Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data
Publication Date
January 30, 2013
Journal
PLOS ONE
Authors
Jessica L. Petersen, James R. Mickelson, E. Gus Cothran, Lisa S. Andersson, et al
Volume
8
Issue
1
Pages
e54997
DOI
https://dx.plos.org/10.1371/journal.pone.0054997
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0054997
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23383025
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3559798
Europe PMC
http://europepmc.org/abstract/MED/23383025
Web of Science
000315563800095
Scopus
84873867256
Mendeley
http://www.mendeley.com/research/genetic-diversity-modern-horse-illustrated-genomewide-snp-data
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Mendeley | Further Information

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Cecilia T.", "last_name"=>"Penedo", "scopus_author_id"=>"57194578674"}, {"first_name"=>"Richard J.", "last_name"=>"Piercy", "scopus_author_id"=>"6603663458"}, {"first_name"=>"Marja", "last_name"=>"Raekallio", "scopus_author_id"=>"6603775616"}, {"first_name"=>"Stefan", "last_name"=>"Rieder", "scopus_author_id"=>"6701509161"}, {"first_name"=>"Knut H.", "last_name"=>"Røed", "scopus_author_id"=>"7006154277"}, {"first_name"=>"Maurizio", "last_name"=>"Silvestrelli", "scopus_author_id"=>"16647447700"}, {"first_name"=>"June", "last_name"=>"Swinburne", "scopus_author_id"=>"6603932878"}, {"first_name"=>"Teruaki", "last_name"=>"Tozaki", "scopus_author_id"=>"56351968100"}, {"first_name"=>"Mark", "last_name"=>"Vaudin", "scopus_author_id"=>"7006138033"}, {"first_name"=>"Claire", "last_name"=>"M. Wade", "scopus_author_id"=>"7102531600"}, {"first_name"=>"Molly E.", "last_name"=>"McCue", "scopus_author_id"=>"16301744300"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84873867256", "sgr"=>"84873867256", "pui"=>"368227259", "isbn"=>"1932-6203", "pmid"=>"23383025", "doi"=>"10.1371/journal.pone.0054997"}, "id"=>"d4afde02-b0eb-39d4-b065-7597979d00c4", "abstract"=>"Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. 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  • {"files"=>["https://ndownloader.figshare.com/files/499783"], "description"=>"<p>Populations (breeds) included in the study, region of breed origin and sampling location, notes on population history relevant to diversity statistics, and breed classification based upon use and phenotype.</p>", "links"=>[], "tags"=>["included", "breed", "sampling", "notes", "classification"], "article_id"=>170240, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jessica L. Petersen", "James R. Mickelson", "E. Gus Cothran", "Lisa S. Andersson", "Jeanette Axelsson", "Ernie Bailey", "Danika Bannasch", "Matthew M. Binns", "Alexandre S. Borges", "Pieter Brama", "Artur da Câmara Machado", "Ottmar Distl", "Michela Felicetti", "Laura Fox-Clipsham", "Kathryn T. Graves", "Gérard Guérin", "Bianca Haase", "Telhisa Hasegawa", "Karin Hemmann", "Emmeline W. Hill", "Tosso Leeb", "Gabriella Lindgren", "Hannes Lohi", "Maria Susana Lopes", "Beatrice A. McGivney", "Sofia Mikko", "Nicholas Orr", "M. Cecilia T Penedo", "Richard J. Piercy", "Marja Raekallio", "Stefan Rieder", "Knut H. Røed", "Maurizio Silvestrelli", "June Swinburne", "Teruaki Tozaki", "Mark Vaudin", "Claire M. Wade", "Molly E. McCue"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054997.t001", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Populations_breeds_included_in_the_study_region_of_breed_origin_and_sampling_location_notes_on_population_history_relevant_to_diversity_statistics_and_breed_classification_based_upon_use_and_phenotype_/170240", "title"=>"Populations (breeds) included in the study, region of breed origin and sampling location, notes on population history relevant to diversity statistics, and breed classification based upon use and phenotype.