@misc{BaslerXenikoudakisWestburyetal.2017, author = {Basler, Nikolas and Xenikoudakis, Georgios and Westbury, Michael V. and Song, Lingfeng and Sheng, Guilian and Barlow, Axel}, title = {Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {715}, issn = {1866-8372}, doi = {10.25932/publishup-42815}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-428151}, pages = {7}, year = {2017}, abstract = {Objective: A key challenge in ancient DNA research is massive microbial DNA contamination from the deposition site which accumulates post mortem in the study organism's remains. Two simple and cost-effective methods to enrich the relative endogenous fraction of DNA in ancient samples involve treatment of sample powder with either bleach or Proteinase K pre-digestion prior to DNA extraction. Both approaches have yielded promising but vary-ing results in other studies. Here, we contribute data on the performance of these methods using a comprehensive and systematic series of experiments applied to a single ancient bone fragment from a giant panda (Ailuropoda melanoleuca).Results: Bleach and pre-digestion treatments increased the endogenous DNA content up to ninefold. However, the absolute amount of DNA retrieved was dramatically reduced by all treatments. We also observed reduced DNA damage patterns in pre-treated libraries compared to untreated ones, resulting in longer mean fragment lengths and reduced thymine over-representation at fragment ends. Guanine-cytosine (GC) contents of both mapped and total reads are consistent between treatments and conform to general expectations, indicating no obvious biasing effect of the applied methods. Our results therefore confirm the value of bleach and pre-digestion as tools in palaeog-enomic studies, providing sufficient material is available.}, language = {en} } @article{ShengBaslerJietal.2019, author = {Sheng, Gui-Lian and Basler, Nikolas and Ji, Xue-Ping and Paijmans, Johanna L. A. and Alberti, Federica and Preick, Michaela and Hartmann, Stefanie and Westbury, Michael V. and Yuan, Jun-Xia and Jablonski, Nina G. and Xenikoudakis, Georgios and Hou, Xin-Dong and Xiao, Bo and Liu, Jian-Hui and Hofreiter, Michael and Lai, Xu-Long and Barlow, Axel}, title = {Paleogenome reveals genetic contribution of extinct giant panda to extant populations}, series = {Current biology}, volume = {29}, journal = {Current biology}, number = {10}, publisher = {Cell Press}, address = {Cambridge}, issn = {0960-9822}, doi = {10.1016/j.cub.2019.04.021}, pages = {1695 -- 1700}, year = {2019}, abstract = {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.}, language = {en} } @article{YuanHouBarlowetal.2019, author = {Yuan, Jun-Xia and Hou, Xin-Dong and Barlow, Axel and Preick, Michaela and Taron, Ulrike H. and Alberti, Federica and Basler, Nikolas and Deng, Tao and Lai, Xu-Long and Hofreiter, Michael and Sheng, Gui-Lian}, title = {Molecular identification of late and terminal Pleistocene Equus ovodovi from northeastern China}, series = {PLOS ONE}, volume = {14}, journal = {PLOS ONE}, number = {5}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0216883}, pages = {12}, year = {2019}, abstract = {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.}, language = {en} } @misc{BarlowShengLaietal.2018, author = {Barlow, Axel and Sheng, Gui-Lian and Lai, Xu-Long and Hofreiter, Michael and Paijmans, Johanna L. A.}, title = {Once lost, twice found: Combined analysis of ancient giant panda sequences characterises extinct clade}, series = {Journal of biogeography}, volume = {46}, journal = {Journal of biogeography}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {0305-0270}, doi = {10.1111/jbi.13486}, pages = {251 -- 253}, year = {2018}, language = {en} } @article{YuanShengPreicketal.2020, author = {Yuan, Junxia and Sheng, Guilian and Preick, Michaela and Sun, Boyang and Hou, Xindong and Chen, Shungang and Taron, Ulrike Helene and Barlow, Axel and Wang, Linying and Hu, Jiaming and Deng, Tao and Lai, Xulong and Hofreiter, Michael}, title = {Mitochondrial genomes of Late Pleistocene caballine horses from China belong to a separate clade}, series = {Quaternary science reviews : the international multidisciplinary research and review journal}, volume = {250}, journal = {Quaternary science reviews : the international multidisciplinary research and review journal}, publisher = {Elsevier}, address = {Amsterdam [u.a.]}, issn = {0277-3791}, doi = {10.1016/j.quascirev.2020.106691}, pages = {8}, year = {2020}, abstract = {There were several species of Equus in northern China during the Late Pleistocene, including Equus przewalskii and Equus dalianensis. A number of morphological studies have been carried out on E. przewalskii and E. dalianensis, but their evolutionary history is still unresolved. In this study, we retrieved near-complete mitochondrial genomes from E. dalianensis and E. przewalskii specimens excavated from Late Pleistocene strata in northeastern China. Phylogenetic analyses revealed that caballoid horses were divided into two subclades: the New World and the Old World caballine horse subclades. The Old World caballine horses comprise of two deep phylogenetic lineages, with modern and ancient Equus caballus and modern E. przewalskii forming lineage I, and the individuals in this study together with one Yakut specimen forming lineage II. Our results indicate that Chinese Late Pleistocene caballoid horses showed a closer relationship to other Eurasian caballine horses than that to Pleistocene horses from North America. In addition, phylogenetic analyses suggested a close relationship between E. dalianensis and the Chinese fossil E. przewalskii, in agreement with previous researches based on morphological analyses. Interestingly, E. dalianensis and the fossil E. przewalskii were intermixed rather than split into distinct lineages, suggesting either that gene flow existed between these two species or that morphology-based species assignment of palaeontological specimens is not always correct. Moreover, Bayesian analysis showed that the divergence time between the New World and the Old World caballoid horses was at 1.02 Ma (95\% CI: 0.86-1.24 Ma), and the two Old World lineages (I \& II) split at 0.88 Ma (95\% CI: 0.69-1.13 Ma), which indicates that caballoid horses seem to have evolved into different populations in the Old World soon after they migrated from North America via the Bering Land Bridge. Finally, the TMRCA of E. dalianensis was estimated at 0.20 Ma (95\% CI: 0.15-0.28 Ma), and it showed a relative low genetic diversity compared with other Equus species.}, language = {en} }