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Bayraktar M, Cebeci Z, Gökçe G. Analysing the genetic diversity and population structure of five native Turkish cattle breeds using SNP data. Reprod Domest Anim 2024; 59:e14545. [PMID: 38426375 DOI: 10.1111/rda.14545] [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: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
The conservation and sustainable utilization of cattle genetic resources necessitate a comprehensive understanding of their genetic diversity and population structure. This study provides an analysis of five native Turkish cattle breeds: Anatolian Black (ANB), Turkish Grey (TUR), Anatolian Southern Yellow (ASY), East Anatolian Red (EAR), and South Anatolian Red (SAN) using 50 K SNP data. These breeds were compared with three European breeds, Simmental (SIM), Holstein (HOL), and Jersey (JER), and three Asian Zebu breeds: Arabic Zebu (ZAR), Nelore (NEL), and Red Sindhi (RSI). Genetic diversity indices demonstrated moderate heterogeneity among the breeds, with TUR exhibiting the highest observed heterozygosity (Ho = 0.35). Wright's Fst values indicated significant genetic differentiation, particularly between Turkish breeds and both European (Fst = 0.035-0.071) and Asian breeds (Fst = 0.025-0.150). Principal component analysis distinguished the unique genetic profiles of each breed cluster. Admixture analysis revealed degrees of shared genetic ancestry, suggesting historical gene flow between Turkish, European, and Asian breeds. Analysis of molecular variance (AMOVA) attributed approximately 58% of the variation to population differences. Nei's genetic distances highlighted the closer genetic relatedness within Turkish breeds (distance ranges between 0.032 and 0.046) and suggested a more relative affinity of TUR with European breeds. The study's phylogenetic assessments elucidate the nuanced genetic relationships among these breeds, with runs of homozygosity (ROH) analysis indicating patterns of ancestral relatedness and moderate levels of inbreeding, particularly evident in Turkish breeds. Our findings provide valuable insights into the genetic landscape of Turkish cattle, offering a crucial foundation for informed conservation and breeding strategies aimed at preserving these breeds' genetic integrity and heritage.
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Affiliation(s)
- Mervan Bayraktar
- Division of Biometry and Genetics, Department of Animal Science, Faculty of Agriculture, Çukurova University, Adana, Turkey
| | - Zeynel Cebeci
- Division of Biometry and Genetics, Department of Animal Science, Faculty of Agriculture, Çukurova University, Adana, Turkey
| | - Gökhan Gökçe
- Division of Animal Husbandry and Breeding, Department of Animal Science, Faculty of Agriculture, Çukurova University, Adana, Turkey
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2
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Janák V, Novák K, Kyselý R. Late History of Cattle Breeds in Central Europe in Light of Genetic and Archaeogenetic Sources-Overview, Thoughts, and Perspectives. Animals (Basel) 2024; 14:645. [PMID: 38396613 PMCID: PMC10886113 DOI: 10.3390/ani14040645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
Although Europe was not a primary centre of cattle domestication, its expansion from the Middle East and subsequent development created a complex pattern of cattle breed diversity. Many isolated populations of local historical breeds still carry the message about the physical and genetic traits of ancient populations. Since the way of life of human communities starting from the eleventh millennium BP was strongly determined by livestock husbandry, the knowledge of cattle diversity through the ages is helpful in the interpretation of many archaeological findings. Historical cattle diversity is currently at the intersection of two leading directions of genetic research. Firstly, it is archaeogenetics attempting to recover and interpret the preserved genetic information directly from archaeological finds. The advanced archaeogenetic approaches meet with the population genomics of extant cattle populations. The immense amount of genetic information collected from living cattle, due to its key economic role, allows for reconstructing the genetic profiles of the ancient populations backwards. The present paper aims to place selected archaeogenetic, genetic, and genomic findings in the picture of cattle history in Central Europe, as suggested by archaeozoological and historical records. Perspectives of the methodical connection between the genetic approaches and the approaches of traditional archaeozoology, such as osteomorphology and osteometry, are discussed. The importance, actuality, and effectiveness of combining different approaches to each archaeological find, such as morphological characterization, interpretation of the historical context, and molecular data, are stressed.
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Affiliation(s)
- Vojtěch Janák
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Letenská 4, 118 00 Praha, Czech Republic
- Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic;
- Department of Archaeology, Faculty of Arts, Charles University, Nám. Jana Palacha 2, 116 38 Praha, Czech Republic
| | - Karel Novák
- Department of Genetics and Breeding, Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic;
| | - René Kyselý
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Letenská 4, 118 00 Praha, Czech Republic
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3
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Zedda N, Meheux K, Blöcher J, Diekmann Y, Gorelik AV, Kalle M, Klein K, Titze AL, Winkelbach L, Naish E, Brou L, Valotteau F, Le Brun-Ricalens F, Burger J, Brami M. Biological and substitute parents in Beaker period adult-child graves. Sci Rep 2023; 13:18765. [PMID: 37907573 PMCID: PMC10618162 DOI: 10.1038/s41598-023-45612-3] [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: 07/18/2023] [Accepted: 10/21/2023] [Indexed: 11/02/2023] Open
Abstract
Joint inhumations of adults and children are an intriguing aspect of the shift from collective to single burial rites in third millennium BC Western Eurasia. Here, we revisit two exceptional Beaker period adult-child graves using ancient DNA: Altwies in Luxembourg and Dunstable Downs in Britain. Ancestry modelling and patterns of shared IBD segments between the individuals examined, and contemporary genomes from Central and Northwest Europe, highlight the continental connections of British Beakers. Although simultaneous burials may involve individuals with no social or biological ties, we present evidence that close blood relations played a role in shaping third millennium BC social systems and burial practices, for example a biological mother and her son buried together at Altwies. Extended family, such as a paternal aunt at Dunstable Downs, could also act as 'substitute parents' in the grave. Hypotheses are explored to explain such simultaneous inhumations. Whilst intercommunity violence, infectious disease and epidemics may be considered as explanations, they fail to account for both the specific, codified nature of this particular form of inhumation, and its pervasiveness, as evidenced by a representative sample of 131 adult-child graves from 88 sites across Eurasia, all dating to the third and second millennia BC.
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Affiliation(s)
- Nicoletta Zedda
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
- Department of Environmental and Prevention Sciences, University of Ferrara, Ferrara, Italy
| | - Katie Meheux
- Institute of Archaeology Library, LCCOS, University College London, London, UK
| | - Jens Blöcher
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Yoan Diekmann
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Alexander V Gorelik
- Vor- Und Frühgeschichtliche Archäologie, Institut Für Altertumswissenschaften, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Martin Kalle
- Vor- Und Frühgeschichtliche Archäologie, Institut Für Altertumswissenschaften, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Kevin Klein
- Vor- Und Frühgeschichtliche Archäologie, Institut Für Altertumswissenschaften, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Anna-Lena Titze
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Laura Winkelbach
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Laurent Brou
- Institut National de Recherches Archéologiques (INRA), Bertrange, Luxembourg
| | - François Valotteau
- Institut National de Recherches Archéologiques (INRA), Bertrange, Luxembourg
| | | | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Maxime Brami
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany.
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4
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Mas-Coma S, Valero MA, Bargues MD. Human and Animal Fascioliasis: Origins and Worldwide Evolving Scenario. Clin Microbiol Rev 2022; 35:e0008819. [PMID: 36468877 PMCID: PMC9769525 DOI: 10.1128/cmr.00088-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Fascioliasis is a plant- and waterborne zoonotic parasitic disease caused by two trematode species: (i) Fasciola hepatica in Europe, Asia, Africa, the Americas, and Oceania and (ii) F. gigantica, which is restricted to Africa and Asia. Fasciolid liver flukes infect mainly herbivores as ruminants, equids, and camelids but also omnivore mammals as humans and swine and are transmitted by freshwater Lymnaeidae snail vectors. Two phases may be distinguished in fasciolid evolution. The long predomestication period includes the F. gigantica origin in east-southern Africa around the mid-Miocene, the F. hepatica origin in the Near-Middle East of Asia around the latest Miocene to Early Pliocene, and their subsequent local spread. The short postdomestication period includes the worldwide spread by human-guided movements of animals in the last 12,000 years and the more recent transoceanic anthropogenic introductions of F. hepatica into the Americas and Oceania and of F. gigantica into several large islands of the Pacific with ships transporting livestock in the last 500 years. The routes and chronology of the spreading waves followed by both fasciolids into the five continents are redefined on the basis of recently generated knowledge of human-guided movements of domesticated hosts. No local, zonal, or regional situation showing disagreement with historical records was found, although in a few world zones the available knowledge is still insufficient. The anthropogenically accelerated evolution of fasciolids allows us to call them "peridomestic endoparasites." The multidisciplinary implications for crucial aspects of the disease should therefore lead the present baseline update to be taken into account in future research studies.
