Molecular Biology and Evolution 18:2327-2330 (2001)
© 2001 Society for Molecular Biology and Evolution
A Site-specific Measure for Rate Difference After Gene Duplication or Speciation
Department of Zoology/Genetics, LHB Center for Bioinformatics and Biological Statistics, Iowa State University
Gene family proliferation by gene (genome) duplication has provided the raw materials for functional innovations (Ohno 1970
; Lundin 1993
; Holland et al. 1994
; Henikoff et al. 1997
; Golding and Dean 1998
). Several models were proposed for functional divergence among member genes (e.g., Li 1983
; Clark 1994
; Hughes 1994
; Fryxell 1996
; Nei, Gu, and Sitnikova 1997
; Force et al. 1999
), but the details remain largely unknown. Gu (1999)
developed a statistical method for testing type I functional divergence, i.e., changes in protein function between two gene clusters result in changes in selective constraints (and therefore shifted evolutionary rates) at some residues. It stands in contrast to type II functional divergence, i.e., changes in protein function between two gene clusters do not alter the level of selective constraints. Amino acid residues with rate shifts are the sites that have either gained
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