Simulating and detecting autocorrelation of molecular evolutionary rates among lineages
Simon YW Ho, Sebastian Duchene, David Duchene
MOLECULAR ECOLOGY RESOURCES | WILEY-BLACKWELL | Published : 2015
Evolutionary timescales can be estimated from genetic data using phylogenetic methods based on the molecular clock. To account for molecular rate variation among lineages, a number of relaxed-clock models have been developed. Some of these models assume that rates vary among lineages in an autocorrelated manner, so that closely related species share similar rates. In contrast, uncorrelated relaxed clocks allow all of the branch-specific rates to be drawn from a single distribution, without assuming any correlation between rates along neighbouring branches. There is uncertainty about which of these two classes of relaxed-clock models are more appropriate for biological data. We present an R p..View full abstract
Awarded by Australian Research Council
We thank three anonymous reviewers for their constructive comments on our study. This work was supported by the Australian Research Council (grant number DP110100383 to S.Y.W.H.), a Francisco Jose de Caldas Scholarship from the Colombian government (S.D.) and by a World Scholars Award from the University of Sydney (S.D.).