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Abstract
The equid family contains only one single extant genus, Equus, including seven living species grouped into horses on the one hand and zebras and asses on the other. In contrast, the equine fossil record shows that an extraordinarily richer diversity existed in the past and provides multiple examples of a highly dynamic evolution punctuated by several waves of explosive radiations and extinctions, cross-continental migrations, and local adaptations. In recent years, genomic technologies have provided new analytical solutions that have enhanced our understanding of equine evolution, including the species radiation within Equus; the extinction dynamics of several lineages; and the domestication history of two individual species, the horse and the donkey. Here, we provide an overview of these recent developments and suggest areas for further research.
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Affiliation(s)
- Pablo Librado
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France;
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France;
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2
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Bennett EA, Champlot S, Peters J, Arbuckle BS, Guimaraes S, Pruvost M, Bar-David S, Davis SJM, Gautier M, Kaczensky P, Kuehn R, Mashkour M, Morales-Muñiz A, Pucher E, Tournepiche JF, Uerpmann HP, Bălăşescu A, Germonpré M, Gündem CY, Hemami MR, Moullé PE, Ötzan A, Uerpmann M, Walzer C, Grange T, Geigl EM. Taming the late Quaternary phylogeography of the Eurasiatic wild ass through ancient and modern DNA. PLoS One 2017; 12:e0174216. [PMID: 28422966 PMCID: PMC5396879 DOI: 10.1371/journal.pone.0174216] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/06/2017] [Indexed: 11/24/2022] Open
Abstract
Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia. Using 229 bp of the mitochondrial hypervariable region, an approach which allowed the inclusion of information from extremely poorly preserved ancient samples, we classify all non-African wild asses into eleven clades that show a clear phylogeographic structure revealing their phylogenetic history. This study places the extinct European wild ass, E. hydruntinus, the phylogeny of which has been debated since the end of the 19th century, into its phylogenetic context within the Asiatic wild asses and reveals recent mitochondrial introgression between populations currently regarded as separate species. The phylogeographic organization of clades resulting from these efforts can be used not only to improve future taxonomic determination of a poorly characterized group of equids, but also to identify historic ranges, interbreeding events between various populations, and the impact of ancient climatic changes. In addition, appropriately placing extant relict populations into a broader phylogeographic and genetic context can better inform ongoing conservation strategies for this highly-endangered species.
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Affiliation(s)
- E. Andrew Bennett
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
| | - Sophie Champlot
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
| | - Joris Peters
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilian University, Munich, Germany
- SNSB, Bavarian State Collection of Anthropology and Palaeoanatomy, München, Germany
| | - Benjamin S. Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Silvia Guimaraes
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
| | - Mélanie Pruvost
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilian University, Munich, Germany
| | - Shirli Bar-David
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | | | - Mathieu Gautier
- Centre de Biologie pour la Gestion des Populations CBGP, Montferrier-sur-Lez, France
| | - Petra Kaczensky
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Ralph Kuehn
- Technische Universität München, AG Molekulare Zoologie/Lehrstuhl für Zoologie, Freising, Germany
| | - Marjan Mashkour
- CNRS and Muséum national d'Histoire naturelle, UMR 7209, Archéozoologie, archéobotanique: sociétés, pratiques et environnements, Département Ecologie et Gestion de la Biodiversité, Paris, France
| | - Arturo Morales-Muñiz
- Laboratory of Archaeozoology, Dept. Biologia, Universidad Autonoma de Madrid, Madrid, Spain
| | | | | | - Hans-Peter Uerpmann
- Eberhard-Karls-Universität Tübingen, Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Tübingen, Germany
| | - Adrian Bălăşescu
- National History Museum of Romania, National Centre of Pluridisciplinary Research, Bucureşti, Romania
| | - Mietje Germonpré
- Royal Belgian Institute of Natural Sciences, Earth and History of Life, Brussels, Belgium
| | - Can Y. Gündem
- Eberhard-Karls-Universität Tübingen, Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Tübingen, Germany
| | - Mahmoud-Reza Hemami
- Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | | | - Aliye Ötzan
- Ankara Üniversitesi Dil ve Tarih-Coğrafya Fakültesi, Ankara, Turkey
| | - Margarete Uerpmann
- Eberhard-Karls-Universität Tübingen, Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Tübingen, Germany
| | - Chris Walzer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Thierry Grange
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
