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Folkertsma R, Charbonnel N, Henttonen H, Heroldová M, Huitu O, Kotlík P, Manzo E, Paijmans JLA, Plantard O, Sándor AD, Hofreiter M, Eccard JA. Genomic signatures of climate adaptation in bank voles. Ecol Evol 2024; 14:e10886. [PMID: 38455148 PMCID: PMC10918726 DOI: 10.1002/ece3.10886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 11/17/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024] Open
Abstract
Evidence for divergent selection and adaptive variation across the landscape can provide insight into a species' ability to adapt to different environments. However, despite recent advances in genomics, it remains difficult to detect the footprints of climate-mediated selection in natural populations. Here, we analysed ddRAD sequencing data (21,892 SNPs) in conjunction with geographic climate variation to search for signatures of adaptive differentiation in twelve populations of the bank vole (Clethrionomys glareolus) distributed across Europe. To identify the loci subject to selection associated with climate variation, we applied multiple genotype-environment association methods, two univariate and one multivariate, and controlled for the effect of population structure. In total, we identified 213 candidate loci for adaptation, 74 of which were located within genes. In particular, we identified signatures of selection in candidate genes with functions related to lipid metabolism and the immune system. Using the results of redundancy analysis, we demonstrated that population history and climate have joint effects on the genetic variation in the pan-European metapopulation. Furthermore, by examining only candidate loci, we found that annual mean temperature is an important factor shaping adaptive genetic variation in the bank vole. By combining landscape genomic approaches, our study sheds light on genome-wide adaptive differentiation and the spatial distribution of variants underlying adaptive variation influenced by local climate in bank voles.
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Affiliation(s)
- Remco Folkertsma
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
- Comparative Cognition Unit, Messerli Research InstituteUniversity of Veterinary Medicine ViennaViennaAustria
| | | | | | - Marta Heroldová
- Department of Forest Ecology, FFWTMendel University in BrnoBrnoCzech Republic
| | - Otso Huitu
- Natural Resources Institute FinlandHelsinkiFinland
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and GeneticsCzech Academy of SciencesLiběchovCzech Republic
| | - Emiliano Manzo
- Fondazione Ethoikos, Convento dell'OsservanzaRadicondoliItaly
| | - Johanna L. A. Paijmans
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
- Present address:
Evolutionary Ecology Group, Department of ZoologyUniversity of CambridgeCambridgeUK
| | | | - Attila D. Sándor
- HUN‐RENClimate Change: New Blood‐Sucking Parasites and Vector‐Borne Pathogens Research GroupBudapestHungary
- Department of Parasitology and ZoologyUniversity of Veterinary MedicineBudapestHungary
- Department of Parasitology and Parasitic DiseasesUniversity of Agricultural Sciences and Veterinary MedicineCluj‐NapocaRomania
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Faculty of ScienceUniversity of PotsdamPotsdamGermany
| | - Jana A. Eccard
- Animal Ecology, Institute for Biochemistry and Biology, Faculty of ScienceBerlin‐Brandenburg Institute for Biodiversity ResearchUniversity of PotsdamPotsdamGermany
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Lucena-Perez M, Paijmans JLA, Nocete F, Nadal J, Detry C, Dalén L, Hofreiter M, Barlow A, Godoy JA. Recent increase in species-wide diversity after interspecies introgression in the highly endangered Iberian lynx. Nat Ecol Evol 2024; 8:282-292. [PMID: 38225424 DOI: 10.1038/s41559-023-02267-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/10/2023] [Indexed: 01/17/2024]
Abstract
Genetic diversity is lost in small and isolated populations, affecting many globally declining species. Interspecific admixture events can increase genetic variation in the recipient species' gene pool, but empirical examples of species-wide restoration of genetic diversity by admixture are lacking. Here we present multi-fold coverage genomic data from three ancient Iberian lynx (Lynx pardinus) approximately 2,000-4,000 years old and show a continuous or recurrent process of interspecies admixture with the Eurasian lynx (Lynx lynx) that increased modern Iberian lynx genetic diversity above that occurring millennia ago despite its recent demographic decline. Our results add to the accumulating evidence for natural admixture and introgression among closely related species and show that this can result in an increase of species-wide genetic diversity in highly genetically eroded species. The strict avoidance of interspecific sources in current genetic restoration measures needs to be carefully reconsidered, particularly in cases where no conspecific source population exists.
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Affiliation(s)
- Maria Lucena-Perez
- Department of Ecology and Evolution, Estación Biológica de Doñana, CSIC, Seville, Spain
| | - Johanna L A Paijmans
- Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Francisco Nocete
- Grupo de Investigación MIDAS, Departamento Historia I (Prehistoria), Universidad de Huelva, Huelva, Spain
| | - Jordi Nadal
- SERP, Departament de Prehistoria, Historia Antiga i Arqueologia, Universitat de Barcelona, Barcelona, Spain
| | - Cleia Detry
- UNIARQ - Centro de Arqueologia da Faculdade de Letras da Universidade de Lisboa, Alameda da Universidade, Lisbon, Portugal
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
| | - Axel Barlow
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, UK
| | - José A Godoy
- Department of Ecology and Evolution, Estación Biológica de Doñana, CSIC, Seville, Spain.
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3
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Major T, Renk P, Reissig J, Paijmans JLA, Morris E, Hofreiter M, Barlow A, Broadley DG, Wüster W. Museum DNA reveals a new, potentially extinct species of rinkhals (Serpentes: Elapidae: Hemachatus) from the Eastern Highlands of Zimbabwe. PLoS One 2023; 18:e0291432. [PMID: 37756254 PMCID: PMC10529548 DOI: 10.1371/journal.pone.0291432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
Genetic information plays a pivotal role in species recognition and delimitation, but rare or extinct animals can be difficult to obtain genetic samples from. While natural history wet collections have proven invaluable in the description of novel species, the use of these historical samples in genetic studies has been greatly impeded by DNA degradation, especially because of formalin-fixation prior to preservation. Here, we use recently developed museum genomics approaches to determine the status of an isolated population of the elapid snake genus Hemachatus from Zimbabwe. We used multiple digestion phases followed by single strand sequencing library construction and hybridisation capture to obtain 12S and 16S rDNA sequences from a poorly preserved tissue sample of this population. Phylogenetic and morphological analyses in an integrated taxonomic framework demonstrate that the Zimbabwean rinkhals population represents an old and highly distinct lineage, which we describe as a new species, Hemachatus nyangensis sp. nov. Our phylogenetic dating analysis is compatible with venom spitting having evolved in response to the threat posed by early hominins, although more data are required for a robust test of this hypothesis. This description demonstrates the power of museum genomics in revealing rare or even extinct species: Hemachatus from Zimbabwe are only known from a small area of the Eastern Highlands known for high endemism. No living specimens have been seen since the 1980s, most likely due to dramatic land-use changes in the Eastern Highlands, suggesting that the species could be extinct. In view of its recognition as a highly distinct lineage, urgent action is required to determine whether any populations survive, and to safeguard remaining habitat.
