TY - JOUR A1 - Barnett, Ross A1 - Westbury, Michael V. A1 - Sandoval-Velasco, Marcela A1 - Vieira, Filipe Garrett A1 - Jeon, Sungwon A1 - Zazula, Grant A1 - Martin, Michael D. A1 - Ho, Simon Y. W. A1 - Mather, Niklas A1 - Gopalakrishnan, Shyam A1 - Ramos-Madrigal, Jazmin A1 - de Manuel, Marc A1 - Zepeda-Mendoza, M. Lisandra A1 - Antunes, Agostinho A1 - Baez, Aldo Carmona A1 - De Cahsan, Binia A1 - Larson, Greger A1 - O'Brien, Stephen J. A1 - Eizirik, Eduardo A1 - Johnson, Warren E. A1 - Koepfli, Klaus-Peter A1 - Wilting, Andreas A1 - Fickel, Jörns A1 - Dalen, Love A1 - Lorenzen, Eline D. A1 - Marques-Bonet, Tomas A1 - Hansen, Anders J. A1 - Zhang, Guojie A1 - Bhak, Jong A1 - Yamaguchi, Nobuyuki A1 - Gilbert, M. Thomas P. T1 - Genomic adaptations and evolutionary history of the extinct scimitar-toothed cat BT - Homotherium latidens JF - Current biology N2 - 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. Y1 - 2020 U6 - https://doi.org/10.1016/j.cub.2020.09.051 SN - 0960-9822 SN - 1879-0445 VL - 30 IS - 24 PB - Cell Press CY - Cambridge 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 - GEN A1 - Beermann, Jan A1 - Westbury, Michael V. A1 - Hofreiter, Michael A1 - Hilgers, Leon A1 - Deister, Fabian A1 - Neumann, Hermann A1 - Raupach, Michael J. T1 - Cryptic species in a well-known habitat BT - applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida) T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1059 KW - multiple sequence alignment KW - Oxidase Subunit-I KW - mitochondrial genome KW - control region KW - Ribosomal-RNA KW - asellota crustacea KW - gammarus crustacea KW - deep-sea KW - DNA KW - evolution Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-460792 SN - 1866-8372 IS - 1059 ER - TY - JOUR A1 - Beermann, Jan A1 - Westbury, Michael V. A1 - Hofreiter, Michael A1 - Hilgers, Leon A1 - Deister, Fabian A1 - Neumann, Hermann A1 - Raupach, Michael J. T1 - Cryptic species in a well-known habitat BT - applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida) JF - Scientific reports N2 - Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research. Y1 - 2018 U6 - https://doi.org/10.1038/s41598-018-25225-x SN - 2045-2322 VL - 8 PB - Nature Publ. Group CY - London ER - TY - GEN A1 - Cahsan, Binia De A1 - Kiemel, Katrin A1 - Westbury, Michael V. A1 - Lauritsen, Maike A1 - Autenrieth, Marijke A1 - Gollmann, Günter A1 - Schweiger, Silke A1 - Stenberg, Marika A1 - Nyström, Per A1 - Drews, Hauke A1 - Tiedemann, Ralph T1 - Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden (Skåne), this population decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after unreported release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (proxy for fitness) of introgressed and nonintrogressed populations and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition and observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency toward higher body weight, relative to regional nonintrogressed populations. These differences were not observed among introgressed and nonintrogressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than Austrian populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of genetically depauperate range margin populations without distortion of local adaptation. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1177 KW - Bombina bombina KW - heat shock protein KW - introgression KW - major histocompatibility complex KW - scaled mass index Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523883 SN - 1866-8372 IS - 14 ER - TY - JOUR A1 - Cahsan, Binia De A1 - Kiemel, Katrin A1 - Westbury, Michael V. A1 - Lauritsen, Maike A1 - Autenrieth, Marijke A1 - Gollmann, Günter A1 - Schweiger, Silke A1 - Stenberg, Marika A1 - Nyström, Per A1 - Drews, Hauke A1 - Tiedemann, Ralph T1 - Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad JF - Ecology and Evolution N2 - Northern range margin populations of the European fire-bellied toad (Bombina bombina) have rapidly declined during recent decades. Extensive agricultural land use has fragmented the landscape, leading to habitat disruption and loss, as well as eutrophication of ponds. In Northern Germany (Schleswig-Holstein) and Southern Sweden (Skåne), this population decline resulted in decreased gene flow from surrounding populations, low genetic diversity, and a putative reduction in adaptive potential, leaving populations vulnerable to future environmental and climatic changes. Previous studies using mitochondrial control region and