A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models.

Area of Science:

• Evolutionary Biology
• Molecular Phylogenetics
• Genomics

Background:

• Molecular clock methods estimate divergence times, crucial for organisms lacking clear fossil records like microbial eukaryotes.
• Oomycetes are fungal-like eukaryotes, vital in ecosystems and including significant plant pathogens.
• Existing oomycete fossil evidence is scarce and taxonomically ambiguous.

Purpose of the Study:

• To estimate divergence times within oomycetes using Bayesian molecular clock methods.
• To investigate the evolutionary history of oomycetes, particularly pathogenic lineages.
• To compare divergence estimates across three distinct molecular clock models.

Main Methods:

• Utilized complete genome sequences of oomycetes, diatoms, and a brown alga.
• Focused on conserved gene expression regulators, including DNA/histone modifiers and transcription factors.
• Applied Bayesian molecular clock analysis with three different clock models.

Main Results:

• Oomycete origins are estimated in the mid-Paleozoic (~430-400 Ma).
• Divergence between major oomycete lineages (peronosporaleans and saprolegnialeans) occurred in the early Mesozoic (~225-190 Ma).
• Strict and random local clock models provided more reliable divergence time estimates.

Conclusions:

• Modern pathogenic oomycetes evolved after their hosts, suggesting environmental factors or horizontal gene transfer drove diversification.
• The oomycete last common ancestor had diverse eukaryotic regulatory proteins, including histone modifiers.
• Canonical DNA methyltransferases were notably absent in the studied oomycete genomes.