TY - JOUR A1 - Kehlmaier, Christian A1 - Barlow, Axel A1 - Hastings, Alexander K. A1 - Vamberger, Melita A1 - Paijmans, Johanna L. A. A1 - Steadman, David W. A1 - Albury, Nancy A. A1 - Franz, Richard A1 - Hofreiter, Michael A1 - Fritz, Uwe T1 - Tropical ancient DNA reveals relationships of the extinct bahamian giant tortoise Chelonoidis alburyorum JF - Proceedings of the Royal Society of London : Series B, Biological sciences N2 - Ancient DNA of extinct species from the Pleistocene and Holocene has provided valuable evolutionary insights. However, these are largely restricted to mammals and high latitudes because DNA preservation in warm climates is typically poor. In the tropics and subtropics, non-avian reptiles constitute a significant part of the fauna and little is known about the genetics of the many extinct reptiles from tropical islands. We have reconstructed the near-complete mitochondrial genome of an extinct giant tortoise from the Bahamas (Chelonoidis alburyorum) using an approximately 1000-year-old humerus from a water-filled sinkhole (blue hole) on Great Abaco Island. Phylogenetic and molecular clock analyses place this extinct species as closely related to Galapagos (C. niger complex) and Chaco tortoises (C. chilensis), and provide evidence for repeated overseas dispersal in this tortoise group. The ancestors of extant Chelonoidis species arrived in South America from Africa only after the opening of the Atlantic Ocean and dispersed from there to the Caribbean and the Galapagos Islands. Our results also suggest that the anoxic, thermally buffered environment of blue holes may enhance DNA preservation, and thus are opening a window for better understanding evolution and population history of extinct tropical species, which would likely still exist without human impact. KW - Bahamas KW - biogeography KW - extinction KW - palaeontology KW - phylogeny Y1 - 2017 U6 - https://doi.org/10.1098/rspb.2016.2235 SN - 0962-8452 SN - 1471-2954 VL - 284 PB - The Royal Society CY - London ER - TY - JOUR A1 - Hofreiter, Michael A1 - Paijmans, Johanna L. A. A1 - Goodchild, Helen A1 - Speller, Camilla F. A1 - Barlow, Axel A1 - González-Fortes, Gloria M. A1 - Thomas, Jessica A. A1 - Ludwig, Arne A1 - Collins, Matthew J. T1 - The future of ancient DNA: Technical advances and conceptual shifts JF - Bioessays : ideas that push the boundaries N2 - 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. KW - ancient DNA KW - hybridisation capture KW - multi-locus data KW - next generation sequencing (NGS) KW - palaeogenomics KW - population genomics Y1 - 2015 U6 - https://doi.org/10.1002/bies.201400160 SN - 0265-9247 SN - 1521-1878 VL - 37 IS - 3 SP - 284 EP - 293 PB - Wiley-Blackwell CY - Hoboken 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 - JOUR A1 - Agne, Stefanie A1 - Naylor, Gavin J. P. A1 - Preick, Michaela A1 - Yang, Lei A1 - Thiel, Ralf A1 - Weigmann, Simon A1 - Paijmans, Johanna L. A. A1 - Barlow, Axel A1 - Hofreiter, Michael A1 - Straube, Nicolas T1 - Taxonomic identification of two poorly known lantern shark species based on mitochondrial DNA from wet-collection paratypes JF - Frontiers in Ecology and Evolution N2 - Etmopteridae (lantern sharks) is the most species-rich family of sharks, comprising more than 50 species. Many species are described from few individuals, and re-collection of specimens is often hindered by the remoteness of their sampling sites. For taxonomic studies, comparative morphological analysis of type specimens housed in natural history collections has been the main source of evidence. In contrast, DNA sequence information has rarely been used. Most lantern shark collection specimens, including the types, were formalin fixed before long-term storage in ethanol solutions. The DNA damage caused by both fixation and preservation of specimens has excluded these specimens from DNA sequence-based phylogenetic analyses so far. However, recent advances in the field of ancient DNA have allowed recovery of wet-collection specimen DNA sequence data. Here we analyse archival mitochondrial DNA sequences, obtained using ancient DNA approaches, of two wet-collection lantern shark paratype specimens, namely Etmopterus litvinovi and E. pycnolepis, for which the type series represent the only known individuals. Target capture of mitochondrial markers from single-stranded DNA libraries allows for phylogenetic placement of both species. Our results suggest synonymy of E. benchleyi with E. litvinovi but support the species status of E. pycnolepis. This revised taxonomy is helpful for future conservation and management efforts, as our