47932
2019
2019
eng
35
8
article
eLife Sciences Publications
Cambridge
1
--
--
--
Demographic reconstruction from ancient DNA supports rapid extinction of the great auk
The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.
eLife
10.7554/eLife.47509
31767056
2050-084X
wos:2019
e47509
WOS:000499713600001
Thomas, JE (reprint author), Bangor Univ, Sch Biol Sci, Mol Ecol & Fisheries Genet Lab, Bangor, Gwynedd, Wales.; Thomas, JE (reprint author), Univ Copenhagen, Nat Hist Museum Denmark, Copenhagen, Denmark., drjethomas@hotmail.com; michael.knapp@otago.ac.nz
NERC Environmental Bioinformatics Centre [NE/L501694/1]; European Research CouncilEuropean Research Council (ERC) [681396]; Genetics Society; European Society for Evolutionary Biology; Royal Society of New ZealandRoyal Society of New Zealand
importub
2020-10-19T10:51:31+00:00
filename=package.tar
bd5e25602bd2c2093e9b0aef42eef778
false
true
Jessica E. Thomas
Gary R. Carvalho
James Haile
Nicolas J. Rawlence
Michael D. Martin
Simon Y. W. Ho
Arnor P. Sigfusson
Vigfus A. Josefsson
Morten Frederiksen
Jannie F. Linnebjerg
Jose A. Samaniego Castruita
Jonas Niemann
Mikkel-Holger S. Sinding
Marcela Sandoval-Velasco
Andre E. R. Soares
Robert Lacy
Christina Barilaro
Juila Best
Dirk Brandis
Chiara Cavallo
Mikelo Elorza
Kimball L. Garrett
Maaike Groot
Friederike Johansson
Jan T. Lifjeld
Goran Nilson
Dale Serjeanston
Paul Sweet
Errol Fuller
Anne Karin Hufthammer
Morten Meldgaard
Jon Fjeldsa
Beth Shapiro
Michael Hofreiter
John R. Stewart
M. Thomas P. Gilbert
Michael Knapp
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Open Access
Import
Gold Open-Access
DOAJ gelistet
46079
2018
2020
eng
28
1059
postprint
1
2020-12-22
2020-12-22
--
Cryptic species in a well-known habitat
Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.
Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe
applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida)
10.25932/publishup-46079
urn:nbn:de:kobv:517-opus4-460792
1866-8372
online registration
Scientific Reports 8 (2018) 6893 DOI: 10.1038/s41598-018-25225-x
6893
<a href="http://publishup.uni-potsdam.de/52917">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
CC-BY - Namensnennung 4.0 International
Jan Beermann
Michael V. Westbury
Michael Hofreiter
Leon Hilgers
Fabian Deister
Hermann Neumann
Michael J. Raupach
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1059
eng
uncontrolled
multiple sequence alignment
eng
uncontrolled
Oxidase Subunit-I
eng
uncontrolled
mitochondrial genome
eng
uncontrolled
control region
eng
uncontrolled
Ribosomal-RNA
eng
uncontrolled
asellota crustacea
eng
uncontrolled
gammarus crustacea
eng
uncontrolled
deep-sea
eng
uncontrolled
DNA
eng
uncontrolled
evolution
Naturwissenschaften und Mathematik
Technik, Technologie
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/46079/pmnr1059.pdf
54834
2017
2017
eng
164
12
6
8
article
MDPI
Basel
1
2017-06-15
2017-06-15
--
An ‛Aukward’ tale
One hundred and seventy-three years ago, the last two Great Auks, Pinguinus impennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which—if any—of Fuller’s candidate skins likely belong to either of the two birds. Using mitochondrial genomes from the five candidate birds (housed in museums in Bremen, Brussels, Kiel, Los Angeles, and Oldenburg) and the organs of the last two known individuals, we partially solve the mystery that has been on Great Auk scholars’ minds for generations and make new suggestions as to the whereabouts of the still-missing skin from these two birds.
Genes
a genetic approach to discover the whereabouts of the Last Great Auks
10.3390/genes8060164
2073-4425
wos:2017
164
WOS:000404456500018
Thomas, JE (reprint author), Bangor Univ, Sch Biol Sci, Mol Ecol & Fisheries Genet Lab, Bangor LL57 2UW, Gwynedd, Wales.; Thomas, JE (reprint author), Univ Copenhagen, Nat Hist Museum Denmark, Oster Voldgade 5-7, DK-1350 Copenhagen K, Denmark., bsp20a@bangor.ac.uk; g.r.carvalho@bangor.ac.uk; drjameshaile@gmail.com; mike.martin@ntnu.no; jose.samaniego@snm.ku.dk; j.niemann@snm.ku.dk; mikkel.sinding@snm.ku.dk; marcela.velasco@snm.ku.dk; nic.rawlence@otago.ac.nz; errolfuller123@btinternet.com; jfjeldsaa@snm.ku.dk; michi@palaeo.eu; jstewart@bournemouth.ac.uk; mtpgilbert@gmail.com; michael.knapp@otago.ac.nz
NERC Ph.D. Studentship [NE/L501694/1]; Genetics Society-Heredity Fieldwork Grant; European Society for Evolutionary Biology-Godfrey Hewitt Mobility Award; Rutherford Discovery Fellowship from the Royal Society of New Zealand
2022-04-19T11:39:40+00:00
sword
importub
filename=package.tar
3a96937fb06e818324f1fbd5bb92f70a
false
true
CC-BY - Namensnennung 4.0 International
Jessica E. Thomas
Gary R. Carvalho
James Haile
Michael D. Martin
Jose A. Samaniego Castruita
Jonas Niemann
Mikkel-Holger S. Sinding
Marcela Sandoval-Velasco
Nicolas J. Rawlence
Errol Fuller
Jon Fjeldsa
Michael Hofreiter
John R. Stewart
M. Thomas P. Gilbert
Michael Knapp
eng
uncontrolled
ancient DNA
eng
uncontrolled
extinct birds
eng
uncontrolled
mitochondrial genome
eng
uncontrolled
museum specimens
eng
uncontrolled
palaeogenomics
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
52917
2018
2018
eng
26
8
article
Nature Publ. Group
London
1
--
--
--
Cryptic species in a well-known habitat
Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.
Scientific reports
applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida)
10.1038/s41598-018-25225-x
29720606
2045-2322
wos:2018
6893
WOS:000431203100022
Beermann, J (reprint author), Alfred Wegener Inst, Helmholtz Ctr Polar & Marine Res, Dept Funct Ecol, POB 120161, D-27515 Bremerhaven, Germany.; Beermann, J (reprint author), Alfred Wegener Inst, Helmholtz Ctr Polar & Marine Res, Biol Anstalt Helgoland, Helgoland, Germany.; Beermann, J (reprint author), Helmholtz Inst Funct Marine Biodivers, Oldenburg, Germany., jan.beermann@awi.de
German Federal Ministry of Education and Research (BMBF)Federal Ministry of Education & Research (BMBF) [03F0664A]; federal state of Niedersachsen
2021-12-01T13:48:14+00:00
sword
importub
filename=package.tar
57542c6f60ad9d7c719af83150f63593
<a href="https://doi.org/10.25932/publishup-46079">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1059</a>
false
true
Jan Beermann
Michael V. Westbury
Michael Hofreiter
Leon Hilgers
Fabian Deister
Hermann Neumann
Michael J. Raupach
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
55172
2017
2017
eng
10
7
article
Nature Publishing Group
London
1
2017-03-22
2017-03-22
--
The evolutionary and phylogeographic history of woolly mammoths
Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0–2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.
Scientific reports
a comprehensive mitogenomic analysis
10.1038/srep44585
28327635
2045-2322
wos:2017
44585
WOS:000397009500001
Shapiro, B (reprint author), Univ Calif Santa Cruz, Dept Ecol & Evolutionary Biol, Santa Cruz, CA 95064 USA., bashapir@ucsc.edu
Packard Foundation; Gordon and Betty Moore Foundation; E.R.C. consolidator grant [310763]; Max-Planck-Society; German Research Foundation [HO 3492/1-1]; NSERC; Canada Research Chair
2022-06-14T11:07:16+00:00
sword
importub
filename=package.tar
e07ee441c826c903edd556de0a5529e1
Shapiro, Beth
false
true
CC-BY - Namensnennung 4.0 International
Dan Chang
Michael Knapp
Jacob Enk
Sebastian Lippold
Martin Kircher
Adrian M. Lister
Ross D. E. MacPhee
Christopher Widga
Paul Czechowski
Robert Sommer
Emily Hodges
Nikolaus Stümpel
Ian Barnes
Love Dalén
Anatoly Derevianko
Mietje Germonpré
Alexandra Hillebrand-Voiculescu
Silviu Constantin
Tatyana Kuznetsova
Dick Mol
Thomas Rathgeber
Wilfried Rosendahl
Alexey N. Tikhonov
Eske Willerslev
Greg Hannon
Carles Lalueza i Fox
Ulrich Joger
Hendrik N. Poinar
Michael Hofreiter
Beth Shapiro
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
43177
2015
2020
eng
14
853
postprint
1
2020-03-18
2020-03-18
--
Re-inventing ancient human DNA
For a long time, the analysis of ancient human DNA represented one of the most controversial disciplines in an already controversial field of research. Scepticism in this field was only matched by the long-lasting controversy over the authenticity of ancient pathogen DNA. This ambiguous view on ancient human DNA had a dichotomous root. On the one hand, the interest in ancient human DNA is great because such studies touch on the history and evolution of our own species. On the other hand, because these studies are dealing with samples from our own species, results are easily compromised by contamination of the experiments with modern human DNA, which is ubiquitous in the environment. Consequently, some of the most disputed studies published - apart maybe from early reports on million year old dinosaur or amber DNA - reported DNA analyses from human subfossil remains. However, the development of so-called next- or second-generation sequencing (SGS) in 2005 and the technological advances associated with it have generated new confidence in the genetic study of ancient human remains. The ability to sequence shorter DNA fragments than with PCR amplification coupled to traditional Sanger sequencing, along with very high sequencing throughput have both reduced the risk of sequencing modern contamination and provided tools to evaluate the authenticity of DNA sequence data. The field is now rapidly developing, providing unprecedented insights into the evolution of our own species and past human population dynamics as well as the evolution and history of human pathogens and epidemics. Here, we review how recent technological improvements have rapidly transformed ancient human DNA research from a highly controversial subject to a central component of modern anthropological research. We also discuss potential future directions of ancient human DNA research.
Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-43177
urn:nbn:de:kobv:517-opus4-431775
1866-8372
Investigative Genetics 6 (2015) 4 DOI: 10.1186/s13323-015-0020-4
4
<a href="http://publishup.uni-potsdam.de/39087">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
CC-BY - Namensnennung 4.0 International
Michael Knapp
Carles Lalueza-Fox
Michael Hofreiter
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
853
eng
uncontrolled
archaic humans
eng
uncontrolled
human evolution
eng
uncontrolled
human population genomics
eng
uncontrolled
next/second-generation sequencing
Biowissenschaften; Biologie
Medizin und Gesundheit
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/43177/pmnr853.pdf
56743
2017
2017
eng
298
299
2
1
2
article
Routledge, Taylor & Francis Group
London
1
2017-05-24
2017-05-24
--
Complete mitochondrial genome of a bat-eared fox (Otocyon megalotis), along with phylogenetic considerations
The bat-eared fox, Otocyon megalotis, is the only member of its genus and is thought to occupy a basal position within the dog family. These factors can lead to challenges in complete mitochondrial reconstructions and accurate phylogenetic positioning. Here, we present the first complete mitochondrial genome of the bat-eared fox recovered using shotgun sequencing and iterative mapping to three distantly related species. Phylogenetic analyses placed the bat-eared fox basal in the Canidae family within the clade including true foxes (Vulpes) and the raccoon dog (Nyctereutes) with high support values. This position is in good agreement with previously published results based on short fragments of mitochondrial and nuclear genes, therefore adding more support to the basal positioning of the bat-eared fox within Canidae.
Mitochondrial DNA. Part B
10.1080/23802359.2017.1331325
2380-2359
wos:2017
WOS:000402042700133
Westbury, M (reprint author), Univ Potsdam, Inst Biochem & Biol, Evolutionary & Adapt Genom, Dept Math & Nat Sci, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany., westbury@uni-potsdam.de
2022-11-18T08:31:13+00:00
sword
importub
filename=package.tar
7f69d6a193fd1565bbbbf34188f9a5e1
2868557-X
false
true
CC-BY - Namensnennung 4.0 International
Michael V. Westbury
Fredrik Dalerumb
Karin Noren
Michael Hofreiter
eng
uncontrolled
Phylogenetics
eng
uncontrolled
mitochondria
eng
uncontrolled
iterative mapping
eng
uncontrolled
Canidae
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
38821
2015
2015
eng
13
6
10
article
PLoS
San Fransisco
1
--
--
--
Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone
The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (similar to 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,0001,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.
PLoS one
10.1371/journal.pone.0129102
26086078
1932-6203
wos:2015
e0129102
WOS:000356567500033
Pinhasi, R (reprint author), Univ Coll Dublin, Sch Archaeol, Dublin 4, Ireland., ron.pinhasi@ucd.ie
(ADNABIOARC) [263441]; ERC grant GeneFlow [310763]
<a href="http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-409557">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 515</a>
Ron Pinhasi
Daniel Fernandes
Kendra Sirak
Mario Novak
Sarah Connell
Songul Alpaslan-Roodenberg
Fokke Gerritsen
Vyacheslav Moiseyev
Andrey Gromov
Pal Raczky
Alexandra Anders
Michael Pietrusewsky
Gary Rollefson
Marija Jovanovic
Hiep Trinhhoang
Guy Bar-Oz
Marc Oxenham
Hirofumi Matsumura
Michael Hofreiter
Institut für Biochemie und Biologie
Referiert
Open Access
37326
2014
2014
eng
8
5
article
Nature Publ. Group
London
1
--
--
--
Identification of the remains of King Richard III
Nature Communications
10.1038/ncomms6631
25463651
2041-1723
wos:2014
5631
WOS:000347226900001
King, TE (reprint author), Univ Leicester, Dept Genet, Univ Rd, Leicester LE1 7RH, Leics, England., tek2@le.ac.uk
University of Leicester; Wellcome Trust; Leverhulme Trust; University of
Leicester, The Richard III Society and Leicester City Council; Austrian
Science Fund (FWF) [P22880-B12]; Netherlands Genomics Initiative
(NGI)/Netherlands Organization for Scientific Research (NWO); European
Union [285487]
Turi E. King
Gloria M. Gonzalez-Fortes
Patricia Balaresque
Mark G. Thomas
David Balding
Pierpaolo Maisano Delser
Rita Neumann
Walther Parson
Michael Knapp
Susan Walsh
Laure Tonasso
John Holt
Manfred Kayser
Jo Appleby
Peter Forster
David Ekserdjian
Michael Hofreiter
Kevin Schuerer
Institut für Biochemie und Biologie
Referiert
40955
2015
2019
eng
13
515
postprint
1
2019-01-17
2019-01-17
--
Optimal ancient DNA yields from the inner ear part of the human petrous bone
The invention and development of next or second generation sequencing methods has resulted in a dramatic transformation of ancient DNA research and allowed shotgun sequencing of entire genomes from fossil specimens. However, although there are exceptions, most fossil specimens contain only low (similar to 1% or less) percentages of endogenous DNA. The only skeletal element for which a systematically higher endogenous DNA content compared to other skeletal elements has been shown is the petrous part of the temporal bone. In this study we investigate whether (a) different parts of the petrous bone of archaeological human specimens give different percentages of endogenous DNA yields, (b) there are significant differences in average DNA read lengths, damage patterns and total DNA concentration, and (c) it is possible to obtain endogenous ancient DNA from petrous bones from hot environments. We carried out intra-petrous comparisons for ten petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,0001,800 calibrated years before present (cal. BP). We obtained shotgun DNA sequences from three distinct areas within the petrous: a spongy part of trabecular bone (part A), the dense part of cortical bone encircling the osseous inner ear, or otic capsule (part B), and the dense part within the otic capsule (part C). Our results confirm that dense bone parts of the petrous bone can provide high endogenous aDNA yields and indicate that endogenous DNA fractions for part C can exceed those obtained for part B by up to 65-fold and those from part A by up to 177-fold, while total endogenous DNA concentrations are up to 126-fold and 109-fold higher for these comparisons. Our results also show that while endogenous yields from part C were lower than 1% for samples from hot (both arid and humid) parts, the DNA damage patterns indicate that at least some of the reads originate from ancient DNA molecules, potentially enabling ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses.
Postprints der Universität Potsdam : Mathematisch-Naturwissenschafliche Reihe
10.25932/publishup-40955
urn:nbn:de:kobv:517-opus4-409557
1866-8372
online registration
PLOS ONE 10 (2015) 6, Art. e0129102 DOI: 10.1371/journal.pone.0129102
e0129102
<a href="http://publishup.uni-potsdam.de/frontdoor/index/index/docId/38821">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
CC-BY - Namensnennung 4.0 International
Ron Pinhasi
Daniel Fernandes
Kendra Sirak
Mario Novak
Sarah Connell
Songül Alpaslan-Roodenberg
Fokke Gerritsen
Vyacheslav Moiseyev
Andrey Gromov
Pál Raczky
Alexandra Anders
Michael Pietrusewsky
Gary Rollefson
Marija Jovanovic
Hiep Trinhhoang
Guy Bar-Oz
Marc Oxenham
Hirofumi Matsumura
Michael Hofreiter
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
515
eng
uncontrolled
genome sequence
eng
uncontrolled
extraction
eng
uncontrolled
patterns
eng
uncontrolled
survival
eng
uncontrolled
damage
Naturwissenschaften und Mathematik
Medizin und Gesundheit
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Open Access
Public Library of Science (PLOS)
Universität Potsdam
https://publishup.uni-potsdam.de/files/40955/pmnr515.pdf
39250
2015
2015
eng
7
1660
370
article
Royal Society
London
1
--
--
--
Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses
Leopard complex spotting is inherited by the incompletely dominant locus, LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in the TRPM1 gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence of LP spotting in Europe dates back to the Pleistocene. We tested for temporal changes in the LP associated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli-Kanligecit (Turkey) dating to 2700-2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However, LP seems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age, LP reappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times.
Philosophical transactions of the Royal Society of London : B, Biological sciences
10.1098/rstb.2013.0386
25487337
0962-8436
1471-2970
wos:2015
UNSP 20130386
WOS:000346147700014
Ludwig, A (reprint author), Leibniz Inst Zoo & Wildlife Res, Dept Evolutionary Genet, Berlin, Germany., ludwig@izw-berlin.de
German Research Foundation [DFG LU 852/7-4]
Arne Ludwig
Monika Reissmann
Norbert Benecke
Rebecca Bellone
Edson Sandoval-Castellanos
Michael Cieslak
Gloria M. González-Fortes
Arturo Morales-Muniz
Michael Hofreiter
Melanie Pruvost
eng
uncontrolled
ancient DNA
eng
uncontrolled
coat colour
eng
uncontrolled
domestication
eng
uncontrolled
Equus
eng
uncontrolled
palaeogenetics
eng
uncontrolled
population
Institut für Biochemie und Biologie
Referiert
39087
2015
2015
eng
11
6
review
BioMed Central
London
1
--
--
--
Re-inventing ancient human DNA
For a long time, the analysis of ancient human DNA represented one of the most controversial disciplines in an already controversial field of research. Scepticism in this field was only matched by the long-lasting controversy over the authenticity of ancient pathogen DNA. This ambiguous view on ancient human DNA had a dichotomous root. On the one hand, the interest in ancient human DNA is great because such studies touch on the history and evolution of our own species. On the other hand, because these studies are dealing with samples from our own species, results are easily compromised by contamination of the experiments with modern human DNA, which is ubiquitous in the environment. Consequently, some of the most disputed studies published - apart maybe from early reports on million year old dinosaur or amber DNA - reported DNA analyses from human subfossil remains. However, the development of so-called next-or second-generation sequencing (SGS) in 2005 and the technological advances associated with it have generated new confidence in the genetic study of ancient human remains. The ability to sequence shorter DNA fragments than with PCR amplification coupled to traditional Sanger sequencing, along with very high sequencing throughput have both reduced the risk of sequencing modern contamination and provided tools to evaluate the authenticity of DNA sequence data. The field is now rapidly developing, providing unprecedented insights into the evolution of our own species and past human population dynamics as well as the evolution and history of human pathogens and epidemics. Here, we review how recent technological improvements have rapidly transformed ancient human DNA research from a highly controversial subject to a central component of modern anthropological research. We also discuss potential future directions of ancient human DNA research.
Investigative Genetics
10.1186/s13323-015-0020-4
25937886
2041-2223
wos:2015
4
WOS:000363734600001
Hofreiter, M (reprint author), Univ Potsdam, Dept Math & Nat Sci Evolutionary & Adapt Genom, Inst Biochem & Biol, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany., michi@palaeo.eu
<a href="https://doi.org/10.25932/publishup-43177">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Wirtschafts- und Sozialwissenschaftliche Reihe ; 121</a>
Michael Knapp
Carles Lalueza-Fox
Michael Hofreiter
eng
uncontrolled
Archaic humans
eng
uncontrolled
Human evolution
eng
uncontrolled
Human population genomics
eng
uncontrolled
Next/second-generation sequencing
Institut für Biochemie und Biologie
Referiert
Open Access
44080
2017
2019
eng
8
793
postprint
1
2019-12-16
2019-12-16
--
A mitogenomic timetree for Darwin's enigmatic South American mammal Macrauchenia patachonica
The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia. Our dated phylogenetic tree places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of B66Ma (95% credibility interval, 56.64-77.83 Ma) obtained for the split between Macrauchenia and other Panperissodactyla. Combined with their morphological distinctiveness, this evidence supports the positioning of Litopterna (possibly in company with other SANU groups) as a separate order within Laurasiatheria. We also show that, when using strict criteria, extinct taxa marked by deep divergence times and a lack of close living relatives may still be amenable to palaeogenomic analysis through iterative mapping against more distant relatives.
Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
urn:nbn:de:kobv:517-opus4-440801
10.25932/publishup-44080
1866-8372
online registration
Nature Communications 8 (2017) Art. 15951 DOI: 10.1038/ncomms15951
false
true
CC-BY - Namensnennung 4.0 International
Michael V. Westbury
Sina Isabelle Baleka
Axel Barlow
Stefanie Hartmann
Johanna L. A. Paijmans
Alejandro Kramarz
Analía M. Forasiepi
Mariano Bond
Javier N. Gelfo
Marcelo A. Reguero
Patricio López-Mendoza
Matias Taglioretti
Fernando Scaglia
Andrés Rinderknecht
Washington Jones
Francisco Mena
Guillaume Billet
Christian de Muizon
José Luis Aguilar
Ross D.E. MacPhee
Michael Hofreiter
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
793
eng
uncontrolled
ancient DNA
eng
uncontrolled
evolutionary history
eng
uncontrolled
genome sequence
eng
uncontrolled
reveals
eng
uncontrolled
contamination
eng
uncontrolled
alignment
eng
uncontrolled
reads
eng
uncontrolled
bones
Naturwissenschaften und Mathematik
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/44080/pmnr793.pdf
46187
2017
2017
eng
3330
+
12
27
article
Cell Press
Cambridge
1
--
--
--
Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics
Saber-toothed cats (Machairodontinae) are among the most widely recognized representatives of the now largely extinct Pleistocene megafauna. However, many aspects of their ecology, evolution, and extinction remain uncertain. Although ancient-DNA studies have led to huge advances in our knowledge of these aspects of many other megafauna species (e.g., mammoths and cave bears), relatively few ancient-DNA studies have focused on saber-toothed cats [1-3], and they have been restricted to short fragments of mitochondrial DNA. Here we investigate the evolutionary history of two lineages of saber-toothed cats (Smilodon and Homotherium) in relation to living carnivores and find that the Machairodontinae form a well-supported clade that is distinct from all living felids. We present partial mitochondrial genomes from one S. populator sample and three Homotherium sp. samples, including the only Late Pleistocene Homotherium sample from Eurasia [4]. We confirm the identification of the unique Late Pleistocene European fossil through ancient-DNA analyses, thus strengthening the evidence that Homotherium occurred in Europe over 200,000 years later than previously believed. This in turn forces a re-evaluation of its demography and extinction dynamics. Within the Machairodontinae, we find a deep divergence between Smilodon and Homotherium (similar to 18 million years) but limited diversity between the American and European Homotherium specimens. The genetic data support the hypothesis that all Late Pleistocene (or post-Villafrancian) Homotherium should be considered a single species, H. latidens, which was previously proposed based on morphological data [5, 6].
