Bayesian relaxed clock estimation of divergence times in foraminifera

Area of Science:

• Evolutionary Biology
• Paleontology
• Molecular Phylogenetics

Background:

• Accurate divergence time estimation is crucial for understanding early eukaryotic speciation dynamics, particularly during the Neo-Proterozoic era.
• Deep divergences are challenging to date due to molecular clock violations and uncertainties in fossil calibrations.
• Foraminifera, unicellular eukaryotes with an excellent fossil record, exhibit high genomic evolutionary rates, complicating divergence dating.

Purpose of the Study:

• To estimate divergence times for Foraminifera using advanced Bayesian molecular dating techniques.
• To reconstruct the phylogeny of Foraminifera and identify major radiation events.
• To assess the robustness of divergence time estimates to prior specifications and evolutionary rate variations.

Main Methods:

• Utilized a Bayesian method incorporating relaxed molecular clock models and multiple flexible fossil calibrations.
• Reconstructed Foraminifera phylogeny using multigene data.
• Employed partitioned Bayesian analysis to accommodate rate heterogeneity among data partitions.

Main Results:

• Foraminifera are estimated to have emerged during the Cryogenian period (650-920 Ma), with a mean origin around 770 Ma, significantly earlier than their first fossil appearance (545 Ma).
• Estimated divergence times for foraminiferal orders generally suggest earlier origins than indicated by the fossil record.
• Posterior time estimates demonstrated robustness to prior specifications, and inter-species variations in evolutionary rates were partially mitigated by the methods used.

Conclusions:

• Bayesian molecular dating with relaxed molecular clocks provides reliable estimates for deep divergences, even with rate heterogeneity and fossil uncertainties.
• The findings suggest an earlier origin for Foraminifera and their major diversification events than previously established.
• Further research incorporating more coding genes is recommended for enhanced precision and resolution of discrepancies between molecular and fossil-based dates.