1
|
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.
Collapse
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
| |
Collapse
|
2
|
Pelayo R, Penedo MCT, Valera M, Molina A, Millon L, Ginja C, Royo LJ. Identification of a new Y chromosome haplogroup in Spanish native cattle. Anim Genet 2017; 48:450-454. [PMID: 28244125 DOI: 10.1111/age.12549] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2017] [Indexed: 11/30/2022]
Abstract
The aim of this work was to perform a thorough analysis of the diversity of Y-haplotypes in Spanish cattle. A total of 207 Bos taurus males were sampled across 25 European breeds, with a special focus on rare, local Spanish populations. Animals were genotyped with five Y-specific microsatellites (INRA189, UMN0103, UMN0307, BM861 and BYM1), two indels (ZFY10 and USP9Y) and one SNP (UTY19). A new haplogroup, distinct from those described by Götherström et al. (2005), was identified and named Y1.2. Samples representing the three B. taurus Y-haplogroups were genotyped for four additional Y chromosome SNPs (rs121919254, rs121919281, rs121919323 and rs137049553). Among these SNPs, only rs121919281 was informative in B. taurus and helped to confirm the new Y1.2 haplogroup. Analysis of a larger dataset of standardized haplotypes for 1507 individuals from 57 populations from Spain, other European countries and Africa showed the new Y1.2 haplogroup to be found exclusively in Spanish breeds. This finding reinforces the importance of local Spanish cattle as reservoirs of genetic diversity as well as the importance of the Iberian Peninsula in the history of cattle.
Collapse
Affiliation(s)
- R Pelayo
- Department of Agroforestry Science, University of Seville, Crta. Utrera, Km 1, 41013, Seville, Spain
| | - M C T Penedo
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - M Valera
- Department of Agroforestry Science, University of Seville, Crta. Utrera, Km 1, 41013, Seville, Spain
| | - A Molina
- Department of Genetics, University of Córdoba, Crta_Nacional IV, km 396, 14071, Córdoba, Spain
| | - L Millon
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - C Ginja
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - L J Royo
- Área de Nutrición, Pastos y Forrajes, SERIDA, Crta de Oviedo s/n, 33300, Villaviciosa (Asturias), Spain
| |
Collapse
|
3
|
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
|
4
|
Rannamäe E, Lõugas L, Niemi M, Kantanen J, Maldre L, Kadõrova N, Saarma U. Maternal and paternal genetic diversity of ancient sheep in Estonia from the Late Bronze Age to the post-medieval period and comparison with other regions in Eurasia. Anim Genet 2016; 47:208-18. [PMID: 26805771 DOI: 10.1111/age.12407] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2015] [Indexed: 12/01/2022]
Abstract
Sheep were among the first domesticated animals to appear in Estonia in the late Neolithic and became one of the most widespread livestock species in the region from the Late Bronze Age onwards. However, the origin and historical expansion of local sheep populations in Estonia remain poorly understood. Here, we analysed fragments of the hypervariable D-loop of mitochondrial DNA (mtDNA; 213 bp) and the Y-chromosome SRY gene (130 bp) extracted from 31 archaeological sheep bones dated from approximately 800 BC to 1700 AD. The ancient DNA data of sheep from Estonia were compared with ancient sheep from Finland as well as a set of contemporary sheep breeds from across Eurasia in order to place them in a wider phylogeographical context. The analysis shows that: (i) 24 successfully amplified and analysed mtDNA sequences of ancient sheep cluster into two haplogroups, A and B, of which B is predominant; (ii) four of the ancient mtDNA haplotypes are novel; (iii) higher mtDNA haplotype diversity occurred during the Middle Ages as compared to other periods, a fact concordant with the historical context of expanding international trade during the Middle Ages; (iv) the proportion of rarer haplotypes declined during the expansion of sheep from the Near Eastern domestication centre to the northern European region; (v) three male samples showed the presence of the characteristic northern European haplotype, SNP G-oY1 of the Y-chromosome, and represent the earliest occurrence of this haplotype. Our results provide the first insight into the genetic diversity and phylogeographical background of ancient sheep in Estonia and provide basis for further studies on the temporal fluctuations of ancient sheep populations.
