TY - JOUR A1 - Beermann, Jan A1 - Westbury, Michael V. A1 - Hofreiter, Michael A1 - Hilgers, Leon A1 - Deister, Fabian A1 - Neumann, Hermann A1 - Raupach, Michael J. T1 - Cryptic species in a well-known habitat BT - applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida) JF - Scientific reports N2 - 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. Y1 - 2018 U6 - https://doi.org/10.1038/s41598-018-25225-x SN - 2045-2322 VL - 8 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Westbury, Michael V. A1 - Dalerumb, Fredrik A1 - Noren, Karin A1 - Hofreiter, Michael T1 - Complete mitochondrial genome of a bat-eared fox (Otocyon megalotis), along with phylogenetic considerations JF - Mitochondrial DNA. Part B N2 - 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. KW - Phylogenetics KW - mitochondria KW - iterative mapping KW - Canidae Y1 - 2017 U6 - https://doi.org/10.1080/23802359.2017.1331325 SN - 2380-2359 VL - 2 IS - 1 SP - 298 EP - 299 PB - Routledge, Taylor & Francis Group CY - London ER - TY - JOUR A1 - Agne, Stefanie A1 - Preick, Michaela A1 - Straube, Nicolas A1 - Hofreiter, Michael T1 - Simultaneous Barcode Sequencing of Diverse Museum Collection Specimens Using a Mixed RNA Bait Set JF - Frontiers in Ecology and Evolution N2 - A growing number of publications presenting results from sequencing natural history collection specimens reflect the importance of DNA sequence information from such samples. Ancient DNA extraction and library preparation methods in combination with target gene capture are a way of unlocking archival DNA, including from formalin-fixed wet-collection material. Here we report on an experiment, in which we used an RNA bait set containing baits from a wide taxonomic range of species for DNA hybridisation capture of nuclear and mitochondrial targets for analysing natural history collection specimens. The bait set used consists of 2,492 mitochondrial and 530 nuclear RNA baits and comprises specific barcode loci of diverse animal groups including both invertebrates and vertebrates. The baits allowed to capture DNA sequence information of target barcode loci from 84% of the 37 samples tested, with nuclear markers being captured more frequently and consensus sequences of these being more complete compared to mitochondrial markers. Samples from dry material had a higher rate of success than wet-collection specimens, although target sequence information could be captured from 50% of formalin-fixed samples. Our study illustrates how efforts to obtain barcode sequence information from natural history collection specimens may be combined and are a way of implementing barcoding inventories of scientific collection material. KW - target capture KW - type specimens KW - molecular species identification KW - museum specimens KW - cross-species capture Y1 - 2022 U6 - https://doi.org/10.3389/fevo.2022.909846 SN - 2296-701X VL - 10 PB - Frontiers Media S.A. CY - Lausanne, Schweiz ER - TY - JOUR A1 - Hilgers, Leon A1 - Hartmann, Stefanie A1 - Hofreiter, Michael A1 - von Rintelen, Thomas T1 - Novel Genes, Ancient Genes, and Gene Co-Option Contributed o the Genetic Basis of the Radula, a Molluscan Innovation JF - Molecular biology and evolution N2 - 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. KW - chitin synthase KW - novelty KW - radula KW - RNAseq KW - shell KW - Tylomelania sarasinorum Y1 - 2018 U6 - https://doi.org/10.1093/molbev/msy052 SN - 0737-4038 SN - 1537-1719 VL - 35 IS - 7 SP - 1638 EP - 1652 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Hofreiter, Michael A1 - Hartmann, Stefanie T1 - Reconstructing protein-coding sequences from ancient DNA JF - Odorant binding and chemosensory proteins N2 - Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including mis-coding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins. KW - re-sequencing KW - mapping KW - genome assembly KW - targeted assembly KW - SRAssembler KW - ancient DNA KW - reference sequence KW - paleogenomics Y1 - 2020 SN - 978-0-12-821157-1 U6 - https://doi.org/10.1016/bs.mie.2020.05.008 SN - 0076-6879 VL - 642 SP - 21 EP - 33 PB - Academic Press, an imprint of Elsevier CY - Cambridge, MA. 