Testing Phylogenetic Hypotheses of the Subgenera of the Freshwater Crayfish Genus Cambarus (Decapoda: Cambaridae)
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{"title"=>"Testing Phylogenetic Hypotheses of the Subgenera of the Freshwater Crayfish Genus Cambarus (Decapoda: Cambaridae)", "type"=>"journal", "authors"=>[{"first_name"=>"Jesse W.", "last_name"=>"Breinholt", "scopus_author_id"=>"26425012000"}, {"first_name"=>"Megan L.", "last_name"=>"Porter", "scopus_author_id"=>"7201467470"}, {"first_name"=>"Keith A.", "last_name"=>"Crandall", "scopus_author_id"=>"7006440923"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"365742272", "sgr"=>"84866878435", "issn"=>"19326203", "pmid"=>"23049950", "scopus"=>"2-s2.0-84866878435", "doi"=>"10.1371/journal.pone.0046105", "isbn"=>"1932-6203"}, "id"=>"e9abb7e2-1a03-3943-b935-00ea382cf6e6", "abstract"=>"BACKGROUND: The genus Cambarus is one of three most species rich crayfish genera in the Northern Hemisphere. The genus has its center of diversity in the Southern Appalachians of the United States and has been divided into 12 subgenera. Using Cambarus we test the correspondence of subgeneric designations based on morphology used in traditional crayfish taxonomy to the underlying evolutionary history for these crayfish. We further test for significant correlation and explanatory power of geographic distance, taxonomic model, and a habitat model to estimated phylogenetic distance with multiple variable regression.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: We use three mitochondrial and one nuclear gene regions to estimate the phylogenetic relationships for species within the genus Cambarus and test evolutionary hypotheses of relationships and associated morphological and biogeographical hypotheses. Our resulting phylogeny indicates that the genus Cambarus is polyphyletic, however we fail to reject the monophyly of Cambarus with a topology test. The majority of the Cambarus subgenera are rejected as monophyletic, suggesting the morphological characters used to define those taxa are subject to convergent evolution. While we found incongruence between taxonomy and estimated phylogenetic relationships, a multiple model regression analysis indicates that taxonomy had more explanatory power of genetic relationships than either habitat or geographic distance.\\n\\nCONCLUSIONS: We find convergent evolution has impacted the morphological features used to delimit Cambarus subgenera. Studies of the crayfish genus Orconectes have shown gonopod morphology used to delimit subgenera is also affected by convergent evolution. This suggests that morphological diagnoses based on traditional crayfish taxonomy might be confounded by convergent evolution across the cambarids and has little utility in diagnosing relationships or defining natural groups. We further suggest that convergent morphological evolution appears to be a common occurrence in invertebrates suggesting the need for careful phylogenetically based interpretations of morphological evolution in invertebrate systematics.", "link"=>"http://www.mendeley.com/research/testing-phylogenetic-hypotheses-subgenera-freshwater-crayfish-genus-cambarus-decapoda-cambaridae", "reader_count"=>38, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>9, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>2, "Student > Master"=>9, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>9, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>2, "Student > Master"=>9, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>29, "Psychology"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Psychology"=>{"Psychology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>29}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"United States"=>2, "Chile"=>1, "Australia"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/569417"], "description"=>"<p><i>Tubericambarus</i> and <i>Glareocola</i> were placed as sister to the subgenera from which they were partitioned <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046105#pone.0046105-Jezerinac1\" target=\"_blank\">[6]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046105#pone.0046105-Bouchard1\" target=\"_blank\">[7]</a>. The monotypic subgenus <i>Exilicambarus</i> is placed in three locations (three possible topologies H1, H2, and H3) based on Bouchard and Hobbs' <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046105#pone.0046105-Bouchard2\" target=\"_blank\">[8]</a> assessment of potential sister taxa.</p>", "links"=>[], "tags"=>["relationships", "subgenera", "genus", "hobbs", "modification", "modified"], "article_id"=>239905, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jesse W. Breinholt", "Megan L. Porter", "Keith A. Crandall"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046105.g002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hypothesized_relationships_among_subgenera_of_the_genus_Cambarus_based_on_Hobbs_3_with_modification_to_include_subgenera_described_and_or_modified_post_Hobbs_3_/239905", "title"=>"Hypothesized relationships among subgenera of the genus <i>Cambarus</i> based on Hobbs [<b>3</b>] with modification to include subgenera described and/or modified post Hobbs [<b>3</b>].