Evolution of Outcrossing in Experimental Populations of Caenorhabditis elegans
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{"title"=>"Evolution of outcrossing in experimental populations of caenorhabditis elegans", "type"=>"journal", "authors"=>[{"first_name"=>"Henrique", "last_name"=>"Teotonio", "scopus_author_id"=>"6603244979"}, {"first_name"=>"Sara", "last_name"=>"Carvalho", "scopus_author_id"=>"16835925200"}, {"first_name"=>"Diogo", "last_name"=>"Manoel", "scopus_author_id"=>"14523096400"}, {"first_name"=>"Miguel", "last_name"=>"Roque", "scopus_author_id"=>"55193503400"}, {"first_name"=>"Ivo M.", "last_name"=>"Chelo", "scopus_author_id"=>"6504697692"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84859977801", "doi"=>"10.1371/journal.pone.0035811", "pui"=>"364662493", "pmid"=>"22540006", "scopus"=>"2-s2.0-84859977801", "issn"=>"19326203", "isbn"=>"2009243285"}, "id"=>"2e8865a1-ee47-3b73-872b-cb8a2f0d548a", "abstract"=>"Caenorhabditis elegans can reproduce exclusively by self-fertilization. Yet, males can be maintained in laboratory populations, a phenomenon that continues to puzzle biologists. In this study we evaluated the role of males in facilitating adaptation to novel environments. For this, we contrasted the evolution of a fitness component exclusive to outcrossing in experimental populations of different mating systems. We introgressed a modifier of outcrossing into a hybrid population derived from several wild isolates to transform the wild-type androdioecious mating system into a dioecious mating system. By genotyping 375 single-nucleotide polymorphisms we show that the two populations had similar standing genetic diversity available for adaptation, despite the occurrence of selection during their derivation. We then performed replicated experimental evolution under the two mating systems from starting conditions of either high or low levels of diversity, under defined environmental conditions of discrete non-overlapping generations, constant density at high population sizes (N = 10(4)), no obvious spatial structure and abundant food resources. During 100 generations measurements of sex ratios and male competitive performance showed: 1) adaptation to the novel environment; 2) directional selection on male frequency under androdioecy; 3) optimal outcrossing rates of 0.5 under androdioecy; 4) the existence of initial inbreeding depression; and finally 5) that the strength of directional selection on male competitive performance does not depend on male frequencies. Taken together, these results suggest that androdioecious males are maintained at intermediate frequencies because outcrossing is adaptive.", "link"=>"http://www.mendeley.com/research/evolution-outcrossing-experimental-populations-caenorhabditis-elegans", "reader_count"=>59, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>11, "Student > Ph. D. Student"=>25, "Student > Postgraduate"=>2, "Student > Master"=>7, "Student > Bachelor"=>8}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>11, "Student > Ph. D. Student"=>25, "Student > Postgraduate"=>2, "Student > Master"=>7, "Student > Bachelor"=>8}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>8, "Mathematics"=>1, "Agricultural and Biological Sciences"=>47, "Neuroscience"=>1}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>47}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Austria"=>1, "United States"=>1, "Poland"=>1, "United Kingdom"=>1, "Portugal"=>2}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/649314"], "description"=>"<p><b>A</b> shows the number of haplotypes, calculated in 10 SNP windows and step sizes of 1 SNP, along the physical distance (see also <b><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035811#pone.0035811.s002\" target=\"_blank\">Figure S2</a></b>); red = androdioecious population; blue = dioecious population. Black line indicates the number of haplotypes among the 16 wild isolates used as parentals. Grey line shows the diversity found among worldwide collections of <i>C. elegans</i> isolates, as recalculated from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035811#pone.0035811-Rockman1\" target=\"_blank\">[40]</a> (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035811#s4\" target=\"_blank\"><b>Materials and Methods</b></a>). Thin colored lines show the number of parental isolate haplotypes identified in the two ancestral populations. <b>B</b>, the grey line indicates the number of shared haplotypes among the two ancestral populations, shown in 10 SNP-wide windows and step sizes of 1 SNP, as calculated by the proportion of the total number of haplotypes common to both populations. Black lines show the <i>F<sub>ST</sub></i> estimated from these shared haplotypes with their significance, obtained by permutation of SNP position within each chromosome, the latter shown as a dashed line. All positions are haplotype centered.</p>", "links"=>[], "tags"=>["differentiation", "ancestral"], "article_id"=>319808, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Henrique Teotonio", "Sara Carvalho", "Diogo Manoel", "Miguel Roque", "Ivo M. Chelo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035811.g003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_diversity_and_differentiation_among_ancestral_populations_/319808", "title"=>"Genetic diversity and differentiation among ancestral populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-23 02:43:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/649126"], "description"=>"<p>In <b>A</b> is represented the SNP frequency difference from the expected frequency among parental wild isolates of a reference allele (N2 wild strain) relative to physical position for chromosome IV (left panels), or chromosome X (right panels). Top panels show observed SNP allele frequencies in