Phylogenetic Distinctiveness of Middle Eastern and Southeast Asian Village Dog Y Chromosomes Illuminates Dog Origins
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{"title"=>"Phylogenetic distinctiveness of Middle Eastern and Southeast Asian village dog Y chromosomes illuminates dog origins", "type"=>"journal", "authors"=>[{"first_name"=>"Sarah K.", "last_name"=>"Brown", "scopus_author_id"=>"7501416848"}, {"first_name"=>"Niels C.", "last_name"=>"Pedersen", "scopus_author_id"=>"7202299909"}, {"first_name"=>"Sardar", "last_name"=>"Jafarishorijeh", "scopus_author_id"=>"54681877300"}, {"first_name"=>"Danika L.", "last_name"=>"Bannasch", "scopus_author_id"=>"6603323478"}, {"first_name"=>"Kristen D.", "last_name"=>"Ahrens", "scopus_author_id"=>"54681565500"}, {"first_name"=>"Jui Te", "last_name"=>"Wu", "scopus_author_id"=>"56093688500"}, {"first_name"=>"Michaella", "last_name"=>"Okon", "scopus_author_id"=>"54682229400"}, {"first_name"=>"Benjamin N.", "last_name"=>"Sacks", "scopus_author_id"=>"7004432277"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"363076103", "sgr"=>"83355167998", "pmid"=>"22194840", "scopus"=>"2-s2.0-83355167998", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0028496", "issn"=>"19326203"}, "id"=>"ea27c21d-6b12-342c-a26d-6e8c57cf4152", "abstract"=>"Modern genetic samples are commonly used to trace dog origins, which entails untested assumptions that village dogs reflect indigenous ancestry or that breed origins can be reliably traced to particular regions. We used high-resolution Y chromosome markers (SNP and STR) and mitochondrial DNA to analyze 495 village dogs/dingoes from the Middle East and Southeast Asia, along with 138 dogs from >35 modern breeds to 1) assess genetic divergence between Middle Eastern and Southeast Asian village dogs and their phylogenetic affinities to Australian dingoes and gray wolves (Canis lupus) and 2) compare the genetic affinities of modern breeds to regional indigenous village dog populations. The Y chromosome markers indicated that village dogs in the two regions corresponded to reciprocally monophyletic clades, reflecting several to many thousand years divergence, predating the Neolithic ages, and indicating long-indigenous roots to those regions. As expected, breeds of the Middle East and East Asia clustered within the respective regional village dog clade. Australian dingoes also clustered in the Southeast Asian clade. However, the European and American breeds clustered almost entirely within the Southeast Asian clade, even sharing many haplotypes, suggesting a substantial and recent influence of East Asian dogs in the creation of European breeds. Comparison to 818 published breed dog Y STR haplotypes confirmed this conclusion and indicated that some African breeds reflect another distinct patrilineal origin. The lower-resolution mtDNA marker consistently supported Y-chromosome results. Both marker types confirmed previous findings of higher genetic diversity in dogs from Southeast Asia than the Middle East. Our findings demonstrate the importance of village dogs as windows into the past and provide a reference against which ancient DNA can be used to further elucidate origins and spread of the domestic dog.", "link"=>"http://www.mendeley.com/research/phylogenetic-distinctiveness-middle-eastern-southeast-asian-village-dog-y-chromosomes-illuminates-do", "reader_count"=>147, "reader_count_by_academic_status"=>{"Unspecified"=>6, "Professor > Associate Professor"=>6, "Researcher"=>42, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>7, "Student > Master"=>24, "Other"=>14, "Student > Bachelor"=>12, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>6, "Professor > Associate Professor"=>6, "Researcher"=>42, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>27, "Student > Postgraduate"=>7, "Student > Master"=>24, "Other"=>14, "Student > Bachelor"=>12, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>6, "Environmental Science"=>25, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>97, "Arts and Humanities"=>3, "Veterinary Science and Veterinary Medicine"=>1, "Psychology"=>3, "Social Sciences"=>5, "Earth and Planetary Sciences"=>4, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>5}, "Psychology"=>{"Psychology"=>3}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>97}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>6}, "Environmental Science"=>{"Environmental Science"=>25}, "Arts and Humanities"=>{"Arts and Humanities"=>3}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "United States"=>1, "Japan"=>1, "United Kingdom"=>1, "United Arab Emirates"=>1, "Portugal"=>1, "India"=>1, "Czech Republic"=>1, "Turkey"=>1, "Belgium"=>1, "Iran"=>1, "China"=>1, "Brazil"=>3, "Peru"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/702473"], "description"=>"<p>Networks of dog (circles) and wolf (squares) NRY SNP-STR haplotypes, including 300 village dogs/dingoes, 124 breed dogs, and 7 wolves. Size of circle is proportional to sample size, except that the larges circle represents 18–50 individuals, and line lengths are proportional to the number of mutational steps. Subclades are numbered corresponding to SNP haplotypes in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028496#pone-0028496-g001\" target=\"_blank\">Figure 1</a>, and are circumscribed by dashed black lines.