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-26 02:45:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/569260"], "description"=>"<p>Counties are colored according to the number of species in that county listed in the SI USNM records with a color scheme scale shown in the lower right corner of figure.</p>", "links"=>[], "tags"=>["created", "openheatmap", "counts", "united", "states", "si", "usnm", "invertebrate", "2012"], "article_id"=>239746, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jesse W. Breinholt", "Megan L. Porter", "Keith A. Crandall"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046105.g001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Choropleth_map_of_the_distribution_of_Cambarus_created_with_the_open_source_web_tool_Openheatmap_http_www_openheatmap_com_using_counts_of_species_in_each_United_States_county_collected_from_the_SI_USNM_Invertebrate_collection_data_base_downloaded_Februar/239746", "title"=>"Choropleth map of the distribution of <i>Cambarus</i> created with the open source web tool Openheatmap (http://www.openheatmap.com/) using counts of species in each United States county collected from the SI USNM Invertebrate collection data base (downloaded February, 2012 from http://collections.mnh.si.edu/search/).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-26 02:42:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/569708"], "description"=>"<p><a href=\"http://www.openheatmap.com/\" target=\"_blank\">http://www.openheatmap.com/</a><b>) using counts of species with distributions in each state.</b> States are colored according to the number of species with distributions in that State with a color scheme scale shown in the lower right corner of each map.</p>", "links"=>[], "tags"=>["maps", "geographic", "resulting", "clades", "bayesian", "created", "openheatmap"], "article_id"=>240197, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jesse W. Breinholt", "Megan L. Porter", "Keith A. Crandall"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046105.g004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Choropleth_maps_to_represent_the_geographic_distribution_of_species_in_resulting_clades_from_the_Bayesian_analysis_Fig_3_created_with_the_open_source_web_tool_Openheatmap_/240197", "title"=>"Choropleth maps to represent the geographic distribution of species in resulting clades from the Bayesian analysis (<b>Fig. 3</b>) created with the open source web tool Openheatmap (", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-26 00:03:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/569875"], "description"=>"<p>Partial Correlation (Partial Corr.), Coefficient (Beta) and Sum of squares (SS) for the observed data. P-values after 10000 randomizations for absolute regression coefficients (2-sided) P(Beta) and for extra sums of squares P(SS).</p>", "links"=>[], "tags"=>["regression", "variables", "geographic", "phylogenetic", "bayesian"], "article_id"=>240369, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jesse W. Breinholt", "Megan L. Porter", "Keith A. Crandall"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046105.t003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_from_multiple_regression_model_for_correlation_of_three_variables_Taxonomic_model_Geographic_distance_Habitat_model_to_Phylogenetic_distance_node_distance_from_Bayesian_topology_/240369", "title"=>"Results from multiple regression model for correlation of three variables (Taxonomic model, Geographic distance, Habitat model) to Phylogenetic distance (node distance from Bayesian topology).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-26 00:06:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/569848"], "description"=>"<p>Table includes the p-value for the AU test and the number (N # of trees) and percent (<i>P</i>p) of trees that fit the given hypothesis from the post-burnin set of Bayesian trees.</p>", "links"=>[], "tags"=>["unbiased", "bayesian", "topological", "topology"], "article_id"=>240343, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jesse W. Breinholt", "Megan L. Porter", "Keith A. Crandall"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046105.t002", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_from_approximately_unbiased_test_AU_test_and_Bayesian_topological_tests_P_p_topology_hypothesis_tests_/240343", "title"=>"Results from approximately unbiased test (AU) test and Bayesian topological tests (<i>P</i>p) topology hypothesis tests.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-26 00:05:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/569907"], "description"=>"*<p>Includes recently described <i>Cambarus</i> species by Cooper and Price <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046105#pone.0046105-Cooper2\" target=\"_blank\">[77]</a>, Loughman et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046105#pone.0046105-Loughman1\" target=\"_blank\">[78]</a>, and Thoma <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046105#pone.0046105-Thoma1\" target=\"_blank\">[79]</a>.