Dating Primate Divergences through an Integrated Analysis of Palaeontological and Molecular Data

Abstract

Estimation of divergence times is usually done using either the fossil record or sequence data from modern species. We provide an integrated analysis of palaeontological and molecular data to give estimates of primate divergence times that utilize both sources of information. The number of preserved primate species discovered in the fossil record, along with their geological age distribution, is combined with the number of extant primate species to provide initial estimates of the primate and anthropoid divergence times. This is done by using a stochastic forwards-modeling approach where speciation and fossil preservation and discovery are simulated forward in time. We use the posterior distribution from the fossil analysis as a prior distribution on node ages in a molecular analysis. Sequence data from two genomic regions (CFTR on human chromosome 7 and the CYP7A1 region on chromosome 8) from 15 primate species are used with the birth-death model implemented in mcmctree in PAML to infer the posterior distribution of the ages of 14 nodes in the primate tree. We find that these age estimates are older than previously reported dates for all but one of these nodes. To perform the inference, a new approximate Bayesian computation (ABC) algorithm is introduced, where the structure of the model can be exploited in an ABC-within-Gibbs algorithm to provide a more efficient analysis.

Conceptual issues in Bayesian divergence time estimation

“…I will also assume that the fossils are direct ancestors that can be assigned to lineages [2,10]. Newer methods [4,5,8,9] allow fossils to be on 'side-branches' which makes the problem more complex but potentially avoids the conflicts between tree topology and calibration priors as outlined below.…”

Primate origins, human origins, and the end of higher taxa

“…Most molecular-clock estimates point to a date of around 85 million years ago for the ancestral euprimate node. [80][81][82] This is some 35 million years before the first appearance of euprimates in the fossil record. Although the validity of these estimates is debated, 83 the surprising recent discovery of a mid-Jurassic placental mammal 84 suggests that the molecular divergence dates may be closer to the truth than the current paleontological estimates.…”

A radiation of arboreal basal eutherian mammals beginning in the Late Cretaceous of India

“…These ancient molecular divergence age estimates and the absence of Cretaceous placentals can be reconciled by proposing that the first 20 to 40 Myr (or 25-50%) of this group's fossil record is missing entirely. A few recent studies using statistical models that incorporate gaps in the fossil record to estimate divergence times, either from fossil occurrences alone or combined with molecular data, have produced results more similar to molecular clock dates (81-88 Mya) for the origin of Primates (4,5), but other quantitative analyses based on the fossil record dispute these early divergence estimates (6)(7)(8). At least 70 species of eutherians (the clade including placentals and their stem relatives) are known from the Late Cretaceous of Laurasia (North America, Europe, and Asia) (9), and although a few have been suggested as possible placentals [e.g., Protungulatum (10)], none are unequivocally supported as a Cretaceous placental mammal (2).…”