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{"title"=>"Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions", "type"=>"journal", "authors"=>[{"first_name"=>"Matthew C.", "last_name"=>"Dulik", "scopus_author_id"=>"24437462400"}, {"first_name"=>"Ludmila P.", "last_name"=>"Osipova", "scopus_author_id"=>"7005170124"}, {"first_name"=>"Theodore G.", "last_name"=>"Schurr", "scopus_author_id"=>"7003287562"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"21412412", "doi"=>"10.1371/journal.pone.0017548", "sgr"=>"79952611182", "isbn"=>"1932-6203", "scopus"=>"2-s2.0-79952611182", "issn"=>"19326203", "pui"=>"361433588"}, "id"=>"e98576a0-dcd9-359a-94b8-09ce307bd439", "abstract"=>"Kazakh populations have traditionally lived as nomadic pastoralists that seasonally migrate across the steppe and surrounding mountain ranges in Kazakhstan and southern Siberia. To clarify their population history from a paternal perspective, we analyzed the non-recombining portion of the Y-chromosome from Kazakh populations living in southern Altai Republic, Russia, using a high-resolution analysis of 60 biallelic markers and 17 STRs. We noted distinct differences in the patterns of genetic variation between maternal and paternal genetic systems in the Altaian Kazakhs. While they possess a variety of East and West Eurasian mtDNA haplogroups, only three East Eurasian paternal haplogroups appear at significant frequencies (C3*, C3c and O3a3c*). In addition, the Y-STR data revealed low genetic diversity within these lineages. Analysis of the combined biallelic and STR data also demonstrated genetic differences among Kazakh populations from across Central Asia. The observed differences between Altaian Kazakhs and indigenous Kazakhs were not the result of admixture between Altaian Kazakhs and indigenous Altaians. Overall, the shared paternal ancestry of Kazakhs differentiates them from other Central Asian populations. In addition, all of them showed evidence of genetic influence by the 13(th) century CE Mongol Empire. Ultimately, the social and cultural traditions of the Kazakhs shaped their current pattern of genetic variation.", "link"=>"http://www.mendeley.com/research/ychromosome-variation-altaian-kazakhs-reveals-common-paternal-gene-pool-kazakhs-influence-mongolian", "reader_count"=>48, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>4, "Researcher"=>6, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>1, "Student > Master"=>9, "Other"=>3, "Student > Bachelor"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>4, "Researcher"=>6, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>1, "Student > Master"=>9, "Other"=>3, "Student > Bachelor"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>25, "Medicine and Dentistry"=>4, "Psychology"=>1, "Social Sciences"=>2, "Computer Science"=>1, "Earth and Planetary Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Social Sciences"=>{"Social Sciences"=>2}, "Psychology"=>{"Psychology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>25}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"Belgium"=>1, "Brazil"=>1, "Mexico"=>1, "Chile"=>1, "Spain"=>1}, "group_count"=>3}

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• http://doi.org/10.1016/j.ajhg.2011.12.014
• http://doi.org/10.1007/s00414-013-0948-y
• http://doi.org/10.1007/s00414-018-1859-8
• http://doi.org/10.1007/s00438-014-0925-2
• http://doi.org/10.1002/ajpa.23789
• http://doi.org/10.1038/jhg.2012.93
• http://doi.org/10.1016/j.gene.2016.11.018
• http://doi.org/10.1038/ejhg.2012.86
• http://doi.org/10.1002/ajpa.22068
• http://doi.org/10.1007/s00414-018-1962-x
• http://doi.org/10.1016/j.ajhg.2016.05.025
• http://doi.org/10.1002/ajpa.23324
• http://doi.org/10.1017/S0016672312000298
• http://doi.org/10.1371/journal.pone.0115265
• http://doi.org/10.1038/ejhg.2015.183
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• http://doi.org/10.1371/journal.pone.0161622
• http://doi.org/10.1038/s41598-017-03176-z
• http://doi.org/10.1371/journal.pone.0076748
• http://doi.org/10.1371/journal.pone.0041252
• http://doi.org/10.1038/srep19998
• http://doi.org/10.1002/ajpa.23151
• http://doi.org/10.1016/j.fsigen.2019.07.017
• http://doi.org/10.1080/1751696X.2014.969506
• http://doi.org/10.1186/s12863-014-0131-6
• http://doi.org/10.1038/s41431-018-0245-9
• http://doi.org/10.1371/journal.pgen.1003634
• http://doi.org/10.1038/jhg.2013.108
• http://doi.org/10.1038/jhg.2016.14

