A Phylogenetic Approach Finds Abundant Interlocus Gene Conversion in Yeast.
Interlocus gene conversion (IGC) homogenizes repeats. While genomes can be repeat-rich, the evolutionary importance of IGC is poorly understood. Additional statistical tools for characterizing it are needed. We propose a composite likelihood strategy for incorporating IGC into widely-used probabilistic models for sequence changes that originate with point mutation. We estimated the percentage of nucleotide substitutions that originate with an IGC event rather than a point mutation in 14 groups of yeast ribosomal protein-coding genes, and found values ranging from 20% to 38%. We designed and applied a procedure to determine whether these percentages are inflated due to artifacts arising from model misspecification. The results of this procedure are consistent with IGC having had an important role in the evolution of each of these 14 gene families. We further investigate the properties of our IGC approach via simulation. In contrast to usual practice, our findings suggest that the IGC should and can be considered when multigene family evolution is investigated.
Bioinformatics Research Center, North Carolina State University Department of Statistics, North Carolina State University.
Xiang
X
Ji
Bioinformatics Research Center, North Carolina State University Department of Biological Sciences, North Carolina State University.
Alexander
A
Griffing
Bioinformatics Research Center, North Carolina State University Department of Statistics, North Carolina State University Department of Biological Sciences, North Carolina State University thorne@statgen.ncsu.edu.
Jeffrey L
JL
Thorne
D001483:Base Sequence / Q000235:genetics; D005075:Biological Evolution; D019143:Evolution, Molecular; D005785:Gene Conversion; D008957:Models, Genetic; D005810:Multigene Family; D009711:Nucleotides / Q000235:genetics; D010802:Phylogeny; D017354:Point Mutation; D012441:Saccharomyces cerevisiae; D017422:Sequence Analysis, DNA / Q000379:methods; D015003:Yeasts / Q000235:genetics*
D009711:Nucleotides
interlocus gene conversion; multigene family evolution