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Chen S, Ren L, Gao Y, Dong G, Sheng G, Han J, Liu X, Chen N, Chen F. Evidence of hybridization of cattle and aurochs on the Tibetan Plateau ∼3750 years ago. Sci Bull (Beijing) 2024:S2095-9273(24)00460-2. [PMID: 39025776 DOI: 10.1016/j.scib.2024.06.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 07/20/2024]
Affiliation(s)
- Shungang Chen
- Group of Alpine Paleoecology and Human Adaptation (ALPHA), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Lele Ren
- School of History and Culture, Lanzhou University, Lanzhou 730000, China
| | - Yu Gao
- Group of Alpine Paleoecology and Human Adaptation (ALPHA), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou 730000, China
| | - Guilian Sheng
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
| | - Jianlin Han
- Yazhouwan National Laboratory, Sanya 572024, China
| | - Xinyi Liu
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Fahu Chen
- Group of Alpine Paleoecology and Human Adaptation (ALPHA), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Abstract
Heat stress is described as the cumulative detrimental effect caused by an imbalance between heat production within the body and heat dissipation. When cattle are exposed to heat stress with skin surface temperatures exceeding 35 °C, gene networks within and across cells respond to environmental heat loads with both intra and extracellular signals that coordinate cellular and whole-animal metabolism changes to store heat and rapidly increase evaporative heat loss. In this study, we examined evidence from genes known to be associated with heat tolerance (Hsp70, HSF1, HspB8, SOD1, PRLH, ATP1A1, MTOR, and EIF2AK4). This information could serve as valuable resource material for breeding programs aimed at increasing the thermotolerance of cattle.
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Affiliation(s)
- LuLan Zeng
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Kaixing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Yuan J, Sun G, Xiao B, Hu J, Wang L, Taogetongqimuge, Bao L, Hou Y, Song S, Jiang S, Wu Y, Pan D, Liu Y, Westbury MV, Lai X, Sheng G. Ancient mitogenomes reveal a high maternal genetic diversity of Pleistocene woolly rhinoceros in Northern China. BMC Ecol Evol 2023; 23:56. [PMID: 37752413 PMCID: PMC10521388 DOI: 10.1186/s12862-023-02168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Woolly rhinoceros (Coelodonta antiquitatis) is a typical indicator of cold-stage climate that was widely distributed in Northern Hemisphere during the Middle-Late Pleistocene. Although a plethora of fossils have been excavated from Northern China, their phylogenetic status, intraspecific diversity and phylogeographical structure are still vague. RESULTS In the present study, we generated four mitogenomes from Late Pleistocene woolly rhinoceros in Northern China and compared them with published data. Bayesian and network analyses indicate that the analyzed individuals contain at least four maternal haplogroups, and Chinese samples fall in three of them. One of our samples belongs to a previously unidentified early diverging clade (haplogroup D), which separated from other woolly rhinoceros around 0.57 Ma (95% CI: 0.76-0.41 Ma). The timing of this clade's origin coincides with the first occurrence of woolly rhinoceros, which are thought to have evolved in Europe. Our other three samples cluster in haplogroup C, previously only identified from one specimen from Wrangel Island (ND030) and initially considered to be an isolated clade. Herein, our findings suggest that ND030 is likely descended from a northward dispersal of the individuals carrying haplogroup C from Northern China. Additionally, Chinese woolly rhinoceros specimens exhibit higher nucleotide diversity than those from Siberia. CONCLUSION Our findings highlight Northern China as a possible refugium and a key evolution center of the Pleistocene woolly rhinoceros.
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Affiliation(s)
- Junxia Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China.
- Bioarchaeology Laboratory, Jilin University, Changchun, 130012, China.
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430078, China.
| | - Guojiang Sun
- 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
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Jiaming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, China
| | - Linying Wang
- 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
- College of Earth and Environmental Science, Lanzhou University, Lanzhou, 730099, China
| | | | - Lei Bao
- Ordos Institute of Cultural Relics and Archaeology, Ordos, 017010, China
| | - Yamei Hou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Shiwen Song
- 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
| | - Shan Jiang
- 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
| | - Yong Wu
- The Third Geological and Mineral Exploration Institute of Gansu Bureau of Geology and Mineral Resources, Lanzhou, 730050, China
| | - Dong Pan
- Palaeontological Fossil Conservation Center, Qinggang County, Suihua, 151600, China
| | - Yang Liu
- School of Sociology & Anthropology, Sun Yat-sen University, Guangzhou, 510275, China
| | | | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430078, China
- School of Earth Science, China University of Geosciences, Wuhan, 430074, 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.
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Zhang Y, Qi S, Liu L, Bao Q, Wu T, Liu W, Zhang Y, Zhao W, Xu Q, Chen G. Genetic Diversity Analysis and Breeding of Geese Based on the Mitochondrial ND6 Gene. Genes (Basel) 2023; 14:1605. [PMID: 37628656 PMCID: PMC10454708 DOI: 10.3390/genes14081605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
To explore the differences in body-weight traits of five goose breeds and analyze their genetic diversity and historical dynamics, we collected body-weight data statistics and used Sanger sequencing to determine the mitochondrial DNA of 100 samples of five typical goose breeds in China and abroad. The results indicated that Lion-Head, Hortobagy, and Yangzhou geese have great breeding potential for body weight. Thirteen polymorphic sites were detected in the corrected 505 bp sequence of the mitochondrial DNA (mtDNA) ND6 gene, accounting for approximately 2.57% of the total number of sites. The guanine-cytosine (GC) content (51.7%) of the whole sequence was higher than the adenine-thymine (AT) content (48.3%), showing a certain GC base preference. There were 11 haplotypes among the five breeds, including one shared haplotype. We analyzed the differences in the distribution of base mismatches among the five breeds and conducted Tajima's D and Fu's Fs neutral tests on the historical dynamics of the populations. The distribution of the mismatch difference presented an unsmooth single peak and the Tajima's D value of the neutral test was negative (D < 0) and reached a significant level, which proves that the population of the three species had expanded; the Lion-Head goose population tends to be stable. The genetic diversity of Lion-Head, Zhedong White, Yangzhou, and Taihu geese was equal to the average diversity of Chinese goose breeds. The Hortobagy goose is a foreign breed with differences in mating line breeding and hybrid advantage utilization.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Guohong Chen
- Key Laboratory for Evaluation and Utilization of Poultry Genetic Resources of Ministry of Agriculture and Rural Affairs, Yangzhou University, Yangzhou 225009, China; (Y.Z.); (S.Q.); (L.L.); (Q.B.); (T.W.); (W.L.); (Y.Z.); (W.Z.); (Q.X.)
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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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Xia X, Qu K, Wang Y, Sinding MHS, Wang F, Hanif Q, Ahmed Z, Lenstra JA, Han J, Lei C, Chen N. Global dispersal and adaptive evolution of domestic cattle: a genomic perspective. STRESS BIOLOGY 2023; 3:8. [PMID: 37676580 PMCID: PMC10441868 DOI: 10.1007/s44154-023-00085-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 03/26/2023] [Indexed: 09/08/2023]
Abstract
Domestic cattle have spread across the globe and inhabit variable and unpredictable environments. They have been exposed to a plethora of selective pressures and have adapted to a variety of local ecological and management conditions, including UV exposure, diseases, and stall-feeding systems. These selective pressures have resulted in unique and important phenotypic and genetic differences among modern cattle breeds/populations. Ongoing efforts to sequence the genomes of local and commercial cattle breeds/populations, along with the growing availability of ancient bovid DNA data, have significantly advanced our understanding of the genomic architecture, recent evolution of complex traits, common diseases, and local adaptation in cattle. Here, we review the origin and spread of domestic cattle and illustrate the environmental adaptations of local cattle breeds/populations.
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Affiliation(s)
- Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong, 675000, China
| | - Yan Wang
- Qingdao Municipal Bureau of Agriculture and Rural Affairs, Qingdao, 266000, China
| | - Mikkel-Holger S Sinding
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Jammu and Kashmir, 12350, Pakistan
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jianlin Han
- Livestock Genetic Program, International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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7
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Origins, timing and introgression of domestic geese revealed by whole genome data. J Anim Sci Biotechnol 2023; 14:26. [PMID: 36782272 PMCID: PMC9926862 DOI: 10.1186/s40104-022-00826-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/14/2022] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Geese are among the most important poultry species in the world. The current generally accepted hypothesis is that the European domestic geese originated from greylag geese (Anser anser), and Chinese domestic geese have two origins, most of which originated from swan geese (Anser cygnoides), and the Yili goose originated from greylag geese. To explain the origin and demographic history of geese, we selected 14 goose breeds from Europe and China and wild populations of swan and greylag geese, and whole genome sequencing data were obtained for 74 samples. RESULTS Population structure analysis and phylogenetic trees showed that the wild ancestor of Chinese domestic geese, except for Yili, is the swan geese, and the wild ancestor of Chinese Yili and European domestic geese is greylag geese. Analysis of the demographic history suggests that the domestication of Chinese geese occurred ~ 3499 years ago and that of the European geese occurred ~ 7552 years ago. Furthermore, gene flow was observed between domestic geese and their wild ancestors. Analysis of introgression showed that Yili geese had been introgressed by Chinese domestic geese, and the body size of Yili geese may be influenced by introgression events of some growth-related genes, including IGF-1. CONCLUSIONS Our study provides evidence for the origin of geese at the genome-wide level and advances the understanding of the history of goose domestication and the traits affected by introgression events.
