Population Genetic Structure and Colonisation History of the Tool-Using New Caledonian Crow
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{"title"=>"Population genetic structure and colonisation history of the tool-using New Caledonian crow", "type"=>"journal", "authors"=>[{"first_name"=>"Jawad", "last_name"=>"Abdelkrim", "scopus_author_id"=>"16318774500"}, {"first_name"=>"Gavin R.", "last_name"=>"Hunt", "scopus_author_id"=>"7202673961"}, {"first_name"=>"Russell D.", "last_name"=>"Gray", "scopus_author_id"=>"7403689938"}, {"first_name"=>"Neil J.", "last_name"=>"Gemmell", "scopus_author_id"=>"7003864817"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203", "pui"=>"364774415", "doi"=>"10.1371/journal.pone.0036608", "scopus"=>"2-s2.0-84860761124", "sgr"=>"84860761124", "issn"=>"19326203", "pmid"=>"22590576"}, "id"=>"fd2a13ca-5f27-31a2-9e4f-f818ff92f015", "abstract"=>"New Caledonian crows exhibit considerable variation in tool making between populations. Here, we present the first study of the species' genetic structure over its geographical distribution. We collected feathers from crows on mainland Grande Terre, the inshore island of Toupéti, and the nearby island of Maré where it is believed birds were introduced after European colonisation. We used nine microsatellite markers to establish the genotypes of 136 crows from these islands and classical population genetic tools as well as Approximate Bayesian Computations to explore the distribution of genetic diversity. We found that New Caledonian crows most likely separate into three main distinct clusters: Grande Terre, Toupéti and Maré. Furthermore, Toupéti and Maré crows represent a subset of the genetic diversity observed on Grande Terre, confirming their mainland origin. The genetic data are compatible with a colonisation of Maré taking place after European colonisation around 1900. Importantly, we observed (1) moderate, but significant, genetic differentiation across Grande Terre, and (2) that the degree of differentiation between populations on the mainland increases with geographic distance. These data indicate that despite individual crows' potential ability to disperse over large distances, most gene flow occurs over short distances. The temporal and spatial patterns described provide a basis for further hypothesis testing and investigation of the geographical variation observed in the tool skills of these crows.", "link"=>"http://www.mendeley.com/research/population-genetic-structure-colonisation-history-toolusing-new-caledonian-crow", "reader_count"=>41, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>9, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>1, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>5, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>9, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>1, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>5, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>4, "Agricultural and Biological Sciences"=>31, "Business, Management and Accounting"=>1, "Psychology"=>3, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>1}, "Psychology"=>{"Psychology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>31}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>4}}, "reader_count_by_country"=>{"Venezuela"=>1, "Czech Republic"=>1, "United States"=>2, "Brazil"=>1, "United Kingdom"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/330534"], "description"=>"<div><p>New Caledonian crows exhibit considerable variation in tool making between populations. Here, we present the first study of the species’ genetic structure over its geographical distribution. We collected feathers from crows on mainland Grande Terre, the inshore island of Toupéti, and the nearby island of Maré where it is believed birds were introduced after European colonisation. We used nine microsatellite markers to establish the genotypes of 136 crows from these islands and classical population genetic tools as well as Approximate Bayesian Computations to explore the distribution of genetic diversity. We found that New Caledonian crows most likely separate into three main distinct clusters: Grande Terre, Toupéti and Maré. Furthermore, Toupéti and Maré crows represent a subset of the genetic diversity observed on Grande Terre, confirming their mainland origin. The genetic data are compatible with a colonisation of Maré taking place after European colonisation around 1900. Importantly, we observed (1) moderate, but significant, genetic differentiation across Grande Terre, and (2) that the degree of differentiation between populations on the mainland increases with geographic distance. These data indicate that despite individual crows’ potential ability to disperse over large distances, most gene flow occurs over short distances. The temporal and spatial patterns described provide a basis for further hypothesis testing and investigation of the geographical variation observed in the tool skills of these crows.