Haplotype Affinities Resolve a Major Component of Goat (Capra hircus) MtDNA D-Loop Diversity and Reveal Specific Features of the Sardinian Stock
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{"title"=>"Haplotype affinities resolve a major component of goat (Capra hircus) mtDNA D-loop diversity and reveal specific features of the Sardinian stock", "type"=>"journal", "authors"=>[{"first_name"=>"Daniela", "last_name"=>"Piras", "scopus_author_id"=>"8874952400"}, {"first_name"=>"Maria Grazia", "last_name"=>"Doro", "scopus_author_id"=>"55000820700"}, {"first_name"=>"Giuseppina", "last_name"=>"Casu", "scopus_author_id"=>"6701318386"}, {"first_name"=>"Paola Maria", "last_name"=>"Melis", "scopus_author_id"=>"7003705036"}, {"first_name"=>"Simona", "last_name"=>"Vaccargiu", "scopus_author_id"=>"7801644706"}, {"first_name"=>"Ignazio", "last_name"=>"Piras", "scopus_author_id"=>"8045819400"}, {"first_name"=>"Debora", "last_name"=>"Parracciani", "scopus_author_id"=>"8786583500"}, {"first_name"=>"Roberta", "last_name"=>"Stradoni", "scopus_author_id"=>"57154108600"}, {"first_name"=>"Bruno", "last_name"=>"Frongia", "scopus_author_id"=>"16642684700"}, {"first_name"=>"Graziano", "last_name"=>"Lai", "scopus_author_id"=>"55001415700"}, {"first_name"=>"Salvatore", "last_name"=>"Sale", "scopus_author_id"=>"55000512900"}, {"first_name"=>"Walter", "last_name"=>"Cattari", "scopus_author_id"=>"55001856500"}, {"first_name"=>"Roberto", "last_name"=>"Piras", "scopus_author_id"=>"55001421000"}, {"first_name"=>"Ombretta", "last_name"=>"Querci", "scopus_author_id"=>"55001856600"}, {"first_name"=>"Piergiorgio", "last_name"=>"Demuro", "scopus_author_id"=>"55001567000"}, {"first_name"=>"Sandro", "last_name"=>"Cui", "scopus_author_id"=>"55000423800"}, {"first_name"=>"Franco", "last_name"=>"Atzori", "scopus_author_id"=>"56950900100"}, {"first_name"=>"Marco", "last_name"=>"Mancosu", "scopus_author_id"=>"54999087500"}, {"first_name"=>"Francesca", "last_name"=>"Marchiori", "scopus_author_id"=>"55002404300"}, {"first_name"=>"Rossana", "last_name"=>"Cammelli", "scopus_author_id"=>"16644690600"}, {"first_name"=>"Alessandra", "last_name"=>"Spiga", "scopus_author_id"=>"56387261600"}, {"first_name"=>"Pier Paolo", "last_name"=>"Loddo", "scopus_author_id"=>"55002941400"}, {"first_name"=>"Gianfranco", "last_name"=>"Pili", "scopus_author_id"=>"55002262000"}, {"first_name"=>"Roberto", "last_name"=>"Boi", "scopus_author_id"=>"35101281200"}, {"first_name"=>"Giuseppe", "last_name"=>"Argiolas", "scopus_author_id"=>"6506936716"}, {"first_name"=>"Paolo", "last_name"=>"Mereu", "scopus_author_id"=>"24778470000"}, {"first_name"=>"Giovanni Giuseppe", "last_name"=>"Leoni", "scopus_author_id"=>"7005529096"}, {"first_name"=>"Salvatore", "last_name"=>"Naitana", "scopus_author_id"=>"56277312600"}, {"first_name"=>"Mario", "last_name"=>"Pirastu", "scopus_author_id"=>"7006656218"}, {"first_name"=>"Andrea", "last_name"=>"Novelletto", "scopus_author_id"=>"7004732668"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84857152189", "pui"=>"364281252", "pmid"=>"22363488", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0030785", "sgr"=>"84857152189"}, "id"=>"d48d27fc-ff0e-3a98-a431-743a6918b579", "abstract"=>"Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1) to provide an operational definition of meaningful mtDNA units within haplogroup A, 2) to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3) to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591) which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity.We identified haplotype groups overrepresented in Sardinian goats as a result of founder effects. We found that breeders maintain diversity of matrilines most likely through equalization of the reproductive potential. Moreover, the relevant amount of inter-farm mtDNA diversity found does not increase proportionally with distance. Our results illustrate the effects of breeding practices on the composition of maternal gene pool and identify mtDNA types that may be considered in projects aimed at retrieving the maternal component of the oldest breeds of Sardinia.", "link"=>"http://www.mendeley.com/research/haplotype-affinities-resolve-major-component-goat-capra-hircus-mtdna-dloop-diversity-reveal-specific", "reader_count"=>17, "reader_count_by_academic_status"=>{"Researcher"=>8, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>2, "Student > Master"=>1, "Student > Bachelor"=>3}, "reader_count_by_user_role"=>{"Researcher"=>8, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>2, "Student > Master"=>1, "Student > Bachelor"=>3}, "reader_count_by_subject_area"=>{"Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>14, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>14}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Finland"=>1, "Indonesia"=>2}, "group_count"=>3}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/679868"], "description"=>"<p>In the background all municipalities are shaded according to the overall number of goats recorded <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030785#pone.0030785-ISTAT1\" target=\"_blank\">[23]</a>, as reported in the left panel (map obtained at <a href=\"http://www.sar.sardegna.it/servizi/sit/datitematici.asp?wgs=1\" target=\"_blank\">http://www.sar.sardegna.it/servizi/sit/datitematici.asp?wgs=1</a>). Sampled municipalities in 5 Sardinian sub regions are shown with the following color codes: Ogliastra-red, Sarrabus-blue, Gerrei-yellow, Iglesiente-purple and Sulcis-green. Detailed names and n. of breeding stations sampled are reported in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030785#pone.0030785.s005\" target=\"_blank\">Table S1</a>.</p>", "links"=>[], "tags"=>["sardinia", "34", "municipalities", "sampling", "was"], "article_id"=>350307, "categories"=>["Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniela Piras", "Maria Grazia Doro", "Giuseppina Casu", "Paola Maria Melis", "Simona Vaccargiu", "Ignazio Piras", "Debora Parracciani", "Roberta Stradoni", "Bruno Frongia", "Graziano Lai", "Salvatore Sale", "Walter Cattari", "Roberto Piras", "Ombretta Querci", "Piergiorgio Demuro", "Sandro Cui", "Franco Atzori", "Marco Mancosu", "Francesca Marchiori", "Rossana Cammelli", "Alessandra Spiga", "Pier Paolo Loddo", "Gianfranco Pili", "Roberto Boi", "Giuseppe Argiolas", "Paolo Mereu", "Giovanni Giuseppe Leoni", "Salvatore Naitana", "Mario Pirastu", "Andrea Novelletto"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030785.g001", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_Sardinia_showing_the_34_municipalities_dotted_where_sampling_was_performed_/350307", "title"=>"Map of Sardinia showing the 34 municipalities (dotted) where sampling was performed.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-17 00:05:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/680007"], "description"=>"<p>Branch length is not proportional to mutational steps. Node size is proportional to haplotype frequency. The correspondence between node clusters and clades in the NJ tree is reported. Unclassified sequences are blackened.</p>", "links"=>[], "tags"=>["joining", "419", "haplotypes", "outgroup"], "article_id"=>350452, "categories"=>["Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniela Piras", "Maria Grazia Doro", "Giuseppina Casu", "Paola Maria Melis", "Simona Vaccargiu", "Ignazio Piras", "Debora Parracciani", "Roberta Stradoni", "Bruno Frongia", "Graziano Lai", "Salvatore Sale", "Walter Cattari", "Roberto Piras", "Ombretta Querci", "Piergiorgio Demuro", "Sandro Cui", "Franco Atzori", "Marco Mancosu", "Francesca Marchiori", "Rossana Cammelli", "Alessandra Spiga", "Pier Paolo Loddo", "Gianfranco Pili", "Roberto Boi", "Giuseppe Argiolas", "Paolo Mereu", "Giovanni Giuseppe Leoni", "Salvatore Naitana", "Mario Pirastu", "Andrea Novelletto"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030785.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Median_joining_network_of_419_haplotypes_and_an_outgroup_obtained_as_described_in_Materials_and_Methods_/350452", "title"=>"Median joining network of 419 haplotypes and an outgroup obtained as described in Materials and Methods.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-17 00:07:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/680165"], "description"=>"<p>Black arrows point to the value obtained in the overall dataset. In the Tajima's D histogram, significant (nominal p<0.05) values are marked with an asterisk and a normal QQ plot is shown in the inset.