TY - GEN A1 - Taron, Ulrike H. A1 - Lell, Moritz A1 - Barlow, Axel A1 - Paijmans, Johanna L. A. T1 - Testing of Alignment Parameters for Ancient Samples BT - Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool T2 - Genes N2 - High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present ‘TAPAS’, (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 415 KW - ancient DNA KW - short-read mapping KW - palaeogenomics KW - alignment sensitivity / specificity Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-409683 ER - TY - JOUR A1 - Paijmans, Johanna L. A. A1 - Barlow, Axel A1 - Förster, Daniel W. A1 - Henneberger, Kirstin A1 - Meyer, Matthias A1 - Nickel, Birgit A1 - Nagel, Doris A1 - Worsøe Havmøller, Rasmus A1 - Baryshnikov, Gennady F. A1 - Joger, Ulrich A1 - Rosendahl, Wilfried A1 - Hofreiter, Michael T1 - Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations JF - BMC Evolutionary Biology N2 - 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. KW - Ancient DNA KW - Hybridisation capture KW - Leopards KW - Mitochondrial genomes KW - Mitogenomes KW - mtDNA KW - Palaeogenetics KW - Panthera pardus Y1 - 2018 U6 - https://doi.org/10.1186/s12862-018-1268-0 SN - 1471-2148 VL - 18 IS - 156 PB - BioMed Central und Springer CY - London, Berlin und Heidelberg ER - TY - JOUR A1 - Taron, Ulrike H. A1 - Lell, Moritz A1 - Barlow, Axel A1 - Paijmans, Johanna L. A. T1 - Testing of Alignment Parameters for Ancient Samples BT - Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool JF - Genes N2 - High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present ‘TAPAS’, (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material. KW - ancient DNA KW - short-read mapping KW - palaeogenomics KW - alignment sensitivity / specificity Y1 - 2018 U6 - https://doi.org/10.3390/genes9030157 SN - 2073-4425 VL - 9 IS - 3 SP - 1 EP - 12 PB - Molecular Diversity Preservation International CY - Basel ER - TY - JOUR A1 - Taron, Ulrike H. A1 - Lell, Moritz A1 - Barlow, Axel A1 - Paijmans, Johanna L. A. T1 - Testing of Alignment Parameters for Ancient Samples BT - Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool JF - Genese N2 - High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present ‘TAPAS’, (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material. KW - ancient DNA KW - short-read mapping KW - palaeogenomics KW - paleogenomics KW - alignment sensitivity/specificity Y1 - 2018 U6 - https://doi.org/10.3390/genes9030157 SN - 2073-4425 VL - 9 IS - 3 PB - MDPI CY - Basel ER - TY - GEN A1 - Barlow, Axel A1 - Sheng, Gui-Lian A1 - Lai, Xu-Long A1 - Hofreiter, Michael A1 - Paijmans, Johanna L. A. T1 - Once lost, twice found: Combined analysis of ancient giant panda sequences characterises extinct clade T2 - Journal of biogeography Y1 - 2018 U6 - https://doi.org/10.1111/jbi.13486 SN - 0305-0270 SN - 1365-2699 VL - 46 IS - 1 SP - 251 EP - 253 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Alberti, Federica A1 - Gonzalez, Javier A1 - Paijmans, Johanna L. A. A1 - Basler, Nikolas A1 - Preick, Michaela A1 - Henneberger, Kirstin A1 - Trinks, Alexandra A1 - Rabeder, Gernot A1 - Conard, Nicholas J. A1 - Muenzel, Susanne C. A1 - Joger, Ulrich A1 - Fritsch, Guido A1 - Hildebrandt, Thomas A1 - Hofreiter, Michael A1 - Barlow, Axel T1 - Optimized DNA sampling of ancient bones using Computed Tomography scans JF - Molecular ecology resources N2 - The prevalence of contaminant microbial DNA in ancient bone samples represents the principal limiting factor for palaeogenomic studies, as it may comprise more than 99% of DNA molecules obtained. Efforts to exclude or reduce this contaminant fraction have been numerous but also variable in their success. Here, we present a simple but highly effective method to increase the relative proportion of endogenous molecules obtained from ancient bones. Using computed tomography (CT) scanning, we identify the densest region of a bone as optimal for sampling. This approach accurately identifies the densest internal regions of petrous bones, which are known to be a source of high-purity ancient DNA. For ancient long bones, CT scans reveal a high-density outermost layer, which has been routinely removed and discarded prior to DNA extraction. For almost all long bones investigated, we find that targeted sampling of this outermost layer provides an increase in endogenous DNA content over that obtained from softer, trabecular bone. This targeted sampling can produce as much as 50-fold increase in the proportion of endogenous DNA, providing a directly proportional reduction in sequencing costs for shotgun sequencing experiments. The observed increases in endogenous DNA proportion are not associated with any reduction in absolute endogenous molecule recovery. Although sampling the outermost layer can result in higher levels of human contamination, some bones were found to have more contamination associated with the internal bone structures. Our method is highly consistent, reproducible and applicable across a wide range of bone types, ages and species. We predict that this discovery will greatly extend the potential to study ancient populations and species in the genomics era. KW - ancient DNA KW - computer tomography KW - palaeogenomics KW - paleogenetics KW - petrous bone Y1 - 2018 U6 - https://doi.org/10.1111/1755-0998.12911 SN - 1755-098X SN - 1755-0998 VL - 18 IS - 6 SP - 1196 EP - 1208 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Thorpe, Roger A1 - Barlow, Axel A1 - Surget-Groba, Yann A1 - Malhotra, Anita T1 - Multilocus phylogeny, species age and