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Affiliation(s)
- Tom Major
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | - Pia Renk
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jens Reissig
- Ultimate Creatures, Kelvin, Sandton, South Africa
| | | | - Ellie Morris
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Axel Barlow
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
| | | | - Wolfgang Wüster
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom
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4
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Agne S, Naylor GJP, Preick M, Yang L, Thiel R, Weigmann S, Paijmans JLA, Barlow A, Hofreiter M, Straube N. Taxonomic Identification of Two Poorly Known Lantern Shark Species Based on Mitochondrial DNA From Wet-Collection Paratypes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.910009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
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.
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Gurke M, Vidal-Gorosquieta A, Paijmans JLA, Wȩcek K, Barlow A, González-Fortes G, Hartmann S, Grandal-d'Anglade A, Hofreiter M. Correction: Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence. PLoS One 2022; 17:e0269578. [PMID: 35653342 PMCID: PMC9162306 DOI: 10.1371/journal.pone.0269578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Hempel E, Westbury MV, Grau JH, Trinks A, Paijmans JLA, Kliver S, Barlow A, Mayer F, Müller J, Chen L, Koepfli KP, Hofreiter M, Bibi F. Diversity and Paleodemography of the Addax ( Addax nasomaculatus), a Saharan Antelope on the Verge of Extinction. Genes (Basel) 2021; 12:genes12081236. [PMID: 34440410 PMCID: PMC8394336 DOI: 10.3390/genes12081236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 12/18/2022] Open
Abstract
Since the 19th century, the addax (Addax nasomaculatus) has lost approximately 99% of its former range. Along with its close relatives, the blue antelope (Hippotragus leucophaeus) and the scimitar-horned oryx (Oryx dammah), the addax may be the third large African mammal species to go extinct in the wild in recent times. Despite this, the evolutionary history of this critically endangered species remains virtually unknown. To gain insight into the population history of the addax, we used hybridization capture to generate ten complete mitochondrial genomes from historical samples and assembled a nuclear genome. We found that both mitochondrial and nuclear diversity are low compared to other African bovids. Analysis of mitochondrial genomes revealed a most recent common ancestor ~32 kya (95% CI 11–58 kya) and weak phylogeographic structure, indicating that the addax likely existed as a highly mobile, panmictic population across its Sahelo–Saharan range in the past. PSMC analysis revealed a continuous decline in effective population size since ~2 Ma, with short intermediate increases at ~500 and ~44 kya. Our results suggest that the addax went through a major bottleneck in the Late Pleistocene, remaining at low population size prior to the human disturbances of the last few centuries.
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Affiliation(s)
- Elisabeth Hempel
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (J.H.G.); (M.H.)
- Museum für Naturkunde, Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany; (F.M.); (J.M.); (F.B.)
- Correspondence:
| | - Michael V. Westbury
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (J.H.G.); (M.H.)
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark;
| | - José H. Grau
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (J.H.G.); (M.H.)
- Museum für Naturkunde, Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany; (F.M.); (J.M.); (F.B.)
| | - Alexandra Trinks
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (J.H.G.); (M.H.)
- Institute of Pathology, Charité–Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany;
| | - Johanna L. A. Paijmans
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (J.H.G.); (M.H.)
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK;
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Acad. Lavrentiev Ave, 630090 Novosibirsk, Russia;
| | - Axel Barlow
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (J.H.G.); (M.H.)
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK;
| | - Frieder Mayer
- Museum für Naturkunde, Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany; (F.M.); (J.M.); (F.B.)
| | - Johannes Müller
- Museum für Naturkunde, Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany; (F.M.); (J.M.); (F.B.)
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China;
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA;
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Front Royal, VA 22630, USA
- Computer Technologies Laboratory, ITMO University, 197101 Saint Petersburg, Russia
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, Germany; (J.H.G.); (M.H.)
| | - Faysal Bibi
- Museum für Naturkunde, Berlin, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany; (F.M.); (J.M.); (F.B.)
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Mengüllüoğlu D, Ambarlı H, Barlow A, Paijmans JLA, Sayar AO, Emir H, Kandemir İ, Hofer H, Fickel J, Förster DW. Mitogenome Phylogeny Including Data from Additional Subspecies Provides New Insights into the Historical Biogeography of the Eurasian lynx Lynx lynx. Genes (Basel) 2021; 12:genes12081216. [PMID: 34440390 PMCID: PMC8392285 DOI: 10.3390/genes12081216] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 11/16/2022] Open
Abstract
Previous molecular studies of the wide-ranging Eurasian lynx Lynx lynx focused mainly on its northern Palearctic populations, with the consequence that the reconstruction of this species’ evolutionary history did not include genetic variation present in its southern Palearctic distribution. We sampled a previously not considered Asian subspecies (L. l. dinniki), added published data from another Asian subspecies (L. l. isabellinus), and reassessed the Eurasian lynx mtDNA phylogeny along with previously published data from northern Palearctic populations. Our mitogenome-based analyses revealed the existence of three major clades (A: Central Asia, B: SE Europe/SW Asia, C: Europe and Northern Asia) and at least five lineages, with diversification in Lynx lynx commencing at least 28kyr earlier than hitherto estimated. The subspecies L. l. isabellinus harbors the most basal matriline, consistent with the origin of Lynx lynx in this subspecies’ current range. L. l. dinniki harbors the second most basal matriline, which is related to, and may be the source of, the mtDNA diversity of the critically endangered Balkan lynx L. l. balcanicus. Our results suggest that the Anatolian peninsula was a glacial refugium for Eurasian lynx, with previously unconsidered implications for the colonization of Europe by this species.
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Affiliation(s)
- Deniz Mengüllüoğlu
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
- Correspondence:
| | - Hüseyin Ambarlı
- Department of Wildlife Ecology and Management, Faculty of Forestry, Düzce University, Düzce 81620, Turkey;
| | - Axel Barlow
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK;
| | - Johanna L. A. Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany;
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Ali Onur Sayar
- Department of Game and Wildlife, Cankiri Karatekin University, Cankiri 18100, Turkey;
| | - Hasan Emir
- Wildlife Department of General Directorate of Nature Conservation and National Parks, Turkish Ministry of Agriculture and Forestry, Ankara 06000, Turkey;
| | - İrfan Kandemir
- Department of Biology, Ankara University, Ankara 06000, Turkey;
| | - Heribert Hofer
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 10315 Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, 10315 Berlin, Germany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany;
| | - Daniel W. Förster
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany; (H.H.); (J.F.); (D.W.F.)
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Taron UH, Salado I, Escobar-Rodríguez M, Westbury MV, Butschkau S, Paijmans JLA, vonHoldt BM, Hofreiter M, Leonard JA. A sliver of the past: The decimation of the genetic diversity of the Mexican wolf. Mol Ecol 2021; 30:6340-6354. [PMID: 34161633 DOI: 10.1111/mec.16037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/21/2021] [Indexed: 01/07/2023]
Abstract
The endangered Mexican wolf (Canis lupus baileyi) is known to carry exceedingly low levels of genetic diversity. This could be (i) the result of long-term evolutionary patterns as they exist at the southernmost limit of the species distribution at a relatively reduced effective size, or (ii) due to rapid population decline caused by human persecution over the last century. If the former, purifying selection is expected to have minimized the impact of inbreeding. If the latter, rapid and recent declines in genetic diversity may have resulted in severe fitness consequences. To differentiate these hypotheses, we conducted comparative whole-genome analyses of five historical Mexican wolves (1907-1917) and 18 contemporary Mexican and grey wolves from North America and Eurasia. Based on whole-genome data, historical and modern Mexican wolves together form a discrete unit. Moreover, we found that modern Mexican wolves have reduced genetic diversity and increased inbreeding relative to the historical population, which was widespread across the southwestern United States and not restricted to Mexico as previously assumed. Finally, although Mexican wolves have evolved in sympatry with coyotes (C. latrans), we observed lower introgression between historical Mexican wolves and coyotes than with modern Mexican wolves, despite similarities in body size. Taken together, our data show that recent population declines probably caused the reduced level of genetic diversity, but not the observed differentiation of the Mexican wolves from other North American wolves.
