12116430

Source:http://linkedlifedata.com/resource/pubmed/id/12116430

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Predicate	Object
rdf:type	pubmed:Citation
lifeskim:mentions	umls-concept:C0028630, umls-concept:C1519068, umls-concept:C1705165, umls-concept:C1705167, umls-concept:C2700061
pubmed:issue	4
pubmed:dateCreated	2002-7-15
pubmed:abstractText	Nucleotide transitions are frequently down-weighted relative to transversions in phylogenetic analysis. This is based on the assumption that transitions, by virtue of their greater evolutionary rate, exhibit relatively more homoplasy and are therefore less reliable phylogenetic characters. Relative amounts of homoplastic and consistent transition and transversion changes in mitochondrial protein coding genes were determined from character-state reconstructions on a highly corroborated phylogeny of mammals. We found that although homoplasy was related to evolutionary rates and was greater for transitions, the absolute number of consistent transitions greatly exceeded the number of consistent transversions. Consequently, transitions provided substantially more useful phylogenetic information than transversions. These results suggest that down-weighting transitions may be unwarranted in many cases. This conclusion was supported by the fact that a range of transition: transversion weighting schemes applied to various mitochondrial genes and genomic partitions rarely provided improvement in phylogenetic estimates relative to equal weighting, and in some cases weighting transitions more heavily than transversions was most effective.
pubmed:language	eng
pubmed:journal	http://linkedlifedata.com/resource/pubmed/journal/9302532
pubmed:citationSubset	IM
pubmed:status	MEDLINE
pubmed:month	Dec
pubmed:issn	1063-5157
pubmed:author	pubmed-author:BroughtonR ERE, pubmed-author:DurrettR TRT, pubmed-author:StanleyS ESE
pubmed:issnType	Print
pubmed:volume	49
pubmed:owner	NLM
pubmed:authorsComplete	Y
pubmed:pagination	617-27
pubmed:dateRevised	2006-11-15
pubmed:meshHeading	pubmed-meshheading:12116430-Base Sequence, pubmed-meshheading:12116430-Mutation, pubmed-meshheading:12116430-Phylogeny
pubmed:year	2000
pubmed:articleTitle	Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis.
pubmed:affiliation	Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853-2701, USA.
pubmed:publicationType	Journal Article, Research Support, U.S. Gov't, Non-P.H.S.