Stochastic mapping of morphological characters.

Many questions in evolutionary biology are best addressed by comparing traits in different species. Often such studies involve mapping characters on phylogenetic trees. Mapping characters on trees allows the nature, number, and timing of the transformations to be identified. The parsimony method is the only method available for mapping morphological characters on phylogenies. Although the parsimony method often makes reasonable reconstructions of the history of a character, it has a number of limitations. These limitations include the inability to consider more than a single change along a branch on a tree and the uncoupling of evolutionary time from amount of character change. We extended a method described by Nielsen (2002, Syst. Biol. 51:729-739) to the mapping of morphological characters under continuous-time Markov models and demonstrate here the utility of the method for mapping characters on trees and for identifying character correlation. (Bayesian estimation; character correlation; character mapping; Markov chain Monte Carlo.) The footprint of natural selection on organisms can of- ten be detected using phylogenetic methods. Correlation in either molecular or morphological characters is taken as evidence of natural selection acting on those charac- ters (Harvey and Pagel, 1991). The correlation might be between a character and the environment, with the re- peated evolution of the character in a particular environ- ment indicating that the trait confers an advantage, or the correlation may be between one character and another. In ribosomal RNA sequences, for example, correlated changes occur in nucleotides paired in the stem struc- tures; natural selection is acting to maintain Watson- Crick pairing of nucleotides in the functionally impor- tant stem structures. In either case-correlation between different characters or the repeated evolution of a charac- ter in a particular environment-phylogenetic methods provide the best framework for the analysis of correlation because they allow the effects of a common phylogenetic history that simultaneously acts on all of the characters to be partitioned from the evolutionary processes gener- ating the character patterns (Felsenstein, 1985). Despite the importance of phylogenetic analysis of character change in evolutionary biology, detection of correlation in characters is fraught with difficulties. One dilemma involves how characters should be mapped onto a phylogenetic tree. Many methods for detecting correlations rely on mapping character changes on a phylogenetic tree using the parsimony method (Ridley, 1983; Maddison, 1990). The parsimony method provides the minimum number of transformations required to explain the evolution of the character on the tree and therefore necessarily underestimates the total number of changes. Furthermore, some methods treat the par- simony mapping of a character as an observation in fur- ther statistical analyses (Ridley, 1983; Maddison, 1990). Although the parsimony method is expected to provide a reasonable mapping of a character when the rates of evolution are low, the fundamental problem with the method is that it does not account for the uncertainty in the process of character change. In effect, the parsimony method wagers all on the mapping requiring the fewest changes, when in reality many other perhaps slightly less parsimonious mappings may be nearly as good or