1
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Brunson K, Witt KE, Monge S, Williams S, Peede D, Odsuren D, Bukhchuluun D, Cameron A, Szpak P, Amartuvshin C, Honeychurch W, Wright J, Pleuger S, Erdene M, Tumen D, Rogers L, Khatanbaatar D, Batdalai B, Galdan G, Janz L. Ancient Mongolian aurochs genomes reveal sustained introgression and management in East Asia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552443. [PMID: 37609302 PMCID: PMC10441390 DOI: 10.1101/2023.08.10.552443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Societies in East Asia have utilized domesticated cattle for over 5000 years, but the genetic history of cattle in East Asia remains understudied. Genome-wide analyses of 23 ancient Mongolian cattle reveal that East Asian aurochs and ancient East Asian taurine cattle are closely related, but neither are closely related to any modern East Asian breeds. We observe binary variation in aurochs diet throughout the early Neolithic, and genomic evidence shows millennia of sustained male-dominated introgression. We identify a unique connection between ancient Mongolian aurochs and the European Hereford breed. These results point to the likelihood of human management of aurochs in Northeast Asia prior to and during the initial adoption of taurine cattle pastoralism.
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Affiliation(s)
| | - Kelsey E. Witt
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University; Clemson, South Carolina 29634, USA
- Center for Computational Molecular Biology, Brown University; Providence 02912, USA
- Department of Ecology, Evolution, and Organismal Biology, Brown University; Providence 02912, USA
| | - Susan Monge
- Department of Anthropology, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Sloan Williams
- Department of Anthropology, University of Illinois Chicago, Chicago, IL 60607, USA
| | - David Peede
- Center for Computational Molecular Biology, Brown University; Providence 02912, USA
- Department of Ecology, Evolution, and Organismal Biology, Brown University; Providence 02912, USA
- Institute at Brown for Environment and Society, Brown University; Providence 02912, USA
| | - Davaakhuu Odsuren
- Department of History, Mongolian National University of Education; Ulaanbaatar, Sukhbaatar district, 210648, Mongolia
- Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar-51, Mongolia
| | - Dashzeveg Bukhchuluun
- Department of Anthropology, Yale University, 10 Sachem St., New Haven, CT 06511, USA
| | - Asa Cameron
- Department of Anthropology, Yale University, 10 Sachem St., New Haven, CT 06511, USA
| | - Paul Szpak
- Department of Anthropology, Trent University; Peterborough K9J 6Y1, Canada
| | - Chunag Amartuvshin
- Department of Anthropology and Archaeology, National University of Mongolia; Ulaanbaatar-51, Mongolia
| | - William Honeychurch
- Department of Anthropology, Yale University, 10 Sachem St., New Haven, CT 06511, USA
| | - Joshua Wright
- Department of Archaeology, University of Aberdeen, King’s College; Aberdeen, AB24 3FX, UK
| | - Sarah Pleuger
- School of History, Classics and Archaeology, University of Edinburgh; Edinburgh EH8 9AG, UK
| | - Myagmar Erdene
- Department of Anthropology and Archaeology, National University of Mongolia; Ulaanbaatar-51, Mongolia
| | - Dashtseveg Tumen
- Department of Anthropology and Archaeology, National University of Mongolia; Ulaanbaatar-51, Mongolia
| | - Leland Rogers
- Department of Anthropology, University of North Carolina Wilmington; Wilmington, NC 28403, USA
| | - Dorjpurev Khatanbaatar
- School of Business Administration and Humanities, The Mongolian University of Science and Technology; Mongolia
| | - Byambatseren Batdalai
- Archaeological Research Center, National University of Mongolia; Ulaanbaatar-51, Mongolia
| | - Ganbaatar Galdan
- Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar-51, Mongolia
| | - Lisa Janz
- Department of Anthropology, University of Toronto Scarborough; Scarborough, ON M1C 1A4, Canada