</p> </div>", "links"=>[], "tags"=>["colonisation", "tool-using", "caledonian", "crow"], "article_id"=>125280, "categories"=>["Evolutionary Biology", "Genetics", "Neuroscience", "Ecology"], "users"=>["Jawad Abdelkrim", "Gavin R. Hunt", "Russell D. Gray", "Neil J. Gemmell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036608", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Population_Genetic_Structure_and_Colonisation_History_of_the_Tool_Using_New_Caledonian_Crow/125280", "title"=>"Population Genetic Structure and Colonisation History of the Tool-Using New Caledonian Crow", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-09 01:28:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/641200"], "description"=>"<p>Values of allelic richness in brackets are calculated only with Grande Terre and Maré samples.</p><p>N: Mean number of samples per locus; Na: Mean number of alleles per locus; Na: Mean number of alleles per locus; Rs: mean allelic richness per locus; Np: Number of private alleles; Ho: observed heterozygosity; He: expected heterozygosity; *departure from Hardy-Weinberg equilibrium.</p>", "links"=>[], "tags"=>["heterozygosity", "caledonian", "crows", "grande"], "article_id"=>311689, "categories"=>["Evolutionary Biology", "Genetics", "Neuroscience", "Ecology"], "users"=>["Jawad Abdelkrim", "Gavin R. Hunt", "Russell D. Gray", "Neil J. Gemmell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036608.t001", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genetic_diversity_and_heterozygosity_in_New_Caledonian_crows_on_Grande_Terre_Toup_ti_and_Mar_/311689", "title"=>"Genetic diversity and heterozygosity in New Caledonian crows on Grande Terre, Toupéti and Maré.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-09 00:28:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/640914"], "description"=>"<p>Location of the 11 sites on the islands of Grande Terre, Toupéti and Maré where crow feathers were collected. The samples sizes (<i>n</i>) are the numbers of individual crows sampled at the sites.</p>", "links"=>[], "tags"=>["caledonia"], "article_id"=>311412, "categories"=>["Evolutionary Biology", "Genetics", "Neuroscience", "Ecology"], "users"=>["Jawad Abdelkrim", "Gavin R. Hunt", "Russell D. Gray", "Neil J. Gemmell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036608.g001", "stats"=>{"downloads"=>4, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Map_of_New_Caledonia_with_sample_locations_/311412", "title"=>"Map of New Caledonia with sample locations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-09 00:23:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/641073"], "description"=>"<p>(a) likelihood of the number of clusters <i>K</i> (mean and standard deviation based on three independent runs) and (b) Variation of ΔK for <i>K</i> = 2 to <i>K</i> = 5 following Evanno <i>et al. </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036608#pone.0036608-Evanno1\" target=\"_blank\">[18]</a>.</p>", "links"=>[], "tags"=>["caledonian"], "article_id"=>311569, "categories"=>["Evolutionary Biology", "Genetics", "Neuroscience", "Ecology"], "users"=>["Jawad Abdelkrim", "Gavin R. Hunt", "Russell D. Gray", "Neil J. Gemmell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036608.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Estimation_of_the_number_of_cluster_identified_in_New_Caledonian_crows_/311569", "title"=>"Estimation of the number of cluster identified in New Caledonian crows.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-09 00:26:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/641139"], "description"=>"<p>Each individual is represented by a vertical line, which is partitioned into segments that represent the individual’s estimated membership fractions in the three clusters. Shades of grey correspond to the three clusters. Black lines separate sampling locations as labelled on the map.</p>", "links"=>[], "tags"=>["clustering"], "article_id"=>311633, "categories"=>["Evolutionary Biology", "Genetics", "Neuroscience", "Ecology"], "users"=>["Jawad Abdelkrim", "Gavin R. Hunt", "Russell D. Gray", "Neil J. Gemmell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036608.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Estimated_population_structure_using_clustering_methods_/311633", "title"=>"Estimated population structure using clustering methods.