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-30 00:04:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/499891"], "description"=>"a<p>Individuals from this breed also included in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1\" target=\"_blank\">[41]</a>;</p>b<p>20 of these individuals were also reported in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1\" target=\"_blank\">[41]</a>;</p>c<p>17 of these individuals were also reported in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1\" target=\"_blank\">[41]</a>;</p>d<p>21 of these individuals were also reported in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1\" target=\"_blank\">[41]</a>;</p>e<p>19 of these individuals were also reported in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1\" target=\"_blank\">[41]</a>.</p><p>F<sub>IS</sub> and f were calculated based upon the primary SNP set (10,536 loci). Samples also used in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054997#pone.0054997-McCue1\" target=\"_blank\">[41]</a> are indicated in the footnotes.</p>*<p>indicates significance at α<0.05 determined by 10,000 permutations.</p>", "links"=>[], "tags"=>["samples", "inbreeding", "estimates", "coefficient", "heterozygosity", "snp", "sets", "pruned", "varying", "levels"], "article_id"=>170334, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jessica L. Petersen", "James R. Mickelson", "E. Gus Cothran", "Lisa S. Andersson", "Jeanette Axelsson", "Ernie Bailey", "Danika Bannasch", "Matthew M. Binns", "Alexandre S. Borges", "Pieter Brama", "Artur da Câmara Machado", "Ottmar Distl", "Michela Felicetti", "Laura Fox-Clipsham", "Kathryn T. Graves", "Gérard Guérin", "Bianca Haase", "Telhisa Hasegawa", "Karin Hemmann", "Emmeline W. Hill", "Tosso Leeb", "Gabriella Lindgren", "Hannes Lohi", "Maria Susana Lopes", "Beatrice A. McGivney", "Sofia Mikko", "Nicholas Orr", "M. Cecilia T Penedo", "Richard J. Piercy", "Marja Raekallio", "Stefan Rieder", "Knut H. Røed", "Maurizio Silvestrelli", "June Swinburne", "Teruaki Tozaki", "Mark Vaudin", "Claire M. Wade", "Molly E. McCue"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054997.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_samples_N_effective_population_size_N_e_individual_inbreeding_estimates_f_inbreeding_coefficient_F_IS_and_expected_heterozygosity_H_e_from_four_SNP_sets_pruned_based_upon_varying_levels_of_LD_/170334", "title"=>"Number of samples (N), effective population size (N<sub>e</sub>), individual inbreeding estimates (f), inbreeding coefficient (F<sub>IS</sub>), and expected heterozygosity (H<sub>e</sub>) from four SNP sets pruned based upon varying levels of LD.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-30 00:05:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/499586"], "description"=>"<p>Pairwise F<sub>ST</sub> values as calculated in Arlequin using 10,536 autosomal SNPs and significance tested using 20,000 permutations. All pairwise values are significantly different from zero. (individual outliers were removed from this analysis).</p>", "links"=>[], "tags"=>["snps", "37"], "article_id"=>170055, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jessica L. Petersen", "James R. Mickelson", "E. Gus Cothran", "Lisa S. Andersson", "Jeanette Axelsson", "Ernie Bailey", "Danika Bannasch", "Matthew M. Binns", "Alexandre S. Borges", "Pieter Brama", "Artur da Câmara Machado", "Ottmar Distl", "Michela Felicetti", "Laura Fox-Clipsham", "Kathryn T. Graves", "Gérard Guérin", "Bianca Haase", "Telhisa Hasegawa", "Karin Hemmann", "Emmeline W. Hill", "Tosso Leeb", "Gabriella Lindgren", "Hannes Lohi", "Maria Susana Lopes", "Beatrice A. McGivney", "Sofia Mikko", "Nicholas Orr", "M. Cecilia T Penedo", "Richard J. Piercy", "Marja Raekallio", "Stefan Rieder", "Knut H. Røed", "Maurizio Silvestrelli", "June Swinburne", "Teruaki