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Corduneanu A, Taulescu M, Ursache TD, Ionică AM, Mihalca AD. Piroplasms in farmed American bison, Bison bison from Romania. Front Vet Sci 2023; 10:1158072. [PMID: 37065243 PMCID: PMC10090506 DOI: 10.3389/fvets.2023.1158072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/13/2023] [Indexed: 03/31/2023] Open
Abstract
The American bison (Bison bison) is the largest terrestrial mammal of North America, with around 350,000 individuals in the wild and in private herds but the knowledge regarding the presence of different vector-borne pathigens in these mammals is very poor. Babesia and Theileria spp. are tick-borne apicomplexan parasites which are considered to be among the most commonly found blood parasites of large ruminants, often with a high economic importance. However, the knowledge on piroplasms of bisons is extremely scarce. The aim of our study was to evaluate the presence of apicomplexan parasites in blood and tissues of farmed American bison from Romania. Overall, we tested 222 blood samples and 11 tissues samples (heart, liver, and spleen) from farmed B. bison raised for meat in Romania. All the samples were analyzed by nPCR targeting the 18SrRNA gene for piroplasmids. All positive samples were sequenced and analyzed phylogenetically. The overall prevalence of infection with piroplasmids in American bison was 1.65%, with Babesia divergens and Theileria sp. identified following sequencing. To our knowledge, this is the first report of piroplasms detected in blood and tissues of farmed B. bison from Europe. Further studies are necessary in order to obtain a better overview on the epidemiological status and clinical relevance of piroplasms in farmed American bisons.
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Affiliation(s)
- Alexandra Corduneanu
- Department of Animal Breeding and Animal Productions, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
- *Correspondence: Alexandra Corduneanu
| | - Marian Taulescu
- Department of Pathology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
- Synevovet, Bucharest, Romania
| | - Teodor Dan Ursache
- Department of Pathology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Angela Monica Ionică
- Molecular Diagnosis Laboratory, Clinical Hospital of Infectious Diseases of Cluj-Napoca, Cluj-Napoca, Romania
| | - Andrei Daniel Mihalca
- Department of Parasitology and Parasitic Diseases, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
- Parasitology Consultancy Group, Coruşu, Romania
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Hou X, Zhao J, Zhang H, Preick M, Hu J, Xiao B, Wang L, Deng M, Liu S, Chang F, Sheng G, Lai X, Hofreiter M, Yuan J. Paleogenomes Reveal a Complex Evolutionary History of Late Pleistocene Bison in Northeastern China. Genes (Basel) 2022; 13:genes13101684. [PMID: 36292570 PMCID: PMC9602171 DOI: 10.3390/genes13101684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022] Open
Abstract
Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct.
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Affiliation(s)
- Xindong Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Jian Zhao
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Michaela Preick
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24–25, 14476 Potsdam, Germany
| | - Jiaming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Earth Sciences, China University of Geosciences, Wuhan 430074, China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Earth Sciences, China University of Geosciences, Wuhan 430074, China
| | - Linying Wang
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Miaoxuan Deng
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Sizhao Liu
- Department of Scientific Research, Dalian Natural History Museum, Dalian 116023, China
| | - Fengqin Chang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Guilian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Earth Sciences, China University of Geosciences, Wuhan 430074, China
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24–25, 14476 Potsdam, Germany
- Correspondence: (M.H.); (J.Y.); Tel.: +49-331-977-6321 (M.H.); +86-027-6788-3022 (J.Y.)
| | - Junxia Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
- Correspondence: (M.H.); (J.Y.); Tel.: +49-331-977-6321 (M.H.); +86-027-6788-3022 (J.Y.)