- * E-mail: (EMG); (TG)
| | - Eva-Maria Geigl
- Institut Jacques Monod, UMR7592, CNRS-Université Paris Diderot, Paris, France
- * E-mail: (EMG); (TG)
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3
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Der Sarkissian C, Vilstrup JT, Schubert M, Seguin-Orlando A, Eme D, Weinstock J, Alberdi MT, Martin F, Lopez PM, Prado JL, Prieto A, Douady CJ, Stafford TW, Willerslev E, Orlando L. Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids. Biol Lett 2015; 11:rsbl.2014.1058. [PMID: 25762573 DOI: 10.1098/rsbl.2014.1058] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hippidions were equids with very distinctive anatomical features. They lived in South America 2.5 million years ago (Ma) until their extinction approximately 10 000 years ago. The evolutionary origin of the three known Hippidion morphospecies is still disputed. Based on palaeontological data, Hippidion could have diverged from the lineage leading to modern equids before 10 Ma. In contrast, a much later divergence date, with Hippidion nesting within modern equids, was indicated by partial ancient mitochondrial DNA sequences. Here, we characterized eight Hippidion complete mitochondrial genomes at 3.4-386.3-fold coverage using target-enrichment capture and next-generation sequencing. Our dataset reveals that the two morphospecies sequenced (H. saldiasi and H. principale) formed a monophyletic clade, basal to extant and extinct Equus lineages. This contrasts with previous genetic analyses and supports Hippidion as a distinct genus, in agreement with palaeontological models. We date the Hippidion split from Equus at 5.6-6.5 Ma, suggesting an early divergence in North America prior to the colonization of South America, after the formation of the Panamanian Isthmus 3.5 Ma and the Great American Biotic Interchange.
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Affiliation(s)
- Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Julia T Vilstrup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark Danish National High-throughput DNA Sequencing Centre, Øster Farimagsgade 2D, 1353 Copenhagen K, Denmark
| | - David Eme
- Université de Lyon, UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Claude Bernard Lyon 1, ENTPE, CNRS, 6 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Jacobo Weinstock
- Faculty of Humanities, University of Southampton, Avenue Campus, Highfield, Southampton SO17 1BF, UK
| | - Maria Teresa Alberdi
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Fabiana Martin
- Centro de Estudios del Hombre Austral, Universidad de Magallanes, Instituto de la Patagonia, Av. Bulnes 01890, Punta Arenas CP 6200000, Chile
| | - Patricio M Lopez
- Instituto de Investigaciones Arqueológicas y Museo Gustavo Le Paige, Universidad Católica del Norte, Calle Gustavo Le Paige No. 380, San Pedro de Atacama, Chile
| | - Jose L Prado
- INCUAPA, CONICET-UNICEN, Del Valle 5737, Olavarría B7400JWI, Argentina
| | - Alfredo Prieto
- Campus Puerto Natales, Km 1.5 Norte, Universidad de Magallanes, Puerto Natales, Chile
| | - Christophe J Douady
- Université de Lyon, UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Claude Bernard Lyon 1, ENTPE, CNRS, 6 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Tom W Stafford
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark Laboratoire AMIS, Université Paul Sabatier 3, Université de Toulouse, UMR CNRS 5288, 37 Allées Jules Guesde, 31073 Toulouse cedex 3, France
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4
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Seguin-Orlando A, Schubert M, Clary J, Stagegaard J, Alberdi MT, Prado JL, Prieto A, Willerslev E, Orlando L. Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes. PLoS One 2013; 8:e78575. [PMID: 24205269 PMCID: PMC3812280 DOI: 10.1371/journal.pone.0078575] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 09/18/2013] [Indexed: 01/09/2023] Open
Abstract
Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.
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Affiliation(s)
- Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Joel Clary
- Centre de Conservation et d’Étude des Collections, Musée des Confluences, Lyon, France
| | | | - Maria T. Alberdi
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
| | - José Luis Prado
- Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano, Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional del Centro de la provincia de Buenos Aires, Olavarría, Argentina
| | - Alfredo Prieto
- Instituto de la Patagonia, Universidad de Magallanes, Punta Arenas, Chile; Programa de Doctorado, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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5
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Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SCA, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM, Fleischer RC, Cooper A, Shapiro B, Orlando L. Mitochondrial phylogenomics of modern and ancient equids. PLoS One 2013; 8:e55950. [PMID: 23437078 PMCID: PMC3577844 DOI: 10.1371/journal.pone.0055950] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 01/07/2013] [Indexed: 11/19/2022] Open
Abstract
The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy’s zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).