</p>", "links"=>[], "tags"=>["breed", "chromosome", "snp-str", "haplotype"], "article_id"=>372841, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sarah K. Brown", "Niels C. Pedersen", "Sardar Jafarishorijeh", "Danika L. Bannasch", "Kristen D. Ahrens", "Jui-Te Wu", "Michaella Okon", "Benjamin N. Sacks"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0028496.g003", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Village_and_breed_dog_Y_chromosome_SNP_STR_haplotype_networks_/372841", "title"=>"Village and breed dog Y chromosome SNP-STR haplotype networks.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-14 00:47:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/702655"], "description"=>"a<p>Haplotype pairs, A16/A17 and A18/A20, were indistinguishable from the 402-bp region examined in our study.</p>", "links"=>[], "tags"=>["mtdna", "haplotypes", "hypervariable", "corresponding", "types", "431", "dogs", "asia"], "article_id"=>373027, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sarah K. Brown", "Niels C. Pedersen", "Sardar Jafarishorijeh", "Danika L. Bannasch", "Kristen D. Ahrens", "Jui-Te Wu", "Michaella Okon", "Benjamin N. Sacks"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0028496.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_mtDNA_haplotypes_402_bp_from_hypervariable_region_I_corresponding_to_universally_occurring_types_UT_14_in_431_village_dogs_from_Southeast_Asia_and_the_Middle_East_/373027", "title"=>"Distribution of mtDNA haplotypes (402-bp from hypervariable region I) corresponding to “universally occurring” types (UT; [14]) in 431 village dogs from Southeast Asia and the Middle East.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-12-14 00:50:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/357534", "https://ndownloader.figshare.com/files/357570", "https://ndownloader.figshare.com/files/357634", "https://ndownloader.figshare.com/files/357680", "https://ndownloader.figshare.com/files/357720", "https://ndownloader.figshare.com/files/357770", "https://ndownloader.figshare.com/files/357817", "https://ndownloader.figshare.com/files/357871", "https://ndownloader.figshare.com/files/357925", "https://ndownloader.figshare.com/files/357973", "https://ndownloader.figshare.com/files/358046", "https://ndownloader.figshare.com/files/358145"], "description"=>"<div><p>Modern genetic samples are commonly used to trace dog origins, which entails untested assumptions that village dogs reflect indigenous ancestry or that breed origins can be reliably traced to particular regions. We used high-resolution Y chromosome markers (SNP and STR) and mitochondrial DNA to analyze 495 village dogs/dingoes from the Middle East and Southeast Asia, along with 138 dogs from >35 modern breeds to 1) assess genetic divergence between Middle Eastern and Southeast Asian village dogs and their phylogenetic affinities to Australian dingoes and gray wolves (<em>Canis lupus</em>) and 2) compare the genetic affinities of modern breeds to regional indigenous village dog populations. The Y chromosome markers indicated that village dogs in the two regions corresponded to reciprocally monophyletic clades, reflecting several to many thousand years divergence, predating the Neolithic ages, and indicating long-indigenous roots to those regions. As expected, breeds of the Middle East and East Asia clustered within the respective regional village dog clade. Australian dingoes also clustered in the Southeast Asian clade. However, the European and American breeds clustered almost entirely within the Southeast Asian clade, even sharing many haplotypes, suggesting a substantial and recent influence of East Asian dogs in the creation of European breeds. Comparison to 818 published breed dog Y STR haplotypes confirmed this conclusion and indicated that some African breeds reflect another distinct patrilineal origin. The lower-resolution mtDNA marker consistently supported Y-chromosome results. Both marker types confirmed previous findings of higher genetic diversity in dogs from Southeast Asia than the Middle East. Our findings demonstrate the importance of village dogs as windows into the past and provide a reference against which ancient DNA can be used to further elucidate origins and spread of the domestic dog.</p> </div>", "links"=>[], "tags"=>["phylogenetic", "distinctiveness", "asian", "chromosomes", "illuminates", "origins"], "article_id"=>130653, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sarah K. Brown", "Niels C. Pedersen", "Sardar Jafarishorijeh", "Danika L. Bannasch", "Kristen D. Ahrens", "Jui-Te Wu", "Michaella Okon", "Benjamin