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Legacies of domestication, Neolithic diffusion and trade between Indian subcontinent and Island Southeast Asia shape maternal genetic diversity of Andaman cattle. PLoS One 2022; 17:e0278681. [PMID: 36490290 PMCID: PMC9733863 DOI: 10.1371/journal.pone.0278681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Andaman cattle is a precious indigenous livestock species endemic to Andaman and Nicobar Islands, India. Till date, origin and genetic makeup of the breed which is warranted for breed conservation is not known. Moreover, the spread of zebu cattle from Indus valley to different parts of Island Southeast Asia (ISEA) is not properly understood. Here, we report the genetic diversity, population structure of Andaman cattle and their evolution in the context of epicentre of zebu domestication and ISEA. High genetic diversity in complete mitochondrial D-loop sequences indicated the ability of the breed to withstand impending climate change. Total 81 haplotypes were detected and all of them except three belonged to Bos indicus. The presence of taurine haplotypes in Andaman cattle indicate introgression by European-derived cattle. A poor phylogenetic signal of Andaman cattle with genetic affinities with cattle of Indian subcontinent and ISEA was observed. The poor phylogenetic structure may be due to multidirectional gene flow from Indian subcontinent and ISEA, with which Andaman shares a close cultural and trade relationship from Neolithic age. We hypothesize that Andaman cattle is the outcome of Neolithic diffusion from centre of zebu domestication along with multidirectional commercial exchange between Indian subcontinent and ISEA.
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Xiang H, Wang Z, Yang L, Zhang X, Zhao X. Using loop-primer mediated PCR to enhance the detection of poorly preserved DNA. Front Genet 2022; 13:1000123. [DOI: 10.3389/fgene.2022.1000123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
Abstract
Ancient DNA is vitally important in evolutionary research, and obtaining authentic ancient DNA sequences is critical for a proper analysis. However, it is difficult to acquire amplicons accurately and efficiently from ancient DNA templates using current techniques. Here, we established a loop-primer-mediated amplification method (L-PCR) to obtain target ancient DNA sequences with high accuracy and efficiency. The method was tested using 66 ancient samples (including 27 pig bones or teeth and 39 chicken bones) and serially diluted modern animal DNA templates. Compared to nested PCR, L-PCR was proven to be more efficient and accurate and could obtain more amplicons from both ancient pig samples and chicken bones and detect as low as 10−3 ng/μl modern pig template DNA. The efficiency was at least 100-fold that of the nested PCR. The results suggest that L-PCR is advantageous for obtaining authentic DNA sequences from poorly preserved or recalcitrant ancient specimens.
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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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11
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Dorji J, Vander Jagt CJ, Chamberlain AJ, Cocks BG, MacLeod IM, Daetwyler HD. Recovery of mitogenomes from whole genome sequences to infer maternal diversity in 1883 modern taurine and indicine cattle. Sci Rep 2022; 12:5582. [PMID: 35379858 PMCID: PMC8980051 DOI: 10.1038/s41598-022-09427-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/18/2022] [Indexed: 11/09/2022] Open
Abstract
Maternal diversity based on a sub-region of mitochondrial genome or variants were commonly used to understand past demographic events in livestock. Additionally, there is growing evidence of direct association of mitochondrial genetic variants with a range of phenotypes. Therefore, this study used complete bovine mitogenomes from a large sequence database to explore the full spectrum of maternal diversity. Mitogenome diversity was evaluated among 1883 animals representing 156 globally important cattle breeds. Overall, the mitogenomes were diverse: presenting 11 major haplogroups, expanding to 1309 unique haplotypes, with nucleotide diversity 0.011 and haplotype diversity 0.999. A small proportion of African taurine (3.5%) and indicine (1.3%) haplogroups were found among the European taurine breeds and composites. The haplogrouping was largely consistent with the population structure derived from alternate clustering methods (e.g. PCA and hierarchical clustering). Further, we present evidence confirming a new indicine subgroup (I1a, 64 animals) mainly consisting of breeds originating from China and characterised by two private mutations within the I1 haplogroup. The total genetic variation was attributed mainly to within-breed variance (96.9%). The accuracy of the imputation of missing genotypes was high (99.8%) except for the relatively rare heteroplasmic genotypes, suggesting the potential for trait association studies within a breed.
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Affiliation(s)
- Jigme Dorji
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
| | - Christy J Vander Jagt
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Benjamin G Cocks
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Iona M MacLeod
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
| | - Hans D Daetwyler
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
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12
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Ji T, Zhang H, Pagel M, Mace R. A phylogenetic analysis of dispersal norms, descent and subsistence in Sino-Tibetans. EVOL HUM BEHAV 2022. [DOI: 10.1016/j.evolhumbehav.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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13
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Yudin NS, Yurchenko AA, Larkin DM. [Signatures of selection and candidate genes for adaptation to extreme environmental factors in the genomes of Turano-Mongolian cattle breeds]. Vavilovskii Zhurnal Genet Selektsii 2021; 25:190-201. [PMID: 34901717 PMCID: PMC8627871 DOI: 10.18699/vj21.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022] Open
Abstract
Changes in the environment force populations of organisms to adapt to new conditions, either through phenotypic plasticity or through genetic or epigenetic changes. Signatures of selection, such as specific changes in the frequency of alleles and haplotypes, as well as the reduction or increase in genetic diversity, help to identify changes in the cattle genome in response to natural and artificial selection, as well as loci and genetic variants directly affecting adaptive and economically important traits. Advances in genetics and biotechnology enable a rapid transfer of unique genetic variants that have originated in local cattle breeds in the process of adaptation to local environments into the genomes of cosmopolitan high-performance breeds, in order to preserve their outstanding performance in new environments. It is also possible to use genomic selection approach to increase the frequency of already present adaptive alleles in cosmopolitan breeds. The review examines recent work on the origin and evolution of Turano-Mongolian cattle breeds, adaptation of Turano-Mongolian cattle to extreme environments, and summarizes available information on potential candidate genes for climate adaptation of Turano-Mongolian breeds, including cold resistance genes, immune response genes, and high-altitude adaptation genes. The authors conclude that the current literature data do not provide preference to one of the two possible scenarios of Turano-Mongolian breed origins: as a result of the domestication of a wild aurochs at East Asia or as a result of the migration of taurine proto-population from the Middle East. Turano-Mongolian breeds show a high degree of adaptation to extreme climatic conditions (cold, heat, lack of oxygen in the highlands) and parasites (mosquitoes, ticks, bacterial and viral infections). As a result of high-density genotyping and sequencing of genomes and transcriptomes, prospective candidate genes and genetic variants involved in adaptation to environmental factors have recently been identified.
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Affiliation(s)
- N S Yudin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Yurchenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D M Larkin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia The Royal Veterinary College, University of London, London, United Kingdom
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14
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Zhang X, Yang L, Hou L, Li H, Xiang H, Zhao X. Ancient Mitogenomes Reveal the Domestication and Distribution of Cattle During the Longshan Culture Period in North China. Front Genet 2021; 12:759827. [PMID: 34887902 PMCID: PMC8650136 DOI: 10.3389/fgene.2021.759827] [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: 08/17/2021] [Accepted: 10/29/2021] [Indexed: 12/30/2022] Open
Abstract
Cattle, as an important tool for agricultural production in ancient China, have a complex history of domestication and distribution in China. Although it is generally accepted that ancient Chinese taurine cattle originated from the Near East, the explanation regarding their spread through China and whether or not this spread was associated with native aurochs during ancient times are still unclear. In this study, we obtained three nearly complete mitochondrial genomes (mitogenomes) from bovine remains dating back ca. 4,000 years at the Taosi and Guchengzhai sites in North China. For the first time at the mitogenome level, phylogenetic analyses confirmed the approximately 4,000-year-old bovines from North China as taurine cattle. All ancient cattle from both sites belonged to the T3 haplogroup, suggesting their origin from the Near East. The high affinity between ancient samples and southern Chinese taurine cattle indicated that ancient Chinese cattle had a genetic contribution to the taurine cattle of South China. A rapid decrease in the female effective population size ca. 4.65 thousand years ago (kya) and a steep increase ca. 1.99 kya occurred in Chinese taurine cattle. Overall, these results provide increasing evidence of the origin of cattle in the middle Yellow River region of China.
