A Bayesian extension of phylogenetic generalized least squares (PGLS): incorporating uncertainty in the comparative study of trait relationships and evolutionary rates

Jesualdo Arturo Fuentes González, P. David Polly & Emília P. Martins
Phylogenetic comparative methods use tree topology, branch lengths, and models of phenotypic change to take into account non-independence in statistical analysis. However, these methods normally assume that trees and models are known without error. Approaches relying on evolutionary regimes also assume specific distributions of character states across a tree, which often result from ancestral state reconstructions that are subject to uncertainty. Several methods have been proposed to deal with some of these sources of uncertainty,...
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