PT  - JOURNAL ARTICLE
AU  - D. S. Caetano
AU  - L. J. Harmon
TI  - Estimating correlated rates of trait evolution with uncertainty
AID  - 10.1101/102939
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 102939
4099  - http://biorxiv.org/content/early/2017/01/25/102939.short
4100  - http://biorxiv.org/content/early/2017/01/25/102939.full
AB  - Correlated evolution among traits can happen due to genetic constraints, ontogeny, and selection and have an important impact on the trajectory of phenotypic evolution. Thus, shifts in the pattern of evolutionary integration may allow the exploration of novel regions of the morphospace by lineages. Here we use phylogenetic trees to study the pace of evolution of several traits and their pattern of evolutionary correlation across clades and over time. We use regimes mapped to the branches of the phylogeny to test for shifts in evolutionary integration. Our approach incorporates the uncertainty related to phylogeny, ancestral state estimates and parameter estimates to produce posterior distributions using Bayesian Markov chain Monte Carlo. We implemented the use of summary statistics to test for regime shifts based on a series of attributes of the model that can be directly relevant to biological hypotheses. In addition, we extend Felsenstein’s pruning algorithm to the case of multivariate Brownian motion models with multiple rate regimes. We performed extensive simulations to explore the performance of the method under a series of scenarios. Finally, we provide two test cases; the evolution of a novel buccal morphology in fishes of the family Centrarchidae and a shift in the trajectory of evolution of traits during the radiation of anole lizards to the Caribbean islands.