</p>", "links"=>[], "tags"=>["dna", "120", "breeding"], "article_id"=>350606, "categories"=>["Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniela Piras", "Maria Grazia Doro", "Giuseppina Casu", "Paola Maria Melis", "Simona Vaccargiu", "Ignazio Piras", "Debora Parracciani", "Roberta Stradoni", "Bruno Frongia", "Graziano Lai", "Salvatore Sale", "Walter Cattari", "Roberto Piras", "Ombretta Querci", "Piergiorgio Demuro", "Sandro Cui", "Franco Atzori", "Marco Mancosu", "Francesca Marchiori", "Rossana Cammelli", "Alessandra Spiga", "Pier Paolo Loddo", "Gianfranco Pili", "Roberto Boi", "Giuseppe Argiolas", "Paolo Mereu", "Giovanni Giuseppe Leoni", "Salvatore Naitana", "Mario Pirastu", "Andrea Novelletto"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030785.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Histograms_of_four_summary_statistics_for_DNA_diversity_from_120_goat_breeding_stations_/350606", "title"=>"Histograms of four summary statistics for DNA diversity from 120 goat breeding stations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-17 00:10:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/680444"], "description"=>"<p>Composition of the sample of individuals yielding the set of mtDNA sequences used in all analyses, by provenance and breed.</p>", "links"=>[], "tags"=>["individuals", "yielding", "mtdna", "sequences", "provenance"], "article_id"=>350891, "categories"=>["Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniela Piras", "Maria Grazia Doro", "Giuseppina Casu", "Paola Maria Melis", "Simona Vaccargiu", "Ignazio Piras", "Debora Parracciani", "Roberta Stradoni", "Bruno Frongia", "Graziano Lai", "Salvatore Sale", "Walter Cattari", "Roberto Piras", "Ombretta Querci", "Piergiorgio Demuro", "Sandro Cui", "Franco Atzori", "Marco Mancosu", "Francesca Marchiori", "Rossana Cammelli", "Alessandra Spiga", "Pier Paolo Loddo", "Gianfranco Pili", "Roberto Boi", "Giuseppe Argiolas", "Paolo Mereu", "Giovanni Giuseppe Leoni", "Salvatore Naitana", "Mario Pirastu", "Andrea Novelletto"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030785.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Composition_of_the_sample_of_individuals_yielding_the_set_of_mtDNA_sequences_used_in_all_analyses_by_provenance_and_breed_/350891", "title"=>"Composition of the sample of individuals yielding the set of mtDNA sequences used in all analyses, by provenance and breed.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-17 00:14:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/680368"], "description"=>"a<p>. Position in the alignment and allelic state (in bold = derived).</p>b<p>. Entries of a 2×2 contingency table, in the order: With defining sub-haplotype AND In the clade, With defining sub-haplotype AND In other clades or unclassified, With other sub-haplotypes AND In the clade, With other sub-haplotypes AND In other clades or unclassified.</p>c<p>. Not calculated, due to mismatch observed variance lower than mean <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030785#pone.0030785-Excoffier1\" target=\"_blank\">[52]</a>.</p>", "links"=>[], "tags"=>["mtdna"], "article_id"=>350812, "categories"=>["Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniela Piras", "Maria Grazia Doro", "Giuseppina Casu", "Paola Maria Melis", "Simona Vaccargiu", "Ignazio Piras", "Debora Parracciani", "Roberta Stradoni", "Bruno Frongia", "Graziano Lai", "Salvatore Sale", "Walter Cattari", "Roberto Piras", "Ombretta Querci", "Piergiorgio Demuro", "Sandro Cui", "Franco Atzori", "Marco Mancosu", "Francesca Marchiori", "Rossana Cammelli", "Alessandra Spiga", "Pier Paolo Loddo", "Gianfranco Pili", "Roberto Boi", "Giuseppe Argiolas", "Paolo Mereu", "Giovanni Giuseppe Leoni", "Salvatore Naitana", "Mario Pirastu", "Andrea Novelletto"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030785.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Properties_of_major_mtDNA_clades_/350812", "title"=>"Properties of major mtDNA clades.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-17 00:13:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/680290"], "description"=>"<p>Analysis of MOlecular VAriance after partitioning according to different criteria.</p>", "links"=>[], "tags"=>["molecular", "variance", "partitioning"], "article_id"=>350730, "categories"=>["Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniela Piras", "Maria Grazia Doro", "Giuseppina Casu", "Paola Maria Melis", "Simona Vaccargiu", "Ignazio Piras", "Debora Parracciani", "Roberta Stradoni", "Bruno Frongia", "Graziano Lai", "Salvatore Sale", "Walter Cattari", "Roberto Piras", "Ombretta Querci", "Piergiorgio Demuro", "Sandro Cui", "Franco Atzori", "Marco Mancosu", "Francesca Marchiori", "Rossana Cammelli", "Alessandra Spiga", "Pier Paolo Loddo", "Gianfranco Pili", "Roberto Boi", "Giuseppe Argiolas", "Paolo Mereu", "Giovanni Giuseppe Leoni", "Salvatore Naitana", "Mario Pirastu", "Andrea Novelletto"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030785.