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Affiliation(s)
- Xing Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Liu Yang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Lingyun Hou
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Xingbo Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
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15
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Cubric‐Curik V, Novosel D, Brajkovic V, Rota Stabelli O, Krebs S, Sölkner J, Šalamon D, Ristov S, Berger B, Trivizaki S, Bizelis I, Ferenčaković M, Rothammer S, Kunz E, Simčič M, Dovč P, Bunevski G, Bytyqi H, Marković B, Brka M, Kume K, Stojanović S, Nikolov V, Zinovieva N, Schönherz AA, Guldbrandtsen B, Čačić M, Radović S, Miracle P, Vernesi C, Curik I, Medugorac I. Large‐scale mitogenome sequencing reveals consecutive expansions of domestic taurine cattle and supports sporadic aurochs introgression. Evol Appl 2021; 15:663-678. [PMID: 35505892 PMCID: PMC9046920 DOI: 10.1111/eva.13315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 10/01/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Vlatka Cubric‐Curik
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Dinko Novosel
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
- Department of Pathology Croatian Veterinary Institute Zagreb Croatia
| | - Vladimir Brajkovic
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Omar Rota Stabelli
- Department of Sustainable Agro‐Ecosystems and Bioresources, Research and Innovation Centre Fondazione Edmund Mach S. Michele all' Adige Italy
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis Gene Center Ludwig Maximilians University Munich Munich Germany
| | - Johann Sölkner
- Division of Livestock Sciences Department of Sustainable Agricultural Systems BOKU‐University of Natural Resources and Life Sciences Vienna Vienna Austria
| | - Dragica Šalamon
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | | | - Beate Berger
- AREC Raumberg‐Gumpenstein Institute of Organic Farming and Biodiversity of Farm Animals Thalheim Austria
| | | | - Iosif Bizelis
- Faculty of Animal Science and Aquaculture Department of Animal Breeding & Husbandry Agricultural University of Athens Athens Greece
| | - Maja Ferenčaković
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Sophie Rothammer
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
| | - Elisabeth Kunz
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
| | - Mojca Simčič
- Biotechnical Faculty Department of Animal Science University of Ljubljana Ljubljana Slovenia
| | - Peter Dovč
- Biotechnical Faculty Department of Animal Science University of Ljubljana Ljubljana Slovenia
| | - Gojko Bunevski
- Faculty of Agricultural Sciences and Food University Ss. Cyril and Methodius Skopje Macedonia
| | - Hysen Bytyqi
- Faculty of Agriculture and Veterinary Department of Animal Science University of Prishtina Prishtina Kosovo
| | - Božidarka Marković
- Biotechnical Faculty Department of Livestock Science University of Montenegro Podgorica Montenegro
| | - Muhamed Brka
- Faculty of Agriculture and Food Science Institute of Animal Sciences University of Sarajevo Sarajevo Bosnia and Herzegovina
| | | | - Srđan Stojanović
- Ministry of Agriculture, Forestry and Water Management Beograd Serbia
| | - Vasil Nikolov
- Executive Agency for Selection and Reproduction in Animal Breeding Sofia Bulgaria
| | - Natalia Zinovieva
- Center of Biotechnology and Molecular Diagnostics of the L.K. Ernst Institute of Animal Husbandry Moscow Region Russia
| | | | - Bernt Guldbrandtsen
- Department of Animal Sciences Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Mato Čačić
- Croatian Agricultural Agency Zagreb Croatia
| | - Siniša Radović
- Institute for Quaternary Palaeontology and Geology Croatian Academy of Sciences and Arts Zagreb Croatia
| | - Preston Miracle
- Department of Archaeology University of Cambridge Cambridge UK
| | - Cristiano Vernesi
- Department of Sustainable Agro‐Ecosystems and Bioresources, Research and Innovation Centre Fondazione Edmund Mach S. Michele all' Adige Italy
| | - Ino Curik
- Department of Animal Science University of Zagreb Faculty of Agriculture Zagreb Croatia
| | - Ivica Medugorac
- Population Genomics Group Faculty of Veterinary Medicine Department of Veterinary Sciences LMU Munich Munich Germany
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16
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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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17
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Roberts NJ, Zhang Y, Convery I, Liang X, Smith D, Jiang G. Cattle Grazing Effects on Vegetation and Wild Ungulates in the Forest Ecosystem of a National Park in Northeastern China. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.680367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is evidence that cattle grazing in forests limits big cat abundance. There is concern, too, about competition with wild ungulate prey through bottom-up effects on vegetation. Hence, there have been calls to remove or control forest livestock grazing in aid of restoring endangered large carnivores and their prey. To help inform scientific debate and decision making, we explored cattle-vegetation-prey dynamics in Northeast Tiger and Leopard National Park, northeast China and present a reappraisal of livestock grazing in the context of coexistence and an integrated approach to land use in China. Inside long-term forest grazing enclosures, wild boar (Sus scrofa) density increased with cattle density. Roe deer (Capreolus pygargus) density and occurrence probability of wild boar and roe deer were not influenced by cattle density. Wild ungulate densities were not related with the number of annual shoots, i.e., forage plant abundance. The presence/absence and abundance of annual shoots was not related with cattle density. Wild ungulate density had mixed associations with vegetation structure; arbor tree diameter at breast height (DBH) and habitat “openness” increased with cattle density. Finally, inside and outside enclosures had different vegetation characteristics and wild boar densities, while roe deer densities were equal. We conclude that cattle density and associated changes to vegetation have positive, negative, and neutral effects on two wild ungulate prey species. Each of these factors warrant consideration in evidence-based management decisions in regard to regulating ungulate community composition to support different large predators as preferred prey in core areas and corridors of habitats.
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18
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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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19
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Gurke M, Vidal-Gorosquieta A, Pajimans JLA, Wȩcek K, Barlow A, González-Fortes G, Hartmann S, Grandal-d’Anglade A, Hofreiter M. Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence. PLoS One 2021; 16:e0249537. [PMID: 33909617 PMCID: PMC8081239 DOI: 10.1371/journal.pone.0249537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/21/2021] [Indexed: 11/19/2022] Open
Abstract
Domestic cattle were brought to Spain by early settlers and agricultural societies. Due to missing Neolithic sites in the Spanish region of Galicia, very little is known about this process in this region. We sampled 18 cattle subfossils from different ages and different mountain caves in Galicia, of which 11 were subject to sequencing of the mitochondrial genome and phylogenetic analysis, to provide insight into the introduction of cattle to this region. We detected high similarity between samples from different time periods and were able to compare the time frame of the first domesticated cattle in Galicia to data from the connecting region of Cantabria to show a plausible connection between the Neolithization of these two regions. Our data shows a close relationship of the early domesticated cattle of Galicia and modern cow breeds and gives a general insight into cattle phylogeny. We conclude that settlers migrated to this region of Spain from Europe and introduced common European breeds to Galicia.
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Affiliation(s)
- Marie Gurke
- Institute of Biochemistry & Biology, University of Potsdam, Potsdam, Germany
| | | | - Johanna L. A. Pajimans
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Karolina Wȩcek
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, Kraków, Poland
| | - Axel Barlow
- School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | | | - Stefanie Hartmann
- Institute of Biochemistry & Biology, University of Potsdam, Potsdam, Germany
| | | | - Michael Hofreiter
- Institute of Biochemistry & Biology, University of Potsdam, Potsdam, Germany
- * E-mail:
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20
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Liu X, Li Z, Yan Y, Li Y, Wu H, Pei J, Yan P, Yang R, Guo X, Lan X. Selection and introgression facilitated the adaptation of Chinese native endangered cattle in extreme environments. Evol Appl 2021; 14:860-873. [PMID: 33767758 PMCID: PMC7980270 DOI: 10.1111/eva.13168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/31/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Although persistent efforts have identified and characterized a few candidate genes and related biological processes with potential functions in the adaptation of many species to extreme environments, few works have been conducted to determine the genomic basis of adaptation in endangered livestock breeds that have been living in extreme conditions for more than thousands of years. To fill this gap, we sequenced the whole genomes of nine individuals from three Chinese native endangered cattle breeds that are living in high-altitude or arid environments. Phylogenetic and evolutionary history analyses of these three and other six breeds showed that the genetic structure of the cattle populations is primarily related to geographic location. Interestingly, we identified pervasive introgression from the yak to Zhangmu cattle (ZMC) that cover several genes (e.g., NOS2, EGLN1 and EPAS1) involved in the hypoxia response and previously identified as positive selection genes in other species, which suggested that the adaptive introgression from yak may have contributed to the adaptation of ZMC to high-altitude environments. In addition, by contrasting the breeds in opposite living conditions, we revealed a set of candidate genes with various functions from hypoxia response, water metabolism, immune response and body shape change to embryo development and skeletal system development, etc., that may be related to high-altitude or arid adaptation. Our research provides new insights into the recovery and adaptation of endangered native cattle and other species in extreme environments and valuable resources for future research on animal husbandry to cope with climate change.
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Affiliation(s)
- Xinfeng Liu
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Zhaohong Li
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Yubin Yan
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Ye Li
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Hui Wu
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Jie Pei
- Lanzhou Institute of Husbandry and Pharmaceutical SciencesChinese Academy of Agricultural SciencesLanzhouChina
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical SciencesChinese Academy of Agricultural SciencesLanzhouChina
| | - Ruolin Yang
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Xian Guo
- Lanzhou Institute of Husbandry and Pharmaceutical SciencesChinese Academy of Agricultural SciencesLanzhouChina
| | - Xianyong Lan
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
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21
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Mannen H, Yonezawa T, Murata K, Noda A, Kawaguchi F, Sasazaki S, Olivieri A, Achilli A, Torroni A. Cattle mitogenome variation reveals a post-glacial expansion of haplogroup P and an early incorporation into northeast Asian domestic herds. Sci Rep 2020; 10:20842. [PMID: 33257722 PMCID: PMC7704668 DOI: 10.1038/s41598-020-78040-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022] Open
Abstract
Surveys of mitochondrial DNA (mtDNA) variation have shown that worldwide domestic cattle are characterized by just a few major haplogroups. Two, T and I, are common and characterize Bos taurus and Bos indicus, respectively, while the other three, P, Q and R, are rare and are found only in taurine breeds. Haplogroup P is typical of extinct European aurochs, while intriguingly modern P mtDNAs have only been found in northeast Asian cattle. These Asian P mtDNAs are extremely rare with the exception of the Japanese Shorthorn breed, where they reach a frequency of 45.9%. To shed light on the origin of this haplogroup in northeast Asian cattle, we completely sequenced 14 Japanese Shorthorn mitogenomes belonging to haplogroup P. Phylogenetic and Bayesian analyses revealed: (1) a post-glacial expansion of aurochs carrying haplogroup P from Europe to Asia; (2) that all Asian P mtDNAs belong to a single sub-haplogroup (P1a), so far never detected in either European or Asian aurochs remains, which was incorporated into domestic cattle of continental northeastern Asia possibly ~ 3700 years ago; and (3) that haplogroup P1a mtDNAs found in the Japanese Shorthorn breed probably reached Japan about 650 years ago from Mongolia/Russia, in agreement with historical evidence.
