Transition-Transversion Bias Is Not Universal: A Counter Example from Grasshopper Pseudogenes
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{"title"=>"Transition-transversion bias is not universal: A counter example from grasshopper pseudogenes", "type"=>"journal", "authors"=>[{"first_name"=>"Irene", "last_name"=>"Keller", "scopus_author_id"=>"7006615706"}, {"first_name"=>"Douda", "last_name"=>"Bensasson", "scopus_author_id"=>"6701392796"}, {"first_name"=>"Richard A.", "last_name"=>"Nichols", "scopus_author_id"=>"7201505539"}], "year"=>2007, "source"=>"PLoS Genetics", "identifiers"=>{"doi"=>"10.1371/journal.pgen.0030022", "sgr"=>"33847289660", "issn"=>"15537390", "pui"=>"46318398", "isbn"=>"1553-7390", "pmid"=>"17274688", "scopus"=>"2-s2.0-33847289660"}, "id"=>"86f474cf-e640-31b9-a7df-5cb944b077e7", "abstract"=>"Comparisons of the DNA sequences of metazoa show an excess of transitional over transversional substitutions. Part of this bias is due to the relatively high rate of mutation of methylated cytosines to thymine. Postmutation processes also introduce a bias, particularly selection for codon-usage bias in coding regions. It is generally assumed, however, that there is a universal bias in favour of transitions over transversions, possibly as a result of the underlying chemistry of mutation. Surprisingly, this underlying trend has been evaluated only in two types of metazoan, namely Drosophila and the Mammalia. Here, we investigate a third group, and find no such bias. We characterize the point substitution spectrum in Podisma pedestris, a grasshopper species with a very large genome. The accumulation of mutations was surveyed in two pseudogene families, nuclear mitochondrial and ribosomal DNA sequences. The cytosine-guanine (CpG) dinucleotides exhibit the high transition frequencies expected of methylated sites. The transition rate at other cytosine residues is significantly lower. After accounting for this methylation effect, there is no significant difference between transition and transversion rates. These results contrast with reports from other taxa and lead us to reject the hypothesis of a universal transition/transversion bias. Instead we suggest fundamental interspecific differences in point substitution processes.", "link"=>"http://www.mendeley.com/research/transitiontransversion-bias-not-universal-counter-example-grasshopper-pseudogenes", "reader_count"=>170, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>7, "Librarian"=>1, "Researcher"=>50, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>53, "Student > Postgraduate"=>2, "Other"=>3, "Student > Master"=>22, "Student > Bachelor"=>13, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>3, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>7, "Librarian"=>1, "Researcher"=>50, "Student > Doctoral Student"=>7, "Student > Ph. D. Student"=>53, "Student > Postgraduate"=>2, "Other"=>3, "Student > Master"=>22, "Student > Bachelor"=>13, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>3, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>21, "Agricultural and Biological Sciences"=>124, "Medicine and Dentistry"=>6, "Social Sciences"=>2, "Computer Science"=>4, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Social Sciences"=>{"Social Sciences"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>124}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>21}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>5}}, "reader_count_by_country"=>{"Colombia"=>1, "United States"=>6, "United Kingdom"=>3, "Kenya"=>1, "Portugal"=>1, "Spain"=>2, "India"=>1, "Canada"=>1, "Netherlands"=>1, "Sweden"=>1, "Brazil"=>3, "France"=>1, "Australia"=>1}, "group_count"=>5}