Collapse
Affiliation(s)
- E Rannamäe
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Jakobi 2, 51014, Tartu, Estonia
| | - L Lõugas
- Department of Archaeobiology, Institute of History, Tallinn University, Rüütli 6, 10130, Tallinn, Estonia
| | - M Niemi
- Department of Forensic Medicine, University of Helsinki, FI-00014, Helsinki, Finland.,Green Technology, Natural Resources Institute Finland, Myllytie 1, FI-31600, Jokioinen, Finland
| | - J Kantanen
- Green Technology, Natural Resources Institute Finland, Myllytie 1, FI-31600, Jokioinen, Finland.,Department of Biology, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - L Maldre
- Department of Archaeobiology, Institute of History, Tallinn University, Rüütli 6, 10130, Tallinn, Estonia
| | - N Kadõrova
- Department of Natural Sciences, Institute of Mathematics and Natural Sciences, Tallinn University, Narva Rd 25, 10120, Tallinn, Estonia
| | - U Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| |
Collapse
|
5
|
Park SDE, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, Murphy A, Braud M, Donoghue MT, Liu Y, Chamberlain AT, Rue-Albrecht K, Schroeder S, Spillane C, Tai S, Bradley DG, Sonstegard TS, Loftus BJ, MacHugh DE. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biol 2015; 16:234. [PMID: 26498365 PMCID: PMC4620651 DOI: 10.1186/s13059-015-0790-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/25/2015] [Indexed: 11/10/2022] Open
Abstract
Background Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0790-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Stephen D E Park
- IdentiGEN Ltd, Unit 2, Trinity Enterprise Centre, Pearse Street, Dublin 2, Ireland.
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. .,Department of Animal Science, University of Connecticut, Storrs, CT, 06029, USA.
| | - Paul A McGettigan
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | | | - Ceiridwen J Edwards
- Research Laboratory for Archaeology and the History of Art, Dyson Perrins Building, South Parks Rd, Oxford, OX1 3QY, UK.
| | - Amanda J Lohan
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Alison Murphy
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Martin Braud
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Mark T Donoghue
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Yuan Liu
- BGI Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Andrew T Chamberlain
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Kévin Rue-Albrecht
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Steven Schroeder
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA.
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Shuaishuai Tai
- BGI Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland.
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA. .,Recombinetics Inc., St. Paul, MN, 55104, USA.
| | - Brendan J Loftus
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland. .,UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| |
Collapse
|
6
|
Bruford MW, Ginja C, Hoffmann I, Joost S, Orozco-terWengel P, Alberto FJ, Amaral AJ, Barbato M, Biscarini F, Colli L, Costa M, Curik I, Duruz S, Ferenčaković M, Fischer D, Fitak R, Groeneveld LF, Hall SJG, Hanotte O, Hassan FU, Helsen P, Iacolina L, Kantanen J, Leempoel K, Lenstra JA, Ajmone-Marsan P, Masembe C, Megens HJ, Miele M, Neuditschko M, Nicolazzi EL, Pompanon F, Roosen J, Sevane N, Smetko A, Štambuk A, Streeter I, Stucki S, Supakorn C, Telo Da Gama L, Tixier-Boichard M, Wegmann D, Zhan X. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025. Front Genet 2015; 6:314. [PMID: 26539210 PMCID: PMC4612686 DOI: 10.3389/fgene.2015.00314] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/05/2015] [Indexed: 12/20/2022] Open
Abstract
Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that “…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.
