Phylogenetic inference and divergence dating of snakes using molecules, morphology and fossils: New insights into convergent evolution of feeding morphology and limb reduction

Abstract

Bayesian divergence time analyses were used to simultaneously infer the phylogenetic relationships and date the major clades of snakes including several important fossils that have not previously been included in divergence dating analyses as terminal taxa. We also explored the effect of using fossilized birth-death (FBD) and uniform tree priors for divergence dating with terminal calibrations. Nonclock and relaxed clock analyses of the combined morphology and molecular data set supported previous molecular phylogenetic hypotheses for the major clades of snakes, including the paraphyly of the traditionally recognized Scolecophidia and Macrostomata. Tip-dating analyses using either a uniform tree prior or FBD prior that assume that all fossils are tips and that extant lineages are randomly sampled resulted in older ages than those inferred using a FBD prior assuming diversified sampling of extant lineages and those estimated by previous studies. We used Bayesian ancestral state reconstruction methods to map the evolution of the ability to consume large prey and the loss of limbs onto our inferred time-calibrated phylogeny. We found strong support for early evolution of the ability to consume large prey, indicating multiple independent losses of this ability. We also found strong support for retention of external hindlimbs until relatively late in snake evolution, indicating multiple independent losses of hindlimbs.