Relaxed Phylogenetics and Dating with Confidence
Publication Date
March 14, 2006
Journal
PLOS Biology
Authors
Alexei J Drummond, Simon Y. W Ho, Matthew J Phillips & Andrew Rambaut
Volume
4
Issue
5
Pages
e88
DOI
https://dx.plos.org/10.1371/journal.pbio.0040088
Publisher URL
http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.0040088
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/16683862
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1395354
Europe PMC
http://europepmc.org/abstract/MED/16683862
Web of Science
000237966900006
Scopus
33344465800
Mendeley
http://www.mendeley.com/research/relaxed-phylogenetics-dating-confidence
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{"title"=>"Relaxed phylogenetics and dating with confidence", "type"=>"journal", "authors"=>[{"first_name"=>"Alexei J.", "last_name"=>"Drummond", "scopus_author_id"=>"26643297100"}, {"first_name"=>"Simon Y.W.", "last_name"=>"Ho", "scopus_author_id"=>"7403716888"}, {"first_name"=>"Matthew J.", "last_name"=>"Phillips", "scopus_author_id"=>"7402769978"}, {"first_name"=>"Andrew", "last_name"=>"Rambaut", "scopus_author_id"=>"7004230842"}], "year"=>2006, "source"=>"PLoS Biology", "identifiers"=>{"pui"=>"43748216", "sgr"=>"33344465800", "issn"=>"15457885", "pmid"=>"16683862", "scopus"=>"2-s2.0-33344465800", "doi"=>"10.1371/journal.pbio.0040088", "isbn"=>"1544-9173"}, "id"=>"db0a497d-f297-3c95-9c02-c04bdbe37154", "abstract"=>"In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of \"relaxed phylogenetics.\" Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.", "link"=>"http://www.mendeley.com/research/relaxed-phylogenetics-dating-confidence", "reader_count"=>2025, "reader_count_by_academic_status"=>{"Unspecified"=>30, "Professor > Associate Professor"=>126, "Librarian"=>2, "Researcher"=>496, "Student > Doctoral Student"=>122, "Student > Ph. D. 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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/474295"], "description"=>"<div><p>In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.</p> </div>", "links"=>[], "tags"=>["relaxed", "phylogenetics", "dating"], "article_id"=>153424, "categories"=>["Evolutionary Biology", "Cancer", "Mathematics", "Genetics", "Biological Sciences", "Ecology"], "users"=>["Alexei J Drummond", "Simon Y. W Ho", "Matthew J Phillips", "Andrew Rambaut"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0040088", "stats"=>{"downloads"=>5, "page_views"=>76, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Relaxed_Phylogenetics_and_Dating_with_Confidence/153424", "title"=>"Relaxed Phylogenetics and Dating with Confidence", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2006-03-14 00:57:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/959589"], "description"=>"<p>The divergence times correspond to the mean posterior estimate of their age in years.\n The yellow bars represent the 95% HPD interval for the divergence time\n estimates. Both the mean and 95% HPD of the divergence times were\n calculated conditional on the existence of the clade defined by the divergence. Each\n node in the tree that has a posterior probability greater than 0.5 is labeled with its\n posterior probability. The sampling times of the tips were assumed to be known\n exactly. Branches colored in red had a posterior rate greater than the average rate,\n whereas branches colored in blue had a lower-than-average rate.</p>", "links"=>[], "tags"=>["69", "influenza", "sequences", "drawn", "randomly", "posterior"], "article_id"=>629602, "categories"=>["Evolutionary Biology", "Virology", "Mathematics", "Genetics", "Biological Sciences", "Ecology"], "users"=>["Alexei J Drummond", "Simon Y. W Ho", "Matthew J Phillips", "Andrew Rambaut"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0040088.g002", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Tree_of_69_Influenza_A_Virus_Sequences_Drawn_Randomly_from_the_Posterior__Distribution_/629602", "title"=>"A Tree of 69 Influenza A Virus Sequences Drawn Randomly from the Posterior\n Distribution", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:44:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/959477"], "description"=>"<p>The timescale is drawn in arbitrary time units. Apart from the branch leading to the\n outgroup, sequence O, all branches are five time units in length.