Reconstructing ancestral ecologies: challenges and possible solutions

There are several ways to extract information about the evolutionary ecology of clades from their phylogenies. Of these, character state optimization and 'ancestor reconstruction' are perhaps the most widely used despite their being fraught with assumptions and potential pitfalls. Requirements for robust inferences of ancestral traits in general (i.e. those applicable to all types of characters) include accurate and robust phylogenetic hypotheses, complete species-level sampling and the appropriate choice of optimality criterion. Ecological characters, however, also require careful consideration of methods for accounting for intraspecific variability. Such methods include 'Presence Coding' and 'Polymorphism Coding' for discrete ecological characters, and 'Range Coding' and 'MaxMin Coding' for continuously variable characters. Ultimately, however, historical inferences such as these are, as with phylogenetic inference itself, associated with a degree of uncertainty. Statistically based uncertainty estimates are available within the context of model-based inference (e.g. maximum likelihood and Bayesian); however, these measures are only as reliable as the chosen model is appropriate. Although generally thought to preclude the possibility of measuring relative uncertainty or support for alternative possible reconstructions, certain useful non-statistical support measures (i.e. 'Sharkey support' and 'Parsimony support') are applicable to parsimony reconstructions.