Did Genetic Drift Drive Increases in Genome Complexity?
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{"title"=>"Did genetic drift drive increases in genome complexity?", "type"=>"journal", "authors"=>[{"first_name"=>"Kenneth D.", "last_name"=>"Whitney", "scopus_author_id"=>"7007180806"}, {"first_name"=>"Theodore", "last_name"=>"Garland", "scopus_author_id"=>"7006148472"}], "year"=>2010, "source"=>"PLoS Genetics", "identifiers"=>{"issn"=>"15537390", "scopus"=>"2-s2.0-77957326306", "sgr"=>"77957326306", "pui"=>"359697323", "isbn"=>"20865118", "pmid"=>"20865118", "doi"=>"10.1371/journal.pgen.1001080"}, "id"=>"b6f36876-dbfa-3f34-b5dc-847a391a3df8", "abstract"=>"Mechanisms underlying the dramatic patterns of genome size variation across the tree of life remain mysterious. Effective population size (N(e)) has been proposed as a major driver of genome size: selection is expected to efficiently weed out deleterious mutations increasing genome size in lineages with large (but not small) N(e). Strong support for this model was claimed from a comparative analysis of N(e)u and genome size for ≈30 phylogenetically diverse species ranging from bacteria to vertebrates, but analyses at that scale have so far failed to account for phylogenetic nonindependence of species. In our reanalysis, accounting for phylogenetic history substantially altered the perceived strength of the relationship between N(e)u and genomic attributes: there were no statistically significant associations between N(e)u and gene number, intron size, intron number, the half-life of gene duplicates, transposon number, transposons as a fraction of the genome, or overall genome size. We conclude that current datasets do not support the hypothesis of a mechanistic connection between N(e) and these genomic attributes, and we suggest that further progress requires larger datasets, phylogenetic comparative methods, more robust estimators of genetic drift, and a multivariate approach that accounts for correlations between putative explanatory variables.", "link"=>"http://www.mendeley.com/research/genetic-drift-drive-increases-genome-complexity", "reader_count"=>250, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>24, "Student > Doctoral Student"=>9, "Researcher"=>66, "Student > Ph. D. Student"=>70, "Student > Postgraduate"=>8, "Student > Master"=>25, "Other"=>3, "Student > Bachelor"=>16, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>20}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>24, "Student > Doctoral Student"=>9, "Researcher"=>66, "Student > Ph. D. Student"=>70, "Student > Postgraduate"=>8, "Student > Master"=>25, "Other"=>3, "Student > Bachelor"=>16, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>20}, "reader_count_by_subject_area"=>{"Unspecified"=>10, "Agricultural and Biological Sciences"=>192, "Philosophy"=>1, "Chemistry"=>1, "Computer Science"=>4, "Earth and Planetary Sciences"=>1, "Economics, Econometrics and Finance"=>1, "Engineering"=>2, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>20, "Mathematics"=>1, "Medicine and Dentistry"=>3, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Sports and Recreations"=>1, "Psychology"=>2, "Social Sciences"=>1, "Immunology and Microbiology"=>4}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Social Sciences"=>{"Social Sciences"=>1}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Psychology"=>{"Psychology"=>2}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>10}, "Environmental Science"=>{"Environmental Science"=>4}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>192}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>20}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "United States"=>16, "United Kingdom"=>6, "Portugal"=>1, "Russia"=>2, "Spain"=>1, "Canada"=>5, "Czech Republic"=>1, "Netherlands"=>1, "Sweden"=>2, "Brazil"=>5, "Poland"=>1, "Australia"=>2, "France"=>1, "Germany"=>4}, "group_count"=>5}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/833919"], "description"=>"<p>Log<sub>10</sub>-transformed dependent variables were regressed on log<sub>10</sub>(<i>N<sub>e</sub>u</i>). Phylogenetic models used arbitrary branch lengths of 1.0 (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#s4\" target=\"_blank\">Materials and Methods</a>). Note that <i>r<sup>2</sup></i> values are not comparable across OLS, PGLS, and RegOU models. Asterisks indicate RegOU models with significantly better fit than OLS models, based on ln likelihood ratio tests (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#s2\" target=\"_blank\">Results</a>); <i>b</i> = regression slope; significant <i>P</i>-values are in bold.</p>†<p>Lynch & Conery <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#pgen.1001080-Lynch3\" target=\"_blank\">[7]</a> reported <i>r<sup>2</sup></i> = 0.659; the discrepancy apparently arises because their analysis used 30 species, only 29 of which were reported in their online supplement.</p>", "links"=>[], "tags"=>["genomic", "attributes", "nonphylogenetic", "phylogenetic"], "article_id"=>504292, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kenneth D. Whitney", "Theodore Garland Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001080.t001", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationships_between_N_e_u_and_genomic_attributes_in_nonphylogenetic_OLS_and_phylogenetic_PGLS_RegOU_models_/504292", "title"=>"Relationships between <i>N<sub>e</sub>u</i> and genomic attributes in nonphylogenetic (OLS) and phylogenetic (PGLS, RegOU) models.