Population Genetics of a Trochid Gastropod Broadens Picture of Caribbean Sea Connectivity
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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/413664"], "description"=>"<div><h3>Background</h3><p>Regional genetic connectivity models are critical for successful conservation and management of marine species. Even though rocky shore invertebrates have been used as model systems to understand genetic structure in some marine environments, our understanding of connectivity in Caribbean communities is based overwhelmingly on studies of tropical fishes and corals. In this study, we investigate population connectivity and diversity of <em>Cittarium pica</em>, an abundant rocky shore trochid gastropod that is commercially harvested across its natural range, from the Bahamas to Venezuela.</p><h3>Methodology/Principal Findings</h3><p>We tested for genetic structure using DNA sequence variation at the mitochondrial COI and 16S loci, AMOVA and distance-based methods. We found substantial differentiation among Caribbean sites. Yet, genetic differentiation was associated only with larger geographic scales within the Caribbean, and the pattern of differentiation only partially matched previous assessments of Caribbean connectivity, including those based on larval dispersal from hydrodynamic models. For instance, the Bahamas, considered an independent region by previous hydrodynamic studies, showed strong association with Eastern Caribbean sites in our study. Further, Bonaire (located in the east and close to the meridional division of the Caribbean basin) seems to be isolated from other Eastern sites.</p><h3>Conclusions/Significance</h3><p>The significant genetic structure and observed in <em>C. pica</em> has some commonalities in pattern with more commonly sampled taxa, but presents features, such as the differentiation of Bonaire, that appear unique. Further, the level of differentiation, together with regional patterns of diversity, has important implications for the application of conservation and management strategies in this commercially harvested species.</p></div>", "links"=>[], "tags"=>["genetics", "trochid", "gastropod", "broadens", "caribbean", "connectivity"], "article_id"=>141708, "categories"=>["Marine Biology"], "users"=>["Edgardo Díaz-Ferguson", "Robert Haney", "John Wares", "Brian Silliman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012675", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Population_Genetics_of_a_Trochid_Gastropod_Broadens_Picture_of_Caribbean_Sea_Connectivity/141708", "title"=>"Population Genetics of a Trochid Gastropod Broadens Picture of Caribbean Sea Connectivity", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-10 00:28:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/830937"], "description"=>"<p><b>Note:</b> Groups of sites were defined based on maximization of between groups variation. As three alternative configurations occurred for both loci with similar values of F<sub>ct</sub>, all three are presented in order of descending F<sub>ct</sub>. Columns indicate sources of genetic variation, the amount of variation accounted for by each source expressed as a percentage, and the fixation indices with associated significance levels determined through 1000 permutations of the data.</p>", "links"=>[], "tags"=>["coi"], "article_id"=>501315, "categories"=>["Marine Biology"], "users"=>["Edgardo Díaz-Ferguson", "Robert Haney", "John Wares", "Brian Silliman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012675.t003", "stats"=>{"downloads"=>3, "page_views"=>61, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SAMOVA_results_for_COI_and_16S_/501315", "title"=>"SAMOVA results for COI and 16S.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-10 00:21:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/830980"], "description"=>"<p><b>Note:</b> Columns indicate sources of genetic variation, the amount of variation accounted for by each source expressed as a percentage, and the fixation indices with associated significance levels determined through 1000 permutations of the data.</p>", "links"=>[], "tags"=>["coi", "16s", "caribbean", "connectivity", "regions"], "article_id"=>501346, "categories"=>["Marine Biology"], "users"=>["Edgardo Díaz-Ferguson", "Robert Haney", "John Wares", "Brian Silliman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012675.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_AMOVA_results_for_C_pica_COI_and_16S_for_the_four_Caribbean_connectivity_regions_9_/501346", "title"=>"AMOVA results for <i>C. pica</i> COI and 16S for the four Caribbean connectivity regions [9].", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-10 00:22:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/830697"], "description"=>"<p>Region I- <b>Bahamas</b> [<b>BSS:</b> San Salvador Bahamas], Region II- Southwestern <b>SW</b> [<b>CR:</b> Punta Cocles, <b>PC:</b> Playa Chiquita, <b>BO:</b> Bocas del Toro], Region III-Panama central <b>PC</b> [<b>BV:</b> Buenaventura-Colon-Panama], Region IV- Eastern <b>E</b> [<b>BN:</b> Bonaire, <b>USVI:</b>Virgin Islands, <b>WPR</b>: Puerto Rico (Guajataca, Aguadilla and La Parguera)].