Can Diversifying Selection Be Distinguished from History in Geographic Clines? A Population Genomic Study of Killifish (Fundulus heteroclitus)
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{"title"=>"Can Diversifying Selection Be Distinguished from History in Geographic Clines? A Population Genomic Study of Killifish (Fundulus heteroclitus)", "type"=>"journal", "authors"=>[{"first_name"=>"Allan E.", "last_name"=>"Strand", "scopus_author_id"=>"7004533128"}, {"first_name"=>"Larissa M.", "last_name"=>"Williams", "scopus_author_id"=>"57199194866"}, {"first_name"=>"Marjorie F.", "last_name"=>"Oleksiak", "scopus_author_id"=>"6602701773"}, {"first_name"=>"Erik E.", "last_name"=>"Sotka", "scopus_author_id"=>"6602951624"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23049770", "doi"=>"10.1371/journal.pone.0045138", "sgr"=>"84866861679", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84866861679", "issn"=>"19326203", "pui"=>"365742257"}, "id"=>"a0f18d9d-2d6e-3c49-a5b0-3dd2991c1271", "abstract"=>"A common geographical pattern of genetic variation is the one-dimensional cline. Clines may be maintained by diversifying selection across a geographical gradient but can also reflect historical processes such as allopatry followed by secondary contact. To identify loci that may be undergoing diversifying selection, we examined the distribution of geographical variation patterns across the range of the killifish (Fundulus heteroclitus) in 310 loci, including microsatellites, allozymes, and single nucleotide polymorphisms. We employed two approaches to detect loci under strong diversifying selection. First, we developed an automated method to identify clinal variation on a per-locus basis and examined the distribution of clines to detect those that exhibited signifcantly steeper slopes. Second, we employed a classic [Formula: see text]-outlier method as a complementary approach. We also assessed performance of these techniques using simulations. Overall, latitudinal clines were detected in nearly half of all loci genotyped (i.e., all eight microsatellite loci, 12 of 16 allozyme loci and 44% of the 285 SNPs). With the exception of few outlier loci (notably mtDNA and malate dehydrogenase), the positions and slopes of Fundulus clines were statistically indistinguishable. The high frequency of latitudinal clines across the genome indicates that secondary contact plays a central role in the historical demography of this species. Our simulation results indicate that accurately detecting diversifying selection using genome scans is extremely difficult in species with a strong signal of secondary contact; neutral evolution under this history produces clines as steep as those expected under selection. Based on these results, we propose that demographic history can explain all clinal patterns observed in F. heteroclitus without invoking natural selection to either establish or maintain the pattern we observe today.", "link"=>"http://www.mendeley.com/research/diversifying-selection-distinguished-history-geographic-clines-population-genomic-study-killifish-fu", "reader_count"=>49, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>6, "Librarian"=>1, "Student > Doctoral Student"=>3, "Researcher"=>12, "Student > Ph. D. Student"=>11, "Other"=>2, "Student > Master"=>4, "Lecturer"=>1, "Professor"=>6, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>6, "Librarian"=>1, "Student > Doctoral Student"=>3, "Researcher"=>12, "Student > Ph. D. Student"=>11, "Other"=>2, "Student > Master"=>4, "Lecturer"=>1, "Professor"=>6, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>38, "Medicine and Dentistry"=>1, "Neuroscience"=>1, "Earth and Planetary Sciences"=>1, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>38}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"United States"=>5, "Japan"=>1, "Brazil"=>1, "United Kingdom"=>1, "Italy"=>1, "Portugal"=>1, "Germany"=>1}, "group_count"=>6}