the ancestral androdioecious population (red). Bottom plots represent observed frequencies in the dioecious population (blue). Gray lines indicate the 95% of simulated data expected under random sampling during the derivation (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035811#s4\" target=\"_blank\"><b>Materials and Methods</b></a>). Gray circles represent SNPs that were lost during the derivation, as measured by a minor allele frequency of <0.026 in either population. The arrow indicates the SNP upon which a selective sweep of the wild isolate N2 allele is modeled during the androdioecious derivation. In <b>B</b>, linkage disequilibrium among pair-wise SNPs is shown in 10 SNP-wide windows with overlapping step sizes of 1 SNP. Values are plotted at the mean physical position of the SNPs present in each window. Gray lines indicate the 95% of simulations data.</p>", "links"=>[], "tags"=>["snp", "allele", "frequencies", "ancestral"], "article_id"=>319617, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Henrique Teotonio", "Sara Carvalho", "Diogo Manoel", "Miguel Roque", "Ivo M. Chelo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035811.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Observed_SNP_allele_frequencies_in_ancestral_populations_/319617", "title"=>"Observed SNP allele frequencies in ancestral populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-23 02:40:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/649670"], "description"=>"<p>In <b>A</b>, the proportion of wild type progeny originated from the competition of experimental males with tester GFP males for the fertilization of standard females (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035811#s4\" target=\"_blank\">Materials and Methods</a>). Dioecious populations are shown in blue, androdioecious populations in red. Empty circles show populations without initial genetic diversity and filled circles populations with initial diversity. Circles and bars represent the average values among replicate populations and associated SEM, respectively. Lines connect the least-square estimates (dots) obtained after ANOVA (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035811#pone-0035811-t001\" target=\"_blank\"><b>Table 1</b></a> for analysis). In <b>B</b>, for the androdioecious populations without standing diversity (empty circles) the least-square estimates of male competitive performance (dots in panel <b>A</b>) are shown against the least-square estimates of male proportions observed (dots in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035811#pone-0035811-g004\" target=\"_blank\"><b>Figure 4B</b></a>). The correlation among both phenotypes in these populations is positive and significant (<i>r</i> = 0.99; <i>t<sub>2</sub></i> = 9.2; <i>p</i> = 0.006). In gray the least-square estimates by replicate population at each generation from a fully nested model (<b><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035811#pone.0035811.s005\" target=\"_blank\">Table S3</a></b>). The correlation among these estimates is not significant. In <b>C</b>, as in <b>B</b>, for androdioecious populations with initial diversity (the correlations among phenotypes are not significant).</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>320163, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Henrique Teotonio", "Sara Carvalho", "Diogo Manoel", "Miguel Roque", "Ivo M. Chelo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035811.g006", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolution_of_male_competitive_performance_/320163", "title"=>"Evolution of male competitive performance.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-23 00:02:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/649258"], "description"=>"<p>Left panel shows the probability distribution of having selection coefficients (<i>s</i>) explaining the allele frequency changes observed during the derivation of the androdioecious population at marker <i>pas15121</i> (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035811#s4\" target=\"_blank\"><b>Materials and Methods</b></a>). Error bars indicate the standard error of the mean of the likelihoods of 100 replicate simulations of the funnel cross, with the dashed line indicating the best estimate of <i>s</i>. Similarly at the right panel, distributions of <i>log10</i> likelihood estimates of allele frequency changes in 19 SNPs, from X-chromosome positions 3,054,487 bp to 5,819,445 bp, for neutral sampling in empty bars, or as grey bars for selection at marker <i>pas15121</i> with <i>s</i> = 0.53. For each of the 100 simulated replicates compound likelihoods are calculated by multiplying the probability of observed frequencies given the simulated frequencies of each marker.</p>", "links"=>[], "tags"=>["n2"], "article_id"=>319751, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Henrique Teotonio", "Sara Carvalho", "Diogo Manoel", "Miguel Roque", "Ivo M. Chelo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035811.g002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Selection_of_the_N2_wild_isolate_pas15121_allele_/319751", "title"=>"Selection of the N2 wild isolate <i>pas15121</i> allele.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-23 02:42:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/649544"], "description"=>"<p><b>A</b> shows the offspring sex ratio of individual dioecious males for the G0 population (n = 27) and three G100 replicate populations (total n = 37). Box-plots of the data at 10, 25, 75, and 90 percentiles are represented, along with outliers (dots), and the mean of each generation (line). In <b>B</b>, the evolution of X-chromosome non-disjunction rates in androdioecious populations is shown. The proportion of males in the grand-progeny of 50 selfing hermaphrodites was scored in populations with (filled circles) or without (empty circles) starting diversity. Symbols indicate the average number of males per replicate population and mating system with SEM. GLM analysis reveals that generation is significant (p = 0.01) as well as block, initial diversity condition, and interaction (all at p<0.001; total residual deviance d.f. = 325).