Collapse
Affiliation(s)
- Michael W Bruford
- School of Biosciences, Cardiff University Cardiff, UK ; Sustainable Places Research Institute, Cardiff University Cardiff, UK
| | - Catarina Ginja
- Faculdade de Ciências, Centro de Ecologia, Evolução e Alterações Ambientais (CE3C), Universidade de Lisboa Lisboa, Portugal ; Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Campus Agrário de Vairão Portugal
| | - Irene Hoffmann
- Food and Agriculture Organization of the United Nations, Animal Genetic Resources Branch, Animal Production and Health Division Rome, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Florian J Alberto
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes Grenoble, France
| | - Andreia J Amaral
- Faculty of Sciences, BioISI- Biosystems and Integrative Sciences Institute, University of Lisbon Campo Grande, Portugal
| | - Mario Barbato
- School of Biosciences, Cardiff University Cardiff, UK
| | | | - Licia Colli
- BioDNA Centro di Ricerca sulla Biodiversità a sul DNA Antico, Istituto di Zootecnica, Università Cattolica del Sacro Cuore di Piacenza Italy
| | - Mafalda Costa
- School of Biosciences, Cardiff University Cardiff, UK
| | - Ino Curik
- Faculty of Agriculture, University of Zagreb Zagreb, Croatia
| | - Solange Duruz
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Daniel Fischer
- Natural Resources Institute Finland (Luke), Green Technology Jokioinen, Finland
| | - Robert Fitak
- Institut für Populationsgenetik Vetmeduni, Vienna, Austria
| | | | | | - Olivier Hanotte
- School of Life Sciences, University of Nottingham Nottingham, UK
| | - Faiz-Ul Hassan
- School of Life Sciences, University of Nottingham Nottingham, UK ; Department of Animal Breeding and Genetics, University of Agriculture Faisalabad, Pakistan
| | - Philippe Helsen
- Centre for Research and Conservation, Royal Zoological Society of Antwerp Antwerp, Belgium
| | - Laura Iacolina
- Department of Chemistry and Bioscience, Aalborg University Aalborg, Denmark
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Green Technology Jokioinen, Finland ; Department of Biology, University of Eastern Finland Kuopio, Finland
| | - Kevin Leempoel
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | | | - Paolo Ajmone-Marsan
- BioDNA Centro di Ricerca sulla Biodiversità a sul DNA Antico, Istituto di Zootecnica, Università Cattolica del Sacro Cuore di Piacenza Italy
| | - Charles Masembe
- Institute of the Environment and Natural Resources, Makerere University Kampala, Uganda
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen University Wageningen, Netherlands
| | - Mara Miele
- School of Planning and Geography, Cardiff University Cardiff, UK
| | | | | | - François Pompanon
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes Grenoble, France
| | - Jutta Roosen
- TUM School of Management, Technische Universität München Munich, Germany
| | - Natalia Sevane
- Department of Animal Production, Veterinary Faculty, Universidad Complutense de Madrid Madrid, Spain
| | | | - Anamaria Štambuk
- Department of Biology, Faculty of Science, University of Zagreb Zagreb, Croatia
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, UK
| | - Sylvie Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - China Supakorn
- School of Life Sciences, University of Nottingham Nottingham, UK ; School of Agricultural Technology, Walailak University Tha Sala, Thailand
| | - Luis Telo Da Gama
- Centre of Research in Animal Health (CIISA) - Faculty of Veterinary Medicine, University of Lisbon Lisbon, Portugal
| | | | - Daniel Wegmann
- Department of Biology, University of Fribourg Fribourg, Switzerland
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences Beijing, China ; Cardiff University - Institute of Zoology, Joint Laboratory for Biocomplexity Research Beijing, China
| |
Collapse
|
7
|
Niemi M, Bläuer A, Iso-Touru T, Harjula J, Nyström Edmark V, Rannamäe E, Lõugas L, Sajantila A, Lidén K, Taavitsainen JP. Temporal fluctuation in North East Baltic Sea region cattle population revealed by mitochondrial and Y-chromosomal DNA analyses. PLoS One 2015; 10:e0123821. [PMID: 25992976 PMCID: PMC4439080 DOI: 10.1371/journal.pone.0123821] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 03/07/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Ancient DNA analysis offers a way to detect changes in populations over time. To date, most studies of ancient cattle have focused on their domestication in prehistory, while only a limited number of studies have analysed later periods. Conversely, the genetic structure of modern cattle populations is well known given the undertaking of several molecular and population genetic studies. RESULTS Bones and teeth from ancient cattle populations from the North-East Baltic Sea region dated to the Prehistoric (Late Bronze and Iron Age, 5 samples), Medieval (14), and Post-Medieval (26) periods were investigated by sequencing 667 base pairs (bp) from the mitochondrial DNA (mtDNA) and 155 bp of intron 19 in the Y-chromosomal UTY gene. Comparison of maternal (mtDNA haplotypes) genetic diversity in ancient cattle (45 samples) with modern cattle populations in Europe and Asia (2094 samples) revealed 30 ancient mtDNA haplotypes, 24 of which were shared with modern breeds, while 6 were unique to the ancient samples. Of seven Y-chromosomal sequences determined from ancient samples, six were Y2 and one Y1 haplotype. Combined data including Swedish samples from the same periods (64 samples) was compared with the occurrence of Y-chromosomal haplotypes in modern cattle (1614 samples). CONCLUSIONS The diversity of haplogroups was highest in the Prehistoric samples, where many haplotypes were unique. The Medieval and Post-Medieval samples also show a high diversity with new haplotypes. Some of these haplotypes have become frequent in modern breeds in the Nordic Countries and North-Western Russia while other haplotypes have remained in only a few local breeds or seem to have been lost. A temporal shift in Y-chromosomal haplotypes from Y2 to Y1 was detected that corresponds with the appearance of new mtDNA haplotypes in the Medieval and Post-Medieval period. This suggests a replacement of the Prehistoric mtDNA and Y chromosomal haplotypes by new types of cattle.
