Conifer Molecular Phylogeny Analysis with Mass-Extinction Detection

A Bayesian method for detecting mass-extinction impacts on molecular phylogenies, developed by Michael R. May and published in 2020. The CoMET model analyzes lineage diversification rates using a compound Poisson process to distinguish background rate variation from extinction events. An empirical application identified a major mass-extinction event in conifers approximately 23 million years ago.

Use Cases

• Apply the CoMET model to molecular phylogenies to detect tree-wide mass-extinction events using event-specific prior distributions.
• Estimate the timing of mass-extinction events from phylogenies in the presence of background speciation and extinction rate variation.
• Distinguish between tree-wide shifts in speciation rate and extinction rate using the Bayesian reversible-jump MCMC algorithm.
• Simulate phylogenies under the episodic stochastic-branching process model to validate the detection power for mass-extinction events.

Strengths

• Method validated via simulation with appropriate (<5%) false-discovery rate for event detection.
• Empirical demonstration provides a specific finding: a conifer mass-extinction event ≈23 Ma.
• Model incorporates three distinct event types: speciation shifts, extinction shifts, and mass extinctions.

Limitations

• Method performance is contingent on the biologically informed priors specified for mass-extinction magnitude.
• The empirical analysis is focused on a single group (conifers), limiting generalizability to other lineages without further study.
• Input data specifics like file formats, sample data, and phylogeny size are not provided.

Provenance

Source

Michael R. May via Dryad

Collection Method

Novel Bayesian statistical framework (CoMET model) applied to molecular phylogenies.

Time Range

Analysis includes an event dated to approximately 23 million years ago.

Freshness

2020-06-24