@misc{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 = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {589}, issn = {1866-8372}, doi = {10.25932/publishup-41413}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414132}, pages = {13}, 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{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{AutenriethHartmannLahetal.2018, author = {Autenrieth, Marijke and Hartmann, Stefanie and Lah, Ljerka and Roos, Anna and Dennis, Alice B. and Tiedemann, Ralph}, title = {High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)}, series = {Molecular ecology resources}, volume = {18}, journal = {Molecular ecology resources}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-098X}, doi = {10.1111/1755-0998.12932}, pages = {1469 -- 1481}, year = {2018}, abstract = {The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50\% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.}, language = {en} } @article{HilgersHartmannHofreiteretal.2018, author = {Hilgers, Leon and Hartmann, Stefanie and Hofreiter, Michael and von Rintelen, Thomas}, title = {Novel Genes, Ancient Genes, and Gene Co-Option Contributed o the Genetic Basis of the Radula, a Molluscan Innovation}, series = {Molecular biology and evolution}, volume = {35}, journal = {Molecular biology and evolution}, number = {7}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0737-4038}, doi = {10.1093/molbev/msy052}, pages = {1638 -- 1652}, year = {2018}, abstract = {The radula is the central foraging organ and apomorphy of the Mollusca. However, in contrast to other innovations, including the mollusk shell, genetic underpinnings of radula formation remain virtually unknown. Here, we present the first radula formative tissue transcriptome using the viviparous freshwater snail Tylomelania sarasinorum and compare it to foot tissue and the shell-building mantle of the same species. We combine differential expression, functional enrichment, and phylostratigraphic analyses to identify both specific and shared genetic underpinnings of the three tissues as well as their dominant functions and evolutionary origins. Gene expression of radula formative tissue is very distinct, but nevertheless more similar to mantle than to foot. Generally, the genetic bases of both radula and shell formation were shaped by novel orchestration of preexisting genes and continuous evolution of novel genes. A significantly increased proportion of radula-specific genes originated since the origin of stem-mollusks, indicating that novel genes were especially important for radula evolution. Genes with radula-specific expression in our study are frequently also expressed during the formation of other lophotrochozoan hard structures, like chaetae (hes1, arx), spicules (gbx), and shells of mollusks (gbx, heph) and brachiopods (heph), suggesting gene co-option for hard structure formation. Finally, a Lophotrochozoa-specific chitin synthase with a myosin motor domain (CS-MD), which is expressed during mollusk and brachiopod shell formation, had radula-specific expression in our study. CS-MD potentially facilitated the construction of complex chitinous structures and points at the potential of molecular novelties to promote the evolution of different morphological innovations.}, 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} }