Genetic Diversity, Population Structure and Wolbachia Infection Status in a Worldwide Sample of Drosophila melanogaster and D. simulans Populations
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{"title"=>"Genetic diversity, population structure and Wolbachia infection status in a worldwide sample of Drosophila melanogaster and D. simulans populations", "type"=>"journal", "authors"=>[{"first_name"=>"Rudi L.", "last_name"=>"Verspoor", "scopus_author_id"=>"53980649200"}, {"first_name"=>"Penelope R.", "last_name"=>"Haddrill", "scopus_author_id"=>"8591519100"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"80053981848", "pmid"=>"22022599", "isbn"=>"1932-6203", "scopus"=>"2-s2.0-80053981848", "issn"=>"19326203", "pui"=>"362735284", "doi"=>"10.1371/journal.pone.0026318"}, "id"=>"8bbc2180-1214-34ec-88b3-860cc7439cdb", "abstract"=>"Drosophila melanogaster and its close relatives have been extremely important model species in the development of population genetic models that serve to explain patterns of diversity in natural populations, a major goal of evolutionary biology. A detailed picture of the evolutionary history of these species is beginning to emerge, as the relative importance of forces including demographic changes and natural selection is established. A continuing aim is to characterise levels of genetic diversity in a large number of populations of these species, covering a wide geographic area. We have used collections from five previously un-sampled wild populations of D. melanogaster and two of D. simulans, across three continents. We estimated levels of genetic diversity within, and divergence between, these populations, and looked for evidence of genetic structure both between ancestral and derived populations, and amongst derived populations. We also investigated the prevalence of infection with the bacterial endosymbiont Wolbachia. We found that D. melanogaster populations from Sub-Saharan Africa are the most diverse, and that divergence is highest between these and non-Sub-Saharan populations. There is strong evidence for structuring of populations between Sub-Saharan Africa and the rest of the world, and some evidence for weak structure amongst derived populations. Populations from Sub-Saharan Africa also differ in the prevalence of Wolbachia infection, with very low levels of infection compared to populations from the rest of the world.", "link"=>"http://www.mendeley.com/research/genetic-diversity-population-structure-wolbachia-infection-status-worldwide-sample-drosophila-melano", "reader_count"=>56, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>5, "Researcher"=>15, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>19, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>5, "Researcher"=>15, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>19, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>48, "Social Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>48}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Brazil"=>1, "Italy"=>1, "United Kingdom"=>1, "Germany"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/726140"], "description"=>"<p>The difference between the maximum likelihood and the likelihood for each estimate of <i>K</i> (the number of populations) is shown. Two analyses were carried out; one including all populations, and one excluding the population from Ghana.</p>", "links"=>[], "tags"=>["populations"], "article_id"=>396502, "categories"=>["Biological Sciences", "Ecology", "Microbiology", "Evolutionary Biology"], "users"=>["Rudi L. Verspoor", "Penelope R. Haddrill"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0026318.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimates_of_the_most_likely_number_of_populations_in_a_worldwide_sample_of_D_melanogaster_/396502", "title"=>"Estimates of the most likely number of populations in a worldwide sample of <i>D. melanogaster</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 13:56:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/726474"], "description"=>"<p>**<i>p</i><0.01, NS  =  non-significant.</p>", "links"=>[], "tags"=>["estimates", "populations", "corrected", "bonferroni"], "article_id"=>396831, "categories"=>["Biological Sciences", "Ecology", "Microbiology", "Evolutionary Biology"], "users"=>["Rudi L. Verspoor", "Penelope R. Haddrill"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0026318.t003", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_F_ST_estimates_between_populations_and_associated_statistical_significance_above_diagonal_corrected_for_multiple_tests_using_a_Bonferroni_correction_/396831", "title"=>"Pairwise <i>F</i><sub>ST</sub> estimates between populations and associated statistical significance (above diagonal), corrected for multiple tests using a Bonferroni correction.