Collapse
Affiliation(s)
- Marianna Niemi
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
- University of Helsinki, Department of Forensic Medicine, Helsinki, Finland
- * E-mail:
| | - Auli Bläuer
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
- Department of Archaeology, University of Turku, Turku, Finland
| | - Terhi Iso-Touru
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
| | - Janne Harjula
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
- Department of Archaeology, University of Turku, Turku, Finland
| | | | - Eve Rannamäe
- Institute of History and Archaeology, University of Tartu, Tartu, Estonia
| | - Lembi Lõugas
- Institute of history, Tallinn University, Tallinn, Estonia
| | - Antti Sajantila
- University of Helsinki, Department of Forensic Medicine, Helsinki, Finland
| | - Kerstin Lidén
- Archaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| | | |
Collapse
|
8
|
Pelayo R, Valera M, Molina A, Royo LJ. Contribution of Lidia cattle breed historical castes to the paternal genetic stock of Spain. Anim Genet 2015; 46:312-5. [PMID: 25728408 DOI: 10.1111/age.12278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2015] [Indexed: 11/29/2022]
Abstract
The main objective of this work was to determine whether the five founding castes defined in the Lidia cattle breed actually have an important contribution to the Spanish paternal genetic stock as well as to the paternal genetic origin support. A total of 1300 Bos taurus male individuals were genotyped for five microsatellites (INRA189, UMN0103, UMN0307, BM861 and BYM1) and one indel (ZFY10). Microsatellite and indel alleles were combined into haplotypes, identifying a total of 38 haplotypes, 11 of them belonging to haplogroup Y1 and 27 to haplogroup Y2. Ten different haplotypes were found in the Lidia cattle breed, with five being exclusive to this breed. Our results agree with different male genetic stocks in the Lidia breed: one hypothetically representing the ancient Iberian bovine genetic stock (Gallardo, Navarra and Cabrera castes and some encastes from Vistahermosa) and a second one that is the result of the more recent breeding strategy of choosing the most aggressive individuals from traditional herds (including some Vistahermosa encastes and the Vazqueña caste). In terms of conservation, it would be better to not consider this breed as a unit but to consider the caste, or even better the encaste, as the target of putative conservation efforts.
Collapse
Affiliation(s)
- R Pelayo
- Department of Agroforestry Science, University of Seville, Seville, Spain
| | | | | | | |
Collapse
|
9
|
Magee DA, MacHugh DE, Edwards CJ. Interrogation of modern and ancient genomes reveals the complex domestic history of cattle. Anim Front 2014. [DOI: 10.2527/af.2014-0017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- David A. Magee
- Animal Genomics Laboratory, School of Agriculture and Food Science, College of Life Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - David E. MacHugh
- Animal Genomics Laboratory, School of Agriculture and Food Science, College of Life Sciences, University College Dublin, Belfield, Dublin 4, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | | |
Collapse
|
10
|
Y chromosome diversity and paternal origin of Chinese cattle. Mol Biol Rep 2013; 40:6633-6. [PMID: 24065546 DOI: 10.1007/s11033-013-2777-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 09/14/2013] [Indexed: 10/26/2022]
Abstract
To determine the Y chromosome genetic diversity and paternal origin of Chinese cattle, 369 bulls from 17 Chinese native cattle breeds and 30 bulls from Holstein and four bulls from Burma were analyzed using a recently discovered USP9Y marker that could distinguish between taurine and indicine cattle more efficiently. In total, the taurine Y1, Y2 haplogroup and indicine Y3 haplogroup were detected in 7 (1.9 %), 193 (52.3 %) and 169 (45.8 %) individuals of 17 Chinese native breeds, respectively, although these frequencies varied amongst the Chinese native cattle breeds examined. Y2 dominates in northern China (91.4 %), while Y3 dominates in southern China (81.2 %). Central China is an admixture zone with Y2 predominating overall (72.0 %). Our results demonstrate that Chinese cattle have two paternal origins, one from B. taurus (Y2) and the other from B. indicus (Y3). The Y1 haplogroup may originate from the imported beef cattle breeds in western countries. The geographical distributions of the Y2 and Y3 haplogroup frequencies reveal a pattern of male indicine introgression from south to north China, and male taurine introgression from north to south China.
