Reconstructing mammalian phylogenies: a detailed comparison of the cytochrome b and cytochrome oxidase subunit I mitochondrial genes

Shanan Tobe, Andrew Kitchener, A.M.T. Linacre

Research output: Contribution to journalArticle

87 Citations (Scopus)

Abstract

The phylogeny and taxonomy of mammalian species were originally based upon shared or derived morphological characteristics. However, genetic analyses have more recently played an increasingly important role in confirming existing or establishing often radically different mammalian groupings and phylogenies. The two most commonly used genetic loci in species identification are the cytochrome oxidase I gene (COI) and the cytochrome b gene (cyt b). For the first time this study provides a detailed comparison of the effectiveness of these two loci in reconstructing the phylogeny of mammals at different levels of the taxonomic hierarchy in order to provide a basis for standardizing methodologies in the future. Interspecific and intraspecific variation is assessed and for the first time, to our knowledge, statistical confidence is applied to sequence comparisons. Comparison of the DNA sequences of 217 mammalian species reveals that cyt b more accurately reconstructs their phylogeny and known relationships between species based on other molecular and morphological analyses at Super Order, Order, Family and generic levels. Cyt b correctly assigned 95.85% of mammal species to Super Order, 94.31% to Order and 98.16% to Family compared to 78.34%, 93.36% and 96.93% respectively for COI. Cyt b also gives better resolution when separating species based on sequence data. Using a Kimura 2-parameter p-distance (x100) threshold of 1.5–2.5, cyt b gives a better resolution for separating species with a lower false positive rate and higher positive predictive value than those of COI.

LanguageEnglish
Article numbere14156
Number of pages14
JournalPLoS One
Volume5
Issue number11
DOIs
Publication statusPublished - 30 Nov 2010

Fingerprint

Cytochromes b
Mitochondrial Genes
Electron Transport Complex IV
Phylogeny
cytochrome b
cytochrome-c oxidase
Genes
phylogeny
Mammals
genes
mammals
Time and motion study
loci
Genetic Loci
Time and Motion Studies
DNA sequences
Taxonomies
interspecific variation
taxonomy
nucleotide sequences

Keywords

  • cytochrome b
  • cytochrome oxidase I
  • phylogeny
  • statistics

Cite this

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Reconstructing mammalian phylogenies : a detailed comparison of the cytochrome b and cytochrome oxidase subunit I mitochondrial genes. / Tobe, Shanan; Kitchener, Andrew; Linacre, A.M.T.

In: PLoS One, Vol. 5, No. 11, e14156, 30.11.2010.

Research output: Contribution to journalArticle

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