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 13:58:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/726284"], "description"=>"<p>The proportion of ancestry for each individual in each of <i>K</i> (the number of populations)  = 2 or <i>K</i> = 3 clusters is shown. Two analyses were carried out; one including all populations (A), and one excluding the population from Ghana (B).</p>", "links"=>[], "tags"=>["microbiology", "Computational biology", "ecology", "Evolutionary biology"], "article_id"=>396641, "categories"=>["Biological Sciences", "Ecology", "Microbiology", "Evolutionary Biology"], "users"=>["Rudi L. Verspoor", "Penelope R. Haddrill"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0026318.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimated_population_structure_in_a_worldwide_sample_of_D_melanogaster_/396641", "title"=>"Estimated population structure in a worldwide sample of <i>D. melanogaster</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 13:57:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/726410"], "description"=>"<p><i>n</i> =  sample size, prevalence given with 95% confidence intervals in parentheses, estimated using the Clopper-Pearson method.</p>", "links"=>[], "tags"=>["females", "populations", "bacterial", "endosymbiont"], "article_id"=>396766, "categories"=>["Biological Sciences", "Ecology", "Microbiology", "Evolutionary Biology"], "users"=>["Rudi L. Verspoor", "Penelope R. Haddrill"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0026318.t001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Infection_status_of_females_in_five_populations_of_D_melanogaster_and_two_populations_of_D_simulans_for_the_bacterial_endosymbiont_Wolbachia_/396766", "title"=>"Infection status of females in five populations of <i>D. melanogaster</i> and two populations of <i>D. simulans</i> for the bacterial endosymbiont <i>Wolbachia</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 13:57:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/726445"], "description"=>"<p><i>n</i> =  sample size, <i>H</i><sub>E</sub>  =  mean expected heterozygosity across loci, <i>H</i><sub>E(RD)</sub>  =  mean expected heterozygosity calculated from 200 datasets generated by randomly discarding one allele at each locus, Zimbabwe data taken from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0026318#pone.0026318-OrozcoterWengel1\" target=\"_blank\">[46]</a>, <i>H</i><sub>E(RD)</sub> and allelic richness were not calculated for the France <i>D. simulans</i> population, because of the small sample size.</p>", "links"=>[], "tags"=>["microbiology", "Computational biology", "ecology", "Evolutionary biology"], "article_id"=>396798, "categories"=>["Biological Sciences", "Ecology", "Microbiology", "Evolutionary Biology"], "users"=>["Rudi L. Verspoor", "Penelope R. Haddrill"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0026318.t002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Microsatellite_diversity_statistics_within_six_D_melanogaster_and_two_D_simulans_populations_/396798", "title"=>"Microsatellite diversity statistics within six <i>D. melanogaster</i> and two <i>D. simulans</i> populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 13:58:00"}

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  • {"unique-ip"=>"6", "full-text"=>"7", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"13", "full-text"=>"11", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

{"start_date"=>"2011-01-01T00:00:00Z", "end_date"=>"2011-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Biogeography", "average_usage"=>[322, 472, 589, 693, 795, 874, 975, 1061, 1132, 1190, 1250, 1315, 1405, 1488, 1571, 1638, 1688, 1753, 1811, 1876, 1942, 2002, 2077, 2200, 2277, 2329, 2423, 2513, 2581, 2651, 2738, 2806, 2855, 2939, 3010, 3070, 3112]}, {"subject_area"=>"/Ecology and environmental sciences/Biogeography", "average_usage"=>[319, 496, 598, 728, 830, 919, 1009, 1088, 1137, 1214, 1289, 1363, 1430, 1507, 1573, 1652, 1718, 1783, 1841, 1916, 1990, 2064, 2144, 2212, 2278, 2339, 2409, 2494, 2577, 2651, 2738, 2806, 2854, 2931, 3000, 3047, 3100]}, {"subject_area"=>"/People and places/Geographical locations", "average_usage"=>[349, 607, 734, 834, 925, 1022, 1116, 1209, 1272, 1340, 1414, 1481, 1562, 1654, 1718, 1792, 1862, 1939, 1999, 2047, 2102, 2155, 2208, 2273, 2334, 2392, 2456, 2533, 2588, 2640, 2688, 2769, 2813, 2872, 2941, 3011, 3083]}]}
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