GENOME-WIDE PHYLOGENETIC RECONSTRUCTION FOR PROCELLARIIFORM SEABIRDS IS ROBUST TO MOLECULAR RATE VARIATION

Abstract

Substitution rates are known to vary across a wide range of organisms, including birds. Physiological and life-history traits that correlate with body mass may be responsible for differences in substitution rate, which can lead to inaccurate reconstructions of evolutionary relationships and obscure the true phylogeny of affected clades. Given the striking 900-fold difference in body mass between the smallest and largest members of the order Procellariiformes, which encompasses petrels, storm petrels and albatrosses, we used genome-scale nuclear DNA sequence data from 4365 ultraconserved element loci (UCEs) in 51 procellariiform species to examine whether phylogenetic reconstruction using massive genome-wide datasets is robust to the presence of extensive rate heterogeneity. In effect, branch length variation in our phylogenetic trees evidences rate variation. Despite this, all phylogenetic analyses (Maximum-likelihood, Bayesian inference and species tree) recovered the same branching topology, including those constrained to have uniform, clock-like substitution rates and those implementing a relaxed clock model that allows rates to vary among lineages. Using Phylogenetic Generalised Least Squares tests, we found that body mass and age at first breeding together explain 64% of the variance in substitution rate. The inferred topology provides a backbone phylogeny for procellariiform seabirds and resolves several controversies about the evolutionary history of the order. We find that the albatrosses are basal, and that the two lineages of storm petrels are not sister to each other. We also find the diving petrels, which have previously been hypothesised as a distinct family, are nestled within the Procellariidae.