A Neutral Model of Transcriptome Evolution
Publication Date
May 11, 2004
Journal
PLOS Biology
Authors
Philipp Khaitovich, Gunter Weiss, Michael Lachmann, Ines Hellmann, et al
Volume
2
Issue
5
Pages
e132
DOI
https://dx.plos.org/10.1371/journal.pbio.0020132
Publisher URL
http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.0020132
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/15138501
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC406393
Europe PMC
http://europepmc.org/abstract/MED/15138501
Web of Science
000221599500018
Scopus
19344372220
Mendeley
http://www.mendeley.com/research/neutral-model-transcriptome-evolution
Events
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Mendeley | Further Information

{"title"=>"A neutral model of transcriptome evolution", "type"=>"journal", "authors"=>[{"first_name"=>"Philipp", "last_name"=>"Khaitovich", "scopus_author_id"=>"6602559039"}, {"first_name"=>"Gunter", "last_name"=>"Weiss", "scopus_author_id"=>"55725480700"}, {"first_name"=>"Michael", "last_name"=>"Lachmann", "scopus_author_id"=>"6603915382"}, {"first_name"=>"Ines", "last_name"=>"Hellmann", "scopus_author_id"=>"6507365203"}, {"first_name"=>"Wolfgang", "last_name"=>"Enard", "scopus_author_id"=>"6508388924"}, {"first_name"=>"Bjoern", "last_name"=>"Muetzel", "scopus_author_id"=>"57199526397"}, {"first_name"=>"Ute", "last_name"=>"Wirkner", "scopus_author_id"=>"6603604548"}, {"first_name"=>"Wilhelm", "last_name"=>"Ansorge", "scopus_author_id"=>"7005995513"}, {"first_name"=>"Svante", "last_name"=>"Pääbo", "scopus_author_id"=>"7006151134"}], "year"=>2004, "source"=>"PLoS Biology", "identifiers"=>{"pmid"=>"15138501", "doi"=>"10.1371/journal.pbio.0020132", "sgr"=>"19344372220", "isbn"=>"1545-7885 (Electronic)", "scopus"=>"2-s2.0-19344372220", "issn"=>"15449173", "pui"=>"39234480"}, "id"=>"025e9524-d011-371f-9c81-6f1bc436dcc7", "abstract"=>"Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for changes in the expression levels of many genes, it is not known whether the majority of changes of gene expression fixed during evolution between species and between various tissues within a species are caused by Darwinian selection or by stochastic processes. We find the following: (1) expression differences between species accumulate approximately linearly with time; (2) gene expression variation among individuals within a species correlates positively with expression divergence between species; (3) rates of expression divergence between species do not differ significantly between intact genes and expressed pseudogenes; (4) expression differences between brain regions within a species have accumulated approximately linearly with time since these regions emerged during evolution. These results suggest that the majority of expression differences observed between species are selectively neutral or nearly neutral and likely to be of little or no functional significance. Therefore, the identification of gene expression differences between species fixed by selection should be based on null hypotheses assuming functional neutrality. Furthermore, it may be possible to apply a molecular clock based on expression differences to infer the evolutionary history of tissues.", "link"=>"http://www.mendeley.com/research/neutral-model-transcriptome-evolution", "reader_count"=>303, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>33, "Researcher"=>90, "Student > Doctoral Student"=>8, "Student > Ph. D. 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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/964569"], "description"=>"<p>Average expression differences within and between primates in brains (A), in liver (B), and for genes in brain for genes with high (red) and low (blue) variation among six humans (C). Colors: red, comparisons between and with humans; blue, comparisons between and with chimpanzees; purple, comparisons between humans and chimpanzees; orange, comparisons between orangutan and rhesus macaque; black, comparisons between experimental duplicates. Vertical error bars for expression indicate 95% confidence intervals calculated by 10,000 bootstraps over genes. Divergence times are according to <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020132#pbio-0020132-Glazko1\" target=\"_blank\">Glazko and Nei (2003</a>).</p>", "links"=>[], "tags"=>["transcriptome", "primates"], "article_id"=>634497, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Philipp Khaitovich", "Gunter Weiss", "Michael Lachmann", "Ines Hellmann", "Wolfgang Enard", "Bjoern Muetzel", "Ute Wirkner", "Wilhelm Ansorge", "Svante Pääbo"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0020132.g001", "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Brain_and_Liver_Transcriptome_Change_among_Primates_as_a_Function_of_Time_/634497", "title"=>"Brain and Liver Transcriptome Change among Primates as a Function of Time", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 09:19:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/964715"], "description"=>"<p>(A) shows the distributions of expression divergence between humans and chimpanzees for intact genes and pseudogenes. (B) shows the distributions of the ratio of expression divergence between humans and chimpanzees and expression diversity within humans for intact genes and pseudogenes.</p>", "links"=>[], "tags"=>["genes"], "article_id"=>634643, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Philipp Khaitovich", "Gunter Weiss", "Michael Lachmann", "Ines Hellmann", "Wolfgang Enard", "Bjoern Muetzel", "Ute Wirkner", "Wilhelm Ansorge", "Svante Pääbo"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0020132.g004", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_between_Intact_Genes_and_Pseudogenes_/634643", "title"=>"Comparison between Intact Genes and Pseudogenes", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 09:21:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/964670"], "description"=>"<p>Average expression differences within and between the mouse species (A) and for genes with high (red) and low (blue) variation among M. musculus individuals (B). Colors: red, comparisons between and with <i>M. musculus;</i> blue, between and with <i>M. spretus;</i> purple, between M. musculus and M. spretus. Vertical error bars for expression indicate 95% confidence intervals calculated by 10,000 bootstraps over genes. Divergence times are according to <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020132#pbio-0020132-She1\" target=\"_blank\">She et al. (1990</a>).