</p>", "links"=>[], "tags"=>["sampled"], "article_id"=>240410, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jesse W. Breinholt", "Megan L. Porter", "Keith A. Crandall"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046105.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_number_of_Cambarus_species_sampled_by_subgenus_/240410", "title"=>"The number of <i>Cambarus</i> species sampled by subgenus.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-26 00:06:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/300723", "https://ndownloader.figshare.com/files/300745", "https://ndownloader.figshare.com/files/300759"], "description"=>"<div><h3>Background</h3><p>The genus <em>Cambarus</em> is one of three most species rich crayfish genera in the Northern Hemisphere. The genus has its center of diversity in the Southern Appalachians of the United States and has been divided into 12 subgenera. Using <em>Cambarus</em> we test the correspondence of subgeneric designations based on morphology used in traditional crayfish taxonomy to the underlying evolutionary history for these crayfish. We further test for significant correlation and explanatory power of geographic distance, taxonomic model, and a habitat model to estimated phylogenetic distance with multiple variable regression.</p> <h3>Methodology/Principal Findings</h3><p>We use three mitochondrial and one nuclear gene regions to estimate the phylogenetic relationships for species within the genus <em>Cambarus</em> and test evolutionary hypotheses of relationships and associated morphological and biogeographical hypotheses. Our resulting phylogeny indicates that the genus <em>Cambarus</em> is polyphyletic, however we fail to reject the monophyly of <em>Cambarus</em> with a topology test. The majority of the <em>Cambarus</em> subgenera are rejected as monophyletic, suggesting the morphological characters used to define those taxa are subject to convergent evolution. While we found incongruence between taxonomy and estimated phylogenetic relationships, a multiple model regression analysis indicates that taxonomy had more explanatory power of genetic relationships than either habitat or geographic distance.</p> <h3>Conclusions</h3><p>We find convergent evolution has impacted the morphological features used to delimit <em>Cambarus</em> subgenera. Studies of the crayfish genus <em>Orconectes</em> have shown gonopod morphology used to delimit subgenera is also affected by convergent evolution. This suggests that morphological diagnoses based on traditional crayfish taxonomy might be confounded by convergent evolution across the cambarids and has little utility in diagnosing relationships or defining natural groups. We further suggest that convergent morphological evolution appears to be a common occurrence in invertebrates suggesting the need for careful phylogenetically based interpretations of morphological evolution in invertebrate systematics.</p> </div>", "links"=>[], "tags"=>["phylogenetic", "hypotheses", "subgenera", "freshwater", "crayfish", "genus"], "article_id"=>119293, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jesse W. Breinholt", "Megan L. Porter", "Keith A. Crandall"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0046105.s001", "https://dx.doi.org/10.1371/journal.pone.0046105.s002", "https://dx.doi.org/10.1371/journal.pone.0046105.s003"], "stats"=>{"downloads"=>8, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Testing_Phylogenetic_Hypotheses_of_the_Subgenera_of_the_Freshwater_Crayfish_Genus_Cambarus_Decapoda_Cambaridae_/119293", "title"=>"Testing Phylogenetic Hypotheses of the Subgenera of the Freshwater Crayfish Genus <em>Cambarus</em> (Decapoda: Cambaridae)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-09-26 02:34:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/569513"], "description"=>"<p>Taxa labels are followed by the US state the sample was collected in, the type of habitat of each species in parenthesis (c = cave, b = burrow, s = stream), and in some cases a number for species with more than one sampled individual. Nodal support is indicated by Bayesian posterior probabilities before the slash and ML bootstrap values after the slash on branches leading to the supported node.</p>", "links"=>[], "tags"=>["phylogenetic", "relationships", "amongst", "subgenera", "crayfish", "genus", "outgroups", "genera"], "article_id"=>239999, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Jesse W. Breinholt", "Megan L. Porter", "Keith A. Crandall"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0046105.g003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayesian_estimate_of_phylogenetic_relationships_amongst_the_species_and_subgenera_of_the_crayfish_genus_Cambarus_with_outgroups_from_other_genera_within_the_family_Cambaridae_/239999", "title"=>"Bayesian estimate of phylogenetic relationships amongst the species and subgenera of the crayfish genus <i>Cambarus</i> with outgroups from other genera within the family Cambaridae.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-26 02:46:39"}

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Relative Metric

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