Vitis Phylogenomics: Hybridization Intensities from a SNP Array Outperform Genotype Calls
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{"title"=>"Vitis phylogenomics: Hybridization intensities from a SNP array outperform genotype calls", "type"=>"journal", "authors"=>[{"first_name"=>"Allison J.", "last_name"=>"Miller", "scopus_author_id"=>"16643004200"}, {"first_name"=>"Naim", "last_name"=>"Matasci", "scopus_author_id"=>"37073060700"}, {"first_name"=>"Heidi", "last_name"=>"Schwaninger", "scopus_author_id"=>"24177530800"}, {"first_name"=>"Mallikarjuna K.", "last_name"=>"Aradhya", "scopus_author_id"=>"6602935044"}, {"first_name"=>"Bernard", "last_name"=>"Prins", "scopus_author_id"=>"6701413609"}, {"first_name"=>"Gan Yuan", "last_name"=>"Zhong", "scopus_author_id"=>"36018035900"}, {"first_name"=>"Charles", "last_name"=>"Simon", "scopus_author_id"=>"7401975324"}, {"first_name"=>"Edward S.", "last_name"=>"Buckler", "scopus_author_id"=>"6603927775"}, {"first_name"=>"Sean", "last_name"=>"Myles", "scopus_author_id"=>"21735079100"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84893580899", "doi"=>"10.1371/journal.pone.0078680", "pui"=>"372309810", "pmid"=>"24236035", "scopus"=>"2-s2.0-84893580899", "issn"=>"19326203", "isbn"=>"1932-6203"}, "id"=>"75a2e8d2-54c2-3058-9fd1-909c6f8d70b1", "abstract"=>"Understanding relationships among species is a fundamental goal of evolutionary biology. Single nucleotide polymorphisms (SNPs) identified through next generation sequencing and related technologies enable phylogeny reconstruction by providing unprecedented numbers of characters for analysis. One approach to SNP-based phylogeny reconstruction is to identify SNPs in a subset of individuals, and then to compile SNPs on an array that can be used to genotype additional samples at hundreds or thousands of sites simultaneously. Although powerful and efficient, this method is subject to ascertainment bias because applying variation discovered in a representative subset to a larger sample favors identification of SNPs with high minor allele frequencies and introduces bias against rare alleles. Here, we demonstrate that the use of hybridization intensity data, rather than genotype calls, reduces the effects of ascertainment bias. Whereas traditional SNP calls assess known variants based on diversity housed in the discovery panel, hybridization intensity data survey variation in the broader sample pool, regardless of whether those variants are present in the initial SNP discovery process. We apply SNP genotype and hybridization intensity data derived from the Vitis9kSNP array developed for grape to show the effects of ascertainment bias and to reconstruct evolutionary relationships among Vitis species. We demonstrate that phylogenies constructed using hybridization intensities suffer less from the distorting effects of ascertainment bias, and are thus more accurate than phylogenies based on genotype calls. Moreover, we reconstruct the phylogeny of the genus Vitis using hybridization data, show that North American subgenus Vitis species are monophyletic, and resolve several previously poorly known relationships among North American species. This study builds on earlier work that applied the Vitis9kSNP array to evolutionary questions within Vitis vinifera and has general implications for addressing ascertainment bias in array-enabled phylogeny reconstruction.", "link"=>"http://www.mendeley.com/research/vitis-phylogenomics-hybridization-intensities-snp-array-outperform-genotype-calls", "reader_count"=>48, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Student > Doctoral Student"=>3, "Researcher"=>10, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>4, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Student > Doctoral Student"=>3, "Researcher"=>10, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>4, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>43, "Medicine and Dentistry"=>1, "Chemistry"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>43}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Hungary"=>1, "United States"=>2, "Uruguay"=>1, "Israel"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1279660"], "description"=>"<p>The proportion of the variance explained is found within parentheses on each axis. <b>A) PCA with all samples included.</b> PC1 clearly separates <i>vinifera</i> and <i>sylvestris</i> from the other wild <i>Vitis</i> species while PC2 separates <i>rotundifolia</i> from all others. <b>B–D) PCA with </b><b><i>rotundifolia</i></b><b>, </b><b><i>sylvestris</i></b><b> and </b><b><i>vinifera</i></b><b> removed.</b> Examining the distances between individual samples in PC space confirms that the curated sample set used in the present study does not likely suffer from mislabeling or curation error that would lead to false phylogenetic inference.