Relationships between Molecular Clock Deviations and High Nonsynonymous to Synonymous Ratios among Some Older Haplogroups

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


This Research Report is available. This report has been submitted for publication outside of IBM and will probably be copyrighted if accepted for publication. It has been issued as a Research Report for early dissemination of its contents. In view of the transfer of copyright to the outside publisher, its distribution outside of IBM prior to publication should be limited to peer communications and specific requests. After outside publication, requests should be filled only by reprints or legally obtained copies of the article (e.g., payment of royalties). I have read and understand this notice and am a member of the scientific community outside or inside of IBM seeking a single copy only.


Questions about this service can be mailed to .