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 23:48:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/833740"], "description"=>"<p>(See <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#s4\" target=\"_blank\">Materials and Methods</a>).</p>", "links"=>[], "tags"=>["lynch", "conery", "dataset", "reconstruction", "genome"], "article_id"=>504108, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kenneth D. Whitney", "Theodore Garland Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001080.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_for_the_species_in_the_Lynch_Conery_dataset_7_with_a_reconstruction_of_genome_sizes_/504108", "title"=>"Phylogeny for the species in the Lynch & Conery dataset [<b>7</b>], with a reconstruction of genome sizes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 23:47:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/833824"], "description"=>"<p>(A) Ordinary least squares regression (OLS); <i>r<sup>2</sup></i> = 0.64, <i>P</i><0.0001. (B) Standardized phylogenetically independent contrasts (equivalent to PGLS) using branch lengths of 1.0; <i>r<sup>2</sup></i> = 0.08, <i>P</i> = 0.138. Values have been “positivized” on the x-axis <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#pgen.1001080-Garland4\" target=\"_blank\">[35]</a>.</p>", "links"=>[], "tags"=>["genome", "22", "eukaryotic", "prokaryotic", "dataset", "lynch", "conery"], "article_id"=>504193, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kenneth D. Whitney", "Theodore Garland Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001080.g003", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_between_N_e_u_and_genome_size_across_22_eukaryotic_and_7_prokaryotic_species_from_the_dataset_of_Lynch_Conery_7_/504193", "title"=>"Relationship between <i>N<sub>e</sub>u</i> and genome size across 22 eukaryotic and 7 prokaryotic species from the dataset of Lynch & Conery [<b>7</b>].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 23:48:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/833666"], "description"=>"<p>In this hypothetical example, eight species have been measured for two traits, x and y, as indicated by pairs of values at the tips of the phylogenetic tree (A). Ordinary least-squares linear regression (OLS) indicates a statistically significant positive relationship (B; <i>r<sup>2</sup></i> = 0.62, <i>P</i> = 0.02), potentially leading to an inference of a positive evolutionary association between x and y. However, inspection of the scatterplot (B) in relation to the phylogenetic relationships of the species (A) indicates that the association between x and y is <i>negative</i> for the four species within each of the two major lineages. Regression through the origin with phylogenetically independent contrasts (computed using <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#pgen.1001080-Midford1\" target=\"_blank\">[34]</a> and setting all branches to length 1.0), which is equivalent to phylogenetic generalized least squares (PGLS) analysis, accounts for the nonindependence of species and indicates no overall evolutionary relationship between the traits (C, standardized contrasts, <i>r<sup>2</sup></i> = 0.01, <i>P</i> = 0.82; basal contrast indicated in red). The apparent pattern across species was driven by positively correlated trait change only at the basal split of the phylogeny; throughout the rest of the phylogeny, the traits mostly changed in <i>opposite</i> directions (A; basal contrast in red). Notes: In A, the estimated nodal values for both traits are shown in parentheses. These are intermediate steps in the independent contrasts algorithm and are not to be taken as optimal estimates of the states at internal nodes; rather, they are a type of “local parsimony” estimate (except the estimate at the basal node, which is equivalent to the estimate under squared-change parsimony). Contrasts are taken between sister nodes on a phylogeny, not along each branch segment <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#pgen.1001080-Felsenstein1\" target=\"_blank\">[15]</a>, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#pgen.1001080-Garland1\" target=\"_blank\">[16]</a>, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001080#pgen.1001080-Garland2\" target=\"_blank\">[18]</a>.</p>", "links"=>[], "tags"=>["phylogenetic", "incorrect", "conclusions", "evolutionary", "associations"], "article_id"=>504034, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Kenneth D. Whitney", "Theodore Garland Jr"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1001080.g001", "stats"=>{"downloads"=>2, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ignoring_phylogenetic_history_can_lead_to_incorrect_conclusions_about_the_nature_of_evolutionary_associations_between_traits_/504034", "title"=>"Ignoring phylogenetic history can lead to incorrect conclusions about the nature of evolutionary associations between traits.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 23:47:28"}

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Relative Metric

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