title: Estimating shifts in diversification rates based on higher-level phylogenies.
abstract: Macroevolutionary studies recently shifted from only reconstructing the past state, i.e. the species phylogeny, to also infer the past speciation and extinction dynamics that gave rise to the phylogeny. Methods for estimating diversification dynamics are sensitive towards incomplete species sampling. We introduce a method to estimate time-dependent diversification rates from phylogenies where clades of a particular age are represented by only one sampled species. A popular example of this type of data is phylogenies on the genus- or family-level, i.e. phylogenies where one species per genus or family is included. We conduct a simulation study to validate our method in a maximum-likelihood framework. Further, this method has already been introduced into the Bayesian package MrBayes, which led to new insights into the evolution of Hymenoptera.
authors.affiliation: Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland tanja.stadler@bsse.ethz.ch.
authors.forename: Tanja
authors.identifier: 0000-0001-6431-535X
authors.initials: T
authors.lastname: Stadler
authors.affiliation: Department of Zoology, Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic.
authors.forename: Jana
authors.initials: J
authors.lastname: Smrckova
mesh_terms: D001499:Bayes Theorem; D005075:Biological Evolution; D003198:Computer Simulation; D053476:Extinction, Biological; D010802:Phylogeny
keywords: extinction; incomplete sampling; inference; phylogenetic tree; speciation