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Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches. DIVERSITY 2021. [DOI: 10.3390/d13080370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Starting four decades ago, studies have examined the ecology and evolutionary dynamics of populations and species using short mitochondrial DNA fragments and stable isotopes. Through technological and analytical advances, the methods and biomolecules at our disposal have increased significantly to now include lipids, whole genomes, proteomes, and even epigenomes. At an unprecedented resolution, the study of ancient biomolecules has made it possible for us to disentangle the complex processes that shaped the ancient faunal diversity across millennia, with the potential to aid in implicating probable causes of species extinction and how humans impacted the genetics and ecology of wild and domestic species. However, even now, few studies explore interdisciplinary biomolecular approaches to reveal ancient faunal diversity dynamics in relation to environmental and anthropogenic impact. This review will approach how biomolecules have been implemented in a broad variety of topics and species, from the extinct Pleistocene megafauna to ancient wild and domestic stocks, as well as how their future use has the potential to offer an enhanced understanding of drivers of past faunal diversity on Earth.
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5
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Scales ZM, Narbay E, Hellberg RS. Use of DNA Barcoding Combined with PCR-SFLP to Authenticate Species in Bison Meat Products. Foods 2021; 10:foods10020347. [PMID: 33562113 PMCID: PMC7915063 DOI: 10.3390/foods10020347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 11/23/2022] Open
Abstract
American bison (Bison bison) meat is susceptible to species mislabeling due to its high value and similar appearance to meat from domestic cattle (Bos taurus). DNA barcoding is commonly used to identify animal species. However, as a result of the historical hybridization of American bison and domestic cattle, additional genetic testing is required for species confirmation. The objective of this study was to perform a market survey of bison meat products and verify the species using DNA barcoding combined with polymerase chain reaction-satellite fragment length polymorphism (PCR-SFLP). Bison products (n = 45) were purchased from a variety of retailers. Samples that were positive for domestic cattle with DNA barcoding were further analyzed with PCR-SFLP. DNA barcoding identified bison in 41 products, red deer (Cervus elaphus) in one product, and domestic cattle in three products. PCR-SFLP confirmed the identification of domestic cattle in two samples, while the third sample was identified as bison with ancestral cattle DNA. Overall, mislabeling was detected in 3 of the 45 samples (6.7%). This study revealed that additional DNA testing of species that have undergone historical hybridization provides improved identification results compared to DNA barcoding alone.
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Abstract
Mobile devices for on-field DNA analysis have been used for medical diagnostics
at the point-of-care, forensic investigations and environmental surveys, but
still have to be validated for ancient DNA studies. We report here on a mobile
laboratory that we setup using commercially available devices, including a
compact real-time PCR machine, and describe procedures to perform DNA extraction
and analysis from a variety of archeological samples within 4 hours. The process
is carried out on 50 mg samples that are identified at the species level using
custom TaqMan real-time PCR assays for mitochondrial DNA fragments. We evaluated
the potential of this approach in museums lacking facilities for DNA studies by
analyzing samples from the Enlène (MIS 2 layer) and the Portel-Ouest cave (MIS 3
deposits), and also performed experiments during an excavation campaign at the
Roc-en-Pail (MIS 5) open-air site. Enlène Bovinae bone samples
only yielded DNA for the extinct steppe bison (Bison priscus),
whereas Portel-Ouest cave coprolites contained cave hyena (Crocuta
crocuta spelaea) DNA together, for some of them, with DNA for the
European bison sister species/subspecies (Bison
schoetensacki/Bb1-X), thus highlighting the cave hyena diet.
Roc-en-Pail Bovinae bone and tooth samples also contained DNA
for the Bison schoetensacki/Bb1-X clade, and
Cervidae bone samples only yielded reindeer
(Rangifer tarandus) DNA. Subsequent DNA sequencing analyses
confirmed that correct species identification had been achieved using our TaqMan
assays, hence validating these assays for future studies. We conclude that our
approach enables the rapid genetic characterization of tens of millennia-old
archeological samples and is expected to be useful for the on-site screening of
museums and freshly excavated samples for DNA content. Because our mobile
laboratory is made up of commercially available instruments, this approach is
easily accessible to other investigators.