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Affiliation(s)
- Santiago Mas-Coma
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
| | - M. Adela Valero
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
| | - M. Dolores Bargues
- Departamento de Parasitologia, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
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Nilson SM, Gandolfi B, Grahn RA, Kurushima JD, Lipinski MJ, Randi E, Waly NE, Driscoll C, Murua Escobar H, Schuster RK, Maruyama S, Labarthe N, Chomel BB, Ghosh SK, Ozpinar H, Rah HC, Millán J, Mendes-de-Almeida F, Levy JK, Heitz E, Scherk MA, Alves PC, Decker JE, Lyons LA. Genetics of randomly bred cats support the cradle of cat domestication being in the Near East. Heredity (Edinb) 2022; 129:346-355. [PMID: 36319737 PMCID: PMC9708682 DOI: 10.1038/s41437-022-00568-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/04/2022] Open
Abstract
Cat domestication likely initiated as a symbiotic relationship between wildcats (Felis silvestris subspecies) and the peoples of developing agrarian societies in the Fertile Crescent. As humans transitioned from hunter-gatherers to farmers ~12,000 years ago, bold wildcats likely capitalized on increased prey density (i.e., rodents). Humans benefited from the cats' predation on these vermin. To refine the site(s) of cat domestication, over 1000 random-bred cats of primarily Eurasian descent were genotyped for single-nucleotide variants and short tandem repeats. The overall cat population structure suggested a single worldwide population with significant isolation by the distance of peripheral subpopulations. The cat population heterozygosity decreased as genetic distance from the proposed cat progenitor's (F.s. lybica) natural habitat increased. Domestic cat origins are focused in the eastern Mediterranean Basin, spreading to nearby islands, and southernly via the Levantine coast into the Nile Valley. Cat population diversity supports the migration patterns of humans and other symbiotic species.
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Affiliation(s)
- Sara M Nilson
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Barbara Gandolfi
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Jennifer D Kurushima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Monika J Lipinski
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Ettore Randi
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg Øst, Denmark
| | - Nashwa E Waly
- Department of Animal Medicine, Faculty of Veterinary Medicine, Assuit University, 71526, Assiut, Egypt
| | | | - Hugo Murua Escobar
- Clinic for Hematology, Oncology and Palliative Care, University Medical Center Rostock, 18055, Rostock, Germany
| | - Rolf K Schuster
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Soichi Maruyama
- Laboratory of Veterinary Public Health, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Norma Labarthe
- Programa de Bioética, Ética Aplicada e Saúde Coletiva, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
- Programa de Pós-Graduação em Medicina Veterinária - Clínica e Reprodução Animal, Faculdade de Veterinária, Universidade Federal Fluminense, Rua Vital Brazil Filho 64, Niterói, RJ, 24230-340, Brazil
| | - Bruno B Chomel
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | | | - Haydar Ozpinar
- Graduate School of Health Sciences, Istanbul Gedik University, 34876, İstanbul, Turkey
| | - Hyung-Chul Rah
- Research Institute of Veterinary Medicine, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, South Korea
| | - Javier Millán
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Miguel Servet 177, 50013, Zaragoza, Spain
- Fundación ARAID, Avda. de Ranillas, 50018, Zaragoza, Spain
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Flavya Mendes-de-Almeida
- Programa de Pós-Graduação em Medicina Veterinária - Clínica e Reprodução Animal, Faculdade de Veterinária, Universidade Federal Fluminense, Rua Vital Brazil Filho 64, Niterói, RJ, 24230-340, Brazil
| | - Julie K Levy
- Maddie's Shelter Medicine Program, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32608, USA
| | | | | | - Paulo C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Associate Lab & Faculdade de Ciências, Universidade do Porto, Campus e Vairão, 4485-661, Vila do Conde, Portugal
- Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
| | - Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA.
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.
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Reference-Guided Draft Genome Assembly, Annotation and SSR Mining Data of the Peruvian Creole Cattle (Bos taurus). DATA 2022. [DOI: 10.3390/data7110155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Peruvian creole cattle (PCC) is a neglected breed and an essential livestock resource in the Andean region of Peru. To develop a modern breeding program and conservation strategies for the PCC, a better understanding of the genetics of this breed is needed. We sequenced the whole genome of the PCC using a de novo assembly approach with a paired-end 150 strategy on the Illumina HiSeq 2500 platform, obtaining 320 GB of sequencing data. A reference scaffolding was used to improve the draft genome. The obtained genome size of the PCC was 2.81 Gb with a contig N50 of 108 Mb and 92.59% complete BUSCOs. This genome size is similar to the genome references of Bos taurus and B. indicus. In addition, we identified 40.22% of repetitive DNA of the genome assembly, of which retroelements occupy 32.39% of the total genome. A total of 19,803 protein-coding genes were annotated in the PCC genome. For SSR data mining, we detected similar statistics in comparison with other breeds. The PCC genome will contribute to a better understanding of the genetics of this species and its adaptation to tough conditions in the Andean ecosystem.
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Behavioural Traits in Bos taurus Cattle, Their Heritability, Potential Genetic Markers, and Associations with Production Traits. Animals (Basel) 2022; 12:ani12192602. [PMID: 36230342 PMCID: PMC9559500 DOI: 10.3390/ani12192602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 11/20/2022] Open
Abstract
Simple Summary Cattle have the potential to seriously injure humans and cause damage to property. The risk of cattle reacting in a dangerous manner can be reduced through genetic selection for cattle which have a better temperament. A literature search was undertaken which returned papers which met the criteria of “Bovine”, “Genetics” and “Behaviour” or terms therein. Behavioural traits were grouped and their heritability, genomic associations and correlations with production traits examined. It was found that heritability estimates were more accurate in studies with large populations (n > 1000). Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible, suggesting that genetic improvement can be undertaken without negatively affecting production. There was variation between the results of the studies examined, and this underlines that any genetic study is population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be required. Abstract People who work with cattle are at severe risk of serious injury due to the size and strength of the cattle. This risk can be minimised by breeding less dangerous cattle, which have a more favourable reaction to humans. This study provides a systematic review of literature pertaining to cattle genetics relating to behaviour. The review protocol was developed using the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) framework, with Population, Exposure and Outcome components identified as Bovine, Genetics and Behaviour respectively. Forty-nine studies were identified in the sifting and assigned non-exclusively to groups of heritability (22), genomic associations (13) and production traits related to behaviour (24). Behavioural traits were clustered into the following groups: “temperament, disposition and/ or docility”, “aggression”, “chute score”, “flight speed”, “milking temperament”, “non-restrained methods” and “restrained methods”. Fourteen papers reported high accuracy (Standard Error ≤ 0.05) estimates of heritability, the majority (n = 12) of these studies measured over 1000 animals. The heritability estimates were found to vary between studies. Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible. These studies suggest that additive improvement of behavioural traits in cattle is possible and would not negatively impact performance. However, the variation between studies demonstrates that the genetic relationships are population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be required.
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Nishikaku K, Yonezawa T, Nishibori M, Harada M, Kawaguchi F, Sasazaki S, Torii Y, Imakawa K, Kawai K, Liu J, Mannen H, Kobayashi T. Phylogenomics and Spatiotemporal Dynamics of Bovine Leukemia Virus Focusing on Asian Native Cattle: Insights Into the Early Origin and Global Dissemination. Front Microbiol 2022; 13:917324. [PMID: 35814709 PMCID: PMC9263593 DOI: 10.3389/fmicb.2022.917324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Bovine leukemia virus (BLV), the causative agent of enzootic bovine leukosis, is currently one of the most important pathogens affecting the cattle industry worldwide. Determining where and in which host it originated, and how it dispersed across continents will provide valuable insights into its historical emergence as the cattle pathogen. Various species in the Bos genus were domesticated in Asia, where they also diversified. As native cattle (taurine cattle, zebu cattle, yak, and water buffalo) are indigenous and adapted to local environments, we hypothesized that Asian native cattle could have harbored BLV and, therefore, that they were important for virus emergence, maintenance, and spread. In this study, phylogeographic and ancestral trait analyses—including sequences obtained from Asian native cattle—were used to reconstruct the evolutionary history of BLV. It was shown that, since its probable emergence in Asia, the virus spread to South America and Europe via international trade of live cattle. It was inferred that zebu cattle were the hosts for the early origin of BLV, while taurine cattle played the significant role in the transmission worldwide. In addition, the results of positive selection analysis indicate that yak had a substantially minor role in the transmission of this virus. In this study, endogenous deltaretrovirus sequences in bats, collected in Asian countries, were also analyzed on whether these sequences were present in the bat genome. Endogenous deltaretrovirus sequences were detected from bat species endemic to specific regions and geographically isolated for a long time. Endogenous deltaretrovirus sequences from these geographically isolated species represent ancient exogenous deltaretroviruses distributions. The phylogenetic analysis revealed that these newly obtained endogenous deltaretrovirus sequences were closely related to those of BLV from Asian native cattle, indicating that BLV-related ancient deltaretroviruses circulated in Asia long before the emergence of BLV. Together, our analyses provide evidence for origin and spatiotemporal dynamics of BLV.