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Affiliation(s)
- Ulrike H Taron
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Salado
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | | | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Butschkau
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
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Baleka S, Herridge VL, Catalano G, Lister AM, Dickinson MR, Di Patti C, Barlow A, Penkman KEH, Hofreiter M, Paijmans JLA. Estimating the dwarfing rate of an extinct Sicilian elephant. Curr Biol 2021; 31:3606-3612.e7. [PMID: 34146486 DOI: 10.1016/j.cub.2021.05.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/29/2021] [Accepted: 05/17/2021] [Indexed: 11/18/2022]
Abstract
Evolution on islands, together with the often extreme phenotypic changes associated with it, has attracted much interest from evolutionary biologists. However, measuring the rate of change of phenotypic traits of extinct animals can be challenging, in part due to the incompleteness of the fossil record. Here, we use combined molecular and fossil evidence to define the minimum and maximum rate of dwarfing in an extinct Mediterranean dwarf elephant from Puntali Cave (Sicily).1 Despite the challenges associated with recovering ancient DNA from warm climates,2 we successfully retrieved a mitogenome from a sample with an estimated age between 175,500 and 50,000 years. Our results suggest that this specific Sicilian elephant lineage evolved from one of the largest terrestrial mammals that ever lived3 to an island species weighing less than 20% of its original mass with an estimated mass reduction between 0.74 and 200.95 kg and height reduction between 0.15 and 41.49 mm per generation. We show that combining ancient DNA with paleontological and geochronological evidence can constrain the timing of phenotypic changes with greater accuracy than could be achieved using any source of evidence in isolation.
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Affiliation(s)
- Sina Baleka
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany; Faculty of Life and Environmental Sciences, University of Iceland, Sæmundargata 2, 101 Reykjavik, Iceland.
| | - Victoria L Herridge
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Giulio Catalano
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Laboratory of Anthropology, Università degli Studi di Palermo, 90128 Palermo, Italy
| | - Adrian M Lister
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Marc R Dickinson
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Carolina Di Patti
- Museo Geologico "G.G. Gemmellaro" - Università degli Studi di Palermo, Corso Tukory 131, 90133 Palermo, Italy
| | - Axel Barlow
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Kirsty E H Penkman
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany.
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Straube N, Lyra ML, Paijmans JLA, Preick M, Basler N, Penner J, Rödel MO, Westbury MV, Haddad CFB, Barlow A, Hofreiter M. Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens. Mol Ecol Resour 2021; 21:2299-2315. [PMID: 34036732 DOI: 10.1111/1755-0998.13433] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 01/02/2023]
Abstract
Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies.
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Affiliation(s)
- Nicolas Straube
- University Museum of Bergen, Bergen, Norway.,SNSB Bavarian State Collection of Zoology, München, Germany
| | - Mariana L Lyra
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil.,Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Johanna L A Paijmans
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michaela Preick
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Nikolas Basler
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Johannes Penner
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,Chair of Wildlife Ecology and Management, Albert Ludwigs University Freiburg, Freiburg, Germany
| | - Mark-Oliver Rödel
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Célio F B Haddad
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil
| | - Axel Barlow
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael Hofreiter
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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11
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Barlow A, Paijmans JLA, Alberti F, Gasparyan B, Bar-Oz G, Pinhasi R, Foronova I, Puzachenko AY, Pacher M, Dalén L, Baryshnikov G, Hofreiter M. Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears. Curr Biol 2021; 31:1771-1779.e7. [PMID: 33592193 DOI: 10.1016/j.cub.2021.01.073] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 10/19/2020] [Accepted: 01/21/2021] [Indexed: 11/18/2022]
Abstract
Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.1 As a consequence, most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a ∼360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals post-divergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.
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Affiliation(s)
- Axel Barlow
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK; Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany.
| | - Johanna L A Paijmans
- School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Federica Alberti
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, 0025, RA, Yerevan, 15 Charents st., Armenia
| | - Guy Bar-Oz
- The Zinman Institute of Archaeology, University of Haifa, 199 Aba-Hushi Avenue, Haifa, Israel 3498838
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Irina Foronova
- V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, 3, Ac. Koptyuga ave., Novosibirsk, Russia 630090
| | - Andrey Y Puzachenko
- Institute of Geography, Russian Academy of Sciences, Staromonetnyy Pereulok, 29, Moscow, Russia 119017
| | - Martina Pacher
- Naturmuseum St. Gallen, Rorschacher Strasse 263, CH-9016 St. Gallen, Switzerland
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Frescativägen 54, 114 18 Stockholm, Sweden
| | - Gennady Baryshnikov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, 199034 St. Petersburg, Russia
| | - Michael Hofreiter
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
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12
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Paijmans JLA, Barlow A, Becker MS, Cahill JA, Fickel J, Förster DWG, Gries K, Hartmann S, Havmøller RW, Henneberger K, Kern C, Kitchener AC, Lorenzen ED, Mayer F, OBrien SJ, von Seth J, Sinding MHS, Spong G, Uphyrkina O, Wachter B, Westbury MV, Dalén L, Bhak J, Manica A, Hofreiter M. African and Asian leopards are highly differentiated at the genomic level. Curr Biol 2021; 31:1872-1882.e5. [PMID: 33848458 DOI: 10.1016/j.cub.2021.03.084] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 02/05/2021] [Accepted: 03/24/2021] [Indexed: 10/21/2022]
Abstract
Leopards are the only big cats still widely distributed across the continents of Africa and Asia. They occur in a wide range of habitats and are often found in close proximity to humans. But despite their ubiquity, leopard phylogeography and population history have not yet been studied with genomic tools. Here, we present population-genomic data from 26 modern and historical samples encompassing the vast geographical distribution of this species. We find that Asian leopards are broadly monophyletic with respect to African leopards across almost their entire nuclear genomes. This profound genetic pattern persists despite the animals' high potential mobility, and despite evidence of transfer of African alleles into Middle Eastern and Central Asian leopard populations within the last 100,000 years. Our results further suggest that Asian leopards originated from a single out-of-Africa dispersal event 500-600 thousand years ago and are characterized by higher population structuring, stronger isolation by distance, and lower heterozygosity than African leopards. Taxonomic categories do not take into account the variability in depth of divergence among subspecies. The deep divergence between the African subspecies and Asian populations contrasts with the much shallower divergence among putative Asian subspecies. Reconciling genomic variation and taxonomy is likely to be a growing challenge in the genomics era.
