TY  - JOUR
A1  - Westbury, Michael V.
A1  - Dalerumb, Fredrik
A1  - Noren, Karin
A1  - Hofreiter, Michael
T1  - Complete mitochondrial genome of a bat-eared fox (Otocyon megalotis), along with phylogenetic considerations
JF  - Mitochondrial DNA. Part B
N2  - 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.
KW  - Phylogenetics
KW  - mitochondria
KW  - iterative mapping
KW  - Canidae
Y1  - 2017
U6  - https://doi.org/10.1080/23802359.2017.1331325
SN  - 2380-2359
VL  - 2
IS  - 1
SP  - 298
EP  - 299
PB  - Routledge, Taylor & Francis Group
CY  - London
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  - Thomas, Jessica E.
A1  - Carvalho, Gary R.
A1  - Haile, James
A1  - Martin, Michael D.
A1  - Castruita, Jose A. Samaniego
A1  - Niemann, Jonas
A1  - Sinding, Mikkel-Holger S.
A1  - Sandoval-Velasco, Marcela
A1  - Rawlence, Nicolas J.
A1  - Fuller, Errol
A1  - Fjeldsa, Jon
A1  - Hofreiter, Michael
A1  - Stewart, John R.
A1  - Gilbert, M. Thomas P.
A1  - Knapp, Michael
T1  - An ‛Aukward’ tale
BT  - a genetic approach to discover the whereabouts of the  Last Great Auks
JF  - Genes
N2  - 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.
KW  - ancient DNA
KW  - extinct birds
KW  - mitochondrial genome
KW  - museum specimens
KW  - palaeogenomics
Y1  - 2017
U6  - https://doi.org/10.3390/genes8060164
SN  - 2073-4425
VL  - 8
IS  - 6
SP  - 164
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Paijmans, Johanna L. A.
A1  - Barnett, Ross
A1  - Gilbert, M. Thomas P.
A1  - Zepeda-Mendoza, M. Lisandra
A1  - Reumer, Jelle W. F.
A1  - de Vos, John
A1  - Zazula, Grant
A1  - Nagel, Doris
A1  - Baryshnikov, Gennady F.
A1  - Leonard, Jennifer A.
A1  - Rohland, Nadin
A1  - Westbury, Michael V.
A1  - Barlow, Axel
A1  - Hofreiter, Michael
T1  - Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics
JF  - Current biology
N2  - 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].
Y1  - 2017
U6  - https://doi.org/10.1016/j.cub.2017.09.033
SN  - 0960-9822
SN  - 1879-0445
VL  - 27
SP  - 3330
EP  - +
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Mohandesan, Elmira
A1  - Speller, Camilla F.
A1  - Peters, Joris
A1  - Uerpmann, Hans-Peter
A1  - Uerpmann, Margarethe
A1  - De Cupere, Bea
A1  - Hofreiter, Michael
A1  - Burger, Pamela A.
T1  - Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel
JF  - Molecular ecology resources
N2  - 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.
KW  - ancient DNA
KW  - Camelus dromedarius
KW  - capture enrichment
KW  - degraded DNA
KW  - mitochondrial genome (mtDNA)
KW  - next-generation sequencing
Y1  - 2017
U6  - https://doi.org/10.1111/1755-0998.12551
SN  - 1755-098X
SN  - 1755-0998
VL  - 17
IS  - 2
SP  - 300
EP  - 313
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Meyer, Matthias
A1  - Palkopoulou, Eleftheria
A1  - Baleka, Sina Isabelle
A1  - Stiller, Mathias
A1  - Penkman, Kirsty E. H.
A1  - Alt, Kurt W.
A1  - Ishida, Yasuko
A1  - Mania, Dietrich
A1  - Mallick, Swapan
A1  - Meijer, Tom
A1  - Meller, Harald
A1  - Nagel, Sarah
A1  - Nickel, Birgit
A1  - Ostritz, Sven
A1  - Rohland, Nadin
A1  - Schauer, Karol
A1  - Schueler, Tim
A1  - Roca, Alfred L.
A1  - Reich, David
A1  - Shapiro, Beth
A1  - Hofreiter, Michael
T1  - Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution
JF  - eLife
N2  - 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.