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Affiliation(s)
- Kohei Nishikaku
- Laboratory of Animal Health, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Japan
| | - Takahiro Yonezawa
- Laboratory of Animal Genetics, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Japan
| | - Masahide Nishibori
- Laboratory of Animal Genetics, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Masashi Harada
- Laboratory Animal Center, Osaka City University Graduate School of Medicine, Osaka, 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
| | - Yasushi Torii
- Laboratory of Animal Health, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Japan
| | - Kazuhiko Imakawa
- Laboratory of Molecular Reproduction, Research Institute of Agriculture, Tokai University, Kumamoto, Japan
| | - Kuniko Kawai
- Department of Biology, School of Biological Science, Tokai University, Sapporo, Japan
| | - Jianquan Liu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry and Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hideyuki Mannen
- Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Tomoko Kobayashi
- Laboratory of Animal Health, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Atsugi, Japan
- *Correspondence: Tomoko Kobayashi,
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9
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The genomic origins of the world's first farmers. Cell 2022; 185:1842-1859.e18. [PMID: 35561686 PMCID: PMC9166250 DOI: 10.1016/j.cell.2022.04.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/04/2022] [Accepted: 04/06/2022] [Indexed: 11/24/2022]
Abstract
The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.
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10
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Siano F, Picariello G, Caruso T, Esposito S, Rescigno C, Addeo F, Vasca E. Proteomics and Integrated Techniques to Characterize Organic Residues in Funerary Findings from Italic Populations of the First Millennium BC. J Proteome Res 2022; 21:1330-1339. [DOI: 10.1021/acs.jproteome.2c00093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco Siano
- Istituto di Scienze dell’Alimentazione, Consiglio Nazionale delle Ricerche, Via Roma 64, 83100 Avellino, Italy
| | - Gianluca Picariello
- Istituto di Scienze dell’Alimentazione, Consiglio Nazionale delle Ricerche, Via Roma 64, 83100 Avellino, Italy
| | - Tonino Caruso
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (Salerno), Italy
| | - Sara Esposito
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (Salerno), Italy
| | - Carlo Rescigno
- Dipartimento di Lettere e Beni Culturali, Università degli Studi della Campania “Luigi Vanvitelli”, Via Raffaele Perla 21, 81055 Santa Maria Capua Vetere (Caserta), Italy
| | - Francesco Addeo
- Dipartimento di Agraria, Università degli Studi di Napoli “Federico II”, Parco Gussone, Via Università 100, 80055 Portici (Napoli), Italy
| | - Ermanno Vasca
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (Salerno), Italy
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Welker MH, Hughes JE, McClure SB. Cooperation and Cattle Herding in Eighteenth Century Acadia: Implications for Archaeological Studies of Agropastoralism. J ETHNOBIOL 2022. [DOI: 10.2993/0278-0771-42.1.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Wang Y, Zhang C, Peng Y, Cai X, Hu X, Bosse M, Zhao Y. Whole‐genome analysis reveals the hybrid formation of Chinese indigenous DHB pigs following human migration. Evol Appl 2022; 15:501-514. [PMID: 35386394 PMCID: PMC8965386 DOI: 10.1111/eva.13366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 12/07/2021] [Accepted: 02/20/2022] [Indexed: 12/01/2022] Open
Abstract
Hybridization is widespread in nature and is a valuable tool in domestic breeding. The DHB (DaHuaBai) pig in South China is the product of such a breeding strategy, resulting in increased body weight compared with other pigs in the surrounding area. We analyzed genomic data from 20 Chinese pig breeds and investigated the genomic architecture after breed formation of DHB. The breed showed inconsistency in genotype and body weight phenotype, in line with selection after hybridization. By quantifying introgression with a haplotype‐based approach, we proposed a two‐step introgression from large‐sized pigs into small‐sized pigs to produce DHB, consistent with the human migration events in Chinese history. Combining with gene prioritization and allele frequency analysis, we identify candidate genes that showed selection after introgression and that may affect body weight, such as IGF1R, SRC, and PCM1. Our research provides an example of a hybrid formation of domestic breeds along with human migration patterns.
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Affiliation(s)
- Yuzhan Wang
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing 100193 China
| | - Chunyuan Zhang
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing 100193 China
| | - Yebo Peng
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing 100193 China
| | - Xinyu Cai
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing 100193 China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing 100193 China
| | - Mirte Bosse
- Animal Breeding and Genomics Centre Wageningen University Wageningen 6708 WD The Netherlands
| | - Yiqiang Zhao
- State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University Beijing 100193 China
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13
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Petretto E, Dettori ML, Pazzola M, Manca F, Amills M, Vacca GM. Mitochondrial DNA diversity of the Sardinian local cattle stock. Sci Rep 2022; 12:2486. [PMID: 35169207 PMCID: PMC8847569 DOI: 10.1038/s41598-022-06420-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/25/2022] [Indexed: 12/14/2022] Open
Abstract
The aim of this research was to characterize the genetic diversity of the Sarda (Sa, n = 131), Sardo Bruna (SB, n = 44) and Sardo Modicana (SM, n = 26) cattle breeds, reared in the island of Sardinia (Italy). A portion of the mitochondrial DNA hypervariable region was sequenced, in order to identify a potential signature of African introgression. The FST coefficients among populations ranged between 0.056 for Sa vs SB and 0.167 for SB vs SM. AMOVA analysis indicated there was a significant differentiation of the three breeds, although most of diversity was gathered at the within-breed level. The Median Joining Network of the Sardinian sequences showed a potential founder effect signature. A MJ network including Sardinian cattle plus African, Italian, Iberian and Asian sequences, revealed the presence of haplogroup T3, already detected in Sa cattle, and the presence of Hg T1 and Hg T1′2′3, in Sa and SB. The presence of a private haplotype belonging to haplogroup T1, which is characteristic of African taurine breeds, may be due to the introgression of Sardinian breeds with African cattle, either directly (most probable source: North African cattle) or indirectly (through a Mediterranean intermediary already introgressed with African blood).
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Affiliation(s)
- Elena Petretto
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Maria Luisa Dettori
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy.
| | - Michele Pazzola
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Fabio Manca
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Marcel Amills
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Giuseppe Massimo Vacca
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
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14
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Nourishing the Human Holobiont to Reduce the Risk of Non-Communicable Diseases: A Cow’s Milk Evidence Map Example. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol2010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The microbiome revolution brought the realization that diet, health, and safety for humans in reality means diet, health, and safety for the human holobiont/superorganism. Eating healthier means much more than just feeding human cells. Our diet must also nourish the combination of our microbiome and our connected physiological systems (e.g., the microimmunosome). For this reason, there has been an interest in returning to ancestral “complete” unprocessed foods enriched in microbes, including raw milks. To contribute to this inevitable “nourishing the holobiont” trend, we introduce a systematic risk–benefit analysis tool (evidence mapping), which facilitates transdisciplinary state-of-the-science decisions that transcend single scientific disciplines. Our prior paper developed an evidence map (a type of risk–benefit mind map) for raw vs. processed/pasteurized human breast milk. In the present paper, we follow with a comprehensive evidence map and narrative for raw/natural vs. processed/pasteurized cow’s milk. Importantly, the evidence maps incorporate clinical data for both infectious and non-communicable diseases and allow the impact of modern agricultural, food management, and medical and veterinary monitoring outcomes to be captured. Additionally, we focus on the impact of raw milks (as “complete” foods) on the microimmunosome, the microbiome-systems biology unit that significantly determines risk of the world’s number one cause of human death, non-communicable diseases.
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15
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16
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Holečková B, Schwarzbacherová V, Galdíková M, Koleničová S, Halušková J, Staničová J, Verebová V, Jutková A. Chromosomal Aberrations in Cattle. Genes (Basel) 2021; 12:1330. [PMID: 34573313 PMCID: PMC8468509 DOI: 10.3390/genes12091330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 02/04/2023] Open
Abstract
Chromosomal aberrations and their mechanisms have been studied for many years in livestock. In cattle, chromosomal abnormalities are often associated with serious reproduction-related problems, such as infertility of carriers and early mortality of embryos. In the present work, we review the mechanisms and consequences of the most important bovine chromosomal aberrations: Robertsonian translocations and reciprocal translocations. We also discuss the application of bovine cell cultures in genotoxicity studies.
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Affiliation(s)
- Beáta Holečková
- Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (V.S.); (M.G.); (S.K.); (J.H.); (A.J.)
| | - Viera Schwarzbacherová
- Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (V.S.); (M.G.); (S.K.); (J.H.); (A.J.)
| | - Martina Galdíková
- Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (V.S.); (M.G.); (S.K.); (J.H.); (A.J.)
| | - Simona Koleničová
- Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (V.S.); (M.G.); (S.K.); (J.H.); (A.J.)
| | - Jana Halušková
- Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (V.S.); (M.G.); (S.K.); (J.H.); (A.J.)
| | - Jana Staničová
- First Faculty of Medicine, Charles University in Prague, Salmovská 1, 121 08 Prague, Czech Republic;
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia;
| | - Valéria Verebová
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia;
| | - Annamária Jutková
- Department of Biology and Physiology, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (V.S.); (M.G.); (S.K.); (J.H.); (A.J.)