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Affiliation(s)
- Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; Department of Genetics & Genome Biology, University of Leicester, Leicester LE1 7RH, UK; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Matthew S Becker
- Zambian Carnivore Programme, PO Box 80 Mfuwe, Eastern Province, Zambia
| | - James A Cahill
- Laboratory of Neurogenetics of Language, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA; Department of Environmental Engineering Sciences, Engineering School of Sustainable Infrastructure and Environment, University of Florida, Gainesville, FL 32611
| | - Joerns Fickel
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Daniel W G Förster
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Katrin Gries
- Der Grüne Zoo Wuppertal, Hubertusallee 30, 42117 Wuppertal, Germany
| | - Stefanie Hartmann
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Rasmus Worsøe Havmøller
- GLOBE institute, University of Copenhagen, Oester Voldgade 5-7, 1350, Copenhagen K, Denmark; Research and Collections, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen OE, Denmark
| | - Kirstin Henneberger
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Christian Kern
- Tierpark Berlin-Friedrichsfelde, Am Tierpark 125, 10319 Berlin, Germany
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK; Institute of Geography, School of Geosciences. Drummond Street, University of Edinburgh EH8 9XP, UK
| | - Eline D Lorenzen
- GLOBE institute, University of Copenhagen, Oester Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Frieder Mayer
- Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung, Invalidenstraße 43, 10115 Berlin, Germany
| | - Stephen J OBrien
- Laboratory of Genomics Diversity, Center for Computer Technologies, ITMO University, 49 Kronverkskiy Pr., St. Petersburg, 197101, Russian Federation; Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, 8000 North Ocean Drive, Ft Lauderdale, Florida 33004 USA
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-10691 Stockholm, Sweden
| | | | - Göran Spong
- Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, 907 83 UMEA, SWEDEN
| | - Olga Uphyrkina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, 159 Stoletiya Street, Vladivostok, 690022, Russia
| | - Bettina Wachter
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Michael V Westbury
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; GLOBE institute, University of Copenhagen, Oester Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-10691 Stockholm, Sweden
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea; Clinomics, UNIST, Ulsan, 44919, Republic of Korea; Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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13
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Taron UH, Paijmans JLA, Barlow A, Preick M, Iyengar A, Drăgușin V, Vasile Ș, Marciszak A, Roblíčková M, Hofreiter M. Ancient DNA from the Asiatic Wild Dog ( Cuon alpinus) from Europe. Genes (Basel) 2021; 12:144. [PMID: 33499169 PMCID: PMC7911384 DOI: 10.3390/genes12020144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/11/2023] Open
Abstract
The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of the dhole is scattered and the identification of fossils can be complicated by an overlap in size and a high morphological similarity between dholes and other canid species. We generated almost complete mitochondrial genomes for six putative dhole fossils from Europe. By using three lines of evidence, i.e., the number of reads mapping to various canid mitochondrial genomes, the evaluation and quantification of the mapping evenness along the reference genomes and phylogenetic analysis, we were able to identify two out of six samples as dhole, whereas four samples represent wolf fossils. This highlights the contribution genetic data can make when trying to identify the species affiliation of fossil specimens. The ancient dhole sequences are highly divergent when compared to modern dhole sequences, but the scarcity of dhole data for comparison impedes a more extensive analysis.
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Affiliation(s)
- Ulrike H. Taron
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
| | - Johanna L. A. Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Michaela Preick
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
| | - Arati Iyengar
- Department of Biological Sciences, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA;
| | - Virgil Drăgușin
- Emil Racoviţă Institute of Speleology, Romanian Academy, 31 Frumoasă Street, 010986 Bucharest, Romania;
- Research Institute of the University of Bucharest, Earth, Environmental and Life Sciences Division, Panduri 90–92, 050663 Bucharest, Romania
| | - Ștefan Vasile
- Department of Geology, Faculty of Geology and Geophysics, University of Bucharest, 1 Nicolae Bălcescu Avenue, 010041 Bucharest, Romania;
| | - Adrian Marciszak
- Department of Paleozoology, Faculty of Biological Sciences, University of Wrocław, Sienkiewicza 21, 50-335 Wrocław, Poland;
| | - Martina Roblíčková
- Moravian Museum, Anthropos Institute, Zelný trh 6, 65937 Brno, Czech Republic;
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24–25, 14476 Potsdam, Germany; (J.L.A.P.); (A.B.); (M.P.); (M.H.)
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14
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Paijmans JLA, Barlow A, Henneberger K, Fickel J, Hofreiter M, Foerster DWG. Ancestral mitogenome capture of the Southeast Asian banded linsang. PLoS One 2020; 15:e0234385. [PMID: 32603327 PMCID: PMC7326216 DOI: 10.1371/journal.pone.0234385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 05/26/2020] [Indexed: 01/21/2023] Open
Abstract
Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.
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Affiliation(s)
- Johanna L. A. Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Leibniz Institute for Zoo- and Wildlife Research, Berlin, Germany
- * E-mail: (JLAP); (AB); (DWGF)
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
- * E-mail: (JLAP); (AB); (DWGF)
| | - Kirstin Henneberger
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Joerns Fickel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Leibniz Institute for Zoo- and Wildlife Research, Berlin, Germany
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Daniel W. G. Foerster
- Leibniz Institute for Zoo- and Wildlife Research, Berlin, Germany
- * E-mail: (JLAP); (AB); (DWGF)
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15
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González-Fortes G, Tassi F, Trucchi E, Henneberger K, Paijmans JLA, Díez-Del-Molino D, Schroeder H, Susca RR, Barroso-Ruíz C, Bermudez FJ, Barroso-Medina C, Bettencourt AMS, Sampaio HA, Grandal-d'Anglade A, Salas A, de Lombera-Hermida A, Fabregas Valcarce R, Vaquero M, Alonso S, Lozano M, Rodríguez-Alvarez XP, Fernández-Rodríguez C, Manica A, Hofreiter M, Barbujani G. A western route of prehistoric human migration from Africa into the Iberian Peninsula. Proc Biol Sci 2020; 286:20182288. [PMID: 30963949 DOI: 10.1098/rspb.2018.2288] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
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.
