Dear all,
I am a newbie to this mailing list and phylogenetic analyses in R and hope you can comment on a question I have. I would like to estimate the rate of evolution of a continous trait and check if the trait evolves faster along some branches of the topology. I already checked with Pagels lambda if the trait evolves according to a Brownian motion model,(i.e. pure drift), which it did not (lambda ~ 0). Modelling the trait evolution under the Ornstein-Uhlenbeck (OU) model provided a significant better fit (p<- 0.01) with a very high alpha parameter of 8.7 (indicating a role of selection in trait evolution). In order to infer now the rate of trait evolution I am searching for a R package that is able to do this inference based on the OU model. However, so far I either just found methods based on the Brownian motion model (e.g. brownie.lite function in phytools, Motmot) or methods that also rely on the reconstruction of ancestral selective regimes beforehand (like mvMORPH or OUwie). I want to keep the model as simple as possible and therefore don't know if it is necessary to also model ancestral selective regimes if I just want to know if the evolutionary rate of the trait varies along branches and which branches show an accelerated rate?! Which programm would you recommend? I would be very thankful for your help and recommendations.
Best wishes,
Belinda
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