SERB, J.M.; OAKLEY, T.H.; Univ. of California, Santa Barbara; Univ. of California, Santa Barbara: Reconciled phylogenetic trees as an emerging analytical framework for evolutionary developmental biology

The field of evolutionary developmental biology has been criticized for its lack of an explicit unifying analytical framework. We suggest that such a framework may exist in the form of a methodology called �reconciled trees,� an analytical approach that can be applied to the diverse disciplines of molecular evolution, parasitology, and biogeography (Page 1993; Page & Charleston 1997, 1998). �Reconciled trees� involves explicit numerical methods for comparing the historical associations between two or more evolutionary lineages: genes within species, parasites within hosts, or species within biogeographic areas. Analysis of these associations through the comparison of phylogenetic topologies provides specific hypotheses to explain incongruence between topologies, and may include evolutionary processes such as horizontal transfer events, gene duplications or extinctions (lineage loss) each which have a specific �cost� set by the user. Here we suggest that the generalized approach of �reconciled trees� can be extended beyond its current use to quantitatively examine historical associations of interest in evo-devo, namely morphological structures within species (Geeta 2003; Oakley 2003) and cell types within species (Arendt 2003). We examined the usefulness of this approach by comparing historical associations between retinal cell types and representative vertebrate species. Seven major retinal cell types were scored for morphological and gene expression characters, analyzed phylogenetically, and �reconciled� with both species and gene trees.