Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis.

Published

Journal Article

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.

Full Text

Duke Authors

Cited Authors

  • Broughton, RE; Stanley, SE; Durrett, RT

Published Date

  • December 2000

Published In

Volume / Issue

  • 49 / 4

Start / End Page

  • 617 - 627

PubMed ID

  • 12116430

Pubmed Central ID

  • 12116430

Electronic International Standard Serial Number (EISSN)

  • 1076-836X

International Standard Serial Number (ISSN)

  • 1063-5157

Digital Object Identifier (DOI)

  • 10.1080/106351500750049734

Language

  • eng