Tozaki", "Mark Vaudin", "Claire M. Wade", "Molly E. McCue"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054997.g004", "stats"=>{"downloads"=>5, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_F_ST_values_based_upon_10_536_SNPs_in_37_horse_populations_/170055", "title"=>"Pairwise F<sub>ST</sub> values based upon 10,536 SNPs in 37 horse populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-30 00:00:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/498891"], "description"=>"<p>Parsimony tree created from 10,066 SNPs and rooted by the domestic ass. Breeds are listed in the legend in order starting from the root and working counterclockwise. Individual outliers with respect to their breeds are noted with arrows. Bootstrap support calculated from 1,000 replicates is shown for major branches when greater than 50%.</p>", "links"=>[], "tags"=>["breed", "relationships", "814", "horses", "illustrated"], "article_id"=>169351, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jessica L. Petersen", "James R. Mickelson", "E. Gus Cothran", "Lisa S. Andersson", "Jeanette Axelsson", "Ernie Bailey", "Danika Bannasch", "Matthew M. Binns", "Alexandre S. Borges", "Pieter Brama", "Artur da Câmara Machado", "Ottmar Distl", "Michela Felicetti", "Laura Fox-Clipsham", "Kathryn T. Graves", "Gérard Guérin", "Bianca Haase", "Telhisa Hasegawa", "Karin Hemmann", "Emmeline W. Hill", "Tosso Leeb", "Gabriella Lindgren", "Hannes Lohi", "Maria Susana Lopes", "Beatrice A. McGivney", "Sofia Mikko", "Nicholas Orr", "M. Cecilia T Penedo", "Richard J. Piercy", "Marja Raekallio", "Stefan Rieder", "Knut H. Røed", "Maurizio Silvestrelli", "June Swinburne", "Teruaki Tozaki", "Mark Vaudin", "Claire M. Wade", "Molly E. McCue"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054997.g001", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Individual_and_breed_relationships_among_814_horses_illustrated_by_parsimony_/169351", "title"=>"Individual and breed relationships among 814 horses illustrated by parsimony.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-30 02:35:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/499402"], "description"=>"<p>Structure output for five values of K investigated. Each individual is represented by one vertical line with the proportion of assignment to each cluster shown on the y axis and colored by cluster. Other values of K are shown in Figure S1 and a summary of assignment of each breed in Tables S1 and S2.</p>", "links"=>[], "tags"=>["clustering", "814", "horses", "38"], "article_id"=>169866, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jessica L. Petersen", "James R. Mickelson", "E. Gus Cothran", "Lisa S. Andersson", "Jeanette Axelsson", "Ernie Bailey", "Danika Bannasch", "Matthew M. Binns", "Alexandre S. Borges", "Pieter Brama", "Artur da Câmara Machado", "Ottmar Distl", "Michela Felicetti", "Laura Fox-Clipsham", "Kathryn T. Graves", "Gérard Guérin", "Bianca Haase", "Telhisa Hasegawa", "Karin Hemmann", "Emmeline W. Hill", "Tosso Leeb", "Gabriella Lindgren", "Hannes Lohi", "Maria Susana Lopes", "Beatrice A. McGivney", "Sofia Mikko", "Nicholas Orr", "M. Cecilia T Penedo", "Richard J. Piercy", "Marja Raekallio", "Stefan Rieder", "Knut H. Røed", "Maurizio Silvestrelli", "June Swinburne", "Teruaki Tozaki", "Mark Vaudin", "Claire M. Wade", "Molly E. McCue"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054997.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayesian_clustering_output_for_five_values_of_K_in_814_horses_of_38_populations_/169866", "title"=>"Bayesian clustering output for five values of K in 814 horses of 38 populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-30 02:44:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/499064"], "description"=>"<p>Majority rule, neighbor joining tree created from 10,536 SNP makers using Nei’s genetic distance and allele frequencies within each population. Percent bootstrap support for all branches calculated from 1,000 replicates is shown.