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Affiliation(s)
- G González-Fortes
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
| | - F Tassi
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
| | - E Trucchi
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
| | - K Henneberger
- 2 Institute for Biochemistry and Biology, University of Potsdam , 14476 Potsdam OT Golm , Germany
| | - J L A Paijmans
- 2 Institute for Biochemistry and Biology, University of Potsdam , 14476 Potsdam OT Golm , Germany
| | - D Díez-Del-Molino
- 3 Department of Bioinformatics and Genetics, Swedish Museum of Natural History , 104 05 Stockholm , Sweden
| | - H Schroeder
- 4 Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen , 1353 Copenhagen K , Denmark
| | - R R Susca
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
| | - C Barroso-Ruíz
- 5 Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH) , 14900 Lucena, Córdoba , Spain
| | - F J Bermudez
- 5 Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH) , 14900 Lucena, Córdoba , Spain
| | - C Barroso-Medina
- 5 Fundación Instituto de Investigación de Prehistoria y Evolución Humana (FIPEH) , 14900 Lucena, Córdoba , Spain
| | - A M S Bettencourt
- 6 Landscape, Heritage and Territory Laboratory-Lab2PT, Department of History, University of Minho , 4700-057 Braga , Portugal
| | - H A Sampaio
- 7 Landscape, Heritage and Territory Laboratory-Lab2PT, Department of Hospitality and Tourism, Polytechnic Institute of Cávado and Ave , Barcelos , Portugal
| | - A Grandal-d'Anglade
- 8 Universitary Institute of Geology, University of Coruña , A Coruña 15081 , Spain
| | - A Salas
- 9 Unidade de Xenética, Instituto de Ciencias Forenses, Universidade de Santiago de Compostela, and GenPoB (IDIS-SERGAS) , Galicia , Spain
| | - A de Lombera-Hermida
- 10 Department of History GEPN-AAT, University of Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - R Fabregas Valcarce
- 10 Department of History GEPN-AAT, University of Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - M Vaquero
- 11 Department of History and History of Art, Rovira i Virgili University , 43002 Tarragona , Spain.,12 Institut Català de Paleoecologia Humana i Evolució Social (IPHES) , 43007 Tarragona , Spain
| | - S Alonso
- 11 Department of History and History of Art, Rovira i Virgili University , 43002 Tarragona , Spain.,12 Institut Català de Paleoecologia Humana i Evolució Social (IPHES) , 43007 Tarragona , Spain
| | - M Lozano
- 11 Department of History and History of Art, Rovira i Virgili University , 43002 Tarragona , Spain.,12 Institut Català de Paleoecologia Humana i Evolució Social (IPHES) , 43007 Tarragona , Spain
| | - X P Rodríguez-Alvarez
- 11 Department of History and History of Art, Rovira i Virgili University , 43002 Tarragona , Spain.,12 Institut Català de Paleoecologia Humana i Evolució Social (IPHES) , 43007 Tarragona , Spain
| | | | - A Manica
- 14 Department of Zoology, University of Cambridge , Cambridge CB2 3EJ , UK
| | - M Hofreiter
- 2 Institute for Biochemistry and Biology, University of Potsdam , 14476 Potsdam OT Golm , Germany
| | - G Barbujani
- 1 Department of Life Science and Biotechnology, University of Ferrara , 44121 Ferrara , Italy
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16
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Xenikoudakis G, Ahmed M, Harris JC, Wadleigh R, Paijmans JLA, Hartmann S, Barlow A, Lerner H, Hofreiter M. Ancient DNA reveals twenty million years of aquatic life in beavers. Curr Biol 2020; 30:R110-R111. [PMID: 32017876 DOI: 10.1016/j.cub.2019.12.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Xenikoudakis et al. report a partial mitochondrial genome of the extinct giant beaver Castoroides and estimate the origin of aquatic behavior in beavers to approximately 20 million years. This time estimate coincides with the extinction of terrestrial beavers and raises the question whether the two events had a common cause.
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Affiliation(s)
- Georgios Xenikoudakis
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.
| | - Mayeesha Ahmed
- Joseph Moore Museum, Earlham College, Richmond, IN 47374, USA
| | | | - Rachel Wadleigh
- Joseph Moore Museum, Earlham College, Richmond, IN 47374, USA; University of Michigan, Ann Arbor, MI 48109, USA
| | - Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Stefanie Hartmann
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Heather Lerner
- Joseph Moore Museum, Earlham College, Richmond, IN 47374, USA.
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
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17
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Barlow A, Hartmann S, Gonzalez J, Hofreiter M, Paijmans JLA. Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates. Genes (Basel) 2020; 11:E50. [PMID: 31906474 PMCID: PMC7017230 DOI: 10.3390/genes11010050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 11/16/2022] Open
Abstract
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.
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18
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Abstract
High-throughput sequencing (HTS) allows fast and cost-efficient sequencing of ancient DNA (aDNA) without prior information about what sequences should be targeted. One necessary step for HTS is the preparation of a sequencing library. Commercial kits are available for this purpose, but many of these are not suitable for aDNA or other types of damaged DNA. Here, we outline a protocol for HTS library preparation that is optimized for ancient DNA. We report the library conversion rate for a range of input template and adapter concentrations. Our results show that the protocol performs at a high efficiency.
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Affiliation(s)
- Kirstin Henneberger
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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19
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Signore AV, Paijmans JLA, Hofreiter M, Fago A, Weber RE, Springer MS, Campbell KL. Emergence of a Chimeric Globin Pseudogene and Increased Hemoglobin Oxygen Affinity Underlie the Evolution of Aquatic Specializations in Sirenia. Mol Biol Evol 2019; 36:1134-1147. [PMID: 30828717 PMCID: PMC6526914 DOI: 10.1093/molbev/msz044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 02/13/2019] [Accepted: 02/27/2019] [Indexed: 12/13/2022] Open
Abstract
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.
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Affiliation(s)
- Anthony V Signore
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada.,School of Biological Sciences, University of Nebraska, Lincoln, NE
| | | | - Michael Hofreiter
- Institute of Biochemistry and Biology, University of Potsdam, Germany
| | - Angela Fago
- Department of Bioscience, Zoophysiology, Aarhus University, Denmark
| | - Roy E Weber
- Department of Bioscience, Zoophysiology, Aarhus University, Denmark
| | - Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA
| | - Kevin L Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
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20
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Abstract
For many archaeological and paleontological samples, the relative content of endogenous compared to contaminant DNA is low. In such cases, enriching sequencing libraries for endogenous DNA, prior to sequencing can make the final research project more cost-effective. Here, we present an in-solution enrichment protocol based on homemade baits that can be applied to recover complete nuclear genomes from ancient remains. The approach is based on the preparation of DNA baits by biotinylated adapter ligation. The procedure has been developed for use with human remains but can be adapted to other species or target regions by choosing the appropriate template DNA from which to build the capture baits. By using homemade rather than commercially acquired baits, this protocol may offer increased flexibility and cost efficiency.
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21
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Paijmans JLA, González Fortes G, Förster DW. Application of Solid-State Capture for the Retrieval of Small-to-Medium Sized Target Loci from Ancient DNA. Methods Mol Biol 2019; 1963:129-139. [PMID: 30875051 DOI: 10.1007/978-1-4939-9176-1_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genetic studies that include ancient samples are often hampered by the low amount of endogenous DNA that ancient samples often contain, relative to co-extracted "contaminant" DNA from other organisms. One approach to mitigate this challenge is to perform hybridization-based capture of target genomic regions using DNA or RNA baits. Such baits are designed to have high sequence similarity to the target genomic regions and can reduce the off-target fraction in DNA sequencing libraries. Here, we present a protocol to use Agilent SureSelect microarrays to enrich ancient DNA libraries for small-to-medium-sized target loci, such as mitochondrial genomes, from ancient DNA extracts. The protocol that we present builds on previously published work by introducing improvements that improve recovery of short DNA fragments while minimizing the cost and duration of the experiment.
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Affiliation(s)
- Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
| | | | - Daniel W Förster
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
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22
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Paijmans JLA, Barlow A, Förster DW, Henneberger K, Meyer M, Nickel B, Nagel D, Worsøe Havmøller R, Baryshnikov GF, Joger U, Rosendahl W, Hofreiter M. Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations. BMC Evol Biol 2018; 18:156. [PMID: 30348080 PMCID: PMC6198532 DOI: 10.1186/s12862-018-1268-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 09/26/2018] [Indexed: 11/17/2022] Open
Abstract
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. Electronic supplementary material The online version of this article (10.1186/s12862-018-1268-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany.
