Abstract:
:Maximum likelihood codon substitution models have proven useful for studying when and how protein function evolves, but they have recently been criticized on a number of fronts. The strengths and weaknesses of such methods must therefore be identified and improved upon. Here, using simulations, we show that the Clade model C versus M1a test for functional divergence among clades is prone to false positives under simple evolutionary conditions. We then propose a new null model (M2a_rel) that better accounts for among-site variation in selective constraint. We show that the revised test has an improved false-positive rate and good power. Applying this test to previously analyzed data sets of primate ribonucleases and mammalian rhodopsins reveals that some conclusions may have been misled by the original method. The improved test should prove useful for identifying patterns of divergence in selective constraint among paralogous gene families and among orthologs from ecologically divergent species.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Weadick CJ,Chang BSdoi
10.1093/molbev/msr311subject
Has Abstractpub_date
2012-05-01 00:00:00pages
1297-300issue
5eissn
0737-4038issn
1537-1719pii
msr311journal_volume
29pub_type
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