Collapse
|
11
|
Niemi M, Bläuer A, Iso-Touru T, Nyström V, Harjula J, Taavitsainen JP, Storå J, Lidén K, Kantanen J. Mitochondrial DNA and Y-chromosomal diversity in ancient populations of domestic sheep (Ovis aries) in Finland: comparison with contemporary sheep breeds. Genet Sel Evol 2013; 45:2. [PMID: 23339395 PMCID: PMC3558444 DOI: 10.1186/1297-9686-45-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 11/30/2012] [Indexed: 11/16/2022] Open
Abstract
Background Several molecular and population genetic studies have focused on the native sheep breeds of Finland. In this work, we investigated their ancestral sheep populations from Iron Age, Medieval and Post-Medieval periods by sequencing a partial mitochondrial DNA D-loop and the 5’-promoter region of the SRY gene. We compared the maternal (mitochondrial DNA haplotypes) and paternal (SNP oY1) genetic diversity of ancient sheep in Finland with modern domestic sheep populations in Europe and Asia to study temporal changes in genetic variation and affinities between ancient and modern populations. Results A 523-bp mitochondrial DNA sequence was successfully amplified for 26 of 36 sheep ancient samples i.e. five, seven and 14 samples representative of Iron Age, Medieval and Post-Medieval sheep, respectively. Genetic diversity was analyzed within the cohorts. This ancient dataset was compared with present-day data consisting of 94 animals from 10 contemporary European breeds and with GenBank DNA sequence data to carry out a haplotype sharing analysis. Among the 18 ancient mitochondrial DNA haplotypes identified, 14 were present in the modern breeds. Ancient haplotypes were assigned to the highly divergent ovine haplogroups A and B, haplogroup B being the major lineage within the cohorts. Only two haplotypes were detected in the Iron Age samples, while the genetic diversity of the Medieval and Post-Medieval cohorts was higher. For three of the ancient DNA samples, Y-chromosome SRY gene sequences were amplified indicating that they originated from rams. The SRY gene of these three ancient ram samples contained SNP G-oY1, which is frequent in modern north-European sheep breeds. Conclusions Our study did not reveal any sign of major population replacement of native sheep in Finland since the Iron Age. Variations in the availability of archaeological remains may explain differences in genetic diversity estimates and patterns within the cohorts rather than demographic events that occurred in the past. Our ancient DNA results fit well with the genetic context of domestic sheep as determined by analyses of modern north-European sheep breeds.
Collapse
Affiliation(s)
- Marianna Niemi
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
| | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Wellmann R, Hartwig S, Bennewitz J. Optimum contribution selection for conserved populations with historic migration. Genet Sel Evol 2012; 44:34. [PMID: 23153196 PMCID: PMC3807754 DOI: 10.1186/1297-9686-44-34] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 10/17/2012] [Indexed: 11/11/2022] Open
Abstract
Background In recent decades, local varieties of domesticated animal species have been frequently crossed with economically superior breeds which has resulted in considerable genetic contributions from migrants. Optimum contribution selection by maximizing gene diversity while constraining breeding values of the offspring or vice versa could eventually lead to the extinction of local breeds with historic migration because maximization of gene diversity or breeding values would be achieved by maximization of migrant contributions. Therefore, other objective functions are needed for these breeds. Results Different objective functions and side constraints were compared with respect to their ability to reduce migrant contributions, to increase the genome equivalents originating from native founders, and to conserve gene diversity. Additionally, a new method for monitoring the development of effective size for breeds with incomplete pedigree records was applied. Approaches were compared for Vorderwald cattle, Hinterwald cattle, and Limpurg cattle. Migrant contributions could be substantially decreased for these three breeds, but the potential to increase the native genome equivalents is limited. Conclusions The most promising approach was constraining migrant contributions while maximizing the conditional probability that two alleles randomly chosen from the offspring population are not identical by descent, given that both descend from native founders.