nuclear transcriptome-wide SNP data detected introgressive hybridization in multiple northern B. bombina populations after unreported release of toads from Austria. Here, we determine the impact of this introgression by comparing the body conditions (proxy for fitness) of introgressed and nonintrogressed populations and the genetic consequences in two candidate genes for putative local adaptation (the MHC II gene as part of the adaptive immune system and the stress response gene HSP70 kDa). We detected regional differences in body condition and observed significantly elevated levels of within individual MHC allele counts in introgressed Swedish populations, associated with a tendency toward higher body weight, relative to regional nonintrogressed populations. These differences were not observed among introgressed and nonintrogressed German populations. Genetic diversity in both MHC and HSP was generally lower in northern than Austrian populations. Our study sheds light on the potential benefits of translocations of more distantly related conspecifics as a means to increase adaptive genetic variability and fitness of genetically depauperate range margin populations without distortion of local adaptation. KW - Bombina bombina KW - heat shock protein KW - introgression KW - major histocompatibility complex KW - scaled mass index Y1 - 2021 SN - 2045-7758 VL - 11 IS - 14 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - JOUR A1 - Cahsan, Binia De A1 - Westbury, Michael V. A1 - Paraskevopoulou, Sofia A1 - Drews, Hauke A1 - Ott, Moritz A1 - Gollmann, Günter A1 - Tiedemann, Ralph T1 - Genomic consequences of human-mediated translocations in margin populations of an endangered amphibian JF - Evolutionary Applications N2 - Due to their isolated and often fragmented nature, range margin populations are especially vulnerable to rapid environmental change. To maintain genetic diversity and adaptive potential, gene flow from disjunct populations might therefore be crucial to their survival. Translocations are often proposed as a mitigation strategy to increase genetic diversity in threatened populations. However, this also includes the risk of losing locally adapted alleles through genetic swamping. Human-mediated translocations of southern lineage specimens into northern German populations of the endangered European fire-bellied toad (Bombina bombina) provide an unexpected experimental set-up to test the genetic consequences of an intraspecific introgression from central population individuals into populations at the species range margin. Here, we utilize complete mitochondrial genomes and transcriptome nuclear data to reveal the full genetic extent of this translocation and the consequences it may have for these populations. We uncover signs of introgression in four out of the five northern populations investigated, including a number of introgressed alleles ubiquitous in all recipient populations, suggesting a possible adaptive advantage. Introgressed alleles dominate at the MTCH2 locus, associated with obesity/fat tissue in humans, and the DSP locus, essential for the proper development of epidermal skin in amphibians. Furthermore, we found loci where local alleles were retained in the introgressed populations, suggesting their relevance for local adaptation. Finally, comparisons of genetic diversity between introgressed and nonintrogressed northern German populations revealed an increase in genetic diversity in all German individuals belonging to introgressed populations, supporting the idea of a beneficial transfer of genetic variation from Austria into North Germany. KW - adaptive introgression KW - admixture KW - Bombina bombina KW - genetic rescue KW - mitogenomes KW - transcriptomics Y1 - 2020 SN - 1752-4563 VL - 14 IS - 6 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - GEN A1 - Cahsan, Binia De A1 - Westbury, Michael V. A1 - Paraskevopoulou, Sofia A1 - Drews, Hauke A1 - Ott, Moritz A1 - Gollmann, Günter A1 - Tiedemann, Ralph T1 - Genomic consequences of human-mediated translocations in margin populations of an endangered amphibian T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Due to their isolated and often fragmented nature, range margin populations are especially vulnerable to rapid environmental change. To maintain genetic diversity and adaptive potential, gene flow from disjunct populations might therefore be crucial to their survival. Translocations are often proposed as a mitigation strategy