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Mapping uncertainty and phylogenetic uncertainty in ancestral character state reconstruction: an example in the moss genus Brachytheciastrum. Systematic Biology 55: 957–971 (2006)
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BibTeX
@MISC{Vanderpoorten06mappinguncertainty,
author = {A. Vanderpoorten and B. Goffinet},
title = {Mapping uncertainty and phylogenetic uncertainty in ancestral character state reconstruction: an example in the moss genus Brachytheciastrum. Systematic Biology 55: 957–971},
year = {2006}
}
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Abstract
Abstract. — The evolution of species traits along a phylogeny can be examined through an increasing number of possible, but not necessarily complementary, approaches. In this paper, we assess whether deriving ancestral states of discrete mor-phological characters from a model whose parameters are (i) optimized by ML on a most likely tree; (ii) optimized by ML onto each of a Bayesian sample of trees; and (iii) sampled by a MCMC visiting the space of a Bayesian sample of trees affects the reconstruction of ancestral states in the moss genus Brachytheciastrum. In the first two methods, the choice of a single- or two-rate model and of a genetic distance (wherein branch lengths are used to determine the probabilities of change) or speciational (wherein changes are only driven by speciation events) model based upon a likelihood-ratio test strongly depended on the sampled trees. Despite these differences in model selection, reconstructions of ancestral character states were strongly correlated to each others across nodes, often at r> 0.9, for all the characters. The Bayesian approach of ancestral character state reconstruction offers, however, a series of advantages over the single-tree approach or the ML model optimization on a Bayesian sample of trees because it does not involve restricting model parameters prior to reconstructing ancestral states, but rather allows a range of model parameters and ancestral character states to be sampled according to their posterior probabilities. From the distribution of the latter, conclusions on trait evolution can be made in a more satis-factorily way than when a substantial part of the uncertainty of the results is obscured by the focus on a single set of model parameters and associated ancestral states. The reconstructions of ancestral character states in Brachytheciastrum reveal ram-
Keyphrases
moss genus brachytheciastrum phylogenetic uncertainty bayesian sample ancestral state model parameter ancestral character state systematic biology ancestral character state reconstruction trait evolution ml model optimization single set speciation event wherein branch length satis-factorily way discrete mor-phological character posterior probability wherein change bayesian approach brachytheciastrum reveal ram genetic distance specie trait two-rate model likely tree model selection single-tree approach substantial part likelihood-ratio test associated ancestral state ancestral character state reconstruction offer