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7
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Delsuc F, Kuch M, Gibb GC, Hughes J, Szpak P, Southon J, Enk J, Duggan AT, Poinar HN. Resolving the phylogenetic position of Darwin's extinct ground sloth ( Mylodon darwinii) using mitogenomic and nuclear exon data. Proc Biol Sci 2019; 285:rspb.2018.0214. [PMID: 29769358 PMCID: PMC5966596 DOI: 10.1098/rspb.2018.0214] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 04/16/2018] [Indexed: 01/18/2023] Open
Abstract
Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first collected its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12 880-year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that this sample was exceptionally well preserved for an ancient subfossil, probably the result of the dry and cold conditions prevailing within the cave. Accordingly, taxonomic assessment of our shotgun metagenomic data showed a very high percentage of endogenous DNA with 22% of the assembled metagenomic contigs assigned to Xenarthra. Additionally, we enriched over 15 kb of sequence data from seven nuclear exons, using target sequence capture designed against a wide xenarthran dataset. Phylogenetic and dating analyses of the mitogenomic dataset including all extant species of xenarthrans and the assembled nuclear supermatrix unambiguously place Mylodon darwinii as the sister-group of modern two-fingered sloths, from which it diverged around 22 million years ago. These congruent results from both the mitochondrial and nuclear data support the diphyly of the two modern sloth lineages, implying the convergent evolution of their unique suspensory behaviour as an adaption to arboreality. Our results offer promising perspectives for whole-genome sequencing of this emblematic extinct taxon.
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Affiliation(s)
- Frédéric Delsuc
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Melanie Kuch
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Gillian C Gibb
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.,Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Jonathan Hughes
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Paul Szpak
- Department of Anthropology, Trent University, Peterborough, ON, Canada
| | - John Southon
- Keck Carbon Cycle Accelerator Mass Spectrometer, Earth Systems Science Department, University of California, Irvine, CA, USA
| | - Jacob Enk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada.,MYcroarray, Ann Arbor, MI, USA
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Hendrik N Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
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8
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Palacio P, Berthonaud V, Guérin C, Lambourdière J, Maksud F, Philippe M, Plaire D, Stafford T, Marsolier-Kergoat MC, Elalouf JM. Genome data on the extinct Bison schoetensacki establish it as a sister species of the extant European bison (Bison bonasus). BMC Evol Biol 2017; 17:48. [PMID: 28187706 PMCID: PMC5303235 DOI: 10.1186/s12862-017-0894-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 01/26/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The European bison (Bison bonasus), now found in Europe and the Caucasus, has been proposed to originate either from the extinct steppe/extant American bison lineage or from the extinct Bison schoetensacki lineage. Bison schoetensacki remains are documented in Eurasian Middle Pleistocene sites, but their presence in Upper Pleistocene sites has been questioned. Despite extensive genetic studies carried out on the steppe and European bison, no remains from the fossil record morphologically identified as Bison schoetensacki has been analyzed up to now. RESULTS In this paper, we analyzed a 36,000-year-old Bison schoetensaki bone sample from the Siréjol cave (France) and a cave hyena coprolite (fossilized feces) found in a nearby cave and containing large amounts of Bovinae DNA. We show that the Bovinae mitochondrial DNA sequences from both samples, including a complete mitochondrial genome sequence, belong to a clade recently reported in the literature. This clade only includes ancient bison specimens without taxonomic identification and displays a sister relationship with the extant European bison. The genetic proximity of Bison schoetensacki with specimens from this clade is corroborated by the analysis of nuclear DNA single nucleotide polymorphisms. CONCLUSIONS This work provides genetic evidence supporting the continuing presence of Bison schoetensacki up to the Upper Pleistocene. Bison schoetensacki turns out to be a sister species of Bison bonasus, excluding the steppe bison Bison priscus as a direct ancestor of the European bison.