</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>320040, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Henrique Teotonio", "Sara Carvalho", "Diogo Manoel", "Miguel Roque", "Ivo M. Chelo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035811.g005", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolution_of_sex_ratio_distorters_/320040", "title"=>"Evolution of sex ratio distorters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-23 00:00:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/333931", "https://ndownloader.figshare.com/files/333967", "https://ndownloader.figshare.com/files/334041", "https://ndownloader.figshare.com/files/334107", "https://ndownloader.figshare.com/files/334266"], "description"=>"<div><p><em>Caenorhabditis elegans</em> can reproduce exclusively by self-fertilization. Yet, males can be maintained in laboratory populations, a phenomenon that continues to puzzle biologists. In this study we evaluated the role of males in facilitating adaptation to novel environments. For this, we contrasted the evolution of a fitness component exclusive to outcrossing in experimental populations of different mating systems. We introgressed a modifier of outcrossing into a hybrid population derived from several wild isolates to transform the wild-type androdioecious mating system into a dioecious mating system. By genotyping 375 single-nucleotide polymorphisms we show that the two populations had similar standing genetic diversity available for adaptation, despite the occurrence of selection during their derivation. We then performed replicated experimental evolution under the two mating systems from starting conditions of either high or low levels of diversity, under defined environmental conditions of discrete non-overlapping generations, constant density at high population sizes (N = 10<sup>4</sup>), no obvious spatial structure and abundant food resources. During 100 generations measurements of sex ratios and male competitive performance showed: 1) adaptation to the novel environment; 2) directional selection on male frequency under androdioecy; 3) optimal outcrossing rates of 0.5 under androdioecy; 4) the existence of initial inbreeding depression; and finally 5) that the strength of directional selection on male competitive performance does not depend on male frequencies. Taken together, these results suggest that androdioecious males are maintained at intermediate frequencies because outcrossing is adaptive.</p> </div>", "links"=>[], "tags"=>["outcrossing", "populations"], "article_id"=>125960, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Henrique Teotonio", "Sara Carvalho", "Diogo Manoel", "Miguel Roque", "Ivo M. Chelo"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0035811.s001", "https://dx.doi.org/10.1371/journal.pone.0035811.s002", "https://dx.doi.org/10.1371/journal.pone.0035811.s003", "https://dx.doi.org/10.1371/journal.pone.0035811.s004", "https://dx.doi.org/10.1371/journal.pone.0035811.s005"], "stats"=>{"downloads"=>10, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Evolution_of_Outcrossing_in_Experimental_Populations_of_Caenorhabditis_elegans_/125960", "title"=>"Evolution of Outcrossing in Experimental Populations of <em>Caenorhabditis elegans</em>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-04-23 01:39:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/649760"], "description"=>"<p>ANOVA of census size, sex ratio and male competitive performance.</p>", "links"=>[], "tags"=>["census"], "article_id"=>320259, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Henrique Teotonio", "Sara Carvalho", "Diogo Manoel", "Miguel Roque", "Ivo M. Chelo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035811.t001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ANOVA_of_census_size_sex_ratio_and_male_competitive_performance_/320259", "title"=>"ANOVA of census size, sex ratio and male competitive performance.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-23 00:04:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/649465"], "description"=>"<p>In <b>A</b>, the census size at the adult stage is shown for dioecious (blue), or androdioecious (red) populations. Empty circles stand for populations without initial diversity; filled circles indicate populations with initial standing diversity. Average values are shown with associated standard error of the mean (SEM) among replicates. Dashed line indicates the overall least-square estimate irrespective of mating system or initial condition of genetic diversity (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035811#pone-0035811-t001\" target=\"_blank\"><b>Table 1</b></a> for analysis). In <b>B</b>, the male proportions measured in all 24 populations (symbols as in <b>A</b>). Lines join the least-square estimates by generation at each treatment (dots).</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>319966, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Henrique Teotonio", "Sara Carvalho", "Diogo Manoel", "Miguel Roque", "Ivo M. Chelo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035811.g004", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolution_of_sex_ratios_/319966", "title"=>"Evolution of sex ratios.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-23 02:46:06"}

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Relative Metric

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