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Affiliation(s)
- Julia T. Vilstrup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mathias Stiller
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Aurelien Ginolhac
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Sandra C. A. Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jacobo Weinstock
- Faculty of Humanities, University of Southampton, Southampton, United Kingdom
| | - Duane Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Alberta, Canada
| | - Sergei K. Vasiliev
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikolai D. Ovodov
- Laboratory of Archaeology and Paleogeography of Central Siberia, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Joel Clary
- Centre de Conservation et d’Étude des Collections, Musée des Confluences, Lyon, France
| | - Kristofer M. Helgen
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington D.C., United States of America
| | - Robert C. Fleischer
- Center for Conservation and Evolutionary Genetics, Smithsonian National Zoological Park, Smithsonian Institution, Washington D.C., United States of America
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, The University of Adelaide, South Australia, Australia
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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Geigl EM, Grange T. Eurasian wild asses in time and space: morphological versus genetic diversity. Ann Anat 2011; 194:88-102. [PMID: 21820882 DOI: 10.1016/j.aanat.2011.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 06/03/2011] [Accepted: 06/05/2011] [Indexed: 10/18/2022]
Abstract
The Equidae have a long evolutionary history that has interested palaeontologists for a long time. Their morphology-based taxonomy, however, is a matter of controversy. Since most equid species are now extinct, the phylogenetic tree based on genetic data can be established only imperfectly via deduction of present day genomes and little is known about the past genetic diversity of these species. Recent studies of ancient DNA preserved in fossil bones have led to a simplification of the phylogenetic tree and the classification system. The situation is still particularly unclear for the wild asses whose geographical distribution in the Pleistocene and the early Holocene stretched from Northern Africa to Eurasia before they became endangered or extinct. Therefore, we performed a phylogeographic study of bone remains of wild asses covering their former geographic range over the past 100,000 years based on the analysis of ancient mitochondrial DNA. Here, we will not show but rather discuss our results calling the morphology-based classification into question and indicating that morphological criteria alone can be an unreliable index in inferring various equid species. Indeed, the diversity of mitochondrial lineages in populations with similar morphology along with genetic signatures shared between morphologically distinct animals reveal a significant morphological plasticity among Equus species. The classification of palaeontological species based on morphological and genetic criteria will be discussed.
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Affiliation(s)
- Eva-Maria Geigl
- Institut Jacques Monod, UMR CNRS Université Paris Diderot, France.
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LIRA JAIME, LINDERHOLM ANNA, OLARIA CARMEN, BRANDSTRÖM DURLING MIKAEL, GILBERT MTHOMASP, ELLEGREN HANS, WILLERSLEV ESKE, LIDÉN KERSTIN, ARSUAGA JUANLUIS, GÖTHERSTRÖM ANDERS. Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses. Mol Ecol 2010; 19:64-78. [DOI: 10.1111/j.1365-294x.2009.04430.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Revising the recent evolutionary history of equids using ancient DNA. Proc Natl Acad Sci U S A 2009; 106:21754-9. [PMID: 20007379 DOI: 10.1073/pnas.0903672106] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rich fossil record of the family Equidae (Mammalia: Perissodactyla) over the past 55 MY has made it an icon for the patterns and processes of macroevolution. Despite this, many aspects of equid phylogenetic relationships and taxonomy remain unresolved. Recent genetic analyses of extinct equids have revealed unexpected evolutionary patterns and a need for major revisions at the generic, subgeneric, and species levels. To investigate this issue we examine 35 ancient equid specimens from four geographic regions (South America, Europe, Southwest Asia, and South Africa), of which 22 delivered 87-688 bp of reproducible aDNA mitochondrial sequence. Phylogenetic analyses support a major revision of the recent evolutionary history of equids and reveal two new species, a South American hippidion and a descendant of a basal lineage potentially related to Middle Pleistocene equids. Sequences from specimens assigned to the giant extinct Cape zebra, Equus capensis, formed a separate clade within the modern plain zebra species, a phenotypicically plastic group that also included the extinct quagga. In addition, we revise the currently recognized extinction times for two hemione-related equid groups. However, it is apparent that the current dataset cannot solve all of the taxonomic and phylogenetic questions relevant to the evolution of Equus. In light of these findings, we propose a rapid DNA barcoding approach to evaluate the taxonomic status of the many Late Pleistocene fossil Equidae species that have been described from purely morphological analyses.
