Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions

TL;DR

This paper evaluates methods for detecting diversification patterns in species, considering both lineage-specific rate shifts and mass extinctions, highlighting their performance and limitations through simulation studies.

Contribution

It compares the effectiveness of existing methods in complex scenarios involving both rate shifts and mass extinctions, revealing their strengths and weaknesses.

Findings

Lineage shifts are more reliably detected than mass extinctions.

Methods tend to over-predict events as scenario complexity increases.

Current methods have good overall performance but need improvement for complex scenarios.

Abstract

Recent methodological advances are enabling better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing frameworks to model this diversity either focus on changes between lineages, neglecting global effects such as mass extinctions, or focus on changes over time which would affect all lineages. Yet it seems probable that both lineages differences and mass extinctions affect the same groups. Here we used simulations to test the performance of two widely used methods, under complex scenarios. We report good performances, although with a tendency to over-predict events when increasing the complexity of the scenario. Overall, we find that lineage shifts are better detected than mass extinctions. This work has significance for assessing the methods currently used for estimating changes in diversification using phylogenies and developing new tests.