Effects of Models of Rate Evolution on Estimation of Divergence Dates with Special Reference to the Metazoan 18S Ribosomal RNA Phylogeny

Abstract

The molecular clock, i.e., constancy of the rate of evolution over time, is commonly assumed in estimating divergence dates. However, this assumption is often violated and has drastic effects on date estimation. Recently, a number of attempts have been made to relax the clock assumption. One approach is to use maximum likelihood, which assigns rates to branches and allows the estimation of both rates and times. An alternative is the Bayes approach, which models the change of the rate over time. A number of models of rate change have been proposed. We have extended and evaluated models of rate evolution, i.e., the lognormal and its recent variant, along with the gamma, the exponential, and the Ornstein-Uhlenbeck processes. These models were first applied to a small hominoid data set, where an empirical Bayes approach was used to estimate the hyperparameters that measure the amount of rate variation. Estimation of divergence times was sensitive to these hyperparameters, especially when the assumed model is close to the clock assumption. The rate and date estimates varied little from model to model, although the posterior Bayes factor indicated the Ornstein-Uhlenbeck process outperformed the other models. To demonstrate the importance of allowing for rate change across lineages, this general approach was used to analyze a larger data set consisting of the 18S ribosomal RNA gene of 39 metazoan species. We obtained date estimates consistent with paleontological records, the deepest split within the group being about 560 million years ago. Estimates of the rates were in accordance with the Cambrian explosion hypothesis and suggested some more recent lineage-specific bursts of evolution.

Estimating metazoan divergence times with a molecular clock

“…3 and 4) have suggested that the last common ancestor of bilaterians (LCB) lived well over one billion years ago (5, 6), whereas others suggest that LCB arose Ϸ900 million years ago (Ma) (e.g., refs. 7-10), and still others are more consistent with an origination closer to the Cambrian (11)(12)(13). These deep estimates for the origin of LCB raise the question of how hundreds of millions of years of bilaterian evolution can escape detection, given that LCB and its near relatives should have had the capability of leaving both body and trace fossils (14)(15)(16).…”

Post-Miocene expansion, colonization, and host switching drove speciation among extant nematodes of the archaic genus Trichinella

“…These values are substantially less than the ML distance (0.2) separating Trichuris muris from Trichuris suis. If the locus evolved in each lineage at Ϸ0.4 ϫ 10 Ϫ9 per site per year (4% over 100 MY), which typifies many metazoan phyla (9), then extant species of Trichinella shared a common ancestor Ϸ16 million years (MY) ago, and encapsulated taxa first began diversifying within the last 9 MY (Table 2). Only by postulating an implausible 18-fold rate decrease in divergence rate could the extant diversity among Trichinella species date to the origins of distinct tetrapod host groups that occurred some 300 MY B.P.…”

“…Several approaches were considered for each data set to derive a temporal range. For SSU rDNA, a per-lineage calibration rate of 0.4 ϫ 10 Ϫ9 per site per year was assumed based on data generally supported for metazoan phyla (9). For mtDNA, data …”

Placing confidence limits on the molecular age of the human–chimpanzee divergence

“…[In the random rate case, the rate at each branch is randomly selected from a uniform distribution of rates so as to introduce a Ϯ40% random noise in evolutionary rate independently for each gene. In the correlated rate, the assignment of lineage-specific rate uses a stationary lognormal distribution in which the rates vary from branch to branch as a random walk for a given gene, so that rates drift up or down along the branches of any lineage (42,43). See Supporting Text.]…”