Current biology
10.1016/j.cub.2017.09.033
29056454
0960-9822
1879-0445
wos:2017
WOS:000414581700024
Paijmans, JLA (reprint author), Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany., paijmans.jla@gmail.com
Programme for research, technological development, and demonstration [FP7-PEOPLE-2011-IEF-298820]; Lundbeck Foundation [R52-A5062]
importub
2020-04-19T23:23:01+00:00
filename=package.tar
bdda58ac132a3b33ed3a95311be35d6a
Johanna L. A. Paijmans
Ross Barnett
M. Thomas P. Gilbert
M. Lisandra Zepeda-Mendoza
Jelle W. F. Reumer
John de Vos
Grant Zazula
Doris Nagel
Gennady F. Baryshnikov
Jennifer A. Leonard
Nadin Rohland
Michael V. Westbury
Axel Barlow
Michael Hofreiter
Institut für Biochemie und Biologie
Referiert
Import
46575
2017
2017
eng
8
8
article
Nature Publ. Group
London
1
--
--
--
A mitogenomic timetree for Darwin’s enigmatic South American mammal Macrauchenia patachonica
The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia. Our dated phylogenetic tree places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of B66Ma (95% credibility interval, 56.64-77.83 Ma) obtained for the split between Macrauchenia and other Panperissodactyla. Combined with their morphological distinctiveness, this evidence supports the positioning of Litopterna (possibly in company with other SANU groups) as a separate order within Laurasiatheria. We also show that, when using strict criteria, extinct taxa marked by deep divergence times and a lack of close living relatives may still be amenable to palaeogenomic analysis through iterative mapping against more distant relatives.
Nature Communications
10.1038/ncomms15951
28654082
2041-1723
wos:2017
15951
WOS:000404129500001
Hofreiter, M (reprint author), Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.; MacPhee, RDE (reprint author), Amer Museum Nat Hist, Dept Mammal, 200 Cent Pk West, New York, NY 10024 USA., macphee@amnh.org; michael.hofreiter@uni-potsdam.de
European Research Council [310763]; National Science Foundation [DEB 1547414]
importub
2020-04-20T02:37:01+00:00
filename=package.tar
a56d32f1a453dea980c7dad7571f416b
Michael V. Westbury
Sina Isabelle Baleka
Axel Barlow
Stefanie Hartmann
Johanna L. A. Paijmans
Alejandro Kramarz
Analia M. Forasiepi
Mariano Bond
Javier N. Gelfo
Marcelo A. Reguero
Patricio Lopez-Mendoza
Matias Taglioretti
Fernando Scaglia
Andres Rinderknecht
Washington Jones
Francisco Mena
Guillaume Billet
Christian de Muizon
Jose Luis Aguilar
Ross D. E. MacPhee
Michael Hofreiter
Institut für Biochemie und Biologie
Referiert
Import
46550
2017
2017
eng
S337
S337
14
3
article
American Assoc. for the Advancement of Science
Washington
1
--
--
--
Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades
Science Advances
10.1126/sciadv.1602878
2375-2548
wos:2017
e1602878
WOS:000411588000014
Campbell, KL (reprint author), Univ Manitoba, Dept Biol Sci, Winnipeg, MB R3T 2N2, Canada., kevin.campbell@umanitoba.ca
Natural Sciences and Engineering Research Council of Canada (NSERC) [238838, 418503]; NSERC Discovery Accelerator Supplement [412336]; Canada Research Chairs program [950-223744]; German Center for Diabetes Research (DZD); NSF [DEB-1457735]; University of Manitoba Undergraduate Research Award; University of Manitoba Graduate Fellowship; Manitoba Graduate Fellowship; Natural Environment Research Council; University of York; NSERC Alexander Graham Bell Canada Graduate Scholarship-Doctoral Program
importub
2020-04-20T02:24:02+00:00
filename=package.tar
7f5d2011f1b3dff48aa567ff92872ebf
Michael J. Gaudry
Martin Jastroch
Jason R. Treberg
Michael Hofreiter
Johanna L. A. Paijmans
James Starrett
Nathan Wales
Anthony V. Signore
Mark S. Springer
Kevin L. Campbell
Institut für Biochemie und Biologie
Referiert
Import
38943
2015
2015
eng
228
228
1
5
58
conferenceobject
NRC Research Press
Ottawa
1
--
--
--
Genomic analyses from highly degraded DNA
Genome
0831-2796
1480-3321
wos:2015
WOS:000360861200162
michi@palaeo.eu
Michael Hofreiter
Axel Barlow
Johanna L. A. Paijmans
Michael V. Westbury
Institut für Biochemie und Biologie
Referiert
49288
2019
2019
eng
1695
1700
12
10
29
article
Cell Press
Cambridge
1
2019-05-09
2019-05-09
--
Paleogenome reveals genetic contribution of extinct giant panda to extant populations
Historically, the giant panda was widely distributed from northern China to southwestern Asia [1]. As a result of range contraction and fragmentation, extant individuals are currently restricted to fragmented mountain ranges on the eastern margin of the Qinghai-Tibet plateau, where they are distributed among three major population clusters [2]. However, little is known about the genetic consequences of this dramatic range contraction. For example, were regions where giant pandas previously existed occupied by ancestors of present-day populations, or were these regions occupied by genetically distinct populations that are now extinct? If so, is there any contribution of these extinct populations to the genomes of giant pandas living today? To investigate these questions, we sequenced the nuclear genome of an similar to 5,000-year-old giant panda from Jiangdongshan, Teng-chong County in Yunnan Province, China. We find that this individual represents a genetically distinct population that diverged prior to the diversification of modern giant panda populations. We find evidence of differential admixture with this ancient population among modern individuals originating from different populations as well as within the same population. We also find evidence for directional gene flow, which transferred alleles from the ancient population into the modern giant panda lineages. A variable proportion of the genomes of extant individuals is therefore likely derived from the ancient population represented by our sequenced individual. Although extant giant panda populations retain reasonable genetic diversity, our results suggest that this represents only part of the genetic diversity this species harbored prior to its recent range contractions.
Current biology
10.1016/j.cub.2019.04.021
31080081
0960-9822
1879-0445
wos:2019
WOS:000468409100030
Sheng, GL (reprint author), China Univ Geosci, State Key Lab Biogeol & Environm Geol, Wuhan 430074, Hubei, Peoples R China.; Barlow, A (reprint author), Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany., glsheng@cug.edu.cn; axel.barlow.ab@gmail.com
National Natural Science Foundation of ChinaNational Natural Science Foundation of China [41672017]; "PPP" project - CSC [2016-2041]; "PPP" project - DAAD [2016-2041]; ERC consolidator grant "gene flow" [310763]; US National Science FoundationNational Science Foundation (NSF) [DEB-0103795]
2021-02-05T08:20:07+00:00
sword
importub
filename=package.tar
7e4ec0e6c679b6a11375939a6e25efb9
Barlow, Axel
false
true
Gui-Lian Sheng
Nikolas Basler
Xue-Ping Ji
Johanna L. A. Paijmans
Federica Alberti
Michaela Preick
Stefanie Hartmann
Michael V. Westbury
Jun-Xia Yuan
Nina G. Jablonski
Georgios Xenikoudakis
Xin-Dong Hou
Bo Xiao
Jian-Hui Liu
Michael Hofreiter
Xu-Long Lai
Axel Barlow
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
41299
2018
2018
eng
2
481
postprint
1
2018-12-03
2018-12-03
--
The complete mitochondrial genome of the common vole, Microtus arvalis (Rodentia: Arvicolinae)
The common vole, Microtus arvalis belongs to the genus Microtus in the subfamily Arvicolinae. In this study, the complete mitochondrial genome of M. arvalis was recovered using shotgun sequencing and an iterative mapping approach using three related species. Phylogenetic analyses using the sequence of 21 arvicoline species place the common vole as a sister species to the East European vole (Microtus levis), but as opposed to previous results we find no support for the recognition of the genus Neodon within the subfamily Arvicolinae, as this is, as well as the genus Lasiopodomys, found within the Microtus genus.
Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
urn:nbn:de:kobv:517-opus4-412994
1866-8372
online registration
Mitochondrial DNA Part B 3 (2018) 1, S.446–447 DOI: 10.1080/23802359.2018.1457994
<a href="http://publishup.uni-potsdam.de/opus4-ubp/frontdoor/index/index/docId/42302">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
CC-BY - Namensnennung 4.0 International
Remco Folkertsma
Michael V. Westbury
Jana Eccard
Michael Hofreiter
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
481
lat
uncontrolled
Microtus arvalis
lat
uncontrolled
Arvicolinae
eng
uncontrolled
mitochondrial genome
eng
uncontrolled
common vole
eng
uncontrolled
phylogeny
Biowissenschaften; Biologie
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Open Access
Taylor & Francis Open Access Agreement
Universität Potsdam
https://publishup.uni-potsdam.de/files/41299/pmnr481.pdf
41413
2018
2019
eng
13
589
postprint
1
2019-02-12
2019-02-12
--
Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena
Hyenas (family Hyaenidae), as the sister group to cats (family Felidae), represent a deeply diverging branch within the cat-like carnivores (Feliformia). With an estimated population size of <10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) represents the rarest of the four extant hyena species and has been listed as Near Threatened by the IUCN. Here, we report a high-coverage genome from a captive bred brown hyena and both mitochondrial and low-coverage nuclear genomes of 14 wild-caught brown hyena individuals from across southern Africa. We find that brown hyena harbor extremely low genetic diversity on both the mitochondrial and nuclear level, most likely resulting from a continuous and ongoing decline in effective population size that started similar to 1 Ma and dramatically accelerated towards the end of the Pleistocene. Despite the strikingly low genetic diversity, we find no evidence of inbreeding within the captive bred individual and reveal phylogeographic structure, suggesting the existence of several potential subpopulations within the species.
Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-41413
urn:nbn:de:kobv:517-opus4-414132
1866-8372
online registration
Molecular Biology and Evolution 35 (2018) 5, pp. 1225–1237 DOI 10.1093/molbev/msy037
<a href="http://publishup.uni-potsdam.de/52981">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
CC-BY-NC - Namensnennung, nicht kommerziell 4.0 International
Michael V. Westbury
Stefanie Hartmann
Axel Barlow
Ingrid Wiesel
Viyanna Leo
Rebecca Welch
Daniel M. Parker
Florian Sicks
Arne Ludwig
Love Dalen
Michael Hofreiter
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
589
eng
uncontrolled
evolution
eng
uncontrolled
hyena
eng
uncontrolled
genomics
eng
uncontrolled
population genomics
eng
uncontrolled
diversity
Biowissenschaften; Biologie
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/41413/pmnr589.pdf
52981
2018
2018
eng
1225
1237
13
5
35
article
Oxford Univ. Press
Oxford
1
--
--
--
Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena
Hyenas (family Hyaenidae), as the sister group to cats (family Felidae), represent a deeply diverging branch within the cat-like carnivores (Feliformia). With an estimated population size of <10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) represents the rarest of the four extant hyena species and has been listed as Near Threatened by the IUCN. Here, we report a high-coverage genome from a captive bred brown hyena and both mitochondrial and low-coverage nuclear genomes of 14 wild-caught brown hyena individuals from across southern Africa. We find that brown hyena harbor extremely low genetic diversity on both the mitochondrial and nuclear level, most likely resulting from a continuous and ongoing decline in effective population size that started similar to 1 Ma and dramatically accelerated towards the end of the Pleistocene. Despite the strikingly low genetic diversity, we find no evidence of inbreeding within the captive bred individual and reveal phylogeographic structure, suggesting the existence of several potential subpopulations within the species.
Molecular biology and evolution
10.1093/molbev/msy037
29528428
0737-4038
1537-1719
wos:2018
WOS:000431889600015
Westbury, MV (reprint author), Univ Copenhagen, Nat Hist Museum Denmark, Copenhagen, Denmark.; Westbury, MV (reprint author), Univ Potsdam, Inst Biochem & Biol, Evolutionary Adapt Genom, Potsdam, Germany., mvwestbury@gmail.com
European Research Council (consolidator grant GeneFlow) [310763]; Science for Life Laboratory; Knut and Alice Wallenberg FoundationKnut & Alice Wallenberg Foundation; National Genomics Infrastructure - Swedish Research Council; Swedish Research CouncilSwedish Research Council; FORMASSwedish Research Council Formas; Uppsala Multidisciplinary Center for Advanced Computational Science
2021-12-06T17:42:57+00:00
sword
importub
filename=package.tar
73b47faad8e9c55e0d3275a75b206f5e
<a href="https://doi.org/10.25932/publishup-41413">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 589 </a>
false
true
CC-BY-NC-ND - Namensnennung, nicht kommerziell, keine Bearbeitungen 4.0 International
Michael V. Westbury
Stefanie Hartmann
Axel Barlow
Ingrid Wiesel
Viyanna Leo
Rebecca Welch
Daniel M. Parker
Florian Sicks
Arne Ludwig
Love Dalen
Michael Hofreiter
eng
uncontrolled
evolution
eng
uncontrolled
hyena
eng
uncontrolled
genomics
eng
uncontrolled
population genomics
eng
uncontrolled
diversity
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
42302
2018
2018
eng
446
447
2
1
3
article
1
2018-04-04
2018-04-04
--
The complete mitochondrial genome of the common vole, Microtus arvalis (Rodentia: Arvicolinae)
The common vole, Microtus arvalis belongs to the genus Microtus in the subfamily Arvicolinae. In this study, the complete mitochondrial genome of M. arvalis was recovered using shotgun sequencing and an iterative mapping approach using three related species. Phylogenetic analyses using the sequence of 21 arvicoline species place the common vole as a sister species to the East European vole (Microtus levis), but as opposed to previous results we find no support for the recognition of the genus Neodon within the subfamily Arvicolinae, as this is, as well as the genus Lasiopodomys, found within the Microtus genus.
Mitochondrial DNA Part B
10.1080/23802359.2018.1457994
2380-2359
Universität Potsdam
PA 2018_77
208.25
<a href="http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-125873">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 481</a>
false
false
CC-BY - Namensnennung 4.0 International
Remco Folkertsma
Michael V. Westbury
Jana Eccard
Michael Hofreiter
lat
uncontrolled
Microtus arvalis
lat
uncontrolled
Arvicolinae
eng
uncontrolled
mitochondrial genome
eng
uncontrolled
common vole
eng
uncontrolled
phylogeny
Biowissenschaften; Biologie
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Publikationsfonds der Universität Potsdam
Open Access
48437
2019
2019
eng
786
793
8
7
30
article
Routledge, Taylor & Francis Group
Abingdon
1
2019-09-23
--
--
Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China
Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290-1180 cal. Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95% credibility interval 117-222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis a slow increase in female effective population size of C. bactrianus from 5000 years ago, which to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.
Mitochondrial DNA Part A
10.1080/24701394.2019.1659250
31542986
2470-1394
2470-1408
wos:2019
WOS:000487318900001
Yuan, JX (reprint author), China Univ Geosci, Fac Mat Sci & Chem, Wuhan, Hubei, Peoples R China., wuhanyjx@126.com
National Natural Science Foundation of ChinaNational Natural Science Foundation of China [41472014, 41672017]; Social Science Foundation of Shaanxi Province, China [2015H012]
importub
2020-11-25T18:46:22+00:00
filename=package.tar
118bff8560af87d006df7e15e890c758
false
true
Shun-Gang Chen
Ji Li
Fan Zhang
Bo Xiao
Jia-Ming Hu
Yin-Qiu Cui
Michael Hofreiter
Xin-Dong Hou
Gui-Lian Sheng
Xu-Long Lai
Jun-Xia Yuan
eng
uncontrolled
Camelus bactrianus
eng
uncontrolled
mitochondrial genome
eng
uncontrolled
ancient DNA
eng
uncontrolled
phylogeny
eng
uncontrolled
maternal lineages
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
46446
2017
2017
eng
9
7
article
Nature Publ. Group
London
1
--
--
--
Origin and dispersal of early domestic pigs in northern China
It is widely accepted that modern pigs were domesticated independently at least twice, and Chinese native pigs are deemed as direct descendants of the first domesticated pigs in the corresponding domestication centers. By analyzing mitochondrial DNA sequences of an extensive sample set spanning 10,000 years, we find that the earliest pigs from the middle Yellow River region already carried the maternal lineages that are dominant in both younger archaeological populations and modern Chinese pigs. Our data set also supports early Neolithic pig utilization and a long-term in situ origin for northeastern Chinese pigs during 8,000-3,500 BP, suggesting a possibly independent domestication in northeast China. Additionally, we observe a genetic replacement in ancient northeast Chinese pigs since 3,500 BP. The results not only provide increasing evidence for pig origin in the middle Yellow River region but also depict an outline for the process of early pig domestication in northeast China.
Scientific reports
10.1038/s41598-017-06056-8
28798357
2045-2322
wos:2017
5602
WOS:000407399600001
Zhao, XB (reprint author), China Agr Univ, Natl Engn Lab Anim Breeding, Beijing 100193, Peoples R China.; Zhao, XB (reprint author), China Agr Univ, Minist Agr, Key Lab Anim Genet Breeding & Reprod, Beijing 100193, Peoples R China.; Zhao, XB (reprint author), China Agr Univ, Coll Anim Sci & Technol, Beijing 100193, Peoples R China.; Hofreiter, M (reprint author), Univ Potsdam, Fac Math & Nat Sci, Inst Biochem & Biol, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany., Michael.hofreiter@uni-potsdam.de; zhxb@cau.edu.cn
National Natural Science Foundation of China [31672379]; National Key Basic Research Program of China [2014CB138500]; China Postdoctoral Science Foundation [2015M581201]
importub
2020-04-20T01:32:02+00:00
filename=package.tar
a33a9b959e1a9df438ed3ce6273297cf
Hai Xiang
Jianqiang Gao
Dawei Cai
Yunbing Luo
Baoquan Yu
Langqing Liu
Ranran Liu
Hui Zhou
Xiaoyong Chen
Weitao Dun
Xi Wang
Michael Hofreiter
Xingbo Zhao
Wirtschaftswissenschaften
Referiert
Import
53320
2018
2018
eng
E2566
E2574
9
11
115
article
National Acad. of Sciences
Washington
1
2018-02-26
2018-02-26
--
A comprehensive genomic history of extinct and living elephants
Proceedings of the National Academy of Sciences of the United States of America
10.1073/pnas.1720554115
29483247
0027-8424
wos:2018
WOS:000427245400014
Palkopoulou, E; Reich, D (reprint author), Harvard Med Sch, Dept Genet, Boston, MA 02115 USA.; Palkopoulou, E; Reich, D (reprint author), Broad Inst MIT & Harvard, Cambridge, MA 02142 USA., elle.palkopoulou@gmail.com; reich@genetics.med.harvard.edu
National Human Genome Research InstituteUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Human Genome Research Institute (NHGRI) [U54 HG003067-08]; US Fish and Wildlife Service African Elephant Conservation FundUS Fish & Wildlife Service; Wellcome TrustWellcome Trust [WT098051, WT108749/Z/15/Z]; European Molecular Biology Laboratory; European Research CouncilEuropean Research Council (ERC) [310763 GeneFlow]; Natural Sciences and Engineering Research Council of CanadaNatural Sciences and Engineering Research Council of Canada [RFMAC-10539150]; Canada Research Chairs programCanada Research Chairs; NSF (HOMINID) Grant [BCS-1032255]; NIH (National Institute of General Medical Sciences) Grant [GM100233]
2022-01-06T12:48:51+00:00
sword
importub
filename=package.tar
012c9c2018c402e1455926599b6541d5
Palkopoulou, Eleftheria
Reich, David
false
true
Eleftheria Palkopoulou
Mark Lipson
Swapan Mallick
Svend Nielsen
Nadin Rohland
Sina Isabelle Baleka
Emil Karpinski
Atma M. Ivancevici
Thu-Hien To
Daniel Kortschak
Joy M. Raison
Zhipeng Qu
Tat-Jun Chin
Kurt W. Alt
Stefan Claesson
Love Dalen
Ross D. E. MacPhee
Harald Meller
Alfred L. Rocar
Oliver A. Ryder
David Heiman
Sarah Young
Matthew Breen
Christina Williams
Bronwen L. Aken
Magali Ruffier
Elinor Karlsson
Jeremy Johnson
Federica Di Palma
Jessica Alfoldi
David L. Adelsoni
Thomas Mailund
Kasper Munch
Kerstin Lindblad-Toh
Michael Hofreiter
Hendrik Poinar
David Reich
eng
uncontrolled
paleogenomics
eng
uncontrolled
elephantid evolution
eng
uncontrolled
mammoth
eng
uncontrolled
admixture
eng
uncontrolled
species divergence
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Bronze Open-Access
53309
2018
2018
eng
7
4
4
article
American Assoc. for the Advancement of Science
Washington
1
2018-03-01
2018-03-01
--
Decline of genetic diversity in ancient domestic stallions in Europe
Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection-initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times.
Science Advances
10.1126/sciadv.aap9691
29675468
2375-2548
wos:2018
eaap9691
WOS:000431374900029
Ludwig, A (reprint author), Leibniz Inst Zoo & Wildlife Res, Dept Evolutionary Genet, D-10315 Berlin, Germany., ludwig@izw-berlin.de
Deutsche ForschungsgemeinschaftGerman Research Foundation (DFG) [LU 85/27-4]; Spanish Ministry of Economy, Industry, and Competitiveness [HAR2014-55722-P, HAR2017-88325-P]; European Research CouncilEuropean Research Council (ERC); Swiss National Science FoundationSwiss National Science Foundation (SNSF)
2022-01-06T08:58:28+00:00
sword
importub
filename=package.tar
cce5ddd7f7b8e4a9f7b515ab12119db7
Ludwig, Arne
false
true
CC-BY-NC - Namensnennung, nicht kommerziell 4.0 International
Saskia Wutke
Edson Sandoval-Castellanos
Norbert Benecke
Hans-Jürgen Döhle
Susanne Friederich
Javier Gonzalez
Michael Hofreiter
Lembi Lougas
Ola Magnell
Anna-Sapfo Malaspinas
Arturo Morales-Muniz
Ludovic Orlando
Monika Reissmann
Alexandra Trinks
Arne Ludwig
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Import
43997
2017
2019
eng
11
791
postprint
1
2019-12-10
2019-12-10
--
Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago
Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently similar to 3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil's Gate, an early Neolithic cave site (dated to similar to 7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.
Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
urn:nbn:de:kobv:517-opus4-439977
10.25932/publishup-43997
1866-8372
online registration
Science Advances 3 (2017) 2, Art. e1601877 DOI: 10.1126/sciadv.1601877
e1601877
<a href="http://publishup.uni-potsdam.de/55424">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
CC-BY - Namensnennung 4.0 International
Veronika Siska
Eppie Ruth Jones
Sungwon Jeon
Youngjune Bhak
Hak-Min Kim
Yun Sung Cho
Hyunho Kim
Kyusang Lee
Elizaveta Veselovskaya
Tatiana Balueva
Marcos Gallego-Llorente
Michael Hofreiter
Daniel G. Bradley
Anders Eriksson
Ron Pinhasi
Jong Bhak
Andrea Manica
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
791
eng
uncontrolled
Mitochondrial-DNA analysis
eng
uncontrolled
positive selection
eng
uncontrolled
jomon skeletons
eng
uncontrolled
ancient DNA
eng
uncontrolled
pigmentation
eng
uncontrolled
population
eng
uncontrolled
admixture
eng
uncontrolled
edar
eng
uncontrolled
gene
eng
uncontrolled
polymorohism
Naturwissenschaften und Mathematik
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/43997/pmnr791.pdf
43995
2017
2019
eng
300
313
14
789
postprint
1
2019-12-10
2019-12-10
--
Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel
The performance of hybridization capture combined with next-generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient-domestic dromedaries with 17-95% length coverage and 1.27-47.1-fold read depths for the covered regions. Using whole-genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1-1.06-fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.
Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
urn:nbn:de:kobv:517-opus4-439955
10.25932/publishup-43995
1866-8372
online registration
Molecular Ecology Resources 17 (2017) 2, S. 300–313 DOI: 10.1111/1755-0998.12551
<a href="http://publishup.uni-potsdam.de/55288">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
CC-BY - Namensnennung 4.0 International
Elmira Mohandesan
Camilla F. Speller
Joris Peters
Hans-Peter Uerpmann
Margarethe Uerpmann
Bea De Cupere
Michael Hofreiter
Pamela A. Burger
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
789
eng
uncontrolled
ancient DNA
eng
uncontrolled
Camelus dromedarius
eng
uncontrolled
capture enrichment
eng
uncontrolled
degraded DNA
eng
uncontrolled
mitochondrial genome (mtDNA)
eng
uncontrolled
next-generation sequencing
Biowissenschaften; Biologie
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/43995/pmnr789.pdf
57626
2020
2020
eng
1071
1073
3
3
190
article
Oxford Univ. Press
Oxford
1
2020-04-09
2020-04-09
--
Comparing mitogenomic timetrees for two African savannah primate genera (Chlorocebus and Papio)
Zoological journal of the Linnean Society
Corrigenda
10.1093/zoolinnean/zlaa026
0024-4082
1096-3642
This is a correction to: Zoological Journal of the Linnean Society. - 181 (2017) 2. - S. 471 – 483, https://doi.org/10.1093/zoolinnean/zlx001
outputup:dataSource:WoS:2020
WOS:000593445900012
Dolotovskaya, S (corresponding author), Leibniz Inst Primate Res, German Primate Ctr, Primate Genet Lab, Kellnerweg 4, D-37077 Gottingen, Germany.
Dolotovskaya, S
2023-01-23T07:35:18+00:00
sword
importub
filename=package.tar
ca8d8ddfa01e6be5bd0595bf9238489d
1471951-4
CC-BY - Namensnennung 4.0 International
Sofya Dolotovskaya
Juan Torroba Bordallo
Tanja Haus
Angela Noll
Michael Hofreiter
Dietmar Zinner
Christian Roos
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
55006
2021
2021
eng
1
20
20
article
Frontiers in Earth Science
Lausanne, Schweiz
1
2021-09-20
2021-09-20
--
Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core
Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental conditions around critical episodes of hominin evolution. Identification of biological taxa based on their sedimentary ancient DNA (sedaDNA) traces can contribute to understand past ecological and climatological conditions of the living environment of our ancestors. However, sedaDNA recovery from tropical environments is challenging because high temperatures, UV irradiation, and desiccation result in highly degraded DNA. Consequently, most of the DNA fragments in tropical sediments are too short for PCR amplification. We analyzed sedaDNA in the upper 70 m of the composite sediment core of the HSPDP drill site at Chew Bahir for eukaryotic remnants. We first tested shotgun high throughput sequencing which leads to metagenomes dominated by bacterial DNA of the deep biosphere, while only a small fraction was derived from eukaryotic, and thus probably ancient, DNA. Subsequently, we performed cross-species hybridization capture of sedaDNA to enrich ancient DNA (aDNA) from eukaryotic remnants for paleoenvironmental analysis, using established barcoding genes (cox1 and rbcL for animals and plants, respectively) from 199 species that may have had relatives in the past biosphere at Chew Bahir. Metagenomes yielded after hybridization capture are richer in reads with similarity to cox1 and rbcL in comparison to metagenomes without prior hybridization capture. Taxonomic assignments of the reads from these hybridization capture metagenomes also yielded larger fractions of the eukaryotic domain. For reads assigned to cox1, inferred wet periods were associated with high inferred relative abundances of putative limnic organisms (gastropods, green algae), while inferred dry periods showed increased relative abundances for insects. These findings indicate that cross-species hybridization capture can be an effective approach to enhance the information content of sedaDNA in order to explore biosphere changes associated with past environmental conditions, enabling such analyses even under tropical conditions.
Frontiers in Earth Science
10.3389/feart.2021.683010
2296-6463
683010
<a href="https://doi.org/10.25932/publishup-55007">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1244</a>
Tiedemann, Ralph
false
false
CC-BY - Namensnennung 4.0 International
Johanna Krüger
Verena Elisabeth Foerster
Martin H. Trauth
Michael Hofreiter
Ralph Tiedemann
eng
uncontrolled
Chew Bahir
eng
uncontrolled
hybridization capture
eng
uncontrolled
ICDP
eng
uncontrolled
paleoclimate
eng
uncontrolled
past biosphere
eng
uncontrolled
sedaDNA
eng
uncontrolled
sediment core
Geowissenschaften
Institut für Biochemie und Biologie
Extern
Referiert
Publikationsfonds der Universität Potsdam
Gold Open-Access
55141
2017
2017
eng
198
198
1
162
other
Wiley
Hoboken
1
--
--
--
The Neolithic transition at the Western edge of Europe
American journal of physical anthropology
0002-9483
1096-8644
wos:2017
86th Annual Meeting of the American-Association-of-Physical-Anthropologists (AAPA)
APR 19-22, 2017
WOS:000423063102373
New Orleans, LA
Horizon, Marie Curie Actions [655478 NeoGenHeritage - H2020-MSCA-IF-2014]
2022-06-10T11:38:05+00:00
sword
importub
filename=package.tar
8abf43271d9d7b7d7d15d523c96f8884
Gloria M. Gonzalez-Fortes
Francesca Tassi
Silvia Ghirotto
Kirstin Henneberger
Michael Hofreiter
Guido Barbujani
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
55288
2017
2017
eng
300
313
14
2
17
article
Wiley
Hoboken
1
2017-06-11
2017-06-11
--
Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel
The performance of hybridization capture combined with next-generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient-domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187-fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient-domestic dromedaries with 17-95% length coverage and 1.27-47.1-fold read depths for the covered regions. Using whole-genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1-1.06-fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.
Molecular ecology resources
10.1111/1755-0998.12551
27289015
1755-098X
1755-0998
wos:2017
WOS:000394880100017
Mohandesan, E; Burger, PA (reprint author), Vetmeduni Vienna, Res Inst Wildlife Ecol, Savoyenstr 1, A-1160 Vienna, Austria.; Mohandesan, E (reprint author), Vetmeduni Vienna, Inst Populat Genet, Vet Pl 1, A-1210 Vienna, Austria., elmira.mohandesan@vetmeduni.ac.at; pamela.burger@vetmeduni.ac.at
2022-06-23T05:26:36+00:00
sword
importub
filename=package.tar
87852463cc6e1b56957fe059f4b3dd6e
<a href="https://doi.org/10.25932/publishup-43995">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 789 </a>
false
true
CC-BY - Namensnennung 4.0 International
Elmira Mohandesan
Camilla F. Speller
Joris Peters
Hans-Peter Uerpmann
Margarethe Uerpmann
Bea De Cupere
Michael Hofreiter
Pamela A. Burger
eng
uncontrolled
ancient DNA
eng
uncontrolled
Camelus dromedarius
eng
uncontrolled
capture enrichment
eng
uncontrolled
degraded DNA
eng
uncontrolled
mitochondrial genome (mtDNA)
eng
uncontrolled
next-generation sequencing
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
55424
2017
2017
eng
10
2
3
article
American Assoc. for the Advancement of Science
Washington
1
2017-02-01
2017-02-01
--
Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago
Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil’s Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.
Science Advances
10.1126/sciadv.1601877
2375-2548
wos:2017
e1601877
WOS:000397039500007
Siska, V; Manica, A (reprint author), Univ Cambridge, Dept Zool, Downing St, Cambridge CB2 3EJ, England.; Bhak, J (reprint author), Ulsan Natl Inst Sci & Technol, Genom Inst, Ulsan 44919, South Korea.; Bhak, J (reprint author), Geromics, Ulsan 44919, South Korea.; Pinhasi, R (reprint author), Univ Coll Dublin, Sch Archaeol, Dublin, Ireland.; Pinhasi, R (reprint author), Univ Coll Dublin, Earth Inst, Dublin, Ireland., vs389@cam.ac.uk; ron.pinhasi@ucd.ie; jongbhak@genomics.org; am315@cam.ac.uk
2022-06-30T13:58:46+00:00
sword
importub
filename=package.tar
48d2210a890bf4e85213401d913148e0
Siska, Veronika
Pinhasi, Ron
Bhak, Jong
Manica, Andrea
<a href="https://doi.org/10.25932/publishup-43997">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 791 </a>
false
true
CC-BY - Namensnennung 4.0 International
Veronika Siska
Eppie Ruth Jones
Sungwon Jeon
Youngjune Bhak
Hak-Min Kim
Yun Sung Cho
Hyunho Kim
Kyusang Lee
Elizaveta Veselovskaya
Tatiana Balueva
Marcos Gallego-Llorente
Michael Hofreiter
Daniel G. Bradley
Anders Eriksson
Ron Pinhasi
Jong Bhak
Andrea Manica
Naturwissenschaften und Mathematik
Institut für Mathematik
Referiert
Import
49231
2019
2019
eng
1419
1435
6
177
article
Cell Press
Cambridge
1
2019-05-02
2019-05-30
--
Tracking five millennia of horse management with extensive ancient genome time series
Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (>= 1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modem legacy of past equestrian civilisations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modem breeding impacted genetic diversity more dramatically than the previous millennia of human management.
Cell
10.1016/j.cell.2019.03.049
31056281
0092-8674
1097-4172
wos:2019
WOS:000469415100010
Orlando, L (reprint author), Univ Paul Sabatier, Univ Toulouse, CNRS, UMR 5288,Lab Anthropobiol Mol & Imagerie Synthese, F-31000 Toulouse, France.; Orlando, L (reprint author), Univ Copenhagen, Lundbeck Fdn, GeoGenet Ctr, DK-1350 Copenhagen K, Denmark., ludovic.orlando@univ-tlse3.fr
Taylor Family-Asia Foundation Endowed Chair in Ecology and Conservation Biology; Marie-Curie Individual FellowshipEuropean Union (EU) [MSCA-IF-67852]; Estonian Research CouncilEstonian Research Council [PRG29]; FCTPortuguese Foundation for Science and Technology [SFRH/BPD/100511/2014]; Ministry of Educations and Science of Russian Federation [33.1907, 2017/P4]; Russian Scientific FoundationRussian Science Foundation (RSF) [18-18-00137]; MINECO/FEDER, UE [BFU2017-86471-P]; Howard Hughes International Early Career; Obra Social CatalunyaGeneralitat de Catalunya; Russian Science FoundationRussian Science Foundation (RSF) [16-18-10265]; SYNTHESYS Project; European Community Research Infrastructure Action under the Seventh Framework "Capacities" Programme; Danish National Research FoundationDanmarks Cited Research Group Program (HCRC) [15-101]; Deanship of Scientific Research, King Saud UniversityDeanship of Scientific Research at King Saud University; Villum Fonden miGENEPI research project; Swiss National Science FoundationSwiss National Science Foundation (SNSF) [CR13I1_140638]; Research Council of NorwayResearch Council of Norway [230821/F20]; Ministerio de Economia y Competitividad, Spain [HAR2016-77600-P]; National Science FoundationNational Science Foundation (NSF) [ANS-1417036]; European Research Council (ERC) under the European UnionEuropean Research Council (ERC) [681605]; [U01 MH106874]
2021-02-03T10:12:41+00:00
sword
importub
filename=package.tar
c9a3b1f3d23545d395a928699b245c6f
Orlando, Ludovic
false
true
CC-BY-NC - Namensnennung, nicht kommerziell 4.0 International
Antoine Fages
Kristian Hanghoj
Naveed Khan
Charleen Gaunitz
Andaine Seguin-Orlando
Michela Leonardi
Christian McCrory Constantz
Cristina Gamba
Khaled A. S. Al-Rasheid
Silvia Albizuri
Ahmed H. Alfarhan
Morten Allentoft
Saleh Alquraishi
David Anthony
Nurbol Baimukhanov
James H. Barrett
Jamsranjav Bayarsaikhan
Norbert Benecke
Eloisa Bernaldez-Sanchez
Luis Berrocal-Rangel
Fereidoun Biglari
Sanne Boessenkool
Bazartseren Boldgiv
Gottfried Brem
Dorcas Brown
Joachim Burger
Eric Crubezy
Linas Daugnora
Hossein Davoudi
Peter de Barros Damgaard
Maria de los Angeles de Chorro y de Villa-Ceballos
Sabine Deschler-Erb
Cleia Detry
Nadine Dill
Maria do Mar Oom
Anna Dohr
Sturla Ellingvag
Diimaajav Erdenebaatar
Homa Fathi
Sabine Felkel
Carlos Fernandez-Rodriguez
Esteban Garcia-Vinas
Mietje Germonpre
Jose D. Granado
Jon H. Hallsson
Helmut Hemmer
Michael Hofreiter
Aleksei Kasparov
Mutalib Khasanov
Roya Khazaeli
Pavel Kosintsev
Kristian Kristiansen
Tabaldiev Kubatbek
Lukas Kuderna
Pavel Kuznetsov
Haeedeh Laleh
Jennifer A. Leonard
Johanna Lhuillier
Corina Liesau von Lettow-Vorbeck
Andrey Logvin
Lembi Lougas
Arne Ludwig
Cristina Luis
Ana Margarida Arruda
Tomas Marques-Bonet
Raquel Matoso Silva
Victor Merz
Enkhbayar Mijiddorj
Bryan K. Miller
Oleg Monchalov
Fatemeh A. Mohaseb
Arturo Morales
Ariadna Nieto-Espinet
Heidi Nistelberger
Vedat Onar
Albina H. Palsdottir
Vladimir Pitulko
Konstantin Pitskhelauri
Melanie Pruvost
Petra Rajic Sikanjic
Anita Rapan Papesa
Natalia Roslyakova
Alireza Sardari
Eberhard Sauer
Renate Schafberg
Amelie Scheu
Jorg Schibler
Angela Schlumbaum
Nathalie Serrand
Aitor Serres-Armero
Beth Shapiro
Shiva Sheikhi Seno
Irina Shevnina
Sonia Shidrang
John Southon
Bastiaan Star
Naomi Sykes
Kamal Taheri
William Taylor
Wolf-Rudiger Teegen
Tajana Trbojevic Vukicevic
Simon Trixl
Dashzeveg Tumen
Sainbileg Undrakhbold
Emma Usmanova
Ali Vahdati
Silvia Valenzuela-Lamas
Catarina Viegas
Barbara Wallner
Jaco Weinstock
Victor Zaibert
Benoit Clavel
Sebastien Lepetz
Marjan Mashkour
Agnar Helgason
Kari Stefansson
Eric Barrey
Eske Willerslev
Alan K. Outram
Pablo Librado
Ludovic Orlando
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
50103
2017
2017
eng
471
483
13
2
181
article
Oxford Univ. Press
Oxford
1
--
2017-04-27
--
Comparing mitogenomic timetrees for two African savannah primate genera (Chlorocebus and Papio)
Complete mitochondrial (mtDNA) genomes have proved to be useful in reconstructing primate phylogenies with higher resolution and confidence compared to reconstructions based on partial mtDNA sequences. Here, we analyse complete mtDNA genomes of African green monkeys (genus Chlorocebus), a widely distributed primate genus in Africa representing an interesting phylogeographical model for the evolution of savannah species. Previous studies on partial mtDNA sequences revealed nine major clades, suggesting several cases of para- and polyphyly among Chlorocebus species. However, in these studies, phylogenetic relationships among several clades were not resolved, and divergence times were not estimated. We analysed complete mtDNA genomes for ten Chlorocebus samples representing major mtDNA clades to find stronger statistical support in the phylogenetic reconstruction than in the previous studies and to estimate divergence times. Our results confirmed para- and polyphyletic relationships of most Chlorocebus species, while the support for the phylogenetic relationships between the mtDNA clades increased compared to the previous studies. Our results indicate an initial west-east division in the northern part of the Chlorocebus range with subsequent divergence into north-eastern and southern clades. This phylogeographic scenario contrasts with that for another widespread African savannah primate genus, the baboons (Papio), for which a dispersal from southern Africa into East and West Africa was suggested.
Zoological Journal of the Linnean Society
10.1093/zoolinnean/zlx001
0024-4082
1096-3642
wos:2017
WOS:000416367300010
Dolotovskaya, S; Roos, C (reprint author), Leibniz Inst Primate Res, German Primate Ctr, Primate Genet Lab, Kellnerweg 4, D-37077 Gottingen, Germany.; Roos, C (reprint author), Leibniz Inst Primate Res, German Primate Ctr, Gene Bank Primates, Kellnerweg 4, D-37077 Gottingen, Germany., s.dolotovskaya@gmail.com; croos@dpz.eu
German Volkswagen Foundation; German Primate Center
2021-03-29T10:13:49+00:00
sword
importub
filename=package.tar
93a6285e9b3c72ee0b44e465513e9d34
false
true
CC-BY - Namensnennung 4.0 International
Sofya Dolotovskaya
Juan Torroba Bordallo
Tanja Haus
Angela Noll
Michael Hofreiter
Dietmar Zinner
Christian Roos
eng
uncontrolled
African green monkeys
eng
uncontrolled
baboons
eng
uncontrolled
mitochondrial genomes
eng
uncontrolled
phylogeny
eng
uncontrolled
phylogeography
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
43159
2014
2021
eng
10
1117
postprint
1
2021-02-09
2021-02-09
--
Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes)
Background
The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures.
Results
To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya.
Conclusions
The results suggests that, as in mice, moa tbx5 is necessary for the induction of forelimbs, but is not sufficient for their outgrowth. Moa Tbx5 may have played an important role in the development of moa’s remnant forelimb girdle, and may be required for the formation of this structure. Our results further show that genetic changes affecting genes other than tbx5 must be responsible for the complete loss of forelimbs in moa.
Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-43159
urn:nbn:de:kobv:517-opus4-431599
1866-8372
online registration
BMC Evolutionary Biology 14 (2014), Art. 75 DOI: 10.1186/1471-2148-14-75
<a href="http://publishup.uni-potsdam.de/37847">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
75
false
true
CC-BY - Namensnennung 4.0 International
Leon Huynen
Takayuki Suzuki
Toshihiko Ogura
Yusuke Watanabe
Craig D. Millar
Michael Hofreiter
Craig Smith
Sara Mirmoeini
David M. Lambert
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1117
eng
uncontrolled
tbx5
eng
uncontrolled
Moa
eng
uncontrolled
gene expression
eng
uncontrolled
ancient DNA
eng
uncontrolled
development
eng
uncontrolled
forelimb
Biowissenschaften; Biologie
Medizin und Gesundheit
open_access
Institut für Biochemie und Biologie
Referiert
BioMed Central
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/43159/pmnr1117.pdf
43892
2015
2020
eng
1510
1522
15
965
postprint
1
2020-07-09
2020-07-09
--
Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100
Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.
Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe
10.25932/publishup-43892
urn:nbn:de:kobv:517-opus4-438920
1866-8372
online registration
Molecular Ecology 24 (2015) 7, 1510-1522 DOI:10.1111/mec.13121
<a href="http://publishup.uni-potsdam.de/39062">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Keine öffentliche Lizenz: Unter Urheberrechtsschutz
S. Elizabeth Alter
Matthias Meyer
Klaas Post
Paul Czechowski
Peter Gravlund
Cork Gaines
Howard C. Rosenbaum
Kristin Kaschner
Samuel T. Turvey
Johannes van der Plicht
Beth Shapiro
Michael Hofreiter
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
965
eng
uncontrolled
ancient DNA
eng
uncontrolled
climate change
eng
uncontrolled
last glacial maximum
eng
uncontrolled
marine mammal
Biowissenschaften; Biologie
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/43892/pmnr965.pdf
43935
2016
2020
eng
9
952
postprint
1
2020-06-10
2020-06-10
--
The genetics of an early Neolithic pastoralist from the Zagros, Iran
The agricultural transition profoundly changed human societies. We sequenced and analysed the first genome (1.39x) of an early Neolithic woman from Ganj Dareh, in the Zagros Mountains of Iran, a site with early evidence for an economy based on goat herding, ca. 10,000 BP. We show that Western Iran was inhabited by a population genetically most similar to hunter-gatherers from the Caucasus, but distinct from the Neolithic Anatolian people who later brought food production into Europe. The inhabitants of Ganj Dareh made little direct genetic contribution to modern European populations, suggesting those of the Central Zagros were somewhat isolated from other populations of the Fertile Crescent. Runs of homozygosity are of a similar length to those from Neolithic farmers, and shorter than those of Caucasus and Western Hunter-Gatherers, suggesting that the inhabitants of Ganj Dareh did not undergo the large population bottleneck suffered by their northern neighbours. While some degree of cultural diffusion between Anatolia, Western Iran and other neighbouring regions is possible, the genetic dissimilarity between early Anatolian farmers and the inhabitants of Ganj Dareh supports a model in which Neolithic societies in these areas were distinct.
Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-43935
urn:nbn:de:kobv:517-opus4-439355
1866-8372
Scientific Reports 6 (2016) 31326 DOI: 10.1038/srep31326
31326
CC-BY - Namensnennung 4.0 International
Marcos Gallego-Llorente
Connell Sarah
Eppie R. Jones
Deborah C. Merrett
Y. Jeon
Anders Eriksson
Veronika Siska
Cristina Gamba
Christopher Meiklejohn
Robert Beyer
Sungwon Jeon
Yun Sung Cho
Michael Hofreiter
Jong Bhak
Andrea Manica
Ron Pinhasi
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
952
eng
uncontrolled
whole-genome association
eng
uncontrolled
ancient
eng
uncontrolled
domestication
eng
uncontrolled
agriculture
eng
uncontrolled
mountains
eng
uncontrolled
diffusion
eng
uncontrolled
migration
eng
uncontrolled
admixture
eng
uncontrolled
patterns
eng
uncontrolled
sequence
eng
uncontrolled
archaeology
eng
uncontrolled
biological anthropology
Naturwissenschaften und Mathematik
Technik, Technologie
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/43935/pmnr952.pdf
44011
2017
2019
eng
1801
1820
21
794
postprint
1
2019-12-16
2019-12-16
--
Paleogenomic evidence for multi-generational mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the lower Danube Basin
The transition from hunting and gathering to farming involved profound cultural and technological changes. In Western and Central Europe, these changes occurred rapidly and synchronously after the arrival of early farmers of Anatolian origin [1-3], who largely replaced the local Mesolithic hunter-gatherers [1, 4-6]. Further east, in the Baltic region, the transition was gradual, with little or no genetic input from incoming farmers [7]. Here we use ancient DNA to investigate the relationship between hunter-gatherers and farmers in the Lower Danube basin, a geographically intermediate area that is characterized by a rapid Neolithic transition but also by the presence of archaeological evidence that points to cultural exchange, and thus possible admixture, between hunter-gatherers and farmers. We recovered four human paleogenomes (1.13 to 4.13 coverage) from Romania spanning a time transect between 8.8 thousand years ago (kya) and 5.4 kya and supplemented them with two Mesolithic genomes (1.73- and 5.33) from Spain to provide further context on the genetic background of Mesolithic Europe. Our results show major Western hunter-gatherer (WHG) ancestry in a Romanian Eneolithic sample with a minor, but sizeable, contribution from Anatolian farmers, suggesting multiple admixture events between hunter-gatherers and farmers. Dietary stableisotope analysis of this sample suggests a mixed terrestrial/ aquatic diet. Our results provide support for complex interactions among hunter-gatherers and farmers in the Danube basin, demonstrating that in some regions, demic and cultural diffusion were not mutually exclusive, but merely the ends of a continuum for the process of Neolithization.
Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
urn:nbn:de:kobv:517-opus4-440115
10.25932/publishup-44011
1866-8372
online registration
Current Biology 27 (2017) 12, S. 1801–1820 DOI: 10.1016/j.cub.2017.05.023
false
true
CC-BY - Namensnennung 4.0 International
Gloria M. González-Fortes
Eppie R. Jones
Emma Lightfoot
Clive Bonsall
Catalin Lazar
Aurora Grandal-d’Anglade
María Dolores Garralda
Labib Drak
Veronika Siska
Angela Simalcsik
Adina Boroneant
Juan Ramón Vidal Romaní
Marcos Vaqueiro Rodríguez
Pablo Arias
Ron Pinhasi
Andrea Manica
Michael Hofreiter
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
794
eng
uncontrolled
ancient DNA
eng
uncontrolled
eneolithic
eng
uncontrolled
neolithic transition
eng
uncontrolled
Romania
eng
uncontrolled
Iron Gates
eng
uncontrolled
mesolithic
Biowissenschaften; Biologie
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/44011/pmnr794.pdf
44013
2017
2019
eng
14
790
postprint
1
2019-12-10
2019-12-10
--
Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution
The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants (Elephas maximus), and many paleontologists place Palaeoloxodon within Elephas. Here, we report the recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils. These fossils were collected at two sites in Germany, Neumark-Nord and Weimar-Ehringsdorf, and likely date to interglacial periods similar to 120 and similar to 244 thousand years ago, respectively. Unexpectedly, nuclear and mitochondrial DNA analyses suggest that P. antiquus was a close relative of extant African forest elephants (Loxodonta cyclotis). Species previously referred to Palaeoloxodon are thus most parsimoniously explained as having diverged from the lineage of Loxodonta, indicating that Loxodonta has not been constrained to Africa. Our results demonstrate that the current picture of elephant evolution is in need of substantial revision.
Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
urn:nbn:de:kobv:517-opus4-440139
10.25932/publishup-44013
1866-8372
online registration
eLife 6 (2017) Art. e25413 DOI: 10.7554/eLife.25413
e25413
CC-BY - Namensnennung 4.0 International
Matthias Meyer
Eleftheria Palkopoulou
Sina Isabelle Baleka
Mathias Stiller
Kirsty E. H. Penkman
Kurt W. Alt
Yasuko Ishida
Dietrich Mania
Swapan Mallick
Tom Meijer
Harald Meller
Sarah Nagel
Birgit Nickel
Sven Ostritz
Nadin Rohland
Karol Schauer
Tim Schüler
Alfred L. Roca
David Reich
Beth Shapiro
Michael Hofreiter
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
790
eng
uncontrolled
genome sequence
eng
uncontrolled
woolly mammoth
eng
uncontrolled
Palaeoloxodon-antiquus
eng
uncontrolled
phylogenetic analysis
eng
uncontrolled
African elephants
eng
uncontrolled
DNA
eng
uncontrolled
Pleistocene
eng
uncontrolled
alignment
eng
uncontrolled
ancient
eng
uncontrolled
reveal
Naturwissenschaften und Mathematik
Technik, Technologie
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/44013/pmnr790.pdf
38996
2015
2015
eng
E1972
E1973
2
16
112
other
National Acad. of Sciences
Washington
1
--
--
--
Reply to Peng et al.: Archaeological contexts should not be ignored for early chicken domestication
Proceedings of the National Academy of Sciences of the United States of America
10.1073/pnas.1502207112
25795244
0027-8424
wos:2015
WOS:000353239100004
Hofreiter, M (reprint author), Univ Potsdam, Fac Math & Nat Sci, Inst Biochem & Biol, D-14476 Potsdam, Germany., michi@palaeo.eu; zhxb@cau.edu.cn
Hai Xiang
Michael Hofreiter
Xingbo Zhao
Institut für Biochemie und Biologie
Referiert
37493
2014
2014
eng
7
10
9
article
PLoS
San Fransisco
1
--
--
--
Phylogenetic distribution of extant richness suggests metamorphosis is a key innovation driving diversification in insects
Insects and their six-legged relatives (Hexapoda) comprise more than half of all described species and dominate terrestrial and freshwater ecosystems. Understanding the macroevolutionary processes generating this richness requires a historical perspective, but the fossil record of hexapods is patchy and incomplete. Dated molecular phylogenies provide an alternative perspective on divergence times and have been combined with birth-death models to infer patterns of diversification across a range of taxonomic groups. Here we generate a dated phylogeny of hexapod families, based on previously published sequence data and literature derived constraints, in order to identify the broad pattern of macroevolutionary changes responsible for the composition of the extant hexapod fauna. The most prominent increase in diversification identified is associated with the origin of complete metamorphosis, confirming this as a key innovation in promoting insect diversity. Subsequent reductions are recovered for several groups previously identified as having a higher fossil diversity during the Mesozoic. In addition, a number of recently derived taxa are found to have radiated following the development of flowering plant (angiosperm) floras during the mid-Cretaceous. These results reveal that the composition of the modern hexapod fauna is a product of a key developmental innovation, combined with multiple and varied evolutionary responses to environmental changes from the mid Cretaceous floral transition onward.
PLoS one
10.1371/journal.pone.0109085
25275450
1932-6203
wos:2014
e109085
WOS:000342591500056
Rainford, JL (reprint author), Univ York, Dept Biol, York YO10 5DD, N Yorkshire, England., jlr516@york.ac.uk
NERC [NE/J500197/1]; National Museums of Scotland; Natural History
Museum, London
James L. Rainford
Michael Hofreiter
David B. Nicholson
Peter J. Mayhew
Institut für Biochemie und Biologie
Referiert
Open Access
38144
2014
2014
eng
7
6169
343
review
American Assoc. for the Advancement of Science
Washington
1
--
--
--
A paleogenomic perspective on evolution and gene function: new insights from ancient DNA
The publication of partial and complete paleogenomes within the last few years has reinvigorated research in ancient DNA. No longer limited to short fragments of mitochondrial DNA, inference of evolutionary processes through time can now be investigated from genome-wide data sampled as far back as 700,000 years. Tremendous insights have been made, in particular regarding the hominin lineage. With rare exception, however, a paleogenomic perspective has been mired by the quality and quantity of recoverable DNA. Though conceptually simple, extracting ancient DNA remains challenging, and sequencing ancient genomes to high coverage remains prohibitively expensive for most laboratories. Still, with improvements in DNA isolation and declining sequencing costs, the taxonomic and geographic purview of paleogenomics is expanding at a rapid pace. With improved capacity to screen large numbers of samples for those with high proportions of endogenous ancient DNA, paleogenomics is poised to become a key technology to better understand recent evolutionary events.
Science
10.1126/science.1236573
24458647
0036-8075
1095-9203
wos:2014
1236573
WOS:000330039300001
Shapiro, B (reprint author), Univ Calif Santa Cruz, Dept Ecol & Evolutionary Biol, Santa Cruz, CA 95064 USA., beth.shapiro@gmail.com
B. Shapiro
Michael Hofreiter
Institut für Biochemie und Biologie
Referiert
38932
2015
2015
eng
E2416
E2416
1
19
112
other
National Acad. of Sciences
Washington
1
--
--
--
Reply to Peters et al.: Further discussions confirm early Holocene chicken domestication in northern China
Proceedings of the National Academy of Sciences of the United States of America
10.1073/pnas.1503956112
25886772
0027-8424
wos:2015
WOS:000354390600003
Hofreiter, M (reprint author), Univ Potsdam, Fac Math & Nat Sci, Inst Biochem & Biol, D-14476 Potsdam, Germany., michi@palaeo.eu; zhxb@cau.edu.cn
Hai Xiang
Jianqiang Gao
Baoquan Yu
Michael Hofreiter
Xingbo Zhao
Institut für Biochemie und Biologie
Referiert
38636
2015
2015
eng
701
710
10
9
93
review
NRC Research Press
Ottawa
1
--
--
--
Resurrecting phenotypes from ancient DNA sequences: promises and perspectives
Anatomical changes in extinct mammalian lineages over evolutionary time, such as the loss of fingers and teeth and the rapid increase in body size that accompanied the late Miocene dispersal of the progenitors of Steller's sea cows (Hydrodamalis gigas (Zimmermann, 1780)) into North Pacific waters and the convergent development of a thick pelage and accompanying reductions in ear and tail surface area of woolly mammoths (Mammuthus primigenius (Blumenbach, 1799)) and woolly rhinoceros (Coelodonta antiquitatis (Blumenbach, 1799)), are prime examples of adaptive evolution underlying the exploitation of new habitats. It is likely, however, that biochemical specializations adopted during these evolutionary transitions were of similar or even greater biological importance. As these "living" processes do not fossilize, direct information regarding the physiological attributes of extinct species has largely remained beyond the range of scientific inquiry. However, the ability to retrieve genomic sequences from ancient DNA samples, combined with ectopic expression systems, now permit the evolutionary origins and structural and functional properties of authentic prehistoric proteins to be examined in great detail. Exponential technical advances in ancient DNA retrieval, enrichment, and sequencing will soon permit targeted generation of complete genomes from hundreds of extinct species across the last one million years that, in combination with emerging in vitro expression, genome engineering, and cell differentiation techniques, promises to herald an exciting new trajectory of evolutionary research at the interface of biochemistry, genomics, palaeontology, and cell biology.
Canadian journal of zoology = Revue canadienne de zoologie
10.1139/cjz-2014-0337
0008-4301
1480-3283
wos:2015
WOS:000360946900004
Campbell, KL (reprint author), Univ Manitoba, Dept Biol Sci, Winnipeg, MB R3T 2N2, Canada., Kevin.Campbell@umanitoba.ca
University of Manitoba Research Grants Program (URGP); Natural Sciences
and Engineering Research Council of Canada (NSERC) Discovery Grant
[238838]; Natural Sciences and Engineering Research Council of Canada
(NSERC) Accelerator Supplement Grant [412336]; ERC consolidator grant
[310763 GeneFlow]
Kevin L. Campbell
Michael Hofreiter
eng
uncontrolled
paleophysiology
eng
uncontrolled
ancient DNA
eng
uncontrolled
extinct species
eng
uncontrolled
adaptation
eng
uncontrolled
protein structure
Institut für Biochemie und Biologie
Referiert
37969
2014
2014
eng
1717
1729
13
7
23
article
Wiley-Blackwell
Hoboken
1
--
--
--
Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe
After centuries of human hunting, the Eurasian beaver Castor fiber had disappeared from most of its original range by the end of the 19th century. The surviving relict populations are characterized by both low genetic diversity and strong phylogeographical structure. However, it remains unclear whether these attributes are the result of a human-induced, late Holocene bottleneck or already existed prior to this reduction in range. To investigate genetic diversity in Eurasian beaver populations during the Holocene, we obtained mitochondrial control region DNA sequences from 48 ancient beaver samples and added 152 modern sequences from GenBank. Phylogeographical analyses of the data indicate a differentiation of European beaver populations into three mitochondrial clades. The two main clades occur in western and eastern Europe, respectively, with an early Holocene contact zone in eastern Europe near a present-day contact zone. A divergent and previously unknown clade of beavers from the Danube Basin survived until at least 6000years ago, but went extinct during the transition to modern times. Finally, we identify a recent decline in effective population size of Eurasian beavers, with a stronger bottleneck signal in the western than in the eastern clade. Our results suggest that the low genetic diversity and the strong phylogeographical structure in recent beavers are artefacts of human hunting-associated population reductions. While beaver populations have been growing rapidly since the late 19th century, genetic diversity within modern beaver populations remains considerably reduced compared to what was present prior to the period of human hunting and habitat reduction.
Molecular ecology
10.1111/mec.12691
24795996
0962-1083
1365-294X
wos:2014
WOS:000333333500009
Horn, S (reprint author), Max Planck Inst Evolutionare Anthropol, Deutsch Pl 6, D-04103 Leipzig, Germany., horn@eva.mpg.de
Max Planck Society; Volkswagen foundation; German Academic Exchange
Service (DAAD); National Science Foundation [0909456]
Susanne Horn
Stefan Prost
Mathias Stiller
Daniel Makowiecki
Tatiana Kuznetsova
Norbert Benecke
Erich Pucher
Anne K. Hufthammer
Charles Schouwenburg
Beth Shapiro
Michael Hofreiter
eng
uncontrolled
Conservation Biology
eng
uncontrolled
Phylogeography
eng
uncontrolled
Conservation Genetics
eng
uncontrolled
Population Genetics - Empirical
Institut für Biochemie und Biologie
Referiert
38502
2015
2015
eng
13302
13307
6
43
112
article
National Acad. of Sciences
Washington
1
--
--
--
DNA capture reveals transoceanic gene flow in endangered river sharks
For over a hundred years, the "river sharks" of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks.
Proceedings of the National Academy of Sciences of the United States of America
10.1073/pnas.1508735112
26460025
0027-8424
wos:2015
WOS:000363458100057
Naylor, GJP (reprint author), Coll Charleston, Hollings Marine Lab, Charleston, SC 29412 USA., naylorg@cofc.edu
National Science Foundation Division of Environmental Biology Award
[1132229]; Innovation Program of Shanghai Municipal Education
Commission; Shanghai Pujiang Program; Program for Professor of Special
Appointment (Eastern Scholar) at Shanghai Institutions of Higher
Learning
Chenhong Li
Shannon Corrigan
Lei Yang
Nicolas Straube
Mark Harris
Michael Hofreiter
William T. White
Gavin J. P. Naylor
eng
uncontrolled
freshwater sharks
eng
uncontrolled
DNA
eng
uncontrolled
museum specimens
Institut für Biochemie und Biologie
Referiert
37847
2014
2014
eng
8
14
article
BioMed Central
London
1
--
--
--
Reconstruction and in vivo analysis of the extinct tbx5 gene from ancient wingless moa (Aves: Dinornithiformes)
Background: The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures.
Results: To determine the sequence of tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya.
BMC evolutionary biology
10.1186/1471-2148-14-75
24885927
1471-2148
wos:2014
75
WOS:000335852600001
Lambert, DM (reprint author), Griffith Univ, Environm Futures Ctr, 170 Kessels Rd, Nathan, Qld 4111, Australia., D.lambert@griffith.edu.au
Australian Research Council (The molecular evolution of wings in ratites) [DP110101364]
<a href="https://doi.org/10.25932/publishup-43159">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1117</a>
Leon Huynen
Takayuki Suzuki
Toshihiko Ogura
Yusuke Watanabe
Craig D. Millar
Michael Hofreiter
Craig Smith
Sara Mirmoeini
David M. Lambert
eng
uncontrolled
tbx5
eng
uncontrolled
Moa
eng
uncontrolled
Gene expression
eng
uncontrolled
Ancient DNA
eng
uncontrolled
Development
eng
uncontrolled
Forelimb
Institut für Biochemie und Biologie
Referiert
Open Access
38744
2015
2015
eng
15
16
article
BioMed Central
London
1
--
--
--
Kiwi genome provides insights into evolution of a nocturnal lifestyle
Background: Kiwi, comprising five species from the genus Apteryx, are endangered, ground-dwelling bird species endemic to New Zealand. They are the smallest and only nocturnal representatives of the ratites. The timing of kiwi adaptation to a nocturnal niche and the genomic innovations, which shaped sensory systems and morphology to allow this adaptation, are not yet fully understood.
Results: We sequenced and assembled the brown kiwi genome to 150-fold coverage and annotated the genome using kiwi transcript data and non-redundant protein information from multiple bird species. We identified evolutionary sequence changes that underlie adaptation to nocturnality and estimated the onset time of these adaptations. Several opsin genes involved in color vision are inactivated in the kiwi. We date this inactivation to the Oligocene epoch, likely after the arrival of the ancestor of modern kiwi in New Zealand. Genome comparisons between kiwi and representatives of ratites, Galloanserae, and Neoaves, including nocturnal and song birds, show diversification of kiwi's odorant receptors repertoire, which may reflect an increased reliance on olfaction rather than sight during foraging. Further, there is an enrichment of genes influencing mitochondrial function and energy expenditure among genes that are rapidly evolving specifically on the kiwi branch, which may also be linked to its nocturnal lifestyle.
Conclusions: The genomic changes in kiwi vision and olfaction are consistent with changes that are hypothesized to occur during adaptation to nocturnal lifestyle in mammals. The kiwi genome provides a valuable genomic resource for future genome-wide comparative analyses to other extinct and extant diurnal ratites.
Genome biology : biology for the post-genomic era
10.1186/s13059-015-0711-4
26201466
1465-6906
1474-760X
wos:2015
147
WOS:000358345900001
Le Duc, D (reprint author), Univ Leipzig, Fac Med, Inst Biochem, Johannisallee 30, D-04103 Leipzig, Germany., diana_leduc@eva.mpg.de; schoberg@medizin.uni-leipzig.de
Deutsche Forschungsgemeinschaft; Medical Faculty, University of Leipzig;
Australian Research Council; Swedish Research Council; NSERC; Max Planck
Society; Sao Paulo Research Foundation (FAPESP) [2011/12500-2]
Diana Le Duc
Gabriel Renaud
Arunkumar Krishnan
Markus Sallman Almen
Leon Huynen
Sonja J. Prohaska
Matthias Ongyerth
Barbara D. Bitarello
Helgi B. Schioth
Michael Hofreiter
Peter F. Stadler
Kay Prüfer
David Lambert
Janet Kelso
Torsten Schöneberg
Institut für Biochemie und Biologie
Referiert
37304
2014
2014
eng
17564
17569
6
49
111
article
National Acad. of Sciences
Washington
1
--
--
--
Early Holocene chicken domestication in northern China
Chickens represent by far the most important poultry species, yet the number, locations, and timings of their domestication have remained controversial for more than a century. Here we report ancient mitochondrial DNA sequences from the earliest archaeological chicken bones from China, dating back to similar to 10,000 B.P. The results clearly show that all investigated bones, including the oldest from the Nanzhuangtou site, are derived from the genus Gallus, rather than any other related genus, such as Phasianus. Our analyses also suggest that northern China represents one region of the earliest chicken domestication, possibly dating as early as 10,000 y B.P. Similar to the evidence from pig domestication, our results suggest that these early domesticated chickens contributed to the gene pool of modern chicken populations. Moreover, our results support the idea that multiple members of the genus Gallus, specifically Gallus gallus and Gallus sonneratii contributed to the gene pool of the modern domestic chicken. Our results provide further support for the growing evidence of an early mixed agricultural complex in northern China.
Proceedings of the National Academy of Sciences of the United States of America
10.1073/pnas.1411882111
25422439
0027-8424
wos:2014
WOS:000345921500053
Hofreiter, M (reprint author), Univ Potsdam, Inst Biochem & Biol, Fac Math & Nat Sci, D-14476 Potsdam, Germany., michi@palaeo.eu; zhxb@cau.edu.cn
National Key Basic Research Program of China [2014CB138500];
Domain-Specific Projects for Transgenic Biological Breeding
[2014ZX08009-002]
Hai Xiang
Jianqiang Gao
Baoquan Yu
Hui Zhou
Dawei Cai
Youwen Zhang
Xiaoyong Chen
Xi Wang
Michael Hofreiter
Xingbo Zhao
eng
uncontrolled
ancient DNA
eng
uncontrolled
chicken
eng
uncontrolled
domestication
eng
uncontrolled
species origin
Institut für Biochemie und Biologie
Referiert
37283
2014
2014
eng
E5661
E5669
9
52
111
article
National Acad. of Sciences
Washington
1
--
--
--
Prehistoric genomes reveal the genetic foundation and cost of horse domestication
Proceedings of the National Academy of Sciences of the United States of America
10.1073/pnas.1416991111
25512547
0027-8424
wos:2014
WOS:000347444400011
Orlando, L (reprint author), Nat Hist Museum Denmark, Ctr GeoGenet, DK-1350 Copenhagen K, Denmark., Lorlando@snm.ku.dk
Danish Council for Independent Research, Natural Sciences (FNU); Danish
National Research Foundation [DNFR94]; Marie-Curie Career Integration
Grant (FP7) [CIG-293845]; International Research Group Program
[IRG14-08]; Deanship of Scientific Research (King Saud University, Saudi
Arabia); Marie-Curie Initial Training Network Grant (EUROTAST) [FP7
ITN-290344]; Marie-Curie Intra-European Fellowships [FP7 IEF-299176, FP7
IEF-302617]; Lundbeck Foundation Grant [R52-A5062]; Swiss National
Science Foundation Grant [31003A-143393]; European Research Council
(ERC) Consolidator Grant [310763]; ERC Starting Grant [260372];
Ministerio de Ciencia e Innovacion (MICINN) Grant [BFU2011-28549];
Packard Foundation; University of California, Santa Cruz
Mikkel Schubert
Hakon Jonsson
Dan Chang
Clio Der Sarkissian
Luca Ermini
Aurelien Ginolhac
Anders Albrechtsen
Isabelle Dupanloup
Adrien Foucal
Bent Larsen Petersen
Matteo Fumagalli
Maanasa Raghavan
Andaine Seguin-Orlando
Thorfinn S. Korneliussen
Amhed M. V. Velazquez
Jesper Stenderup
Cindi A. Hoover
Carl-Johan Rubin
Ahmed H. Alfarhan
Saleh A. Alquraishi
Khaled A. S. Al-Rasheid
David E. MacHugh
Ted Kalbfleisch
James N. MacLeod
Edward M. Rubin
Thomas Sicheritz-Ponten
Leif Andersson
Michael Hofreiter
Tomas Marques-Bonet
M. Thomas P. Gilbert
Rasmus Nielsen
Laurent Excoffier
Eske Willerslev
Beth Shapiro
Ludovic Orlando
Institut für Biochemie und Biologie
Referiert
38409
2015
2015
eng
505
515
11
4
7
article
Springer
Heidelberg
1
--
--
--
Burial condition is the most important factor for mtDNA PCR amplification success in Palaeolithic equid remains from the Alpine foreland
Faunal remains from Palaeolithic sites are important genetic sources to study preglacial and postglacial populations and to investigate the effect of climate change and human impact. Post mortem decay, resulting in fragmented and chemically modified DNA, is a key obstacle in ancient DNA analyses. In the absence of reliable methods to determine the presence of endogenous DNA in sub-fossil samples, temporal and spatial surveys of DNA survival on a regional scale may help to estimate the potential of faunal remains from a given time period and region. We therefore investigated PCR amplification success, PCR performance and post mortem damage in c. 47,000 to c. 12,000-year-old horse remains from 14 Palaeolithic sites along the Swiss Jura Mountains in relation to depositional context, tissue type, storage time and age, potentially influencing DNA preservation. The targeted 75 base pair mitochondrial DNA fragment could be amplified solely from equid remains from caves and not from any of the open dry and (temporary) wetland sites. Whether teeth are better than bones cannot be ultimately decided; however, both storage time after excavation and age significantly affect PCR amplification and performance, albeit not in a linear way. This is best explained by the-inevitable-heterogeneity of the data set. The extent of post mortem damage is not related to any of the potential impact factors. The results encourage comprehensive investigations of Palaeolithic cave sites, even from temperate regions.
