Population Connectivity and Phylogeography of a Coastal Fish, Atractoscion aequidens (Sciaenidae), across the Benguela Current Region: Evidence of an Ancient Vicariant Event
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{"title"=>"Population connectivity and phylogeography of a coastal fish, Atractoscion aequidens (Sciaenidae), across the Benguela Current region: Evidence of an ancient vicariant event", "type"=>"journal", "authors"=>[{"first_name"=>"Romina", "last_name"=>"Henriques", "scopus_author_id"=>"57006339000"}, {"first_name"=>"Warren M.", "last_name"=>"Potts", "scopus_author_id"=>"8521312400"}, {"first_name"=>"Carmen V.", "last_name"=>"Santos", "scopus_author_id"=>"36656292800"}, {"first_name"=>"Warwick H.H.", "last_name"=>"Sauer", "scopus_author_id"=>"35944523200"}, {"first_name"=>"Paul W.", "last_name"=>"Shaw", "scopus_author_id"=>"7401651625"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"372566210", "issn"=>"19326203", "isbn"=>"1932-6203", "doi"=>"10.1371/journal.pone.0087907", "scopus"=>"2-s2.0-84895893963", "pmid"=>"24586296", "sgr"=>"84895893963"}, "id"=>"47d52fc7-91fa-3ee1-88a6-81619ccb3495", "abstract"=>"Contemporary patterns of genetic diversity and population connectivity within species can be influenced by both historical and contemporary barriers to gene flow. In the marine environment, present day oceanographic features such as currents, fronts and upwelling systems can influence dispersal of eggs/larvae and/juveniles/adults, shaping population substructuring. The Benguela Current system in the southeastern Atlantic is one of the oldest upwelling systems in the world, and provides a unique opportunity to investigate the relative influence of contemporary and historical mechanisms shaping the evolutionary history of warm-temperate fish species. Using the genetic variation in the mitochondrial DNA Control Region and eight nuclear microsatellite DNA loci, we identified the presence of two highly divergent populations in a vagile and warm-temperate fish species, Atractoscion aequidens, across the Benguela region. The geographical distributions of the two populations, on either side of the perennial upwelling cell, suggest a strong correlation between the oceanographic features of the system and the breakdown of gene flow within this species. Genetic divergence (mtDNA φ ST = 0.902, microsatellite F ST = 0.055: probability of genetic homogeneity for either marker = p<0.001), absence of migrants (less than 1% per generation) between populations and coalescent estimates of time since most recent common ancestor suggest that the establishment of the main oceanographic features of the system (2 million years ago), particularly the strengthening and position of the perennial upwelling cell, is the most likely mechanism behind the observed isolation. Concordance between mitochondrial and nuclear genetic markers indicates that isolation and divergence of the northern and southern Benguela populations of A. aequidens occurred deep in the past and has continued to the present day. These findings suggest that the Benguela Current system may constitute an ancient and impermeable barrier to gene flow for warm-temperate fish species.", "link"=>"http://www.mendeley.com/research/population-connectivity-phylogeography-coastal-fish-atractoscion-aequidens-sciaenidae-across-benguel", "reader_count"=>71, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>12, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>4, "Other"=>4, "Student > Master"=>16, "Student > Bachelor"=>7, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>12, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>4, "Other"=>4, "Student > Master"=>16, "Student > Bachelor"=>7, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>12, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>48, "Arts and Humanities"=>1, "Physics and Astronomy"=>1}, "reader_count_by_subdiscipline"=>{"Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>48}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>12}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Sweden"=>1, "Brazil"=>1, "South Africa"=>1, "Mexico"=>1, "Portugal"=>1, "Germany"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1393753"], "description"=>"<p>Sampling strategy for <i>A. aequidens</i> across the Benguela Current region, highlighting sampling sites (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087907#pone-0087907-t001\" target=\"_blank\">Table 1</a> for sampling codes), and their position relative to the major oceanographic features of the system: position of the Benguela and Agulhas Currents, central Namibia upwelling cell, and continental platform width.