@misc{XenikoudakisAhmedHarrisetal.2020, author = {Xenikoudakis, Georgios and Ahmed, Mayeesha and Harris, Jacob Colt and Wadleigh, Rachel and Paijmans, Johanna L. A. and Hartmann, Stefanie and Barlow, Axel and Lerner, Heather and Hofreiter, Michael}, title = {Ancient DNA reveals twenty million years of aquatic life in beavers}, series = {Current biology : CB}, volume = {30}, journal = {Current biology : CB}, number = {3}, publisher = {Current Biology Ltd.}, address = {London}, issn = {0960-9822}, doi = {10.1016/j.cub.2019.12.041}, pages = {R110 -- R111}, year = {2020}, abstract = {Xenikoudakis et al. report a partial mitochondrial genome of the extinct giant beaver Castoroides and estimate the origin of aquatic behavior in beavers to approximately 20 million years. This time estimate coincides with the extinction of terrestrial beavers and raises the question whether the two events had a common cause.}, language = {en} } @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{BarlowCahillHartmannetal.2018, author = {Barlow, Axel and Cahill, James A. and Hartmann, Stefanie and Theunert, Christoph and Xenikoudakis, Georgios and Gonzalez-Fortes, Gloria M. and Paijmans, Johanna L. A. and Rabeder, Gernot and Frischauf, Christine and Garcia-Vazquez, Ana and Murtskhvaladze, Marine and Saarma, Urmas and Anijalg, Peeter and Skrbinsek, Tomaz and Bertorelle, Giorgio and Gasparian, Boris and Bar-Oz, Guy and Pinhasi, Ron and Slatkin, Montgomery and Dalen, Love and Shapiro, Beth and Hofreiter, Michael}, title = {Partial genomic survival of cave bears in living brown bears}, series = {Nature Ecology \& Evolution}, volume = {2}, journal = {Nature Ecology \& Evolution}, number = {10}, publisher = {Nature Publ. Group}, address = {London}, issn = {2397-334X}, doi = {10.1038/s41559-018-0654-8}, pages = {1563 -- 1570}, year = {2018}, abstract = {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.}, language = {en} }