Biology subjects

Harmon, L. J.

Publications and source records attributed to Harmon, L. J..

4 recordsLinked to original sources

bioRxiv2018

Macroevolutionary diversification rates show time-dependency

For centuries, biologists have been captivated by the vast disparity in species richness between different groups of organisms. Variation in diversity is widely attributed to differences between groups in how fast they speciate or go extinct. Such macroevolutionary rates have been estimated for thousands of groups and have been correlated with an incredible variety of organismal traits. Here we analyze a large collection of phylogenetic trees and fossil time series and report a hidden generality amongst these seemingly idiosyncratic results: speciation and extinction rates follow a scaling law where both depend strongly on the age of the group in which they are measured, with the fastest rates in the youngest clades. Using a series of simulations and sensitivity analyses, we demonstrate that the time-dependency is unlikely to be a result of simple statistical artifacts. As such, this time-scaling has profound implications for the interpretation of rate estimates and suggests there might be general laws governing macroevolutionary dynamics.

evolutionary biology↗

bioRxiv2018

The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates

Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. However, the effect that the selection of these priors has on the inference of comparative parameters has not been thoroughly investigated. Such uncertainty may systematically bias phylogenetic reconstruction and, subsequently, parameter estimation. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we use BEAST to simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation rates and extinction rates) from these trees. When substitution rate heterogeneity is large, parameter estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.

evolutionary biology↗

bioRxiv2017

Fighting over food unites the birds of North America in a continental dominance hierarchy

The study of aggressive interactions between species has, to date, usually been restricted to interactions among small numbers of ecologically close competitors. Nothing is known about interspecific dominance hierarchies that include numerous, ecologically varied species. Such hierarchies are of interest because they could be used to address a variety of research questions, e.g. do similarly ranked species tend to avoid each other in time or space, and what will happen when such species come into contact as climates change? Here, we propose a method for creating a continental-scale hierarchy, and we make initial analyses based on this hierarchy. We quantified the extent to which a dominance hierarchy of feeder birds was linear, as intransitivities can promote local species coexistence. Using the existing network of citizen scientists participating in Project FeederWatch, we collected the data with which to create a continent-spanning interspecific dominance hierarchy that included species that do not currently have overlapping geographic distributions. Overall, the hierarchy was nearly linear, and largely predicted by body mass, although there were clade-specific deviations from the average mass-dominance relationship. Most of the small number of intransitive relationships in the hierarchy were based on small samples of observations. Few observations were made of interactions between close relatives and ecological competitors like Melanerpes woodpeckers and chickadees, as such species often have only marginally overlapping geographic distributions. Yet, these species ranks--emergent properties of the interaction network--were usually in agreement with published literature on dominance relationships between them. Interspecific dominance hierarchy, aggression, displacement, citizen science\n\nLAY SUMMARYWhen it comes to fighting over food, bigger is better but woodpeckers are best. The outcome of aggressive encounters between birds frequently determines which individual gains access to contested resources like food, but until now, little was known about such encounters between individuals of different species. We partnered with citizen scientists to record interspecific behavioral interactions at bird feeders around North America, and assembled these interactions into a continental dominance hierarchy.

ecology↗

bioRxiv2017

Estimating correlated rates of trait evolution with uncertainty

Correlated evolution among traits, which can happen due to genetic constraints, ontogeny, and selection, can have an important impact on the trajectory of phenotypic evolution. For example, shifts in the pattern of evolutionary integration may allow the exploration of novel regions of the morphospace by lineages. Here we use phylogenetic trees to study the pace of evolution of several traits and their pattern of evolutionary correlation across clades and over time. We use regimes mapped to the branches of the phylogeny to test for shifts in evolutionary integration. Our approach incorporates the uncertainty related to phylogeny, ancestral state estimates and parameter estimates to produce posterior distributions using Bayesian Markov chain Monte Carlo. We implemented the use of summary statistics to test for regime shifts based on a series of attributes of the model that can be directly relevant to biological hypotheses. In addition, we extend Felsensteins pruning algorithm to the case of multivariate Brownian motion models with multiple rate regimes. We performed extensive simulations to explore the performance of the method under a series of scenarios. Finally, we provide two test cases; the evolution of a novel buccal morphology in fishes of the family Centrarchidae and a shift in the trajectory of evolution of traits during the radiation of anole lizards to and from the Caribbean islands.

evolutionary biology↗