Improved Resolution Haplogroup G Phylogeny in the Y Chromosome, Revealed by a Set of Newly Characterized SNPs
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{"title"=>"Improved resolution haplogroup G phylogeny in the Y chromosome, revealed by a set of newly characterized SNPs", "type"=>"journal", "authors"=>[{"first_name"=>"Lynn M.", "last_name"=>"Sims", "scopus_author_id"=>"23111687700"}, {"first_name"=>"Dennis", "last_name"=>"Garvey", "scopus_author_id"=>"36805382800"}, {"first_name"=>"Jack", "last_name"=>"Ballantyne", "scopus_author_id"=>"7103216781"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"67149134679", "scopus"=>"2-s2.0-67149134679", "pui"=>"354729038", "pmid"=>"19495413", "doi"=>"10.1371/journal.pone.0005792", "issn"=>"19326203"}, "id"=>"bd89f9c8-cac9-36ae-91d2-68f8b5e385c7", "abstract"=>"BACKGROUND: Y-SNP haplogroup G (hgG), defined by Y-SNP marker M201, is relatively uncommon in the United States general population, with only 8 additional sub-markers characterized. Many of the previously described eight sub-markers are either very rare (2-4%) or do not distinguish between major populations within this hg. In fact, prior to the current study, only 2% of our reference Caucasian population belonged to hgG and all of these individuals were in sub-haplogroup G2a, defined by P15. Additional Y-SNPs are needed in order to differentiate between individuals within this haplogroup. PRINCIPAL FINDINGS: In this work we have investigated whether we could differentiate between a population of 63 hgG individuals using previously uncharacterized Y-SNPs. We have designed assays to test these individuals using all known hgG SNPs (n = 9) and an additional 16 unreported/undefined Y-SNPS. Using a combination of DNA sequence and genetic genealogy databases, we have uncovered a total of 15 new hgG SNPs that had been previously reported but not phylogenetically characterized. Ten of the new Y-SNPs are phylogenetically equivalent to M201, one is equivalent to P15 and, interestingly, four create new, separate haplogroups. Three of the latter are more common than many of the previously defined Y-SNPs. Y-STR data from these individuals show that DYS385*12 is present in (70%) of G2a3b1-U13 individuals while only 4% of non-G2a3b1-U13 individuals posses the DYS385*12 allele. CONCLUSIONS: This study uncovered several previously undefined Y-SNPs by using data from several database sources. The new Y-SNPs revealed in this paper will be of importance to those with research interests in population biology and human evolution.", "link"=>"http://www.mendeley.com/research/improved-resolution-haplogroup-g-phylogeny-y-chromosome-revealed-set-newly-characterized-snps", "reader_count"=>25, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>6, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>1, "Other"=>3, "Student > Master"=>2, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>6, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>1, "Other"=>3, "Student > Master"=>2, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Agricultural and Biological Sciences"=>22, "Physics and Astronomy"=>1, "Chemistry"=>1, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>22}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>2, "United Kingdom"=>2}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/895018"], "description"=>"†<p>SNP is listed as: ancestral>derived.</p>*<p>U20 and U33 were amplified at 56°C annealing temperature and U23 was amplified at 57°C for only 35 cycles.</p>", "links"=>[], "tags"=>["snp", "indicated"], "article_id"=>565476, "categories"=>["Infectious Diseases", "Evolutionary Biology"], "users"=>["Lynn M. Sims", "Dennis Garvey", "Jack Ballantyne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005792.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_Y_SNPS_their_associated_database_references_and_location_of_the_SNP_within_the_product_for_the_indicated_primers_/565476", "title"=>"List of Y-SNPS, their associated database references, and location of the SNP within the product for the indicated primers.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-21 05:40:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/894960"], "description"=>"<p>The haplogroup names are assigned base on the most recent haplogroup tree by Karafet et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005792#pone.0005792-Karafet1\" target=\"_blank\">[13]</a>.</p>", "links"=>[], "tags"=>["trees", "frequencies", "haplogroup", "individuals", "characterized"], "article_id"=>565412, "categories"=>["Infectious Diseases", "Evolutionary Biology"], "users"=>["Lynn M. Sims", "Dennis Garvey", "Jack Ballantyne"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0005792.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_Trees_Indicating_the_Frequencies_of_Haplogroup_G_Individuals_with_B_and_without_A_the_Newly_Characterized_Y_SNPs_/565412", "title"=>"Phylogenetic Trees Indicating the Frequencies of Haplogroup G Individuals with (B) and without (A) the Newly Characterized Y-SNPs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 05:39:58"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"10", "full-text"=>"14", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2012", "month"=>"7"}
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Relative Metric

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