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Affiliation(s)
- Pauline Palacio
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Véronique Berthonaud
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Claude Guérin
- CNRS-UMR 5276, Laboratoire de Géologie de Lyon: Terre, planètes, environnement, Département des Sciences de la Terre, Université Claude Bernard, Lyon I, 27-43 Boulevard du 11 Novembre, 69622, Villeurbanne cedex, France
| | - Josie Lambourdière
- Service de Systématique Moléculaire, UMS 2700 CNRS-MNHN, CP26, 57 Rue Cuvier, 75231, Paris Cedex 05, France
| | - Frédéric Maksud
- Service Régional de l'Archéologie, 32 rue de la Dalbade, BP811 31080, Toulouse cedex 6, France
| | - Michel Philippe
- Centre de Conservation et d'Étude sur les Collections, 13A rue Bancel, 69007, Lyon, France
| | - Delphine Plaire
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,CNRS-UMR 7206, Eco-anthropologie et Ethnobiologie, Département Hommes, Natures et Sociétés, Musée de l'Homme, 17 place du Trocadéro et du 11 novembre, 75016, Paris, France
| | - Thomas Stafford
- Stafford Research, 200 Acadia Avenue, Lafayette, CO, 80026, USA
| | - Marie-Claude Marsolier-Kergoat
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,CNRS-UMR 7206, Eco-anthropologie et Ethnobiologie, Département Hommes, Natures et Sociétés, Musée de l'Homme, 17 place du Trocadéro et du 11 novembre, 75016, Paris, France
| | - Jean-Marc Elalouf
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France. .,CNRS-UMR 7206, Eco-anthropologie et Ethnobiologie, Département Hommes, Natures et Sociétés, Musée de l'Homme, 17 place du Trocadéro et du 11 novembre, 75016, Paris, France.
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9
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Massilani D, Guimaraes S, Brugal JP, Bennett EA, Tokarska M, Arbogast RM, Baryshnikov G, Boeskorov G, Castel JC, Davydov S, Madelaine S, Putelat O, Spasskaya NN, Uerpmann HP, Grange T, Geigl EM. Past climate changes, population dynamics and the origin of Bison in Europe. BMC Biol 2016; 14:93. [PMID: 27769298 PMCID: PMC5075162 DOI: 10.1186/s12915-016-0317-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/11/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Climatic and environmental fluctuations as well as anthropogenic pressure have led to the extinction of much of Europe's megafauna. The European bison or wisent (Bison bonasus), one of the last wild European large mammals, narrowly escaped extinction at the onset of the 20th century owing to hunting and habitat fragmentation. Little is known, however, about its origin, evolutionary history and population dynamics during the Pleistocene. RESULTS Through ancient DNA analysis we show that the emblematic European bison has experienced several waves of population expansion, contraction, and extinction during the last 50,000 years in Europe, culminating in a major reduction of genetic diversity during the Holocene. Fifty-seven complete and partial ancient mitogenomes from throughout Europe, the Caucasus, and Siberia reveal that three populations of wisent (Bison bonasus) and steppe bison (B. priscus) alternately occupied Western Europe, correlating with climate-induced environmental changes. The Late Pleistocene European steppe bison originated from northern Eurasia, whereas the modern wisent population emerged from a refuge in the southern Caucasus after the last glacial maximum. A population overlap during a transition period is reflected in ca. 36,000-year-old paintings in the French Chauvet cave. Bayesian analyses of these complete ancient mitogenomes yielded new dates of the various branching events during the evolution of Bison and its radiation with Bos, which lead us to propose that the genetic affiliation between the wisent and cattle mitogenomes result from incomplete lineage sorting rather than post-speciation gene flow. CONCLUSION The paleogenetic analysis of bison remains from the last 50,000 years reveals the influence of climate changes on the dynamics of the various bison populations in Europe, only one of which survived into the Holocene, where it experienced severe reductions in its genetic diversity. The time depth and geographical scope of this study enables us to propose temperate Western Europe as a suitable biotope for the wisent compatible with its reintroduction.
