Inferring Branch-Specific Rates of Lineage Diversification Under the Birth-Death-Shift Process

Area of Science:

• Evolutionary Biology
• Phylogenetics
• Computational Biology

Background:

• Estimating speciation and extinction rates is crucial for understanding biodiversity.
• Existing models often struggle to account for rate variations across all lineages (extant, extinct, and unsampled).

Purpose of the Study:

• To introduce a novel stochastic-diversification model, the birth-death-shift (BDS) process.
• To develop a Bayesian framework for estimating lineage-specific diversification rates, accommodating rate shifts.

Main Methods:

• Developed the birth-death-shift (BDS) process model.
• Employed a Bayesian statistical framework for parameter estimation using phylogenies of extant lineages.
• Validated the model using simulation studies and applied it to a primate dataset.

Main Results:

• The BDS process effectively estimates diversification rates that vary across extant, extinct, and unsampled lineages.
• Branch-specific diversification rate estimates were robust to prior assumptions regarding the number of rate shifts.
• The model implementation in RevBayes offers a statistically coherent approach.

Conclusions:

• The BDS process provides a flexible and statistically sound method for inferring complex diversification dynamics.
• This approach enhances our ability to study evolutionary history and biodiversity patterns.
• The model is a valuable tool for evolutionary biologists analyzing phylogenetic data.