Statistical Parsimony Networks and Species Assemblages in Cephalotrichid Nemerteans (Nemertea)
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{"title"=>"Statistical parsimony networks and species assemblages in cephalotrichid nemerteans (Nemertea)", "type"=>"journal", "authors"=>[{"first_name"=>"Haixia", "last_name"=>"Chen", "scopus_author_id"=>"35209832200"}, {"first_name"=>"Malin", "last_name"=>"Strand", "scopus_author_id"=>"8909306200"}, {"first_name"=>"Jon L.", "last_name"=>"Norenburg", "scopus_author_id"=>"6602129265"}, {"first_name"=>"Shichun", "last_name"=>"Sun", "scopus_author_id"=>"55797566800"}, {"first_name"=>"Hiroshi", "last_name"=>"Kajihara", "scopus_author_id"=>"56125557700"}, {"first_name"=>"Alexey V.", "last_name"=>"Chernyshev", "scopus_author_id"=>"8704649800"}, {"first_name"=>"Svetlana A.", "last_name"=>"Maslakova", "scopus_author_id"=>"6507760148"}, {"first_name"=>"Per", "last_name"=>"Sundberg", "scopus_author_id"=>"7004094193"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pmid"=>"20877627", "pui"=>"359826753", "scopus"=>"2-s2.0-77958505557", "doi"=>"10.1371/journal.pone.0012885", "isbn"=>"1932-6203", "sgr"=>"77958505557"}, "id"=>"78125062-8082-3ca6-bbdf-dfa0c0c92f6f", "abstract"=>"BACKGROUND: It has been suggested that statistical parsimony network analysis could be used to get an indication of species represented in a set of nucleotide data, and the approach has been used to discuss species boundaries in some taxa.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: Based on 635 base pairs of the mitochondrial protein-coding gene cytochrome c oxidase I (COI), we analyzed 152 nemertean specimens using statistical parsimony network analysis with the connection probability set to 95%. The analysis revealed 15 distinct networks together with seven singletons. Statistical parsimony yielded three networks supporting the species status of Cephalothrix rufifrons, C. major and C. spiralis as they currently have been delineated by morphological characters and geographical location. Many other networks contained haplotypes from nearby geographical locations. Cladistic structure by maximum likelihood analysis overall supported the network analysis, but indicated a false positive result where subnetworks should have been connected into one network/species. This probably is caused by undersampling of the intraspecific haplotype diversity.\\n\\nCONCLUSIONS/SIGNIFICANCE: Statistical parsimony network analysis provides a rapid and useful tool for detecting possible undescribed/cryptic species among cephalotrichid nemerteans based on COI gene. It should be combined with phylogenetic analysis to get indications of false positive results, i.e., subnetworks that would have been connected with more extensive haplotype sampling.", "link"=>"http://www.mendeley.com/research/statistical-parsimony-networks-species-assemblages-cephalotrichid-nemerteans-nemertea", "reader_count"=>52, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>14, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>1, "Student > Master"=>6, "Student > Bachelor"=>6, "Professor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>14, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>1, "Student > Master"=>6, "Student > Bachelor"=>6, "Professor"=>5}, "reader_count_by_subject_area"=>{"Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>46, "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"=>46}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Brazil"=>1, "Mexico"=>1, "Malaysia"=>1, "Portugal"=>1, "Germany"=>2, "Spain"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/412786"], "description"=>"<div><h3>Background</h3><p>It has been suggested that statistical parsimony network analysis could be used to get an indication of species represented in a set of nucleotide data, and the approach has been used to discuss species boundaries in some taxa.</p><h3>Methodology/Principal Findings</h3><p>Based on 635 base pairs of the mitochondrial protein-coding gene cytochrome <em>c</em> oxidase I (COI), we analyzed 152 nemertean specimens using statistical parsimony network analysis with the connection probability set to 95%. The analysis revealed 15 distinct networks together with seven singletons. Statistical parsimony yielded three networks supporting the species status of <em>Cephalothrix rufifrons</em>, <em>C. major</em> and <em>C. spiralis</em> as they currently have been delineated by morphological characters and geographical location. Many other networks contained haplotypes from nearby geographical locations. Cladistic structure by maximum likelihood analysis overall supported the network analysis, but indicated a false positive result where subnetworks should have been connected into one network/species. This probably is caused by undersampling of the intraspecific haplotype diversity.</p><h3>Conclusions/Significance</h3><p>Statistical parsimony network analysis provides a rapid and useful tool for detecting possible undescribed/cryptic species among cephalotrichid nemerteans based on COI gene. It should be combined with phylogenetic analysis to get indications of false positive results, i.e., subnetworks that would have been connected with more extensive haplotype sampling.