results indicate a larger distribution range of E. litvinovi. This study further demonstrates the importance of wet-collection type specimens as genetic resource for taxonomic research. KW - type specimens KW - Etmopterus litvinovi KW - Etmopterus pycnolepis KW - deep-sea KW - sharks KW - archival DNA Y1 - 2022 U6 - https://doi.org/10.3389/fevo.2022.910009 SN - 2296-701X VL - 10 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Beck, Samantha V. A1 - Carvalho, Gary R. A1 - Barlow, Axel A1 - Ruber, Lukas A1 - Tan, Heok Hui A1 - Nugroho, Estu A1 - Wowor, Daisy A1 - Nor, Siti Azizah Mohd A1 - Herder, Fabian A1 - Muchlisin, Zainal A. A1 - de Bruyn, Mark T1 - Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish, Aplocheilus panchax JF - PLoS one Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0179557 SN - 1932-6203 VL - 12 PB - PLoS CY - San Fransisco 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 - JOUR A1 - Sheng, Gui-Lian A1 - Basler, Nikolas A1 - Ji, Xue-Ping A1 - Paijmans, Johanna L. A. A1 - Alberti, Federica A1 - Preick, Michaela A1 - Hartmann, Stefanie A1 - Westbury, Michael V. A1 - Yuan, Jun-Xia A1 - Jablonski, Nina G. A1 - Xenikoudakis, Georgios A1 - Hou, Xin-Dong A1 - Xiao, Bo A1 - Liu, Jian-Hui A1 - Hofreiter, Michael A1 - Lai, Xu-Long A1 - Barlow, Axel T1 - Paleogenome reveals genetic contribution of extinct giant panda to extant populations JF - Current biology N2 - 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. Y1 - 2019 U6 - https://doi.org/10.1016/j.cub.2019.04.021 SN - 0960-9822 SN - 1879-0445 VL - 29 IS - 10 SP - 1695 EP - 1700 PB - Cell Press CY - Cambridge 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 - Maddock, Simon T. A1 - Childerstone, Aaron A1 - Fry, Bryan Grieg A1 - Williams, David J. A1 - Barlow, Axel A1 - Wuester, Wolfgang T1 - Multi-locus phylogeny and species delimitation of Australo-Papuan blacksnakes (Pseudechis Wagler, 1830: Elapidae: Serpentes) JF - Molecular phylogenetics and evolution N2 - Genetic analyses of Australasian organisms have resulted in the identification of extensive cryptic diversity across the continent. The venomous elapid snakes are among the best-studied organismal groups in this region, but many knowledge gaps persist: for instance, despite their iconic status, the species-level diversity among Australo-Papuan blacksnakes (Pseudechis) has remained poorly understood due to the existence of a group of cryptic species within the P. australis species complex, collectively termed "pygmy mulga snakes". Using two mitochondrial and three nuclear loci we assess species boundaries within the genus using Bayesian species delimitation methods and reconstruct their phylogenetic history using multispecies coalescent approaches. Our analyses support the recognition of 10 species, including all of the currently described pygmy mulga snakes and one undescribed species from the Northern Territory of Australia. Phylogenetic relationships within the genus are broadly consistent with previous work, with the recognition of three major groups, the viviparous red-bellied black snake P. porphyriacus forming the sister species to two clades consisting of ovoviviparous species. KW - Australia KW - New Guinea KW - Molecular phylogenetics KW - BPP KW - Snakes KW - Multispecies coalescent Y1 - 2017 U6 - https://doi.org/10.1016/j.ympev.2016.09.005 SN - 1055-7903 SN - 1095-9513 VL - 107 SP - 48 EP - 55 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Yuan, Jun-Xia A1 - Hou, Xin-Dong A1 - Barlow, Axel A1 - Preick, Michaela A1 - Taron, Ulrike H. A1 - Alberti, Federica A1 - Basler, Nikolas A1 - Deng, Tao A1 - Lai, Xu-Long A1 - Hofreiter, Michael A1 - Sheng, Gui-Lian T1 - Molecular identification of late and terminal Pleistocene Equus ovodovi from northeastern China JF - PLOS ONE N2 - The extant diversity of horses (family Equidae) represents a small fraction of that occurring over their evolutionary history. One such lost lineage is the subgenus Sussemionus, which is thought to have become extinct during the Middle Pleistocene. However, recent molecular studies and morphological analysis have revealed that one of their representatives, E. ovodovi, did exist in Siberia during the Late Pleistocene. Fossil materials of E. ovodovi have thus far only been found in Russia. In this study, we extracted DNA from three equid fossil specimens excavated from northeastern China dated at 12,770-12,596, 29,525-28,887 and 40,201-38,848 cal. yBP, respectively, and retrieved three near-complete mitochondrial genomes from the specimens. Phylogenetic analyses cluster the Chinese haplotypes together with previously