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Affiliation(s)
- Diyendo Massilani
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France
| | - Silvia Guimaraes
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France
| | - Jean-Philip Brugal
- CNRS, USR 3336 IFRA (Institut Français de Recherche en Afrique), Nairobi, Kenya.,Aix-Marseille Université, UMR 7269 LAMPEA (Labo.Méd.de Préhistoire, Europe-Afrique) Maison Méditerranéenne des Sciences de l'Homme, BP 674, 13094, Aix-en-Provence, cedex 2, France
| | - E Andrew Bennett
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France
| | - Malgorzata Tokarska
- Mammal Research Institute Polish Academy of Sciences, Genetics and Evolution Department, Waszkiewicza 1, 17-230, Bialowieza, Poland
| | - Rose-Marie Arbogast
- CNRS/UMR 7044/MISHA, 5 allée du Général Rouvillois, 67083, Strasbourg, France
| | - Gennady Baryshnikov
- Zoological Institute, Russian Academy of Sciences, 199034, Saint Petersburg, Russia
| | - Gennady Boeskorov
- Diamond and Precious Metal Geology Institute of the Siberian Branch of the RAS, Yakutsk, Russia
| | - Jean-Christophe Castel
- Muséum d'histoire naturelle de Genève (MHN), Département d'Archéozoologie, Route de Malagnou 1, 1208, Geneva, Switzerland
| | - Sergey Davydov
- North-East Science Station, Pacific Institute of Geography, Far East Branch, Russ. Ac. Sci., 678830, Cherskiy, Russia
| | - Stéphane Madelaine
- Musée national de Préhistoire, 24620, Les Eyzies de Tayac-Sireuil, France
| | - Olivier Putelat
- Archéologie Alsace, 11 rue Jean-François Champollion, 67600, Sélestat, France.,UMR 7041 ArScan - Archéologies environnementales - Maison de l'Archéologie et de l'Ethnologie, 92023, Nanterre, France
| | - Natalia N Spasskaya
- Zoological Museum of Moscow Lomonosow, State University, Bolshaya Nikitskaya Str. 6, Moscow, 125009, Russia
| | - Hans-Peter Uerpmann
- Institut für Ur- und Frühgeschichte und Archäologie des Mittelalters, Abteilung Ältere Urgeschichte und Quartärökologie, Zentrum für Naturwissenschaftliche Archäologie, Rümelinstr. 23, 72070, Tübingen, Germany
| | - Thierry Grange
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France.
| | - Eva-Maria Geigl
- Institut Jacques Monod, UMR7592, CNRS, University Paris Diderot, Epigenome and Paleogenome group, 15 rue Hélène Brion, 75013, Paris, France.
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Soubrier J, Gower G, Chen K, Richards SM, Llamas B, Mitchell KJ, Ho SYW, Kosintsev P, Lee MSY, Baryshnikov G, Bollongino R, Bover P, Burger J, Chivall D, Crégut-Bonnoure E, Decker JE, Doronichev VB, Douka K, Fordham DA, Fontana F, Fritz C, Glimmerveen J, Golovanova LV, Groves C, Guerreschi A, Haak W, Higham T, Hofman-Kamińska E, Immel A, Julien MA, Krause J, Krotova O, Langbein F, Larson G, Rohrlach A, Scheu A, Schnabel RD, Taylor JF, Tokarska M, Tosello G, van der Plicht J, van Loenen A, Vigne JD, Wooley O, Orlando L, Kowalczyk R, Shapiro B, Cooper A. Early cave art and ancient DNA record the origin of European bison. Nat Commun 2016; 7:13158. [PMID: 27754477 PMCID: PMC5071849 DOI: 10.1038/ncomms13158] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/09/2016] [Indexed: 11/09/2022] Open
Abstract
The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (<11.7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison (Bison priscus) and ancestors of modern cattle (aurochs, Bos primigenius) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21-18 kya).
