Placental mammal diversification and the Cretaceous–Tertiary boundary

TLDR: The largest available molecular data set for placental mammals is investigated, which includes segments of 19 nuclear and three mitochondrial genes for representatives of all extant placental orders and permits simultaneous constraints from the fossil record and allows rates of molecular evolution to vary on different branches of a phylogenetic tree.

Abstract: Competing hypotheses for the timing of the placental mammal radiation focus on whether extant placental orders originated and diversified before or after the Cretaceous-Tertiary (K/T) boundary. Molecular studies that have addressed this issue suffer from single calibration points, unwarranted assumptions about the molecular clock, and/or taxon sampling that lacks representatives of all placental orders. We investigated this problem using the largest available molecular data set for placental mammals, which includes segments of 19 nuclear and three mitochondrial genes for representatives of all extant placental orders. We used the Thorne/Kishino method, which permits simultaneous constraints from the fossil record and allows rates of molecular evolution to vary on different branches of a phylogenetic tree. Analyses that used different sets of fossil constraints, different priors for the base of Placentalia, and different data partitions all support interordinal divergences in the Cretaceous followed by intraordinal diversification mostly after the K/T boundary. Four placental orders show intraordinal diversification that predates the K/T boundary, but only by an average of 10 million years. In contrast to some molecular studies that date the rat–mouse split as old as 46 million years, our results show improved agreement with the fossil record and place this split at 16–23 million years. To test the hypothesis that molecular estimates of Cretaceous divergence times are an artifact of increased body size subsequent to the K/T boundary, we also performed analyses with a “K/T body size” taxon set. In these analyses, interordinal splits remained in the Cretaceous.