TY  - JOUR
A1  - Palkopoulou, Eleftheria
A1  - Lipson, Mark
A1  - Mallick, Swapan
A1  - Nielsen, Svend
A1  - Rohland, Nadin
A1  - Baleka, Sina Isabelle
A1  - Karpinski, Emil
A1  - Ivancevici, Atma M.
A1  - Thu-Hien To, 
A1  - Kortschak, Daniel
A1  - Raison, Joy M.
A1  - Qu, Zhipeng
A1  - Chin, Tat-Jun
A1  - Alt, Kurt W.
A1  - Claesson, Stefan
A1  - Dalen, Love
A1  - MacPhee, Ross D. E.
A1  - Meller, Harald
A1  - Rocar, Alfred L.
A1  - Ryder, Oliver A.
A1  - Heiman, David
A1  - Young, Sarah
A1  - Breen, Matthew
A1  - Williams, Christina
A1  - Aken, Bronwen L.
A1  - Ruffier, Magali
A1  - Karlsson, Elinor
A1  - Johnson, Jeremy
A1  - Di Palma, Federica
A1  - Alfoldi, Jessica
A1  - Adelsoni, David L.
A1  - Mailund, Thomas
A1  - Munch, Kasper
A1  - Lindblad-Toh, Kerstin
A1  - Hofreiter, Michael
A1  - Poinar, Hendrik
A1  - Reich, David
T1  - A comprehensive genomic history of extinct and living elephants
JF  - Proceedings of the National Academy of Sciences of the United States of America
KW  - paleogenomics
KW  - elephantid evolution
KW  - mammoth
KW  - admixture
KW  - species divergence
Y1  - 2018
U6  - https://doi.org/10.1073/pnas.1720554115
SN  - 0027-8424
VL  - 115
IS  - 11
SP  - E2566
EP  - E2574
PB  - National Acad. of Sciences
CY  - Washington
ER  - 
TY  - JOUR
A1  - Chang, Dan
A1  - Knapp, Michael
A1  - Enk, Jacob
A1  - Lippold, Sebastian
A1  - Kircher, Martin
A1  - Lister, Adrian M.
A1  - MacPhee, Ross D. E.
A1  - Widga, Christopher
A1  - Czechowski, Paul
A1  - Sommer, Robert
A1  - Hodges, Emily
A1  - Stümpel, Nikolaus
A1  - Barnes, Ian
A1  - Dalén, Love
A1  - Derevianko, Anatoly
A1  - Germonpré, Mietje
A1  - Hillebrand-Voiculescu, Alexandra
A1  - Constantin, Silviu
A1  - Kuznetsova, Tatyana
A1  - Mol, Dick
A1  - Rathgeber, Thomas
A1  - Rosendahl, Wilfried
A1  - Tikhonov, Alexey N.
A1  - Willerslev, Eske
A1  - Hannon, Greg
A1  - Lalueza i Fox, Carles
A1  - Joger, Ulrich
A1  - Poinar, Hendrik N.
A1  - Hofreiter, Michael
A1  - Shapiro, Beth
T1  - The evolutionary and phylogeographic history of woolly mammoths
BT  - a comprehensive mitogenomic analysis
JF  - Scientific reports
N2  - 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.
Y1  - 2017
U6  - https://doi.org/10.1038/srep44585
SN  - 2045-2322
VL  - 7
PB  - Nature Publishing Group
CY  - London
ER  - 
TY  - JOUR
A1  - Barnett, Ross
A1  - Westbury, Michael V.
A1  - Sandoval-Velasco, Marcela
A1  - Vieira, Filipe Garrett
A1  - Jeon, Sungwon
A1  - Zazula, Grant
A1  - Martin, Michael D.
A1  - Ho, Simon Y. W.
A1  - Mather, Niklas
A1  - Gopalakrishnan, Shyam
A1  - Ramos-Madrigal, Jazmin
A1  - de Manuel, Marc
A1  - Zepeda-Mendoza, M. Lisandra
A1  - Antunes, Agostinho
A1  - Baez, Aldo Carmona
A1  - De Cahsan, Binia
A1  - Larson, Greger
A1  - O'Brien, Stephen J.
A1  - Eizirik, Eduardo
A1  - Johnson, Warren E.
A1  - Koepfli, Klaus-Peter
A1  - Wilting, Andreas
A1  - Fickel, Jörns
A1  - Dalen, Love
A1  - Lorenzen, Eline D.
A1  - Marques-Bonet, Tomas
A1  - Hansen, Anders J.
A1  - Zhang, Guojie
A1  - Bhak, Jong
A1  - Yamaguchi, Nobuyuki
A1  - Gilbert, M. Thomas P.
T1  - Genomic adaptations and evolutionary history of the extinct scimitar-toothed cat
BT  - Homotherium latidens
JF  - Current biology
N2  - Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1-4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6-8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a -7x nuclear genome and a similar to 38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (similar to 22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11-14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.
Y1  - 2020
U6  - https://doi.org/10.1016/j.cub.2020.09.051
SN  - 0960-9822
SN  - 1879-0445
VL  - 30
IS  - 24
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  - 
TY  - GEN
A1  - Westbury, Michael V.
A1  - Hartmann, Stefanie
A1  - Barlow, Axel
A1  - Wiesel, Ingrid
A1  - Leo, Viyanna
A1  - Welch, Rebecca
A1  - Parker, Daniel M.
A1  - Sicks, Florian
A1  - Ludwig, Arne
A1  - Dalen, Love
A1  - Hofreiter, Michael
T1  - Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 589 
KW  - evolution
KW  - hyena
KW  - genomics
KW  - population genomics
KW  - diversity
Y1  - 2019
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-414132
SN  - 1866-8372
IS  - 589
ER  - 
TY  - JOUR
A1  - Westbury, Michael V.
A1  - Hartmann, Stefanie
A1  - Barlow, Axel
A1  - Wiesel, Ingrid
A1  - Leo, Viyanna
A1  - Welch, Rebecca
A1  - Parker, Daniel M.
A1  - Sicks, Florian
A1  - Ludwig, Arne
A1  - Dalen, Love
A1  - Hofreiter, Michael
T1  - Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena
JF  - Molecular biology and evolution
N2  - 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.
KW  - evolution
KW  - hyena
KW  - genomics
KW  - population genomics
KW  - diversity
Y1  - 2018
U6  - https://doi.org/10.1093/molbev/msy037
SN  - 0737-4038
SN  - 1537-1719
VL  - 35
IS  - 5
SP  - 1225
EP  - 1237
PB  - Oxford Univ. Press
CY  - Oxford
ER  -