title: Quantifying Age-dependent Extinction from Species Phylogenies.
abstract: Several ecological factors that could play into species extinction are expected to correlate with species age, i.e., time elapsed since the species arose by speciation. To date, however, statistical tools to incorporate species age into likelihood-based phylogenetic inference have been lacking. We present here a computational framework to quantify age-dependent extinction through maximum likelihood parameter estimation based on phylogenetic trees, assuming species lifetimes are gamma distributed. Testing on simulated trees shows that neglecting age dependence can lead to biased estimates of key macroevolutionary parameters. We then apply this method to two real data sets, namely a complete phylogeny of birds (class Aves) and a clade of self-compatible and -incompatible nightshades (Solanaceae), gaining initial insights into the extent to which age-dependent extinction may help explain macroevolutionary patterns. Our methods have been added to the R package TreePar.
authors.affiliation: Institute for Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland; helen.alexander@env.ethz.ch.
authors.forename: Helen K
authors.initials: HK
authors.lastname: Alexander
authors.affiliation: Laboratoire de Probabilités et Modèles Aléatoires CNRS UMR 7599, UPMC Univ Paris 06, Paris, France; Center for Interdisciplinary Research in Biology CNRS UMR 7241, Collège de France, Paris, France; and.
authors.forename: Amaury
authors.initials: A
authors.lastname: Lambert
authors.affiliation: Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland;
authors.forename: Tanja
authors.initials: T
authors.lastname: Stadler
mesh_terms: D000818:Animals; D005075:Biological Evolution; D001717:Birds / Q000145:classification; D002965:Classification / Q000379:methods*; D003198:Computer Simulation; D053476:Extinction, Biological; D016013:Likelihood Functions; D008954:Models, Biological; D010802:Phylogeny; D019657:Solanaceae / Q000145:classification; D013995:Time
keywords: Aves; Solanaceae; coalescent point process; diversification; macroevolution; maximum likelihood estimation; phylogenetics