Molecular Identification of Birds: Performance of Distance-Based DNA Barcoding in Three Genes to Delimit Parapatric Species
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{"title"=>"Molecular identification of birds: Performance of distance-based DNA barcoding in three genes to delimit parapatric species", "type"=>"journal", "authors"=>[{"first_name"=>"Mansour", "last_name"=>"Aliabadian", "scopus_author_id"=>"8858277600"}, {"first_name"=>"Mohammad", "last_name"=>"Kaboli", "scopus_author_id"=>"12792359400"}, {"first_name"=>"Vincent", "last_name"=>"Nijman", "scopus_author_id"=>"6603777959"}, {"first_name"=>"Miguel", "last_name"=>"Vences", "scopus_author_id"=>"7006129560"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-58149477880", "pmid"=>"19127298", "sgr"=>"58149477880", "doi"=>"10.1371/journal.pone.0004119", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203", "pui"=>"354058834"}, "id"=>"8912a435-130e-330a-bdf6-1999c9bc652c", "abstract"=>"Background DNA barcoding based on the mitochondrial cytochrome oxidase subunit I gene (cox1 or COI) has been successful in species identification across a wide array of taxa but in some cases failed to delimit the species boundaries of closely allied allopatric species or of hybridising sister species. Methodology/Principal Findings In this study we extend the sample size of prior studies in birds for cox1 (2776 sequences, 756 species) and target especially species that are known to occur parapatrically, and/or are known to hybridise, on a Holarctic scale. In order to obtain a larger set of taxa (altogether 2719 species), we include also DNA sequences of two other mitochondrial genes: cytochrome b (cob) (4614 sequences, 2087 species) and 16S (708 sequences, 498 species). Our results confirm the existence of a wide gap between intra- and interspecies divergences for both cox1 and cob, and indicate that distance-based DNA barcoding provides sufficient information to identify and delineate bird species in 98% of all possible pairwise comparisons. This DNA barcoding gap was not statistically influenced by the number of individuals sequenced per species. However, most of the hybridising parapatric species pairs have average divergences intermediate between intraspecific and interspecific distances for both cox1 and cob. Conclusions/Significance DNA barcoding, if used as a tool for species discovery, would thus fail to identify hybridising parapatric species pairs. However, most of them can probably still assigned to known species by character-based approaches, although development of complementary nuclear markers will be necessary to account for mitochondrial introgression in hybridising species.", "link"=>"http://www.mendeley.com/research/molecular-identification-birds-performance-distancebased-dna-barcoding-three-genes-delimit-parapatri", "reader_count"=>189, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>11, "Researcher"=>45, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>45, "Student > Postgraduate"=>6, "Student > Master"=>36, "Other"=>4, "Student > Bachelor"=>13, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>4, "Professor"=>16}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>11, "Researcher"=>45, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>45, "Student > Postgraduate"=>6, "Student > Master"=>36, "Other"=>4, "Student > Bachelor"=>13, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>4, "Professor"=>16}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Engineering"=>2, "Environmental Science"=>15, "Biochemistry, Genetics and Molecular Biology"=>19, "Agricultural and Biological Sciences"=>139, "Medicine and Dentistry"=>3, "Arts and Humanities"=>1, "Business, Management and Accounting"=>1, "Physics and Astronomy"=>1, "Social Sciences"=>1, "Earth and Planetary Sciences"=>1, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>139}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>19}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>15}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Republic of Singapore"=>1, "Colombia"=>1, "United States"=>6, "Japan"=>1, "Malaysia"=>1, "Switzerland"=>1, "Portugal"=>1, "Russia"=>1, "India"=>2, "Spain"=>1, "Canada"=>1, "Czech Republic"=>1, "Korea (South)"=>1, "Iran"=>1, "Belgium"=>1, "Brazil"=>6, "Denmark"=>1, "Italy"=>3, "France"=>2, "Germany"=>1}, "group_count"=>6}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/911189"], "description"=>"<p>White bars are comparisons between pairs of parapatric species and grey bars are comparisons within each of these species.</p>", "links"=>[], "tags"=>["pairwise", "comparisons", "parapatric"], "article_id"=>581649, "categories"=>["Ecology", "Molecular Biology", "Evolutionary Biology"], "users"=>["Mansour Aliabadian", "Mohammad Kaboli", "Vincent Nijman", "Miguel Vences"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004119.g002", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_K2P_Pairwise_comparisons_among_parapatric_bird_species_in_a_cox1_b_cob_and_c_16S_genes_/581649", "title"=>"K2P Pairwise comparisons among parapatric bird species in (a) <i>cox1</i>, (b) <i>cob</i>, and (c) <i>16S</i> genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-01-07 00:27:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/911291"], "description"=>"<p>Number of individuals and taxa employed in this study.</p>", "links"=>[], "tags"=>["individuals", "taxa", "employed"], "article_id"=>581749, "categories"=>["Ecology", "Molecular Biology", "Evolutionary Biology"], "users"=>["Mansour Aliabadian", "Mohammad Kaboli", "Vincent Nijman", "Miguel Vences"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004119.t003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_individuals_and_taxa_employed_in_this_study_/581749", "title"=>"Number of individuals and taxa employed in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-01-07 00:29:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/911082"], "description"=>"<p>Black bars are comparisons among intraspecific sequences (left axis) and grey bars represent comparisons among different species (right axis).