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9
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Orlando L, Male D, Alberdi MT, Prado JL, Prieto A, Cooper A, Hänni C. Ancient DNA Clarifies the Evolutionary History of American Late Pleistocene Equids. J Mol Evol 2008; 66:533-8. [DOI: 10.1007/s00239-008-9100-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Revised: 02/20/2008] [Accepted: 02/28/2008] [Indexed: 10/22/2022]
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10
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Kuehn R, Kaczensky P, Lkhagvasuren D, Pietsch S, Walzer C. Differentiation of Meat Samples from Domestic Horses (Equus caballus) and Asiatic Wild Asses (Equus hemionus) Using a Species-Specific Restriction Site in the Mitochondrial Cytochrome b Region. MONGOLIAN JOURNAL OF BIOLOGICAL SCIENCES 2006; 4:57-62. [PMID: 22059088 DOI: 10.22353/mjbs.2006.04.16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Recent studies suggest that Asiatic wild asses (Equus hemionus) are being increasingly poached in a commercial fashion. Part of the meat is believed to reach the meat markets in the capital Ulaanbaatar. To test this hypothesis, we collected 500 meat samples between February and May 2006. To differentiate between domestic horse (Equus caballus) and wild ass meat, we developed a restriction fragment length polymorphism (RFLP) assay based on the polymerase chain reaction (PCR). We amplified and sequenced a cytochrome b fragment (335 bp) and carried out a multialignment of the generated sequences for the domestic horse, the Asiatic wild ass, the domestic donkey (Equus asinus) and the Przewalski's horse (Equus ferus przewalskii). We detected a species-specific restriction site (AatII) for the Asiatic wild ass, resulting in a specific restriction fragment length polymorphism (RFLP) band pattern. This RFLP assay represents a rapid and cost-effective method to detect wild ass meat. All of the 500 meat samples we collected and analysed within this pilot project proved to be domestic horsemeat as declared by the sales people. Thus, either the assumption that wild ass meat is sold as "cheap horse meat" is wrong, or we picked the wrong markets, products or season.
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Affiliation(s)
- Ralph Kuehn
- Molecular Zoology, Chair of Zoology, Technische Universität München, Am Hochanger 13, D-85354 Freising, Germany,
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11
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Orlando L, Mashkour M, Burke A, Douady CJ, Eisenmann V, Hänni C. Geographic distribution of an extinct equid (Equus hydruntinus: Mammalia, Equidae) revealed by morphological and genetical analyses of fossils. Mol Ecol 2006; 15:2083-93. [PMID: 16780426 DOI: 10.1111/j.1365-294x.2006.02922.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Equus hydruntinus inhabited Europe and the Middle East for more than 300 000 years. For a long time, palaeontological data failed to place E. hydruntinus into the equid phylogenetic tree, confronted with the fact that it shares primitive Equus characters with both zebras and asses, and derived characters with asses and hemiones. However, the study of a recently discovered skull points to a relationship with hemiones. Extraction of DNA from ancient samples from Crimea (E. hydruntinus) and Iran (E. cf. hydruntinus) yielded 134-288 bp of the mtDNA control region and 143 bp of the cytochrome b gene. This DNA analysis supports the proximity of E. hydruntinus and Equus hemionus suggested by skull and limb bone analyses, and rejects proximity to either Equus burchelli or the asses suggested by tooth morphology. Dental morphology may thus be of poor taxonomical value if used alone for establishing equid phylogenetic relationships. Furthermore, the small genetic distance between E. cf. hydruntinus of Iran and the classical E. hydruntinus of Crimea suggests that both samples belong to the same species. Accordingly, the geographic range of E. hydruntinus -- until now believed to be restricted to Europe, Israel, and Turkey -- can be extended towards East as far as Iran.
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Affiliation(s)
- Ludovic Orlando
- Paléogénétique et Evolution moléculaire, CNRS UMR 5161, INRA LA 1237, Laboratoire de Biologie Moléculaire de la Cellule, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon cedex 07, France.
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12
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Kuehn R, Ludt CJ, Schroeder W, Rottmann O. Molecular phylogeny of Megaloceros giganteus--the giant deer or just a giant red deer? Zoolog Sci 2006; 22:1031-44. [PMID: 16219984 DOI: 10.2108/zsj.22.1031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Two fragments of mitochondrial DNA (mtDNA) of the cytochrome b gene (137 bp and 167 bp) were successfully isolated and sequenced from antlers and bones of five specimens of the Giant Deer (Megaloceros giganteus) to examine the phylogenetic position of Megaloceros giganteus within the family Cervidae. This is the first report on ancient DNA (aDNA) sequences from Megaloceros giganteus. A phylogenetic analysis based on parameter-rich models describes the evolutionary relationships between five individuals of fossil Megaloceros giganteus and 37 individuals of 11 extant species of the family Cervidae. The results support a "Cervus-Megaloceros" clade. The phylogenetic positions of sympatric Megaloceros and Cervus elaphus specimens in particular indicate either that the Megaloceros mtDNA gene pool did not evolve for a substantial time period as an entity distinct from Cervus elaphus until its extinction, or that Megaloceros contributed mtDNA to Cervus elaphus or vice versa. The results of this study allow the conclusion that the European Megaloceros giganteus is more related to its modern regional counterparts of the species of Cervus elaphus than recent claims have suggested.
