LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies

Abstract

Rates of species origination and extinction can vary over time during evolutionary radiations, and it is possible to reconstruct the history of diversification using molecular phylogenies of extant taxa only. Maximum likelihood methods provide a useful framework for inferring temporal variation in diversification rates. LASER is a package for the R programming environment that implements maximum likelihood methods based on the birth-death process to test whether diversification rates have changed over time. LASER contrasts the likelihood of phylogenetic data under models where diversification rates have changed over time to alternative models where rates have remained constant over time. Major strengths of the package include the ability to detect temporal increases in diversification rates and the inference of diversification parameters under multiple rate-variable models of diversification. The program and associated documentation are freely available from the R package archive at http://cran.r-project.org.

Keywords: Maximum likelihood; birth-death process; diversification; phylogeny.

Figure 1

Distribution of the ΔAIC_RC test statistic for 5000 rate-constant phylogenies of the same size as the Enallagma phylogeny. The calculated ΔAIC_RC for Enallagma was 13.0372 and indicates a highly significant temporal increase in the net diversification rate over time (p = 0.0016).