The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation

Area of Science:

• Evolutionary Biology
• Molecular Phylogenetics
• Eukaryotic Diversity

Background:

• Establishing the evolutionary relationships and divergence times of major eukaryotic lineages is a long-standing challenge in evolutionary biology.
• Early ribosomal RNA (rRNA) gene phylogenies suggested complexity evolved early, but later analyses revealed artifacts in these trees.
• Current understanding, based on multiple genes, suggests six major eukaryotic groups, but their interrelationships and divergence timing remain uncertain.

Purpose of the Study:

• To re-analyze existing molecular clock datasets to assess the reliability of estimated eukaryotic divergence times.
• To identify sources of error in molecular dating and their impact on confidence intervals for divergence dates.
• To outline requirements for more accurate dating of early eukaryotic evolution.

Main Methods:

• Re-analysis of datasets from published molecular clock studies.
• Systematic evaluation of error sources in molecular divergence time estimation, including calibration fossils, tree topology, substitution models, and rate variation.
• Assessment of the impact of these errors on confidence intervals and the variability of estimated dates.

Main Results:

• When various error sources are properly accounted for, confidence intervals on inferred eukaryotic divergence dates become very large.
• Estimated divergence dates vary significantly depending on the specific methods and assumptions employed in molecular clock analyses.
• The reliability of current molecular clock estimates for deep eukaryotic divergences is limited by numerous potential biases.

Conclusions:

• Accurate dating of major eukaryotic lineage divergences requires a robust phylogenetic tree and improved calibration points.
• More sophisticated relaxed molecular clock methods and broader gene sampling across microbial eukaryotes are essential.
• A richer Proterozoic fossil record of microbial eukaryotes is crucial for reliable calibration of molecular clocks.