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      Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia

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          Abstract

          A fine-grained mitochondrial DNA phylogenomic analysis was conducted in domestic pigs and wild boars, revealing that pig domestication in East Asia occurred in the Mekong and the middle and downstream regions of the Yangtze river.

          Abstract

          Background

          Previously reported evidence indicates that pigs were independently domesticated in multiple places throughout the world. However, a detailed picture of the origin and dispersal of domestic pigs in East Asia has not yet been reported.

          Results

          Population phylogenomic analysis was conducted in domestic pigs and wild boars by screening the haplogroup-specific mutation motifs inferred from a phylogenetic tree of pig complete mitochondrial DNA (mtDNA) sequences. All domestic pigs are clustered into single clade D (which contains subclades D1, D2, D3, and D4), with wild boars from East Asia being interspersed. Three haplogroups within D1 are dominant in the Mekong region (D1a2 and D1b) and the middle and downstream regions of the Yangtze River (D1a1a), and may represent independent founders of domestic pigs. None of the domestic pig samples from North East Asia, the Yellow River region, and the upstream region of the Yangtze River share the same haplogroup status with the local wild boars. The limited regional distributions of haplogroups D1 (including its subhaplogroups), D2, D3, and D4 in domestic pigs suggest at least two different in situ domestication events.

          Conclusion

          The use of fine-grained mtDNA phylogenomic analysis of wild boars and domestic pigs is a powerful tool with which to discern the origin of domestic pigs. Our findings show that pig domestication in East Asia mainly occurred in the Mekong region and the middle and downstream regions of the Yangtze River.

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          Most cited references58

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          DnaSP, DNA polymorphism analyses by the coalescent and other methods.

          DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (approximately 5 Mb per sequence); (2) conducting a large number of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical outputs for an easy visualization of results. The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp
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            Evidence for two independent domestications of cattle.

            The origin and taxonomic status of domesticated cattle are controversial. Zebu and taurine breeds are differentiated primarily by the presence or absence of a hump and have been recognized as separate species (Bos indicus and Bos taurus). However, the most widely held view is that both types of cattle derive from a single domestication event 8000-10,000 years ago. We have examined mtDNA sequences from representatives of six European (taurine) breeds, three Indian (zebu) breeds, and four African (three zebu, one taurine) breeds. Similar levels of average sequence divergence were observed among animals within each of the major continental groups: 0.41% (European), 0.38% (African), and 0.42% (Indian). However, the sequences fell into two very distinct geographic lineages that do not correspond with the taurine-zebu dichotomy: all European and African breeds are in one lineage, and all Indian breeds are in the other. There was little indication of breed clustering within either lineage. Application of a molecular clock suggests that the two major mtDNA clades diverged at least 200,000, and possibly as much as 1 million, years ago. This relatively large divergence is interpreted most simply as evidence for two separate domestication events, presumably of different subspecies of the aurochs, Bos primigenius. The clustering of all African zebu mtDNA sequences within the taurine lineage is attributed to ancestral crossbreeding with the earlier B. taurus inhabitants of the continent.
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              Mitochondrial portraits of human populations using median networks.

              Analysis of variation in the hypervariable region of mitochondrial DNA (mtDNA) has emerged as an important tool for studying human evolution and migration. However, attempts to reconstruct optimal intraspecific mtDNA phylogenies frequently fail because parallel mutation events partly obscure the true evolutionary pathways. This makes it inadvisable to present a single phylogenetic tree at the expense of neglecting equally acceptable ones. As an alternative, we propose a novel network approach for portraying mtDNA relationships. For small sample sizes (< approximately 50), an unmodified median network contains all most parsimonious trees, displays graphically the full information content of the sequence data, and can easily be generated by hand. For larger sample sizes, we reduce the complexity of the network by identifying parallelisms. This reduction procedure is guided by a compatibility argument and an additional source of phylogenetic information: the frequencies of the mitochondrial haplotypes. As a spin-off, our approach can also assist in identifying sequencing errors, which manifest themselves in implausible network substructures. We illustrate the advantages of our approach with several examples from existing data sets.
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                Author and article information

                Journal
                Genome Biol
                Genome Biology
                BioMed Central
                1465-6906
                1465-6914
                2007
                19 November 2007
                : 8
                : 11
                : R245
                Affiliations
                [1 ]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
                [2 ]Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, 2 North Greenlake Street, Kunming 650091, China
                [3 ]The Graduate School of the Chinese Academy of Sciences, 19 Yuquan Street, Beijing, 100039, China
                [4 ]Center for Pharmacogenomics, Department of Psychiatry and Behavioral Science, University of Miami Miller School of Medicine, 1580 NW 10 th Ave., Miami, Florida 33136, USA
                [5 ]Key Laboratory of Animal Models and Human Disease Mechanisms, 32 East Jiaochang Road, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
                [6 ]China Agriculture University, 2 West Yuanmingyuan Street, Beijing 10094, China
                [7 ]College of Life Sciences, Sun Yat-sen University, 135 West Xin'gang Street, Guangzhou 510275, China
                Article
                gb-2007-8-11-r245
                10.1186/gb-2007-8-11-r245
                2258183
                18021448
                c005778f-6986-4047-a40c-b2ffb7ccd55d
                Copyright © 2007 Wu et al; licensee BioMed Central Ltd.

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 8 November 2006
                : 8 February 2007
                : 19 November 2007
                Categories
                Research

                Genetics
                Genetics

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