</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Coastal ecology", "Evolutionary biology", "Evolutionary processes", "Genetic drift", "natural selection", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "population genetics", "Effective population size", "Gene flow", "haplotypes", "Marine biology", "Fisheries science", "Marine conservation", "Population biology", "Zoology", "Ichthyology", "regions"], "article_id"=>940656, "categories"=>["Biological Sciences"], "users"=>["Romina Henriques", "Warren M. Potts", "Carmen V. Santos", "Warwick H. H. Sauer", "Paul W. Shaw"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087907.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Oceanographic_regions_sampled_/940656", "title"=>"Oceanographic regions sampled.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-20 04:14:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1393754"], "description"=>"<p>Assignment values for each individual fish obtained from STRUCTURE, based on genotypes from eight nuclear microsatellite loci, for <i>K</i> = 2. Cluster 1 (dark grey) are all northern (Angola) population fish; Cluster 2 (light grey) are all southern (South Africa) population fish.</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Coastal ecology", "Evolutionary biology", "Evolutionary processes", "Genetic drift", "natural selection", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "population genetics", "Effective population size", "Gene flow", "haplotypes", "Marine biology", "Fisheries science", "Marine conservation", "Population biology", "Zoology", "Ichthyology", "clusters", "observed", "populations", "benguela"], "article_id"=>940657, "categories"=>["Biological Sciences"], "users"=>["Romina Henriques", "Warren M. Potts", "Carmen V. Santos", "Warwick H. H. Sauer", "Paul W. Shaw"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087907.g002", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_genetic_clusters_observed_within_A_aequidens_populations_across_the_Benguela_region_/940657", "title"=>"Number of genetic clusters observed within <i>A. aequidens</i> populations across the Benguela region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-20 04:14:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1393755"], "description"=>"<p>Haplotype network based on 583 bp of mtDNA CR sequences. Node sizes are proportional to number of individuals observed for that haplotype and colour codes refer to sampling site (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087907#pone-0087907-t001\" target=\"_blank\">Table 1</a> for site designations). Red dots correspond to missing (non-sampled) haplotypes.</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Coastal ecology", "Evolutionary biology", "Evolutionary processes", "Genetic drift", "natural selection", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "population genetics", "Effective population size", "Gene flow", "haplotypes", "Marine biology", "Fisheries science", "Marine conservation", "Population biology", "Zoology", "Ichthyology", "sampled", "benguela"], "article_id"=>940658, "categories"=>["Biological Sciences"], "users"=>["Romina Henriques", "Warren M. Potts", "Carmen V. Santos", "Warwick H. H. Sauer", "Paul W. Shaw"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087907.g003", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Haplotype_network_for_A_aequidens_sampled_across_the_Benguela_region_/940658", "title"=>"Haplotype network for <i>A. aequidens</i> sampled across the Benguela region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-20 04:14:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1393756"], "description"=>"<p>BSPs showing changes in effective population size (N<sub>e</sub>*μ) over time (KY). The solid line indicates the median estimate, and the 95% HPD interval is depicted in blue.</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Coastal ecology", "Evolutionary biology", "Evolutionary processes", "Genetic drift", "natural selection", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "population genetics", "Effective population size", "Gene flow", "haplotypes", "Marine biology", "Fisheries science", "Marine conservation", "Population biology", "Zoology", "Ichthyology", "skyline", "populations", "benguela"], "article_id"=>940659, "categories"=>["Biological Sciences"], "users"=>["Romina Henriques", "Warren M. Potts", "Carmen V. Santos", "Warwick H. H. Sauer", "Paul W. Shaw"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087907.g004", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayesian_Skyline_Plots_BSPs_for_the_two_populations_of_A_aequidens_across_the_Benguela_region_/940659", "title"=>"Bayesian Skyline Plots (BSPs) for the two populations of <i>A. aequidens</i> across the Benguela region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-20 04:14:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1393757"], "description"=>"<p>Statistically significant results (<i>p</i><0.05) in bold.