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 - 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 - Hartmann, Stefanie A1 - Preick, Michaela A1 - Abelt, Silke A1 - Scheffel, André A1 - Hofreiter, Michael T1 - Annotated genome sequences of the carnivorous plant Roridula gorgonias and a non-carnivorous relative, Clethra arborea JF - BMC Research Notes N2 - Objective Plant carnivory is distributed across the tree of life and has evolved at least six times independently, but sequenced and annotated nuclear genomes of carnivorous plants are currently lacking. We have sequenced and structurally annotated the nuclear genome of the carnivorous Roridula gorgonias and that of a non-carnivorous relative, Madeira’s lily-of-the-valley-tree, Clethra arborea, both within the Ericales. This data adds an important resource to study the evolutionary genetics of plant carnivory across angiosperm lineages and also for functional and systematic aspects of plants within the Ericales. Results Our assemblies have total lengths of 284 Mbp (R. gorgonias) and 511 Mbp (C. arborea) and show high BUSCO scores of 84.2% and 89.5%, respectively. We used their predicted genes together with publicly available data from other Ericales’ genomes and transcriptomes to assemble a phylogenomic data set for the inference of a species tree. However, groups of orthologs showed a marked absence of species represented by a transcriptome. We discuss possible reasons and caution against combining predicted genes from genome- and transriptome-based assemblies. KW - Carnivorous plant KW - Roridula gorgonias KW - Clethra arborea KW - Genome assembly KW - Transcriptome assembly KW - Phylogenomics KW - Orthologous Matrix (OMA) Project Y1 - 2020 U6 - https://doi.org/10.1186/s13104-020-05254-4 SN - 1756-0500 VL - 13 PB - Biomed Central CY - London 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 - TY - JOUR A1 - Signore, Anthony V. A1 - Paijmans, Johanna L. A. A1 - Hofreiter, Michael A1 - Fago, Angela A1 - Weber, Roy E. A1 - Springer, Mark S. A1 - Campbell, Kevin L. T1 - Emergence of a chimeric globin pseudogene and increased Hemoglobin Oxygen Affinity Underlie the evolution of aquatic specializations in Sirenia JF - Molecular biology and evolution N2 - As limits on O2 availability during submergence impose severe constraints on aerobic respiration, the oxygen binding globin proteins of marine mammals are expected to have evolved under strong evolutionary pressures during their land-to-sea transition. Here, we address this question for the order Sirenia by retrieving, annotating, and performing detailed selection analyses on the globin repertoire of the extinct Steller’s sea cow (Hydrodamalis gigas), dugong (Dugong dugon), and Florida manatee (Trichechus manatus latirostris) in relation to their closest living terrestrial relatives (elephants and hyraxes). These analyses indicate most loci experienced elevated nucleotide substitution rates during their transition to a fully aquatic lifestyle. While most of these genes evolved under neutrality or strong purifying selection, the rate of nonsynonymous/synonymous replacements increased in two genes (Hbz-T1 and Hba-T1) that encode the α-type chains of hemoglobin (Hb) during each stage of life. Notably, the relaxed evolution of Hba-T1 is temporally coupled with the emergence of a chimeric pseudogene (Hba-T2/Hbq-ps) that contributed to the tandemly linked Hba-T1 of stem sirenians via interparalog gene conversion. Functional tests on recombinant Hb proteins from extant and ancestral sirenians further revealed that the molecular remodeling of Hba-T1 coincided with increased Hb–O2 affinity in early sirenians. Available evidence suggests that this trait evolved to maximize O2 extraction from finite lung stores and suppress tissue O2 offloading, thereby facilitating the low metabolic intensities of extant sirenians. In contrast, the derived reduction in Hb–O2 affinity in (sub)Arctic Steller’s sea cows is consistent with fueling increased thermogenesis by these once colossal marine herbivores. KW - ancient DNA KW - aquatic adaptation KW - gene conversion KW - hemoglobin KW - oxygen affinity KW - molecular evolution KW - myoglobin KW - neuroglobin KW - cytoglobin KW - pseudogene Y1 - 2019 U6 - https://doi.org/10.1093/molbev/msz044 SN - 0737-4038 SN - 1537-1719 VL - 36 IS - 6 SP - 1134 EP - 1147 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Gonzalez-Fortes, Gloria M. A1 - Tassi, F. A1 - Trucchi, E. A1 - Henneberger, K. A1 - Paijmans, Johanna L. A. A1 - Diez-del-Molino, D. A1 - Schroeder, H. A1 - Susca, R. R. A1 - Barroso-Ruiz, C. A1 - Bermudez, F. J. A1 - Barroso-Medina, C. A1 - Bettencourt, A. M. S. A1 - Sampaio, H. A. A1 - Salas, A. A1 - de Lombera-Hermida, A. A1 - Fabregas Valcarce, Ramón A1 - Vaquero, M. A1 - Alonso, S. A1 - Lozano, Marina A1 - Rodriguez-Alvarez, Xose Pedro A1 - Fernandez-Rodriguez, C. A1 - Manica, Andrea A1 - Hofreiter, Michael A1 - Barbujani, Guido T1 - A western route of prehistoric human migration from Africa into the Iberian Peninsula JF - Proceedings of the Royal Society of London : B, Biological sciences N2 - Being at the western fringe of Europe, Iberia had a peculiar prehistory and a complex pattern of Neolithization. A few studies, all based on modern populations, reported the presence of DNA of likely African origin in this region, generally concluding it was the result of recent gene flow, probably during the Islamic period. Here, we provide evidence of much older gene flow from Africa to Iberia by sequencing whole genomes from four human remains from northern Portugal and southern Spain dated around 4000 years BP (from the Middle Neolithic to the Bronze Age). We found one of them to carry an unequivocal sub-Saharan mitogenome of most probably West or West-Central African origin, to our knowledge never reported before in prehistoric remains outside Africa. Our analyses of ancient nuclear genomes show small but significant levels of sub-Saharan African affinity in several ancient Iberian samples, which indicates that what we detected was not an occasional individual phenomenon, but an admixture event recognizable at the population level. We interpret this result as evidence of an early migration process from Africa into the Iberian Peninsula through a western route, possibly across the Strait of Gibraltar. KW - palaeogenome KW - Africa KW - Iberia KW - mitochondrial DNA KW - gene flow KW - admixture Y1 - 2019 U6 - https://doi.org/10.1098/rspb.2018.2288 SN - 0962-8452 SN - 1471-2954 VL - 286 IS - 1895 PB - Royal Society 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 - 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 - Grau, José Horacio A1 - Hackl, Thomas A1 - Koepfli, Klaus-Peter A1 - Hofreiter, Michael T1 - Improving draft genome contiguity with reference-derived in silico mate-pair libraries JF - GigaScience N2 - Background Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available. Findings In order to improve genome contiguity, we have developed Cross-Species Scaffolding—a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico. Conclusions We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ∼30x coverage of shotgun sequencing data. KW - genome assembly KW - mate-pairs KW - in silico KW - scaffolding KW - shotgun sequencing Y1 - 2018 U6 - https://doi.org/10.1093/gigascience/giy029 SN - 2047-217X VL - 7 IS - 5 SP - 1 EP - 6 PB - Oxford University Press CY - Oxford 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 - Folkertsma, Remco A1 - Westbury, Michael V. A1 - Eccard, Jana A1 - Hofreiter, Michael T1 - The complete mitochondrial genome of the common vole, Microtus arvalis (Rodentia: Arvicolinae) JF - Mitochondrial DNA Part B N2 - The common vole, Microtus arvalis belongs to the genus Microtus in the subfamily Arvicolinae. In this study, the complete mitochondrial genome of M. arvalis was recovered using shotgun sequencing and an iterative mapping approach using three related species. Phylogenetic analyses using the sequence of 21 arvicoline species place the common vole as a sister species to the East European vole (Microtus levis), but as opposed to previous results we find no support for the recognition of the genus Neodon within the subfamily Arvicolinae, as this is, as well as the genus Lasiopodomys, found within the Microtus