Y1  - 2017
U6  - https://doi.org/10.7554/eLife.25413
SN  - 2050-084X
VL  - 6
PB  - eLife Sciences Publications
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Librado, Pablo
A1  - Gamba, Cristina
A1  - Gaunitz, Charleen
A1  - Sarkissian, Clio Der
A1  - Pruvost, Melanie
A1  - Albrechtsen, Anders
A1  - Fages, Antoine
A1  - Khan, Naveed
A1  - Schubert, Mikkel
A1  - Jagannathan, Vidhya
A1  - Serres-Armero, Aitor
A1  - Kuderna, Lukas F. K.
A1  - Povolotskaya, Inna S.
A1  - Seguin-Orlando, Andaine
A1  - Lepetz, Sebastien
A1  - Neuditschko, Markus
A1  - Theves, Catherine
A1  - Alquraishi, Saleh A.
A1  - Alfarhan, Ahmed H.
A1  - Al-Rasheid, Khaled A. S.
A1  - Rieder, Stefan
A1  - Samashev, Zainolla
A1  - Francfort, Henri-Paul
A1  - Benecke, Norbert
A1  - Hofreiter, Michael
A1  - Ludwig, Arne
A1  - Keyser, Christine
A1  - Marques-Bonet, Tomas
A1  - Ludes, Bertrand
A1  - Crubezy, Eric
A1  - Leeb, Tosso
A1  - Willerslev, Eske
A1  - Orlando, Ludovic
T1  - Ancient genomic changes associated with domestication of the horse
JF  - Science
N2  - 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.
Y1  - 2017
U6  - https://doi.org/10.1126/science.aam5298
SN  - 0036-8075
SN  - 1095-9203
VL  - 356
SP  - 442
EP  - 445
PB  - American Assoc. for the Advancement of Science
CY  - Washington
ER  - 
TY  - JOUR
A1  - Kehlmaier, Christian
A1  - Barlow, Axel
A1  - Hastings, Alexander K.
A1  - Vamberger, Melita
A1  - Paijmans, Johanna L. A.
A1  - Steadman, David W.
A1  - Albury, Nancy A.
A1  - Franz, Richard
A1  - Hofreiter, Michael
A1  - Fritz, Uwe
T1  - Tropical ancient DNA reveals relationships of the extinct bahamian giant tortoise Chelonoidis alburyorum
JF  - Proceedings of the Royal Society of London : Series B, Biological sciences
N2  - 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.
KW  - Bahamas
KW  - biogeography
KW  - extinction
KW  - palaeontology
KW  - phylogeny
Y1  - 2017
U6  - https://doi.org/10.1098/rspb.2016.2235
SN  - 0962-8452
SN  - 1471-2954
VL  - 284
PB  - The Royal Society
CY  - London
ER  - 
TY  - JOUR
A1  - González-Fortes, Gloria M.
A1  - Jones, Eppie R.
A1  - Lightfoot, Emma
A1  - Bonsall, Clive
A1  - Lazar, Catalin
A1  - Dolores Garralda, Maria
A1  - Drak, Labib
A1  - Siska, Veronika
A1  - Simalcsik, Angela
A1  - Boroneant, Adina
A1  - Vidal Romani, Juan Ramon
A1  - Vaqueiro Rodriguez, Marcos
A1  - Arias, Pablo
A1  - Pinhasi, Ron
A1  - Manica, Andrea
A1  - Hofreiter, Michael
T1  - Paleogenomic Evidence for Multi-generational Mixing between Neolithic Farmers and Mesolithic Hunter-Gatherers in the Lower Danube Basin
JF  - Current biology
N2  - 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.
Y1  - 2017
U6  - https://doi.org/10.1016/j.cub.2017.05.023
SN  - 0960-9822
SN  - 1879-0445
VL  - 27
SP  - 1801
EP  - +
PB  - Cell Press
CY  - Cambridge
ER  - 
TY  - GEN
A1  - Gonzalez-Fortes, Gloria M.
A1  - Tassi, Francesca
A1  - Ghirotto, Silvia
A1  - Henneberger, Kirstin
A1  - Hofreiter, Michael
A1  - Barbujani, Guido
T1  - The Neolithic transition at the Western edge of Europe
T2  - American journal of physical anthropology
Y1  - 2017
SN  - 0002-9483
SN  - 1096-8644
VL  - 162
SP  - 198
EP  - 198
PB  - Wiley
CY  - Hoboken
ER  -