</p>", "links"=>[], "tags"=>["rooted", "binary", "simulating"], "article_id"=>629497, "categories"=>["Evolutionary Biology", "Virology", "Mathematics", "Genetics", "Biological Sciences", "Ecology"], "users"=>["Alexei J Drummond", "Simon Y. W Ho", "Matthew J Phillips", "Andrew Rambaut"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0040088.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Rooted_Binary_Tree_Used_for_Simulating_Sequence_Evolution_/629497", "title"=>"The Rooted Binary Tree Used for Simulating Sequence Evolution", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:43:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/959872"], "description"=>"<p>Each of the 12 categories has equal probability ( <i>p</i> = 1/12). The\n <i>i</i><sup>th</sup> rate category (numbered from left to right)\n corresponds to the (I − 0.5)/12 quantile of the lognormal distribution. </p>", "links"=>[], "tags"=>["lognormal", "discretized", "12"], "article_id"=>629890, "categories"=>["Evolutionary Biology", "Virology", "Mathematics", "Genetics", "Biological Sciences", "Ecology"], "users"=>["Alexei J Drummond", "Simon Y. W Ho", "Matthew J Phillips", "Andrew Rambaut"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0040088.g005", "stats"=>{"downloads"=>6, "page_views"=>132, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Lognormal_Distribution_Discretized_into_12_Rate_Categories_/629890", "title"=>"A Lognormal Distribution Discretized into 12 Rate Categories", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:46:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/959689"], "description"=>"<p>(A) The combined prior distribution of divergence times for the MAP tree topology.\n The green bars represent the 95% HPD interval for the divergence times. (B)\n The posterior distribution of the divergence times. The divergence times correspond to\n the mean posterior estimate of their age in millions of years. The yellow bars\n represent the 95% HPD interval for the divergence time estimates. Both the\n mean and 95% HPD of the divergence times were calculated conditional on the\n existence of the clade defined by the divergence. Each node in the tree is labeled\n with its posterior probability if it is greater than 0.5. The three nodes with\n normally distributed calibration priors are indicated by orange bars. Branches colored\n in red had a posterior rate greater than the average rate, whereas branches colored in\n blue had a lower-than-average rate.</p>", "links"=>[], "tags"=>["17", "marsupials", "placental"], "article_id"=>629710, "categories"=>["Evolutionary Biology", "Virology", "Mathematics", "Genetics", "Biological Sciences", "Ecology"], "users"=>["Alexei J Drummond", "Simon Y. W Ho", "Matthew J Phillips", "Andrew Rambaut"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0040088.g003", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Analysis_of_17_Marsupials_and_Seven_Placental_Mammals_/629710", "title"=>"The Analysis of 17 Marsupials and Seven Placental Mammals", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:44:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/959767"], "description"=>"<p>The datasets are as follows: (A) bacterial, (B) yeast, (C) plant, (D) metazoan, and\n (E) primate.</p>", "links"=>[], "tags"=>["phylogenies"], "article_id"=>629791, "categories"=>["Evolutionary Biology", "Virology", "Mathematics", "Genetics", "Biological Sciences", "Ecology"], "users"=>["Alexei J Drummond", "Simon Y. W Ho", "Matthew J Phillips", "Andrew Rambaut"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0040088.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_8220_True_8221_Phylogenies_for_the_Large_Datasets_/629791", "title"=>"The “True” Phylogenies for the Large Datasets", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 08:45:24"}

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Relative Metric

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F1000Prime | Further Information

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CrossRef
Time
2020-08-25 04:19:47 UTC
Target URL
http://doi.crossref.org/servlet/getForwardLinks?usr=plos&pwd=Sp5BS5-wNH6_jJ&doi=10.1371%2Fjournal.pbio.0040088
Trace

/app/models/concerns/networkable.rb:21:in `get_result'
/app/models/source.rb:165:in `get_data'
/app/models/retrieval_status.rb:47:in `perform_get_data'
/app/jobs/source_job.rb:52:in `block (2 levels) in perform'
/app/jobs/source_job.rb:51:in `block in perform'
/app/jobs/source_job.rb:35:in `each'
/app/jobs/source_job.rb:35:in `perform'