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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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Aurochs roamed along the SW coast of Andalusia (Spain) during Late Pleistocene. Sci Rep 2022; 12:9911. [PMID: 35701579 PMCID: PMC9198092 DOI: 10.1038/s41598-022-14137-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/16/2022] [Indexed: 11/09/2022] Open
Abstract
In the Iberian Peninsula the fossil record of artiodactyls spans over 53 million years. During the Pleistocene, wild cattle species such as Bison and especially Bos became common. In Late Pleistocene, the aurochs (Bos primigenius) was widespread and the only bovine living along the large river valleys of southern Iberia. Although commonly found in fossil sites and especially in cave bone assemblages, the trace fossil record of aurochs was known worldwide only from the Holocene. Large bovine and roe deer/caprine tracks were found in at least five horizons of the early Late Pleistocene (MIS 5) beach and eolian deposits of Cape Trafalgar (Cadiz Province, South of Spain). The large bovine tracks are formally described as Bovinichnus uripeda igen. et isp. nov. and compared with the record of aurochs tracks, large red deer tracks and steppe bison biogeographical distribution in Iberia. Aurochs were the most likely producers of the newly described Trafalgar Trampled Surface (TTS) and some of the large artiodactyl tracks in the Matalascañas Trampled Surface, representing the oldest aurochs track record known. This new evidence, together with comparisons with the record of possible aurochs tracks in the Mid-Late Pleistocene coastal deposits from the Asperillo cliff section in Matalascañas (Huelva Province, SW Spain) and bone assemblages known in Gibraltar, point to a recurrent use of the coastal habitat by these large artiodactyls in SW Iberia.
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Sinding MHS, Ciucani MM, Ramos-Madrigal J, Carmagnini A, Rasmussen JA, Feng S, Chen G, Vieira FG, Mattiangeli V, Ganjoo RK, Larson G, Sicheritz-Pontén T, Petersen B, Frantz L, Gilbert MTP, Bradley DG. Kouprey ( Bos sauveli) genomes unveil polytomic origin of wild Asian Bos. iScience 2021; 24:103226. [PMID: 34712923 PMCID: PMC8531564 DOI: 10.1016/j.isci.2021.103226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/11/2021] [Accepted: 10/01/2021] [Indexed: 12/30/2022] Open
Abstract
The evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct kouprey (Bos sauveli) and analyzed them alongside other Bos and Bison genomes. We found that B. sauveli possessed genomic signatures characteristic of an independent species closely related to Bos javanicus and Bos gaurus. We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow. Finally, we detected significant gene flow from an unsampled Asian Bos-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the Bos complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so. We generated two genomes from the likely extinct kouprey (Bos sauveli) Extensive mt and nuclear-genome-wide incomplete lineage sorting across wild Asian Bos Initial polytomic diversification of the wild Asian Bos—kouprey, banteng, and gaur
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Affiliation(s)
| | | | | | - Alberto Carmagnini
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Jacob Agerbo Rasmussen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Guangji Chen
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | | | | | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Thomas Sicheritz-Pontén
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Bent Petersen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - M. Thomas P. Gilbert
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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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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Neov B, Spassov N, Hristova L, Hristov P, Radoslavov G. New data on the evolutionary history of the European bison ( Bison bonasus) based on subfossil remains from Southeastern Europe. Ecol Evol 2021; 11:2842-2848. [PMID: 33767840 PMCID: PMC7981210 DOI: 10.1002/ece3.7241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 01/07/2021] [Accepted: 01/15/2021] [Indexed: 11/11/2022] Open
Abstract
The origin and evolutionary history of the European bison Bison bonasus (wisent) have become clearer after several morphological, genomic, and paleogenomic studies in the last few years, but these paleogenomic studies have raised new questions about the evolution of the species. Here, we present additional information about the population diversity of the species based on the analysis of new subfossil Holocene remains from the Balkan Peninsula. Seven ancient samples excavated from caves in Western Stara Planina in Bulgaria were investigated by mitochondrial D-loop (HVR1) sequence analysis. The samples were dated to 3,800 years BP by radiocarbon analysis. Additionally, a phylogenetic analysis was performed to investigate the genetic relationship among the investigated samples and all mitochondrial DNA sequences from the genus Bison available in GenBank. The results clustered with the sequences from the extinct Holocene South-Eastern (Balkan) wisent to the fossil Alpine population from France, Austria, and Switzerland, but not with those from the recent Central European (North Sea) one and the now extinct Caucasian population. In conclusion, these data indicate that the Balkan wisent that existed in historical time represented a relict and probably an isolated population of the Late Pleistocene-Holocene South-Western mountainous population of the wisent.
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Affiliation(s)
- Boyko Neov
- Department of Animal Diversity and ResourcesInstitute of Biodiversity and Ecosystem ResearchBulgarian Academy of SciencesSofiaBulgaria
| | - Nikolai Spassov
- Palaeontology and Mineralogy DepartmentNational Museum of Natural HistoryBulgarian Academy of SciencesSofiaBulgaria
| | - Latinka Hristova
- Palaeontology and Mineralogy DepartmentNational Museum of Natural HistoryBulgarian Academy of SciencesSofiaBulgaria
| | - Peter Hristov
- Department of Animal Diversity and ResourcesInstitute of Biodiversity and Ecosystem ResearchBulgarian Academy of SciencesSofiaBulgaria
| | - Georgi Radoslavov
- Department of Animal Diversity and ResourcesInstitute of Biodiversity and Ecosystem ResearchBulgarian Academy of SciencesSofiaBulgaria
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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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