Identification of parallel amino acid substitutions accompanying parallel phenotypic evolution is of considerable interest to molecular evolutionists because such parallel substitutions are likely to be adaptive and functionally important ( Stewart et al., 1987; Yokoyama and Yokoyama, 1990; Zhang and Kumar, 1997 ). In 2006, I reported that the gene encoding pancreatic ribonuclease (RNase1) was duplicated independently in Asian and African colobine monkeys ( Zhang, 2006 ). Statistical analyses of DNA sequences, functional assays of reconstructed ancestral proteins, and site-directed mutagenesis showed that the new genes acquired enhanced digestive efficiencies through three parallel amino acid replacements driven by positive selection. They also lost a non-digestive function independently, under a relaxed selective constraint. In a recent Short Communication, Xu and colleagues suggested that the independent duplications that I reported were actually only one duplication event and that the adaptive parallel substitutions I described were no longer existent or were explainable by hypermutations at CpG sites ( Xu et al., 2009 ). Xu et al.’s claims were not supported by available evidence. Below, I provide a detailed response and offer additional phylogenetic evidence for parallel adaptive evolution of digestive RNases in Asian and African colobines. In my original analysis (
Molecular Phylogenetics and Evolution – Elsevier
Published: Nov 1, 2009
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