</p>", "links"=>[], "tags"=>["components", "1030", "samples", "3231"], "article_id"=>849836, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Allison J. Miller", "Naim Matasci", "Heidi Schwaninger", "Mallikarjuna K. Aradhya", "Bernard Prins", "Gan-Yuan Zhong", "Charles Simon", "Edward S. Buckler", "Sean Myles"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0078680.g001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principal_components_analysis_PCA_of_1030_Vitis_samples_using_3231_SNPs_/849836", "title"=>"Principal components analysis (PCA) of 1030 <i>Vitis</i> samples using 3231 SNPs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-13 04:05:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/1279674"], "description"=>"<div><p>Understanding relationships among species is a fundamental goal of evolutionary biology. Single nucleotide polymorphisms (SNPs) identified through next generation sequencing and related technologies enable phylogeny reconstruction by providing unprecedented numbers of characters for analysis. One approach to SNP-based phylogeny reconstruction is to identify SNPs in a subset of individuals, and then to compile SNPs on an array that can be used to genotype additional samples at hundreds or thousands of sites simultaneously. Although powerful and efficient, this method is subject to ascertainment bias because applying variation discovered in a representative subset to a larger sample favors identification of SNPs with high minor allele frequencies and introduces bias against rare alleles. Here, we demonstrate that the use of hybridization intensity data, rather than genotype calls, reduces the effects of ascertainment bias. Whereas traditional SNP calls assess known variants based on diversity housed in the discovery panel, hybridization intensity data survey variation in the broader sample pool, regardless of whether those variants are present in the initial SNP discovery process. We apply SNP genotype and hybridization intensity data derived from the Vitis9kSNP array developed for grape to show the effects of ascertainment bias and to reconstruct evolutionary relationships among <i>Vitis</i> species. We demonstrate that phylogenies constructed using hybridization intensities suffer less from the distorting effects of ascertainment bias, and are thus more accurate than phylogenies based on genotype calls. Moreover, we reconstruct the phylogeny of the genus <i>Vitis</i> using hybridization data, show that North American subgenus <i>Vitis</i> species are monophyletic, and resolve several previously poorly known relationships among North American species. This study builds on earlier work that applied the Vitis9kSNP array to evolutionary questions within <i>Vitis vinifera</i> and has general implications for addressing ascertainment bias in array-enabled phylogeny reconstruction.</p></div>", "links"=>[], "tags"=>["hybridization", "intensities", "snp", "outperform", "genotype", "calls"], "article_id"=>849850, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Allison J. Miller", "Naim Matasci", "Heidi Schwaninger", "Mallikarjuna K. Aradhya", "Bernard Prins", "Gan-Yuan Zhong", "Charles Simon", "Edward S. Buckler", "Sean Myles"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0078680", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Vitis_Phylogenomics_Hybridization_Intensities_from_a_SNP_Array_Outperform_Genotype_Calls/849850", "title"=>"<i>Vitis</i> Phylogenomics: Hybridization Intensities from a SNP Array Outperform Genotype Calls", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-13 04:05:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/1279669"], "description"=>"<p>Each dot represents a pairwise comparison between two species. Pairwise comparisons involving <i>V. vinifera</i> or <i>V. sylvestris</i> are highlighted in red. Genetic distances for <i>V. vinifera</i> and <i>V. sylvestris</i> based on intensity values are systematically elevated compared to other pairwise comparisons.</p>", "links"=>[], "tags"=>["metrics", "genotype", "calls", "hybridization"], "article_id"=>849845, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Allison J. Miller", "Naim Matasci", "Heidi Schwaninger", "Mallikarjuna K. Aradhya", "Bernard Prins", "Gan-Yuan Zhong", "Charles Simon", "Edward S. Buckler", "Sean Myles"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0078680.g006", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_genetic_distance_metrics_based_on_genotype_calls_and_hybridization_intensities_/849845", "title"=>"Comparison of genetic distance metrics based on genotype calls and hybridization intensities.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-13 04:05:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/1279668"], "description"=>"<p>A) Neighbour-joining (NJ) tree from <i>F<sub>ST</sub></i> estimates derived from SNP genotype calls from the Vitis9KSNP array. B) NJ tree from a distance measure derived from hybridization intensities from the Vitis9KSNP array.</p>", "links"=>[], "tags"=>["phylogenetic", "snp", "genotype", "calls", "differs", "generated", "hybridization"], "article_id"=>849844, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Allison J. Miller", "Naim Matasci", "Heidi Schwaninger", "Mallikarjuna K. Aradhya", "Bernard Prins", "Gan-Yuan Zhong", "Charles Simon", "Edward S. Buckler", "Sean Myles"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0078680.g005", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_phylogenetic_tree_of_Vitis_based_on_SNP_genotype_calls_differs_from_the_phylogenetic_generated_using_array_hybridization_intensities_/849844", "title"=>"The phylogenetic tree of <i>Vitis</i> based on SNP genotype calls differs from the phylogenetic generated using array hybridization intensities.