Congruence test of molecular clock calibration hypotheses based on Bayes factor comparisons

Abstract

Molecular clock calibration is a crucial step for placing phylogenetic trees in the temporal framework required to test evolutionary hypotheses and estimate evolutionary rates. In general, most authors agree that the best approach is to incorporate multiple calibrations to avoid the risk of bias associated with a single dating source. However, the indiscriminate inclusion of as many calibration points as possible can lead to tree shape distortion and an overestimation of the variation in evolutionary rates among branches due to errors in the geological, paleontological or paleogeographic information used for dating. We present a test of congruence among calibration hypotheses to assist their filtering prior to molecular clock analysis, which we have called Bayes Factor Cluster Analysis (BFCA). This is a heuristic method based on the comparison of pairwise calibrations hypotheses by Bayes factors that allows identifying sets of congruent calibrations. We have tested BFCA through simulation using beast and mcmctree programs and analysed a real case of multiple calibration hypotheses to date the evolution of the genus Carabus (Coleoptera: Carabidae). The analyses of simulated data showed the predictability of change in Bayes factors when comparing alternative calibration hypotheses on a particular tree topology, and thus the suitability of BFCA in identifying unreliable calibrations, especially in cases with limited variation in evolutionary rates among branches. The exclusion of inconsistent calibrations as identified by BFCA produced significant changes in the estimation of divergence times and evolutionary rates in the genus Carabus, illustrating the importance of filtering calibrations before analyses. The method has been implemented in an open-source R package called bfca to simplify its application. © 2013 British Ecological Society.