Archaeological and anthropological sciences
10.1007/s12520-014-0213-4
1866-9557
1866-9565
wos:2015
WOS:000365796700008
Elsner, J (reprint author), Univ Basel, Integrat Prehist & Archaeol Sci, Spalenring 145, CH-4055 Basel, Switzerland., Julia.Elsner@unibas.ch
Swiss National Science Foundation [K-31K1_120528/1]; Freiwillige Akademische Gesellschaft Basel, Nikolaus; Bertha Burckhardt-Burgin-Foundation
<a href="http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429763">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 727</a>
Julia Elsner
Joerg Schibler
Michael Hofreiter
Angela Schlumbaum
eng
uncontrolled
Ancient DNA
eng
uncontrolled
DNA preservation
eng
uncontrolled
Horse
eng
uncontrolled
Cave
eng
uncontrolled
Switzerland
Institut für Biochemie und Biologie
Referiert
40732
2016
2018
eng
17
postprint
1
2018-06-19
2018-06-19
--
Phylogenetic analyses suggest that diversification and body size evolution are independent in insects
Background:
Skewed body size distributions and the high relative richness of small-bodied taxa are a fundamental
property of a wide range of animal clades. The evolutionary processes responsible for generating these distributions
are well described in vertebrate model systems but have yet to be explored in detail for other major terrestrial
clades. In this study, we explore the macro-evolutionary patterns of body size variation across families of Hexapoda
(insects and their close relatives), using recent advances in phylogenetic understanding, with an aim to investigate
the link between size and diversity within this ancient and highly diverse lineage.
Results:
The maximum, minimum and mean-log body lengths of hexapod families are all approximately log-normally
distributed, consistent with previous studies at lower taxonomic levels, and contrasting with skewed distributions
typical of vertebrate groups. After taking phylogeny and within-tip variation into account, we find no evidence for a
negative relationship between diversification rate and body size, suggesting decoupling of the forces controlling these
two traits. Likelihood-based modeling of the log-mean body size identifies distinct processes operating within
Holometabola and Diptera compared with other hexapod groups, consistent with accelerating rates of size evolution
within these clades, while as a whole, hexapod body size evolution is found to be dominated by neutral processes
including significant phylogenetic conservatism.
Conclusions:
Based on our findings we suggest that the use of models derived from well-studied but atypical clades,
such as vertebrates may lead to misleading conclusions when applied to other major terrestrial lineages. Our results
indicate that within hexapods, and within the limits of current systematic and phylogenetic knowledge, insect
diversification is generally unfettered by size-biased macro-evolutionary processes, and that these processes over large
timescales tend to converge on apparently neutral evolutionary processes. We also identify limitations on available
data within the clade and modeling approaches for the resolution of trees of higher taxa, the resolution of which may
collectively enhance our understanding of this key component of terrestrial ecosystems.
BMC evolutionary biology
urn:nbn:de:kobv:517-opus4-407328
online registration
BMC Evolutionary Biology 16 (2016); DOI: 10.1186/s12862-015-0570-3
CC-BY - Namensnennung 4.0 International
James L. Rainford
Michael Hofreiter
Peter J. Mayhew
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
441
eng
uncontrolled
body size
eng
uncontrolled
diversification
eng
uncontrolled
hexapoda
eng
uncontrolled
insects
eng
uncontrolled
phylogeny
Biowissenschaften; Biologie
Medizin und Gesundheit
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Institut für Biochemie und Biologie
Referiert
Open Access
BioMed Central
Universität Potsdam
https://publishup.uni-potsdam.de/files/40732/pmnr_441.online.pdf
44675
2016
2016
eng
8846
8856
11
6
article
Wiley-Blackwell
Hoboken
1
--
--
--
Does cooperation mean kinship between spatially discrete ant nests?
Eusociality is one of the most complex forms of social organization, characterized by cooperative and reproductive units termed colonies. Altruistic behavior of workers within colonies is explained by inclusive fitness, with indirect fitness benefits accrued by helping kin. Members of a social insect colony are expected to be more closely related to one another than they are to other conspecifics. In many social insects, the colony can extend to multiple socially connected but spatially separate nests (polydomy). Social connections, such as trails between nests, promote cooperation and resource exchange, and we predict that workers from socially connected nests will have higher internest relatedness than those from socially unconnected, and noncooperating, nests. We measure social connections, resource exchange, and internest genetic relatedness in the polydomous wood ant Formica lugubris to test whether (1) socially connected but spatially separate nests cooperate, and (2) high internest relatedness is the underlying driver of this cooperation. Our results show that socially connected nests exhibit movement of workers and resources, which suggests they do cooperate, whereas unconnected nests do not. However, we find no difference in internest genetic relatedness between socially connected and unconnected nest pairs, both show high kinship. Our results suggest that neighboring pairs of connected nests show a social and cooperative distinction, but no genetic distinction. We hypothesize that the loss of a social connection may initiate ecological divergence within colonies. Genetic divergence between neighboring nests may build up only later, as a consequence rather than a cause of colony separation.
Ecology and evolution
10.1002/ece3.2590
28035273
2045-7758
wos2016:2019
WOS:000392063300017
Procter, DS (reprint author), Univ York, York Ctr Complex Syst Anal, York, N Yorkshire, England.; Procter, DS (reprint author), Univ York, Dept Biol, York, N Yorkshire, England., duncan.procter@bristol.ac.uk
Natural Environment Research Council [NE/J017094/1]; Forest Research; Royal Society
importub
2020-03-22T12:10:01+00:00
filename=package.tar
f6940b5f91ce3b4a4cad2abd1427ca29
Duncan S. Procter
Joan E. Cottrell
Kevin Watts
Michael Hofreiter
Elva J. H. Robinson
eng
uncontrolled
colony organization
eng
uncontrolled
eusociality
eng
uncontrolled
Formica lugubris
eng
uncontrolled
kin selection
eng
uncontrolled
polydomy
eng
uncontrolled
social organization
Institut für Biochemie und Biologie
Referiert
Import
44657
2016
2016
eng
9
6
article
Nature Publ. Group
London
1
--
--
--
Spotted phenotypes in horses lost attractiveness in the Middle Ages
Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in similar to 3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genotype analyses show a significant increase in spotted coats in early domestic horses (Copper Age to Iron Age). In contrast, medieval horses carried significantly fewer alleles for these phenotypes, whereas solid phenotypes (i.e., chestnut) became dominant. This shift may have been supported because of (i) pleiotropic disadvantages, (ii) a reduced need to separate domestic horses from their wild counterparts, (iii) a lower religious prestige, or (iv) novel developments in weaponry. These scenarios may have acted alone or in combination. However, the dominance of chestnut is a remarkable feature of the medieval horse population.
Scientific reports
10.1038/srep38548
27924839
2045-2322
wos2016:2019
38548
WOS:000389525100002
Ludwig, A (reprint author), Leibniz Inst Zoo & Wildlife Res, Dept Evolutionary Genet, D-10315 Berlin, Germany., ludwig@izw-berlin.de
Deutsche Forschungsgemeinschaft [LU 852/7-4]
importub
2020-03-22T12:01:02+00:00
filename=package.tar
2e8d69317be8062de1e7aaa81c881544
Saskia Wutke
Norbert Benecke
Edson Sandoval-Castellanos
Hans-Jürgen Döhle
Susanne Friederich
Javier Esteban Gonzalez Soto
Jon Hallsteinn Hallsson
Michael Hofreiter
Lembi Lougas
Ola Magnell
Arturo Morales-Muniz
Ludovic Orlando
Albina Hulda Palsdottir
Monika Reissmann
Matej Ruttkay
Alexandra Trinks
Arne Ludwig
Institut für Biochemie und Biologie
Referiert
Import
45062
2016
2016
eng
R697
R699
3
26
other
Cell Press
Cambridge
1
--
--
--
The origin of ambling horses
Horseback riding is the most fundamental use of domestic horses and has had a huge influence on the development of human societies for millennia. Over time, riding techniques and the style of riding improved. Therefore, horses with the ability to perform comfortable gaits (e.g. ambling or pacing), so-called ‘gaited’ horses, have been highly valued by humans, especially for long distance travel. Recently, the causative mutation for gaitedness in horses has been linked to a substitution causing a premature stop codon in the DMRT3 gene (DMRT3_Ser301STOP) [1]. In mice, Dmrt3 is expressed in spinal cord interneurons and plays an important role in the development of limb movement coordination [1]. Genotyping the position in 4396 modern horses from 141 breeds revealed that nowadays the mutated allele is distributed worldwide with an especially high frequency in gaited horses and breeds used for harness racing [2]. Here, we examine historic horse remains for the DMRT3 SNP, tracking the origin of gaitedness to Medieval England between 850 and 900 AD. The presence of the corresponding allele in Icelandic horses (9th–11th century) strongly suggests that ambling horses were brought from the British Isles to Iceland by Norse people. Considering the high frequency of the ambling allele in early Icelandic horses, we believe that Norse settlers selected for this comfortable mode of horse riding soon after arrival. The absence of the allele in samples from continental Europe (including Scandinavia) at this time implies that ambling horses may have spread from Iceland and maybe also the British Isles across the continent at a later date.
Current biology
10.1016/j.cub.2016.07.001
27505236
0960-9822
1879-0445
wos2016:2019
WOS:000381241100004
Ludwig, A (reprint author), Leibniz Inst Zoo & Wildlife Res, Dept Evolutionary Genet, Alfred Kowalke Str 17, D-10315 Berlin, Germany.; Hofreiter, M (reprint author), Univ Potsdam, Inst Biochem & Biol, Fac Math & Nat Sci, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany., michi@palaeo.eu; ludwig@izw-berlin.de
importub
2020-03-22T15:23:01+00:00
filename=package.tar
357c8fe89ebcadef456bf9153ecbc709
Saskia Wutke
Leif Andersson
Norbert Benecke
Edson Sandoval-Castellanos
Javier Gonzalez
Jon Hallsteinn Hallsson
Lembi Lougas
Ola Magnell
Arturo Morales-Muniz
Ludovic Orlando
Albina Hulda Palsdottir
Monika Reissmann
Mariana B. Munoz-Rodriguez
Matej Ruttkay
Alexandra Trinks
Michael Hofreiter
Arne Ludwig
Institut für Biochemie und Biologie
Referiert
Import
45231
2016
2016
eng
6707
6712
6
113
article
National Acad. of Sciences
Washington
1
--
--
--
Ancient and modern DNA reveal dynamics of domestication and cross-continental dispersal of the dromedary
Dromedaries have been fundamental to the development of human societies in arid landscapes and for long-distance trade across hostile hot terrains for 3,000 y. Today they continue to be an important livestock resource in marginal agro-ecological zones. However, the history of dromedary domestication and the influence of ancient trading networks on their genetic structure have remained elusive. We combined ancient DNA sequences of wild and early-domesticated dromedary samples from arid regions with nuclear microsatellite and mitochondrial genotype information from 1,083 extant animals collected across the species’ range. We observe little phylogeographic signal in the modern population, indicative of extensive gene flow and virtually affecting all regions except East Africa, where dromedary populations have remained relatively isolated. In agreement with archaeological findings, we identify wild dromedaries from the southeast Arabian Peninsula among the founders of the domestic dromedary gene pool. Approximate Bayesian computations further support the “restocking from the wild” hypothesis, with an initial domestication followed by introgression from individuals from wild, now-extinct populations. Compared with other livestock, which show a long history of gene flow with their wild ancestors, we find a high initial diversity relative to the native distribution of the wild ancestor on the Arabian Peninsula and to the brief coexistence of early-domesticated and wild individuals. This study also demonstrates the potential to retrieve ancient DNA sequences from osseous remains excavated in hot and dry desert environments.
Proceedings of the National Academy of Sciences of the United States of America
10.1073/pnas.1519508113
27162355
0027-8424
wos2016:2019
WOS:000377948800047
Hanotte, O (reprint author), Univ Nottingham, Genet Ecol & Evolut, Sch Life Sci, Nottingham NG7 2RD, England.; Burger, PA (reprint author), Vetmeduni Vienna, Res Inst Wildlife Ecol, A-1160 Vienna, Austria., olivier.hanotte@nottingham.ac.uk; pamela.burger@vetmeduni.ac.at
Grant KFU from King Faisal University, Saudi Arabia [F289]; Natural Environment Research Council, Sheffield University, United Kingdom [NBAF419]; European Research Council Consolidator Grant [310763]; Austrian Science Fund [P21084-B17, P24706-B25]; Austrian Programme for Advanced Research and Technology Fellowship from the Austrian Academy of Sciences [1106/12]
importub
2020-03-22T16:48:01+00:00
filename=package.tar
50978bcf708e96d82821b3a0420af4f9
Faisal Almathen
Pauline Charruau
Elmira Mohandesan
Joram M. Mwacharo
Pablo Orozco-terWengel
Daniel Pitt
Abdussamad M. Abdussamad
Margarethe Uerpmann
Hans-Peter Uerpmann
Bea De Cupere
Peter Magee
Majed A. Alnaqeeb
Bashir Salim
Abdul Raziq
Tadelle Dessie
Omer M. Abdelhadi
Mohammad H. Banabazi
Marzook Al-Eknah
Chris Walzer
Bernard Fayer
Michael Hofreiter
Joris Peters
Olivier Hanotte
Pamela A. Burger
eng
uncontrolled
anthropogenic admixture
eng
uncontrolled
Camelus dromedarius
eng
uncontrolled
demographic history
eng
uncontrolled
paleogenetics
eng
uncontrolled
wild dromedary
Institut für Biochemie und Biologie
Referiert
Import
44975
2016
2016
eng
11
371
review
Royal Society
London
1
--
--
--
Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans
Philosophical transactions of the Royal Society of London : B, Biological sciences
10.1098/rstb.2015.0332
0962-8436
1471-2970
wos2016:2019
20150332
WOS:000381779700010
Speller, C (reprint author), Univ York, Dept Archaeol, BioArCh, Environm Bldg, York Y010 5DD, N Yorkshire, England.; Hofreiter, M (reprint author), Univ Potsdam, Fac Math & Nat Sci, Inst Biochem & Biol, D-14476 Potsdam, Germany., camilla.speller@york.ac.uk; michael.hofreiter@uni-potsdam.de
European Research Council [ORCA FP7-PEOPLE-2011-IIF 299075]; Labex Archimede programme at the University Paul-Valery Montpellier 3 [IA- ANR-11-LABX-0032-01]; Project MORSE [CEP&S 2011-ANR-279 11-CEPL-006];
importub
2020-03-22T14:40:01+00:00
filename=package.tar
cb4b43f75e9d86c32963933fa48abf61
Camilla Speller
Youri van den Hurk
Anne Charpentier
Ana Rodrigues
Armelle Gardeisen
Barbara Wilkens
Krista McGrath
Keri Rowsell
Luke Spindler
Matthew J. Collins
Michael Hofreiter
eng
uncontrolled
ancient DNA
eng
uncontrolled
archaeozoology
eng
uncontrolled
cetaceans
eng
uncontrolled
collagen peptide mass fingerprinting
eng
uncontrolled
species identification
eng
uncontrolled
zooarchaeology by mass spectrometry
Institut für Biochemie und Biologie
Referiert
Import
45694
2016
2016
eng
47
55
17
16
article
BioMed Central
London
1
--
--
--
Phylogenetic analyses suggest that diversification and body size evolution are independent in insects
Background: Skewed body size distributions and the high relative richness of small-bodied taxa are a fundamental property of a wide range of animal clades. The evolutionary processes responsible for generating these distributions are well described in vertebrate model systems but have yet to be explored in detail for other major terrestrial clades. In this study, we explore the macro-evolutionary patterns of body size variation across families of Hexapoda (insects and their close relatives), using recent advances in phylogenetic understanding, with an aim to investigate the link between size and diversity within this ancient and highly diverse lineage. Results: The maximum, minimum and mean-log body lengths of hexapod families are all approximately log-normally distributed, consistent with previous studies at lower taxonomic levels, and contrasting with skewed distributions typical of vertebrate groups. After taking phylogeny and within-tip variation into account, we find no evidence for a negative relationship between diversification rate and body size, suggesting decoupling of the forces controlling these two traits. Likelihood-based modeling of the log-mean body size identifies distinct processes operating within Holometabola and Diptera compared with other hexapod groups, consistent with accelerating rates of size evolution within these clades, while as a whole, hexapod body size evolution is found to be dominated by neutral processes including significant phylogenetic conservatism. Conclusions: Based on our findings we suggest that the use of models derived from well-studied but atypical clades, such as vertebrates may lead to misleading conclusions when applied to other major terrestrial lineages. Our results indicate that within hexapods, and within the limits of current systematic and phylogenetic knowledge, insect diversification is generally unfettered by size-biased macro-evolutionary processes, and that these processes over large timescales tend to converge on apparently neutral evolutionary processes. We also identify limitations on available data within the clade and modeling approaches for the resolution of trees of higher taxa, the resolution of which may collectively enhance our understanding of this key component of terrestrial ecosystems.
BMC evolutionary biology
10.1186/s12862-015-0570-3
26746988
1471-2148
wos2016:2019
8
WOS:000367779100001
Mayhew, PJ (reprint author), Univ York, Dept Biol, York YO10 5DD, N Yorkshire, England., peter.mayhew@york.ac.uk
NERC [NE/J500197/1]
importub
2020-03-22T20:40:01+00:00
filename=package.tar
c71581270d5eeee82a43d88396c75eda
James L. Rainford
Michael Hofreiter
Peter J. Mayhew
eng
uncontrolled
Body size
eng
uncontrolled
Diversification
eng
uncontrolled
Hexapoda
eng
uncontrolled
Insects
eng
uncontrolled
Phylogeny
Institut für Biochemie und Biologie
Referiert
Import
46210
2017
2017
eng
2893
2907
15
34
article
Oxford Univ. Press
Oxford
1
--
--
--
Spatiotemporal Dynamics of Genetic Variation in the Iberian Lynx along Its Path to Extinction Reconstructed with Ancient DNA
There is the tendency to assume that endangered species have been both genetically and demographically healthier in the past, so that any genetic erosion observed today was caused by their recent decline. The Iberian lynx (Lynx pardinus) suffered a dramatic and continuous decline during the 20th century, and now shows extremely low genome- and species-wide genetic diversity among other signs of genomic erosion. We analyze ancient (N = 10), historical (N = 245), and contemporary (N = 172) samples with microsatellite and mitogenome data to reconstruct the species' demography and investigate patterns of genetic variation across space and time. Iberian lynx populations transitioned from low but significantly higher genetic diversity than today and shallow geographical differentiation millennia ago, through a structured metapopulation with varying levels of diversity during the last centuries, to two extremely genetically depauperate and differentiated remnant populations by 2002. The historical subpopulations show varying extents of genetic drift in relation to their recent size and time in isolation, but these do not predict whether the populations persisted or went finally extinct. In conclusion, current genetic patterns were mainly shaped by genetic drift, supporting the current admixture of the two genetic pools and calling for a comprehensive genetic management of the ongoing conservation program. This study illustrates how a retrospective analysis of demographic and genetic patterns of endangered species can shed light onto their evolutionary history and this, in turn, can inform conservation actions.
Molecular biology and evolution
10.1093/molbev/msx222
28962023
0737-4038
1537-1719
wos:2017
WOS:000416178700012
Godoy, JA (reprint author), CSIC, Donana Biol Stn EBD, Dept Integrat Ecol, Seville, Spain., godoy@ebd.csic.es
Spanish Direction General de Investigation Cientifica y Tecnica [CGL2006-10853/BOS, CGL2010-21540/BOS]; Spanish Ministerio de Ciencia e Innovation (MICINN) [CGL2013-47755-P]; Fundacion BBVA through a project on ancient lynx genetics; CSIC (Spanish National Research Council); Programa Internacional de Becas "La Caixa-Severo Ochoa"; Ministerio de Ciencia e Innovation (MICINN) [HAR2014-55131]; Generalitat de Catalunya [SGR2014-108]; LIFE project [LIFE-NAT 06/E/000209, LIFE10 NAT/E/000570]
importub
2020-04-19T23:34:02+00:00
filename=package.tar
4b963219599735cc840ff588d2b9de97
Mireia Casas-Marce
Elena Marmesat
Laura Soriano
Begona Martinez-Cruz
Maria Lucena-Perez
Francisco Nocete
Antonio Rodriguez-Hidalgo
Antoni Canals
Jordi Nadal
Cleia Detry
Eloisa Bernaldez-Sanchez
Carlos Fernandez-Rodriguez
Manuel Perez-Ripoll
Mathias Stiller
Michael Hofreiter
Alejandro Rodriguez
Eloy Revilla
Miguel Delibes
Jose A. Godoy
eng
uncontrolled
Iberian lynx
eng
uncontrolled
ancient DNA
eng
uncontrolled
paleogenetics
eng
uncontrolled
genetic erosion
eng
uncontrolled
endangered species
Institut für Biochemie und Biologie
Referiert
Import
39062
2015
2015
eng
1510
1522
13
7
24
article
Wiley-Blackwell
Hoboken
1
--
--
--
Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100
Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.
Molecular ecology
10.1111/mec.13121
25753251
0962-1083
1365-294X
wos:2015
WOS:000351631500009
Alter, SE (reprint author), CUNY York Coll, Dept Biol, 94-20 Guy R Brewer Blvd, Jamaica, NY 11415 USA., sealter@gmail.com
Max Planck Society; Packard Foundation; European Research Council [310763]
<a href="https://doi.org/10.25932/publishup-43892">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 965</a>
S. Elizabeth Alter
Matthias Meyer
Klaas Post
Paul Czechowski
Peter Gravlund
Cork Gaines
Howard C. Rosenbaum
Kristin Kaschner
Samuel T. Turvey
Johannes van der Plicht
Beth Shapiro
Michael Hofreiter
eng
uncontrolled
ancient DNA
eng
uncontrolled
climate change
eng
uncontrolled
last glacial maximum
eng
uncontrolled
marine mammal
Institut für Biochemie und Biologie
Referiert
39249
2015
2015
eng
6
1660
370
preprint
Royal Society
London
1
--
--
--
Ancient DNA: the first three decades
Philosophical transactions of the Royal Society of London : B, Biological sciences
10.1098/rstb.2013.0371
25487324
0962-8436
1471-2970
wos:2015
20130371
WOS:000346147700001
Hagelberg, E (reprint author), Univ Oslo, Dept Biosci, POB 1066, N-0316 Oslo, Norway., erika.hagelberg@ibv.uio.no
Erika Hagelberg
Michael Hofreiter
Christine Keyser
eng
uncontrolled
ancient DNA
eng
uncontrolled
human evolutionary genetics
eng
uncontrolled
palaeogenomics
Institut für Biochemie und Biologie
Referiert
39251
2015
2015
eng
7
1660
370
article
Royal Society
London
1
--
--
--
Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing
Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.