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• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/67447eb5-11f9-4a62-8059-b3ad80f5e258", "title"=>"Media Coverage of This Article", "body"=>"The following article represents some of the media coverage that has occurred for this paper:\n\nPublication: For what they were we are \nTitle: “For what they were... we are: Y-DNA of Khazaks from Altay Republic”\nhttp://forwhattheywereweare.blogspot.co.uk/2011/03/y-dna-of-khazaks-from-altay-republic.html\n\nIf you see any additional coverage of this paper in the press or blogosphere, please reply to this thread and add the link to the article. \n", "isRemoved"=>false, "created"=>"2013-04-01T18:23:47Z", "lastModified"=>"2013-04-01T18:23:47Z", "creator"=>{"userId"=>"80539"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"PLOS ONE Staff"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0017548", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2013-04-01T18:23:47Z", "replies"=>[]}

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• {"title"=>"Haplogroup Q-M346", "url"=>"http://en.wikipedia.org/wiki/Haplogroup_Q-M346", "timestamp"=>"2019-02-18T16:09:10Z"}
• {"title"=>"Haplogroup C-M217", "url"=>"http://en.wikipedia.org/wiki/Haplogroup_C-M217", "timestamp"=>"2019-03-20T23:49:06Z"}
• {"title"=>"Haplogroup G (Y-DNA) by country", "url"=>"http://en.wikipedia.org/wiki/Haplogroup_G_(Y-DNA)_by_country", "timestamp"=>"2019-02-19T13:23:04Z"}
• {"title"=>"Haplogroup T-M184", "url"=>"http://en.wikipedia.org/wiki/Haplogroup_T-M184", "timestamp"=>"2019-03-20T19:05:35Z"}

