Estimating metazoan divergence times with a molecular clock

TLDR

Accurately dating the origin of bilaterally symmetrical animals is essential for understanding early animal evolution, yet fossil evidence places the earliest bilaterians at ~555 Ma while vertebrate–dipteran molecular clocks suggest a 900 Ma split, highlighting a significant rate disparity between vertebrates and invertebrates. The authors used a concatenated alignment of seven amino‑acid genes from 23 bilaterian taxa, anchored by 11 invertebrate calibration points, to estimate the last common ancestor of bilaterians at 573–656 Ma, contingent on the rate‑heterogeneity scaling parameter. They found that dipteran evolutionary rates match other invertebrates but are higher than vertebrates, and that the estimated bilaterian ancestor age of 573–656 Ma aligns with the fossil record, supporting the idea that the Cambrian explosion partly reflects bilaterian diversification.

Abstract

Accurately dating when the first bilaterally symmetrical animals arose is crucial to our understanding of early animal evolution. The earliest unequivocally bilaterian fossils are approximately 555 million years old. In contrast, molecular-clock analyses calibrated by using the fossil record of vertebrates estimate that vertebrates split from dipterans (Drosophila) approximately 900 million years ago (Ma). Nonetheless, comparative genomic analyses suggest that a significant rate difference exists between vertebrates and dipterans, because the percentage difference between the genomes of mosquito and fly is greater than between fish and mouse, even though the vertebrate divergence is almost twice that of the dipteran. Here we show that the dipteran rate of molecular evolution is similar to other invertebrate taxa (echinoderms and bivalve molluscs) but not to vertebrates, which significantly decreased their rate of molecular evolution with respect to invertebrates. Using a data set consisting of the concatenation of seven different amino acid sequences from 23 ingroup taxa (giving a total of 11 different invertebrate calibration points scattered throughout the bilaterian tree and across the Phanerozoic), we estimate that the last common ancestor of bilaterians arose somewhere between 573 and 656 Ma, depending on the value assigned to the parameter scaling molecular substitution rate heterogeneity. These results are in accord with the known fossil record and support the view that the Cambrian explosion reflects, in part, the diversification of bilaterian phyla.