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Affiliation(s)
- Ralph Kuehn
- Department of Ecosystem and Landscape Management, Wildlife Biology and Wildlife Management Unit, Technische Universität München-Weihenstephan, Freising, Germany.
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Weinstock J, Willerslev E, Sher A, Tong W, Ho SY, Rubenstein D, Storer J, Burns J, Martin L, Bravi C, Prieto A, Froese D, Scott E, Xulong L, Cooper A. Evolution, systematics, and phylogeography of pleistocene horses in the new world: a molecular perspective. PLoS Biol 2005; 3:e241. [PMID: 15974804 PMCID: PMC1159165 DOI: 10.1371/journal.pbio.0030241] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2005] [Accepted: 05/06/2005] [Indexed: 11/18/2022] Open
Abstract
The rich fossil record of horses has made them a classic example of evolutionary processes. However, while the overall picture of equid evolution is well known, the details are surprisingly poorly understood, especially for the later Pliocene and Pleistocene, c. 3 million to 0.01 million years (Ma) ago, and nowhere more so than in the Americas. There is no consensus on the number of equid species or even the number of lineages that existed in these continents. Likewise, the origin of the endemic South American genus Hippidion is unresolved, as is the phylogenetic position of the “stilt-legged” horses of North America. Using ancient DNA sequences, we show that, in contrast to current models based on morphology and a recent genetic study, Hippidion was phylogenetically close to the caballine (true) horses, with origins considerably more recent than the currently accepted date of c. 10 Ma. Furthermore, we show that stilt-legged horses, commonly regarded as Old World migrants related to the hemionid asses of Asia, were in fact an endemic North American lineage. Finally, our data suggest that there were fewer horse species in late Pleistocene North America than have been named on morphological grounds. Both caballine and stilt-legged lineages may each have comprised a single, wide-ranging species. Ancient DNA simplifies the systematics of horses present in the New Word during the Pleistocene and reveals that the stilt- legged horse is native to the continent and not a Eurasian migrant.
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Affiliation(s)
- Jaco Weinstock
- 1 Ancient Biomolecules Centre, Department of Zoology, University of Oxford, United Kingdom
| | - Eske Willerslev
- 1 Ancient Biomolecules Centre, Department of Zoology, University of Oxford, United Kingdom
| | - Andrei Sher
- 2 Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Wenfei Tong
- 3 Department of Ecology and Evolutionary Biology, Princeton University, United States of America
| | - Simon Y.W Ho
- 1 Ancient Biomolecules Centre, Department of Zoology, University of Oxford, United Kingdom
| | - Dan Rubenstein
- 3 Department of Ecology and Evolutionary Biology, Princeton University, United States of America
| | - John Storer
- 4 Government of the Yukon, Cultural Services Branch, Whitehorse, Canada
| | - James Burns
- 5 Quaternary Paleontology Program, Provincial Museum of Alberta, Edmonton, Canada
| | - Larry Martin
- 6 Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Claudio Bravi
- 7 Instituto Multidisciplinario de Biologia Celular (IMBICE), La Plata, Argentina
| | - Alfredo Prieto
- 8 Instituto de la Patagonia, Universidad de Magallanes, Punta Arenas, Chile
| | - Duane Froese
- 9 Department of Earth and Atmospheric Science, University of Alberta, Canada
| | - Eric Scott
- 10 San Bernardino County Museum, Redlands, California, United States of America
| | - Lai Xulong
- 11 China University of Geosciences, Wuhan, China
| | - Alan Cooper
- 1 Ancient Biomolecules Centre, Department of Zoology, University of Oxford, United Kingdom
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Alberdi MT, Prado JL, Prieto A. Considerations on the paper "Morphological convergence in Hippidion and Equus (Amerhippus) South American equids elucidated by ancient DNA analysis'', by Ludovic Orlando, Véra Eisenmann, Frédéric Reynier, Paul Sondaar, Catherine Hänni. J Mol Evol 2005; 61:145-7. [PMID: 15980958 DOI: 10.1007/s00239-004-0216-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Accepted: 02/25/2005] [Indexed: 11/29/2022]
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