</p>", "links"=>[], "tags"=>["joining", "calculated", "snp", "frequencies", "38"], "article_id"=>169528, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jessica L. Petersen", "James R. Mickelson", "E. Gus Cothran", "Lisa S. Andersson", "Jeanette Axelsson", "Ernie Bailey", "Danika Bannasch", "Matthew M. Binns", "Alexandre S. Borges", "Pieter Brama", "Artur da Câmara Machado", "Ottmar Distl", "Michela Felicetti", "Laura Fox-Clipsham", "Kathryn T. Graves", "Gérard Guérin", "Bianca Haase", "Telhisa Hasegawa", "Karin Hemmann", "Emmeline W. Hill", "Tosso Leeb", "Gabriella Lindgren", "Hannes Lohi", "Maria Susana Lopes", "Beatrice A. McGivney", "Sofia Mikko", "Nicholas Orr", "M. Cecilia T Penedo", "Richard J. Piercy", "Marja Raekallio", "Stefan Rieder", "Knut H. Røed", "Maurizio Silvestrelli", "June Swinburne", "Teruaki Tozaki", "Mark Vaudin", "Claire M. Wade", "Molly E. McCue"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054997.g002", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distance_based_neighbor_joining_tree_calculated_from_SNP_frequencies_in_38_horse_populations_/169528", "title"=>"Distance based, neighbor joining tree calculated from SNP frequencies in 38 horse populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-30 02:38:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/480011", "https://ndownloader.figshare.com/files/480015", "https://ndownloader.figshare.com/files/480020", "https://ndownloader.figshare.com/files/480027", "https://ndownloader.figshare.com/files/480033", "https://ndownloader.figshare.com/files/480037", "https://ndownloader.figshare.com/files/480040", "https://ndownloader.figshare.com/files/480045", "https://ndownloader.figshare.com/files/480048"], "description"=>"<div><p>Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F<sub>ST</sub> calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.</p> </div>", "links"=>[], "tags"=>["illustrated", "genome-wide", "snp", "data"], "article_id"=>154917, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jessica L. Petersen", "James R. Mickelson", "E. Gus Cothran", "Lisa S. Andersson", "Jeanette Axelsson", "Ernie Bailey", "Danika Bannasch", "Matthew M. Binns", "Alexandre S. Borges", "Pieter Brama", "Artur da Câmara Machado", "Ottmar Distl", "Michela Felicetti", "Laura Fox-Clipsham", "Kathryn T. Graves", "Gérard Guérin", "Bianca Haase", "Telhisa Hasegawa", "Karin Hemmann", "Emmeline W. Hill", "Tosso Leeb", "Gabriella Lindgren", "Hannes Lohi", "Maria Susana Lopes", "Beatrice A. McGivney", "Sofia Mikko", "Nicholas Orr", "M. Cecilia T Penedo", "Richard J. Piercy", "Marja Raekallio", "Stefan Rieder", "Knut H. Røed", "Maurizio Silvestrelli", "June Swinburne", "Teruaki Tozaki", "Mark Vaudin", "Claire M. Wade", "Molly E. McCue"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0054997.s001", "https://dx.doi.org/10.1371/journal.pone.0054997.s002", "https://dx.doi.org/10.1371/journal.pone.0054997.s003", "https://dx.doi.org/10.1371/journal.pone.0054997.s004", "https://dx.doi.org/10.1371/journal.pone.0054997.s005", "https://dx.doi.org/10.1371/journal.pone.0054997.s006", "https://dx.doi.org/10.1371/journal.pone.0054997.s007", "https://dx.doi.org/10.1371/journal.pone.0054997.s008", "https://dx.doi.org/10.1371/journal.pone.0054997.s009"], "stats"=>{"downloads"=>15, "page_views"=>54, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genetic_Diversity_in_the_Modern_Horse_Illustrated_from_Genome_Wide_SNP_Data__/154917", "title"=>"Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-01-30 01:21:57"}

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Relative Metric

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