TY - GEN A1 - Barlow, Axel A1 - Sheng, Gui-Lian A1 - Lai, Xu-Long A1 - Hofreiter, Michael A1 - Paijmans, Johanna L. A. T1 - Once lost, twice found: Combined analysis of ancient giant panda sequences characterises extinct clade T2 - Journal of biogeography Y1 - 2018 U6 - https://doi.org/10.1111/jbi.13486 SN - 0305-0270 SN - 1365-2699 VL - 46 IS - 1 SP - 251 EP - 253 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Yuan, Jun-Xia A1 - Hou, Xin-Dong A1 - Barlow, Axel A1 - Preick, Michaela A1 - Taron, Ulrike H. A1 - Alberti, Federica A1 - Basler, Nikolas A1 - Deng, Tao A1 - Lai, Xu-Long A1 - Hofreiter, Michael A1 - Sheng, Gui-Lian T1 - Molecular identification of late and terminal Pleistocene Equus ovodovi from northeastern China JF - PLOS ONE N2 - 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. Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0216883 SN - 1932-6203 VL - 14 IS - 5 PB - PLoS CY - San Fransisco 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 - Chen, Shun-Gang A1 - Li, Ji A1 - Zhang, Fan A1 - Xiao, Bo A1 - Hu, Jia-Ming A1 - Cui, Yin-Qiu A1 - Hofreiter, Michael A1 - Hou, Xin-Dong A1 - Sheng, Gui-Lian A1 - Lai, Xu-Long A1 - Yuan, Jun-Xia T1 - Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China JF - Mitochondrial DNA Part A N2 - 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. KW - Camelus bactrianus KW - mitochondrial genome KW - ancient DNA KW - phylogeny KW - maternal lineages Y1 - 2019 U6 - https://doi.org/10.1080/24701394.2019.1659250 SN - 2470-1394 SN - 2470-1408 VL - 30 IS - 7 SP - 786 EP - 793 PB - Routledge, Taylor & Francis Group CY - Abingdon ER -