N. Sacks"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0028496.s001", "https://dx.doi.org/10.1371/journal.pone.0028496.s002", "https://dx.doi.org/10.1371/journal.pone.0028496.s003", "https://dx.doi.org/10.1371/journal.pone.0028496.s004", "https://dx.doi.org/10.1371/journal.pone.0028496.s005", "https://dx.doi.org/10.1371/journal.pone.0028496.s006", "https://dx.doi.org/10.1371/journal.pone.0028496.s007", "https://dx.doi.org/10.1371/journal.pone.0028496.s008", "https://dx.doi.org/10.1371/journal.pone.0028496.s009", "https://dx.doi.org/10.1371/journal.pone.0028496.s010", "https://dx.doi.org/10.1371/journal.pone.0028496.s011", "https://dx.doi.org/10.1371/journal.pone.0028496.s012"], "stats"=>{"downloads"=>20, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Phylogenetic_Distinctiveness_of_Middle_Eastern_and_Southeast_Asian_Village_Dog_Y_Chromosomes_Illuminates_Dog_Origins/130653", "title"=>"Phylogenetic Distinctiveness of Middle Eastern and Southeast Asian Village Dog Y Chromosomes Illuminates Dog Origins", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-12-14 00:10:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/702544"], "description"=>"<p>Samples include 428 village dogs, dingoes, and breed dogs genotyped in this study and 818 published breed dog haplotypes <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028496#pone.0028496-Bannasch1\" target=\"_blank\">[21]</a>, color coded according to putative region of breed origin (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028496#pone.0028496.s012\" target=\"_blank\">Table S10</a>). Size of circle is proportional to sample size, except that the largest circle represents 18–50 individuals, and line lengths are proportional to the number of mutational steps.</p>", "links"=>[], "tags"=>["chromosome", "str", "haplotype", "putative", "geographic", "breed"], "article_id"=>372910, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sarah K. Brown", "Niels C. Pedersen", "Sardar Jafarishorijeh", "Danika L. Bannasch", "Kristen D. Ahrens", "Jui-Te Wu", "Michaella Okon", "Benjamin N. Sacks"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0028496.g004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Y_chromosome_STR_haplotype_network_indicating_putative_geographic_origin_of_breed_dogs_/372910", "title"=>"Y chromosome STR haplotype network indicating putative geographic origin of breed dogs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-14 00:48:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/702398"], "description"=>"<p>Networks of 300 village dog/dingo (circles) and 7 wolf (squares) (a) NRY STR haplotypes and (b) NRY SNP-STR haplotypes, including (a,b) 164 Southeast Asian village dogs/dingoes, 136 Middle Eastern village dogs, 1 Chinese wolf, 3 Iranian wolves, and 3 Canadian wolves. Size of circle is proportional to sample size, except that the largest circle represents 18–50 individuals, and line lengths are proportional to the number of mutational steps. (b) NRY SNP-STR subclades corresponding to numbered SNP haplotypes in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028496#pone-0028496-g001\" target=\"_blank\">Figure 1</a> are circumscribed by dashed black lines.</p>", "links"=>[], "tags"=>["chromosome", "str", "snp-str", "haplotype"], "article_id"=>372769, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sarah K. Brown", "Niels C. Pedersen", "Sardar Jafarishorijeh", "Danika L. Bannasch", "Kristen D. Ahrens", "Jui-Te Wu", "Michaella Okon", "Benjamin N. Sacks"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0028496.g002", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Village_dog_Y_chromosome_STR_and_SNP_STR_haplotype_networks_/372769", "title"=>"Village dog Y chromosome STR and SNP-STR haplotype networks.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-14 00:46:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/702344"], "description"=>"<p>Samples include Southeast Asian village dogs (<i>n</i> = 159), Australian dingoes (<i>n</i> = 5), Middle Eastern village dogs (<i>n</i> = 136), wolves (<i>n</i> = 7), dhole (<i>n</i> = 1) and black-backed jackal (<i>n</i> = 1), which form a primarily Middle East village dog clade, including wolf and outgroup taxa, and a primarily Southeast Asian village dog clade. The 8 haplotypes were based on 11 SNP mutations and included 6 found previously (haplotypes 1–9, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028496#pone.0028496-Natanaelsson1\" target=\"_blank\">[25]</a>) and 3 new ones (haplotypes 10–12; reflected previously as unsampled nodes). Haplotypes 1–4 could not be distinguished based on the 11 sites genotyped in our study. Size of circle is proportional to sample size. Haplotypes of 48 village dogs were incomplete and imputed based on 8–10 SNPs and associations with similar STR haplotypes (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028496#pone.0028496.s009\" target=\"_blank\">Table S7</a>).</p>", "links"=>[], "tags"=>["chromosome", "snp", "haplotype", "dogs"], "article_id"=>372713, "categories"=>["Ecology", "Genetics", "Evolutionary Biology"], "users"=>["Sarah K. Brown", "Niels C. Pedersen", "Sardar Jafarishorijeh", "Danika L. Bannasch", "Kristen D. Ahrens", "Jui-Te Wu", "Michaella Okon", "Benjamin N. Sacks"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0028496.g001", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Y_chromosome_SNP_haplotype_network_of_village_dogs_and_wild_canids_/372713", "title"=>"Y chromosome SNP haplotype network of village dogs and wild canids.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-12-14 00:45:13"}

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