The Population Genetics of dN/dS
Publication Date
December 12, 2008
Journal
PLOS Genetics
Authors
Sergey Kryazhimskiy & Joshua B. Plotkin
Volume
4
Issue
12
Pages
e1000304
DOI
http://doi.org/10.1371/journal.pgen.1000304
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1000304
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/19081788
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596312
Europe PMC
http://europepmc.org/abstract/MED/19081788
Web of Science
000263667900019
Scopus
58149168840
Mendeley
http://www.mendeley.com/research/population-genetics-dnds
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CiteULike | Further Information

Mendeley | Further Information

{"title"=>"The population genetics of dN/dS", "type"=>"journal", "authors"=>[{"first_name"=>"Sergey", "last_name"=>"Kryazhimskiy", "scopus_author_id"=>"20734712600"}, {"first_name"=>"Joshua B.", "last_name"=>"Plotkin", "scopus_author_id"=>"7006104476"}], "year"=>2008, "source"=>"PLoS Genetics", "identifiers"=>{"doi"=>"10.1371/journal.pgen.1000304", "pui"=>"354027908", "pmid"=>"19081788", "sgr"=>"58149168840", "isbn"=>"1553-7404 (Electronic)", "scopus"=>"2-s2.0-58149168840", "issn"=>"15537390"}, "id"=>"c3c7349c-1208-3a3a-95e9-6281834d85b9", "abstract"=>"Evolutionary pressures on proteins are often quantified by the ratio of substitution rates at non-synonymous and synonymous sites. The dN/dS ratio was originally developed for application to distantly diverged sequences, the differences among which represent substitutions that have fixed along independent lineages. Nevertheless, the dN/dS measure is often applied to sequences sampled from a single population, the differences among which represent segregating polymorphisms. Here, we study the expected dN/dS ratio for samples drawn from a single population under selection, and we find that in this context, dN/dS is relatively insensitive to the selection coefficient. Moreover, the hallmark signature of positive selection over divergent lineages, dN/dS>1, is violated within a population. For population samples, the relationship between selection and dN/dS does not follow a monotonic function, and so it may be impossible to infer selection pressures from dN/dS. These results have significant implications for the interpretation of dN/dS measurements among population-genetic samples.", "link"=>"http://www.mendeley.com/research/population-genetics-dnds", "reader_count"=>828, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>68, "Librarian"=>1, "Student > Doctoral Student"=>26, "Researcher"=>243, "Student > Ph. D. Student"=>270, "Student > Postgraduate"=>24, "Student > Master"=>86, "Other"=>15, "Student > Bachelor"=>47, "Lecturer"=>7, "Lecturer > Senior Lecturer"=>3, "Professor"=>37}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>68, "Librarian"=>1, "Student > Doctoral Student"=>26, "Researcher"=>243, "Student > Ph. D. Student"=>270, "Student > Postgraduate"=>24, "Student > Master"=>86, "Other"=>15, "Student > Bachelor"=>47, "Lecturer"=>7, "Lecturer > Senior Lecturer"=>3, "Professor"=>37}, "reader_count_by_subject_area"=>{"Agricultural and Biological Sciences"=>672, "Arts and Humanities"=>2, "Business, Management and Accounting"=>1, "Chemistry"=>6, "Computer Science"=>17, "Economics, Econometrics and Finance"=>1, "Engineering"=>5, "Environmental Science"=>12, "Biochemistry, Genetics and Molecular Biology"=>60, "Mathematics"=>7, "Medicine and Dentistry"=>27, "Design"=>1, "Physics and Astronomy"=>6, "Social Sciences"=>1, "Immunology and Microbiology"=>8, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>27}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>6}, "Mathematics"=>{"Mathematics"=>7}, "Environmental Science"=>{"Environmental Science"=>12}, "Arts and Humanities"=>{"Arts and Humanities"=>2}, "Design"=>{"Design"=>1}, "Engineering"=>{"Engineering"=>5}, "Chemistry"=>{"Chemistry"=>6}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>8}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>672}, "Computer Science"=>{"Computer Science"=>17}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>60}}, "reader_count_by_country"=>{"United States"=>51, "Thailand"=>1, "Portugal"=>2, "Saudi Arabia"=>1, "Netherlands"=>4, "Sweden"=>7, "Austria"=>2, "Vietnam"=>1, "Korea (South)"=>1, "China"=>2, "Brazil"=>16, "Poland"=>1, "France"=>9, "Nigeria"=>1, "Colombia"=>1, "Hungary"=>1, "Sri Lanka"=>1, "Japan"=>4, "United Kingdom"=>17, "Switzerland"=>4, "Spain"=>5, "India"=>1, "French Polynesia"=>1, "Canada"=>1, "Czech Republic"=>1, "Turkey"=>1, "Belgium"=>2, "Norway"=>1, "Finland"=>1, "Denmark"=>3, "Uganda"=>1, "Italy"=>2, "Mexico"=>4, "Australia"=>2, "Germany"=>10}, "group_count"=>27}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/913716"], "description"=>"<p>The dashed line shows the expected dN/dS ratio for samples from divergent lineages, given by Equation (2). The solid lines show the expected dN/dS ratio for within-population samples, given by Equation (5), under two mutation rates.</p>", "links"=>[], "tags"=>["scaled"], "article_id"=>584185, "categories"=>["Molecular Biology", "Genetics"], "users"=>["Sergey Kryazhimskiy", "Joshua B. Plotkin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000304.g001", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_relationship_between_the_scaled_selection_coefficient_947_and_the_expected_dN_dS_ratio_/584185", "title"=>"The relationship between the scaled selection coefficient, <i>γ</i>, and the expected dN/dS ratio.