Combined phylogeny of ray-finned fishes (Actinopterygii) and the use of morphological characters in large-scale analyses.

This study evaluates the phylogeny of ray-finned fishes (Actinopterygii) combining most available information (44 markers from nuclear and mitochondrial DNA and 274 morphological characters). The molecular partition of the dataset was produced through a pipeline (GB-to-TNT) that allows the fast building of large matrices from GenBank format. The analysed dataset has 8104 species, including representatives of all orders and 95% of the 475 families of Actinopterygii, making it the most diverse phylogenetic dataset analysed to date for this clade of fishes. Analysed morphological characters are features historically considered diagnostic for families or orders, which can be unequivocally coded from the literature. Analyses are by parsimony under several weighting schemes. General results agree with previous classifications, especially for groups with better gene sampling and those long thought (from morphological evidence) to be monophyletic. Many clades have low support and some orders are not recovered as monophyletic. Additional data and synthetic studies of homology are needed to obtain synapomorphies and diagnoses for most clades.