Estimating Divergence Dates and Substitution Rates in the Drosophila Phylogeny

Abstract

An absolute timescale for evolution is essential if we are to associate evolutionary phenomena, such as adaptation or speciation, with potential causes, such as geological activity or climatic change. Timescales in most phylogenetic studies use geologically dated fossils or phylogeographic events as calibration points, but more recently, it has also become possible to use experimentally derived estimates of the mutation rate as a proxy for substitution rates. The large radiation of drosophilid taxa endemic to the Hawaiian islands has provided multiple calibration points for the Drosophila phylogeny, thanks to the "conveyor belt" process by which this archipelago forms and is colonized by species. However, published date estimates for key nodes in the Drosophila phylogeny vary widely, and many are based on simplistic models of colonization and coalescence or on estimates of island age that are not current. In this study, we use new sequence data from seven species of Hawaiian Drosophila to examine a range of explicit coalescent models and estimate substitution rates. We use these rates, along with a published experimentally determined mutation rate, to date key events in drosophilid evolution. Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25–40 Ma) is closer to being compatible with independent fossil-derived dates (20–50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty. We find that Hawaiian-calibrated dates are extremely sensitive to model choice and give rise to point estimates that range between 26 and 192 Ma, depending on the details of the model. Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates. As either source of error will bias estimates of divergence time, we suggest mutation rate estimates be used until better models are available.

Genome comparisons indicate recent transfer ofwRi‐likeWolbachiabetween sister speciesDrosophila suzukiiandD. subpulchrella

“…Using the Obbard et al. (2012) summary of available estimates for D. melanogaster and D. simulans divergence and our relative chronogram for D. subpulchrella and D. suzukii (Fig. 2c), we infer divergence times for D. subpulchrella and D. suzukii ranging from about 1 to 9 million years, two orders of magnitude larger than our estimates for w Suz versus w Spc.…”

“…(2012), who inferred that Wolbachia substitution rates were roughly 10‐fold lower than the noncoding nuclear mutation rate for D. melanogaster , which is often considered a reasonable approximation for the rate of third‐position substitutions (at least for fourfold degenerate sites, Obbard et al. 2012). This is clearly inconsistent with the three‐order‐of‐magnitude difference we estimate (Table 3).…”

“…Using our k s from Table 1 with the Nasonia calibration, the estimated divergence for w Suz and w Spc is 6,400 years, which is consistent with our Drosophila calibration. These analyses suggest that w Suz and w Spc diverged on the order of 1,000–10,000 years ago, orders of magnitude shorter than typical time scales for Drosophila speciation (10 5 –10 6  years, Coyne & Orr, 2004, p. 75; Obbard et al., 2012). Molecular estimates of Drosophila divergence times generally depend on speculative inferences from the phylogeography of the Hawaiian Drosophila radiation (Obbard et al., 2012).…”

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

“…A number of other estimates on the divergence time between subgenus Sophophora and subgenus Drosophila can be found in the literature (e.g. 63 Mya, Gao, Hu, Toda, Katoh & Tamura, 2011; and 25–40 Mya, Obbard et al., 2012; 40 Mya, Russo, Takezaki & Nei, 1995). However, the same plateau feature could still be observed using these other estimates, suggesting it was underpinned mainly by the expression variances among the species pairs (i.e.…”

Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification

“…In order to investigate the evolution of H3K27me3 patterns across the genome, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) for H3K27me3 in four species, D. melanogaster, D. simulans, D. yakuba, and D. pseudoobscura, with divergence times ranging from less than 5 million years (Myr) to more than 35 Myr (Tamura et al 2004;Obbard et al 2012). To determine whether and how H3K27me3 changes might alter gene expression, we also performed RNA sequencing (RNAseq) in all species.…”