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany
| | - Daniel W Förster
- Leibniz Institute for Zoo- and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315, Berlin, Germany
| | - Kirstin Henneberger
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Doris Nagel
- Institute for Paleontology, University of Vienna, Althanstrasse 14, Vienna, A-1090, Austria
| | - Rasmus Worsøe Havmøller
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Gennady F Baryshnikov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, 199034, St. Petersburg, Russia
| | - Ulrich Joger
- State Natural History Museum, Pockelsstr. 10, 38106, Braunschweig, Germany
| | - Wilfried Rosendahl
- Reiss-Engelhorn Museen and Curt-Engelhorn-Centre for Archaeometry, C4 8, 68159, Mannheim, Germany
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany
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23
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Barlow A, Cahill JA, Hartmann S, Theunert C, Xenikoudakis G, Fortes GG, Paijmans JLA, Rabeder G, Frischauf C, Grandal-d'Anglade A, García-Vázquez A, Murtskhvaladze M, Saarma U, Anijalg P, Skrbinšek T, Bertorelle G, Gasparian B, Bar-Oz G, Pinhasi R, Slatkin M, Dalén L, Shapiro B, Hofreiter M. Partial genomic survival of cave bears in living brown bears. Nat Ecol Evol 2018; 2:1563-1570. [PMID: 30150744 DOI: 10.1038/s41559-018-0654-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/27/2018] [Indexed: 02/06/2023]
Abstract
Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.
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Affiliation(s)
- Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
| | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Stefanie Hartmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Christoph Theunert
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Gloria G Fortes
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | - Gernot Rabeder
- Institute of Palaeontology, University of Vienna, Vienna, Austria
| | | | | | - Ana García-Vázquez
- Instituto Universitario de Xeoloxía, Universidade da Coruña, A Coruña, Spain
| | | | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Peeter Anijalg
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tomaž Skrbinšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Boris Gasparian
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Ron Pinhasi
- Earth Institute, University College Dublin, Dublin, Ireland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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24
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Förster DW, Bull JK, Lenz D, Autenrieth M, Paijmans JLA, Kraus RHS, Nowak C, Bayerl H, Kuehn R, Saveljev AP, Sindičić M, Hofreiter M, Schmidt K, Fickel J. Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species. Mol Ecol Resour 2018; 18:1356-1373. [PMID: 29978939 DOI: 10.1111/1755-0998.12924] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/28/2018] [Accepted: 06/05/2018] [Indexed: 11/29/2022]
Abstract
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.
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Affiliation(s)
- Daniel W Förster
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - James K Bull
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Dorina Lenz
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Marijke Autenrieth
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Robert H S Kraus
- Department of Biology, University of Konstanz, Konstanz, Germany.,Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology, Radolfzell, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany
| | - Helmut Bayerl
- Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technical University of Munich, Freising, Germany
| | - Ralph Kuehn
- Unit of Molecular Zoology, Chair of Zoology, Department of Animal Science, Technical University of Munich, Freising, Germany.,Department of Fish, Wildlife and Conservation Ecology, New Mexico State University, Las Cruces, New Mexico
| | - Alexander P Saveljev
- Department of Animal Ecology, Russian Research Institute of Game Management and Fur Farming, Kirov, Russia
| | - Magda Sindičić
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Krzysztof Schmidt
- Mammal Research Institute, Polish Academy of Sciences, Białowieza, Poland
| | - Jörns Fickel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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25
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Alberti F, Gonzalez J, Paijmans JLA, Basler N, Preick M, Henneberger K, Trinks A, Rabeder G, Conard NJ, Münzel SC, Joger U, Fritsch G, Hildebrandt T, Hofreiter M, Barlow A. Optimized DNA sampling of ancient bones using Computed Tomography scans. Mol Ecol Resour 2018; 18:1196-1208. [DOI: 10.1111/1755-0998.12911] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Federica Alberti
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Javier Gonzalez
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | | | - Nikolas Basler
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Michaela Preick
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Kirstin Henneberger
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Alexandra Trinks
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
- Evolutionary Biology; IRI for the Life Sciences; Humboldt University Berlin; Berlin Germany
| | - Gernot Rabeder
- Department of Palaeontology; Geozentrum; University of Vienna; Vienna Austria
| | - Nicholas J. Conard
- Institute for Archaeological Sciences; Archaeozoology; University of Tübingen; Tübingen Germany
| | - Susanne C. Münzel
- Institute for Archaeological Sciences; Archaeozoology; University of Tübingen; Tübingen Germany
| | - Ulrich Joger
- Staatliches Naturhistorisches Museum Braunschweig; Braunschweig Germany
| | - Guido Fritsch
- Leibniz Institute for Zoo and Wildlife Research; Berlin Germany
| | | | - Michael Hofreiter
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Axel Barlow
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam Germany
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26
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Taron UH, Lell M, Barlow A, Paijmans JLA. Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool. Genes (Basel) 2018. [PMID: 29533977 PMCID: PMC5867878 DOI: 10.3390/genes9030157] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
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.
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Affiliation(s)
- Ulrike H Taron
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
| | - Moritz Lell
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
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27
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Wecek K, Hartmann S, Paijmans JLA, Taron U, Xenikoudakis G, Cahill JA, Heintzman PD, Shapiro B, Baryshnikov G, Bunevich AN, Crees JJ, Dobosz R, Manaserian N, Okarma H, Tokarska M, Turvey ST, Wójcik JM, Zyla W, Szymura JM, Hofreiter M, Barlow A. Complex Admixture Preceded and Followed the Extinction of Wisent in the Wild. Mol Biol Evol 2017; 34:598-612. [PMID: 28007976 PMCID: PMC5356474 DOI: 10.1093/molbev/msw254] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Retracing complex population processes that precede extreme bottlenecks may be impossible using data from living individuals. The wisent (Bison bonasus), Europe’s largest terrestrial mammal, exemplifies such a population history, having gone extinct in the wild but subsequently restored by captive breeding efforts. Using low coverage genomic data from modern and historical individuals, we investigate population processes occurring before and after this extinction. Analysis of aligned genomes supports the division of wisent into two previously recognized subspecies, but almost half of the genomic alignment contradicts this population history as a result of incomplete lineage sorting and admixture. Admixture between subspecies populations occurred prior to extinction and subsequently during the captive breeding program. Admixture with the Bos cattle lineage is also widespread but results from ancient events rather than recent hybridization with domestics. Our study demonstrates the huge potential of historical genomes for both studying evolutionary histories and for guiding conservation strategies.