</p>", "links"=>[], "tags"=>["pairwise", "distances"], "article_id"=>581542, "categories"=>["Ecology", "Molecular Biology", "Evolutionary Biology"], "users"=>["Mansour Aliabadian", "Mohammad Kaboli", "Vincent Nijman", "Miguel Vences"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004119.g001", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_K2P_pairwise_distances_in_a_cox1_b_cob_and_c_16S_genes_/581542", "title"=>"K2P pairwise distances in (a) <i>cox1</i>, (b) <i>cob</i>, and (c) <i>16S</i> genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-01-07 00:25:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/911265"], "description"=>"<p>Mean K2P pairwise distances between species in parapatric species pairs in three genes, <i>cox1</i>, <i>cob</i>, and <i>16S</i>.</p>", "links"=>[], "tags"=>["k2p", "pairwise", "distances", "parapatric", "pairs"], "article_id"=>581719, "categories"=>["Ecology", "Molecular Biology", "Evolutionary Biology"], "users"=>["Mansour Aliabadian", "Mohammad Kaboli", "Vincent Nijman", "Miguel Vences"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004119.t001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mean_K2P_pairwise_distances_between_species_in_parapatric_species_pairs_in_three_genes_cox1_cob_and_16S_/581719", "title"=>"Mean K2P pairwise distances between species in parapatric species pairs in three genes, <i>cox1</i>, <i>cob</i>, and <i>16S</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-01-07 00:28:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/911343"], "description"=>"<p>Presented are mean±standard deviation (number of comparisons).</p>", "links"=>[], "tags"=>["distances", "parapatric", "pairs", "non-parapatric", "comparing", "hybridise", "intrageneric", "intraspecific", "hybridising", "non-hybridising"], "article_id"=>581784, "categories"=>["Ecology", "Molecular Biology", "Evolutionary Biology"], "users"=>["Mansour Aliabadian", "Mohammad Kaboli", "Vincent Nijman", "Miguel Vences"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004119.t002", "stats"=>{"downloads"=>9, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_K2P_distances_of_species_in_parapatric_species_pairs_and_among_non_parapatric_species_comparing_parapatric_species_pairs_that_do_hybridise_with_those_that_do_not_and_with_intrageneric_excluding_parapatric_species_intraspecific_excluding_parapatric_specie/581784", "title"=>"K2P distances of species in parapatric species pairs and among non-parapatric species, comparing parapatric species pairs that do hybridise with those that do not, and with intrageneric (excluding parapatric species), intraspecific (excluding parapatric species), intraspecific in hybridising parapatric species, and intraspecific in non-hybridising parapatric species (** = 0.01, t-test).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-01-07 00:29:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/450440", "https://ndownloader.figshare.com/files/450468", "https://ndownloader.figshare.com/files/450602", "https://ndownloader.figshare.com/files/450803"], "description"=>"<div><h3>Background</h3><p>DNA barcoding based on the mitochondrial cytochrome oxidase subunit I gene (<em>cox1</em> or COI) has been successful in species identification across a wide array of taxa but in some cases failed to delimit the species boundaries of closely allied allopatric species or of hybridising sister species.</p><h3>Methodology/Principal Findings</h3><p>In this study we extend the sample size of prior studies in birds for <em>cox1</em> (2776 sequences, 756 species) and target especially species that are known to occur parapatrically, and/or are known to hybridise, on a Holarctic scale. In order to obtain a larger set of taxa (altogether 2719 species), we include also DNA sequences of two other mitochondrial genes: cytochrome <em>b</em> (<em>cob</em>) (4614 sequences, 2087 species) and <em>16S</em> (708 sequences, 498 species). Our results confirm the existence of a wide gap between intra- and interspecies divergences for both <em>cox1</em> and <em>cob</em>, and indicate that distance-based DNA barcoding provides sufficient information to identify and delineate bird species in 98% of all possible pairwise comparisons. This DNA barcoding gap was not statistically influenced by the number of individuals sequenced per species. However, most of the hybridising parapatric species pairs have average divergences intermediate between intraspecific and interspecific distances for both <em>cox1</em> and <em>cob</em>.</p><h3>Conclusions/Significance</h3><p>DNA barcoding, if used as a tool for species discovery, would thus fail to identify hybridising parapatric species pairs. However, most of them can probably still assigned to known species by character-based approaches, although development of complementary nuclear markers will be necessary to account for mitochondrial introgression in hybridising species.</p></div>", "links"=>[], "tags"=>["molecular", "distance-based", "dna", "barcoding", "genes", "delimit", "parapatric"], "article_id"=>148783, "categories"=>["Ecology", "Molecular Biology", "Evolutionary Biology"], "users"=>["Mansour Aliabadian", "Mohammad Kaboli", "Vincent Nijman", "Miguel Vences"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0004119.s001", "https://dx.doi.org/10.1371/journal.pone.0004119.s002", "https://dx.doi.org/10.1371/journal.pone.0004119.s003", "https://dx.doi.org/10.1371/journal.pone.0004119.s004"], "stats"=>{"downloads"=>21, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Molecular_Identification_of_Birds_Performance_of_Distance_Based_DNA_Barcoding_in_Three_Genes_to_Delimit_Parapatric_Species/148783", "title"=>"Molecular Identification of Birds: Performance of Distance-Based DNA Barcoding in Three Genes to Delimit Parapatric Species", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-01-07 02:26:23"}

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Relative Metric

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