genus. KW - Microtus arvalis KW - Arvicolinae KW - mitochondrial genome KW - common vole KW - phylogeny Y1 - 2018 U6 - https://doi.org/10.1080/23802359.2018.1457994 SN - 2380-2359 VL - 3 IS - 1 SP - 446 EP - 447 ER - TY - JOUR A1 - Gamba, Cristina A1 - Jones, Eppie R. A1 - Teasdale, Matthew D. A1 - McLaughlin, Russell L. A1 - González-Fortes, Gloria M. A1 - Mattiangeli, Valeria A1 - Domboroczki, Laszlo A1 - Kovari, Ivett A1 - Pap, Ildiko A1 - Anders, Alexandra A1 - Whittle, Alasdair A1 - Dani, Janos A1 - Raczky, Pal A1 - Higham, Thomas F. G. A1 - Hofreiter, Michael A1 - Bradley, Daniel G. A1 - Pinhasi, Ron T1 - Genome flux and stasis in a five millennium transect of European prehistory JF - Nature Communications N2 - The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (similar to 22x) and seven to similar to 1x coverage, to investigate the impact of these on Europe's genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence. Y1 - 2014 U6 - https://doi.org/10.1038/ncomms6257 SN - 2041-1723 VL - 5 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Lucena-Perez, María A1 - Bazzicalupo, Enrico A1 - Paijmans, Johanna A1 - Kleinman-Ruiz, Daniel A1 - Dalén, Love A1 - Hofreiter, Michael A1 - Delibes, Miguel A1 - Clavero, Miguel A1 - Godoy, José A. T1 - Ancient genome provides insights into the history of Eurasian lynx in Iberia and Western Europe JF - Quaternary science reviews : the international multidisciplinary research and review journal N2 - The Eurasian lynx (Lynx lynx) is one of the most widely distributed felids in the world. However, most of its populations started to decline a few millennia ago. Historical declines have been especially severe in Europe, and particularly in Western Europe, from where the species disappeared in the last few centuries. Here, we analyze the genome of an Eurasian lynx inhabiting the Iberian Peninsula 2500 ya, to gain insights into the phylogeographic position and genetic status of this extinct population. Also, we contextualize previous ancient data in the light of new phylogeographic studies of the species. Our results suggest that the Iberian population is part of an extinct European lineage closely related to the current Carpathian-Baltic lineages. Also, this sample holds the lowest diversity reported for the species so far, and similar to that of the highly endangered Iberian lynx. A combination of historical factors, such as a founder effect while colonizing the peninsula, together with intensified human impacts during the Holocene in the Cantabrian strip, could have led to a genetic impoverishment of the population and precipitated its extinction. Mitogenomic lineages distribution in space and time support the long-term coexistence of several lineages of Eurasian lynx in Western Europe with fluctuating ranges. While mitochondrial sequences related to the lineages currently found in Balkans and Caucasus were predominant during the Pleistocene, those more closely related to the lineage currently distributed in Central Europe prevailed during the Holocene. The use of ancient genomics has proven to be a useful tool to understand the biogeographic pattern of the Eurasian lynx in the past. Y1 - 2022 U6 - https://doi.org/10.1016/j.quascirev.2022.107518 SN - 0277-3791 SN - 1873-457X VL - 285 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Förster, Daniel W. A1 - Bull, James K. A1 - Lenz, Dorina A1 - Autenrieth, Marijke A1 - Paijmans, Johanna L. A. A1 - Kraus, Robert H. S. A1 - Nowak, Carsten A1 - Bayerl, Helmut A1 - Kühn, Ralph A1 - Saveljev, Alexander P. A1 - Sindicic, Magda A1 - Hofreiter, Michael A1 - Schmidt, Krzysztof A1 - Fickel, Jörns T1 - Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species JF - Molecular ecology resources N2 - Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species’ European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species. KW - CDS KW - conservation genetics KW - Eurasian lynx KW - genetic monitoring KW - hybridization capture KW - single nucleotide polymorphism Y1 - 2018 U6 - https://doi.org/10.1111/1755-0998.12924 SN - 1755-098X SN - 1755-0998 VL - 18 IS - 6 SP - 1356 EP - 1373 PB - Wiley CY - Hoboken ER -