published Russian E. ovodovi, strongly supporting the assignment of these samples to this taxon. The molecular identification of E. ovodovi in northeastern China extends the known geographical range of this fossil species by several thousand kilometers to the east. The estimated coalescence time of all E. ovodovi haplotypes is approximately 199 Kya, with the Chinese haplotypes coalescing approximately 130 Kya. With a radiocarbon age of 12,770-12,596 cal. yBP, the youngest sample in this study represents the first E. ovodovi sample dating to the terminal Pleistocene, moving the extinction date of this species forwards considerably compared to previously documented fossils. Overall, comparison of our three mitochondrial genomes with the two published ones suggests a genetic diversity similar to several extant species of the genus Equus. Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0216883 SN - 1932-6203 VL - 14 IS - 5 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Yuan, Junxia A1 - Sheng, Guilian A1 - Preick, Michaela A1 - Sun, Boyang A1 - Hou, Xindong A1 - Chen, Shungang A1 - Taron, Ulrike Helene A1 - Barlow, Axel A1 - Wang, Linying A1 - Hu, Jiaming A1 - Deng, Tao A1 - Lai, Xulong A1 - Hofreiter, Michael T1 - Mitochondrial genomes of Late Pleistocene caballine horses from China belong to a separate clade JF - Quaternary science reviews : the international multidisciplinary research and review journal N2 - There were several species of Equus in northern China during the Late Pleistocene, including Equus przewalskii and Equus dalianensis. A number of morphological studies have been carried out on E. przewalskii and E. dalianensis, but their evolutionary history is still unresolved. In this study, we retrieved near-complete mitochondrial genomes from E. dalianensis and E. przewalskii specimens excavated from Late Pleistocene strata in northeastern China. Phylogenetic analyses revealed that caballoid horses were divided into two subclades: the New World and the Old World caballine horse subclades. The Old World caballine horses comprise of two deep phylogenetic lineages, with modern and ancient Equus caballus and modern E. przewalskii forming lineage I, and the individuals in this study together with one Yakut specimen forming lineage II. Our results indicate that Chinese Late Pleistocene caballoid horses showed a closer relationship to other Eurasian caballine horses than that to Pleistocene horses from North America. In addition, phylogenetic analyses suggested a close relationship between E. dalianensis and the Chinese fossil E. przewalskii, in agreement with previous researches based on morphological analyses. Interestingly, E. dalianensis and the fossil E. przewalskii were intermixed rather than split into distinct lineages, suggesting either that gene flow existed between these two species or that morphology-based species assignment of palaeontological specimens is not always correct. Moreover, Bayesian analysis showed that the divergence time between the New World and the Old World caballoid horses was at 1.02 Ma (95% CI: 0.86-1.24 Ma), and the two Old World lineages (I & II) split at 0.88 Ma (95% CI: 0.69-1.13 Ma), which indicates that caballoid horses seem to have evolved into different populations in the Old World soon after they migrated from North America via the Bering Land Bridge. Finally, the TMRCA of E. dalianensis was estimated at 0.20 Ma (95% CI: 0.15-0.28 Ma), and it showed a relative low genetic diversity compared with other Equus species. KW - Equus dalianensis KW - Equus przewalskii KW - Pleistocene caballine horses KW - ancient DNA KW - phylogenetic relationship KW - divergence time Y1 - 2020 U6 - https://doi.org/10.1016/j.quascirev.2020.106691 SN - 0277-3791 VL - 250 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Zancolli, Giulia A1 - Baker, Timothy G. A1 - Barlow, Axel A1 - Bradley, Rebecca K. A1 - Calvete, Juan J. A1 - Carter, Kimberley C. A1 - de Jager, Kaylah A1 - Owens, John Benjamin A1 - Price, Jenny Forrester A1 - Sanz, Libia A1 - Scholes-Higham, Amy A1 - Shier, Liam A1 - Wood, Liam A1 - Wüster, Catharine E. A1 - Wüster, Wolfgang T1 - Is Hybridization a Source of Adaptive Venom Variation in Rattlesnakes? A Test, Using a Crotalus scutulatus x viridis Hybrid Zone in Southwestern New Mexico JF - Toxins N2 - 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. KW - adaptation KW - Crotalus KW - evolution KW - hybridization KW - introgression KW - Mojave toxin KW - molecular evolution KW - venom Y1 - 2016 U6 - https://doi.org/10.3390/toxins8060188 SN - 2072-6651 VL - 8 PB - MDPI CY - Basel 