title: Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions.
abstract: BACKGROUND
  Recent methodological advances allow 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.
  
  
  RESULTS
  Here we used simulations to test the performance of two widely used methods under complex scenarios of diversification. We report good performances, although with a tendency to over-predict events with increasing complexity of the scenario.
  
  
  CONCLUSIONS
  Overall, we find that lineage shifts are better detected than mass extinctions. This work has significance to assess the methods currently used to estimate changes in diversification using phylogenetic trees. Our results also point toward the need to develop new models of diversification to expand our capabilities to analyse realistic and complex evolutionary scenarios.
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland. sacha.laurent@unil.ch.|Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, 1015, Switzerland. sacha.laurent@unil.ch.
authors.forename: Sacha
authors.initials: S
authors.lastname: Laurent
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland. marc.robinson-rechavi@unil.ch.|Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, 1015, Switzerland. marc.robinson-rechavi@unil.ch.
authors.forename: Marc
authors.initials: M
authors.lastname: Robinson-Rechavi
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland. nicolas.salamin@unil.ch.|Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, 1015, Switzerland. nicolas.salamin@unil.ch.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Salamin
mesh_terms: D005075:Biological Evolution; D003198:Computer Simulation; D053476:Extinction, Biological; D049810:Genetic Speciation; D008957:Models, Genetic; D010802:Phylogeny