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Affiliation(s)
- Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan.
| | - Takahiro Yonezawa
- Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Japan
| | - Kako Murata
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Aoi Noda
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Fuki Kawaguchi
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Shinji Sasazaki
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
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22
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Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
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Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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23
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Verdugo MP, Mullin VE, Scheu A, Mattiangeli V, Daly KG, Maisano Delser P, Hare AJ, Burger J, Collins MJ, Kehati R, Hesse P, Fulton D, Sauer EW, Mohaseb FA, Davoudi H, Khazaeli R, Lhuillier J, Rapin C, Ebrahimi S, Khasanov M, Vahidi SMF, MacHugh DE, Ertuğrul O, Koukouli-Chrysanthaki C, Sampson A, Kazantzis G, Kontopoulos I, Bulatovic J, Stojanović I, Mikdad A, Benecke N, Linstädter J, Sablin M, Bendrey R, Gourichon L, Arbuckle BS, Mashkour M, Orton D, Horwitz LK, Teasdale MD, Bradley DG. Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent. SCIENCE (NEW YORK, N.Y.) 2020; 365:173-176. [PMID: 31296769 DOI: 10.1126/science.aav1002] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 06/14/2019] [Indexed: 11/02/2022]
Abstract
Genome-wide analysis of 67 ancient Near Eastern cattle, Bos taurus, remains reveals regional variation that has since been obscured by admixture in modern populations. Comparisons of genomes of early domestic cattle to their aurochs progenitors identify diverse origins with separate introgressions of wild stock. A later region-wide Bronze Age shift indicates rapid and widespread introgression of zebu, Bos indicus, from the Indus Valley. This process was likely stimulated at the onset of the current geological age, ~4.2 thousand years ago, by a widespread multicentury drought. In contrast to genome-wide admixture, mitochondrial DNA stasis supports that this introgression was male-driven, suggesting that selection of arid-adapted zebu bulls enhanced herd survival. This human-mediated migration of zebu-derived genetics has continued through millennia, altering tropical herding on each continent.
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Affiliation(s)
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland.,Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Amelie Scheu
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland.,Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Kevin G Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Pierpaolo Maisano Delser
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland.,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Andrew J Hare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Matthew J Collins
- BioArCh, University of York, York YO10 5DD, UK.,Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
| | - Ron Kehati
- 448 Shvil Hachalav Street, Nir Banim 7952500, Israel
| | - Paula Hesse
- Jewish Studies Program, Department of Classics and Ancient Mediterranean Studies, The Pennsylvania State University, University Park, PA 16802, USA
| | - Deirdre Fulton
- Department of Religion, Baylor University, Waco, TX 76798, USA
| | - Eberhard W Sauer
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Fatemeh A Mohaseb
- Archéozoologie et Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France.,Bioarchaeology Laboratory, Central Laboratory, University of Tehran, 1417634934 Tehran, Iran
| | - Hossein Davoudi
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, 1417634934 Tehran, Iran.,Osteology Department, National Museum of Iran, 1136918111 Tehran, Iran.,Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, 111-14115 Tehran, Iran
| | - Roya Khazaeli
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, 1417634934 Tehran, Iran
| | - Johanna Lhuillier
- Archéorient Université Lyon 2, CNRS UMR 5133, Maison de l'Orient et de la Méditerranée, 69365 Lyon, France
| | - Claude Rapin
- Archéologie d'Orient et d'Occident (AOROC, UMR 8546, CNRS ENS), Centre d'archéologie, 75005 Paris, France
| | - Saeed Ebrahimi
- Faculty of Literature and Humanities, Islamic Azad University, 1711734353 Tehran, Iran
| | - Mutalib Khasanov
- Uzbekistan Institute of Archaeology of the Academy of Sciences of the Republic of Uzbekistan, 703051 Samarkand, Uzbekistan
| | - S M Farhad Vahidi
- Agricultural Biotechnology Research Institute of Iran-North branch (ABRII), Agricultural Research, Education and Extension Organization, 4188958883 Rasht, Iran
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin D04 V1W8, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin D04 V1W8, Ireland
| | - Okan Ertuğrul
- Veterinary Faculty, Ankara University, 06110 Ankara, Turkey
| | - Chaido Koukouli-Chrysanthaki
- Hellenic Ministry of Culture and Sports, Department of Prehistoric and Classical Antiquities, and Museums, Serres 62 122, Greece
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of the Aegean, 85132 Rhodes, Greece
| | - George Kazantzis
- Archaeological Museum of Aeani, 500 04, Kozani, Western Macedonia, Greece
| | | | - Jelena Bulatovic
- Laboratory for Bioarchaeology, Department of Archaeology, University of Belgrade, 11000 Belgrade, Serbia
| | | | - Abdesalam Mikdad
- Institut National des Sciences de l'Archéologie et du Patrimoine de Maroc (INSAP) Hay Riad, Madinat al Ifrane, Rabat Instituts, 10000 Rabat, Morocco
| | - Norbert Benecke
- Department of Natural Sciences, German Archaeological Institute, 14195 Berlin, Germany
| | - Jörg Linstädter
- Deutsches Archäologisches Institut, Kommission für Archäologie Außereuropäischer Kulturen (KAAK), 53173 Bonn, Germany
| | - Mikhail Sablin
- Zoological Institute of the Russian Academy of Sciences, 199034 St Petersburg, Russia
| | - Robin Bendrey
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK.,Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Lionel Gourichon
- Université Côte d'Azur, CNRS, CEPAM (UMR 7264), 06357 Nice, France
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marjan Mashkour
- Archéozoologie et Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France.,Bioarchaeology Laboratory, Central Laboratory, University of Tehran, 1417634934 Tehran, Iran.,Osteology Department, National Museum of Iran, 1136918111 Tehran, Iran
| | - David Orton
- BioArCh, University of York, York YO10 5DD, UK
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, 9190401 Jerusalem, Israel
| | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland.,BioArCh, University of York, York YO10 5DD, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland.
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24
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Robins A. The Alpha Hypothesis: Did Lateralized Cattle-Human Interactions Change the Script for Western Culture? Animals (Basel) 2019; 9:E638. [PMID: 31480488 PMCID: PMC6769460 DOI: 10.3390/ani9090638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/16/2019] [Accepted: 08/27/2019] [Indexed: 11/16/2022] Open
Abstract
Domestic cattle possess lateralized cognitive processing of human handlers. This has been recently demonstrated in the preference for large groups of cattle to view a human closely within the predominantly left visual field. By contrast, the same stimulus viewed predominantly within the right visual field promotes a significantly greater frequency of dispersal from a standing position, including flight responses. The respective sets of behaviours correspond with the traditional terms of "near side" for the left side of cattle and horses, and the "off" or "far side" for the right side. These traditional terms of over 300 years usage in the literature communicate functional practicalities for handling livestock and the recognition of lateralized cognitive processing. In this review, the possibility of even earlier recognition and the significance of laterality in cattle-human interaction was argued, from the earliest representations of the letter "A", originally illustrated from nearly 4000 years before the present time as the head of an ox as viewed not from the front or from the right, but from the left (near) side. By extension, this knowledge of lateralization in cattle may represent the earliest written example of applied ethology-the study of the behaviour of animals under human management.
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Affiliation(s)
- Andrew Robins
- Centre for Animal Welfare and Ethics, School of Veterinary Science, University of Queensland, Gatton Campus, Gatton, Queensland 4343, Australia.
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25
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Yudin NS, Larkin DM. Whole genome studies of origin, selection and adaptation of the Russian cattle breeds. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.525] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Our review presents several recent studies on the genetic history and signatures of selection in genomes of the native Russian cattle breeds. Most of these works are not easily accessible for the Russian-speaking audience. We describe the origins of appearance of the Russian cattle breeds from the genetics perspective. We point to the links between most of the Russian breeds with the taurine breeds of the European origin and for some Russian breeds with the breeds of the Asian origin. We describe major phylogenetic clusters of the Russian breeds and point to those that still maintain their unique genetics, meaning that their preservation is a priority. In addition, we review the results of the search for signatures of selection in genomes of the Russian cattle breeds. Some unique signatures of selection present in the genomes of so-called “turano-mongolian” cattle (i. e. the Yakut cattle) are described which allowed the Yakut cattle to adapt to harsh environments found above the Polar Circle. Signatures of selection which could help other cattle breeds of the Russian origin to adapt to various climatic condition of the Russian Federation are reviewed. The Russian cattle genomes also contain known signatures of selection related to cattle domestication about 8–10 thousand years ago. The most profound ones include genes related to changes of the coat colour. This phenotype in many cases could be related to the distinction of the first domesticated populations and lead to the formation of so-called land races (primitive breeds). Whole-genome association studies of Russian cattle breeds pointed to a novel gene which could be related to the “white-faced” phenotype and to a gene which is related to body temperature support under the acute cold stress. The data presented in our review could be used for identification of genetic markers to focus on in future efforts on designing new highly productive cattle breeds adapted to climates of the Russian Federation and other countries with similar climates.
