Testing macro–evolutionary models using incomplete molecular phylogenies

Abstract

Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversi¢cation. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Speci¢cally, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, ¢rst, the adverse e¡ects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.

Diversification of clearwing butterflies with the rise of the Andes

“…To test whether diversification rates have changed over time the gamma (γ) statistic was calculated (Pybus & Harvey, 2000) for different taxonomic groups using ape 3.0‐9. Positive and negative values of γ indicate an increasing and decreasing diversification rate towards the present respectively.…”

A molecular assessment of phylogenetic relationships and lineage accumulation rates within the family Salamandridae (Amphibia, Caudata)

“…For each of these trees, we quantiWed the LTT patterns using the statistic (Pybus and Harvey, 2000;Pybus et al, 2002). Trees exhibiting increased speciation rates during all or a portion of their history (or decreased extinction rates) are expected to produce concave LTT plots and a > 0, whereas trees that exhibit a decrease in speciation rates (or increased extinction rates) are expected to produce a convex LTT plot and a < 0.…”

“…Therefore, we also investigated patterns of lineage accumulation in the early evolutionary history of the Salamandridae by calculating for the Wrst two-thirds of each tree (starting from the deepest node to a cumulative branch length of 0.67). Gamma statistics were used in a constant-rate (CR) test (Pybus and Harvey, 2000) to assess whether the rates of lineage accumulation over time have changed. Because we have nearly complete species sampling for the family, the CR test is appropriate without having to perform a Monte Carlo simulation to account for missing lineages.…”

“…Plotting lineage accumulation as a function of estimated divergence time and integrating this information with null models of the birth and death of lineages (Nee et al, 1992) permit statistical testing of hypotheses of lineage diversiWcation over time (Paradis, 1997;Pybus and Harvey, 2000;Pybus et al, 2002). These phylogenetic approaches have yielded important insight in the tempo of evolutionary diversiWcation in diverse organismal groups including iguanian lizards (Harmon et al, 2003), marine Wshes (Ruber and Zardoya, 2005), mosses (Shaw et al, 2003), and plethodontid salamanders (Kozak et al, 2006).…”

Modeling lineage and phenotypic diversification in the New World monkey (Platyrrhini, Primates) radiation

“…Morphological and phylogenetic studies have hypothesized that the diversification of 1 statistic (Pybus and Harvey, 2000), whether the pattern of lineage diversification in the 1 platyrrhine tree departs from what is expected under the most simple model, Pure-Birth 2 (PB), in which each species has a constant probability λ (speciation rate) of generating 3…”