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_MOlecular_VAriance_after_partitioning_according_to_different_criteria_/350730", "title"=>"Analysis of MOlecular VAriance after partitioning according to different criteria.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-17 00:12:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/347083", "https://ndownloader.figshare.com/files/347102", "https://ndownloader.figshare.com/files/347110", "https://ndownloader.figshare.com/files/347128", "https://ndownloader.figshare.com/files/347143", "https://ndownloader.figshare.com/files/347152", "https://ndownloader.figshare.com/files/347169", "https://ndownloader.figshare.com/files/347183", "https://ndownloader.figshare.com/files/347208", "https://ndownloader.figshare.com/files/347236", "https://ndownloader.figshare.com/files/347269", "https://ndownloader.figshare.com/files/347282", "https://ndownloader.figshare.com/files/347299"], "description"=>"<div><p>Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1) to provide an operational definition of meaningful mtDNA units within haplogroup A, 2) to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3) to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591) which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using Bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity.</p> <p>We identified haplotype groups overrepresented in Sardinian goats as a result of founder effects. We found that breeders maintain diversity of matrilines most likely through equalization of the reproductive potential. Moreover, the relevant amount of inter-farm mtDNA diversity found does not increase proportionally with distance. Our results illustrate the effects of breeding practices on the composition of maternal gene pool and identify mtDNA types that may be considered in projects aimed at retrieving the maternal component of the oldest breeds of Sardinia.</p> </div>", "links"=>[], "tags"=>["haplotype", "affinities", "mtdna", "d-loop", "features", "sardinian"], "article_id"=>128598, "categories"=>["Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Daniela Piras", "Maria Grazia Doro", "Giuseppina Casu", "Paola Maria Melis", "Simona Vaccargiu", "Ignazio Piras", "Debora Parracciani", "Roberta Stradoni", "Bruno Frongia", "Graziano Lai", "Salvatore Sale", "Walter Cattari", "Roberto Piras", "Ombretta Querci", "Piergiorgio Demuro", "Sandro Cui", "Franco Atzori", "Marco Mancosu", "Francesca Marchiori", "Rossana Cammelli", "Alessandra Spiga", "Pier Paolo Loddo", "Gianfranco Pili", "Roberto Boi", "Giuseppe Argiolas", "Paolo Mereu", "Giovanni Giuseppe Leoni", "Salvatore Naitana", "Mario Pirastu", "Andrea Novelletto"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0030785.s001", "https://dx.doi.org/10.1371/journal.pone.0030785.s002", "https://dx.doi.org/10.1371/journal.pone.0030785.s003", "https://dx.doi.org/10.1371/journal.pone.0030785.s004", "https://dx.doi.org/10.1371/journal.pone.0030785.s005", "https://dx.doi.org/10.1371/journal.pone.0030785.s006", "https://dx.doi.org/10.1371/journal.pone.0030785.s007", "https://dx.doi.org/10.1371/journal.pone.0030785.s008", "https://dx.doi.org/10.1371/journal.pone.0030785.s009", "https://dx.doi.org/10.1371/journal.pone.0030785.s010", "https://dx.doi.org/10.1371/journal.pone.0030785.s011", "https://dx.doi.org/10.1371/journal.pone.0030785.s012", "https://dx.doi.org/10.1371/journal.pone.0030785.s013"], "stats"=>{"downloads"=>8, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Haplotype_Affinities_Resolve_a_Major_Component_of_Goat_Capra_hircus_MtDNA_D_Loop_Diversity_and_Reveal_Specific_Features_of_the_Sardinian_Stock/128598", "title"=>"Haplotype Affinities Resolve a Major Component of Goat (<em>Capra hircus</em>) MtDNA D-Loop Diversity and Reveal Specific Features of the Sardinian Stock", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-02-17 02:23:18"}

PMC Usage Stats | Further Information

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