TY  - GEN
A1  - Xenikoudakis, Georgios
A1  - Ahmed, Mayeesha
A1  - Harris, Jacob Colt
A1  - Wadleigh, Rachel
A1  - Paijmans, Johanna L. A.
A1  - Hartmann, Stefanie
A1  - Barlow, Axel
A1  - Lerner, Heather
A1  - Hofreiter, Michael
T1  - Ancient DNA reveals twenty million years of aquatic life in beavers
T2  - Current biology : CB
N2  - 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.
Y1  - 2020
U6  - https://doi.org/10.1016/j.cub.2019.12.041
SN  - 0960-9822
SN  - 1879-0445
VL  - 30
IS  - 3
SP  - R110
EP  - R111
PB  - Current Biology Ltd.
CY  - London
ER  - 
TY  - GEN
A1  - Westbury, Michael V.
A1  - Baleka, Sina Isabelle
A1  - Barlow, Axel
A1  - Hartmann, Stefanie
A1  - Paijmans, Johanna L. A.
A1  - Kramarz, Alejandro
A1  - Forasiepi, Analía M.
A1  - Bond, Mariano
A1  - Gelfo, Javier N.
A1  - Reguero, Marcelo A.
A1  - López-Mendoza, Patricio
A1  - Taglioretti, Matias
A1  - Scaglia, Fernando
A1  - Rinderknecht, Andrés
A1  - Jones, Washington
A1  - Mena, Francisco
A1  - Billet, Guillaume
A1  - de Muizon, Christian
A1  - Aguilar, José Luis
A1  - MacPhee, Ross D.E.
A1  - Hofreiter, Michael
T1  - A mitogenomic timetree for Darwin's enigmatic South American mammal Macrauchenia patachonica
T2  - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 793 
KW  - ancient DNA
KW  - evolutionary history
KW  - genome sequence
KW  - reveals
KW  - contamination
KW  - alignment
KW  - reads
KW  - bones
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-440801
SN  - 1866-8372
IS  - 793
ER  - 
TY  - GEN
A1  - Barlow, Axel
A1  - Hartmann, Stefanie
A1  - Gonzalez, Javier
A1  - Hofreiter, Michael
A1  - Paijmans, Johanna L. A.
T1  - Consensify
BT  - a method for generating pseudohaploid genome sequences from palaeogenomic datasets with reduced error rates
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1033 
KW  - palaeogenomics
KW  - ancient DNA
KW  - sequencing error
KW  - error reduction
KW  - D statistics
KW  - bioinformatics
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-472521
SN  - 1866-8372
IS  - 1033
ER  - 
TY  - JOUR
A1  - Westbury, Michael V.
A1  - Baleka, Sina Isabelle
A1  - Barlow, Axel
A1  - Hartmann, Stefanie
A1  - Paijmans, Johanna L. A.
A1  - Kramarz, Alejandro
A1  - Forasiepi, Analia M.
A1  - Bond, Mariano
A1  - Gelfo, Javier N.
A1  - Reguero, Marcelo A.
A1  - Lopez-Mendoza, Patricio
A1  - Taglioretti, Matias
A1  - Scaglia, Fernando
A1  - Rinderknecht, Andres
A1  - Jones, Washington
A1  - Mena, Francisco
A1  - Billet, Guillaume
A1  - de Muizon, Christian
A1  - Luis Aguilar, Jose
A1  - MacPhee, Ross D. E.
A1  - Hofreiter, Michael
T1  - A mitogenomic timetree for Darwin’s enigmatic South American mammal  Macrauchenia patachonica
JF  - Nature Communications
N2  - 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.
Y1  - 2017
U6  - https://doi.org/10.1038/ncomms15951
SN  - 2041-1723
VL  - 8
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Barlow, Axel
A1  - Hartmann, Stefanie
A1  - Gonzalez, Javier
A1  - Hofreiter, Michael
A1  - Paijmans, Johanna L. A.
T1  - Consensify
BT  - a method for generating pseudohaploid genome sequences from palaeogenomic datasets with reduced error rates
JF  - Genes / Molecular Diversity Preservation International
N2  - 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.
KW  - palaeogenomics
KW  - ancient DNA
KW  - sequencing error
KW  - error reduction
KW  - D statistics
KW  - bioinformatics
Y1  - 2020
U6  - https://doi.org/10.3390/genes11010050
SN  - 2073-4425
VL  - 11
IS  - 1
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Sheng, Gui-Lian
A1  - Basler, Nikolas
A1  - Ji, Xue-Ping
A1  - Paijmans, Johanna L. A.
A1  - Alberti, Federica
A1  - Preick, Michaela
A1  - Hartmann, Stefanie
A1  - Westbury, Michael V.
A1  - Yuan, Jun-Xia
A1  - Jablonski, Nina G.
A1  - Xenikoudakis, Georgios
A1  - Hou, Xin-Dong
A1  - Xiao, Bo
A1  - Liu, Jian-Hui
A1  - Hofreiter, Michael
A1  - Lai, Xu-Long
A1  - Barlow, Axel
T1  - Paleogenome reveals genetic contribution of extinct giant panda to extant populations
JF  - Current biology
N2  - 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.
Y1  - 2019
U6  - https://doi.org/10.1016/j.cub.2019.04.021
SN  - 0960-9822
SN  - 1879-0445
VL  - 29
IS  - 10
SP  - 1695
EP  - 1700
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Barlow, Axel
A1  - Cahill, James A.
A1  - Hartmann, Stefanie
A1  - Theunert, Christoph
A1  - Xenikoudakis, Georgios
A1  - Gonzalez-Fortes, Gloria M.
A1  - Paijmans, Johanna L. A.
A1  - Rabeder, Gernot
A1  - Frischauf, Christine
A1  - Garcia-Vazquez, Ana
A1  - Murtskhvaladze, Marine
A1  - Saarma, Urmas
A1  - Anijalg, Peeter
A1  - Skrbinsek, Tomaz
A1  - Bertorelle, Giorgio
A1  - Gasparian, Boris
A1  - Bar-Oz, Guy
A1  - Pinhasi, Ron
A1  - Slatkin, Montgomery
A1  - Dalen, Love
A1  - Shapiro, Beth
A1  - Hofreiter, Michael
T1  - Partial genomic survival of cave bears in living brown bears
JF  - Nature Ecology & Evolution
N2  - Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.
Y1  - 2018
U6  - https://doi.org/10.1038/s41559-018-0654-8
SN  - 2397-334X
VL  - 2
IS  - 10
SP  - 1563
EP  - 1570
PB  - Nature Publ. Group
CY  - London
ER  -