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17
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Clemente F, Unterländer M, Dolgova O, Amorim CEG, Coroado-Santos F, Neuenschwander S, Ganiatsou E, Cruz Dávalos DI, Anchieri L, Michaud F, Winkelbach L, Blöcher J, Arizmendi Cárdenas YO, Sousa da Mota B, Kalliga E, Souleles A, Kontopoulos I, Karamitrou-Mentessidi G, Philaniotou O, Sampson A, Theodorou D, Tsipopoulou M, Akamatis I, Halstead P, Kotsakis K, Urem-Kotsou D, Panagiotopoulos D, Ziota C, Triantaphyllou S, Delaneau O, Jensen JD, Moreno-Mayar JV, Burger J, Sousa VC, Lao O, Malaspinas AS, Papageorgopoulou C. The genomic history of the Aegean palatial civilizations. Cell 2021; 184:2565-2586.e21. [PMID: 33930288 PMCID: PMC8127963 DOI: 10.1016/j.cell.2021.03.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/17/2020] [Accepted: 03/18/2021] [Indexed: 12/30/2022]
Abstract
The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.
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Affiliation(s)
- Florian Clemente
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Martina Unterländer
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece; Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Olga Dolgova
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Carlos Eduardo G Amorim
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Francisco Coroado-Santos
- CE3C, Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal
| | - Samuel Neuenschwander
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Elissavet Ganiatsou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Diana I Cruz Dávalos
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Lucas Anchieri
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Frédéric Michaud
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Laura Winkelbach
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Jens Blöcher
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Yami Ommar Arizmendi Cárdenas
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Eleni Kalliga
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Angelos Souleles
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Ioannis Kontopoulos
- Center for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | | | - Olga Philaniotou
- Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of the Aegean, 85132 Rhodes, Greece
| | - Dimitra Theodorou
- Ephorate of Antiquities of Kozani, Hellenic Ministry of Culture and Sports, 50004 Kozani, Greece
| | - Metaxia Tsipopoulou
- Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece
| | - Ioannis Akamatis
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Paul Halstead
- Department of Archaeology, University of Sheffield, Minalloy House, 10-16 Regent St., Sheffield S1 3NJ, UK
| | - Kostas Kotsakis
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Dushka Urem-Kotsou
- Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Diamantis Panagiotopoulos
- Institute of Classical Archaeology, University of Heidelberg, Marstallhof 4, 69117 Heidelberg, Germany
| | - Christina Ziota
- Ephorate of Antiquities of Florina, Hellenic Ministry of Culture and Sports, 53100 Florina, Greece
| | - Sevasti Triantaphyllou
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - J Víctor Moreno-Mayar
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Center for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark; National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Vitor C Sousa
- CE3C, Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece.
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18
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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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19
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Malomane DK, Weigend S, Schmitt AO, Weigend A, Reimer C, Simianer H. Genetic diversity in global chicken breeds in relation to their genetic distances to wild populations. Genet Sel Evol 2021; 53:36. [PMID: 33853523 PMCID: PMC8048360 DOI: 10.1186/s12711-021-00628-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 03/30/2021] [Indexed: 12/03/2022] Open
Abstract
Background Migration of a population from its founder population is expected to cause a reduction of its genetic diversity and facilitates differentiation between the population and its founder population, as predicted by the theory of genetic isolation by distance. Consistent with that theory, a model of expansion from a single founder predicts that patterns of genetic diversity in populations can be explained well by their geographic expansion from their founders, which is correlated with genetic differentiation. Methods To investigate this in chicken, we estimated the relationship between the genetic diversity of 160 domesticated chicken populations and their genetic distances to wild chicken populations. Results Our results show a strong inverse relationship, i.e. 88.6% of the variation in the overall genetic diversity of domesticated chicken populations was explained by their genetic distance to the wild populations. We also investigated whether the patterns of genetic diversity of different types of single nucleotide polymorphisms (SNPs) and genes are similar to that of the overall genome. Among the SNP classes, the non-synonymous SNPs deviated most from the overall genome. However, genetic distance to the wild chicken still explained more variation in domesticated chicken diversity across all SNP classes, which ranged from 83.0 to 89.3%. Conclusions Genetic distance between domesticated chicken populations and their wild relatives can predict the genetic diversity of the domesticated populations. On the one hand, genes with little genetic variation across populations, regardless of the genetic distance to the wild population, are associated with major functions such as brain development. Changes in such genes may be detrimental to the species. On the other hand, genetic diversity seems to change at a faster rate within genes that are associated with e.g. protein transport and protein and lipid metabolic processes. In general, such genes may be flexible to changes according to the populations’ needs. These results contribute to the knowledge of the evolutionary patterns of different functional genomic regions in the chicken. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00628-z.
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Affiliation(s)
- Dorcus Kholofelo Malomane
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany. .,Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.
| | - Steffen Weigend
- Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | - Armin Otto Schmitt
- Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Breeding Informatics Group, Department of Animal Sciences, Georg August-Universität Goettingen, Goettingen, Germany
| | - Annett Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | - Christian Reimer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Henner Simianer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
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20
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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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21
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Genetic Diversity of Historical and Modern Populations of Russian Cattle Breeds Revealed by Microsatellite Analysis. Genes (Basel) 2020; 11:genes11080940. [PMID: 32824045 PMCID: PMC7463645 DOI: 10.3390/genes11080940] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 01/24/2023] Open
Abstract
Analysis of ancient and historical DNA has great potential to trace the genetic diversity of local cattle populations during their centuries-long development. Forty-nine specimens representing five cattle breeds (Kholmogor, Yaroslavl, Great Russian, Novgorod, and Holland), dated from the end of the 19th century to the first half of the 20th century, were genotyped for nine polymorphic microsatellite loci. Using a multiple-tube approach, we determined the consensus genotypes of all samples/loci analysed. Amplification errors, including allelic drop-out (ADO) and false alleles (FA), occurred with an average frequency of 2.35% and 0.79%, respectively. A significant effect of allelic length on ADO rate (r2 = 0.620, p = 0.05) was shown. We did not observe significant differences in genetic diversity among historical samples and modern representatives of Kholmogor and Yaroslavl breeds. The unbiased expected heterozygosity values were 0.726–0.774 and 0.708–0.739; the allelic richness values were 2.716–2.893 and 2.661–2.758 for the historical and modern samples, respectively. Analyses of FST and Jost’s D genetic distances, and the results of STRUCTURE clustering, showed the maintenance of a part of historical components in the modern populations of Kholmogor and Yaroslavl cattle. Our study contributes to the conservation of biodiversity in the local Russian genetic resources of cattle.
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22
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Schou MF, Kristensen TN, Hoffmann AA. Patterns of environmental variance across environments and traits in domestic cattle. Evol Appl 2020; 13:1090-1102. [PMID: 32431754 PMCID: PMC7232762 DOI: 10.1111/eva.12924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 01/07/2023] Open
Abstract
The variance in phenotypic trait values is a product of environmental and genetic variation. The sensitivity of traits to environmental variation has a genetic component and is likely to be under selection. However, there are few studies investigating the evolution of this sensitivity, in part due to the challenges of estimating the environmental variance. The livestock literature provides a wealth of studies that accurately partition components of phenotypic variance, including the environmental variance, in well-defined environments. These studies involve breeds that have been under strong selection on mean phenotype in optimal environments for many generations, and therefore represent an opportunity to study the potential evolution of trait sensitivity to environmental conditions. Here, we use literature on domestic cattle to examine the evolution of micro-environmental variance (CVR-the coefficient of residual variance) by testing for differences in expression of CVR in animals from the same breed reared in different environments. Traits that have been under strong selection did not follow a null expectation of an increase in CVR in heterogenous environments (e.g., grazing), a pattern that may reflect evolution of increased uniformity in heterogeneous environments. When comparing CVR across environments of different levels of optimality, here measured by trait mean, we found a reduction in CVR in the more optimal environments for both life history and growth traits. Selection aimed at increasing trait means in livestock breeds typically occurs in the more optimal environments, and we therefore suspect that the decreased CVR is a consequence of evolution of the expression of micro-environmental variance in this environment. Our results highlight the heterogeneity in micro-environmental variance across environments and point to possible connections to the intensity of selection on trait means.
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Affiliation(s)
- Mads F. Schou
- Department of Chemistry and BioscienceAalborg UniversityAalborg EastDenmark
- Department of BiologyLund UniversityLundSweden
| | | | - Ary A. Hoffmann
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVICAustralia
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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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Mkize LS, Zishiri OT. Population genetic structure and maternal lineage of South African crossbred Nguni cattle using the cytochrome b gene in mtDNA. Trop Anim Health Prod 2020; 52:2079-2089. [PMID: 32048149 DOI: 10.1007/s11250-020-02231-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/30/2020] [Indexed: 10/25/2022]
Abstract
The Nguni cattle breed predominates South Africa and is endowed with traits favourable against environmental stressors such as heat stress and resistance to diseases. Interventions to improve production have led to the erosion of the genetic integrity of local breeds and the introduction of exotic breeds has proved ineffective as they fail to perform well due to different climatic conditions and production systems. In this study, the genetic structure and genetic lineage of Nguni crossbreds from 6 populations were assessed using the mitochondrial cytochrome b gene. Twelve polymorphic sites were detected resulting in 11 haplotypes with haplotype and nucleotide diversities of 0.550 ± 0.135 and 0.0019 ± 0.0011, respectively. Only 2 of the 6 populations displayed recent population expansion events, whereas the majority adhered to neutral evolution. The basal haplotype contained approximately 60% of the studied populations and there were four unique haplotypes that were revealed. A possible Nguni descript haplotype was uncovered, and this haplotype was found in all populations but was however devoid of individuals from around the world. The genetic structure of the populations was rather low (average pairwise FST = 0.066 and Slatkins FST = 0.094), and approximately 96% of the total genetic variation was accounted for by differences within populations. Phylogenetic analyses supported the clustering of all the samples within the Bos taurus clade and no Bos indicus haplotype was detected. Furthermore, no intermediate haplotype of taurine and indicine was detected. Overall, the maternal lineage of the crossbreds points to a taurine origin and the low genetic diversity depicts the retention of the Nguni genetic pool and possibly its superior adaptive traits.
