A model with many small shifts for estimating species-specific diversification rates

Area of Science:

• Evolutionary Biology
• Phylogenetics
• Biodiversity Science

Background:

• Understanding biodiversity requires analyzing diversification rate variations across evolutionary history.
• Previous phylogenetic methods focused on major shifts, potentially overlooking smaller, frequent rate changes.

Purpose of the Study:

• To develop and validate a new Bayesian approach (ClaDS) for estimating branch-specific diversification rates.
• To investigate the contribution of small versus large shifts to diversification rate heterogeneity in birds.

Main Methods:

• Developed ClaDS, a Bayesian method modeling diversification rate changes at each speciation event.
• Validated ClaDS performance using Monte Carlo simulations for inferring rate changes.
• Applied ClaDS to avian phylogenies to analyze diversification rates across the entire bird radiation.

Main Results:

• ClaDS accurately infers both small and large diversification rate changes.
• Diversification rates are highly heterogeneous within evolutionarily restricted avian groups.
• Intraclade variation accounts for 76% of branch-specific rate variation in birds, indicating numerous small shifts.

Conclusions:

• Biodiversity patterns are shaped by frequent, smaller diversification rate shifts rather than rare, large ones.
• The ClaDS method provides a powerful tool for dissecting diversification dynamics.
• Intraclade variation is a major driver of evolutionary diversification in birds.