@misc{GallegoLlorenteSarahJonesetal.2016, author = {Gallego-Llorente, Marcos and Sarah, Connell and Jones, Eppie R. and Merrett, Deborah C. and Jeon, Y. and Eriksson, Anders and Siska, Veronika and Gamba, Cristina and Meiklejohn, Christopher and Beyer, Robert and Jeon, Sungwon and Cho, Yun Sung and Hofreiter, Michael and Bhak, Jong and Manica, Andrea and Pinhasi, Ron}, title = {The genetics of an early Neolithic pastoralist from the Zagros, Iran}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {952}, issn = {1866-8372}, doi = {10.25932/publishup-43935}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-439355}, pages = {9}, year = {2016}, abstract = {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.}, language = {en} } @article{BarnettWestburySandovalVelascoetal.2020, author = {Barnett, Ross and Westbury, Michael V. and Sandoval-Velasco, Marcela and Vieira, Filipe Garrett and Jeon, Sungwon and Zazula, Grant and Martin, Michael D. and Ho, Simon Y. W. and Mather, Niklas and Gopalakrishnan, Shyam and Ramos-Madrigal, Jazmin and de Manuel, Marc and Zepeda-Mendoza, M. Lisandra and Antunes, Agostinho and Baez, Aldo Carmona and De Cahsan, Binia and Larson, Greger and O'Brien, Stephen J. and Eizirik, Eduardo and Johnson, Warren E. and Koepfli, Klaus-Peter and Wilting, Andreas and Fickel, J{\"o}rns and Dalen, Love and Lorenzen, Eline D. and Marques-Bonet, Tomas and Hansen, Anders J. and Zhang, Guojie and Bhak, Jong and Yamaguchi, Nobuyuki and Gilbert, M. Thomas P.}, title = {Genomic adaptations and evolutionary history of the extinct scimitar-toothed cat}, series = {Current biology}, volume = {30}, journal = {Current biology}, number = {24}, publisher = {Cell Press}, address = {Cambridge}, issn = {0960-9822}, doi = {10.1016/j.cub.2020.09.051}, pages = {14}, year = {2020}, abstract = {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.}, language = {en} } @misc{SiskaJonesJeonetal.2017, author = {Siska, Veronika and Jones, Eppie Ruth and Jeon, Sungwon and Bhak, Youngjune and Kim, Hak-Min and Cho, Yun Sung and Kim, Hyunho and Lee, Kyusang and Veselovskaya, Elizaveta and Balueva, Tatiana and Gallego-Llorente, Marcos and Hofreiter, Michael and Bradley, Daniel G. and Eriksson, Anders and Pinhasi, Ron and Bhak, Jong and Manica, Andrea}, title = {Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {791}, issn = {1866-8372}, doi = {10.25932/publishup-43997}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-439977}, pages = {11}, year = {2017}, abstract = {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.}, language = {en} } @article{SiskaJonesJeonetal.2017, author = {Siska, Veronika and Jones, Eppie Ruth and Jeon, Sungwon and Bhak, Youngjune and Kim, Hak-Min and Cho, Yun Sung and Kim, Hyunho and Lee, Kyusang and Veselovskaya, Elizaveta and Balueva, Tatiana and Gallego-Llorente, Marcos and Hofreiter, Michael and Bradley, Daniel G. and Eriksson, Anders and Pinhasi, Ron and Bhak, Jong and Manica, Andrea}, title = {Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago}, series = {Science Advances}, volume = {3}, journal = {Science Advances}, number = {2}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {2375-2548}, doi = {10.1126/sciadv.1601877}, pages = {10}, year = {2017}, abstract = {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.}, language = {en} }