This study presents an exhaustive computation of the deviations of substitution counts from what would be expected by a maximum likelihood Poisson regression model of a molecular clock, together with a similar computation of nonsynonymous to synonymous substitutions on each node, and their deviation from expectation determined from the entire phylogenetic tree. We show that the observed deviating nodes shows significant overlap, primarily in leaf nodes, suggesting most nonsynonymous substitutions are recent, and not yet excluded by selection pressure, in agreement with prior studies. We have verified prior studies also reporting some deviations of nonsynonymous to synonymous substitution ratios between northern and temperate climes, but, at the finer level of analysis, show that some of the groups of clades lumped by environment in previous studies are actually heterogeneous in their deviations, tending not to support environmental selection. We have also identified deviations in older interior clades that share relationships with each other, suggesting drift effects fixing nonsynonymous substitutions before selection removed them from the population.
By: Daniel E. Platt
Published in: RC24556 in 2008
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