Inferring species trees from gene trees: a phylogenetic analysis of the Elapidae (Serpentes) based on the amino acid sequences of venom proteins.

Toward the goal of recovering the phylogenetic relationships among elapid snakes, we separately found the shortest trees from the amino acid sequences for the venom proteins phospholipase A2 and the short neurotoxin, collectively representing 32 species in 16 genera. We then applied a method we term gene tree parsimony for inferring species trees from gene trees that works by finding the species tree which minimizes the number of deep coalescences or gene duplications plus unsampled sequences necessary to fit each gene tree to the species tree. This procedure, which is both logical and generally applicable, avoids many of the problems of previous approaches for inferring species trees from gene trees. The results support a division of the elapids examined into sister groups of the Australian and marine (laticaudines and hydrophiines) species, and the African and Asian species. Within the former clade, the sea snakes are shown to be diphyletic, with the laticaudines and hydrophiines having separate origins. This finding is corroborated by previous studies, which provide support for the usefulness of gene tree parsimony.