to increase genetic diversity in threatened populations. However, this also includes the risk of losing locally adapted alleles through genetic swamping. Human-mediated translocations of southern lineage specimens into northern German populations of the endangered European fire-bellied toad (Bombina bombina) provide an unexpected experimental set-up to test the genetic consequences of an intraspecific introgression from central population individuals into populations at the species range margin. Here, we utilize complete mitochondrial genomes and transcriptome nuclear data to reveal the full genetic extent of this translocation and the consequences it may have for these populations. We uncover signs of introgression in four out of the five northern populations investigated, including a number of introgressed alleles ubiquitous in all recipient populations, suggesting a possible adaptive advantage. Introgressed alleles dominate at the MTCH2 locus, associated with obesity/fat tissue in humans, and the DSP locus, essential for the proper development of epidermal skin in amphibians. Furthermore, we found loci where local alleles were retained in the introgressed populations, suggesting their relevance for local adaptation. Finally, comparisons of genetic diversity between introgressed and nonintrogressed northern German populations revealed an increase in genetic diversity in all German individuals belonging to introgressed populations, supporting the idea of a beneficial transfer of genetic variation from Austria into North Germany. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1168 KW - adaptive introgression KW - admixture KW - Bombina bombina KW - genetic rescue KW - mitogenomes KW - transcriptomics Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523140 SN - 1866-8372 IS - 6 ER - TY - JOUR A1 - De Cahsan, Binia A1 - Westbury, Michael V. A1 - Drews, Hauke A1 - Tiedemann, Ralph T1 - The complete mitochondrial genome of a European fire-bellied toad (Bombina bombina) from Germany JF - Mitochondrial DNA Part B N2 - The European fire-bellied toad, Bombina bombina, is a small aquatic toad belonging to the family Bombinatoridae. The species is native to the lowlands of Central and Eastern Europe, where population numbers have been in decline in recent past decades. Here, we present the first complete mitochondrial genome of the endangered European fire-bellied toad from Northern Germany recovered using iterative mapping. Phylogenetic analyses including other representatives of the Bombinatoridae placed our German specimen as sister to a Polish B. bombina sequence with high support. This finding is congruent with the postulated Pleistocene history of the species. Our complete mitochondrial genome represents an important resource for further population analysis of the European fire-bellied toad, especially those found within Germany. KW - Bombina bombina KW - Fire-bellied toad KW - mitogenome KW - conservation genetics KW - population delimitation Y1 - 2019 U6 - https://doi.org/10.1080/23802359.2018.1547143 SN - 2380-2359 VL - 4 IS - 1 SP - 498 EP - 500 PB - Taylor & Francis Group CY - London ER - TY - GEN A1 - De Cahsan, Binia A1 - Westbury, Michael V. A1 - Drews, Hauke A1 - Tiedemann, Ralph T1 - The complete mitochondrial genome of a European fire-bellied toad (Bombina bombina) from Germany T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - The European fire-bellied toad, Bombina bombina, is a small aquatic toad belonging to the family Bombinatoridae. The species is native to the lowlands of Central and Eastern Europe, where population numbers have been in decline in recent past decades. Here, we present the first complete mitochondrial genome of the endangered European fire-bellied toad from Northern Germany recovered using iterative mapping. Phylogenetic analyses including other representatives of the Bombinatoridae placed our German specimen as sister to a Polish B. bombina sequence with high support. This finding is congruent with the postulated Pleistocene history of the species. Our complete mitochondrial genome represents an important resource for further population analysis of the European fire-bellied toad, especially those found within Germany. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 532 KW - Bombina bombina KW - Fire-bellied toad KW - mitogenome KW - conservation genetics KW - population delimitation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-423222 SN - 1866-8372 IS - 532 ER -