</p>", "links"=>[], "tags"=>["locations", "regions"], "article_id"=>501071, "categories"=>["Marine Biology"], "users"=>["Edgardo Díaz-Ferguson", "Robert Haney", "John Wares", "Brian Silliman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012675.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sampling_locations_and_regions_for_C_pica_in_the_Caribbean_/501071", "title"=>"Sampling locations and regions for <i>C. pica</i> in the Caribbean.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-10 00:17:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/831017"], "description"=>"<p><b>Note:</b> All p-values were determined with 1000 permutations of haplotypes among populations and significance is indicated with one or two asterisks (*p<0.05 and **p<0.01). Values for COI are in the upper triangular matrix and those for 16S are in the lower matrix. Refer to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012675#pone-0012675-g001\" target=\"_blank\">Figure 1</a> for locality abbreviations.</p>", "links"=>[], "tags"=>["matrices", "pairwise", "coi", "16s"], "article_id"=>501387, "categories"=>["Marine Biology"], "users"=>["Edgardo Díaz-Ferguson", "Robert Haney", "John Wares", "Brian Silliman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012675.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Triangular_matrices_of_pairwise_F_st_values_for_COI_and_16S_between_populations_/501387", "title"=>"Triangular matrices of pairwise F<sub>st</sub> values for COI and 16S between populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-10 00:23:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/831044"], "description"=>"<p><b>Note:</b> Significant p-values (p<0.05 and p<0.01) are indicated with one or two asterisks, and based on permutation test results.</p>", "links"=>[], "tags"=>["parameters", "regions", "undifferentiated", "nucleotide"], "article_id"=>501418, "categories"=>["Marine Biology"], "users"=>["Edgardo Díaz-Ferguson", "Robert Haney", "John Wares", "Brian Silliman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012675.t004", "stats"=>{"downloads"=>5, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_regional_genetic_parameters_for_regions_with_multiple_undifferentiated_populations_including_values_of_nucleotide_diversity_Tajima_s_D_T_and_Fu_s_F_s_/501418", "title"=>"Summary of regional genetic parameters for regions with multiple undifferentiated populations, including values of nucleotide diversity (π), Tajima's D<sub>T</sub> and Fu's F<sub>s</sub>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-10 00:23:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/830888"], "description"=>"<p><b>*</b> indicates the maximal F<sub>CT</sub> groupings based on the COI and 16S data, while the shaded region delineates the structure expected from hydrodynamic models of larval dispersal in the Caribbean.</p>", "links"=>[], "tags"=>["numbers", "groups", "samova", "coi"], "article_id"=>501253, "categories"=>["Marine Biology"], "users"=>["Edgardo Díaz-Ferguson", "Robert Haney", "John Wares", "Brian Silliman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012675.g003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Values_of_F_CT_for_alternative_numbers_of_groups_in_SAMOVA_for_COI_and_16S_/501253", "title"=>"Values of F<sub>CT</sub> for alternative numbers of groups in SAMOVA for COI and 16S.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-10 00:20:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/830768"], "description"=>"<p>Each haplotype is labeled and represented by a circle and its area is proportional to its relative frequency by location. For a given haplotype, color coding indicates in what proportion it is found at different sites. Numbers correspond to the positions of mutations occurring in the studied COI and 16S fragments. Median vectors (<b>mv</b>) are represented as small red circles. The sequences (haplotypes) by site have GenBank Accession Nos <i>GU726381</i>-<i>GU726460</i> (COI) and <i>GU733509-GU733607</i> (16S).</p>", "links"=>[], "tags"=>["networks", "coi", "16s"], "article_id"=>501139, "categories"=>["Marine Biology"], "users"=>["Edgardo Díaz-Ferguson", "Robert Haney", "John Wares", "Brian Silliman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012675.g002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Median_joining_networks_for_COI_a_and_16S_b_C_pica_haplotypes_/501139", "title"=>"Median-joining networks for COI (a) and 16S (b) <i>C. pica</i> haplotypes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-10 00:18:59"}

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Relative Metric

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