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Affiliation(s)
- Karolina Wecek
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Kraków, Poland.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Stefanie Hartmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Ulrike Taron
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
| | - Peter D Heintzman
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA.,University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, CA
| | - Gennady Baryshnikov
- Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, Petersberg, Russia
| | | | - Jennifer J Crees
- Zoological Society of London, Institute of Zoology, Regent's Park, London, United Kingdom
| | - Roland Dobosz
- Upper Silesian Museum, Bytom, Poland.,Department of Zoology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Ninna Manaserian
- Institute of Zoology Armenian National Academy of Sciences, Yerevan, Armenia
| | - Henryk Okarma
- Institute of Nature Conservation Polish Academy of Sciences, Kraków, Poland
| | | | - Samuel T Turvey
- Zoological Society of London, Institute of Zoology, Regent's Park, London, United Kingdom
| | - Jan M Wójcik
- Mammal Research Institute Polish Academy of Sciences, Bialowieza, Poland
| | | | - Jacek M Szymura
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Kraków, Poland
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Gaudry MJ, Jastroch M, Treberg JR, Hofreiter M, Paijmans JLA, Starrett J, Wales N, Signore AV, Springer MS, Campbell KL. Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades. Sci Adv 2017; 3:e1602878. [PMID: 28706989 PMCID: PMC5507634 DOI: 10.1126/sciadv.1602878] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 06/21/2017] [Indexed: 05/08/2023]
Abstract
Mitochondrial uncoupling protein 1 (UCP1) is essential for nonshivering thermogenesis in brown adipose tissue and is widely accepted to have played a key thermoregulatory role in small-bodied and neonatal placental mammals that enabled the exploitation of cold environments. We map ucp1 sequences from 133 mammals onto a species tree constructed from a ~51-kb sequence alignment and show that inactivating mutations have occurred in at least 8 of the 18 traditional placental orders, thereby challenging the physiological importance of UCP1 across Placentalia. Selection and timetree analyses further reveal that ucp1 inactivations temporally correspond with strong secondary reductions in metabolic intensity in xenarthrans and pangolins, or in six other lineages coincided with a ~30 million-year episode of global cooling in the Paleogene that promoted sharp increases in body mass and cladogenesis evident in the fossil record. Our findings also demonstrate that members of various lineages (for example, cetaceans, horses, woolly mammoths, Steller's sea cows) evolved extreme cold hardiness in the absence of UCP1-mediated thermogenesis. Finally, we identify ucp1 inactivation as a historical contingency that is linked to the current low species diversity of clades lacking functional UCP1, thus providing the first evidence for species selection related to the presence or absence of a single gene product.
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Affiliation(s)
- Michael J. Gaudry
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Martin Jastroch
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Parkring 13, 85748 Garching, Germany
- Department of Animal Physiology, Faculty of Biology, Philipps University of Marburg, D-35032 Marburg, Germany
| | - Jason R. Treberg
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Michael Hofreiter
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | | | - James Starrett
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Anthony V. Signore
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Mark S. Springer
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Kevin L. Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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Kehlmaier C, Barlow A, Hastings AK, Vamberger M, Paijmans JLA, Steadman DW, Albury NA, Franz R, Hofreiter M, Fritz U. Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum. Proc Biol Sci 2017; 284:20162235. [PMID: 28077774 PMCID: PMC5247498 DOI: 10.1098/rspb.2016.2235] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 11/29/2016] [Indexed: 12/13/2022] Open
Abstract
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 1 000-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 Galápagos (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 Galápagos 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.
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Affiliation(s)
- Christian Kehlmaier
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109 Dresden, Germany
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, OT Golm, Germany
| | - Alexander K Hastings
- Virginia Museum of Natural History, 21 Starling Avenue, Martinsville, VA 24112, USA
| | - Melita Vamberger
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109 Dresden, Germany
| | - Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, OT Golm, Germany
| | - David W Steadman
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Nancy A Albury
- National Museum of The Bahamas, Marsh Harbour, Abaco, The Bahamas
| | - Richard Franz
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476 Potsdam, OT Golm, Germany
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109 Dresden, Germany
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30
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Springer MS, Signore AV, Paijmans JLA, Vélez-Juarbe J, Domning DP, Bauer CE, He K, Crerar L, Campos PF, Murphy WJ, Meredith RW, Gatesy J, Willerslev E, MacPhee RDE, Hofreiter M, Campbell KL. Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia. Mol Phylogenet Evol 2015; 91:178-93. [PMID: 26050523 DOI: 10.1016/j.ympev.2015.05.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 05/22/2015] [Accepted: 05/28/2015] [Indexed: 01/02/2023]
Abstract
The recently extinct (ca. 1768) Steller's sea cow (Hydrodamalis gigas) was a large, edentulous North Pacific sirenian. The phylogenetic affinities of this taxon to other members of this clade, living and extinct, are uncertain based on previous morphological and molecular studies. We employed hybridization capture methods and second generation sequencing technology to obtain >30kb of exon sequences from 26 nuclear genes for both H. gigas and Dugong dugon. We also obtained complete coding sequences for the tooth-related enamelin (ENAM) gene. Hybridization probes designed using dugong and manatee sequences were both highly effective in retrieving sequences from H. gigas (mean=98.8% coverage), as were more divergent probes for regions of ENAM (99.0% coverage) that were designed exclusively from a proboscidean (African elephant) and a hyracoid (Cape hyrax). New sequences were combined with available sequences for representatives of all other afrotherian orders. We also expanded a previously published morphological matrix for living and fossil Sirenia by adding both new taxa and nine new postcranial characters. Maximum likelihood and parsimony analyses of the molecular data provide robust support for an association of H. gigas and D. dugon to the exclusion of living trichechids (manatees). Parsimony analyses of the morphological data also support the inclusion of H. gigas in Dugongidae with D. dugon and fossil dugongids. Timetree analyses based on calibration density approaches with hard- and soft-bounded constraints suggest that H. gigas and D. dugon diverged in the Oligocene and that crown sirenians last shared a common ancestor in the Eocene. The coding sequence for the ENAM gene in H. gigas does not contain frameshift mutations or stop codons, but there is a transversion mutation (AG to CG) in the acceptor splice site of intron 2. This disruption in the edentulous Steller's sea cow is consistent with previous studies that have documented inactivating mutations in tooth-specific loci of a variety of edentulous and enamelless vertebrates including birds, turtles, aardvarks, pangolins, xenarthrans, and baleen whales. Further, branch-site dN/dS analyses provide evidence for positive selection in ENAM on the stem dugongid branch where extensive tooth reduction occurred, followed by neutral evolution on the Hydrodamalis branch. Finally, we present a synthetic evolutionary tree for living and fossil sirenians showing several key innovations in the history of this clade including character state changes that parallel those that occurred in the evolutionary history of cetaceans.
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Affiliation(s)
- Mark S Springer
- Department of Biology, University of California, Riverside, CA 92521, USA.