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Affiliation(s)
| | - D. M. Larkin
- Royal Veterinary College, University of London; Institute of Cytology and Genetics, SB RAS
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26
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Weldenegodguad M, Popov R, Pokharel K, Ammosov I, Ming Y, Ivanova Z, Kantanen J. Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions. Front Genet 2019; 9:728. [PMID: 30687392 PMCID: PMC6336893 DOI: 10.3389/fgene.2018.00728] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/22/2018] [Indexed: 12/30/2022] Open
Abstract
Northern Fennoscandia and the Sakha Republic in the Russian Federation represent the northernmost regions on Earth where cattle farming has been traditionally practiced. In this study, we performed whole-genome sequencing to genetically characterize three rare native breeds Eastern Finncattle, Western Finncattle and Yakutian cattle adapted to these northern Eurasian regions. We examined the demographic history, genetic diversity and unfolded loci under natural or artificial selection. On average, we achieved 13.01-fold genome coverage after mapping the sequencing reads on the bovine reference genome (UMD 3.1) and detected a total of 17.45 million single nucleotide polymorphisms (SNPs) and 1.95 million insertions-deletions (indels). We observed that the ancestral species (Bos primigenius) of Eurasian taurine cattle experienced two notable prehistorical declines in effective population size associated with dramatic climate changes. The modern Yakutian cattle exhibited a higher level of within-population variation in terms of number of SNPs and nucleotide diversity than the contemporary European taurine breeds. This result is in contrast to the results of marker-based cattle breed diversity studies, indicating assortment bias in previous analyses. Our results suggest that the effective population size of the ancestral Asiatic taurine cattle may have been higher than that of the European cattle. Alternatively, our findings could indicate the hybrid origins of the Yakutian cattle ancestries and possibly the lack of intensive artificial selection. We identified a number of genomic regions under selection that may have contributed to the adaptation to the northern and subarctic environments, including genes involved in disease resistance, sensory perception, cold adaptation and growth. By characterizing the native breeds, we were able to obtain new information on cattle genomes and on the value of the adapted breeds for the conservation of cattle genetic resources.
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Affiliation(s)
- Melak Weldenegodguad
- Department of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ruslan Popov
- Yakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), Yakutsk, Russia
| | - Kisun Pokharel
- Department of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Innokentyi Ammosov
- Board of Agricultural Office of Eveno-Bytantaj Region, Batagay-Alyta, Russia
| | - Yao Ming
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | - Zoya Ivanova
- Yakutian Research Institute of Agriculture (FGBNU Yakutskij NIISH), Yakutsk, Russia
| | - Juha Kantanen
- Department of Production Systems, Natural Resources Institute Finland (Luke), Helsinki, Finland
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27
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Renaud G, Schubert M, Sawyer S, Orlando L. Authentication and Assessment of Contamination in Ancient DNA. Methods Mol Biol 2019; 1963:163-194. [PMID: 30875054 DOI: 10.1007/978-1-4939-9176-1_17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Contamination from both present-day humans and postmortem microbial sources is a common challenge in ancient DNA studies. Here we present a suite of tools to assist in the assessment of contamination in ancient DNA data sets. These tools perform standard tests of authenticity of ancient DNA data including detecting the presence of postmortem damage signatures in sequence alignments and quantifying the amount of present-day human contamination.
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Affiliation(s)
- Gabriel Renaud
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Susanna Sawyer
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark.
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, University Paul Sabatier, Toulouse, France.
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28
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Cai Y, Jiao T, Lei Z, Liu L, Zhao S. Maternal genetic and phylogenetic characteristics of domesticated cattle in northwestern China. PLoS One 2018; 13:e0209645. [PMID: 30589861 PMCID: PMC6307701 DOI: 10.1371/journal.pone.0209645] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 12/10/2018] [Indexed: 11/19/2022] Open
Abstract
Northwestern China, an important part of the Silk Road, was the birthplace of the Zhouzu farming culture. The domestication of cattle as an important aspect of farming culture has had a long history in northwestern China. In this study, we assessed the maternal structure and phylogeny of cattle by analyzing the mitochondrial DNA hypervariable segment I (HVS-I) in 698 native cattle from eight areas of northwestern China. The phylogenetic analyses revealed two highly divergent mtDNA clades: clade T, which had four sub-clades (Ta—Td), and clade I. The cattle domesticated from Bos taurus showed a clear dominant distribution pattern in northwestern China. The nucleotide diversity of the Bos indicus clade was lower than that of clades from Bos taurus. In summary, our results suggest that the native cattle of northwestern China were domesticated from two different maternal ancestors, Bos taurus and Bos indicus, which migrated to the central plains of China from the north and south, respectively, with Bos taurus remaining at the edges of the region. The population expansion of the cattle domesticated from Bos taurus occurred in the Longdong region of Gansu Province, and these cattle formed four relatively independent evolutionary branches. Subsequent to this expansion event, Bos indicus migrated from southern to northern China.
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Affiliation(s)
- Yuan Cai
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, PR China
| | - Ting Jiao
- College of Grassland, Gansu Agricultural University, Lanzhou, Gansu, PR China
| | - Zhaomin Lei
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, PR China
| | - Li Liu
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, PR China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, Gansu, PR China
- * E-mail:
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29
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Xu L, Zhang W, Shen H, Zhang Y, Zhao Y, Jia Y, Gao X, Zhu B, Xu L, Zhang L, Gao H, Li J, Chen Y. Genome-wide scanning reveals genetic diversity and signatures of selection in Chinese indigenous cattle breeds. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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30
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Yurchenko AA, Daetwyler HD, Yudin N, Schnabel RD, Vander Jagt CJ, Soloshenko V, Lhasaranov B, Popov R, Taylor JF, Larkin DM. Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation. Sci Rep 2018; 8:12984. [PMID: 30154520 PMCID: PMC6113280 DOI: 10.1038/s41598-018-31304-w] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/16/2018] [Indexed: 01/08/2023] Open
Abstract
Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data to other breeds of European and Asian origins we found known and novel candidate genes that could potentially be related to domestication, economically important traits and environmental adaptations in cattle. The Russian cattle breed genomes contained regions under putative selection with genes that may be related to adaptations to harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic signatures of selective sweeps near key genes related to economically important traits, such as the milk production (e.g., DGAT1, ABCG2), growth (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate genes which should be included in future studies attempting to identify genes to improve the extant breeds and facilitate generation of commercial breeds that fit better into the environments of Russia and other countries with similar climates.
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Affiliation(s)
- Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, 3083, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, 3083, Victoria, Australia
| | - Nikolay Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211-5300, USA
| | - Christy J Vander Jagt
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, 3083, Victoria, Australia
| | | | | | - Ruslan Popov
- Yakutian Research Institute of Agriculture, 677001, Yakutsk, Russia
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211-5300, USA
| | - Denis M Larkin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090, Novosibirsk, Russia.
- Royal Veterinary College, University of London, NW01 0TU, London, UK.
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31
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Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia. Nat Commun 2018; 9:2337. [PMID: 29904051 PMCID: PMC6002414 DOI: 10.1038/s41467-018-04737-0] [Citation(s) in RCA: 185] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 05/10/2018] [Indexed: 02/07/2023] Open
Abstract
Cattle domestication and the complex histories of East Asian cattle breeds warrant further investigation. Through analysing the genomes of 49 modern breeds and eight East Asian ancient samples, worldwide cattle are consistently classified into five continental groups based on Y-chromosome haplotypes and autosomal variants. We find that East Asian cattle populations are mainly composed of three distinct ancestries, including an earlier East Asian taurine ancestry that reached China at least ~3.9 kya, a later introduced Eurasian taurine ancestry, and a novel Chinese indicine ancestry that diverged from Indian indicine approximately 36.6–49.6 kya. We also report historic introgression events that helped domestic cattle from southern China and the Tibetan Plateau achieve rapid adaptation by acquiring ~2.93% and ~1.22% of their genomes from banteng and yak, respectively. Our findings provide new insights into the evolutionary history of cattle and the importance of introgression in adaptation of cattle to new environmental challenges in East Asia. There are various indigenous cattle breeds in East Asia which have a complex history. Here, the authors analyse the genomes of 49 modern breeds and eight ancient samples and identify three distinct ancestries and multiple adaptive introgressions from other bovine species.
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32
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Yudin NS, Belonogova NM, Larkin DM. Genes related to the white face colour pattern in eight Russian cattle breeds. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
One of the major effects of domestication is change of animal coat colour to up to complete white colour of the whole body. It is possible that white colour of livestock animals had aesthetic significance for humans as well. The first step towards detection of genes and mutations controlling white colouring in animals is the genome-wide association studies. These studies, however, have not been done for the cattle breeds native to the Russian Federation. The aim of this study was therefore to identify genomic intervals and candidate genes that could be responsible for white face colouring in eight Russian cattle breeds. The data on genome-wide genotyping of 131,709 high-quality single nucleotide polymorphisms (SNPs) on 148 animas have been used in the program EMMAX. Association analysis has been performed using two related phenotypes: a) the white face with the rest of the body of any colour and b) white face with the rest of the body of different (non-white) colour. In the first case, the only statistically significant marker found was the SNP BovineHD0500019319 located on cattle chromosome (BTA) 5. The same SNP was the most significant within the cluster of three SNPs on BTA5: 68,803,879–69,365,854 associated also with the second phenotype. Five genes were found within this interval in the cattle genome, out of which the most likely functional candidate was SLC41A2, with the SNP BovineHD0500019319 found within its intronic sequence. SLC41A2 encodes a magnesium transporter protein. However, the function of this gene is not well established. Other members of this gene family are the key genes controlling differences in human skin and animal coat colour. Additional significant association signals with the second phenotype have been detected in BTA 1–4, 6–15, 18, 19, 24, 27, and 29. Overall, 37 genomic intervals have been detected associated with white face colouring in eight Russian native cattle breeds.