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  • {"month"=>"6", "year"=>"2018", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"59"}
  • {"month"=>"7", "year"=>"2018", "pdf_views"=>"7", "xml_views"=>"4", "html_views"=>"44"}
  • {"month"=>"8", "year"=>"2018", "pdf_views"=>"18", "xml_views"=>"1", "html_views"=>"50"}
  • {"month"=>"9", "year"=>"2018", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"36"}
  • {"month"=>"10", "year"=>"2018", "pdf_views"=>"18", "xml_views"=>"0", "html_views"=>"60"}
  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"45"}
  • {"month"=>"12", "year"=>"2018", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"32"}
  • {"month"=>"1", "year"=>"2019", "pdf_views"=>"25", "xml_views"=>"0", "html_views"=>"69"}
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  • {"month"=>"3", "year"=>"2019", "pdf_views"=>"17", "xml_views"=>"1", "html_views"=>"57"}
  • {"month"=>"4", "year"=>"2019", "pdf_views"=>"19", "xml_views"=>"0", "html_views"=>"95"}
  • {"month"=>"5", "year"=>"2019", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"64"}
  • {"month"=>"6", "year"=>"2019", "pdf_views"=>"11", "xml_views"=>"0", "html_views"=>"48"}
  • {"month"=>"7", "year"=>"2019", "pdf_views"=>"13", "xml_views"=>"0", "html_views"=>"60"}
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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/952967"], "description"=>"<p>Frequency of the different point substitutions in <i>Podisma</i> (black) and <i>Drosophila</i> (grey) (data from Petrov and Hartl [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030022#pgen-0030022-b009\" target=\"_blank\">9</a>]) expressed as a percentage of the average substitution rate.</p>", "links"=>[], "tags"=>["substitution", "patterns", "grasshopper"], "article_id"=>623280, "categories"=>["Evolutionary Biology"], "users"=>["Irene Keller", "Douda Bensasson", "Richard A Nichols"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030022.g003", "stats"=>{"downloads"=>3, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neutral_Point_Substitution_Patterns_in_the_Grasshopper_Podisma_and_the_Fruit_Fly_Drosophila_/623280", "title"=>"Neutral Point Substitution Patterns in the Grasshopper <i>Podisma</i> and the Fruit Fly <i>Drosophila</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:49:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/952911"], "description"=>"<p>Maximum likelihood estimates of the frequency (with associated standard errors) of the different substitutions in grasshopper pseudogenes expressed as a percentage of the average substitution rate (C:G → T:A substitutions at CpG sites are excluded) (light grey, transversions; dark grey, transitions).</p>", "links"=>[], "tags"=>["substitution", "grasshopper", "pseudogenes"], "article_id"=>623227, "categories"=>["Evolutionary Biology"], "users"=>["Irene Keller", "Douda Bensasson", "Richard A Nichols"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030022.g002", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neutral_Point_Substitution_Pattern_in_Grasshopper_Pseudogenes_Accounting_for_Multiple_Substitutions_/623227", "title"=>"Neutral Point Substitution Pattern in Grasshopper Pseudogenes Accounting for Multiple Substitutions", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:48:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/952802"], "description"=>"<p>(A and B) Frequency of the different substitutions in rDNA pseudogenes (black) and Numts (grey) expressed as a percentage of the average substitution rate.</p>", "links"=>[], "tags"=>["substitution", "patterns", "types", "grasshopper"], "article_id"=>623118, "categories"=>["Evolutionary Biology"], "users"=>["Irene Keller", "Douda Bensasson", "Richard A Nichols"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030022.g001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neutral_Point_Substitution_Patterns_in_Two_Types_of_Grasshopper_Pseudogenes_/623118", "title"=>"Neutral Point Substitution Patterns in Two Types of Grasshopper Pseudogenes", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:47:56"}

PMC Usage Stats | Further Information

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  • {"scanned-page-browse"=>"0", "month"=>"7", "cited-by"=>"0", "abstract"=>"0", "full-text"=>"5", "unique-ip"=>"8", "pdf"=>"6", "year"=>"2010", "figure"=>"0", "scanned-summary"=>"0", "supp-data"=>"0"}
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  • {"scanned-page-browse"=>"0", "month"=>"9", "cited-by"=>"0", "abstract"=>"1", "full-text"=>"16", "unique-ip"=>"17", "pdf"=>"12", "year"=>"2010", "figure"=>"0", "scanned-summary"=>"0", "supp-data"=>"0"}
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  • {"unique-ip"=>"33", "full-text"=>"37", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"21", "full-text"=>"21", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"19", "full-text"=>"20", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

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