Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms.
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...This approach is known as the covarion model in the context of DNA sequence evolution (Fitch and Markowitz 1970) or the hidden rates model in the context of binary characters (Beaulieu et al. 2014)....
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Cites methods from "Identifying hidden rate changes in ..."
...Covarion methods (e.g., Penny et al. 2001; Beaulieu et al. 2013) could be adapted to model the effect of hidden variables....
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...Here we use the Akaike Information Criterion (Akaike 1974) to compare the log-likelihoods of different models....
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...The AIC weight (wi), which represents the relative likelihood that model i is the best model given a set of models (Burnham and Anderson 2002), was calculated for all models....
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...A maximum likelihood (ML) phylogenetic analysis of the total sequence alignment was performed using RAxML (v.7.2.6; Stamatakis 2006), and tree searches were conducted under the GTR+CAT approximation of rate heterogeneity, partitioned by gene region....
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