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.

FIGURE 1.

Marginal posterior distributions for the primate (t₁) and anthropoid (t₂) divergence times. Results are shown for 3 modeling scenarios. Dates are in units of millions of years.

FIGURE 2.

Rooted tree showing mean estimates of node ages t₁,…,t₁₄ obtained when using the Poisson sampling model to provide prior distributions for the t₁ and t₂ node ages. The numbers in parentheses after the species name indicate that the sequence for that species is only available at that locus. Species without labels have data for both loci.

FIGURE 3.

Figure showing the posterior date estimates of 7 nodes in the primate phylogeny (see Table 4). For each node, 5 different estimates are shown, depending on which prior distribution was used in the molecular analysis. In order (from top to bottom), they are the estimates from the Poisson, K-T, binomial, gamma, and bounds models. The white hatch shows the posterior mean age estimate, and the black box shows posterior 95% CI. For the primate (t₁) and anthropoid (t₂) divergences, the 95% CI from the fossil calibrations are shown as grey lines. The arrowheads show estimates taken from the literature (gray arrowhead, Steiper and Young 2009 and black arrowhead, Steiper and Young 2006). The node labels correspond to those given in Table 4.

FIGURE 4.

Infinite site plot. Posterior 95% CI width against posterior means of node ages for the Poisson sampling model.