</p></div>", "links"=>[], "tags"=>["parsimony", "networks", "assemblages", "cephalotrichid", "nemerteans"], "article_id"=>141544, "categories"=>["Evolutionary Biology", "Inorganic Chemistry", "Molecular Biology", "Marine Biology", "Ecology"], "users"=>["Haixia Chen", "Malin Strand", "Jon L. Norenburg", "Shichun Sun", "Hiroshi Kajihara", "Alexey V. Chernyshev", "Svetlana A. Maslakova", "Per Sundberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012885", "stats"=>{"downloads"=>10, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Statistical_Parsimony_Networks_and_Species_Assemblages_in_Cephalotrichid_Nemerteans_Nemertea_/141544", "title"=>"Statistical Parsimony Networks and Species Assemblages in Cephalotrichid Nemerteans (Nemertea)", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-21 00:25:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/829395"], "description"=>"<p>Number of individuals, haplotypes and haplotype diversity (<i>h</i>) in each haplotype network (Networks 1–15) and mean nucleotide Kimura-2-parameters (K2P) distances for COI gene within haplotype network.</p>", "links"=>[], "tags"=>["haplotypes", "haplotype", "nucleotide", "kimura-2-parameters", "distances", "coi"], "article_id"=>499753, "categories"=>["Evolutionary Biology", "Inorganic Chemistry", "Molecular Biology", "Marine Biology", "Ecology"], "users"=>["Haixia Chen", "Malin Strand", "Jon L. Norenburg", "Shichun Sun", "Hiroshi Kajihara", "Alexey V. Chernyshev", "Svetlana A. Maslakova", "Per Sundberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012885.t001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_individuals_haplotypes_and_haplotype_diversity_h_in_each_haplotype_network_Networks_1_15_and_mean_nucleotide_Kimura_2_parameters_K2P_distances_for_COI_gene_within_haplotype_network_/499753", "title"=>"Number of individuals, haplotypes and haplotype diversity (<i>h</i>) in each haplotype network (Networks 1–15) and mean nucleotide Kimura-2-parameters (K2P) distances for COI gene within haplotype network.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-21 02:42:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/829282"], "description"=>"<p>Branch support values (>80%) are shown on the branches. Abbreviations as per <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012885#pone.0012885.s001\" target=\"_blank\">Table S1</a>. Branch lengths are proportional to genetic distance, branch lengths to Networks 7 (h53–54) and 20 (h88) are drawn to 1/3 of actual length for convenience.</p>", "links"=>[], "tags"=>["cladogram", "90", "haplotypes", "152", "coi"], "article_id"=>499642, "categories"=>["Evolutionary Biology", "Inorganic Chemistry", "Molecular Biology", "Marine Biology", "Ecology"], "users"=>["Haixia Chen", "Malin Strand", "Jon L. Norenburg", "Shichun Sun", "Hiroshi Kajihara", "Alexey V. Chernyshev", "Svetlana A. Maslakova", "Per Sundberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012885.g002", "stats"=>{"downloads"=>2, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Unrooted_cladogram_from_maximum_likelihood_analysis_of_the_90_unique_haplotypes_of_152_COI_sequences_/499642", "title"=>"Unrooted cladogram from maximum likelihood analysis of the 90 unique haplotypes of 152 COI sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-21 02:40:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/829114"], "description"=>"<p>Each bar indicates one missing unsampled haplotype. Two or more names in one frame indicate identical genotypes. The names in frames correspond to those labcodes in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012885#pone.0012885.s001\" target=\"_blank\">Table S1</a> (Species name plus the abbreviation of the locality and number). Abbreviations as per <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012885#pone.0012885.s001\" target=\"_blank\">Table S1</a>.</p>", "links"=>[], "tags"=>["networks", "coi", "parsimony"], "article_id"=>499476, "categories"=>["Evolutionary Biology", "Inorganic Chemistry", "Molecular Biology", "Marine Biology", "Ecology"], "users"=>["Haixia Chen", "Malin Strand", "Jon L. Norenburg", "Shichun Sun", "Hiroshi Kajihara", "Alexey V. Chernyshev", "Svetlana A. Maslakova", "Per Sundberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012885.g001", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Haplotype_networks_for_the_COI_gene_in_this_study_under_the_95_parsimony_criterion_/499476", "title"=>"Haplotype networks for the COI gene in this study under the 95% parsimony criterion.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-21 02:37:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/829358"], "description"=>"<p>N1–22 indicates Networks 1–22 (Networks 1–14, See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012885#pone-0012885-g001\" target=\"_blank\">Figure 1</a>); N15, <i>C</i>. <i>simula</i> CA1 (<i>C. simula</i> CA2, <i>C</i>. sp. FL7, <i>C</i>. sp. FL8); N16, <i>C</i>. sp. SPA; N17–18, <i>C</i>. sp. PAN1, 2; N19–20, <i>C</i>. sp. JAP-SE1, 2; N21, <i>C</i>. sp. VIE; N22, <i>C</i>. <i>fasciculus</i> JAP-F33. Abbreviations as per <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012885#pone.0012885.s001\" target=\"_blank\">Table S1</a>.</p>", "links"=>[], "tags"=>["distances", "coi", "haplotype"], "article_id"=>499717, "categories"=>["Evolutionary Biology", "Inorganic Chemistry", "Molecular Biology", "Marine Biology", "Ecology"], "users"=>["Haixia Chen", "Malin Strand", "Jon L. Norenburg", "Shichun Sun", "Hiroshi Kajihara", "Alexey V. Chernyshev", "Svetlana A. Maslakova", "Per Sundberg"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012885.t002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Kimura_2_parameters_K2P_distances_for_COI_gene_between_haplotype_networks_species_/499717", "title"=>"Kimura-2-parameters (K2P) distances for COI gene between haplotype networks/species.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-21 02:41:57"}

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Relative Metric

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