Phylogenetic Data for Diversification Rate Analysis with Fossils

A dataset supporting the inference of speciation and extinction rate variation using the fossilized birth-death process. It includes phylogenies for both extant and extinct species, implemented and tested within the BAMM computational framework. The data was authored by Jonathan S. Mitchell and last updated in June 2020.

Use Cases

• Apply the fossilized birth-death process model to phylogenies containing both extant and extinct taxa to estimate extinction rates.
• Use the BAMM framework with reversible jump Markov chain Monte Carlo to simulate posterior distributions of macroevolutionary rate regimes from branching times and tree topology.
• Evaluate model performance on phylogenies simulated under various diversification scenarios to test inference reliability.
• Assess the impact of including fossil observations on the accuracy of extinction rate estimates compared to analyses using only living species.

Strengths

• Data is derived from a peer-reviewed methodological framework for macroevolutionary analysis published in 2020.
• Specifically designed to handle phylogenies that include both extant and extinct species, addressing a known limitation in the field.
• The associated model implementation has been tested for robustness against certain violations like heterogeneity in preservation rates.

Limitations

• The specific size, row count, column structure, and file formats of the dataset are unknown from the provided input.
• As a methodological dataset from 2020, it may not incorporate the most recent fossil discoveries or phylogenetic methods.
• Potential limitations in model assumptions, such as the specified number of fossil occurrences, could affect inferences as noted in the source description.

Provenance

Source

Dryad digital repository.

Collection Method

Generated through simulation and analysis using the BAMM computational framework for macroevolutionary study.

Freshness

Last updated on 2020-06-30.