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Affiliation(s)
| | - Oliver Tendayi Zishiri
- School of Life Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, 4000, South Africa.
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25
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Population Structure and Genetic Diversity of Italian Beef Breeds as a Tool for Planning Conservation and Selection Strategies. Animals (Basel) 2019; 9:ani9110880. [PMID: 31671823 PMCID: PMC6912484 DOI: 10.3390/ani9110880] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 02/01/2023] Open
Abstract
The aim was to investigate the population structure of eight beef breeds: three local Tuscan breeds under extinction, Calvana (CAL), Mucca Pisana (MUP), and Pontremolese (PON); three local unselected breeds reared in Sardinia, Sarda (SAR), Sardo Bruna (SAB), and Sardo Modicana (SAM); and two cosmopolitan breeds, Charolais (CHA) and Limousine (LIM), reared in the same regions. An effective population size ranges between 14.62 (PON) to 39.79 (SAM) in local breeds, 90.29 for CHA, and 135.65 for LIM. The average inbreeding coefficients were higher in Tuscan breeds (7.25%, 5.10%, and 3.64% for MUP, CAL, and PON, respectively) compared to the Sardinian breeds (1.23%, 1.66%, and 1.90% in SAB, SAM, and SAR, respectively), while for CHA and LIM they were <1%. The highest rates of mating between half-siblings were observed for CAL and MUP (~9% and 6.5%, respectively), while the highest rate of parent-offspring mating was ~8% for MUP. Our findings describe the urgent situation of the three Tuscan breeds and support the application of conservation measures and/or the development of breeding programs. Development of breeding strategies is suggested for the Sardinian breeds.
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26
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Upadhyay M, Bortoluzzi C, Barbato M, Ajmone‐Marsan P, Colli L, Ginja C, Sonstegard TS, Bosse M, Lenstra JA, Groenen MAM, Crooijmans RPMA. Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs. Evol Appl 2019; 12:951-963. [PMID: 31080507 PMCID: PMC6503822 DOI: 10.1111/eva.12770] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 12/23/2018] [Accepted: 12/27/2018] [Indexed: 01/10/2023] Open
Abstract
The divergence between indicine cattle (Bos indicus) and taurine cattle (Bos taurus) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non-European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole-genome sequencing data. Additionally, we also employed unlinked and phased SNP-based approaches on high-density SNP array data to characterize non-European cattle ancestry in several southern European cattle breeds. Using heterozygosity-based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross-bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non-European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might account for the presence of non-European cattle ancestry in these cattle breeds.
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Affiliation(s)
- Maulik Upadhyay
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
| | - Chiara Bortoluzzi
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Mario Barbato
- Department of Animal Science, Food and Nutrition – DIANA, Nutrigenomics and Proteomics Research Centre – PRONUTRIGEN, Biodiversity and Ancient DNA Research Centre – BioDNAUniversità Cattolica del Sacro CuorePiacenzaItaly
| | - Paolo Ajmone‐Marsan
- Department of Animal Science, Food and Nutrition – DIANA, Nutrigenomics and Proteomics Research Centre – PRONUTRIGEN, Biodiversity and Ancient DNA Research Centre – BioDNAUniversità Cattolica del Sacro CuorePiacenzaItaly
| | - Licia Colli
- Department of Animal Science, Food and Nutrition – DIANA, Nutrigenomics and Proteomics Research Centre – PRONUTRIGEN, Biodiversity and Ancient DNA Research Centre – BioDNAUniversità Cattolica del Sacro CuorePiacenzaItaly
| | - Catarina Ginja
- CIBIO‐InBIO—Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairaoPortugal
| | | | - Mirte Bosse
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | | | - Martien A. M. Groenen
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
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27
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Schou MF, Hoffmann AA, Kristensen TN. Genetic correlations and their dependence on environmental similarity-Insights from livestock data. Evolution 2019; 73:1672-1678. [PMID: 31144765 DOI: 10.1111/evo.13762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/11/2019] [Indexed: 11/27/2022]
Abstract
Genetic correlations for a trait across environments are predicted to decrease as environments diverge. However, estimates of genetic correlations from natural populations are typically defined across a limited environmental range and prone to very large standard errors, making it difficult to test this prediction. We address the importance of environmental distance on genetic correlations by employing data from domestic cattle in which abundant and accurate estimates are available from a wide range of environments. Three production traits related to milk yield show a clear decrease in genetic correlations with increasing environmental divergence. This pattern was also evident for growth traits and other yield traits but not for traits related to reproduction, morphology, physiology, or disease. We suspect that this reflects weaker selection on these latter trait classes compared to production traits, or alternatively the effects of selection are constrained by unfavorable genetic correlations between traits. The results support the notion that traits that historically have been under strong directional selection in a small range of frequently encountered environments will evolve high genetic correlations across these environments, while exposure to uncommon (and dissimilar) environments lead to a reranking of gene effects and a decrease in genetic correlations across environments.
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Affiliation(s)
- Mads F Schou
- Department of Chemistry and Bioscience, Aalborg University, DK-9220, Aalborg East, Denmark.,Department of Biology, Lund University, Lund, SE-22362, Sweden
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
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28
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da Fonseca RR, Ureña I, Afonso S, Pires AE, Jørsboe E, Chikhi L, Ginja C. Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle. BMC Genomics 2019; 20:334. [PMID: 31053061 PMCID: PMC6500009 DOI: 10.1186/s12864-019-5685-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Iberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns. RESULTS We sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant gene flow or admixture from African taurine cattle and include mtDNA and Y-chromosome haplotypes from multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes within all analyzed taurine breeds, potentially reflecting male-biased gene flow. CONCLUSIONS Our results show that an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries. We also found that the levels of differentiation of autosomes vs sex chromosomes across all studied taurine and indicine breeds are likely to have been affected by widespread breeding practices associated with male-biased gene flow.
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Affiliation(s)
- Rute R. da Fonseca
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Irene Ureña
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Sandra Afonso
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Ana Elisabete Pires
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
- LARC, Laboratório de Arqueociências, Direcção Geral do Património Cultural, Lisbon, Portugal
| | - Emil Jørsboe
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lounès Chikhi
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS. 118 route de Narbonne, Bat 4R1, 31062 Toulouse cedex 9, France
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande n°6, P-2780-156 Oeiras, Portugal
| | - Catarina Ginja
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
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29
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Bosse M, Megens H, Derks MFL, de Cara ÁMR, Groenen MAM. Deleterious alleles in the context of domestication, inbreeding, and selection. Evol Appl 2019; 12:6-17. [PMID: 30622631 PMCID: PMC6304688 DOI: 10.1111/eva.12691] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 05/30/2018] [Accepted: 06/12/2018] [Indexed: 12/21/2022] Open
Abstract
Each individual has a certain number of harmful mutations in its genome. These mutations can lower the fitness of the individual carrying them, dependent on their dominance and selection coefficient. Effective population size, selection, and admixture are known to affect the occurrence of such mutations in a population. The relative roles of demography and selection are a key in understanding the process of adaptation. These are factors that are potentially influenced and confounded in domestic animals. Here, we hypothesize that the series of events of bottlenecks, introgression, and strong artificial selection associated with domestication increased mutational load in domestic species. Yet, mutational load is hard to quantify, so there are very few studies available revealing the relevance of evolutionary processes. The precise role of artificial selection, bottlenecks, and introgression in further increasing the load of deleterious variants in animals in breeding and conservation programmes remains unclear. In this paper, we review the effects of domestication and selection on mutational load in domestic species. Moreover, we test some hypotheses on higher mutational load due to domestication and selective sweeps using sequence data from commercial pig and chicken lines. Overall, we argue that domestication by itself is not a prerequisite for genetic erosion, indicating that fitness potential does not need to decline. Rather, mutational load in domestic species can be influenced by many factors, but consistent or strong trends are not yet clear. However, methods emerging from molecular genetics allow discrimination of hypotheses about the determinants of mutational load, such as effective population size, inbreeding, and selection, in domestic systems. These findings make us rethink the effect of our current breeding schemes on fitness of populations.
