Computational protocol: Rates of morphological evolution in Captorhinidae: an adaptive radiation of Permian herbivores

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Protocol publication

[…] A dietary character with three states, carnivore, herbivore and omnivore, was scored for all taxa present in the phylogeny. Ancestral character states were deduced using conditional (joint) likelihood, employing the ace function in the ape package () in R. This function allow three models of discrete character change: an equal rates model (transitions between all states in all directions are equally probable), a symmetrical model (transitions between two character states occur with equal probability in either direction, but different pairs of character states have different probabilities of transition) and an all-rates-different model (each transition has a different probability). In order to deduce which model was best for the data available, these models were fit to the captorhinid phylogeny using likelihood methods, employing the fitDiscrete function in the R package geiger (). The Akaike weights were used to deduce the best fitting model.Since this likelihood ancestral state reconstruction produced uncertain results surrounding the character state at three nodes (see below), an alternative Bayesian approach for optimizing the dietary character at these nodes was used as an independent test in the program BayesTraits V2 (). A reversible jump Markov chain Monte Carlo (RJ MCMC) approach was used to reconstruct the ancestral states of the discrete character, allowing different combinations of character states to have different transition rates. The analysis was run for 10,000,000 iterations with 100,000 discarded as burn-in, sampling every 1,000 generations. These results are presented in the , and the analyses described below are based on the likelihood results. […]

Pipeline specifications

Software tools APE, GEIGER, BayesTraits
Application Phylogenetics
Diseases Nephrosis, Lipoid