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/568488"], "description"=>"<p>Sources and types of data employed in this study.</p>", "links"=>[], "tags"=>["types", "employed"], "article_id"=>238982, "categories"=>["Information And Computing Sciences", "Inorganic Chemistry", "Genetics", "Evolutionary Biology"], "users"=>["Allan E. Strand", "Larissa M. Williams", "Marjorie F. Oleksiak", "Erik E. Sotka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045138.t001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sources_and_types_of_data_employed_in_this_study_/238982", "title"=>"Sources and types of data employed in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-26 02:29:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/568311"], "description"=>"<p>For all simulations presented, ancestral populations are split into two relictual populations 100,000 generations in the past. At 10,000 generations before present, each of these daughter populations split into 20 linearly arranged populations (only 8 of the resulting 40 populations are indicated). Gene flow between populations continued at the same rate throughout the 10,000 generations.</p>", "links"=>[], "tags"=>["simulation"], "article_id"=>238807, "categories"=>["Information And Computing Sciences", "Inorganic Chemistry", "Genetics", "Evolutionary Biology"], "users"=>["Allan E. Strand", "Larissa M. Williams", "Marjorie F. Oleksiak", "Erik E. Sotka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045138.g003", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Demographic_model_for_simulation_study_/238807", "title"=>"Demographic model for simulation study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-26 02:26:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/300370", "https://ndownloader.figshare.com/files/300382", "https://ndownloader.figshare.com/files/300390"], "description"=>"<div><p>A common geographical pattern of genetic variation is the one-dimensional cline. Clines may be maintained by diversifying selection across a geographical gradient but can also reflect historical processes such as allopatry followed by secondary contact. To identify loci that may be undergoing diversifying selection, we examined the distribution of geographical variation patterns across the range of the killifish (<em>Fundulus heteroclitus</em>) in 310 loci, including microsatellites, allozymes, and single nucleotide polymorphisms. We employed two approaches to detect loci under strong diversifying selection. First, we developed an automated method to identify clinal variation on a per-locus basis and examined the distribution of clines to detect those that exhibited signifcantly steeper slopes. Second, we employed a classic -outlier method as a complementary approach. We also assessed performance of these techniques using simulations. Overall, latitudinal clines were detected in nearly half of all loci genotyped (i.e., all eight microsatellite loci, 12 of 16 allozyme loci and 44% of the 285 SNPs). With the exception of few outlier loci (notably mtDNA and malate dehydrogenase), the positions and slopes of <em>Fundulus</em> clines were statistically indistinguishable. The high frequency of latitudinal clines across the genome indicates that secondary contact plays a central role in the historical demography of this species. Our simulation results indicate that accurately detecting diversifying selection using genome scans is extremely difficult in species with a strong signal of secondary contact; neutral evolution under this history produces clines as steep as those expected under selection. Based on these results, we propose that demographic history can explain all clinal patterns observed in <em>F. heteroclitus</em> without invoking natural selection to either establish or maintain the pattern we observe today.</p> </div>", "links"=>[], "tags"=>["diversifying", "distinguished", "geographic", "genomic", "killifish"], "article_id"=>119226, "categories"=>["Information And Computing Sciences", "Inorganic Chemistry", "Genetics", "Evolutionary Biology"], "users"=>["Allan E. Strand", "Larissa M. Williams", "Marjorie F. Oleksiak", "Erik E. Sotka"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0045138.s001", "https://dx.doi.org/10.1371/journal.pone.0045138.s002", "https://dx.doi.org/10.1371/journal.pone.0045138.s003"], "stats"=>{"downloads"=>4, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Can_Diversifying_Selection_Be_Distinguished_from_History_in_Geographic_Clines_A_Population_Genomic_Study_of_Killifish_Fundulus_heteroclitus_/119226", "title"=>"Can Diversifying Selection Be Distinguished from History in Geographic Clines? A Population Genomic Study of Killifish (<em>Fundulus heteroclitus</em>)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-09-26 02:33:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/568169"], "description"=>"<p>A) Location of sampled populations. B) Allele frequences of clinal loci used in the Genomic Co-Co plot analysis. mtDNA and Mdh allozyme clines are highlighted in black, and Ldh allozyme and Ldh SNP clines are highlighted in red.</p>", "links"=>[], "tags"=>["locations", "allele", "frequencies"], "article_id"=>238667, "categories"=>["Information And Computing Sciences", "Inorganic Chemistry", "Genetics", "Evolutionary Biology"], "users"=>["Allan E. Strand", "Larissa M. Williams", "Marjorie F. Oleksiak", "Erik E. Sotka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045138.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sampling_locations_and_allele_frequencies_in_Fundulus_heteroclitus_/238667", "title"=>"Sampling locations and allele frequencies in <i>Fundulus heteroclitus</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-26 02:24:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/568368"], "description"=>"<p>In the sub-figure on the left the stepping-stone dispersal rate is 0.4 (); on the right, is equal to 4. In each sub-figure, panel <b>A</b> illustrates the distribution of allele frequencies along the cline for simulated loci. All clines are adjusted so that higher allele frequencies are on the left. Bold lines indicate loci deemed to be under diversifying selection by fdist2. Panel <b>B</b> shows the distribution of cline midpoints and slopes estimated using broken stick models applied to the clines in panel <b>A</b>. Panel <b>C</b> shows the results of fdist2 applied to these clines.</p>", "links"=>[], "tags"=>["genetics and genomics", "marine and aquatic sciences", "computer science", "Evolutionary biology"], "article_id"=>238861, "categories"=>["Information And Computing Sciences", "Inorganic Chemistry", "Genetics", "Evolutionary Biology"], "users"=>["Allan E. Strand", "Larissa M. Williams", "Marjorie F. Oleksiak", "Erik E. Sotka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045138.g004", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summaries_of_two_simulations_/238861", "title"=>"Summaries of two simulations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-26 02:27:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/568242"], "description"=>"<p>Contours of 75, 95 and 99% are shown on the co-co plot. Mean F<i><sub>ST</sub></i> is dotted and 99% C.I. lines are in black on the fdist2 panel. Outlier loci are in red (95% C.I.), non-outlier loci are in grey, and Ldh allozyme and SNPs are blue.</p>", "links"=>[], "tags"=>["outlier", "loci", "genomic", "co-co", "fdist2"], "article_id"=>238734, "categories"=>["Information And Computing Sciences", "Inorganic Chemistry", "Genetics", "Evolutionary Biology"], "users"=>["Allan E. Strand", "Larissa M. Williams", "Marjorie F. Oleksiak", "Erik E. Sotka"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045138.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_outlier_loci_based_on_Genomic_Co_Co_plot_left_panel_and_fdist2_right_panel_analyses_/238734", "title"=>"Identification of outlier loci based on Genomic Co-Co plot (left panel) and fdist2 (right panel) analyses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-26 02:25:34"}

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Relative Metric

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