</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Coastal ecology", "Evolutionary biology", "Evolutionary processes", "Genetic drift", "natural selection", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "population genetics", "Effective population size", "Gene flow", "haplotypes", "Marine biology", "Fisheries science", "Marine conservation", "Population biology", "Zoology", "Ichthyology", "benguela", "subsystem", "populations", "mtdna", "cr", "neutrality", "mismatch", "mutation", "ci"], "article_id"=>940660, "categories"=>["Biological Sciences"], "users"=>["Romina Henriques", "Warren M. Potts", "Carmen V. Santos", "Warwick H. H. Sauer", "Paul W. Shaw"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087907.t005", "stats"=>{"downloads"=>4, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_demographic_history_for_northern_Angola_northern_Namibia_and_southern_South_Africa_Benguela_subsystem_populations_of_A_aequidens_based_on_mtDNA_CR_sequence_variation_genetic_diversity_h_and_960_neutrality_tests_Tajima_s_D_and_Fu_s_F_S_mismatch_di/940660", "title"=>"Genetic demographic history for northern (Angola/northern Namibia) and southern (South Africa) Benguela subsystem populations of <i>A. aequidens</i>, based on mtDNA CR sequence variation: genetic diversity (<i>h</i> and <i>π</i>); neutrality tests (Tajima's <i>D</i> and Fu's <i>F<sub>S</sub></i>); mismatch distribution parameters (<i>θ<sub>0</sub></i> = population size before expansion in mutation units, <i>θ<sub>1</sub></i> = population size after expansion in mutation units; and time since expansion (<i>T<sub>exp</sub></i> in Ka; 95% CI in brackets).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-20 04:14:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1393758"], "description"=>"<p>Values significantly greater than zero (<i>p</i><0.05) in bold.</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Coastal ecology", "Evolutionary biology", "Evolutionary processes", "Genetic drift", "natural selection", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "population genetics", "Effective population size", "Gene flow", "haplotypes", "Marine biology", "Fisheries science", "Marine conservation", "Population biology", "Zoology", "Ichthyology", "differentiation", "samples", "mtdna", "cr", "sequences", "microsatellite", "loci"], "article_id"=>940661, "categories"=>["Biological Sciences"], "users"=>["Romina Henriques", "Warren M. Potts", "Carmen V. Santos", "Warwick H. H. Sauer", "Paul W. Shaw"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087907.t004", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_differentiation_966_ST_between_A_aequidens_samples_based_on_mtDNA_CR_sequences_below_diagonal_and_eight_nuclear_microsatellite_loci_above_diagonal_F_ST_D_est_/940661", "title"=>"Genetic differentiation (<i>φ</i><sub>ST</sub>) between <i>A. aequidens</i> samples based on mtDNA CR sequences (below diagonal) and eight nuclear microsatellite loci (above diagonal: <i>F</i><sub>ST</sub> (<i>D</i><sub>est</sub>)).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-20 04:14:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1393759"], "description"=>"<p>Estimates of time since divergence between northern and southern subsystem <i>A. aequidens</i> populations: Ln(likelihood) – posterior likelihood of the calibration method employed; estimated time since most recent common ancestor (<i>tmrca</i> - Ma), and estimated divergence rate (% per My).</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Coastal ecology", "Evolutionary biology", "Evolutionary processes", "Genetic drift", "natural selection", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "population genetics", "Effective population size", "Gene flow", "haplotypes", "Marine biology", "Fisheries science", "Marine conservation", "Population biology", "Zoology", "Ichthyology", "divergence", "subsystem", "posterior", "calibration"], "article_id"=>940662, "categories"=>["Biological Sciences"], "users"=>["Romina Henriques", "Warren M. Potts", "Carmen V. Santos", "Warwick H. H. Sauer", "Paul W. Shaw"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087907.t006", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimates_of_time_since_divergence_between_northern_and_southern_subsystem_A_aequidens_populations_Ln_likelihood_posterior_likelihood_of_the_calibration_method_employed_estimated_time_since_most_recent_common_ancestor_tmrca_Ma_and_estimated_divergence_ra/940662", "title"=>"Estimates of time since divergence between northern and southern subsystem <i>A. aequidens</i> populations: Ln(likelihood) – posterior likelihood of the calibration method employed; estimated time since most recent common ancestor (<i>tmrca</i> - Ma), and estimated divergence rate (% per My).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-20 04:14:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1393760"], "description"=>"<p>Sampling strategy for <i>A. aequidens</i> across the Benguela Current region: sampling locations, sample code and sample size.