Universal Pacemaker of Genome Evolution
Publication Date
November 29, 2012
Journal
PLOS Computational Biology
Authors
Sagi Snir, Yuri I. Wolf & Eugene V. Koonin
Volume
8
Issue
11
Pages
e1002785
DOI
https://dx.plos.org/10.1371/journal.pcbi.1002785
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1002785
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23209393
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3510094
Europe PMC
http://europepmc.org/abstract/MED/23209393
Web of Science
000311897100043
Scopus
84870689997
Mendeley
http://www.mendeley.com/research/universal-pacemaker-genome-evolution
Events
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/534520"], "description"=>"<p><i>dfit</i>: log<sub>10</sub>(<i>E</i><sup>2</sup><i><sub>MC,k</sub></i>/<i>E</i><sup>2</sup><i><sub>UPM,k</sub></i>). <i>afit</i>: −(log<sub>10</sub>(<i>E</i><sup>2</sup><i><sub>MC,k</sub></i>)+log<sub>10</sub>(<i>E</i><sup>2</sup><i><sub>UPM,k</sub></i>))/2.</p>", "links"=>[], "tags"=>["goodness", "upm", "mc", "plotted"], "article_id"=>205013, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Sagi Snir", "Yuri I. Wolf", "Eugene V. Koonin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002785.g004", "stats"=>{"downloads"=>4, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_goodness_of_fit_for_the_UPM_vs_the_MC_model_dfit_plotted_against_the_average_goodness_of_fit_afit_/205013", "title"=>"Relative goodness of fit for the UPM vs the MC model (<i>dfit</i>) plotted against the average goodness of fit (<i>afit</i>).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-29 01:23:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/286742", "https://ndownloader.figshare.com/files/286915", "https://ndownloader.figshare.com/files/286960", "https://ndownloader.figshare.com/files/287023", "https://ndownloader.figshare.com/files/287161", "https://ndownloader.figshare.com/files/287235"], "description"=>"<div><p>A fundamental observation of comparative genomics is that the distribution of evolution rates across the complete sets of orthologous genes in pairs of related genomes remains virtually unchanged throughout the evolution of life, from bacteria to mammals. The most straightforward explanation for the conservation of this distribution appears to be that the relative evolution rates of all genes remain nearly constant, or in other words, that evolutionary rates of different genes are strongly correlated within each evolving genome. This correlation could be explained by a model that we denoted Universal PaceMaker (UPM) of genome evolution. The UPM model posits that the rate of evolution changes synchronously across genome-wide sets of genes in all evolving lineages. Alternatively, however, the correlation between the evolutionary rates of genes could be a simple consequence of molecular clock (MC). We sought to differentiate between the MC and UPM models by fitting thousands of phylogenetic trees for bacterial and archaeal genes to supertrees that reflect the dominant trend of vertical descent in the evolution of archaea and bacteria and that were constrained according to the two models. The goodness of fit for the UPM model was better than the fit for the MC model, with overwhelming statistical significance, although similarly to the MC, the UPM is strongly overdispersed. Thus, the results of this analysis reveal a universal, genome-wide pacemaker of evolution that could have been in operation throughout the history of life.</p> </div>", "links"=>[], "tags"=>["pacemaker", "genome", "evolution"], "article_id"=>116515, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Sagi Snir", "Yuri I. Wolf", "Eugene V. Koonin"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002785.s001", "https://dx.doi.org/10.1371/journal.pcbi.1002785.s002", "https://dx.doi.org/10.1371/journal.pcbi.1002785.s003", "https://dx.doi.org/10.1371/journal.pcbi.1002785.s004", "https://dx.doi.org/10.1371/journal.pcbi.1002785.s005", "https://dx.doi.org/10.1371/journal.pcbi.1002785.s006"], "stats"=>{"downloads"=>18, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Universal_Pacemaker_of_Genome_Evolution__/116515", "title"=>"Universal Pacemaker of Genome Evolution", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-11-29 01:48:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/534280"], "description"=>"<p>A. A gene tree (GT). After the comparison with the supertree (ST), the GT is reduced to the maximum agreement subtree (MAST, highlighted in yellow). The reduced GT edge highlighted in red corresponds to two edges in the original GT. B. Supertree (ST). Mapping of the reduced GT onto the ST is highlighted; two sections of ST that consist of multiple edges mapping to a single edge of the reduced GT are highlighted in blue and green, respectively.