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Affiliation(s)
- Mirte Bosse
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Hendrik‐Jan Megens
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Martijn F. L. Derks
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
| | - Ángeles M. R. de Cara
- Centre d’Ecologie Fonctionnelle et EvolutiveCNRSUniversité de MontpellierUniversité Paul Valéry Montpellier 3EPHE, IRDMontpellierFrance
| | - Martien A. M. Groenen
- Animal Breeding and GenomicsWageningen University & ResearchWageningenThe Netherlands
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30
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Penso-Dolfin L, Moxon S, Haerty W, Di Palma F. The evolutionary dynamics of microRNAs in domestic mammals. Sci Rep 2018; 8:17050. [PMID: 30451897 PMCID: PMC6242877 DOI: 10.1038/s41598-018-34243-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022] Open
Abstract
MiRNAs are crucial regulators of gene expression found across both the plant and animal kingdoms. While the number of annotated miRNAs deposited in miRBase has greatly increased in recent years, few studies provided comparative analyses across sets of related species, or investigated the role of miRNAs in the evolution of gene regulation. We generated small RNA libraries across 5 mammalian species (cow, dog, horse, pig and rabbit) from 4 different tissues (brain, heart, kidney and testis). We identified 1676 miRBase and 413 novel miRNAs by manually curating the set of computational predictions obtained from miRCat and miRDeep2. Our dataset spanning five species has enabled us to investigate the molecular mechanisms and selective pressures driving the evolution of miRNAs in mammals. We highlight the important contributions of intronic sequences (366 orthogroups), duplication events (135 orthogroups) and repetitive elements (37 orthogroups) in the emergence of new miRNA loci. We use this framework to estimate the patterns of gains and losses across the phylogeny, and observe high levels of miRNA turnover. Additionally, the identification of lineage-specific losses enables the characterisation of the selective constraints acting on the associated target sites. Compared to the miRBase subset, novel miRNAs tend to be more tissue specific. 20 percent of novel orthogroups are restricted to the brain, and their target repertoires appear to be enriched for neuron activity and differentiation processes. These findings may reflect an important role for young miRNAs in the evolution of brain expression plasticity. Many seed sequences appear to be specific to either the cow or the dog. Analyses on the associated targets highlight the presence of several genes under artificial positive selection, suggesting an involvement of these miRNAs in the domestication process. Altogether, we provide an overview on the evolutionary mechanisms responsible for miRNA turnover in 5 domestic species, and their possible contribution to the evolution of gene regulation.
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Affiliation(s)
- Luca Penso-Dolfin
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, United Kingdom.
| | - Simon Moxon
- University of East Anglia, Norwich Research Park, Norwich, NR47TJ, United Kingdom
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, United Kingdom
| | - Federica Di Palma
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, United Kingdom.
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31
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Ollivier M, Tresset A, Frantz LAF, Bréhard S, Bălăşescu A, Mashkour M, Boroneanţ A, Pionnier-Capitan M, Lebrasseur O, Arbogast RM, Bartosiewicz L, Debue K, Rabinovich R, Sablin MV, Larson G, Hänni C, Hitte C, Vigne JD. Dogs accompanied humans during the Neolithic expansion into Europe. Biol Lett 2018; 14:20180286. [PMID: 30333260 PMCID: PMC6227856 DOI: 10.1098/rsbl.2018.0286] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/24/2018] [Indexed: 12/11/2022] Open
Abstract
Near Eastern Neolithic farmers introduced several species of domestic plants and animals as they dispersed into Europe. Dogs were the only domestic species present in both Europe and the Near East prior to the Neolithic. Here, we assessed whether early Near Eastern dogs possessed a unique mitochondrial lineage that differentiated them from Mesolithic European populations. We then analysed mitochondrial DNA sequences from 99 ancient European and Near Eastern dogs spanning the Upper Palaeolithic to the Bronze Age to assess if incoming farmers brought Near Eastern dogs with them, or instead primarily adopted indigenous European dogs after they arrived. Our results show that European pre-Neolithic dogs all possessed the mitochondrial haplogroup C, and that the Neolithic and Post-Neolithic dogs associated with farmers from Southeastern Europe mainly possessed haplogroup D. Thus, the appearance of haplogroup D most probably resulted from the dissemination of dogs from the Near East into Europe. In Western and Northern Europe, the turnover is incomplete and haplogroup C persists well into the Chalcolithic at least. These results suggest that dogs were an integral component of the Neolithic farming package and a mitochondrial lineage associated with the Near East was introduced into Europe alongside pigs, cows, sheep and goats. It got diluted into the native dog population when reaching the Western and Northern margins of Europe.
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Affiliation(s)
- Morgane Ollivier
- CNRS/ENS de Lyon, PALGENE, ENS de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Anne Tresset
- CNRS/MNHN/SUs - UMR 7209 AASPE, 55 rue Buffon, 75005 Paris, France
| | - Laurent A F Frantz
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford OX1 3QY, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | | | - Adrian Bălăşescu
- Romanian Academy of Sciences, 11 Henri Coandă St., Sector 1, 010667 Bucharest, Romania
| | - Marjan Mashkour
- CNRS/MNHN/SUs - UMR 7209 AASPE, 55 rue Buffon, 75005 Paris, France
| | - Adina Boroneanţ
- Romanian Academy of Sciences, 11 Henri Coandă St., Sector 1, 010667 Bucharest, Romania
| | | | - Ophélie Lebrasseur
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford OX1 3QY, UK
| | - Rose-Marie Arbogast
- CNRS - UMR 7044 MISHA, 5 allée du Général Rouvillois, 67083 Strasbourg, France
| | - László Bartosiewicz
- Osteoarchaeological Research Laboratory, University of Stockholm, Stockholm, Sweden
| | - Karyne Debue
- CNRS/MNHN/SUs - UMR 7209 AASPE, 55 rue Buffon, 75005 Paris, France
| | - Rivka Rabinovich
- Institute of Archaeology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Mikhail V Sablin
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint Petersburg, Russia
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford OX1 3QY, UK
| | | | | | - Jean-Denis Vigne
- CNRS/MNHN/SUs - UMR 7209 AASPE, 55 rue Buffon, 75005 Paris, France
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32
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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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33
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Daly KG, Maisano Delser P, Mullin VE, Scheu A, Mattiangeli V, Teasdale MD, Hare AJ, Burger J, Verdugo MP, Collins MJ, Kehati R, Erek CM, Bar-Oz G, Pompanon F, Cumer T, Çakırlar C, Mohaseb AF, Decruyenaere D, Davoudi H, Çevik Ö, Rollefson G, Vigne JD, Khazaeli R, Fathi H, Doost SB, Rahimi Sorkhani R, Vahdati AA, Sauer EW, Azizi Kharanaghi H, Maziar S, Gasparian B, Pinhasi R, Martin L, Orton D, Arbuckle BS, Benecke N, Manica A, Horwitz LK, Mashkour M, Bradley DG. Ancient goat genomes reveal mosaic domestication in the Fertile Crescent. Science 2018; 361:85-88. [PMID: 29976826 DOI: 10.1126/science.aas9411] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/13/2018] [Accepted: 06/04/2018] [Indexed: 12/16/2022]
Abstract
Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.
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Affiliation(s)
- Kevin G Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Pierpaolo Maisano Delser
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Amelie Scheu
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | | | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,BioArCh, University of York, York YO10 5DD, UK
| | - Andrew J Hare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, 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
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | | | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Mount Carmel, Haifa, Israel
| | - François Pompanon
- Université Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Tristan Cumer
- Université Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Canan Çakırlar
- Groningen Institute of Archaeology, Groningen University, Groningen, Netherlands
| | - Azadeh Fatemeh Mohaseb
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France.,Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Delphine Decruyenaere
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France
| | - Hossein Davoudi
- Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran.,Osteology Department, National Museum of Iran, Tehran, Iran
| | - Özlem Çevik
- Trakya Universitesi, Edebiyat Fakültesi, Arkeoloi Bölümü, Edirne, Turkey
| | - Gary Rollefson
- Department of Anthropology, Whitman College, Walla Walla, WA 99362, USA
| | - Jean-Denis Vigne
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France
| | - Roya Khazaeli
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Homa Fathi
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Sanaz Beizaee Doost
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | | | - Ali Akbar Vahdati
- Provincial Office of the Iranian Center for Cultural Heritage, Handicrafts and Tourism Organisation, North Khorassan, Bojnord, Iran
| | - Eberhard W Sauer
- School of History, Classics and Archaeology, University of Edinburgh, William Robertson Wing, Old Medical School, Edinburgh EH8 9AG, UK
| | | | - Sepideh Maziar
- Institut für Archäologische Wissenschaften, Goethe Universität, Frankfurt am Main, Germany
| | - Boris Gasparian
- Institute of Archaeology and Ethnology, National Academy of Sciences of the Republic of Armenia, Yerevan 0025, Republic of Armenia
| | - Ron Pinhasi
- Department of Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Louise Martin
- Institute of Archeology, University College London, London, UK
| | - David Orton
- BioArCh, University of York, York YO10 5DD, UK
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina, Chapel Hill, NC, USA
| | - Norbert Benecke
- Department of Natural Sciences, German Archaeological Institute, 14195 Berlin, Germany
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France.,Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran.,Osteology Department, National Museum of Iran, Tehran, Iran
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria. Proc Natl Acad Sci U S A 2018. [PMID: 29531040 PMCID: PMC5879695 DOI: 10.1073/pnas.1719880115] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Many modern European states trace their roots back to a period known as the Migration Period that spans from Late Antiquity to the early Middle Ages. We have conducted the first population-level analysis of people from this era, generating genomic data from 41 graves from archaeological sites in present-day Bavaria in southern Germany mostly dating to around 500 AD. While they are predominantly of northern/central European ancestry, we also find significant evidence for a nonlocal genetic provenance that is highly enriched among resident Early Medieval women, demonstrating artificial skull deformation. We infer that the most likely origin of the majority of these women was southeastern Europe, resolving a debate that has lasted for more than half a century. Modern European genetic structure demonstrates strong correlations with geography, while genetic analysis of prehistoric humans has indicated at least two major waves of immigration from outside the continent during periods of cultural change. However, population-level genome data that could shed light on the demographic processes occurring during the intervening periods have been absent. Therefore, we generated genomic data from 41 individuals dating mostly to the late 5th/early 6th century AD from present-day Bavaria in southern Germany, including 11 whole genomes (mean depth 5.56×). In addition we developed a capture array to sequence neutral regions spanning a total of 5 Mb and 486 functional polymorphic sites to high depth (mean 72×) in all individuals. Our data indicate that while men generally had ancestry that closely resembles modern northern and central Europeans, women exhibit a very high genetic heterogeneity; this includes signals of genetic ancestry ranging from western Europe to East Asia. Particularly striking are women with artificial skull deformations; the analysis of their collective genetic ancestry suggests an origin in southeastern Europe. In addition, functional variants indicate that they also differed in visible characteristics. This example of female-biased migration indicates that complex demographic processes during the Early Medieval period may have contributed in an unexpected way to shape the modern European genetic landscape. Examination of the panel of functional loci also revealed that many alleles associated with recent positive selection were already at modern-like frequencies in European populations ∼1,500 years ago.