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Affiliation(s)
- N. S. Yudin
- Institute of Cytology and Genetics SB RAS; Novosibirsk State University
| | | | - D. M. Larkin
- Institute of Cytology and Genetics SB RAS; Royal Veterinary College, University of London
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33
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Taron UH, Lell M, Barlow A, Paijmans JLA. Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool. Genes (Basel) 2018. [PMID: 29533977 PMCID: PMC5867878 DOI: 10.3390/genes9030157] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present 'TAPAS', (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material.
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Affiliation(s)
- Ulrike H Taron
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
| | - Moritz Lell
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
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34
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The mtDNA haplogroup P of modern Asian cattle: A genetic legacy of Asian aurochs? PLoS One 2018; 13:e0190937. [PMID: 29304129 PMCID: PMC5755918 DOI: 10.1371/journal.pone.0190937] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/22/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Aurochs (Bos primigenius) were distributed throughout large parts of Eurasia and Northern Africa during the late Pleistocene and the early Holocene, and all modern cattle are derived from the aurochs. Although the mtDNA haplogroups of most modern cattle belong to haplogroups T and I, several additional haplogroups (P, Q, R, C and E) have been identified in modern cattle and aurochs. Haplogroup P was the most common haplogroup in European aurochs, but so far, it has been identified in only three of >3,000 submitted haplotypes of modern Asian cattle. METHODOLOGY We sequenced the complete mtDNA D-loop region of 181 Japanese Shorthorn cattle and analyzed these together with representative bovine mtDNA sequences. The haplotype P of Japanese Shorthorn cattle was analyzed along with that of 36 previously published European aurochs and three modern Asian cattle sequences using the hypervariable 410 bp of the D-loop region. CONCLUSIONS We detected the mtDNA haplogroup P in Japanese Shorthorn cattle with an extremely high frequency (83/181). Phylogenetic networks revealed two main clusters, designated as Pa for haplogroup P in European aurochs and Pc in modern Asian cattle. We also report the genetic diversity of haplogroup P compared with the sequences of extinct aurochs. No shared haplotypes are observed between the European aurochs and the modern Asian cattle. This finding suggests the possibility of local and secondary introgression events of haplogroup P in northeast Asian cattle, and will contribute to a better understanding of its origin and genetic diversity.
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Mei C, Wang H, Liao Q, Wang L, Cheng G, Wang H, Zhao C, Zhao S, Song J, Guang X, Liu GE, Li A, Wu X, Wang C, Fang X, Zhao X, Smith SB, Yang W, Tian W, Gui L, Zhang Y, Hill RA, Jiang Z, Xin Y, Jia C, Sun X, Wang S, Yang H, Wang J, Zhu W, Zan L. Genetic Architecture and Selection of Chinese Cattle Revealed by Whole Genome Resequencing. Mol Biol Evol 2017; 35:688-699. [PMID: 29294071 DOI: 10.1093/molbev/msx322] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The bovine genetic resources in China are diverse, but their value and potential are yet to be discovered. To determine the genetic diversity and population structure of Chinese cattle, we analyzed the whole genomes of 46 cattle from six phenotypically and geographically representative Chinese cattle breeds, together with 18 Red Angus cattle genomes, 11 Japanese black cattle genomes and taurine and indicine genomes available from previous studies. Our results showed that Chinese cattle originated from hybridization between Bos taurus and Bos indicus. Moreover, we found that the level of genetic variation in Chinese cattle depends upon the degree of indicine content. We also discovered many potential selective sweep regions associated with domestication related to breed-specific characteristics, with selective sweep regions including genes associated with coat color (ERCC2, MC1R, ZBTB17, and MAP2K1), dairy traits (NCAPG, MAPK7, FST, ITFG1, SETMAR, PAG1, CSN3, and RPL37A), and meat production/quality traits (such as BBS2, R3HDM1, IGFBP2, IGFBP5, MYH9, MYH4, and MC5R). These findings substantially expand the catalogue of genetic variants in cattle and reveal new insights into the evolutionary history and domestication traits of Chinese cattle.
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Affiliation(s)
- Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hongcheng Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qijun Liao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chunping Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | | | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, Maryland, USA
| | | | - George E Liu
- Animal Genomics and Improvement Laboratory, USDA-ARS, Maryland, USA
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xueli Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | | | - Xin Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Department of Animal Science, McGill University, Montreal, Canada
| | - Stephen B Smith
- Department of Animal Science, Texas A&M University, Texas, USA
| | - Wucai Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wanqiang Tian
- Yangling Vocational & Technical College, Yangling, China
| | - Linsheng Gui
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yingying Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Rodney A Hill
- School of Biomedical Sciences, Charles Sturt University, New South Wales, Australia
| | - Zhongliang Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yaping Xin
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Cunling Jia
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiuzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shuhui Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | | | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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36
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MacHugh DE, Larson G, Orlando L. Taming the Past: Ancient DNA and the Study of Animal Domestication. Annu Rev Anim Biosci 2016; 5:329-351. [PMID: 27813680 DOI: 10.1146/annurev-animal-022516-022747] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the last decade, ancient DNA research has been revolutionized by the availability of increasingly powerful DNA sequencing and ancillary genomics technologies, giving rise to the new field of paleogenomics. In this review, we show how our understanding of the genetic basis of animal domestication and the origins and dispersal of livestock and companion animals during the Upper Paleolithic and Neolithic periods is being rapidly transformed through new scientific knowledge generated with paleogenomic methods. These techniques have been particularly informative in revealing high-resolution patterns of artificial and natural selection and evidence for significant admixture between early domestic animal populations and their wild congeners.
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Affiliation(s)
- David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland; .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, United Kingdom;
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark; .,Université de Toulouse, University Paul Sabatier, Laboratoire AMIS, CNRS UMR 5288, 31000 Toulouse, France
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37
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O'Sullivan NJ, Teasdale MD, Mattiangeli V, Maixner F, Pinhasi R, Bradley DG, Zink A. A whole mitochondria analysis of the Tyrolean Iceman's leather provides insights into the animal sources of Copper Age clothing. Sci Rep 2016; 6:31279. [PMID: 27537861 PMCID: PMC4989873 DOI: 10.1038/srep31279] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 07/15/2016] [Indexed: 02/07/2023] Open
Abstract
The attire of the Tyrolean Iceman, a 5,300-year-old natural mummy from the Ötzal Italian Alps, provides a surviving example of ancient manufacturing technologies. Research into his garments has however, been limited by ambiguity surrounding their source species. Here we present a targeted enrichment and sequencing of full mitochondrial genomes sampled from his clothes and quiver, which elucidates the species of production for nine fragments. Results indicate that the majority of the samples originate from domestic ungulate species (cattle, sheep and goat), whose recovered haplogroups are now at high frequency in today’s domestic populations. Intriguingly, the hat and quiver samples were produced from wild species, brown bear and roe deer respectively. Combined, these results suggest that Copper Age populations made considered choices of clothing material from both the wild and domestic populations available to them. Moreover, these results show the potential for the recovery of complete mitochondrial genomes from degraded prehistoric artefacts.
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Affiliation(s)
- Niall J O'Sullivan
- Institute for Mummies and the Iceman, EURAC research, 39100 Bolzano, Italy.,School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Matthew D Teasdale
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Frank Maixner
- Institute for Mummies and the Iceman, EURAC research, 39100 Bolzano, Italy
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Daniel G Bradley
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Albert Zink
- Institute for Mummies and the Iceman, EURAC research, 39100 Bolzano, Italy
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38
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Mohandesan E, Speller CF, Peters J, Uerpmann HP, Uerpmann M, De Cupere B, Hofreiter M, Burger PA. Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel. Mol Ecol Resour 2016; 17:300-313. [PMID: 27289015 PMCID: PMC5324683 DOI: 10.1111/1755-0998.12551] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/28/2016] [Accepted: 05/06/2016] [Indexed: 12/29/2022]
Abstract
The performance of hybridization capture combined with next‐generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient‐domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187‐fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient‐domestic dromedaries with 17–95% length coverage and 1.27–47.1‐fold read depths for the covered regions. Using whole‐genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1–1.06‐fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.