</p>", "links"=>[], "tags"=>["transcriptome", "mice"], "article_id"=>634597, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Philipp Khaitovich", "Gunter Weiss", "Michael Lachmann", "Ines Hellmann", "Wolfgang Enard", "Bjoern Muetzel", "Ute Wirkner", "Wilhelm Ansorge", "Svante Pääbo"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0020132.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Brain_Transcriptome_Change_among_Mice_as_a_Function_of_Time_/634597", "title"=>"Brain Transcriptome Change among Mice as a Function of Time", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 09:20:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/964755"], "description"=>"<div><p>(A) Schematic evolutionary tree for six human brain regions: B.44, Brodmann's area 44; PFC, prefrontal cortex; ACC, anterior cingulate cortex; PVC, primary visual cortex; CN, caudate nucleus; and CB, cerebellum. Numbers indicate approximate divergence time in millions of years (<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020132#pbio-0020132-Butler1\" target=\"_blank\">Butler and Hodos 1996</a>; <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020132#pbio-0020132-Nieuwenhuys1\" target=\"_blank\">Nieuwenhuys et al. 1998</a>).</p>\n <p>(B) Average expression differences among brain regions in humans (red) and in chimpanzees (blue).</p>\n <p>(C) Average expression differences among brain regions in <i>M. musculus.</i> Error bars for expression indicate 95% confidence intervals calculated from 10,000 bootstrap replications over genes.</p></div>", "links"=>[], "tags"=>["regions", "evolutionary"], "article_id"=>634678, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Philipp Khaitovich", "Gunter Weiss", "Michael Lachmann", "Ines Hellmann", "Wolfgang Enard", "Bjoern Muetzel", "Ute Wirkner", "Wilhelm Ansorge", "Svante Pääbo"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0020132.g005", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transcriptome_Change_among_Brain_Regions_as_a_Function_of_Evolutionary_Time_/634678", "title"=>"Transcriptome Change among Brain Regions as a Function of Evolutionary Time", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 09:21:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/964620"], "description"=>"<p>Colors and symbols as in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020132#pbio-0020132-g001\" target=\"_blank\">Figure 1</a> except orange, which indicates comparisons between chimpanzee and both macaque species, and blue, which indicates comparisons between rhesus macaque and crab-eating macaque. Divergence times are according to <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020132#pbio-0020132-Hayasaka1\" target=\"_blank\">Hayasaka et al. (1996</a>) and <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020132#pbio-0020132-Glazko1\" target=\"_blank\">Glazko and Nei (2003</a>).</p>", "links"=>[], "tags"=>["transcriptome", "cdna"], "article_id"=>634545, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Philipp Khaitovich", "Gunter Weiss", "Michael Lachmann", "Ines Hellmann", "Wolfgang Enard", "Bjoern Muetzel", "Ute Wirkner", "Wilhelm Ansorge", "Svante Pääbo"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0020132.g002", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Brain_Transcriptome_Change_as_Measured_by_cDNA_Arrays_/634545", "title"=>"Brain Transcriptome Change as Measured by cDNA Arrays", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-22 09:19:51"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"10", "full-text"=>"6", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"3", "year"=>"2015", "month"=>"11"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"12"}
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  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"13", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"3"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"4"}
  • {"unique-ip"=>"2", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"5"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"6"}
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  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
  • {"unique-ip"=>"6", "full-text"=>"10", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
  • {"unique-ip"=>"9", "full-text"=>"13", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2016", "month"=>"11"}
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  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"2"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"3"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"4"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"5"}
  • {"unique-ip"=>"3", "full-text"=>"5", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"6"}
  • {"unique-ip"=>"4", "full-text"=>"6", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"7"}
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  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"13", "full-text"=>"8", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"6", "full-text"=>"4", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
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  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"9", "full-text"=>"10", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"12", "full-text"=>"12", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"9", "full-text"=>"7", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"14", "full-text"=>"12", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"24", "full-text"=>"23", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"11", "full-text"=>"11", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"16", "full-text"=>"17", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"19", "full-text"=>"19", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"10", "full-text"=>"7", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}

Relative Metric

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