</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Coastal ecology", "Evolutionary biology", "Evolutionary processes", "Genetic drift", "natural selection", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "population genetics", "Effective population size", "Gene flow", "haplotypes", "Marine biology", "Fisheries science", "Marine conservation", "Population biology", "Zoology", "Ichthyology", "benguela", "sampling"], "article_id"=>940663, "categories"=>["Biological Sciences"], "users"=>["Romina Henriques", "Warren M. Potts", "Carmen V. Santos", "Warwick H. H. Sauer", "Paul W. Shaw"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087907.t001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sampling_strategy_for_A_aequidens_across_the_Benguela_Current_region_sampling_locations_sample_code_and_sample_size_/940663", "title"=>"Sampling strategy for <i>A. aequidens</i> across the Benguela Current region: sampling locations, sample code and sample size.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-20 04:14:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1393761"], "description"=>"<p>Genetic diversity at eight microsatellite loci in <i>A. aequidens</i>: n – number of individuals genotyped; Na – number of alleles; AR – allelic richness for a minimum of 47 individuals; H<sub>E</sub> – expected heterozygosity; H<sub>O</sub> – observed heterozygosity; F<sub>IS</sub> – inbreeding coefficient (significant deviations to Hardy-Weinberg expectations in bold, <i>p</i><0.05).</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Coastal ecology", "Evolutionary biology", "Evolutionary processes", "Genetic drift", "natural selection", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "population genetics", "Effective population size", "Gene flow", "haplotypes", "Marine biology", "Fisheries science", "Marine conservation", "Population biology", "Zoology", "Ichthyology", "microsatellite", "loci", "individuals", "na", "ar", "allelic", "richness", "47", "observed", "inbreeding", "coefficient", "deviations", "hardy-weinberg", "expectations"], "article_id"=>940664, "categories"=>["Biological Sciences"], "users"=>["Romina Henriques", "Warren M. Potts", "Carmen V. Santos", "Warwick H. H. Sauer", "Paul W. Shaw"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087907.t003", "stats"=>{"downloads"=>13, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_diversity_at_eight_microsatellite_loci_in_A_aequidens_n_number_of_individuals_genotyped_Na_number_of_alleles_AR_allelic_richness_for_a_minimum_of_47_individuals_H_E_8211_expected_heterozygosity_H_O_8211_observed_heterozygosity_F_IS_8211_inbreedin/940664", "title"=>"Genetic diversity at eight microsatellite loci in <i>A. aequidens</i>: n – number of individuals genotyped; Na – number of alleles; AR – allelic richness for a minimum of 47 individuals; H<sub>E</sub> – expected heterozygosity; H<sub>O</sub> – observed heterozygosity; F<sub>IS</sub> – inbreeding coefficient (significant deviations to Hardy-Weinberg expectations in bold, <i>p</i><0.05).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-20 04:14:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1393762"], "description"=>"<p>Mitochondrial genetic diversity within the Control Region (CR) of <i>A. aequidens</i> from sites (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087907#pone-0087907-t001\" target=\"_blank\">Table 1</a> for codes) within the northern and southern Benguela subsystems: n – number of individuals; H – number of haplotypes; PH – number of haplotypes private to sites within subsystems; <i>h</i> – haplotype diversity; <i>π</i> - nucleotide diversity.</p>", "links"=>[], "tags"=>["ecology", "biogeography", "Coastal ecology", "Evolutionary biology", "Evolutionary processes", "Genetic drift", "natural selection", "Forms of evolution", "Divergent evolution", "Organismal evolution", "Animal evolution", "population genetics", "Effective population size", "Gene flow", "haplotypes", "Marine biology", "Fisheries science", "Marine conservation", "Population biology", "Zoology", "Ichthyology", "sites", "benguela", "ph", "haplotype", "nucleotide"], "article_id"=>940665, "categories"=>["Biological Sciences"], "users"=>["Romina Henriques", "Warren M. Potts", "Carmen V. Santos", "Warwick H. H. Sauer", "Paul W. Shaw"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087907.t002", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mitochondrial_genetic_diversity_within_the_Control_Region_CR_of_A_aequidens_from_sites_see_Table_1_for_codes_within_the_northern_and_southern_Benguela_subsystems_n_number_of_individuals_H_number_of_haplotypes_PH_number_of_haplotypes_private_to_sites_with/940665", "title"=>"Mitochondrial genetic diversity within the Control Region (CR) of <i>A. aequidens</i> from sites (see Table 1 for codes) within the northern and southern Benguela subsystems: n – number of individuals; H – number of haplotypes; PH – number of haplotypes private to sites within subsystems; <i>h</i> – haplotype diversity; <i>π</i> - nucleotide diversity.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-20 04:14:06"}

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