Biology subjects

Michael R. May

Publications and source records attributed to Michael R. May.

3 recordsLinked to original sources

bioRxiv2015

TESS: Bayesian inference of lineage diversification rates from (incompletely sampled) molecular phylogenies in R

SummaryMany fundamental questions in evolutionary biology entail estimating rates of lineage diversification (speciation - extinction). We develop a flexible Bayesian framework for specifying an effectively infinite array of diversification models--where rates are constant, vary continuously, or change episodically through time--and implement numerical methods to estimate parameters of these models from molecular phylogenies, even when species sampling is incomplete. Additionally we provide robust methods for comparing the relative and absolute fit of competing branching-process models to a given tree, thereby providing rigorous tests of biological hypotheses regarding patterns and processes of lineage diversification.\n\nAvailability and implementationthe source code for TESS is freely available at http://cran.r-project.org/web/packages/TESS/.\n\nContactSebastian.Hoehna@gmail.com

Bioinformatics↗

bioRxiv2015

A Bayesian Approach for Detecting Mass-Extinction Events When Rates of Lineage Diversification Vary

The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting mass-extinction events from phylogenies estimated from molecular sequence data. We develop our approach in a Bayesian statistical framework, which enables us to harness prior information on the frequency and magnitude of mass-extinction events. The approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between rate-shift events. We model three types of events: (1) instantaneous tree-wide shifts in speciation rate; (2) instantaneous tree-wide shifts in extinction rate, and; (3) instantaneous tree-wide mass-extinction events. Each of the events is described by a separate compound Poisson process (CPP) model, where the waiting times between each event are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-type specific prior distribution. Parameters of the model are then estimated using a reversible-jump Markov chain Monte Carlo (rjMCMC) algorithm. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events, provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e., below 5%) false discovery rate even in the case of background diversification rate variation. Finally, we provide an empirical application of this approach to conifers, which reveals that this group has experienced two major episodes of mass extinction. This new approach--the CPP on Mass Extinction Times (CoMET) model--provides an effective tool for identifying mass-extinction events from molecular phylogenies, even when the history of those groups includes more prosaic temporal variation in diversification rate.

Evolutionary Biology↗

bioRxiv2015

Bayesian Inference of Divergence Times and Feeding Evolution in Grey Mullets (Mugilidae)

Grey mullets (Mugilidae, Ovalentariae) are coastal fishes found in near-shore environments of tropical, subtropical, and temperate regions within marine, brackish, and freshwater habitats throughout the world. This group is noteworthy both for the highly conserved morphology of its members--which complicates species identification and delimitation--and also for the uncommon herbivorous or detritivorous diet of most mullets. In this study, we first attempt to identify the number of mullet species, and then--for the resulting species--estimate a densely sampled time-calibrated phylogeny using three mitochondrial gene regions and three fossil calibrations. Our results identify two major subgroups of mullets that diverged in the Paleocene/Early Eocene, followed by an Eocene/Oligocene radiation across both tropical and subtropical habitats. We use this phylogeny to explore the evolution of feeding preference in mullets, which indicates multiple independent origins of both herbivorous and detritivorous diets within this group. We also explore correlations between feeding preference and other variables, including body size, habitat (marine, brackish, or freshwater), and geographic distribution (tropical, subtropical, or temperate). Our analyses reveal: (1) a positive correlation between trophic index and habitat (with herbivorous and/or detritivorous species predominantly occurring in marine habitats); (2) a negative correlation between trophic index and geographic distribution (with herbivorous species occurring predominantly in subtropical and temperate regions), and; (3) a negative correlation between body size and geographic distribution (with larger species occurring predominantly in subtropical and temperate regions).

Evolutionary Biology↗