期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 18, 期 8, 页码 1464-1473出版社
OXFORD UNIV PRESS
DOI: 10.1093/oxfordjournals.molbev.a003932
关键词
heterogeneous GC content; unequal base composition; maximum-likelihood phylogeny; nonhomogeneous phylogeny models; molecular phylogeny; Drosophilidae
资金
- NIGMS NIH HHS [GM42397] Funding Source: Medline
Compositional changes are a major feature of genome evolution. Overlooking nucleotide composition differences among sequences can seriously mislead phylogenetic reconstructions. Large compositional variation exists among the members of the family Drosophilidae. Until now, however, base composition differences have been largely neglected in the formulations of the nucleotide substitution process used to reconstruct the phylogeny of this important group of species. The present study adopts a maximum-likelihood framework of phylogenetic inference in order to analyze five nuclear gene regions and shows that (1) the pattern of compositional variation in the Drosophilidae, does not match the phylogeny of the species; (2) accounting for the heterogeneous GC content with Galtier and Gouy's nucleotide substitution model leads to a tree that differs in significant aspects from the tree inferred when the nucleotide composition differences are ignored, even though both phylogenetic hypotheses attain strong nodal support in the bootstrap analyses; and (3) the LogDet distance correction cannot completely overcome the distorting effects of the compositional variation that exist, among the species of the Drosophilidae. Our analyses confidently place the Chymomyza genus as an outgroup closer than the genus Scaptodrosophila to the Drosophila genus and conclusively support the monophyly of the Sophophora subgenus.
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