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-12 01:09:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/451440", "https://ndownloader.figshare.com/files/451664"], "description"=>"<div><p>Evolutionary pressures on proteins are often quantified by the ratio of substitution rates at non-synonymous and synonymous sites. The dN/dS ratio was originally developed for application to distantly diverged sequences, the differences among which represent substitutions that have fixed along independent lineages. Nevertheless, the dN/dS measure is often applied to sequences sampled from a single population, the differences among which represent segregating polymorphisms. Here, we study the expected dN/dS ratio for samples drawn from a single population under selection, and we find that in this context, dN/dS is relatively insensitive to the selection coefficient. Moreover, the hallmark signature of positive selection over divergent lineages, dN/dS>1, is violated within a population. For population samples, the relationship between selection and dN/dS does not follow a monotonic function, and so it may be impossible to infer selection pressures from dN/dS. These results have significant implications for the interpretation of dN/dS measurements among population-genetic samples.</p></div>", "links"=>[], "tags"=>["genetics"], "article_id"=>148980, "categories"=>["Molecular Biology", "Genetics"], "users"=>["Sergey Kryazhimskiy", "Joshua B. Plotkin"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000304.s001", "https://dx.doi.org/10.1371/journal.pgen.1000304.s002"], "stats"=>{"downloads"=>8, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Population_Genetics_of_dN_dS/148980", "title"=>"The Population Genetics of dN/dS", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-12-12 02:29:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/913894"], "description"=>"<p>Wright-Fisher simulations based on the full genetic code were performed as described for two independent populations (middle column) and a single population (right column). The table shows the most-likely dN/dS value as estimated by PAML for two sampled sequences, as well as a 95% confidence interval obtained from the <i>χ</i><sup>2</sup> distribution. For each value of <i>γ</i>, the first line corresponds to simulations with <i>μ</i> = 10<sup>−7</sup>, and the second line corresponds to simulations with <i>μ</i> = 10<sup>−6</sup>.</p>", "links"=>[], "tags"=>["scaled", "paml", "simulated"], "article_id"=>584357, "categories"=>["Molecular Biology", "Genetics"], "users"=>["Sergey Kryazhimskiy", "Joshua B. Plotkin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000304.t001", "stats"=>{"downloads"=>7, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_relationship_between_the_scaled_selection_coefficient_947_and_the_dN_dS_ratio_as_estimated_by_the_PAML_package_from_simulated_data_/584357", "title"=>"The relationship between the scaled selection coefficient, <i>γ</i>, and the dN/dS ratio as estimated by the PAML package from simulated data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-12-12 01:12:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/913827"], "description"=>"<p>Black squares show the mean±two standard errors of the observed dN/dS ratio. The predicted dN/dS ratios for divergent lineages are shown in dashed lines (Equation 2); the predicted dN/dS ratios for a single population are shown in solid lines (Equation 5). Left column corresponds to results for two independent populations; right column corresponds to results for a single population. Top panels show results for <i>θ</i> = 0.1; bottom panels show results for <i>θ</i> = 0.01. The simulations for two populations were performed at <i>L</i> = 10<sup>3</sup> independent sites, and the simulations for a single population were performed at <i>L</i> = 10<sup>4</sup> independent sites.</p>", "links"=>[], "tags"=>["scaled", "simulated", "wright-fisher"], "article_id"=>584289, "categories"=>["Molecular Biology", "Genetics"], "users"=>["Sergey Kryazhimskiy", "Joshua B. Plotkin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000304.g003", "stats"=>{"downloads"=>2, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_relationship_between_the_scaled_selection_coefficient_947_and_the_dN_dS_ratio_in_simulated_Wright_Fisher_populations_/584289", "title"=>"The relationship between the scaled selection coefficient, <i>γ</i>, and the dN/dS ratio in simulated Wright-Fisher populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-12 01:11:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/913771"], "description"=>"<p>Black squares show the mean±two standard errors of the observed dN/dS ratio. Left panel shows results for <i>θ</i> = 0.1; right panel shows results for <i>θ</i> = 0.01. Simulations were performed at <i>L</i> = 10<sup>3</sup> independent sites.</p>", "links"=>[], "tags"=>["within-population", "simulated", "wright-fisher"], "article_id"=>584233, "categories"=>["Molecular Biology", "Genetics"], "users"=>["Sergey Kryazhimskiy", "Joshua B. Plotkin"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000304.g002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_behavior_of_the_within_population_dN_dS_ratio_for_large_947_in_simulated_Wright_Fisher_populations_/584233", "title"=>"The behavior of the within-population dN/dS ratio for large <i>γ</i> in simulated Wright-Fisher populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-12 01:10:33"}

PMC Usage Stats | Further Information

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Relative Metric

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