Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence.

ABSTRACT: Molecular phylogenetics is often used to estimate the time since the divergence of modern gene sequences. For highly diverged sequences, such phylogenetic techniques sometimes estimate surprisingly recent divergence times. In the case of viruses, independent evidence indicates that the estimates of deep divergence times from molecular phylogenetics are sometimes too recent. This discrepancy is caused in part by inadequate models of purifying selection leading to branch-length underestimation. Here we examine the effect on branch-length estimation of using models that incorporate experimental measurements of purifying selection. We find that models informed by experimentally measured site-specific amino-acid preferences estimate longer deep branches on phylogenies of influenza virus hemaggl

SUBMITTER: Hilton SK 

PROVIDER: S-EPMC6220371 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature