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MBE Advance Access published online on December 8, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi065
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Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved.
Accepted December 6, 2004

Research Article

The Impact of Taxon Sampling on the Estimation of Rates of Evolution at Sites

C. Blouin 1*, D. Butt 2, and A.J. Roger 3

1 Genome Atlantic, Dept. of Biochemistry and Molecular Biology, Dalhousie University, Canada, 5850 University, Ave., B3H 1X5; Faculty of Computer Science, Dalhousie University, Canada, 6050 University Ave., B3H 1W5
2 Faculty of Computer Science, Dalhousie University, Canada, 6050 University Ave., B3H 1W5
3 Genome Atlantic, Dept. of Biochemistry and Molecular Biology, Dalhousie University, Canada, 5850 University, Ave., B3H 1X5; Canadian Institute for Advanced Research, Program in Evolutionary Biology


  Abstract

The function of individual sites within a protein influences their rate of accepted point mutations. During the computation of phylogenetic likelihoods, rate heterogeneity can be modeled on a site-per-site basis with relative rates drawn from a discretized -distribution. Site-rate estimates (e.g. the rate of highest posterior probability given the data at a site) can then be used as a measure of evolutionary constraints imposed by function. However, if the sequence availability is limited, the evaluation of rates is subject to sampling error. This paper presents a simulation study that evaluates the robustness of evolutionary site rate estimates for both small and phylogenetically unbalanced samples. The sampling error on rate estimates was first evaluated for alignments that included 5-45 sequences, sampled by jackknifing, from a master alignment containing 968 sequences. We observed that the potentially enhanced resolution amongst site rates due to the inclusion of a larger number of rate categories is negated by the difficulty to correctly estimate intermediate rates. This effect is marked for datasets with less than 30 sequences. Although the computation of likelihood theoretically accounts for phylogenetic distances through branch lengths, the introduction of a single long-branch outlier sequence had a significant negative effect on site rate estimates. Finally, the presence of a shift in rate of evolution between related lineages can be diagnostic of a gain/loss of function within a protein family. Our analyses indicate that detecting these rate shifts is a harder problem than estimating rates. This is so, partially, because the difference in rates depends on two rate estimates, each with an intrinsic uncertainty. The performances of four methods to detect these site rate shifts are evaluated and compared. Guidelines to prepare datasets minimally influenced by error introduced by sequence sampling are suggested.

Keywords: protein; evolutionary rate; functional divergence; maximum likelihood; simulation.
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