Primate Phylogenetic Data for Speciation Duration Estimation

Simulated and primate phylogenetic data support a study estimating speciation duration using a protracted birth-death model. The work implements a likelihood method from Lambert et al. (2014) to estimate parameters like speciation-initiation rate and extinction rate. The author, Rampal S. Etienne, applied the approach to a primate phylogeny and validated estimates with simulations.

Use Cases

• Fit the protracted birth-death model to phylogenetic branching times to estimate the rate of completion of speciation.
• Use simulated phylogenies of extant species to assess bias in estimates of the speciation-initiation rate and the extinction rate.
• Calculate the duration of speciation for a primate clade by combining estimated model parameters.
• Validate the implemented likelihood method by comparing estimated durations of speciation from simulations against known values.

Strengths

• Data underpins a peer-reviewed methodological implementation for the protracted speciation model.
• Includes application to a real primate phylogeny, enabling empirical validation.
• Simulated phylogenies allow for direct assessment of parameter estimation bias.

Limitations

• The primate phylogeny is a single clade, limiting generalizability to other taxonomic groups.
• Simulation results indicate phylogenies often lack information for unbiased estimates of certain parameters like speciation-initiation rate.
• The core data (phylogenetic branching times) is not explicitly provided in the input, requiring user acquisition.

Provenance

Source

Rampal S. Etienne

Collection Method

Likelihood computation on phylogenetic branching times under a protracted birth-death model, applied to simulated and primate phylogenies.

Freshness

Last updated on 2020-06-24.