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Affiliation(s)
- Elmira Mohandesan
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria.,Institute of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Joris Peters
- Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität München (LMU Munich), 80539, Munich, Germany.,Staatliche Naturwissenschaftliche Sammlungen Bayerns, Bavarian State Collection of Anthropology and Palaeoanatomy, 80333, Munich, Germany
| | - Hans-Peter Uerpmann
- Abteilung Archäozoologie, Institut für Naturwissenschaftliche Archäologie, Eberhard-Karls-Universität Tübingen, Rümelinstrasse 23, 7207, Tübingen, Germany
| | - Margarethe Uerpmann
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, Bavarian State Collection of Anthropology and Palaeoanatomy, 80333, Munich, Germany
| | - Bea De Cupere
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000, Brussels, Belgium
| | - Michael Hofreiter
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK.,Evolutionary and Adaptive Genomics, Department of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Street 24-25, Potsdam, 14476, Germany
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria
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Gasc C, Peyretaillade E, Peyret P. Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms. Nucleic Acids Res 2016; 44:4504-18. [PMID: 27105841 PMCID: PMC4889952 DOI: 10.1093/nar/gkw309] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/07/2016] [Accepted: 04/12/2016] [Indexed: 12/25/2022] Open
Abstract
The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. Among these strategies, hybridization capture has proven to be an innovative and efficient tool for targeting and enriching specific biomarkers in complex DNA mixtures. It has been successfully applied in numerous areas of biology, such as exome resequencing for the identification of mutations underlying Mendelian or complex diseases and cancers, and its usefulness has been demonstrated in the agronomic field through the linking of genetic variants to agricultural phenotypic traits of interest. Moreover, hybridization capture has provided access to underexplored, but relevant fractions of genomes through its ability to enrich defined targets and their flanking regions. Finally, on the basis of restricted genomic information, this method has also allowed the expansion of knowledge of nonreference species and ancient genomes and provided a better understanding of metagenomic samples. In this review, we present the major advances and discoveries permitted by hybridization capture and highlight the potency of this approach in all areas of biology.
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Affiliation(s)
- Cyrielle Gasc
- EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France
| | | | - Pierre Peyret
- EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France
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40
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Olivieri A, Gandini F, Achilli A, Fichera A, Rizzi E, Bonfiglio S, Battaglia V, Brandini S, De Gaetano A, El-Beltagi A, Lancioni H, Agha S, Semino O, Ferretti L, Torroni A. Mitogenomes from Egyptian Cattle Breeds: New Clues on the Origin of Haplogroup Q and the Early Spread of Bos taurus from the Near East. PLoS One 2015; 10:e0141170. [PMID: 26513361 PMCID: PMC4626031 DOI: 10.1371/journal.pone.0141170] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/04/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Genetic studies support the scenario that Bos taurus domestication occurred in the Near East during the Neolithic transition about 10 thousand years (ky) ago, with the likely exception of a minor secondary event in Italy. However, despite the proven effectiveness of whole mitochondrial genome data in providing valuable information concerning the origin of taurine cattle, until now no population surveys have been carried out at the level of mitogenomes in local breeds from the Near East or surrounding areas. Egypt is in close geographic and cultural proximity to the Near East, in particular the Nile Delta region, and was one of the first neighboring areas to adopt the Neolithic package. Thus, a survey of mitogenome variation of autochthonous taurine breeds from the Nile Delta region might provide new insights on the early spread of cattle rearing outside the Near East. METHODOLOGY Using Illumina high-throughput sequencing we characterized the mitogenomes from two cattle breeds, Menofi (N = 17) and Domiaty (N = 14), from the Nile Delta region. Phylogenetic and Bayesian analyses were subsequently performed. CONCLUSIONS Phylogenetic analyses of the 31 mitogenomes confirmed the prevalence of haplogroup T1, similar to most African cattle breeds, but showed also high frequencies for haplogroups T2, T3 and Q1, and an extremely high haplotype diversity, while Bayesian skyline plots pointed to a main episode of population growth ~12.5 ky ago. Comparisons of Nile Delta mitogenomes with those from other geographic areas revealed that (i) most Egyptian mtDNAs are probably direct local derivatives from the founder domestic herds which first arrived from the Near East and the extent of gene flow from and towards the Nile Delta region was limited after the initial founding event(s); (ii) haplogroup Q1 was among these founders, thus proving that it underwent domestication in the Near East together with the founders of the T clades.
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Affiliation(s)
- Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
- * E-mail:
| | - Francesca Gandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, United Kingdom
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Alessandro Fichera
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Ermanno Rizzi
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (Milano), Italy
- Fondazione Telethon, Milano, Italy
| | - Silvia Bonfiglio
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Stefania Brandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Anna De Gaetano
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Ahmed El-Beltagi
- Animal Production Research Institute (APRI), Ministry of Agriculture, Cairo, Egypt
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Saif Agha
- Department of Animal Production, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
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41
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Park SDE, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, Murphy A, Braud M, Donoghue MT, Liu Y, Chamberlain AT, Rue-Albrecht K, Schroeder S, Spillane C, Tai S, Bradley DG, Sonstegard TS, Loftus BJ, MacHugh DE. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biol 2015; 16:234. [PMID: 26498365 PMCID: PMC4620651 DOI: 10.1186/s13059-015-0790-2] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/25/2015] [Indexed: 11/10/2022] Open
Abstract
Background Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0790-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephen D E Park
- IdentiGEN Ltd, Unit 2, Trinity Enterprise Centre, Pearse Street, Dublin 2, Ireland.
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. .,Department of Animal Science, University of Connecticut, Storrs, CT, 06029, USA.
| | - Paul A McGettigan
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | | | - Ceiridwen J Edwards
- Research Laboratory for Archaeology and the History of Art, Dyson Perrins Building, South Parks Rd, Oxford, OX1 3QY, UK.
| | - Amanda J Lohan
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Alison Murphy
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Martin Braud
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Mark T Donoghue
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Yuan Liu
- BGI Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Andrew T Chamberlain
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Kévin Rue-Albrecht
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Steven Schroeder
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA.
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Shuaishuai Tai
- BGI Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland.
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA. .,Recombinetics Inc., St. Paul, MN, 55104, USA.
| | - Brendan J Loftus
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland. .,UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
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42
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Lv FH, Peng WF, Yang J, Zhao YX, Li WR, Liu MJ, Ma YH, Zhao QJ, Yang GL, Wang F, Li JQ, Liu YG, Shen ZQ, Zhao SG, Hehua E, Gorkhali NA, Farhad Vahidi SM, Muladno M, Naqvi AN, Tabell J, Iso-Touru T, Bruford MW, Kantanen J, Han JL, Li MH. Mitogenomic Meta-Analysis Identifies Two Phases of Migration in the History of Eastern Eurasian Sheep. Mol Biol Evol 2015; 32:2515-33. [PMID: 26085518 PMCID: PMC4576706 DOI: 10.1093/molbev/msv139] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Despite much attention, history of sheep (Ovis aries) evolution, including its dating, demographic trajectory and geographic spread, remains controversial. To address these questions, we generated 45 complete and 875 partial mitogenomic sequences, and performed a meta-analysis of these and published ovine mitochondrial DNA sequences (n = 3,229) across Eurasia. We inferred that O. orientalis and O. musimon share the most recent female ancestor with O. aries at approximately 0.790 Ma (95% CI: 0.637-0.934 Ma) during the Middle Pleistocene, substantially predating the domestication event (∼8-11 ka). By reconstructing historical variations in effective population size, we found evidence of a rapid population increase approximately 20-60 ka, immediately before the Last Glacial Maximum. Analyses of lineage expansions showed two sheep migratory waves at approximately 4.5-6.8 ka (lineages A and B: ∼6.4-6.8 ka; C: ∼4.5 ka) across eastern Eurasia, which could have been influenced by prehistoric West-East commercial trade and deliberate mating of domestic and wild sheep, respectively. A continent-scale examination of lineage diversity and approximate Bayesian computation analyses indicated that the Mongolian Plateau region was a secondary center of dispersal, acting as a "transportation hub" in eastern Eurasia: Sheep from the Middle Eastern domestication center were inferred to have migrated through the Caucasus and Central Asia, and arrived in North and Southwest China (lineages A, B, and C) and the Indian subcontinent (lineages B and C) through this region. Our results provide new insights into sheep domestication, particularly with respect to origins and migrations to and from eastern Eurasia.
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Affiliation(s)
- Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wei-Feng Peng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Wen-Rong Li
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ming-Jun Liu
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Yue-Hui Ma
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Qian-Jun Zhao
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Guang-Li Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China College of Life Sciences, Shangqiu Normal University, Shangqiu, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Sheng-Guo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Eer Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Neena A Gorkhali
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council, Kathmandu, Nepal
| | - S M Farhad Vahidi
- Agricultural Biotechnology Research Institute of Iran-North Branch (ABRII), Rasht, Iran
| | - Muhammad Muladno
- Department of Animal Technology and Production Science, Bogor Agricultural University, Darmaga Campus, Bogor, Indonesia
| | - Arifa N Naqvi
- Faculty of Life Sciences, Karakoram International University, Gilgit, Baltistan, Pakistan
| | - Jonna Tabell
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland
| | - Terhi Iso-Touru
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland
| | - Michael W Bruford
- School of Biosciences and Sustainable Places Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland Department of Biology, University of Eastern Finland, Kuopio, Finland
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
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43
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Orlando L, Gilbert MTP, Willerslev E. Reconstructing ancient genomes and epigenomes. Nat Rev Genet 2015; 16:395-408. [PMID: 26055157 DOI: 10.1038/nrg3935] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information, aDNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes.