</p>", "links"=>[], "tags"=>["trees"], "article_id"=>204784, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Sagi Snir", "Yuri I. Wolf", "Eugene V. Koonin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002785.g001", "stats"=>{"downloads"=>1, "page_views"=>35, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_trees_and_the_supertree_/204784", "title"=>"Gene trees and the supertree.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-29 01:19:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/534333"], "description"=>"<p>A. Under the Molecular Clock model, gene-specific evolution rates (colored lines) remain constant; at any point in time (shown as dots), the relative rates of gene evolution are also constant. B. Under the Universal Pacemaker model, gene-specific evolution rates can change arbitrarily but by the same amount across the entire genome; at any point in time, the relative rates of gene evolution remain constant.</p>", "links"=>[], "tags"=>["molecular", "pacemaker", "models", "genome"], "article_id"=>204829, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Sagi Snir", "Yuri I. Wolf", "Eugene V. Koonin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002785.g002", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Universal_Molecular_Clock_and_Universal_Pacemaker_models_of_genome_evolution_/204829", "title"=>"The Universal Molecular Clock and Universal Pacemaker models of genome evolution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-29 01:20:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/534683"], "description"=>"<p>Comparison of the Molecular Clock and Universal Pacemaker models of genome evolution.</p>", "links"=>[], "tags"=>["molecular", "pacemaker", "models", "genome"], "article_id"=>205180, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Sagi Snir", "Yuri I. Wolf", "Eugene V. Koonin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002785.t001", "stats"=>{"downloads"=>3, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_Molecular_Clock_and_Universal_Pacemaker_models_of_genome_evolution_/205180", "title"=>"Comparison of the Molecular Clock and Universal Pacemaker models of genome evolution.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-11-29 01:26:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/534604"], "description"=>"<p>The curve was smoothed using the Gaussian-kernel method.</p>", "links"=>[], "tags"=>["rates", "2294", "fitting", "trees", "upm"], "article_id"=>205098, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Sagi Snir", "Yuri I. Wolf", "Eugene V. Koonin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002785.g005", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_distribution_of_the_relative_evolution_rates_r_k_values_for_2294_gene_families_obtained_by_fitting_gene_trees_to_the_UPM_unconstrained_supertree_/205098", "title"=>"The distribution of the relative evolution rates (<i>r<sub>k</sub></i> values) for 2294 gene families obtained by fitting gene trees to the UPM (unconstrained) supertree.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-29 01:24:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/534417"], "description"=>"<p>The curve was smoothed using the Gaussian-kernel method.</p>", "links"=>[], "tags"=>["ratios", "2294"], "article_id"=>204917, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Sagi Snir", "Yuri I. Wolf", "Eugene V. Koonin"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002785.g003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_distribution_of_the_E_2_MC_k_E_2_UPM_k_ratios_for_2294_gene_families_/204917", "title"=>"The distribution of the <i>E</i><sup>2</sup><i><sub>MC,k</sub></i>/<i>E</i><sup>2</sup><i><sub>UPM,k</sub></i> ratios for 2294 gene families.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-11-29 01:21:57"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[324, 551, 679, 782, 879, 971, 1064, 1154, 1245, 1328, 1406, 1476, 1541, 1617, 1683, 1754, 1818, 1893, 1962, 2025, 2092, 2164, 2227, 2294, 2355]}, {"subject_area"=>"/Medicine and health sciences/Medical devices and equipment", "average_usage"=>[241, 488, 601, 701, 777, 867, 943, 1011, 1074, 1140, 1183, 1219, 1283, 1338, 1408, 1471, 1600, 1656, 1718, 1766, 1836, 1906, 1985, 2041, 2105]}]}
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