| | - Anthony V Signore
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Johanna L A Paijmans
- Department of Biology, The University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Jorge Vélez-Juarbe
- Department of Mammalogy, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | - Daryl P Domning
- Laboratory of Evolutionary Biology, Department of Anatomy, Howard University, Washington, DC 20059, USA; Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Cameron E Bauer
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Kai He
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Lorelei Crerar
- Department of Biology, George Mason University, Fairfax, VA 22030, USA
| | - Paula F Campos
- Center for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Robert W Meredith
- Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, USA
| | - John Gatesy
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Eske Willerslev
- Center for GeoGenetics, Natural History Museum, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY 10024, USA
| | - Michael Hofreiter
- Department of Biology, The University of York, Wentworth Way, Heslington, York YO10 5DD, UK; Adaptive and Evolutionary Genomics, Institute for Biochemistry and Biology, Faculty of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Strasse 24-24, 14476 Potsdam, Germany
| | - Kevin L Campbell
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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Paijmans JLA, Fickel J, Courtiol A, Hofreiter M, Förster DW. Impact of enrichment conditions on cross-species capture of fresh and degraded DNA. Mol Ecol Resour 2015; 16:42-55. [DOI: 10.1111/1755-0998.12420] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 04/21/2015] [Accepted: 04/23/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Johanna L. A. Paijmans
- Department of Biology; University of York; York YO10 5DD UK
- Institute for Biochemistry and Biology; University of Potsdam; Karl-Liebknecht-Str 24-25 14476 Potsdam Germany
| | - Joerns Fickel
- Institute for Biochemistry and Biology; University of Potsdam; Karl-Liebknecht-Str 24-25 14476 Potsdam Germany
- Evolutionary Genetics Department, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17; 10315 Berlin Germany
| | - Alexandre Courtiol
- Evolutionary Genetics Department, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17; 10315 Berlin Germany
| | - Michael Hofreiter
- Department of Biology; University of York; York YO10 5DD UK
- Institute for Biochemistry and Biology; University of Potsdam; Karl-Liebknecht-Str 24-25 14476 Potsdam Germany
| | - Daniel W. Förster
- Evolutionary Genetics Department, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17; 10315 Berlin Germany
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32
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Abstract
Ancient mitochondrial DNA has been used in a wide variety of paleontological and archeological studies, ranging from population dynamics of extinct species to patterns of domestication. Most of these studies have traditionally been based on the analysis of short fragments from the mitochondrial control region, analyzed using PCR coupled with Sanger sequencing. With the introduction of high-throughput sequencing, as well as new enrichment technologies, the recovery of full mitochondrial genomes (mitogenomes) from ancient specimens has become significantly less complicated. Here we present a protocol to build ancient extracts into Illumina high-throughput sequencing libraries, and subsequent Agilent array-based capture to enrich for the desired mitogenome. Both are based on previously published protocols, with the introduction of several improvements aimed to increase the recovery of short DNA fragments, while keeping the cost and effort requirements low. This protocol was designed for enrichment of mitochondrial DNA in ancient or other degraded samples. However, the protocols can be easily adapted for using for building libraries for shotgun-sequencing of whole genomes, or enrichment of other genomic regions.
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Affiliation(s)
| | - Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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Hofreiter M, Paijmans JLA, Goodchild H, Speller CF, Barlow A, Fortes GG, Thomas JA, Ludwig A, Collins MJ. The future of ancient DNA: Technical advances and conceptual shifts. Bioessays 2014; 37:284-93. [PMID: 25413709 DOI: 10.1002/bies.201400160] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
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 0.7× coverage (mammoth) in 2008 to more than 50× 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.
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Affiliation(s)
- Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany; Department of Biology, University of York, York, UK
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34
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Bellone RR, Holl H, Setaluri V, Devi S, Maddodi N, Archer S, Sandmeyer L, Ludwig A, Foerster D, Pruvost M, Reissmann M, Bortfeldt R, Adelson DL, Lim SL, Nelson J, Haase B, Engensteiner M, Leeb T, Forsyth G, Mienaltowski MJ, Mahadevan P, Hofreiter M, Paijmans JLA, Gonzalez-Fortes G, Grahn B, Brooks SA. Evidence for a retroviral insertion in TRPM1 as the cause of congenital stationary night blindness and leopard complex spotting in the horse. PLoS One 2013; 8:e78280. [PMID: 24167615 PMCID: PMC3805535 DOI: 10.1371/journal.pone.0078280] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 09/10/2013] [Indexed: 12/21/2022] Open
Abstract
Leopard complex spotting is a group of white spotting patterns in horses caused by an incompletely dominant gene (LP) where homozygotes (LP/LP) are also affected with congenital stationary night blindness. Previous studies implicated Transient Receptor Potential Cation Channel, Subfamily M, Member 1 (TRPM1) as the best candidate gene for both CSNB and LP. RNA-Seq data pinpointed a 1378 bp insertion in intron 1 of TRPM1 as the potential cause. This insertion, a long terminal repeat (LTR) of an endogenous retrovirus, was completely associated with LP, testing 511 horses (χ2=1022.00, p<<0.0005), and CSNB, testing 43 horses (χ2=43, p<<0.0005). The LTR was shown to disrupt TRPM1 transcription by premature poly-adenylation. Furthermore, while deleterious transposable element insertions should be quickly selected against the identification of this insertion in three ancient DNA samples suggests it has been maintained in the horse gene pool for at least 17,000 years. This study represents the first description of an LTR insertion being associated with both a pigmentation phenotype and an eye disorder.
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Affiliation(s)
- Rebecca R. Bellone
- Department of Biology, University of Tampa, Tampa, Florida, United States of America
- * E-mail:
| | - Heather Holl
- Department of Animal Science, Cornell University, Ithaca, New York, United States of America
| | - Vijayasaradhi Setaluri
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Sulochana Devi
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Nityanand Maddodi
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, United States of America
| | | | - Lynne Sandmeyer
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Daniel Foerster
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Melanie Pruvost
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Epigenomic and Palaeogenomic Group, Institut Jacques Monod, Paris, France
| | - Monika Reissmann
- Department of Breeding Biology and Molecular Genetics, Humboldt University Berlin, Berlin, Germany
| | - Ralf Bortfeldt
- Department of Breeding Biology and Molecular Genetics, Humboldt University Berlin, Berlin, Germany
| | - David L. Adelson
- School of Molecular and Biomedical Science, the University of Adelaide, South Australia, Australia
| | - Sim Lin Lim
- School of Molecular and Biomedical Science, the University of Adelaide, South Australia, Australia
| | - Janelle Nelson
- Department of Biology, University of Tampa, Tampa, Florida, United States of America
| | - Bianca Haase
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | | | - Tosso Leeb
- Institute of Genetics, University of Bern, Bern, Switzerland
| | - George Forsyth
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Michael J. Mienaltowski
- Department of Molecular Pharmacology & Physiology, College of Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Padmanabhan Mahadevan
- Department of Biology, University of Tampa, Tampa, Florida, United States of America
| | | | | | | | - Bruce Grahn
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Samantha A. Brooks
- Department of Animal Science, Cornell University, Ithaca, New York, United States of America
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Jenkins DL, Davis LG, Stafford TW, Campos PF, Hockett B, Jones GT, Cummings LS, Yost C, Connolly TJ, Yohe RM, Gibbons SC, Raghavan M, Rasmussen M, Paijmans JLA, Hofreiter M, Kemp BM, Barta JL, Monroe C, Gilbert MTP, Willerslev E. Clovis age Western Stemmed projectile points and human coprolites at the Paisley Caves. Science 2012; 337:223-8. [PMID: 22798611 DOI: 10.1126/science.1218443] [Citation(s) in RCA: 185] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The Paisley Caves in Oregon record the oldest directly dated human remains (DNA) in the Western Hemisphere. More than 100 high-precision radiocarbon dates show that deposits containing artifacts and coprolites ranging in age from 12,450 to 2295 (14)C years ago are well stratified. Western Stemmed projectile points were recovered in deposits dated to 11,070 to 11,340 (14)C years ago, a time contemporaneous with or preceding the Clovis technology. There is no evidence of diagnostic Clovis technology at the site. These two distinct technologies were parallel developments, not the product of a unilinear technological evolution. "Blind testing" analysis of coprolites by an independent laboratory confirms the presence of human DNA in specimens of pre-Clovis age. The colonization of the Americas involved multiple technologically divergent, and possibly genetically divergent, founding groups.
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Affiliation(s)
- Dennis L Jenkins
- Museum of Natural and Cultural History, University of Oregon, Eugene, OR 97403, USA.
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