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Affiliation(s)
- Ludovic Orlando
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark. [2] Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, 37 allées Jules Guesde, 31000 Toulouse, France
| | - M Thomas P Gilbert
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark. [2] Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen 1350C, Denmark
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Zhou L, Wang SB, Jian J, Geng QC, Wen J, Song Q, Wu Z, Li GJ, Liu YQ, Dunwell JM, Zhang J, Feng JY, Niu Y, Zhang L, Ren WL, Zhang YM. Identification of domestication-related loci associated with flowering time and seed size in soybean with the RAD-seq genotyping method. Sci Rep 2015; 5:9350. [PMID: 25797785 PMCID: PMC4369735 DOI: 10.1038/srep09350] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 03/02/2015] [Indexed: 12/02/2022] Open
Abstract
Flowering time and seed size are traits related to domestication. However, identification of domestication-related loci/genes of controlling the traits in soybean is rarely reported. In this study, we identified a total of 48 domestication-related loci based on RAD-seq genotyping of a natural population comprising 286 accessions. Among these, four on chromosome 12 and additional two on chromosomes 11 and 15 were associated with flowering time, and four on chromosomes 11 and 16 were associated with seed size. Of the five genes associated with flowering time and the three genes associated with seed size, three genes Glyma11g18720, Glyma11g15480 and Glyma15g35080 were homologous to Arabidopsis genes, additional five genes were found for the first time to be associated with these two traits. Glyma11g18720 and Glyma05g28130 were co-expressed with five genes homologous to flowering time genes in Arabidopsis, and Glyma11g15480 was co-expressed with 24 genes homologous to seed development genes in Arabidopsis. This study indicates that integration of population divergence analysis, genome-wide association study and expression analysis is an efficient approach to identify candidate domestication-related genes.
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Affiliation(s)
- Ling Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Shi-Bo Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | | | - Qing-Chun Geng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Jia Wen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705, USA
| | | | - Guang-Jun Li
- College of Life Science, Linyi University, Linyi 276005, China
| | - Yu-Qin Liu
- Crop Research Institute, Linyi Academy of Agricultural Sciences, Linyi 276012, China
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Reading RG6 6AR, United Kingdom
| | - Jin Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian-Ying Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuan Niu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen-Long Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuan-Ming Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Der Sarkissian C, Allentoft ME, Ávila-Arcos MC, Barnett R, Campos PF, Cappellini E, Ermini L, Fernández R, da Fonseca R, Ginolhac A, Hansen AJ, Jónsson H, Korneliussen T, Margaryan A, Martin MD, Moreno-Mayar JV, Raghavan M, Rasmussen M, Velasco MS, Schroeder H, Schubert M, Seguin-Orlando A, Wales N, Gilbert MTP, Willerslev E, Orlando L. Ancient genomics. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130387. [PMID: 25487338 PMCID: PMC4275894 DOI: 10.1098/rstb.2013.0387] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.
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Affiliation(s)
- Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - María C Ávila-Arcos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ross Barnett
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Luca Ermini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ruth Fernández
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Rute da Fonseca
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Aurélien Ginolhac
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Hákon Jónsson
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Michael D Martin
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- 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
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval Velasco
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- 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
| | - Nathan Wales
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - 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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Abstract
Ancient mitochondrial DNA has been used in a wide variety of paleontological and archeological studies, ranging from population dynamics of extinct species to patterns of domestication. Most of these studies have traditionally been based on the analysis of short fragments from the mitochondrial control region, analyzed using PCR coupled with Sanger sequencing. With the introduction of high-throughput sequencing, as well as new enrichment technologies, the recovery of full mitochondrial genomes (mitogenomes) from ancient specimens has become significantly less complicated. Here we present a protocol to build ancient extracts into Illumina high-throughput sequencing libraries, and subsequent Agilent array-based capture to enrich for the desired mitogenome. Both are based on previously published protocols, with the introduction of several improvements aimed to increase the recovery of short DNA fragments, while keeping the cost and effort requirements low. This protocol was designed for enrichment of mitochondrial DNA in ancient or other degraded samples. However, the protocols can be easily adapted for using for building libraries for shotgun-sequencing of whole genomes, or enrichment of other genomic regions.
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Affiliation(s)
| | - Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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47
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Major transitions in human evolution revisited: a tribute to ancient DNA. J Hum Evol 2014; 79:4-20. [PMID: 25532800 DOI: 10.1016/j.jhevol.2014.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 06/06/2014] [Accepted: 06/19/2014] [Indexed: 11/23/2022]
Abstract
The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long population history. However, by combining this information with genomic data from ancient remains, one can now directly access our evolutionary past and reveal our population history in much greater detail. This review outlines the main recent achievements in ancient DNA research and illustrates how the field recently moved from the polymerase chain reaction (PCR) amplification of short mitochondrial fragments to whole-genome sequencing and thereby revisited our own history. Ancient DNA research has revealed the routes that our ancestors took when colonizing the planet, whom they admixed with, how they domesticated plant and animal species, how they genetically responded to changes in lifestyle, and also, which pathogens decimated their populations. These approaches promise to soon solve many pending controversies about our own origins that are indecipherable from modern patterns of genetic variation alone, and therefore provide an extremely powerful toolkit for a new generation of molecular anthropologists.
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48
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King TE, Fortes GG, Balaresque P, Thomas MG, Balding D, Delser PM, Neumann R, Parson W, Knapp M, Walsh S, Tonasso L, Holt J, Kayser M, Appleby J, Forster P, Ekserdjian D, Hofreiter M, Schürer K. Identification of the remains of King Richard III. Nat Commun 2014; 5:5631. [PMID: 25463651 PMCID: PMC4268703 DOI: 10.1038/ncomms6631] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 10/21/2014] [Indexed: 12/21/2022] Open
Abstract
In 2012, a skeleton was excavated at the presumed site of the Grey Friars friary in Leicester, the last-known resting place of King Richard III. Archaeological, osteological and radiocarbon dating data were consistent with these being his remains. Here we report DNA analyses of both the skeletal remains and living relatives of Richard III. We find a perfect mitochondrial DNA match between the sequence obtained from the remains and one living relative, and a single-base substitution when compared with a second relative. Y-chromosome haplotypes from male-line relatives and the remains do not match, which could be attributed to a false-paternity event occurring in any of the intervening generations. DNA-predicted hair and eye colour are consistent with Richard's appearance in an early portrait. We calculate likelihood ratios for the non-genetic and genetic data separately, and combined, and conclude that the evidence for the remains being those of Richard III is overwhelming.
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Affiliation(s)
- Turi E. King
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
- School of Archaeology and Ancient History, University of Leicester, Leicester LE1 7RH, UK
| | - Gloria Gonzalez Fortes
- Department of Biology, University of York, York YO10 5DD, UK
- Institute of Biochemistry and Biology, Universität Potsdam, Karl-Liebknechtstr. 24-25, 14476 Potsdam, Germany
| | - Patricia Balaresque
- UMR5288-CNRS/Université Paul Sabatier-Toulouse 3 Laboratoire Anthropologie Moléculaire et Imagerie de Synthèse Faculté de Médecine Purpam 37, allées Jules Guesde, 31073 Toulouse, France
| | - Mark G. Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - David Balding
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | | | - Rita Neumann
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstraße 44, A-6020 Innsbruck, Austria
- Pennsylvania State University, Eberly College of Science, Thomas Bldg, #517, University Park, Pennsylvania 16802, USA
| | - Michael Knapp
- School of Biological Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Susan Walsh
- Molecular Anthropology Laboratory, Department of Anthropology, Yale University, Yale, New Haven, Connecticut 06511, USA
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Laure Tonasso
- UMR5288-CNRS/Université Paul Sabatier-Toulouse 3 Laboratoire Anthropologie Moléculaire et Imagerie de Synthèse Faculté de Médecine Purpam 37, allées Jules Guesde, 31073 Toulouse, France
| | - John Holt
- Space Research Centre, University of Leicester, Leicester LE1 7RH, UK
| | - Manfred Kayser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Centre Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Jo Appleby
- School of Archaeology and Ancient History, University of Leicester, Leicester LE1 7RH, UK
| | - Peter Forster
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
- Murray Edwards College, University of Cambridge, Cambridge CB3 0DF, UK
| | - David Ekserdjian
- Department of the History of Art and Film, University of Leicester, Leicester LE1 7RH, UK
| | - Michael Hofreiter
- Department of Biology, University of York, York YO10 5DD, UK
- Institute of Biochemistry and Biology, Universität Potsdam, Karl-Liebknechtstr. 24-25, 14476 Potsdam, Germany
| | - Kevin Schürer
- Centre for English Local History, University of Leicester, Leicester LE1 7RH, UK
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49
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Larson G, Fuller DQ. The Evolution of Animal Domestication. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-110512-135813] [Citation(s) in RCA: 322] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Greger Larson
- Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham DH1 3LE, United Kingdom;
| | - Dorian Q. Fuller
- Institute of Archaeology, University College London, London WC1H 0PY, United Kingdom
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50
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Orlando L, Cooper A. Using Ancient DNA to Understand Evolutionary and Ecological Processes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-120213-091712] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies of population genetics have revealed dynamic patterns of change in many large vertebrates, featuring localized extinctions, migrations, and population bottlenecks. The pronounced climate cycles of the Late Pleistocene have played a key role, reducing the taxonomic and genetic diversity of many taxa and shaping modern populations. Importantly, the complex series of events revealed by ancient DNA data is seldom reflected in current biogeographic patterns. DNA preserved in ancient sediments and coprolites has been used to characterize a range of paleoenvironments and reconstruct functional relationships in paleoecological systems. In the near future, genome-level surveys of ancient populations will play an increasingly important role in revealing, calibrating, and testing evolutionary processes.
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Affiliation(s)
- Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark;,
| | - Alan Cooper
- Australian Center for Ancient DNA, University of Adelaide, Adelaide, South Australia
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