Philosophical transactions of the Royal Society of London : B, Biological sciences
10.1098/rstb.2013.0379
25487331
0962-8436
1471-2970
wos:2015
20130379
WOS:000346147700008
Bradley, DG (reprint author), Univ Dublin Trinity Coll, Smurfit Inst Genet, Dublin 2, Ireland., dbradley@tcd.ie
ERC [295729-CodeX]; EU Marie Curie Fellowship Palimpsest; EU Marie Curie
ETN LeCHE Fellowship
Matthew David Teasdale
N. L. van Doorn
S. Fiddyment
C. C. Webb
Michael Hofreiter
Matthew J. Collins
Daniel G. Bradley
eng
uncontrolled
parchment
eng
uncontrolled
next generation sequencing
eng
uncontrolled
ancient DNA
eng
uncontrolled
ZooMS
eng
uncontrolled
sheep
Institut für Biochemie und Biologie
Referiert
39190
2015
2015
eng
210
216
7
54
article
Elsevier
London
1
--
--
--
Palaeolithic dogs and Pleistocene wolves revisited: a reply to Morey (2014)
This is a reply to the comments of Morey (2014) on our identification of Palaeolithic dogs from several European Palaeolithic sites. In his comments Morey (2014) presents some misrepresentations and misunderstandings that we remedy here. In contrast to what Morey (2014) propounds, our results suggest that the domestication of the wolf was a long process that started early in the Upper Palaeolithic and that since that time two sympatric canid morphotypes can be seen in Eurasian sites: Pleistocene wolves and Palaeolithic dogs. Contrary to Morey (2014), we are convinced that the study of this domestication process should be multidisciplinary. (C) 2014 Elsevier Ltd. All rights reserved.
Journal of archaeological science
10.1016/j.jas.2014.11.035
0305-4403
1095-9238
wos:2015
WOS:000350182900019
Germonpre, M (reprint author), Royal Belgian Inst Nat Sci, Directorate Earth & Hist Life, Vautierstr 29, B-1000 Brussels, Belgium., mietje.germonpre@naturalsciences.be
Mietje Germonpre
Mikhail V. Sablin
Martina Laznickova-Galetova
Viviane Despres
Rhiannon E. Stevens
Mathias Stiller
Michael Hofreiter
eng
uncontrolled
Canid morphotype
eng
uncontrolled
Dog
eng
uncontrolled
Domestication
eng
uncontrolled
Palaeolithic
eng
uncontrolled
Pleistocene
eng
uncontrolled
Wolf
Institut für Biochemie und Biologie
Referiert
42976
2015
2019
eng
505
515
11
727
postprint
1
2019-06-17
2019-06-17
--
Burial condition is the most important factor for mtDNA PCR amplification success in Palaeolithic equid remains from the Alpine foreland
Faunal remains from Palaeolithic sites are important genetic sources to study preglacial and postglacial populations and to investigate the effect of climate change and human impact. Post mortem decay, resulting in fragmented and chemically modified DNA, is a key obstacle in ancient DNA analyses. In the absence of reliable methods to determine the presence of endogenous DNA in sub-fossil samples, temporal and spatial surveys of DNA survival on a regional scale may help to estimate the potential of faunal remains from a given time period and region. We therefore investigated PCR amplification success, PCR performance and post mortem damage in c. 47,000 to c. 12,000-year-old horse remains from 14 Palaeolithic sites along the Swiss Jura Mountains in relation to depositional context, tissue type, storage time and age, potentially influencing DNA preservation. The targeted 75 base pair mitochondrial DNA fragment could be amplified solely from equid remains from caves and not from any of the open dry and (temporary) wetland sites. Whether teeth are better than bones cannot be ultimately decided; however, both storage time after excavation and age significantly affect PCR amplification and performance, albeit not in a linear way. This is best explained by the—inevitable—heterogeneity of the data set. The extent of post mortem damage is not related to any of the potential impact factors. The results encourage comprehensive investigations of Palaeolithic cave sites, even from temperate regions.
Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-42976
urn:nbn:de:kobv:517-opus4-429763
1866-8372
online registration
Archaeological and anthropological sciences 7 (2015) 4, S. 505–515 DOI: 10.1007/s12520-014-0213-4
<a href="http://publishup.uni-potsdam.de/opus4-ubp/frontdoor/index/index/docId/38409">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
false
true
CC-BY - Namensnennung 4.0 International
Julia Elsner
Jörg Schibler
Michael Hofreiter
Angela Schlumbaum
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
727
eng
uncontrolled
ancient DNA
eng
uncontrolled
DNA preservation
eng
uncontrolled
horse
eng
uncontrolled
cave
eng
uncontrolled
Switzerland
Geschichte des Altertums bis ca. 499, Archäologie
open_access
Institut für Biochemie und Biologie
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/42976/pmnr727.pdf
41921
2018
2018
eng
1
6
5
7
article
Oxford University Press
Oxford
1
2018-04-21
2018-04-21
--
Improving draft genome contiguity with reference-derived in silico mate-pair libraries
Background
Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available.
Findings
In order to improve genome contiguity, we have developed Cross-Species Scaffolding—a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico.
Conclusions
We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ∼30x coverage of shotgun sequencing data.
GigaScience
10.1093/gigascience/giy029
2047-217X
online registration
<a href="http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-419225">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 477</a>
CC-BY - Namensnennung 4.0 International
José Horacio Grau
Thomas Hackl
Klaus-Peter Koepfli
Michael Hofreiter
eng
uncontrolled
genome assembly
eng
uncontrolled
mate-pairs
eng
uncontrolled
in silico
eng
uncontrolled
scaffolding
eng
uncontrolled
shotgun sequencing
Biowissenschaften; Biologie
Medizin und Gesundheit
open_access
Institut für Biochemie und Biologie
Referiert
Open Access
41922
2018
2018
eng
6
postprint
1
2018-11-09
2018-11-09
--
Improving draft genome contiguity with reference-derived in silico mate-pair libraries
Background
Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available.
Findings
In order to improve genome contiguity, we have developed Cross-Species Scaffolding—a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico.
Conclusions
We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ∼30x coverage of shotgun sequencing data.
GigaScience
urn:nbn:de:kobv:517-opus4-419225
online registration
GigaScience 7 (2018) 5, S. 1–6 DOI: 10.1093/gigascience/giy029
<a href="http://publishup.uni-potsdam.de/opus4-ubp/frontdoor/index/index/docId/41921">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
CC-BY - Namensnennung 4.0 International
José Horacio Grau
Thomas Hackl
Klaus-Peter Koepfli
Michael Hofreiter
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
477
eng
uncontrolled
genome assembly
eng
uncontrolled
mate-pairs
eng
uncontrolled
in silico
eng
uncontrolled
scaffolding
eng
uncontrolled
shotgun sequencing
Biowissenschaften; Biologie
Medizin und Gesundheit
open_access
Institut für Biochemie und Biologie
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/41922/pmnr477.online.pdf
46597
2017
2017
eng
14
6
article
eLife Sciences Publications
Cambridge
1
--
--
--
Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution
The straight-tusked elephants Palaeoloxodon spp. were widespread across Eurasia during the Pleistocene. Phylogenetic reconstructions using morphological traits have grouped them with Asian elephants (Elephas maximus), and many paleontologists place Palaeoloxodon within Elephas. Here, we report the recovery of full mitochondrial genomes from four and partial nuclear genomes from two P. antiquus fossils. These fossils were collected at two sites in Germany, Neumark-Nord and Weimar-Ehringsdorf, and likely date to interglacial periods similar to 120 and similar to 244 thousand years ago, respectively. Unexpectedly, nuclear and mitochondrial DNA analyses suggest that P. antiquus was a close relative of extant African forest elephants (Loxodonta cyclotis). Species previously referred to Palaeoloxodon are thus most parsimoniously explained as having diverged from the lineage of Loxodonta, indicating that Loxodonta has not been constrained to Africa. Our results demonstrate that the current picture of elephant evolution is in need of substantial revision.
eLife
10.7554/eLife.25413
2050-084X
wos:2017
e25413
WOS:000402722800001
Meyer, M (reprint author), Max Planck Inst Evolutionary Anthropolgy, Leipzig, Germany.; Hofreiter, M (reprint author), Univ Potsdam, Dept Math & Nat Sci, Inst Biochem & Biol, Evolutionary Adapt Genom, Potsdam, Germany., mmeyer@eva.mpg.de; michael.hofreiter@uni-potsdam.de
Max Planck Society; Gordon and Betty Moore Foundation; US Fish and Wildlife Service [AFE1606-F16AP00909]; Wellcome Trust; Leverhulme Trust; European Research Council [310763 GeneFlow]
importub
2020-04-20T02:48:01+00:00
filename=package.tar
adc7aa008e25f60d2aa1a8e6e08215aa
Matthias Meyer
Eleftheria Palkopoulou
Sina Isabelle Baleka
Mathias Stiller
Kirsty E. H. Penkman
Kurt W. Alt
Yasuko Ishida
Dietrich Mania
Swapan Mallick
Tom Meijer
Harald Meller
Sarah Nagel
Birgit Nickel
Sven Ostritz
Nadin Rohland
Karol Schauer
Tim Schueler
Alfred L. Roca
David Reich
Beth Shapiro
Michael Hofreiter
Institut für Biochemie und Biologie
Referiert
Import
46648
2017
2017
eng
17246
17256
15
12
article
PLoS
San Fransisco
1
--
--
--
Ancient mtDNA diversity reveals specific population development of wild horses in Switzerland after the Last Glacial Maximum
PLoS one
10.1371/journal.pone.0177458
28542345
1932-6203
wos:2017
e0177458
WOS:000402061500025
Elsner, J (reprint author), Univ Basel, Integrat Prehist & Archaeol Sci, Basel, Switzerland., Julia.Elsner@email.de
Swiss National Science Foundation [K-31K1_120528/1]; Freiwillige Akademische Gesellschaft Basel; Bertha Burckhardt-Burgin-Foundation; Nikolaus
importub
2020-04-20T03:13:02+00:00
filename=package.tar
6c3b802b79647a68d9cc5f14d786ade4
Julia Elsner
Michael Hofreiter
Joerg Schibler
Angela Schlumbaum
Institut für Biochemie und Biologie
Referiert
Import
46712
2017
2017
eng
442
445
4
356
article
American Assoc. for the Advancement of Science
Washington
1
--
--
--
Ancient genomic changes associated with domestication of the horse
The genomic changes underlying both early and late stages of horse domestication remain largely unknown. We examined the genomes of 14 early domestic horses from the Bronze and Iron Ages, dating to between similar to 4.1 and 2.3 thousand years before present. We find early domestication selection patterns supporting the neural crest hypothesis, which provides a unified developmental origin for common domestic traits. Within the past 2.3 thousand years, horses lost genetic diversity and archaic DNA tracts introgressed from a now-extinct lineage. They accumulated deleterious mutations later than expected under the cost-of-domestication hypothesis, probably because of breeding from limited numbers of stallions. We also reveal that Iron Age Scythian steppe nomads implemented breeding strategies involving no detectable inbreeding and selection for coat-color variation and robust forelimbs.
Science
10.1126/science.aam5298
28450643
0036-8075
1095-9203
wos:2017
WOS:000400143000055
Orlando, L (reprint author), Nat Hist Museum Denmark, Ctr GeoGenet, Oster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.; Orlando, L (reprint author), Univ Paul Sabatier, Univ Toulouse, Lab Anthropobiol Mol & Imagerie Synth, CNRS,UMR 5288, F-31000 Toulouse, France., lorlando@snm.ku.dk
Danish Council for Independent Research, Natural Sciences [4002-00152B]; International Highly cited Research Group Program (grant HCRC) [15-101]; Deanship of Scientific Research, King Saud University; Villum Fonden miGENEPI; European Research Council [ERC-CoG-2015-681605]; Marie-Curie Intra-European fellowship [FP7-IEF-328024]; MINECO [BFU2014-55090-P]; Deutsche Forschungsgemeinschaft [LU 852/7-4]; SYNTHESYS Project - European Community Research Infrastructure Action under the Framework Programme 7 "Capacities" Program; ICREA
importub
2020-04-20T03:45:01+00:00
filename=package.tar
7c8464f2a595b9075ad560618da7073a
Pablo Librado
Cristina Gamba
Charleen Gaunitz
Clio Der Sarkissian
Melanie Pruvost
Anders Albrechtsen
Antoine Fages
Naveed Khan
Mikkel Schubert
Vidhya Jagannathan
Aitor Serres-Armero
Lukas F. K. Kuderna
Inna S. Povolotskaya
Andaine Seguin-Orlando
Sebastien Lepetz
Markus Neuditschko
Catherine Theves
Saleh A. Alquraishi
Ahmed H. Alfarhan
Khaled A. S. Al-Rasheid
Stefan Rieder
Zainolla Samashev
Henri-Paul Francfort
Norbert Benecke
Michael Hofreiter
Arne Ludwig
Christine Keyser
Tomas Marques-Bonet
Bertrand Ludes
Eric Crubezy
Tosso Leeb
Eske Willerslev
Ludovic Orlando
Institut für Biochemie und Biologie
Referiert
Import
46583
2017
2017
eng
1801
+
20
27
article
Cell Press
Cambridge
1
--
--
--
Paleogenomic Evidence for Multi-generational Mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the Lower Danube Basin
The transition from hunting and gathering to farming involved profound cultural and technological changes. In Western and Central Europe, these changes occurred rapidly and synchronously after the arrival of early farmers of Anatolian origin [1-3], who largely replaced the local Mesolithic hunter-gatherers [1, 4-6]. Further east, in the Baltic region, the transition was gradual, with little or no genetic input from incoming farmers [7]. Here we use ancient DNA to investigate the relationship between hunter-gatherers and farmers in the Lower Danube basin, a geographically intermediate area that is characterized by a rapid Neolithic transition but also by the presence of archaeological evidence that points to cultural exchange, and thus possible admixture, between hunter-gatherers and farmers. We recovered four human paleogenomes (1.13 to 4.13 coverage) from Romania spanning a time transect between 8.8 thousand years ago (kya) and 5.4 kya and supplemented them with two Mesolithic genomes (1.73- and 5.33) from Spain to provide further context on the genetic background of Mesolithic Europe. Our results show major Western hunter-gatherer (WHG) ancestry in a Romanian Eneolithic sample with a minor, but sizeable, contribution from Anatolian farmers, suggesting multiple admixture events between hunter-gatherers and farmers. Dietary stableisotope analysis of this sample suggests a mixed terrestrial/ aquatic diet. Our results provide support for complex interactions among hunter-gatherers and farmers in the Danube basin, demonstrating that in some regions, demic and cultural diffusion were not mutually exclusive, but merely the ends of a continuum for the process of Neolithization.
Current biology
10.1016/j.cub.2017.05.023
28552360
0960-9822
1879-0445
wos:2017
WOS:000403567800026
Gonzalez-Fortes, G (reprint author), Univ Ferrara, Dept Life Sci & Biotechnol, Via L Borsari 46, I-44100 Ferrara, Italy.; Gonzalez-Fortes, G; Hofreiter, M (reprint author), Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.; Gonzalez-Fortes, G; Jones, ER; Manica, A (reprint author), Univ Cambridge, Dept Zool, Downing St, Cambridge CB2 3EJ, England.; Pinhasi, R (reprint author), Univ Coll Dublin, Sch Archaeol, Dublin 4, Ireland.; Pinhasi, R (reprint author), Univ Coll Dublin, Earth Inst, Dublin 4, Ireland.; Pinhasi, R (reprint author), Univ Vienna, Dept Anthropol, Althanstr 14, A-1090 Vienna, Austria., gnzgrm@unife.it; erj35@cam.ac.uk; ron.pinhasi@ucd.ie; am315@cam.ac.uk; michi@palaeo.eu
European Research Council (ERC) [ERC-2010-StG 263441]; MSC Individual Fellowship [655478]; Herchel Smith Research Fellowship; ERC [310763, 647797]; Gates Cambridge Trust; MEN-UEFISCDI [PN-II-PT-PCCA-2013-4-2302]; project BIOGEOS of the Spanish MINECO [CGL2014-57209-P]; project CoChange of the Spanish State Plan for R+D+i (MINECO) [HAR2014-51830-P]
importub
2020-04-20T02:41:01+00:00
filename=package.tar
2ef37bc37ced6232f226cfe0a4dfdec8
Gloria M. González-Fortes
Eppie R. Jones
Emma Lightfoot
Clive Bonsall
Catalin Lazar
Maria Dolores Garralda
Labib Drak
Veronika Siska
Angela Simalcsik
Adina Boroneant
Juan Ramon Vidal Romani
Marcos Vaqueiro Rodriguez
Pablo Arias
Ron Pinhasi
Andrea Manica
Michael Hofreiter
Institut für Biochemie und Biologie
Referiert
Import
55007
2021
2022
eng
1
20
20
postprint
Universitätsverlag Potsdam
Potsdam
1
2022-05-23
2022-05-23
--
Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core
Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental conditions around critical episodes of hominin evolution. Identification of biological taxa based on their sedimentary ancient DNA (sedaDNA) traces can contribute to understand past ecological and climatological conditions of the living environment of our ancestors. However, sedaDNA recovery from tropical environments is challenging because high temperatures, UV irradiation, and desiccation result in highly degraded DNA. Consequently, most of the DNA fragments in tropical sediments are too short for PCR amplification. We analyzed sedaDNA in the upper 70 m of the composite sediment core of the HSPDP drill site at Chew Bahir for eukaryotic remnants. We first tested shotgun high throughput sequencing which leads to metagenomes dominated by bacterial DNA of the deep biosphere, while only a small fraction was derived from eukaryotic, and thus probably ancient, DNA. Subsequently, we performed cross-species hybridization capture of sedaDNA to enrich ancient DNA (aDNA) from eukaryotic remnants for paleoenvironmental analysis, using established barcoding genes (cox1 and rbcL for animals and plants, respectively) from 199 species that may have had relatives in the past biosphere at Chew Bahir. Metagenomes yielded after hybridization capture are richer in reads with similarity to cox1 and rbcL in comparison to metagenomes without prior hybridization capture. Taxonomic assignments of the reads from these hybridization capture metagenomes also yielded larger fractions of the eukaryotic domain. For reads assigned to cox1, inferred wet periods were associated with high inferred relative abundances of putative limnic organisms (gastropods, green algae), while inferred dry periods showed increased relative abundances for insects. These findings indicate that cross-species hybridization capture can be an effective approach to enhance the information content of sedaDNA in order to explore biosphere changes associated with past environmental conditions, enabling such analyses even under tropical conditions.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-55007
urn:nbn:de:kobv:517-opus4-550071
1866-8372
Version of record
683010
<a href="http://publishup.uni-potsdam.de/opus4-ubp/frontdoor/index/index/docId/55006">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Tiedemann, Ralph
false
true
CC-BY - Namensnennung 4.0 International
Johanna Krüger
Verena Elisabeth Foerster
Martin H. Trauth
Michael Hofreiter
Ralph Tiedemann
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1244
eng
uncontrolled
Chew Bahir
eng
uncontrolled
hybridization capture
eng
uncontrolled
ICDP
eng
uncontrolled
paleoclimate
eng
uncontrolled
past biosphere
eng
uncontrolled
sedaDNA
eng
uncontrolled
sediment core
Geowissenschaften
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/55007/pmnr1244.pdf
50375
2020
2021
eng
8
postprint
1
2021-04-16
2021-04-16
--
Annotated genome sequences of the carnivorous plant Roridula gorgonias and a non-carnivorous relative, Clethra arborea
Objective
Plant carnivory is distributed across the tree of life and has evolved at least six times independently, but sequenced and annotated nuclear genomes of carnivorous plants are currently lacking. We have sequenced and structurally annotated the nuclear genome of the carnivorous Roridula gorgonias and that of a non-carnivorous relative, Madeira’s lily-of-the-valley-tree, Clethra arborea, both within the Ericales. This data adds an important resource to study the evolutionary genetics of plant carnivory across angiosperm lineages and also for functional and systematic aspects of plants within the Ericales.
Results
Our assemblies have total lengths of 284 Mbp (R. gorgonias) and 511 Mbp (C. arborea) and show high BUSCO scores of 84.2% and 89.5%, respectively. We used their predicted genes together with publicly available data from other Ericales’ genomes and transcriptomes to assemble a phylogenomic data set for the inference of a species tree. However, groups of orthologs showed a marked absence of species represented by a transcriptome. We discuss possible reasons and caution against combining predicted genes from genome- and transriptome-based assemblies.
Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-50375
urn:nbn:de:kobv:517-opus4-503752
1866-8372
BMC Research Notes 13 (2020), Art. 426 DOI: 10.1186/s13104-020-05254-4
426
<a href="http://publishup.uni-potsdam.de/50374">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
false
true
CC-BY - Namensnennung 4.0 International
Stefanie Hartmann
Michaela Preick
Silke Abelt
André Scheffel
Michael Hofreiter
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1141
eng
uncontrolled
Carnivorous plant
eng
uncontrolled
Roridula gorgonias
eng
uncontrolled
Clethra arborea
eng
uncontrolled
Genome assembly
eng
uncontrolled
Transcriptome assembly
eng
uncontrolled
Phylogenomics
eng
uncontrolled
Orthologous Matrix (OMA) Project
Biowissenschaften; Biologie
Medizin und Gesundheit
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/50375/pmnr1141.pdf
57459
2022
2022
eng
5
10
article
Frontiers Media S.A.
Lausanne, Schweiz
1
2022-06-17
2022-06-17
--
Simultaneous Barcode Sequencing of Diverse Museum Collection Specimens Using a Mixed RNA Bait Set
A growing number of publications presenting results from sequencing natural history collection specimens reflect the importance of DNA sequence information from such samples. Ancient DNA extraction and library preparation methods in combination with target gene capture are a way of unlocking archival DNA, including from formalin-fixed wet-collection material. Here we report on an experiment, in which we used an RNA bait set containing baits from a wide taxonomic range of species for DNA hybridisation capture of nuclear and mitochondrial targets for analysing natural history collection specimens. The bait set used consists of 2,492 mitochondrial and 530 nuclear RNA baits and comprises specific barcode loci of diverse animal groups including both invertebrates and vertebrates. The baits allowed to capture DNA sequence information of target barcode loci from 84% of the 37 samples tested, with nuclear markers being captured more frequently and consensus sequences of these being more complete compared to mitochondrial markers. Samples from dry material had a higher rate of success than wet-collection specimens, although target sequence information could be captured from 50% of formalin-fixed samples. Our study illustrates how efforts to obtain barcode sequence information from natural history collection specimens may be combined and are a way of implementing barcoding inventories of scientific collection material.
