A phylogenetic method linking nucleotide substitution rates to continuous trait evolution

Author(s): Patrick Gemmell

Affiliation(s): Harvard University



We present a R/C++ software method that relates nucleotide substitution rates to changes in a continuous trait of interest. The method takes as input a multiple sequence alignment of conserved elements, continuous trait data observed in extant species, and a background phylogeny and substitution process. Gibbs sampling is used to assign conservation states (background, conserved, accelerated) to lineages and explore whether the assigned states are associated with increases or decreases in the rate of trait evolution. The approach is illustrated using publicly available mammalian body-size and lifespan data, previously analyzed with respect to protein coding genes. We think these sorts of methods will ultimately increase our understanding of natural history as well as shine a spotlight on parts of our own genome that are of biomedical interest.