Collapse
Affiliation(s)
- Robin Wellmann
- Institute of Animal Husbandry and Animal Breeding, University of Hohenheim, D-70599 Stuttgart, Germany.
| | | | | |
Collapse
|
13
|
Rizzi E, Lari M, Gigli E, De Bellis G, Caramelli D. Ancient DNA studies: new perspectives on old samples. Genet Sel Evol 2012; 44:21. [PMID: 22697611 PMCID: PMC3390907 DOI: 10.1186/1297-9686-44-21] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 06/14/2012] [Indexed: 11/24/2022] Open
Abstract
In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.
Collapse
Affiliation(s)
- Ermanno Rizzi
- Institute for Biomedical Technologies, National Research Council, Via F.lli Cervi 93, Segrate, Milan 20090, Italy
| | | | | | | | | |
Collapse
|
14
|
Svensson EM, Telldahl Y, Sjöling E, Sundkvist A, Hulth H, Sjøvold T, Götherström A. Coat colour and sex identification in horses from Iron Age Sweden. Ann Anat 2012; 194:82-7. [PMID: 22154005 DOI: 10.1016/j.aanat.2011.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 11/04/2011] [Accepted: 11/04/2011] [Indexed: 10/15/2022]
Abstract
Domestication of animals and plants marked a turning point in human prehistory. To date archaeology, archaeozoology and genetics have shed light on when and where all of our major livestock species were domesticated. Phenotypic changes associated with domestication have occurred in all farm animals. Coat colour is one of the traits that have been subjected to the strongest human selection throughout history. Here we use genotyping of coat colour SNPs in horses to investigate whether there were any regional differences or preferences for specific colours associated with specific cultural traditions in Iron Age Sweden. We do this by identifying the sex and coat colour of horses sacrificed at Skedemosse, Öland (Sweden) during the Iron Age, as well as in horses from two sites in Uppland, Ultuna and Valsgärde (dated to late Iron Age). We show that bay, black and chestnut colours were all common and two horses with tobiano spotting were found. We also show how the combination of sex identification with genotyping of just a few SNPs underlying the basic coat colours can be used to identify the minimum number of individuals at a site on a higher level than morphological methods alone. Although separated by 500 km and from significantly different archaeological contexts the horses at Skedemosse and Ultuna are quite homogenous when it comes to coat colour phenotypes, indicating that there were no clear geographical variation in coat colouration in Sweden during the late Iron Age and early Viking Age.
Collapse
Affiliation(s)
- Emma M Svensson
- Department of Evolutionary Biology, EBC, Uppsala University, Sweden.
| | | | | | | | | | | | | |
Collapse
|
15
|
Telldahl Y, Svensson E, Götherström A, Storå J. Typing late prehistoric cows and bulls--osteology and genetics of cattle at the Eketorp ringfort on the Öland island in Sweden. PLoS One 2011; 6:e20748. [PMID: 21731623 PMCID: PMC3120812 DOI: 10.1371/journal.pone.0020748] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 05/12/2011] [Indexed: 11/18/2022] Open
Abstract
Human management of livestock and the presence of different breeds have been discussed in archaeozoology and animal breeding. Traditionally osteometrics has been the main tool in addressing these questions. We combine osteometrics with molecular sex identifications of 104 of 340 morphometrically analysed bones in order to investigate the use of cattle at the Eketorp ringfort on the Öland island in Sweden. The fort is dated to 300-1220/50 A.D., revealing three different building phases. In order to investigate specific patterns and shifts through time in the use of cattle the genetic data is evaluated in relation to osteometric patterns and occurrence of pathologies on cattle metapodia. Males were genotyped for a Y-chromosomal SNP in UTY19 that separates the two major haplogroups, Y1 and Y2, in taurine cattle. A subset of the samples were also genotyped for one SNP involved in coat coloration (MC1R), one SNP putatively involved in resistance to cattle plague (TLR4), and one SNP in intron 5 of the IGF-1 gene that has been associated to size and reproduction.The results of the molecular analyses confirm that the skeletal assemblage from Eketorp is dominated by skeletal elements from females, which implies that dairying was important. Pathological lesions on the metapodia were classified into two groups; those associated with the use as draught animals and those lesions without a similar aetiology. The results show that while bulls both exhibit draught related lesions and other types of lesions, cows exhibit other types of lesions. Interestingly, a few elements from females exhibit draught related lesions. We conclude that this reflects the different use of adult female and male cattle.Although we note some variation in the use of cattle at Eketorp between Iron Age and Medieval time we have found little evidence for the use of different types of animals for specific purposes. The use of specific (genetic) breeds seems to be a phenomenon that developed later than the Eketorp settlement.
Collapse
Affiliation(s)
- Ylva Telldahl
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
| | | | | | | |
Collapse
|
16
|
Edwards CJ, Ginja C, Kantanen J, Pérez-Pardal L, Tresset A, Stock F, Gama LT, Penedo MCT, Bradley DG, Lenstra JA, Nijman IJ. Dual origins of dairy cattle farming--evidence from a comprehensive survey of European Y-chromosomal variation. PLoS One 2011; 6:e15922. [PMID: 21253012 PMCID: PMC3016991 DOI: 10.1371/journal.pone.0015922] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 11/29/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Diversity patterns of livestock species are informative to the history of agriculture and indicate uniqueness of breeds as relevant for conservation. So far, most studies on cattle have focused on mitochondrial and autosomal DNA variation. Previous studies of Y-chromosomal variation, with limited breed panels, identified two Bos taurus (taurine) haplogroups (Y1 and Y2; both composed of several haplotypes) and one Bos indicus (indicine/zebu) haplogroup (Y3), as well as a strong phylogeographic structuring of paternal lineages. METHODOLOGY AND PRINCIPAL FINDINGS Haplogroup data were collected for 2087 animals from 138 breeds. For 111 breeds, these were resolved further by genotyping microsatellites INRA189 (10 alleles) and BM861 (2 alleles). European cattle carry exclusively taurine haplotypes, with the zebu Y-chromosomes having appreciable frequencies in Southwest Asian populations. Y1 is predominant in northern and north-western Europe, but is also observed in several Iberian breeds, as well as in Southwest Asia. A single Y1 haplotype is predominant in north-central Europe and a single Y2 haplotype in central Europe. In contrast, we found both Y1 and Y2 haplotypes in Britain, the Nordic region and Russia, with the highest Y-chromosomal diversity seen in the Iberian Peninsula. CONCLUSIONS We propose that the homogeneous Y1 and Y2 regions reflect founder effects associated with the development and expansion of two groups of dairy cattle, the pied or red breeds from the North Sea and Baltic coasts and the spotted, yellow or brown breeds from Switzerland, respectively. The present Y1-Y2 contrast in central Europe coincides with historic, linguistic, religious and cultural boundaries.
Collapse
Affiliation(s)
- Ceiridwen J. Edwards
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Research Laboratory for Archaeology, University of Oxford, Oxford, United Kingdom
| | - Catarina Ginja
- Veterinary Genetics Laboratory, University of California Davis, Davis, California, United States of America
- Departamento de Genética, Melhoramento Animal e Reprodução, Instituto Nacional dos Recursos Biológicos, Fonte Boa, Vale de Santarém, Portugal
| | - Juha Kantanen
- Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
| | | | - Anne Tresset
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, CNRS Muséum National d'Histoire Naturelle, Paris, France
| | - Frauke Stock
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Luis T. Gama
- Departamento de Genética, Melhoramento Animal e Reprodução, Instituto Nacional dos Recursos Biológicos, Fonte Boa, Vale de Santarém, Portugal
| | - M. Cecilia T. Penedo
- Veterinary Genetics Laboratory, University of California Davis, Davis, California, United States of America
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Isaäc J. Nijman
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
17
|
Ajmone-Marsan P, Garcia JF, Lenstra JA. On the origin of cattle: How aurochs became cattle and colonized the world. Evol Anthropol 2010. [DOI: 10.1002/evan.20267] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
18
|
Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S. Genetic diversity in farm animals--a review. Anim Genet 2010; 41 Suppl 1:6-31. [PMID: 20500753 DOI: 10.1111/j.1365-2052.2010.02038.x] [Citation(s) in RCA: 293] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.
