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 - GEN A1 - Basler, Nikolas A1 - Xenikoudakis, Georgios A1 - Westbury, Michael V. A1 - Song, Lingfeng A1 - Sheng, Guilian A1 - Barlow, Axel T1 - Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 715 KW - ancient DNA (aDNA) KW - bleach KW - pre-digestion KW - endogenous content KW - palaeogenomics KW - paleogenomics KW - next generation sequencing (NGS) KW - giant panda KW - Ailuropoda melanoleuca Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-428151 SN - 1866-8372 IS - 715 ER - TY - JOUR A1 - Folkertsma, Remco A1 - Westbury, Michael V. A1 - Eccard, Jana A1 - Hofreiter, Michael T1 - The complete mitochondrial genome of the common vole, Microtus arvalis (Rodentia: Arvicolinae) JF - Mitochondrial DNA Part B N2 - The common vole, Microtus arvalis belongs to the genus Microtus in the subfamily Arvicolinae. In this study, the complete mitochondrial genome of M. arvalis was recovered using shotgun sequencing and an iterative mapping approach using three related species. Phylogenetic analyses using the sequence of 21 arvicoline species place the common vole as a sister species to the East European vole (Microtus levis), but as opposed to previous results we find no support for the recognition of the genus Neodon within the subfamily Arvicolinae, as this is, as well as the genus Lasiopodomys, found within the Microtus genus. KW - Microtus arvalis KW - Arvicolinae KW - mitochondrial genome KW - common vole KW - phylogeny Y1 - 2018 U6 - https://doi.org/10.1080/23802359.2018.1457994 SN - 2380-2359 VL - 3 IS - 1 SP - 446 EP - 447 ER - TY - GEN A1 - Folkertsma, Remco A1 - Westbury, Michael V. A1 - Eccard, Jana A1 - Hofreiter, Michael T1 - The complete mitochondrial genome of the common vole, Microtus arvalis (Rodentia: Arvicolinae) T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The common vole, Microtus arvalis belongs to the genus Microtus in the subfamily Arvicolinae. In this study, the complete mitochondrial genome of M. arvalis was recovered using shotgun sequencing and an iterative mapping approach using three related species. Phylogenetic analyses using the sequence of 21 arvicoline species place the common vole as a sister species to the East European vole (Microtus levis), but as opposed to previous results we find no support for the recognition of the genus Neodon within the subfamily Arvicolinae, as this is, as well as the genus Lasiopodomys, found within the Microtus genus. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 481 KW - Microtus arvalis KW - Arvicolinae KW - mitochondrial genome KW - common vole KW - phylogeny Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-412994 SN - 1866-8372 IS - 481 ER -