Binary-state speciation and extinction method is conditionally robust to realistic violations of its assumptions

Area of Science:

• Evolutionary Biology
• Phylogenetics
• Computational Biology

Background:

• Phylogenetic comparative methods test evolutionary hypotheses without extensive fossil records.
• These methods often assume stable or increasing clade diversity, which is not always accurate.
• The Binary State Speciation and Extinction (BiSSE) model is a common tool for analyzing diversification rates.

Purpose of the Study:

• To evaluate the accuracy of the BiSSE method in detecting diversification rate differences under declining diversity.
• To assess BiSSE's performance when speciation rates decline below extinction rates, leading to richness loss.
• To test BiSSE's ability to detect symmetric and asymmetric speciation rates in simulated clades.

Main Methods:

• Simulated hypothetical clades with varying diversification rate trajectories.
• Included scenarios with declining positive net diversification rates.
• Simulated scenarios where speciation rates fall below extinction rates.
• Analyzed both symmetric and asymmetric speciation rate simulations.

Main Results:

• BiSSE models fit well for neutral characters when net diversification rates remain positive.
• When net diversification becomes negative, BiSSE may incorrectly favor non-neutral character models.
• BiSSE's accuracy in detecting speciation rate asymmetry improves with clade age, even in declining clades.

Conclusions:

• BiSSE is most reliable for clades of intermediate age, before diversity decline.
• Using BiSSE on older, declining clades risks inferring false evolutionary rate differences.
• Caution is needed when inferring past diversification patterns for extant groups that have declined in diversity, especially without fossil data.