Collapse
Affiliation(s)
- L F Groeneveld
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Hoeltystr. 10, 31535 Neustadt, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Pérez-Pardal L, Royo LJ, Beja-Pereira A, Curik I, Traoré A, Fernández I, Sölkner J, Alonso J, Álvarez I, Bozzi R, Chen S, Ponce de León FA, Goyache F. Y-specific microsatellites reveal an African subfamily in taurine (Bos taurus) cattle. Anim Genet 2010; 41:232-41. [DOI: 10.1111/j.1365-2052.2009.01988.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
20
|
Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA. Proc Natl Acad Sci U S A 2010; 107:7686-91. [PMID: 20404179 DOI: 10.1073/pnas.0912264107] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The establishment of agricultural economies based upon domestic animals began independently in many parts of the world and led to both increases in human population size and the migration of people carrying domestic plants and animals. The precise circumstances of the earliest phases of these events remain mysterious given their antiquity and the fact that subsequent waves of migrants have often replaced the first. Through the use of more than 1,500 modern (including 151 previously uncharacterized specimens) and 18 ancient (representing six East Asian archeological sites) pig (Sus scrofa) DNA sequences sampled across East Asia, we provide evidence for the long-term genetic continuity between modern and ancient Chinese domestic pigs. Although the Chinese case for independent pig domestication is supported by both genetic and archaeological evidence, we discuss five additional (and possibly) independent domestications of indigenous wild boar populations: one in India, three in peninsular Southeast Asia, and one off the coast of Taiwan. Collectively, we refer to these instances as "cryptic domestication," given the current lack of corroborating archaeological evidence. In addition, we demonstrate the existence of numerous populations of genetically distinct and widespread wild boar populations that have not contributed maternal genetic material to modern domestic stocks. The overall findings provide the most complete picture yet of pig evolution and domestication in East Asia, and generate testable hypotheses regarding the development and spread of early farmers in the Far East.
Collapse
|
21
|
Pérez-Pardal L, Royo LJ, Beja-Pereira A, Chen S, Cantet RJC, Traoré A, Curik I, Sölkner J, Bozzi R, Fernández I, Alvarez I, Gutiérrez JP, Gómez E, Ponce de León FA, Goyache F. Multiple paternal origins of domestic cattle revealed by Y-specific interspersed multilocus microsatellites. Heredity (Edinb) 2010; 105:511-9. [PMID: 20332805 DOI: 10.1038/hdy.2010.30] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In this study, we show how Y-specific interspersed multilocus microsatellites, which are loci that yield several amplified bands differing in size from the same male individual and PCR reaction, are a powerful source of information for tracing the history of cattle. Our results confirm the existence of three main groups of sires, which are separated by evolutionary time and clearly predate domestication. These three groups are consistent with the haplogroups previously identified by Götherström et al. (2005) using five Y-specific segregating sites: Y1 and Y2 in taurine (Bos taurus) cattle and Y3 in zebu (Bos indicus) cattle. The zebu cattle cluster clearly originates from a domestication process that was geographically and temporally separated from that of taurine clusters. Our analyses further suggest that: (i) introgression of wild sire genetic material into domesticated herds may have a significant role in the formation of modern cattle, including the formation of the Y1 haplogroup; (ii) a putative domestication event in Africa probably included local Y2-like wild sires; (iii) the West African zebu cattle Y-chromosome may have partially originated from an ancient introgression of humped cattle into Africa; and (iv) the high genetic similarity among Asian zebu sires is consistent with a single domestication process.
Collapse
Affiliation(s)
- L Pérez-Pardal
- Área de Genética y Reproducción Animal, SERIDA, Camino de Rioseco, Camino de Rioseco 1225, Gijón, Asturias, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|