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• {"files"=>["https://ndownloader.figshare.com/files/396090", "https://ndownloader.figshare.com/files/396127"], "description"=>"<div><p>Kazakh populations have traditionally lived as nomadic pastoralists that seasonally migrate across the steppe and surrounding mountain ranges in Kazakhstan and southern Siberia. To clarify their population history from a paternal perspective, we analyzed the non-recombining portion of the Y-chromosome from Kazakh populations living in southern Altai Republic, Russia, using a high-resolution analysis of 60 biallelic markers and 17 STRs. We noted distinct differences in the patterns of genetic variation between maternal and paternal genetic systems in the Altaian Kazakhs. While they possess a variety of East and West Eurasian mtDNA haplogroups, only three East Eurasian paternal haplogroups appear at significant frequencies (C3*, C3c and O3a3c*). In addition, the Y-STR data revealed low genetic diversity within these lineages. Analysis of the combined biallelic and STR data also demonstrated genetic differences among Kazakh populations from across Central Asia. The observed differences between Altaian Kazakhs and indigenous Kazakhs were not the result of admixture between Altaian Kazakhs and indigenous Altaians. Overall, the shared paternal ancestry of Kazakhs differentiates them from other Central Asian populations. In addition, all of them showed evidence of genetic influence by the 13^th century CE Mongol Empire. Ultimately, the social and cultural traditions of the Kazakhs shaped their current pattern of genetic variation.</p> </div>", "links"=>[], "tags"=>["y-chromosome", "altaian", "kazakhs", "reveals", "paternal", "mongolian", "expansions"], "article_id"=>138240, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew C. Dulik", "Ludmila P. Osipova", "Theodore G. Schurr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017548.s001", "https://dx.doi.org/10.1371/journal.pone.0017548.s002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Y_Chromosome_Variation_in_Altaian_Kazakhs_Reveals_a_Common_Paternal_Gene_Pool_for_Kazakhs_and_the_Influence_of_Mongolian_Expansions/138240", "title"=>"Y-Chromosome Variation in Altaian Kazakhs Reveals a Common Paternal Gene Pool for Kazakhs and the Influence of Mongolian Expansions", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-03-11 02:17:20"}
• {"files"=>["https://ndownloader.figshare.com/files/791290"], "description"=>"<p>The asterisks (*) denote the locations of Altaian Kazakh populations sampled for this study. The locations of comparative Kazakh populations are shown with each corresponding number: Altaian Kazakh [this study], Kazakh1 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017548#pone.0017548-Wells1\" target=\"_blank\">[10]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017548#pone.0017548-Zerjal1\" target=\"_blank\">[13]</a>, Kazakh2 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017548#pone.0017548-PerezLezaun1\" target=\"_blank\">[12]</a>, Kazakh3 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017548#pone.0017548-Chaix1\" target=\"_blank\">[11]</a>, Kazakh4 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017548#pone.0017548-Zhong1\" target=\"_blank\">[40]</a>, and Kazakh5 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017548#pone.0017548-Malyarchuk1\" target=\"_blank\">[41]</a>. Kazakh1 represents samples that were collected from four locations <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017548#pone.0017548-Wells1\" target=\"_blank\">[10]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017548#pone.0017548-Zerjal1\" target=\"_blank\">[13]</a>.</p>", "links"=>[], "tags"=>["populations"], "article_id"=>461663, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew C. Dulik", "Ludmila P. Osipova", "Theodore G. Schurr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017548.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Kazakh_populations_analyzed_in_this_study_/461663", "title"=>"Kazakh populations analyzed in this study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-11 00:27:43"}
• {"files"=>["https://ndownloader.figshare.com/files/791386"], "description"=>"<p>Reduced median-median joining network of Altaian Kazakhs using 14-STR haplotypes.</p>", "links"=>[], "tags"=>["median-median", "joining", "altaian", "kazakhs", "14-str"], "article_id"=>461751, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew C. Dulik", "Ludmila P. Osipova", "Theodore G. Schurr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017548.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reduced_median_median_joining_network_of_Altaian_Kazakhs_using_14_STR_haplotypes_/461751", "title"=>"Reduced median-median joining network of Altaian Kazakhs using 14-STR haplotypes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-11 00:29:11"}
• {"files"=>["https://ndownloader.figshare.com/files/791488"], "description"=>"<p>Reduced median-median joining network of Altaian and Indigenous Kazakh populations using 5-STR haplotypes.</p>", "links"=>[], "tags"=>["median-median", "joining", "altaian", "kazakh", "populations", "5-str"], "article_id"=>461854, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew C. Dulik", "Ludmila P. Osipova", "Theodore G. Schurr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017548.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reduced_median_median_joining_network_of_Altaian_and_Indigenous_Kazakh_populations_using_5_STR_haplotypes_/461854", "title"=>"Reduced median-median joining network of Altaian and Indigenous Kazakh populations using 5-STR haplotypes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-11 00:30:54"}
• {"files"=>["https://ndownloader.figshare.com/files/791579"], "description"=>"<p>Principal component analysis plot of genetic distances based on Y-chromosome haplogroup frequencies in Central Asian and Mongolian populations.</p>", "links"=>[], "tags"=>["distances", "y-chromosome", "haplogroup", "frequencies", "asian", "mongolian"], "article_id"=>461944, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew C. Dulik", "Ludmila P. Osipova", "Theodore G. Schurr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017548.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principal_component_analysis_plot_of_genetic_distances_based_on_Y_chromosome_haplogroup_frequencies_in_Central_Asian_and_Mongolian_populations_/461944", "title"=>"Principal component analysis plot of genetic distances based on Y-chromosome haplogroup frequencies in Central Asian and Mongolian populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-11 00:32:24"}