Frontiers in Ecology and Evolution
10.3389/fevo.2022.909846
2296-701X
Agne, Stefanie
909846
<a href="https://doi.org/10.25932/publishup-57460">Zweitveröffentlichung in der Schriftenreihe Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1293</a>
CC-BY - Namensnennung 4.0 International
Stefanie Agne
Michaela Preick
Nicolas Straube
Michael Hofreiter
eng
uncontrolled
target capture
eng
uncontrolled
type specimens
eng
uncontrolled
molecular species identification
eng
uncontrolled
museum specimens
eng
uncontrolled
cross-species capture
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Extern
Referiert
Publikationsfonds der Universität Potsdam
Gold Open-Access
57460
2022
2022
eng
5
1293
postprint
1
2023-01-11
2023-01-11
--
Simultaneous Barcode Sequencing of Diverse Museum Collection Specimens Using a Mixed RNA Bait Set
A growing number of publications presenting results from sequencing natural history collection specimens reflect the importance of DNA sequence information from such samples. Ancient DNA extraction and library preparation methods in combination with target gene capture are a way of unlocking archival DNA, including from formalin-fixed wet-collection material. Here we report on an experiment, in which we used an RNA bait set containing baits from a wide taxonomic range of species for DNA hybridisation capture of nuclear and mitochondrial targets for analysing natural history collection specimens. The bait set used consists of 2,492 mitochondrial and 530 nuclear RNA baits and comprises specific barcode loci of diverse animal groups including both invertebrates and vertebrates. The baits allowed to capture DNA sequence information of target barcode loci from 84% of the 37 samples tested, with nuclear markers being captured more frequently and consensus sequences of these being more complete compared to mitochondrial markers. Samples from dry material had a higher rate of success than wet-collection specimens, although target sequence information could be captured from 50% of formalin-fixed samples. Our study illustrates how efforts to obtain barcode sequence information from natural history collection specimens may be combined and are a way of implementing barcoding inventories of scientific collection material.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-57460
urn:nbn:de:kobv:517-opus4-574600
1866-8372
Agne, Stefanie
Version of record
<a href="https://publishup.uni-potsdam.de/57459">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
CC-BY - Namensnennung 4.0 International
Stefanie Agne
Michaela Preick
Nicolas Straube
Michael Hofreiter
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1293
eng
uncontrolled
target capture
eng
uncontrolled
type specimens
eng
uncontrolled
molecular species identification
eng
uncontrolled
museum specimens
eng
uncontrolled
cross-species capture
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/57460/pmnr1293.pdf
52645
2018
2018
eng
1638
1652
15
7
35
article
Oxford Univ. Press
Oxford
1
2018-04-17
2018-04-17
--
Novel Genes, Ancient Genes, and Gene Co-Option Contributed o the Genetic Basis of the Radula, a Molluscan Innovation
The radula is the central foraging organ and apomorphy of the Mollusca. However, in contrast to other innovations, including the mollusk shell, genetic underpinnings of radula formation remain virtually unknown. Here, we present the first radula formative tissue transcriptome using the viviparous freshwater snail Tylomelania sarasinorum and compare it to foot tissue and the shell-building mantle of the same species. We combine differential expression, functional enrichment, and phylostratigraphic analyses to identify both specific and shared genetic underpinnings of the three tissues as well as their dominant functions and evolutionary origins. Gene expression of radula formative tissue is very distinct, but nevertheless more similar to mantle than to foot. Generally, the genetic bases of both radula and shell formation were shaped by novel orchestration of preexisting genes and continuous evolution of novel genes. A significantly increased proportion of radula-specific genes originated since the origin of stem-mollusks, indicating that novel genes were especially important for radula evolution. Genes with radula-specific expression in our study are frequently also expressed during the formation of other lophotrochozoan hard structures, like chaetae (hes1, arx), spicules (gbx), and shells of mollusks (gbx, heph) and brachiopods (heph), suggesting gene co-option for hard structure formation. Finally, a Lophotrochozoa-specific chitin synthase with a myosin motor domain (CS-MD), which is expressed during mollusk and brachiopod shell formation, had radula-specific expression in our study. CS-MD potentially facilitated the construction of complex chitinous structures and points at the potential of molecular novelties to promote the evolution of different morphological innovations.
Molecular biology and evolution
10.1093/molbev/msy052
29672732
0737-4038
1537-1719
wos:2018
WOS:000441141400007
Hilgers, L (reprint author), Museum Nat Kunde Berlin, Leibniz Inst Evolut & Biodivers Sci, Berlin, Germany.; Hilgers, L (reprint author), Univ Potsdam, Inst Biochem & Biol, Adapt Evolutionary Genom Dept, Potsdam, Germany., leon.hilgers@mfn-berlin.de
German Research Council (DFG)German Research Foundation (DFG) [Ri 1738/9-1]
2021-11-15T11:29:40+00:00
sword
importub
filename=package.tar
5888cd7247f8842cc7257a209187347d
Hilgers, Leon
CC-BY-NC - Namensnennung, nicht kommerziell 4.0 International
Leon Hilgers
Stefanie Hartmann
Michael Hofreiter
Thomas von Rintelen
eng
uncontrolled
chitin synthase
eng
uncontrolled
novelty
eng
uncontrolled
radula
eng
uncontrolled
RNAseq
eng
uncontrolled
shell
eng
uncontrolled
Tylomelania sarasinorum
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
56931
2020
2020
eng
21
33
13
642
article
Academic Press, an imprint of Elsevier
Cambridge, MA.
1
2020-06-19
2020-06-19
--
Reconstructing protein-coding sequences from ancient DNA
Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including mis-coding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins.
Odorant binding and chemosensory proteins
10.1016/bs.mie.2020.05.008
32828254
978-0-12-821157-1
0076-6879
outputup:dataSource:PubMed:2020
WOS:000612528800003
Hofreiter, M (corresponding author), Univ Potsdam, Inst Biochem & Biol, Evolutionary Adapt Genom, Potsdam, Germany., mhofreit@uni-potsdam.de
Hofreiter, Michael
2022-12-01T09:18:38+00:00
sword
importub
filename=package.tar
06d698075cf9ccdf866c5ebff9737e33
416178-6
2221516-5
false
true
Michael Hofreiter
Stefanie Hartmann
eng
uncontrolled
re-sequencing
eng
uncontrolled
mapping
eng
uncontrolled
genome assembly
eng
uncontrolled
targeted assembly
eng
uncontrolled
SRAssembler
eng
uncontrolled
ancient DNA
eng
uncontrolled
reference sequence
eng
uncontrolled
paleogenomics
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
61012
2020
2020
eng
R110
R111
2
3
30
other
Current Biology Ltd.
London
1
2020-02-03
2020-02-03
--
Ancient DNA reveals twenty million years of aquatic life in beavers
Xenikoudakis et al. report a partial mitochondrial genome of the extinct giant beaver Castoroides and estimate the origin of aquatic behavior in beavers to approximately 20 million years. This time estimate coincides with the extinction of terrestrial beavers and raises the question whether the two events had a common cause.
Current biology : CB
10.1016/j.cub.2019.12.041
32017876
0960-9822
1879-0445
outputup:dataSource:WoS:2020
WOS:000511287900007
Xenikoudakis, G (corresponding author), Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany.; Lerner, H (corresponding author), Earlham Coll, Joseph Moore Museum, Richmond, IN 47374 USA., geoxenik@gmail.com; hlerner@gmail.com
Xenikoudakis, Georgios
Lerner, Heather
2023-10-05T11:19:23+00:00
sword
importub
filename=package.tar
82505b7325a3b383515bca1298a2798a
2019214-9
1071731-6
false
true
Georgios Xenikoudakis
Mayeesha Ahmed
Jacob Colt Harris
Rachel Wadleigh
Johanna L. A. Paijmans
Stefanie Hartmann
Axel Barlow
Heather Lerner
Michael Hofreiter
Biowissenschaften; Biologie
Institut für Informatik und Computational Science
Institut für Biochemie und Biologie
Referiert
Import
42255
2019
2019
eng
12
505
postprint
1
2019-01-10
2019-01-10
--
Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations
Background
Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts?
Results
In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these.
Conclusions
The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.
Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
1866-8372
10.25932/publishup-42255
urn:nbn:de:kobv:517-opus4-422555
BMC Evolutionary Biology 18 (2018) 156 DOI: 10.1186/s12862-018-1268-0
<a href="http://publishup.uni-potsdam.de/opus4-ubp/frontdoor/index/index/docId/42256">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
CC-BY - Namensnennung 4.0 International
Johanna L. A. Paijmans
Axel Barlow
Daniel W. Förster
Kirstin Henneberger
Matthias Meyer
Birgit Nickel
Doris Nagel
Rasmus Worsøe Havmøller
Gennady F. Baryshnikov
Ulrich Joger
Wilfried Rosendahl
Michael Hofreiter
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
505
eng
uncontrolled
Ancient DNA
eng
uncontrolled
Hybridisation capture
eng
uncontrolled
Leopards
eng
uncontrolled
Mitochondrial genomes
eng
uncontrolled
Mitogenomes
eng
uncontrolled
mtDNA
eng
uncontrolled
Palaeogenetics
eng
uncontrolled
Panthera pardus
Biowissenschaften; Biologie
Medizin und Gesundheit
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/42255/pmnr505.pdf
43881
2015
2020
eng
284
295
12
908
postprint
1
2020-05-25
2020-05-25
--
The future of ancient DNA
Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.
Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe
technical advances and conceptual shifts
10.25932/publishup-43881
urn:nbn:de:kobv:517-opus4-438816
1866-8372
BioEssays 37 (2015) 3, 284-293 DOI: 10.1002/bies.201400160
<a href="http://publishup.uni-potsdam.de/39132">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Keine öffentliche Lizenz: Unter Urheberrechtsschutz
Michael Hofreiter
Johanna L. A. Paijmans
Helen Goodchild
Camilla F. Speller
Axel Barlow
Gloria M. Gonzalez-Fortes
Jessica A. Thomas
Arne Ludwig
Matthew J. Collins
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
908
eng
uncontrolled
ancient DNA
eng
uncontrolled
hybridisation capture
eng
uncontrolled
multi-locus data
eng
uncontrolled
next generation sequencing (NGS)
eng
uncontrolled
palaeogenomics
eng
uncontrolled
population genomics
Chemie und zugeordnete Wissenschaften
Biowissenschaften; Biologie
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Open Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/43881/pmnr908.pdf
42256
2018
2018
eng
12
156
18
article
BioMed Central und Springer
London, Berlin und Heidelberg
1
2018-10-23
2018-10-23
--
Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations
Background
Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts?
Results
In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these.
Conclusions
The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.
BMC Evolutionary Biology
10.1186/s12862-018-1268-0
1471-2148
Universität Potsdam
PA 2018_58
1661.24
<a href="http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-422555">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 505</a>
CC-BY - Namensnennung 4.0 International
Johanna L. A. Paijmans
Axel Barlow
Daniel W. Förster
Kirstin Henneberger
Matthias Meyer
Birgit Nickel
Doris Nagel
Rasmus Worsøe Havmøller
Gennady F. Baryshnikov
Ulrich Joger
Wilfried Rosendahl
Michael Hofreiter
eng
uncontrolled
Ancient DNA
eng
uncontrolled
Hybridisation capture
eng
uncontrolled
Leopards
eng
uncontrolled
Mitochondrial genomes
eng
uncontrolled
Mitogenomes
eng
uncontrolled
mtDNA
eng
uncontrolled
Palaeogenetics
eng
uncontrolled
Panthera pardus
Biowissenschaften; Biologie
Medizin und Gesundheit
open_access
Mathematisch-Naturwissenschaftliche Fakultät
Referiert
Publikationsfonds der Universität Potsdam
Open Access
47252
2020
2020
eng
24
1033
postprint
1
2020-12-14
2020-12-14
--
Consensify
A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.
Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
a method for generating pseudohaploid genome sequences from palaeogenomic datasets with reduced error rates
10.25932/publishup-47252
urn:nbn:de:kobv:517-opus4-472521
1866-8372
online registration
Genes 11 (2020) 1, 50 DOI:10.3390/genes11010050
50
true
true
CC-BY - Namensnennung 4.0 International
Axel Barlow
Stefanie Hartmann
Javier Gonzalez
Michael Hofreiter
Johanna L. A. Paijmans
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1033
eng
uncontrolled
palaeogenomics
eng
uncontrolled
ancient DNA
eng
uncontrolled
sequencing error
eng
uncontrolled
error reduction
eng
uncontrolled
D statistics
eng
uncontrolled
bioinformatics
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/47252/pmnr1033.pdf
44915
2016
2016
eng
4907
4918
12
25
article
Wiley-Blackwell
Hoboken
1
--
--
--
Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears
Ancient DNA studies have revolutionized the study of extinct species and populations, providing insights on phylogeny, phylogeography, admixture and demographic history. However, inferences on behaviour and sociality have been far less frequent. Here, we investigate the complete mitochondrial genomes of extinct Late Pleistocene cave bears and middle Holocene brown bears that each inhabited multiple geographically proximate caves in northern Spain. In cave bears, we find that, although most caves were occupied simultaneously, each cave almost exclusively contains a unique lineage of closely related haplotypes. This remarkable pattern suggests extreme fidelity to their birth site in cave bears, best described as homing behaviour, and that cave bears formed stable maternal social groups at least for hibernation. In contrast, brown bears do not show any strong association of mitochondrial lineage and cave, suggesting that these two closely related species differed in aspects of their behaviour and sociality. This difference is likely to have contributed to cave bear extinction, which occurred at a time in which competition for caves between bears and humans was likely intense and the ability to rapidly colonize new hibernation sites would have been crucial for the survival of a species so dependent on caves for hibernation as cave bears. Our study demonstrates the potential of ancient DNA to uncover patterns of behaviour and sociality in ancient species and populations, even those that went extinct many tens of thousands of years ago.
Molecular ecology
10.1111/mec.13800
27506329
0962-1083
1365-294X
wos2016:2019
WOS:000384810000016
Fortes, GG; Barlow, A (reprint author), Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam Ot Golm, Germany.; Fortes, GG (reprint author), Univ Ferrara, Dept Biol & Evolut, I-44121 Ferrara, Italy.; Fortes, GG (reprint author), Univ A Coruna, Inst Univ Xeoloxia, La Coruna 15081, Spain., ggfortes14@gmail.com; axel.barlow.ab@gmail.com
Xunta de Galicia, Conselleria de Economia e Industria [10 PXIB 162 125]; Ministerio de Economia y Competitividad [MINECO CGL2014-57209-P]; European Science Foundation Research Networking Programmes (ConGenOmics) [5882]; ERC consolidator grant GeneFlow [310763]; KARSTHIVES Project - CNCS-UEFISCDI [PCCE_ID_31/2010]
importub
2020-03-22T14:10:01+00:00
filename=package.tar
12f4c099a00e9e6314559b59d47ad5a2
Gloria M. González-Fortes
Ben Kolbe
Daniel Fernandes
Ioana N. Meleg
Ana Garcia-Vazquez
Ana C. Pinto-Llona
Silviu Constantin
Trino J. de Torres
Jose E. Ortiz
Christine Frischauf
Gernot Rabeder
Michael Hofreiter
Axel Barlow
eng
uncontrolled
ancient DNA
eng
uncontrolled
extinction
eng
uncontrolled
homing
eng
uncontrolled
sociality
eng
uncontrolled
Ursus arctos
eng
uncontrolled
Ursus spelaeus
Institut für Biochemie und Biologie
Referiert
Import
45863
2016
2016
eng
42
55
14
16
article
Wiley-Blackwell
Hoboken
1
--
--
--
Impact of enrichment conditions on cross-species capture of fresh and degraded DNA
Abstract
By combining high-throughput sequencing with target enrichment (‘hybridization capture’), researchers are able to obtain molecular data from genomic regions of interest for projects that are otherwise constrained by sample quality (e.g. degraded and contamination-rich samples) or a lack of a priori sequence information (e.g. studies on nonmodel species). Despite the use of hybridization capture in various fields of research for many years, the impact of enrichment conditions on capture success is not yet thoroughly understood. We evaluated the impact of a key parameter – hybridization temperature – on the capture success of mitochondrial genomes across the carnivoran family Felidae. Capture was carried out for a range of sample types (fresh, archival, ancient) with varying levels of sequence divergence between bait and target (i.e. across a range of species) using pools of individually indexed libraries on Agilent SureSelect™ arrays. Our results suggest that hybridization capture protocols require specific optimization for the sample type that is being investigated. Hybridization temperature affected the proportion of on-target sequences following capture: for degraded samples, we obtained the best results with a hybridization temperature of 65 °C, while a touchdown approach (65 °C down to 50 °C) yielded the best results for fresh samples. Evaluation of capture performance at a regional scale (sliding window approach) revealed no significant improvement in the recovery of DNA fragments with high sequence divergence from the bait at any of the tested hybridization temperatures, suggesting that hybridization temperature may not be the critical parameter for the enrichment of divergent fragments.
Molecular ecology resources
10.1111/1755-0998.12420
25925277
1755-098X
1755-0998
wos2016:2019
WOS:000369141000007
Paijmans, JLA (reprint author), Univ York, Dept Biol, York YO10 5DD, N Yorkshire, England.; Paijmans, JLA (reprint author), Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.; Forster, DW (reprint author), Leibniz Inst Zoo & Wildlife Res, Evolutionary Genet Dept, Alfred Kowalke Str 17, D-10315 Berlin, Germany., paijmans.jla@gmail.com; dwgfoerster@gmail.com
National Science Foundation (DEB) [1132229]; Leibniz Association [SAW-2013-IZW-2]
importub
2020-03-22T22:05:01+00:00
filename=package.tar
175b68ffd1cc73f96dc8cbe201ff33bd
Johanna L. A. Paijmans
Jörns Fickel
Alexandre Courtiol
Michael Hofreiter
Daniel W. Foerster
eng
uncontrolled
degraded DNA
eng
uncontrolled
Felidae
eng
uncontrolled
hybridization capture
eng
uncontrolled
mitogenomes
eng
uncontrolled
next-generation sequencing
eng
uncontrolled
sequence enrichment
Institut für Biochemie und Biologie
Referiert
Import
55504
2017
2017
eng
8
284
article
The Royal Society
London
1
2017-01-11
2017-01-11
--
Tropical ancient DNA reveals relationships of the extinct bahamian giant tortoise Chelonoidis alburyorum
Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island. Phylogenetic and molecular clock analyses place this extinct species as closely related to Galapagos (C. niger complex) and Chaco tortoises (C. chilensis), and provide evidence for repeated overseas dispersal in this tortoise group. The ancestors of extant Chelonoidis species arrived in South America from Africa only after the opening of the Atlantic Ocean and dispersed from there to the Caribbean and the Galapagos Islands. Our results also suggest that the anoxic, thermally buffered environment of blue holes may enhance DNA preservation, and thus are opening a window for better understanding evolution and population history of extinct tropical species, which would likely still exist without human impact.
Proceedings of the Royal Society of London : Series B, Biological sciences
10.1098/rspb.2016.2235
0962-8452
1471-2954
wos:2017
20162235
WOS:000393400500019
Fritz, U (reprint author), Senckenberg Dresden, Museum Zool, AB Meyer Bldg, D-01109 Dresden, Germany., ufritz@senckenberg.de
2022-07-07T11:23:23+00:00
sword
importub
filename=package.tar
1d53d15b400ad4c9b4f0f2b65b6ca663
Fritz, Uwe
false
true
Christian Kehlmaier
Axel Barlow
Alexander K. Hastings
Melita Vamberger
Johanna L. A. Paijmans
David W. Steadman
Nancy A. Albury
Richard Franz
Michael Hofreiter
Uwe Fritz
eng
uncontrolled
Bahamas
eng
uncontrolled
biogeography
eng
uncontrolled
extinction
eng
uncontrolled
palaeontology
eng
uncontrolled
phylogeny
Biowissenschaften; Biologie
Tiere (Zoologie)
Institut für Biochemie und Biologie
Referiert
Import
50374
2020
2020
eng
6
13
article
Biomed Central
London
1
2020-09-10
2020-09-10
--
Annotated genome sequences of the carnivorous plant Roridula gorgonias and a non-carnivorous relative, Clethra arborea
Objective
Plant carnivory is distributed across the tree of life and has evolved at least six times independently, but sequenced and annotated nuclear genomes of carnivorous plants are currently lacking. We have sequenced and structurally annotated the nuclear genome of the carnivorous Roridula gorgonias and that of a non-carnivorous relative, Madeira’s lily-of-the-valley-tree, Clethra arborea, both within the Ericales. This data adds an important resource to study the evolutionary genetics of plant carnivory across angiosperm lineages and also for functional and systematic aspects of plants within the Ericales.
Results
Our assemblies have total lengths of 284 Mbp (R. gorgonias) and 511 Mbp (C. arborea) and show high BUSCO scores of 84.2% and 89.5%, respectively. We used their predicted genes together with publicly available data from other Ericales’ genomes and transcriptomes to assemble a phylogenomic data set for the inference of a species tree. However, groups of orthologs showed a marked absence of species represented by a transcriptome. We discuss possible reasons and caution against combining predicted genes from genome- and transriptome-based assemblies.
BMC Research Notes
10.1186/s13104-020-05254-4
1756-0500
Universität Potsdam
PA 2020_137
1178.56
426
<a href="https://doi.org/10.25932/publishup-50375">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1141</a>
false
false
CC-BY - Namensnennung 4.0 International
Stefanie Hartmann
Michaela Preick
Silke Abelt
André Scheffel
Michael Hofreiter
eng
uncontrolled
Carnivorous plant
eng
uncontrolled
Roridula gorgonias
eng
uncontrolled
Clethra arborea
eng
uncontrolled
Genome assembly
eng
uncontrolled
Transcriptome assembly
eng
uncontrolled
Phylogenomics
eng
uncontrolled
Orthologous Matrix (OMA) Project
Biowissenschaften; Biologie
Medizin und Gesundheit
open_access
Institut für Biochemie und Biologie
Referiert
Publikationsfonds der Universität Potsdam
Gold Open-Access
43799
2014
2014
eng
9
1332
5
postprint
1
2014-10-21
2014-10-21
--
Genome flux and stasis in a five millennium transect of European prehistory
The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (similar to 22x) and seven to similar to 1x coverage, to investigate the impact of these on Europe's genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-43799
urn:nbn:de:kobv:517-opus4-437999
1866-8372
online registration
Version of record
<a href="https://publishup.uni-potsdam.de/37505">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Pinhasi, Ron
Bradley, Daniel G.
Nature Communications 5, 5257 (2014) DOI: 10.1038/ncomms6257
false
true
CC-BY - Namensnennung 4.0 International
Cristina Gamba
Eppie R. Jones
Matthew D. Teasdale
Russell L. McLaughlin
Gloria M. González-Fortes
Valeria Mattiangeli
László Domboróczki
Ivett Kővári
Ildikó Pap
Alexandra Anders
Alasdair Whittle
János Dani
Pál Raczky
Thomas F. G. Higham
Michael Hofreiter
Daniel G. Bradley
Ron Pinhasi
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1332
eng
uncontrolled
ancient DNA
eng
uncontrolled
lactase-persistence
eng
uncontrolled
positive selection
eng
uncontrolled
patterns
eng
uncontrolled
sequence
eng
uncontrolled
farmers
eng
uncontrolled
pigmentation
eng
uncontrolled
homozygosity
eng
uncontrolled
ancestry
eng
uncontrolled
skin
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/43799/zmnr1332.pdf
43931
2015
2015
eng
8
1334
postprint
1
2015-11-16
2015-11-16
--
Upper Palaeolithic genomes reveal deep roots of modern Eurasians
We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-43931
urn:nbn:de:kobv:517-opus4-439317
1866-8372
online registration
Manica, Andrea
Pinhasi, Ron
Bradley, Daniel G.
Version of record
<a href="https://publishup.uni-potsdam.de/38466">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Nature Communications 6, (2015) 8912 DOI:10.1038/ncomms9912
false
true
CC-BY - Namensnennung 4.0 International
Eppie R. Jones
Gloria M. González-Fortes
Sarah Connell
Veronika Siska
Anders Eriksson
Rui Martiniano
Russell L. McLaughlin
Marcos Gallego Llorente
Lara M. Cassidy
Cristina Gamba
Tengiz Meshveliani
Ofer Bar-Yosef
Werner Müller
Anna Belfer-Cohen
Zinovi Matskevich
Nino Jakeli
Thomas F. G. Higham
Mathias Currat
David Lordkipanidze
Michael Hofreiter
Andrea Manica
Ron Pinhasi
Daniel G. Bradley
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1334
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/43931/zmnr1334.pdf
38466
2015
2015
eng
8
6
article
Nature Publishing Group
London
1
2015-11-16
2015-11-16
--
Upper Palaeolithic genomes reveal deep roots of modern Eurasians
We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic-Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers similar to 45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers similar to 25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe similar to 3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.