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35
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Di Lorenzo P, Lancioni H, Ceccobelli S, Colli L, Cardinali I, Karsli T, Capodiferro MR, Sahin E, Ferretti L, Ajmone Marsan P, Sarti FM, Lasagna E, Panella F, Achilli A. Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin. PLoS One 2018; 13:e0192567. [PMID: 29462170 PMCID: PMC5819780 DOI: 10.1371/journal.pone.0192567] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/25/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Over the past 15 years, 300 out of 6000 breeds of all farm animal species identified by the Food and Agriculture Organization of the United Nations (FAO) have gone extinct. Among cattle, many Podolian breeds are seriously endangered in various European areas. Podolian cattle include a group of very ancient European breeds, phenotypically close to the aurochs ancestors (Bos primigenius). The aim of the present study was to assess the genetic diversity of Podolian breeds and to reconstruct their origin. METHODOLOGY The mitochondrial DNA (mtDNA) control-regions of 18 Podolian breeds have been phylogenetically assessed. Nine non-Podolian breeds have been also included for comparison. CONCLUSION The overall analysis clearly highlights some peculiarities in the mtDNA gene pool of some Podolian breeds. In particular, a principal component analysis point to a genetic proximity between five breeds (Chianina, Marchigiana, Maremmana, Podolica Italiana and Romagnola) reared in Central Italy and the Turkish Grey. We here propose the suggestive hypothesis of a dual ancestral contribution to the present gene pool of Podolian breeds, one deriving from Eastern European cattle; the other arising from the arrival of Middle Eastern cattle into Central Italy through a different route, perhaps by sea, ferried by Etruscan boats. The historical migration of Podolian cattle from North Eastern Europe towards Italy has not cancelled the mtDNA footprints of this previous ancient migration.
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Affiliation(s)
- Piera Di Lorenzo
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
- * E-mail: (HL); (AA)
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Licia Colli
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, Italy
- Biodiversity and Ancient DNA Research Center–BioDNA, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, Perugia, Italy
| | - Taki Karsli
- Department of Animal Science, Faculty of Agriculture, University of Akdeniz, Antalya, Turkey
| | | | - Emine Sahin
- Korkuteli Vocational School, University of Akdeniz, Antalya, Turkey
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
| | - Paolo Ajmone Marsan
- Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, Italy
- Biodiversity and Ancient DNA Research Center–BioDNA, Università Cattolica del S. Cuore, Piacenza, Italy
| | - Francesca Maria Sarti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Francesco Panella
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, Pavia, Italy
- * E-mail: (HL); (AA)
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36
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37
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Botigué LR, Song S, Scheu A, Gopalan S, Pendleton AL, Oetjens M, Taravella AM, Seregély T, Zeeb-Lanz A, Arbogast RM, Bobo D, Daly K, Unterländer M, Burger J, Kidd JM, Veeramah KR. Ancient European dog genomes reveal continuity since the Early Neolithic. Nat Commun 2017; 8:16082. [PMID: 28719574 PMCID: PMC5520058 DOI: 10.1038/ncomms16082] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/25/2017] [Indexed: 12/19/2022] Open
Abstract
Europe has played a major role in dog evolution, harbouring the oldest uncontested Palaeolithic remains and having been the centre of modern dog breed creation. Here we sequence the genomes of an Early and End Neolithic dog from Germany, including a sample associated with an early European farming community. Both dogs demonstrate continuity with each other and predominantly share ancestry with modern European dogs, contradicting a previously suggested Late Neolithic population replacement. We find no genetic evidence to support the recent hypothesis proposing dual origins of dog domestication. By calibrating the mutation rate using our oldest dog, we narrow the timing of dog domestication to 20,000-40,000 years ago. Interestingly, we do not observe the extreme copy number expansion of the AMY2B gene characteristic of modern dogs that has previously been proposed as an adaptation to a starch-rich diet driven by the widespread adoption of agriculture in the Neolithic.
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Affiliation(s)
- Laura R Botigué
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - Shiya Song
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Amelie Scheu
- Palaeogenetics Group, Johannes Gutenberg-University Mainz, 55099 Mainz, Germany.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Shyamalika Gopalan
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - Amanda L Pendleton
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Matthew Oetjens
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Angela M Taravella
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Timo Seregély
- Department of Prehistoric Archaeology, Institute of Archaeology, Heritage Sciences and Art History, University of Bamberg, 96045 Bamberg, Germany
| | - Andrea Zeeb-Lanz
- Generaldirektion Kulturelles Erbe Rheinland-Pfalz, Direktion Landesarchäologie, Außenstelle Speyer, 67346 Speyer, Germany
| | | | - Dean Bobo
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - Kevin Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Martina Unterländer
- Palaeogenetics Group, Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Joachim Burger
- Palaeogenetics Group, Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Jeffrey M Kidd
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
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38
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The Evolutionary Origin and Genetic Makeup of Domestic Horses. Genetics 2017; 204:423-434. [PMID: 27729493 DOI: 10.1534/genetics.116.194860] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/17/2016] [Indexed: 12/21/2022] Open
Abstract
The horse was domesticated only 5.5 KYA, thousands of years after dogs, cattle, pigs, sheep, and goats. The horse nonetheless represents the domestic animal that most impacted human history; providing us with rapid transportation, which has considerably changed the speed and magnitude of the circulation of goods and people, as well as their cultures and diseases. By revolutionizing warfare and agriculture, horses also deeply influenced the politico-economic trajectory of human societies. Reciprocally, human activities have circled back on the recent evolution of the horse, by creating hundreds of domestic breeds through selective programs, while leading all wild populations to near extinction. Despite being tightly associated with humans, several aspects in the evolution of the domestic horse remain controversial. Here, we review recent advances in comparative genomics and paleogenomics that helped advance our understanding of the genetic foundation of domestic horses.
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39
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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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40
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Di Lorenzo P, Lancioni H, Ceccobelli S, Curcio L, Panella F, Lasagna E. Uniparental genetic systems: a male and a female perspective in the domestic cattle origin and evolution. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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41
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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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Broushaki F, Thomas MG, Link V, López S, van Dorp L, Kirsanow K, Hofmanová Z, Diekmann Y, Cassidy LM, Díez-del-Molino D, Kousathanas A, Sell C, Robson HK, Martiniano R, Blöcher J, Scheu A, Kreutzer S, Bollongino R, Bobo D, Davudi H, Munoz O, Currat M, Abdi K, Biglari F, Craig OE, Bradley DG, Shennan S, Veeramah K, Mashkour M, Wegmann D, Hellenthal G, Burger J. Early Neolithic genomes from the eastern Fertile Crescent. Science 2016; 353:499-503. [PMID: 27417496 PMCID: PMC5113750 DOI: 10.1126/science.aaf7943] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/05/2016] [Indexed: 01/06/2023]
Abstract
We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46,000 to 77,000 years ago and show affinities to modern-day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in southwestern Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.