• {"files"=>["https://ndownloader.figshare.com/files/791699"], "description"=>"<p>Multidimensional scaling plot of R_ST values estimated from Y-STR haplotypes in Central Asian and Mongolian populations.</p>", "links"=>[], "tags"=>["scaling", "y-str", "haplotypes", "asian", "mongolian"], "article_id"=>462070, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew C. Dulik", "Ludmila P. Osipova", "Theodore G. Schurr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017548.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multidimensional_scaling_plot_of_R_ST_values_estimated_from_Y_STR_haplotypes_in_Central_Asian_and_Mongolian_populations_/462070", "title"=>"Multidimensional scaling plot of R_ST values estimated from Y-STR haplotypes in Central Asian and Mongolian populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-11 00:34:30"}
• {"files"=>["https://ndownloader.figshare.com/files/791781"], "description"=>"<p>Note: Categories for “Geography” – Central Asia; Altai; Mongolia.</p><p>“Language” – Turkic; Mongolic.</p><p>“Ethnicity” – Kazakh; Kyrgyz; Uzbek; Uyghur; Kara-kalpak; Turkmen; Mongolian.</p><p>“Modified Ethnicity” – Altaian Kazakh + Kazakh1; Kazakh2 + Kazakh3; Kyrgyz; Uzbek; Uyghur; Kara-kalpak; Turkmen; Mongolian.</p>", "links"=>[], "tags"=>["molecular", "variance", "y-str", "haplotypes", "asian", "mongolian"], "article_id"=>462148, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew C. Dulik", "Ludmila P. Osipova", "Theodore G. Schurr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017548.t006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_molecular_variance_results_of_Y_STR_haplotypes_in_Central_Asian_and_Mongolian_populations_/462148", "title"=>"Analysis of molecular variance results of Y-STR haplotypes in Central Asian and Mongolian populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-11 00:35:48"}
• {"files"=>["https://ndownloader.figshare.com/files/791817"], "description"=>"<p>*TMRCAs were estimated using the rho statistic in Network v 4.5.1.6. TMRCA estimates using Batwing are represented by median values and 95% confidence intervals. All TMRCAs are expressed in years before present (BP).</p>", "links"=>[], "tags"=>["estimates", "altaian", "kazakh", "haplotype", "clusters", "14-str", "haplotypes", "rho"], "article_id"=>462180, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew C. Dulik", "Ludmila P. Osipova", "Theodore G. Schurr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017548.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_TMRCA_estimates_of_Altaian_Kazakh_haplotype_clusters_from_14_STR_haplotypes_using_Rho_statistics_and_Batwing_/462180", "title"=>"TMRCA estimates of Altaian Kazakh haplotype clusters from 14-STR haplotypes using Rho statistics and Batwing.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-11 00:36:20"}
• {"files"=>["https://ndownloader.figshare.com/files/791846"], "description"=>"<p>*TMRCAs were estimated using the rho statistic in Network v 4.5.1.6. TMRCA estimates using Batwing are represented by median values and 95% confidence intervals. All TMRCAs are expressed in years before present (BP).</p>", "links"=>[], "tags"=>["estimates", "5-str", "haplotypes", "rho"], "article_id"=>462217, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew C. Dulik", "Ludmila P. Osipova", "Theodore G. Schurr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017548.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_TMRCA_estimates_from_5_STR_haplotypes_using_Rho_statistics_and_Batwing_/462217", "title"=>"TMRCA estimates from 5-STR haplotypes using Rho statistics and Batwing.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-11 00:36:57"}
• {"files"=>["https://ndownloader.figshare.com/files/791875"], "description"=>"<p>Summary statistics among four Kazakh populations.</p>", "links"=>[], "tags"=>["kazakh"], "article_id"=>462244, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew C. Dulik", "Ludmila P. Osipova", "Theodore G. Schurr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017548.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_statistics_among_four_Kazakh_populations_/462244", "title"=>"Summary statistics among four Kazakh populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-11 00:37:24"}
• {"files"=>["https://ndownloader.figshare.com/files/791910"], "description"=>"<p>*Haplogroups E, O1 and O2a are not shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017548#pone-0017548-t002\" target=\"_blank\">Table 2</a> because they are not present in Kazakh populations, although they are part of the 14-haplogroup profile used in the haplogroup analysis and PCA.</p>†<p>SNP data was not available for Kazakh2 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017548#pone.0017548-Chaix1\" target=\"_blank\">[11]</a> and Kazakh3 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017548#pone.0017548-Wells1\" target=\"_blank\">[10]</a>.</p>", "links"=>[], "tags"=>["haplogroup", "classification", "kazakh"], "article_id"=>462283, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew C. Dulik", "Ludmila P. Osipova", "Theodore G. Schurr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017548.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Low_resolution_haplogroup_classification_for_Kazakh_populations_/462283", "title"=>"Low-resolution haplogroup classification for Kazakh populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-11 00:38:03"}
• {"files"=>["https://ndownloader.figshare.com/files/791939"], "description"=>"<p>High-resolution haplogroup classification for Altaian Kazakhs (by location).</p>", "links"=>[], "tags"=>["haplogroup", "classification", "altaian", "kazakhs"], "article_id"=>462306, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Matthew C. Dulik", "Ludmila P. Osipova", "Theodore G. Schurr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017548.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_High_resolution_haplogroup_classification_for_Altaian_Kazakhs_by_location_/462306", "title"=>"High-resolution haplogroup classification for Altaian Kazakhs (by location).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-11 00:38:26"}

PMC Usage Stats | Further Information

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Relative Metric

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F1000Prime