Dokument-ID Dokumenttyp Verfasser/Autoren Herausgeber Haupttitel Abstract Auflage Verlagsort Verlag Erscheinungsjahr Seitenzahl Schriftenreihe Titel Schriftenreihe Bandzahl ISBN Quelle der Hochschulschrift Konferenzname Quelle:Titel Quelle:Jahrgang Quelle:Heftnummer Quelle:Erste Seite Quelle:Letzte Seite URN DOI Abteilungen OPUS4-40759 misc Zancolli, Giulia; Baker, Timothy G.; Barlow, Axel; Bradley, Rebecca K.; Calvete, Juan J.; Carter, Kimberley C.; de Jager, Kaylah; Owens, John Benjamin; Price, Jenny Forrester; Sanz, Libia; Scholes-Higham, Amy; Shier, Liam; Wood, Liam; Wüster, Catharine E.; Wüster, Wolfgang Is hybridization a source of adaptive venom variation in rattlesnakes? Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species. 2016 16 Toxins urn:nbn:de:kobv:517-opus4-407595 Mathematisch-Naturwissenschaftliche Fakultät OPUS4-42255 misc Paijmans, Johanna L. A.; Barlow, Axel; Förster, Daniel W.; Henneberger, Kirstin; Meyer, Matthias; Nickel, Birgit; Nagel, Doris; Worsøe Havmøller, Rasmus; Baryshnikov, Gennady F.; Joger, Ulrich; Rosendahl, Wilfried; Hofreiter, Michael Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations Background Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts? Results In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these. Conclusions The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies. 2019 12 Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe 505 urn:nbn:de:kobv:517-opus4-422555 10.25932/publishup-42255 Mathematisch-Naturwissenschaftliche Fakultät OPUS4-43881 misc Hofreiter, Michael; Paijmans, Johanna L. A.; Goodchild, Helen; Speller, Camilla F.; Barlow, Axel; Gonzalez-Fortes, Gloria M.; Thomas, Jessica A.; Ludwig, Arne; Collins, Matthew J. The future of ancient DNA Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics. 2015 12 Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe 908 284 295 urn:nbn:de:kobv:517-opus4-438816 10.25932/publishup-43881 Mathematisch-Naturwissenschaftliche Fakultät OPUS4-44080 misc Westbury, Michael V.; Baleka, Sina Isabelle; Barlow, Axel; Hartmann, Stefanie; Paijmans, Johanna L. A.; Kramarz, Alejandro; Forasiepi, Analía M.; Bond, Mariano; Gelfo, Javier N.; Reguero, Marcelo A.; López-Mendoza, Patricio; Taglioretti, Matias; Scaglia, Fernando; Rinderknecht, Andrés; Jones, Washington; Mena, Francisco; Billet, Guillaume; de Muizon, Christian; Aguilar, José Luis; MacPhee, Ross D.E.; Hofreiter, Michael A mitogenomic timetree for Darwin's enigmatic South American mammal Macrauchenia patachonica The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia. Our dated phylogenetic tree places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of B66Ma (95% credibility interval, 56.64-77.83 Ma) obtained for the split between Macrauchenia and other Panperissodactyla. Combined with their morphological distinctiveness, this evidence supports the positioning of Litopterna (possibly in company with other SANU groups) as a separate order within Laurasiatheria. We also show that, when using strict criteria, extinct taxa marked by deep divergence times and a lack of close living relatives may still be amenable to palaeogenomic analysis through iterative mapping against more distant relatives. 2017 8 Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe 793 urn:nbn:de:kobv:517-opus4-440801 10.25932/publishup-44080 Mathematisch-Naturwissenschaftliche Fakultät OPUS4-42815 misc Basler, Nikolas; Xenikoudakis, Georgios; Westbury, Michael V.; Song, Lingfeng; Sheng, Guilian; Barlow, Axel Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone 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. 2017 7 Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe 715 urn:nbn:de:kobv:517-opus4-428151 10.25932/publishup-42815 Mathematisch-Naturwissenschaftliche Fakultät OPUS4-42256 Wissenschaftlicher Artikel Paijmans, Johanna L. A.; Barlow, Axel; Förster, Daniel W.; Henneberger, Kirstin; Meyer, Matthias; Nickel, Birgit; Nagel, Doris; Worsøe Havmøller, Rasmus; Baryshnikov, Gennady F.; Joger, Ulrich; Rosendahl, Wilfried; Hofreiter, Michael Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations Background Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts? Results In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these. Conclusions The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies. London, Berlin und Heidelberg BioMed Central und Springer 2018 12 BMC Evolutionary Biology 18 156 10.1186/s12862-018-1268-0 Mathematisch-Naturwissenschaftliche Fakultät OPUS4-41413 misc Westbury, Michael V.; Hartmann, Stefanie; Barlow, Axel; Wiesel, Ingrid; Leo, Viyanna; Welch, Rebecca; Parker, Daniel M.; Sicks, Florian; Ludwig, Arne; Dalen, Love; Hofreiter, Michael Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena 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. 2018 13 Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe 589 urn:nbn:de:kobv:517-opus4-414132 10.25932/publishup-41413 Mathematisch-Naturwissenschaftliche Fakultät