@article{WestburyDalerumbNorenetal.2017, author = {Westbury, Michael V. and Dalerumb, Fredrik and Noren, Karin and Hofreiter, Michael}, title = {Complete mitochondrial genome of a bat-eared fox (Otocyon megalotis), along with phylogenetic considerations}, series = {Mitochondrial DNA. Part B}, volume = {2}, journal = {Mitochondrial DNA. Part B}, number = {1}, publisher = {Routledge, Taylor \& Francis Group}, address = {London}, issn = {2380-2359}, doi = {10.1080/23802359.2017.1331325}, pages = {298 -- 299}, year = {2017}, abstract = {The bat-eared fox, Otocyon megalotis, is the only member of its genus and is thought to occupy a basal position within the dog family. These factors can lead to challenges in complete mitochondrial reconstructions and accurate phylogenetic positioning. Here, we present the first complete mitochondrial genome of the bat-eared fox recovered using shotgun sequencing and iterative mapping to three distantly related species. Phylogenetic analyses placed the bat-eared fox basal in the Canidae family within the clade including true foxes (Vulpes) and the raccoon dog (Nyctereutes) with high support values. This position is in good agreement with previously published results based on short fragments of mitochondrial and nuclear genes, therefore adding more support to the basal positioning of the bat-eared fox within Canidae.}, language = {en} } @article{BarnettWestburySandovalVelascoetal.2020, author = {Barnett, Ross and Westbury, Michael V. and Sandoval-Velasco, Marcela and Vieira, Filipe Garrett and Jeon, Sungwon and Zazula, Grant and Martin, Michael D. and Ho, Simon Y. W. and Mather, Niklas and Gopalakrishnan, Shyam and Ramos-Madrigal, Jazmin and de Manuel, Marc and Zepeda-Mendoza, M. Lisandra and Antunes, Agostinho and Baez, Aldo Carmona and De Cahsan, Binia and Larson, Greger and O'Brien, Stephen J. and Eizirik, Eduardo and Johnson, Warren E. and Koepfli, Klaus-Peter and Wilting, Andreas and Fickel, J{\"o}rns and Dalen, Love and Lorenzen, Eline D. and Marques-Bonet, Tomas and Hansen, Anders J. and Zhang, Guojie and Bhak, Jong and Yamaguchi, Nobuyuki and Gilbert, M. Thomas P.}, title = {Genomic adaptations and evolutionary history of the extinct scimitar-toothed cat}, series = {Current biology}, volume = {30}, journal = {Current biology}, number = {24}, publisher = {Cell Press}, address = {Cambridge}, issn = {0960-9822}, doi = {10.1016/j.cub.2020.09.051}, pages = {14}, year = {2020}, abstract = {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.}, language = {en} } @article{WestburyHartmannBarlowetal.2018, author = {Westbury, Michael V. and Hartmann, Stefanie and Barlow, Axel and Wiesel, Ingrid and Leo, Viyanna and Welch, Rebecca and Parker, Daniel M. and Sicks, Florian and Ludwig, Arne and Dalen, Love and Hofreiter, Michael}, title = {Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena}, series = {Molecular biology and evolution}, volume = {35}, journal = {Molecular biology and evolution}, number = {5}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0737-4038}, doi = {10.1093/molbev/msy037}, pages = {1225 -- 1237}, year = {2018}, abstract = {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.}, language = {en} } @article{BeermannWestburyHofreiteretal.2018, author = {Beermann, Jan and Westbury, Michael V. and Hofreiter, Michael and Hilgers, Leon and Deister, Fabian and Neumann, Hermann and Raupach, Michael J.}, title = {Cryptic species in a well-known habitat}, series = {Scientific reports}, volume = {8}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-018-25225-x}, pages = {26}, year = {2018}, abstract = {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.}, language = {en} } @article{CahsanKiemelWestburyetal.2021, author = {Cahsan, Binia De and Kiemel, Katrin and Westbury, Michael V. and Lauritsen, Maike and Autenrieth, Marijke and Gollmann, G{\"u}nter and Schweiger, Silke and Stenberg, Marika and Nystr{\"o}m, Per and Drews, Hauke and Tiedemann, Ralph}, title = {Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad}, series = {Ecology and Evolution}, volume = {11}, journal = {Ecology and Evolution}, number = {14}, publisher = {John Wiley \& Sons, Inc.}, address = {New Jersey}, issn = {2045-7758}, pages = {15}, year = {2021}, abstract = {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 (Sk{\aa}ne), 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.}, language = {en} } @misc{CahsanKiemelWestburyetal.2021, author = {Cahsan, Binia De and Kiemel, Katrin and Westbury, Michael V. and Lauritsen, Maike and Autenrieth, Marijke and Gollmann, G{\"u}nter and Schweiger, Silke and Stenberg, Marika and Nystr{\"o}m, Per and Drews, Hauke and Tiedemann, Ralph}, title = {Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {14}, issn = {1866-8372}, doi = {10.25932/publishup-52388}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-523883}, pages = {17}, year = {2021}, abstract = {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 (Sk{\aa}ne), 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.}, language = {en} } @article{CahsanWestburyParaskevopoulouetal.2021, author = {Cahsan, Binia De and Westbury, Michael V. and Paraskevopoulou, Sofia and Drews, Hauke and Ott, Moritz and Gollmann, G{\"u}nter and Tiedemann, Ralph}, title = {Genomic consequences of human-mediated translocations in margin populations of an endangered amphibian}, series = {Evolutionary Applications}, volume = {14}, journal = {Evolutionary Applications}, number = {6}, publisher = {John Wiley \& Sons, Inc.}, address = {New Jersey}, issn = {1752-4563}, pages = {12}, year = {2021}, abstract = {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.}, language = {en} } @misc{CahsanWestburyParaskevopoulouetal.2021, author = {Cahsan, Binia De and Westbury, Michael V. and Paraskevopoulou, Sofia and Drews, Hauke and Ott, Moritz and Gollmann, G{\"u}nter and Tiedemann, Ralph}, title = {Genomic consequences of human-mediated translocations in margin populations of an endangered amphibian}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {6}, issn = {1866-8372}, doi = {10.25932/publishup-52314}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-523140}, pages = {14}, year = {2021}, abstract = {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.}, 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} } @misc{BeermannWestburyHofreiteretal.2018, author = {Beermann, Jan and Westbury, Michael V. and Hofreiter, Michael and Hilgers, Leon and Deister, Fabian and Neumann, Hermann and Raupach, Michael J.}, title = {Cryptic species in a well-known habitat}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {1059}, issn = {1866-8372}, doi = {10.25932/publishup-46079}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-460792}, pages = {28}, year = {2018}, abstract = {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.}, language = {en} }