biogeography of the Lesser Antillean anoles JF - Molecular phylogenetics and evolution N2 - Lesser Antillean anoles provide classic examples of island radiations. A detailed knowledge of their phylogeny and biogeography, in particular how the age of species relate to the ages of their respective islands and the age of their radiation, is essential to elucidate the tempo and mechanisms of these radiations. We conduct a large-scale phylogenetic and phylogeographic investigation of the Lesser Antillean anoles using multiple genetic markers and comprehensive geographic sampling of most species. The multilocus phylogeny gives the first well-supported reconstruction of the interspecific relationships, and the densely sampled phylogeography reveals a highly dynamic system, driven by overseas dispersal, with several alternative post-dispersal colonisation trajectories. These radiations currently occupy both the outer-older (Eocene to Miocene), and the inner-younger (< 8mybp), Lesser Antillean arcs. The origin of these radiations corresponds with the age of the ancient outer arc. However, the ages of extant species (compatible with the age of other small terrestrial amniotes) are much younger, about the age of the emergence of the younger arc, or less. The difference between the age of the radiation and the age of the extant species suggests substantial species turnover on older arc islands, most likely through competitive replacement. Although extant anoles are extremely speciose, this may represent only a fraction of their biodiversity over time. While paraphyly enables us to infer several recent colonization events, the absence of the younger arc islands and extant species at the earlier and middle stages of the radiation, does not allow the earlier inter-island colonization to be reliably inferred. Reproductive isolation in allopatry takes a very considerable time (in excess of 8my) and sympatry appears to occur only late in the radiation. The resolved multilocus phylogeny, and relative species age, raise difficulties for some earlier hypotheses regarding size evolution, and provide no evidence for within-island speciation. KW - Anolis KW - Multilocus phylogeny KW - Lesser antilles KW - Species age KW - Species turnover KW - Island colonization Y1 - 2018 U6 - https://doi.org/10.1016/j.ympev.2018.06.014 SN - 1055-7903 SN - 1095-9513 VL - 127 SP - 682 EP - 695 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Wuster, Wolfgang A1 - Chirio, Laurent A1 - Trape, Jean-Francois A1 - Ineich, Ivan A1 - Jackson, Kate A1 - Greenbaum, Eli A1 - Barron, Cesar A1 - Kusamba, Chifundera A1 - Nagy, Zoltan T. A1 - Storey, Richard A1 - Hall, Cara A1 - Wuster, Catharine E. A1 - Barlow, Axel A1 - Broadley, Donald G. T1 - Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae) JF - Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists N2 - Cobras are among the most widely known venomous snakes, and yet their taxonomy remains incompletely understood, particularly in Africa. Here, we use a combination of mitochondrial and nuclear gene sequences and morphological data to diagnose species limits within the African forest cobra, Naja (Boulengerina) melanoleuca. Mitochondrial DNA sequences reveal deep divergences within this taxon. Congruent patterns of variation in mtDNA, nuclear genes and morphology support the recognition of five separate species, confirming the species status of N. subfulva and N. peroescobari, and revealing two previously unnamed West African species, which are described as new: Naja (Boulengerina) guineensis sp. nov. Broadley, Trape, Chirio, Ineich & Wuster, from the Upper Guinea forest of West Africa, and Naja (Boulengerina) savannula sp. nov. Broadley, Trape, Chirio & Wuster, a banded form from the savanna-forest mosaic of the Guinea and Sudanian savannas of West Africa. The discovery of cryptic diversity in this iconic group highlights our limited understanding of tropical African biodiversity, hindering our ability to conserve it effectively. KW - Integrative taxonomy KW - Africa KW - Naja melanoleuca KW - Naja guineensis sp nov. KW - Naja savannula sp nov. KW - Elapidae KW - systematics Y1 - 2018 U6 - https://doi.org/10.11646/zootaxa.4455.1.3 SN - 1175-5326 SN - 1175-5334 VL - 4455 IS - 1 SP - 68 EP - 98 PB - Magnolia Press CY - Auckland ER - TY - JOUR A1 - Barlow, Axel A1 - Cahill, James A. A1 - Hartmann, Stefanie A1 - Theunert, Christoph A1 - Xenikoudakis, Georgios A1 - Gonzalez-Fortes, Gloria M. A1 - Paijmans, Johanna L. A. A1 - Rabeder, Gernot A1 - Frischauf, Christine A1 - Garcia-Vazquez, Ana A1 - Murtskhvaladze, Marine A1 - Saarma, Urmas A1 - Anijalg, Peeter A1 - Skrbinsek, Tomaz A1 - Bertorelle, Giorgio A1 - Gasparian, Boris A1 - Bar-Oz, Guy A1 - Pinhasi, Ron A1 - Slatkin, Montgomery A1 - Dalen, Love A1 - Shapiro, Beth A1 - Hofreiter, Michael T1 - Partial genomic survival of cave bears in living brown bears JF - Nature Ecology & Evolution N2 - 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. Y1 - 2018 U6 - https://doi.org/10.1038/s41559-018-0654-8 SN - 2397-334X VL - 2 IS - 10 SP - 1563 EP - 1570 PB - Nature Publ. Group CY - London ER - 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 - JOUR 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 JF - Molecular biology and evolution 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. KW - evolution KW - hyena KW - genomics KW - population genomics KW - diversity Y1 - 2018 U6 - https://doi.org/10.1093/molbev/msy037 SN - 0737-4038 SN - 1537-1719 VL - 35 IS - 5 SP - 1225 EP - 1237 PB - Oxford Univ. Press CY - Oxford ER -