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Affiliation(s)
- Julien Soubrier
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Graham Gower
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Kefei Chen
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephen M. Richards
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Kieren J. Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Simon Y. W. Ho
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Russian Academy of Sciences, 202 8 Marta Street, 620144 Ekaterinburg, Russia
| | - Michael S. Y. Lee
- School of Biological Sciences, Flinders University, South Australia 5001, Australia
- Earth Sciences Section, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Gennady Baryshnikov
- Zoological Institute RAS, Universitetskaya Naberezhnaya 1, 199034 St Petersburg, Russia
| | - Ruth Bollongino
- Palaeogenetics Group, Institute of Anthropology, University of Mainz D-55128, Mainz, Germany
| | - Pere Bover
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
- Department of Biodiversity and Conservation, Institut Mediterrani d'Estudis Avançats (CSIC-UIB), Cr. Miquel Marquès 21, 07190 Esporles, Illes Balears
| | - Joachim Burger
- Palaeogenetics Group, Institute of Anthropology, University of Mainz D-55128, Mainz, Germany
| | - David Chivall
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Evelyne Crégut-Bonnoure
- Museum Requien, 67 rue Joseph Vernet, 84000 Avignon, France
- Laboratoire TRACES UMR5608, Université Toulouse Jean Jaurès - Maison de la Recherche, 5 allée Antonio Machado, 31058 Toulouse, France
| | - Jared E. Decker
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | | | - Katerina Douka
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Damien A. Fordham
- Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Federica Fontana
- Dipartimento di Studi Umanistici, Università degli Studi di Ferrara, 12 Via Paradiso, 44121 Ferrara, Italy
| | - Carole Fritz
- CNRS, TRACES, UMR 5608 et CREAP, MSHS Toulouse, USR 3414, Maison de la Recherche, 5 allées Antonio Machado, 31058 Toulouse, France
| | - Jan Glimmerveen
- CERPOLEX/Mammuthus, Anna Paulownastraat 25A, NL-2518 BA Den Haag, The Netherlands
| | | | - Colin Groves
- School of Archaeology and Anthropology, Australian National University, Building 14, Canberra, Australian National University 0200, Australia
| | - Antonio Guerreschi
- Dipartimento di Studi Umanistici, Università degli Studi di Ferrara, 12 Via Paradiso, 44121 Ferrara, Italy
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Emilia Hofman-Kamińska
- Mammal Research Institute, Polish Academy of Sciences, Waszkiewicza 1c, 17-230 Białowieża, Poland
| | - Alexander Immel
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Marie-Anne Julien
- Department of Archaeology, Centre for the Archaeology of Human Origins, University of Southampton, Avenue Campus, Southampton SO17 1BF, UK
- Unité Histoire naturelle de l'Homme préhistorique (UMR 7194), Sorbonne Universités, Muséum national d'Histoire narurelle, CNRS, 1 rue René Panhard, 75013 Paris, France
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Oleksandra Krotova
- Department of Stone Age, Institute of Archaeology, National Ukrainian Academy of Science, 04210 Kiev, Ukraine
| | - Frauke Langbein
- Institute for Archaeological Sciences, Archaeo and Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
| | - Adam Rohrlach
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Amelie Scheu
- Palaeogenetics Group, Institute of Anthropology, University of Mainz D-55128, Mainz, Germany
| | - Robert D. Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Jeremy F. Taylor
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Małgorzata Tokarska
- Mammal Research Institute, Polish Academy of Sciences, Waszkiewicza 1c, 17-230 Białowieża, Poland
| | - Gilles Tosello
- Chercheur associé, CREAP, MSHS Toulouse, URS 3414, Maison de la Recherche, 5 allées Antonio Machado, 31058 Toulouse, France
| | - Johannes van der Plicht
- Centre for Isotope Research, Radiocarbon Laboratory, University of Groningen, Nijenborg 4, NI-9747 AG Groningen, The Netherlands
| | - Ayla van Loenen
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jean-Denis Vigne
- Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Sorbonne Universités, UMR7209, ‘Archéozoologie, archéobotanique: sociétés, pratiques et environnements', CP56, 55 rue Buffon, 75005 Paris, France
| | - Oliver Wooley
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, ØsterVoldgade 5-7, Copenhagen 1350K, Denmark
- Université de Toulouse, University Paul Sabatier, Laboratoire AMIS, CNRS UMR 5288, 37 Allées Jules Guesde, Toulouse 31000, France
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, Waszkiewicza 1c, 17-230 Białowieża, Poland
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
- UCSC Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
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