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Abstract
BackgroundMolecular clock methodologies allow for the estimation of divergence times across a variety of organisms; this can be particularly useful for groups lacking robust fossil histories, such as microbial eukaryotes with few distinguishing morphological traits. Here we have used a Bayesian molecular clock method under three distinct clock models to estimate divergence times within oomycetes, a group of fungal-like eukaryotes that are ubiquitous in the environment and include a number of devastating pathogenic species. The earliest fossil evidence for oomycetes comes from the Lower Devonian (~400 Ma), however the taxonomic affinities of these fossils are unclear.ResultsComplete genome sequences were used to identify orthologous proteins among oomycetes, diatoms, and a brown alga, with a focus on conserved regulators of gene expression such as DNA and histone modifiers and transcription factors. Our molecular clock estimates place the origin of oomycetes by at least the mid-Paleozoic (~430-400 Ma), with the divergence between two major lineages, the peronosporaleans and saprolegnialeans, in the early Mesozoic (~225-190 Ma). Divergence times estimated under the three clock models were similar, although only the strict and random local clock models produced reliable estimates for most parameters.ConclusionsOur molecular timescale suggests that modern pathogenic oomycetes diverged well after the origin of their respective hosts, indicating that environmental conditions or perhaps horizontal gene transfer events, rather than host availability, may have driven lineage diversification. Our findings also suggest that the last common ancestor of oomycetes possessed a full complement of eukaryotic regulatory proteins, including those involved in histone modification, RNA interference, and tRNA and rRNA methylation; interestingly no match to canonical DNA methyltransferases could be identified in the oomycete genomes studied here.
Highlights
Molecular clock methodologies allow for the estimation of divergence times across a variety of organisms; this can be useful for groups lacking robust fossil histories, such as microbial eukaryotes with few distinguishing morphological traits
Bayesian relaxed clock methods allow rates to vary among lineages but assume autocorrelation by drawing the rate of a descendent branch from a distribution whose mean is determined by the rate of the parent branch [7,8]; other Bayesian methods relax this assumption of autocorrelation for the co-estimation of phylogeny and divergence times [9]
A total of 70 genes involved in the regulation of gene expression were examined for homology in Phytophthora infestans (Table 2); homologs of two genes (Drosha-like; TFIIH, Ssl1 subunit) could not be identified in P. infestans but were present in other oomycetes
Summary
Molecular clock methodologies allow for the estimation of divergence times across a variety of organisms; this can be useful for groups lacking robust fossil histories, such as microbial eukaryotes with few distinguishing morphological traits. We have used a Bayesian molecular clock method under three distinct clock models to estimate divergence times within oomycetes, a group of fungal-like eukaryotes that are ubiquitous in the environment and include a number of devastating pathogenic species. Bayesian relaxed clock methods allow rates to vary among lineages but assume autocorrelation by drawing the rate of a descendent branch from a distribution whose mean is determined by the rate of the parent branch [7,8]; other Bayesian methods relax this assumption of autocorrelation for the co-estimation of phylogeny and divergence times [9]. A random local clock model approach has been proposed which allows rate changes to occur along any branch in a phylogeny; this method allows users to directly test various local clock scenarios against a strict clock model of no rate changes [10]
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