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Affiliation(s)
- Farnaz Broushaki
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Vivian Link
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Saioa López
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lucy van Dorp
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Karola Kirsanow
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Zuzana Hofmanová
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Yoan Diekmann
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lara M. Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - David Díez-del-Molino
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - Athanasios Kousathanas
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
| | - Christian Sell
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Harry K. Robson
- BioArCh, Department of Archaeology, University of York, York, YO10 5YW, UK
| | - Rui Martiniano
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jens Blöcher
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Amelie Scheu
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Susanne Kreutzer
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Ruth Bollongino
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Dean Bobo
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794- 5245, USA
| | - Hossein Davudi
- Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran
| | - Olivia Munoz
- UMR 7041 ArScAn -VEPMO, Maison de l’Archéologie et de l’Ethnologie, 21 allée de l’Université, 92023 Nanterre, France
| | - Mathias Currat
- Department of Genetics & Evolution-Anthropology Unit, University of Geneva, 1211 Geneva, Switzerland
| | - Kamyar Abdi
- Samuel Jordan Center for Persian Studies and Culture, University of California-lrvine, Irvine, CA 92697-3370, USA
| | - Fereidoun Biglari
- Paleolithic Department, National Museum of Iran, 113617111, Tehran, Iran
| | - Oliver E. Craig
- BioArCh, Department of Archaeology, University of York, York, YO10 5YW, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Stephen Shennan
- Institute of Archaeology, University College London, London WC1H 0PY, UK
| | - Krishna Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794- 5245, USA
| | - Marjan Mashkour
- CNRS/MNHN/SUs – UMR 7209, Archéozoologie et Archéobotanique, Sociétés, Pratiques et Environnements, Département Ecologie et Gestion de la Biodiversité, 55 rue Buffon, 75005 Paris, France
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Joachim Burger
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
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VandeHaar M, Armentano L, Weigel K, Spurlock D, Tempelman R, Veerkamp R. Harnessing the genetics of the modern dairy cow to continue improvements in feed efficiency. J Dairy Sci 2016; 99:4941-4954. [DOI: 10.3168/jds.2015-10352] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 12/28/2015] [Indexed: 01/09/2023]
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Lancioni H, Di Lorenzo P, Cardinali I, Ceccobelli S, Capodiferro MR, Fichera A, Grugni V, Semino O, Ferretti L, Gruppetta A, Attard G, Achilli A, Lasagna E. Survey of uniparental genetic markers in the Maltese cattle breed reveals a significant founder effect but does not indicate local domestication. Anim Genet 2016; 47:267-9. [DOI: 10.1111/age.12408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie; Università degli Studi di Perugia; Perugia 06123 Italy
| | - Piera Di Lorenzo
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali; Università degli Studi di Perugia; Perugia 06121 Italy
| | - Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie; Università degli Studi di Perugia; Perugia 06123 Italy
| | - Simone Ceccobelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali; Università degli Studi di Perugia; Perugia 06121 Italy
| | - Marco Rosario Capodiferro
- Dipartimento di Chimica, Biologia e Biotecnologie; Università degli Studi di Perugia; Perugia 06123 Italy
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”; Università degli Studi di Pavia; Pavia 27100 Italy
| | - Alessandro Fichera
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”; Università degli Studi di Pavia; Pavia 27100 Italy
| | - Viola Grugni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”; Università degli Studi di Pavia; Pavia 27100 Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”; Università degli Studi di Pavia; Pavia 27100 Italy
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”; Università degli Studi di Pavia; Pavia 27100 Italy
| | - Anthony Gruppetta
- Department of Rural Sciences and Food Systems; Institute of Earth Systems; University of Malta; Msida MSD 2080 Malta
| | - George Attard
- Department of Rural Sciences and Food Systems; Institute of Earth Systems; University of Malta; Msida MSD 2080 Malta
| | - Alessandro Achilli
- Dipartimento di Chimica, Biologia e Biotecnologie; Università degli Studi di Perugia; Perugia 06123 Italy
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”; Università degli Studi di Pavia; Pavia 27100 Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali; Università degli Studi di Perugia; Perugia 06121 Italy
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Omrak A, Günther T, Valdiosera C, Svensson EM, Malmström H, Kiesewetter H, Aylward W, Storå J, Jakobsson M, Götherström A. Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool. Curr Biol 2015; 26:270-275. [PMID: 26748850 DOI: 10.1016/j.cub.2015.12.019] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/07/2015] [Accepted: 12/09/2015] [Indexed: 10/22/2022]
Abstract
Anatolia and the Near East have long been recognized as the epicenter of the Neolithic expansion through archaeological evidence. Recent archaeogenetic studies on Neolithic European human remains have shown that the Neolithic expansion in Europe was driven westward and northward by migration from a supposed Near Eastern origin [1-5]. However, this expansion and the establishment of numerous culture complexes in the Aegean and Balkans did not occur until 8,500 before present (BP), over 2,000 years after the initial settlements in the Neolithic core area [6-9]. We present ancient genome-wide sequence data from 6,700-year-old human remains excavated from a Neolithic context in Kumtepe, located in northwestern Anatolia near the well-known (and younger) site Troy [10]. Kumtepe is one of the settlements that emerged around 7,000 BP, after the initial expansion wave brought Neolithic practices to Europe. We show that this individual displays genetic similarities to the early European Neolithic gene pool and modern-day Sardinians, as well as a genetic affinity to modern-day populations from the Near East and the Caucasus. Furthermore, modern-day Anatolians carry signatures of several admixture events from different populations that have diluted this early Neolithic farmer component, explaining why modern-day Sardinian populations, instead of modern-day Anatolian populations, are genetically more similar to the people that drove the Neolithic expansion into Europe. Anatolia's central geographic location appears to have served as a connecting point, allowing a complex contact network with other areas of the Near East and Europe throughout, and after, the Neolithic.
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Affiliation(s)
- Ayça Omrak
- Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 114 18, Stockholm, Sweden.
| | - Torsten Günther
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Cristina Valdiosera
- Department of Archaeology, Environment and Community Planning, La Trobe University, VIC 3086, Melbourne, Australia; Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Emma M Svensson
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Ullsväg 26, 75007, Uppsala, Sweden
| | - Helena Malmström
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Henrike Kiesewetter
- Project Troia, Institute of Prehistory, Early History, and Medieval Archaeology, Tübingen University, Schloss-Burgsteige 11, 72070, Tuebingen, Germany
| | - William Aylward
- Biotechnology Center and Department of Classics and Ancient Near Eastern Studies, University of Wisconsin-Madison, 1220 Linden Drive, Madison, WI 53706, USA
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 114 18, Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, 114 18, Stockholm, Sweden.
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46
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Hristov P, Spassov N, Iliev N, Radoslavov G. An independent event of Neolithic cattle domestication on the South-eastern Balkans: evidence from prehistoric aurochs and cattle populations. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:383-391. [PMID: 26711535 DOI: 10.3109/19401736.2015.1127361] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Neolithic/Chalcolithic livestock domestication is an important issue for understanding the mode of life and economics of ancient human communities. The Balkans appears to be a crucial point for clarifying the socio-economical interrelations between the Oldest Middle Eastern/Anatolian and newly formed cultures in Europe. Two main hypotheses regarding the early history of cattle domestication, from their ancestor - the aurochs, have been discussed: multipoint domestication centers or single point origin and subsequent worldwide dissemination. In this study, we provide molecular data about the Balkan aurochs for the first time as well as additional information for the Neolithic/Chalcolithic cattle populations in this geographic location. A total of seventeen samples from different ancient settlements were analyzed according to D-loop control region. The results did not show different genetic profile of wild and domestic populations. All haplotypes were found to belong to the basic macro-haplogroup T. The majority of specimens (n = 14) were defined to form a new Balkan-specific T6 haplogroup. Only two of the ancient samples analyzed were assigned to the T3 haplotype predominating in Europe. We attempt to throw new light on the earliest cattle domestication events in Europe, thus, the results presented are discussed in two directions: (a) The possibility of local independent domestication processes in Neolithic South-Eastern Europe; (b) The single point domestication in the Middle East and subsequent cattle dissemination in Europe. Our data does not exclude the possibility for independent domestication events followed by a second wave of parallel dissemination of cattle herds via the Mediterranean route.
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Affiliation(s)
- Peter Hristov
- a Department of Animal Diversity and Resources , Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences , Sofia 1113 , Bulgaria
| | - Nikolai Spassov
- b Palaeontology and Mineralogy Department , National Museum of Natural History, Bulgarian Academy of Sciences , 1 "Tsar Osvoboditel" Blvd , Sofia 1000 , Bulgaria
| | - Nikolai Iliev
- b Palaeontology and Mineralogy Department , National Museum of Natural History, Bulgarian Academy of Sciences , 1 "Tsar Osvoboditel" Blvd , Sofia 1000 , Bulgaria
| | - Georgi Radoslavov
- a Department of Animal Diversity and Resources , Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences , Sofia 1113 , Bulgaria
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47
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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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48
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Abstract
The first genome sequence of the extinct European wild aurochs reveals the genetic foundation of native British and Irish landraces of cattle. See related Research article: www.dx.doi.org/10.1186/s13059-015-0790-2
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Affiliation(s)
- Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, ØsterVoldgade 5-7, 1350K, Copenhagen, Denmark. .,Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, CNRS UMR 5288, 37 Allées Jules Guesde, 31000, Toulouse, France.
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