Nature Communications
10.1038/ncomms9912
2041-1723
26567969
wos:2015
8912
WOS:000366378900014
Bradley, DG (reprint author), Univ Dublin Trinity Coll, Smurfit Inst Genet, Dublin 2, Ireland., am315@cam.ac.uk; ron.pinhasi@ucd.ie; dbradley@tcd.ie
European Research Council (ERC) [ERC-2010-StG 263441]; ERC [295729-CodeX, 310763-GeneFlow, 647787-LocalAdaptation]; National Geographic Global Exploration Fund [grant-GEFNE78-13]; Gates Cambridge Trust; BBSRC DTP studentship; Irish Research Council for Humanities and Social Sciences (IRCHSS) ERC Support Programme; Marie-Curie Intra-European Fellowships [FP7-IEF-328024]; BEAN project of the Marie Curie ITN [289966]; Irish Research Council [GOIPG/2013/1219]; ALS Association of America [2284]; Fondation Thierry Latran (ALSIBD); Swiss NSF grant [31003A_156853]
<a href="https://doi.org/10.25932/publishup-43931">Zweitveröffentlichung in der Schriftenreihe Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1334</a>
Manica, Andrea
Pinhasi, Ron
Bradley, Daniel G.
CC-BY - Namensnennung 4.0 International
Eppie R. Jones
Gloria M. González-Fortes
Sarah Connell
Veronika Siska
Anders Eriksson
Rui Martiniano
Russell L. McLaughlin
Marcos Gallego Llorente
Lara M. Cassidy
Cristina Gamba
Tengiz Meshveliani
Ofer Bar-Yosef
Werner Mueller
Anna Belfer-Cohen
Zinovi Matskevich
Nino Jakeli
Thomas F. G. Higham
Mathias Currat
David Lordkipanidze
Michael Hofreiter
Andrea Manica
Ron Pinhasi
Daniel G. Bradley
Naturwissenschaften und Mathematik
Institut für Biochemie und Biologie
Extern
Referiert
Gold Open-Access
60987
2020
2020
eng
22
1
11
article
MDPI
Basel
1
--
2020-01-02
--
Consensify
A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.
Genes / Molecular Diversity Preservation International
a method for generating pseudohaploid genome sequences from palaeogenomic datasets with reduced error rates
10.3390/genes11010050
31906474
2073-4425
outputup:dataSource:WoS:2020
50
WOS:000514898000072
Barlow, A; Paijmans, JLA (corresponding author), Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.; Barlow, A (corresponding author), Nottingham Trent Univ, Sch Sci & Technol, Clifton Lane, Nottingham NG11 8NS, England.; Paijmans, JLA (corresponding author), Univ Leicester, Dept Genet & Genome Biol, Leicester LE1 7RH, Leics, England., axel.barlow.ab@gmail.com; stefanie.hartmann@uni-potsdam.de; <br /> thinocorus@googlemail.com; mhofreit@uni-potsdam.de; <br /> paijmans.jla@gmail.com
University of Leicester [M38DF64]; European Research Council (ERC); consolidator grant 'gene flow'European Research Council (ERC) [310763]
Barlow, Axel
Paijmans, Johanna L. A.
2023-10-04T09:54:17+00:00
sword
importub
filename=package.tar
b6a4b8468c0fdca6a99b142ec12aaabf
2527218-4
false
true
CC-BY - Namensnennung 4.0 International
Axel Barlow
Stefanie Hartmann
Javier Gonzalez
Michael Hofreiter
Johanna L. A. Paijmans
eng
uncontrolled
palaeogenomics
eng
uncontrolled
ancient DNA
eng
uncontrolled
sequencing error
eng
uncontrolled
error reduction
eng
uncontrolled
D statistics
eng
uncontrolled
bioinformatics
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
47443
2020
2019
eng
12
6
15
article
PLOS
San Francisco, California, US
1
2020-06-30
2019-07-31
--
Ancestral mitogenome capture of the Southeast Asian banded linsang
Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.
PLoS ONE
10.1371/journal.pone.0234385
1932-6203
e0234385
<a href="https://doi.org/10.25932/publishup-47444">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 972</a>
Universität Potsdam
PA 2020_068
1389.76
CC-BY - Namensnennung 4.0 International
Johanna L. A. Paijmans
Axel Barlow
Kirstin Henneberger
Jörns Fickel
Michael Hofreiter
Daniel W. G. Foerste
eng
uncontrolled
Shotgun sequencing
eng
uncontrolled
Mitochondria
eng
uncontrolled
Phylogenetics
eng
uncontrolled
Phylogenetic analysis
eng
uncontrolled
Paleogenetics
eng
uncontrolled
Sequence alignment
eng
uncontrolled
Genomics
eng
uncontrolled
Museum collections
Naturwissenschaften und Mathematik
Medizin und Gesundheit
Institut für Biochemie und Biologie
Referiert
Publikationsfonds der Universität Potsdam
Gold Open-Access
38584
2015
2015
eng
178
193
16
91
article
Elsevier
San Diego
1
--
--
--
Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia
The recently extinct (ca. 1768) Steller's sea cow (Hydrodamalis gigas) was a large, edentulous North Pacific sirenian. The phylogenetic affinities of this taxon to other members of this clade, living and extinct, are uncertain based on previous morphological and molecular studies. We employed hybridization capture methods and second generation sequencing technology to obtain >30 kb of exon sequences from 26 nuclear genes for both H. gigas and Dugong dugon. We also obtained complete coding sequences for the tooth-related enamelin (ENAM) gene. Hybridization probes designed using dugong and manatee sequences were both highly effective in retrieving sequences from H. gigas (mean = 98.8% coverage), as were more divergent probes for regions of ENAM (99.0% coverage) that were designed exclusively from a proboscidean (African elephant) and a hyracoid (Cape hyrax). New sequences were combined with available sequences for representatives of all other afrotherian orders. We also expanded a previously published morphological matrix for living and fossil Sirenia by adding both new taxa and nine new postcranial characters. Maximum likelihood and parsimony analyses of the molecular data provide robust support for an association of H. gigas and D. dugon to the exclusion of living trichechids (manatees). Parsimony analyses of the morphological data also support the inclusion of H. gigas in Dugongidae with D. dugon and fossil dugongids. Timetree analyses based on calibration density approaches with hard- and soft-bounded constraints suggest that H. gigas and D. dugon diverged in the Oligocene and that crown sirenians last shared a common ancestor in the Eocene. The coding sequence for the ENAM gene in H. gigas does not contain frameshift mutations or stop codons, but there is a transversion mutation (AG to CG) in the acceptor splice site of intron 2. This disruption in the edentulous Steller's sea cow is consistent with previous studies that have documented inactivating mutations in tooth-specific loci of a variety of edentulous and enamelless vertebrates including birds, turtles, aardvarks, pangolins, xenarthrans, and baleen whales. Further, branch-site dN/dS analyses provide evidence for positive selection in ENAM on the stem dugongid branch where extensive tooth reduction occurred, followed by neutral evolution on the Hydrodamalis branch. Finally, we present a synthetic evolutionary tree for living and fossil sirenians showing several key innovations in the history of this clade including character state changes that parallel those that occurred in the evolutionary history of cetaceans. (C) 2015 Elsevier Inc. All rights reserved.
Molecular phylogenetics and evolution
10.1016/j.ympev.2015.05.022
26050523
1055-7903
1095-9513
wos:2015
WOS:000358270900014
Springer, MS (reprint author), Univ Calif Riverside, Dept Biol, Riverside, CA 92521 USA., mark.springer@ucc.edu; Kevin.Campbell@umanitoba.ca
NSF (United States) [EF0629860, EAR-PF1249920, DEB1132229]; NSERC
(Canada) Discovery and Accelerator Supplement Grants; NSERC Alexander
Graham Bell Canada Graduate Scholarship
Mark S. Springer
Anthony V. Signore
Johanna L. A. Paijmans
Jorge Velez-Juarbe
Daryl P. Domning
Cameron E. Bauer
Kai He
Lorelei Crerar
Paula F. Campos
William J. Murphy
Robert W. Meredith
John Gatesy
Eske Willerslev
Ross D. E. MacPhee
Michael Hofreiter
Kevin L. Campbell
Institut für Biochemie und Biologie
Referiert
39132
2015
2015
eng
284
293
10
3
37
article
Wiley-Blackwell
Hoboken
1
--
--
--
The future of ancient DNA: Technical advances and conceptual shifts
Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.
Bioessays : ideas that push the boundaries
10.1002/bies.201400160
25413709
0265-9247
1521-1878
wos:2015
WOS:000349954100011
Hofreiter, M (reprint author), Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany., michael.hofreiter@uni-potsdam.de
DFG [DFG 852/7-4]; Marie-Curie grant ORCA [FP7-PEOPLE-2011-IIF 299075]; ERC [310763 GeneFlow]
<a href="https://doi.org/10.25932/publishup-43881">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 908</a>
Michael Hofreiter
Johanna L. A. Paijmans
Helen Goodchild
Camilla F. Speller
Axel Barlow
Gloria M. González-Fortes
Jessica A. Thomas
Arne Ludwig
Matthew J. Collins
eng
uncontrolled
ancient DNA
eng
uncontrolled
hybridisation capture
eng
uncontrolled
multi-locus data
eng
uncontrolled
next generation sequencing (NGS)
eng
uncontrolled
palaeogenomics
eng
uncontrolled
population genomics
Institut für Biochemie und Biologie
Referiert
34617
2013
2013
eng
7
6
4
article
Nature Publ. Group
London
1
--
--
--
Morphological and genetic evidence for early Holocene cattle management in northeastern China
The domestication of cattle is generally accepted to have taken place in two independent centres: around 10,500 years ago in the Near East, giving rise to modern taurine cattle, and two millennia later in southern Asia, giving rise to zebu cattle. Here we provide firmly dated morphological and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent C-14 dates. Using Illumina high-throughput sequencing coupled with DNA hybridization capture, we characterize 15,406 bp of the mitogenome with on average 16.7-fold coverage. Phylogenetic analyses reveal a hitherto unknown mitochondrial haplogroup that falls outside the known taurine diversity. Our data suggest that the first attempts to manage cattle in northern China predate the introduction of domestic cattle that gave rise to the current stock by several thousand years.
Nature Communications
10.1038/ncomms3755
2041-1723
wos:2011-2013
2755
WOS:000328023000026
Hofreiter, M (reprint author), Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht St 24-25, D-14476 Potsdam, Germany., michael.hofreiter@york.ac.uk
NSFC [41030102, 40903004, 31072001]; CAS
Hucai Zhang
Johanna L. A. Paijmans
Fengqin Chang
Xiaohong Wu
Guangjie Chen
Chuzhao Lei
Xiujuan Yang
Zhenyi Wei
Daniel G. Bradley
Ludovic Orlando
Terry O'Connor
Michael Hofreiter
Institut für Biochemie und Biologie
Referiert
47444
2020
2020
eng
14
972
postprint
1
2020-08-14
2020-08-14
--
Ancestral mitogenome capture of the Southeast Asian banded linsang
Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.
Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-47444
urn:nbn:de:kobv:517-opus4-474441
1866-8372
e0234385
PLoS ONE 15(2020) 6, Art. e0234385 DOI:10.1371/journal.pone.0234385
<a href="http://publishup.uni-potsdam.de/47443">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
true
true
CC-BY - Namensnennung 4.0 International
Johanna L. A. Paijmans
Axel Barlow
Kirstin Henneberger
Jörns Fickel
Michael Hofreiter
Daniel W. G. Foerste
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
972
eng
uncontrolled
Shotgun sequencing
eng
uncontrolled
Mitochondria
eng
uncontrolled
Phylogenetics
eng
uncontrolled
Phylogenetic analysis
eng
uncontrolled
Paleogenetics
eng
uncontrolled
Sequence alignment
eng
uncontrolled
Genomics
eng
uncontrolled
Museum collections
Naturwissenschaften und Mathematik
Medizin und Gesundheit
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/47444/pmnr972.pdf
49140
2019
2019
eng
1134
1147
14
6
36
article
Oxford Univ. Press
Oxford
1
2019-03-04
2019-03-04
--
Emergence of a chimeric globin pseudogene and increased Hemoglobin Oxygen Affinity Underlie the evolution of aquatic specializations in Sirenia
As limits on O2 availability during submergence impose severe constraints on aerobic respiration, the oxygen binding globin proteins of marine mammals are expected to have evolved under strong evolutionary pressures during their land-to-sea transition. Here, we address this question for the order Sirenia by retrieving, annotating, and performing detailed selection analyses on the globin repertoire of the extinct Steller’s sea cow (Hydrodamalis gigas), dugong (Dugong dugon), and Florida manatee (Trichechus manatus latirostris) in relation to their closest living terrestrial relatives (elephants and hyraxes). These analyses indicate most loci experienced elevated nucleotide substitution rates during their transition to a fully aquatic lifestyle. While most of these genes evolved under neutrality or strong purifying selection, the rate of nonsynonymous/synonymous replacements increased in two genes (Hbz-T1 and Hba-T1) that encode the α-type chains of hemoglobin (Hb) during each stage of life. Notably, the relaxed evolution of Hba-T1 is temporally coupled with the emergence of a chimeric pseudogene (Hba-T2/Hbq-ps) that contributed to the tandemly linked Hba-T1 of stem sirenians via interparalog gene conversion. Functional tests on recombinant Hb proteins from extant and ancestral sirenians further revealed that the molecular remodeling of Hba-T1 coincided with increased Hb–O2 affinity in early sirenians. Available evidence suggests that this trait evolved to maximize O2 extraction from finite lung stores and suppress tissue O2 offloading, thereby facilitating the low metabolic intensities of extant sirenians. In contrast, the derived reduction in Hb–O2 affinity in (sub)Arctic Steller’s sea cows is consistent with fueling increased thermogenesis by these once colossal marine herbivores.
Molecular biology and evolution
10.1093/molbev/msz044
30828717
0737-4038
1537-1719
wos:2019
WOS:000473587400003
Campbell, KL (reprint author), Univ Manitoba, Dept Biol Sci, Winnipeg, MB, Canada., Kevin.Campbell@umanitoba.ca
National Sciences and Engineering Research Council (NSERC) of CanadaNatural Sciences and Engineering Research Council of Canada [RGPIN/238838-2011, RGPIN/412336-2011]; NSERCNatural Sciences and Engineering Research Council of Canada; NSFNational Science Foundation (NSF) [EF0629860]; National Science Foundation DEB award [1132229]; Aarhus University, Faculty of Science and Technology Grant; Danish Council for Independent Research Grant [DFF-4181-00094]
2021-01-28T06:27:47+00:00
sword
importub
filename=package.tar
19aa59702685dfc69c895848d001b3d6
Campbell, Kevin L.
false
true
CC-BY-NC-ND - Namensnennung, nicht kommerziell, keine Bearbeitungen 4.0 International
Anthony V. Signore
Johanna L. A. Paijmans
Michael Hofreiter
Angela Fago
Roy E. Weber
Mark S. Springer
Kevin L. Campbell
eng
uncontrolled
ancient DNA
eng
uncontrolled
aquatic adaptation
eng
uncontrolled
gene conversion
eng
uncontrolled
hemoglobin
eng
uncontrolled
oxygen affinity
eng
uncontrolled
molecular evolution
eng
uncontrolled
myoglobin
eng
uncontrolled
neuroglobin
eng
uncontrolled
cytoglobin
eng
uncontrolled
pseudogene
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
50423
2019
2019
eng
10
1895
286
article
Royal Society
London
1
2019-01-23
2019-01-30
--
A western route of prehistoric human migration from Africa into the Iberian Peninsula
Being at the western fringe of Europe, Iberia had a peculiar prehistory and a complex pattern of Neolithization. A few studies, all based on modern populations, reported the presence of DNA of likely African origin in this region, generally concluding it was the result of recent gene flow, probably during the Islamic period. Here, we provide evidence of much older gene flow from Africa to Iberia by sequencing whole genomes from four human remains from northern Portugal and southern Spain dated around 4000 years BP (from the Middle Neolithic to the Bronze Age). We found one of them to carry an unequivocal sub-Saharan mitogenome of most probably West or West-Central African origin, to our knowledge never reported before in prehistoric remains outside Africa. Our analyses of ancient nuclear genomes show small but significant levels of sub-Saharan African affinity in several ancient Iberian samples, which indicates that what we detected was not an occasional individual phenomenon, but an admixture event recognizable at the population level. We interpret this result as evidence of an early migration process from Africa into the Iberian Peninsula through a western route, possibly across the Strait of Gibraltar.
Proceedings of the Royal Society of London : B, Biological sciences
10.1098/rspb.2018.2288
30963949
0962-8452
1471-2954
wos:2019
20182288
WOS:000465430300005
Gonzalez Fortes, G; Barbujani, G (reprint author), Univ Ferrara, Dept Life Sci & Biotechnol, I-44121 Ferrara, Italy., gnzgrm@unife.it; g.barbujani@unife.it
Marie Sklodowska-Curie Individual Fellowship (NeoGenHeritage) [655478]; European Research Council (ERC)European Research Council (ERC) [310763-GeneFlow, 295733-LanGeLin, 647787-LocalAdaptation]; Spanish MINECO [CGL2014-57209-P, HAR2010-21786/HIST]; Xunta de GaliciaXunta de Galicia
2021-04-20T08:47:47+00:00
sword
importub
filename=package.tar
006c0d40ec475928caae363b6a09f147
false
true
Gloria M. Gonzalez-Fortes
F. Tassi
E. Trucchi
K. Henneberger
Johanna L. A. Paijmans
D. Diez-del-Molino
H. Schroeder
R. R. Susca
C. Barroso-Ruiz
F. J. Bermudez
C. Barroso-Medina
A. M. S. Bettencourt
H. A. Sampaio
A. Salas
A. de Lombera-Hermida
Ramón Fabregas Valcarce
M. Vaquero
S. Alonso
Marina Lozano
Xose Pedro Rodriguez-Alvarez
C. Fernandez-Rodriguez
Andrea Manica
Michael Hofreiter
Guido Barbujani
eng
uncontrolled
palaeogenome
eng
uncontrolled
Africa
eng
uncontrolled
Iberia
eng
uncontrolled
mitochondrial DNA
eng
uncontrolled
gene flow
eng
uncontrolled
admixture
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Bronze Open-Access
49337
2019
2019
eng
12
5
14
article
PLoS
San Fransisco
1
--
2019-05-16
--
Molecular identification of late and terminal Pleistocene Equus ovodovi from northeastern China
The extant diversity of horses (family Equidae) represents a small fraction of that occurring over their evolutionary history. One such lost lineage is the subgenus Sussemionus, which is thought to have become extinct during the Middle Pleistocene. However, recent molecular studies and morphological analysis have revealed that one of their representatives, E. ovodovi, did exist in Siberia during the Late Pleistocene. Fossil materials of E. ovodovi have thus far only been found in Russia. In this study, we extracted DNA from three equid fossil specimens excavated from northeastern China dated at 12,770-12,596, 29,525-28,887 and 40,201-38,848 cal. yBP, respectively, and retrieved three near-complete mitochondrial genomes from the specimens. Phylogenetic analyses cluster the Chinese haplotypes together with previously published Russian E. ovodovi, strongly supporting the assignment of these samples to this taxon. The molecular identification of E. ovodovi in northeastern China extends the known geographical range of this fossil species by several thousand kilometers to the east. The estimated coalescence time of all E. ovodovi haplotypes is approximately 199 Kya, with the Chinese haplotypes coalescing approximately 130 Kya. With a radiocarbon age of 12,770-12,596 cal. yBP, the youngest sample in this study represents the first E. ovodovi sample dating to the terminal Pleistocene, moving the extinction date of this species forwards considerably compared to previously documented fossils. Overall, comparison of our three mitochondrial genomes with the two published ones suggests a genetic diversity similar to several extant species of the genus Equus.
PLOS ONE
10.1371/journal.pone.0216883
31095634
1932-6203
wos:2019
e0216883
WOS:000468030100050
Sheng, GL (reprint author), China Univ Geosci, State Key Lab Biogeol & Environm Geol, Wuhan, Hubei, Peoples R China.; Hofreiter, M (reprint author), Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany., michael.hofreiter@uni-potsdam.de; glsheng@cug.edu.cn
National Natural Science Foundation of ChinaNational Natural Science Foundation of China [41472014, 41672017]; China Scholarship CouncilChina Scholarship Council [2016-2041]; DAADDeutscher Akademischer Austausch Dienst (DAAD) [2016-2041]
2021-02-09T12:15:58+00:00
sword
importub
filename=package.tar
3d032f785646900733dfd676401e6287
Hofreiter, Michael
Sheng, Gui-Lian
false
true
CC-BY - Namensnennung 4.0 International
Jun-Xia Yuan
Xin-Dong Hou
Axel Barlow
Michaela Preick
Ulrike H. Taron
Federica Alberti
Nikolas Basler
Tao Deng
Xu-Long Lai
Michael Hofreiter
Gui-Lian Sheng
Naturwissenschaften und Mathematik
Institut für Biochemie und Biologie
Referiert
Import
DOAJ gelistet
50800
2018
2018
eng
251
253
3
1
46
other
Wiley
Hoboken
1
--
2018-12-05
--
Once lost, twice found: Combined analysis of ancient giant panda sequences characterises extinct clade
Journal of biogeography
10.1111/jbi.13486
0305-0270
1365-2699
wos:2019
WOS:000456346000020
Barlow, A (reprint author), Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany., axel.barlow.ab@gmail.com
National Natural Science Foundation of ChinaNational Natural Science Foundation of China [41672017]
2021-05-26T11:37:19+00:00
sword
importub
filename=package.tar
bbd6439e3e3ee3fb24cb6a85b63c9e45
false
true
Axel Barlow
Gui-Lian Sheng
Xu-Long Lai
Michael Hofreiter
Johanna L. A. Paijmans
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Bronze Open-Access
51257
2018
2018
eng
1196
1208
13
6
18
article
Wiley
Hoboken
1
--
2018-06-07
--
Optimized DNA sampling of ancient bones using Computed Tomography scans
The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era.
Molecular ecology resources
10.1111/1755-0998.12911
29877032
1755-098X
1755-0998
wos:2018
WOS:000449535600003
Hofreiter, M; Barlow, A (reprint author), Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany.; Hildebrandt, T (reprint author), Forsch Verbund Berli eV, Leibniz Inst Zoo & Wildlife Res, Alfred Kowalke Str 17, D-10315 Berlin, Germany., hildebrand@izw-berlin.de; michi@palaeo.eu; axel.barlow.ab@gmail.com
ERC consolidator grant GeneFlow [310763]; Klaus Tschira foundation [00.298.2016]
2021-07-08T16:42:08+00:00
sword
importub
filename=package.tar
d7f2cca9f650e212a70d03859c858db5
Barlow, Axel
Hofreiter, Michael
Hildebrandt, Thomas
false
true
Federica Alberti
Javier Gonzalez
Johanna L. A. Paijmans
Nikolas Basler
Michaela Preick
Kirstin Henneberger
Alexandra Trinks
Gernot Rabeder
Nicholas J. Conard
Susanne C. Muenzel
Ulrich Joger
Guido Fritsch
Thomas Hildebrandt
Michael Hofreiter
Axel Barlow
eng
uncontrolled
ancient DNA
eng
uncontrolled
computer tomography
eng
uncontrolled
palaeogenomics
eng
uncontrolled
paleogenetics
eng
uncontrolled
petrous bone
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Green Open-Access