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 - Gurke, Marie A1 - Vidal-Gorosquieta, Amalia A1 - Pajimans, Johanna L. A. A1 - Wȩcek, Karolina A1 - Barlow, Axel A1 - González-Fortes, Gloria M. A1 - Hartmann, Stefanie A1 - Grandal-d’Anglade, Aurora A1 - Hofreiter, Michael T1 - Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence JF - PLoS ONE N2 - Domestic cattle were brought to Spain by early settlers and agricultural societies. Due to missing Neolithic sites in the Spanish region of Galicia, very little is known about this process in this region. We sampled 18 cattle subfossils from different ages and different mountain caves in Galicia, of which 11 were subject to sequencing of the mitochondrial genome and phylogenetic analysis, to provide insight into the introduction of cattle to this region. We detected high similarity between samples from different time periods and were able to compare the time frame of the first domesticated cattle in Galicia to data from the connecting region of Cantabria to show a plausible connection between the Neolithization of these two regions. Our data shows a close relationship of the early domesticated cattle of Galicia and modern cow breeds and gives a general insight into cattle phylogeny. We conclude that settlers migrated to this region of Spain from Europe and introduced common European breeds to Galicia. KW - Haplogroups KW - Mitochondria KW - Cattle KW - Genomics KW - Domestic animals KW - Livestock KW - Single nucleotide polymorphisms KW - Neolithic period Y1 - 2020 U6 - https://doi.org/10.1371/journal.pone.0249537 SN - 1932-6203 VL - 16 IS - 4 PB - Public Library of Science CY - San Francisco 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 - 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 - TY - JOUR A1 - Paijmans, Johanna L. A. A1 - Barnett, Ross A1 - Gilbert, M. Thomas P. A1 - Zepeda-Mendoza, M. Lisandra A1 - Reumer, Jelle W. F. A1 - de Vos, John A1 - Zazula, Grant A1 - Nagel, Doris A1 - Baryshnikov, Gennady F. A1 - Leonard, Jennifer A. A1 - Rohland, Nadin A1 - Westbury, Michael V. A1 - Barlow, Axel A1 - Hofreiter, Michael T1 - Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics JF - Current biology N2 - Saber-toothed cats (Machairodontinae) are among the most widely recognized representatives of the now largely extinct Pleistocene megafauna. However, many aspects of their ecology, evolution, and extinction remain uncertain. Although ancient-DNA studies have led to huge advances in our knowledge of these aspects of many other megafauna species (e.g., mammoths and cave bears), relatively few ancient-DNA studies have focused on saber-toothed cats [1-3], and they have been restricted to short fragments of mitochondrial DNA. Here we investigate the evolutionary history of two lineages of saber-toothed cats (Smilodon and Homotherium) in relation to living carnivores and find that the Machairodontinae form a well-supported clade that is distinct from all living felids. We present partial mitochondrial genomes from one S. populator sample and three Homotherium sp. samples, including the only Late Pleistocene Homotherium sample from Eurasia [4]. We confirm the identification of the unique Late Pleistocene European fossil through ancient-DNA analyses, thus strengthening the evidence that Homotherium occurred in Europe over 200,000 years later than previously believed. This in turn forces a re-evaluation of its demography and extinction dynamics. Within the Machairodontinae, we find a deep divergence between Smilodon and Homotherium (similar to 18 million years) but limited diversity between the American and European Homotherium specimens. The genetic data support the hypothesis that all Late Pleistocene (or post-Villafrancian) Homotherium should be considered a single species, H. latidens, which was previously proposed based on morphological data [5, 6]. Y1 - 2017 U6 - https://doi.org/10.1016/j.cub.2017.09.033 SN - 0960-9822 SN - 1879-0445 VL - 27 SP - 3330 EP - + PB - Cell Press CY - Cambridge ER - TY - JOUR A1 - Barlow, Axel A1 - Hartmann, Stefanie A1 - Gonzalez, Javier A1 - Hofreiter, Michael A1 - Paijmans, Johanna L. A. T1 - Consensify BT - a method for generating pseudohaploid genome sequences from palaeogenomic datasets with reduced error rates JF - Genes / Molecular Diversity Preservation International N2 - A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes. KW - palaeogenomics KW - ancient DNA KW - sequencing error KW - error reduction KW - D statistics KW - bioinformatics Y1 - 2020 U6 - https://doi.org/10.3390/genes11010050 SN - 2073-4425 VL - 11 IS - 1 PB - MDPI CY - Basel ER -