PT  - JOURNAL ARTICLE
AU  - Sacha Laurent
AU  - Marc Robinson-Rechavi
AU  - Nicolas Salamin
TI  - Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions
AID  - 10.1101/004572
DP  - 2014 Jan 01
TA  - bioRxiv
PG  - 004572
4099  - http://biorxiv.org/content/early/2014/11/24/004572.short
4100  - http://biorxiv.org/content/early/2014/11/24/004572.full
AB  - 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.