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-13 04:05:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/1279664"], "description"=>"<p><b>A</b>) Between-species comparisons with <i>vinifera</i> or <i>sylvestris</i> involve far fewer monomorphic SNPs than other comparisons. The number of monomorphic SNPs was calculated for every pairwise comparison between species. Because <i>vinifera</i> and <i>sylvestris</i> show an excess of intermediate frequency alleles compared to other <i>Vitis</i> species using the Vitis9KSNP array, comparisons involving <i>vinifera</i> or <i>sylvestris</i> display fewer monomorphic sites relative to comparisons involving other species pairs. <b>B</b>) The dotted lines indicated by “min” and “max” are the minimum and maximum <i>F<sub>ST</sub></i> values from comparisons between <i>vinifera</i> or <i>sylvestris</i> and other species. The ascertainment bias results in intermediate <i>F<sub>ST</sub></i> estimates with relatively little variation for pairwise comparisons between species involving <i>vinifera</i> or <i>sylvestris</i>.</p>", "links"=>[], "tags"=>["ascertainment", "vitis9ksnp"], "article_id"=>849840, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Allison J. Miller", "Naim Matasci", "Heidi Schwaninger", "Mallikarjuna K. Aradhya", "Bernard Prins", "Gan-Yuan Zhong", "Charles Simon", "Edward S. Buckler", "Sean Myles"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0078680.g003", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evidence_of_ascertainment_bias_from_the_Vitis9KSNP_array_/849840", "title"=>"Evidence of ascertainment bias from the Vitis9KSNP array.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-13 04:05:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/1279662"], "description"=>"<p>MAF allele frequencies for other species look similar to <i>V. coignetiae</i> and <i>V. riparia</i> with a severe deficit of intermediate frequency alleles compared to <i>vinifera</i> and <i>sylvestris</i>.</p>", "links"=>[], "tags"=>["allele", "asia"], "article_id"=>849838, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Allison J. Miller", "Naim Matasci", "Heidi Schwaninger", "Mallikarjuna K. Aradhya", "Bernard Prins", "Gan-Yuan Zhong", "Charles Simon", "Edward S. Buckler", "Sean Myles"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0078680.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Minor_allele_frequency_MAF_for_vinifera_and_sylvestris_and_two_representative_taxa_V_coignetiae_from_Asia_and_V_riparia_from_North_America_/849838", "title"=>"Minor allele frequency (MAF) for <i>vinifera</i> and <i>sylvestris</i> and two representative taxa, <i>V. coignetiae</i> from Asia and <i>V. riparia</i> from North America.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-13 04:05:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/1279671"], "description"=>"<p>Accessions used in the SNP Analyses.</p>", "links"=>[], "tags"=>["snp"], "article_id"=>849847, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Allison J. Miller", "Naim Matasci", "Heidi Schwaninger", "Mallikarjuna K. Aradhya", "Bernard Prins", "Gan-Yuan Zhong", "Charles Simon", "Edward S. Buckler", "Sean Myles"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0078680.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Accessions_used_in_the_SNP_Analyses_/849847", "title"=>"Accessions used in the SNP Analyses.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-11-13 04:05:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/1279666"], "description"=>"<p>MDS plots of genetic distances among <i>Vitis</i> species using SNP genotype calls (A and B) and array hybridization intensities (C and D). A) MDS of <i>F<sub>ST</sub></i> distances among all species calculated from genotype calls. B) Same as A) but without <i>rotundifolia</i>. C) MDS of genetic distances among all species based on intensity values. D) Same as C) but without <i>rotundifolia</i>.</p>", "links"=>[], "tags"=>["distances", "snp", "genotype", "calls", "hybridization", "intensities", "mds", "calculated"], "article_id"=>849842, "categories"=>["Biological Sciences", "Ecology", "Earth and Environmental Sciences"], "users"=>["Allison J. Miller", "Naim Matasci", "Heidi Schwaninger", "Mallikarjuna K. Aradhya", "Bernard Prins", "Gan-Yuan Zhong", "Charles Simon", "Edward S. Buckler", "Sean Myles"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0078680.g004", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MDS_plots_of_genetic_distances_among_Vitis_species_using_SNP_genotype_calls_A_and_B_and_array_hybridization_intensities_C_and_D_A_MDS_of_F_ST_distances_among_all_species_calculated_from_genotype_calls_B_Same_as_A_but_without_rotundifolia_C_MDS_of_genetic/849842", "title"=>"MDS plots of genetic distances among <i>Vitis</i> species using SNP genotype calls (A and B) and array hybridization intensities (C and D). A) MDS of <i>F<sub>ST</sub></i> distances among all species calculated from genotype calls. B) Same as A) but without <i>rotundifolia</i>. C) MDS of genetic distances among all species based on intensity values. D) Same as C) but without <i>rotundifolia</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-11-13 04:05:38"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"14", "full-text"=>"13", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
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Relative Metric

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