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-09 00:27:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/641236"], "description"=>"<p>The strength of the correlation (<i>r</i><sup>2</sup>) is estimated using reduced major axis regression and the significance (<i>p</i>) of the <i>Z</i> statistics is evaluated through randomization procedure. All combinations of normal and log-transformed distances are reported.</p>", "links"=>[], "tags"=>["geographic", "distances", "grande", "terre"], "article_id"=>311726, "categories"=>["Evolutionary Biology", "Genetics", "Neuroscience", "Ecology"], "users"=>["Jawad Abdelkrim", "Gavin R. Hunt", "Russell D. Gray", "Neil J. Gemmell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036608.t003", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Correlation_between_genetic_Jost_s_i_D_i_and_geographic_distances_on_Grande_Terre_with_and_without_Toup_ti_/311726", "title"=>"Correlation between genetic (Jost’s <i>D</i>) and geographic distances on Grande Terre with and without Toupéti.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-09 00:28:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/641265"], "description"=>"<p>Fst values are indicated below diagonal.</p><p>Values in bold are significantly greater than zero (<i>p</i> value &lt;0.05).</p>", "links"=>[], "tags"=>["differentiation", "pairs", "locations"], "article_id"=>311755, "categories"=>["Evolutionary Biology", "Genetics", "Neuroscience", "Ecology"], "users"=>["Jawad Abdelkrim", "Gavin R. Hunt", "Russell D. Gray", "Neil J. Gemmell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036608.t002", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genetic_differentiation_measured_by_Jost_s_i_D_i_above_diagonal_between_pairs_of_locations_with_at_least_five_samples_/311755", "title"=>"Genetic differentiation measured by Jost’s <i>D</i> (above diagonal) between pairs of locations with at least five samples.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-09 00:29:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/641340"], "description"=>"<p>Posterior distributions are estimated for the most likely scenario (i.e. scenario 1). The mean and median are given, along with 95% credibility intervals. All times (teuro, t1, t2, db and M) are in generations.</p><p>NGT: current effective size of Grande Terre.</p><p>NM0: current effective size of Maré.</p><p>NT: current effective size of Toupéti.</p><p>NM1: effective size of Maré during the post-colonisation bottleneck.</p><p>teuro: constrained colonisation time on Maré around 1900 in scenario 1, corresponding to 30 to 50 generations.</p><p>db: duration of the post-colonisation bottleneck.</p><p>t1: time before present of colonisation of Maré in scenario 2, 3 and 4.</p><p>t2: time before present of colonisation of Toupéti.</p><p>M: time of second colonisation on Maré in scenario 3 after the first one at t1.</p><p>r: admixture rate during the second colonisation event on Maré in scenario 3.</p>", "links"=>[], "tags"=>["posterior", "distributions", "parameters", "abc"], "article_id"=>311833, "categories"=>["Evolutionary Biology", "Genetics", "Neuroscience", "Ecology"], "users"=>["Jawad Abdelkrim", "Gavin R. Hunt", "Russell D. Gray", "Neil J. Gemmell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036608.t004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Prior_and_posterior_distributions_of_demographic_and_historic_parameters_used_in_ABC_analyses_/311833", "title"=>"Prior and posterior distributions of demographic and historic parameters used in ABC analyses.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-09 00:30:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/641308"], "description"=>"<p>The logistic regression used to compute posterior probabilities considered the 40 000 simulated data sets closest to the observed data (1% of the total number of simulations performed for the four scenarios). Scenario 1 is favoured among the four competing scenarios, closely followed by scenario 2.</p>", "links"=>[], "tags"=>["posterior", "probabilities", "intervals", "logistic", "regression"], "article_id"=>311794, "categories"=>["Evolutionary Biology", "Genetics", "Neuroscience", "Ecology"], "users"=>["Jawad Abdelkrim", "Gavin R. Hunt", "Russell D. Gray", "Neil J. Gemmell"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036608.t005", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Relative_posterior_probabilities_with_95_credibility_intervals_for_each_scenario_using_logistic_regression_approaches_/311794", "title"=>"Relative posterior probabilities with 95% credibility intervals for each scenario using logistic regression approaches.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-09 00:29:54"}

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Relative Metric

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