Biology subjects

Harmon, L. J.

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

12 recordsLinked to original sources

bioRxiv2026

Unlocking a flexible set of phylogenetic models for discrete and continuous trait evolution using discretized stochastic diffusion

The practical utility of many modern phylogenetic comparative methods can depend on how accurately mathematical models capture the evolutionary process of traits. Boucher and Demery (2016) described a new quantitative trait model for testing hypotheses about constraint on phenotypic character evolution: Brownian motion with reflective limits. Since their analytic solution for the probability function under this bounded scenario was intractable for reasonably-sized trees, Boucher and Demery (2016) also identified a creative technique for computing the likelihood of their model. The basis of this method derives from the convergence of an equal-rates, symmetric, ordered Markov chain and continuous stochastic diffusion in the limit as the number of lattice states in the chain goes to{infty} (or, alternatively, as their widths decrease towards zero). We realized that this general approach had the potential to unlock a surprisingly large number of additional models for the phylogenetic comparative analysis of discrete and continuous trait data, and we explore several of these in the present article. Specifically, we examine application of this discretized diffusion approximation to the threshold model from evolutionary quantitative genetics, to a new "semi-threshold" trait evolution model, to a joint model where the rate of evolution for a continuous trait depends on the value of a co-evolving discrete character, along with a separate model where precisely the converse is true, and to a discrete-character-dependent multi-trend trended continuous trait evolution model. We conclude with some context for the origins of our article and discussion of other possible applications of this powerful approach.

evolutionary biology↗

bioRxiv2025

Is Evolution Predictable? Experiments in an Evolutionary Video Game

The outcome of evolution sometimes appears to be predictable, as in the evolution of the same characteristics independently in convergent evolution. Other times, evolutions path depends on starting conditions or chance events, and some forms evolve just once and never appear again. Is convergence, and by implication, predictability, a common characteristic of the evolutionary process? We aimed to answer this question by using an evolutionary video game titled Project Hastur as a study system. In this video game, the enemies evolve traits to help them combat the players strategy. We determined whether the same environmental pressures (in this case, player strategy) lead to predictable evolution. We conducted a series of experiments with three different playing styles and four different evolutionary treatments with varying kinds of selection pressure, each with several replicates. For each replicate, enemies from the first and final generations were categorized into types using k-means clustering. The Euclidean distance between the cluster centroids and the sum of squares values were recorded for each replicate and compared among evolutionary treatments using Wilcoxon rank sum tests. Evolutionary predictability was evaluated using permutation tests. We found that fitness functions in Project Hastur led to incredible, but unpredictable, diversity. The fitness landscape changes between replicates, even within the same experimental treatment and regardless of player strategy, resulting in enemies with an unpredictable array of trait values.

evolutionary biology↗

bioRxiv2025

SSARP: An R Package for Easily Creating Species- and Speciation- Area Relationships Using Web Databases

A universal method of quantifying patterns of biodiversity on islands is the species-area relationship (SAR). SARs visualize the relationship between species richness (the number of species) and the area of the land mass on which they live. An extension of this visualization, the speciation-area relationship (SpAR), helps researchers determine trends in speciation rate over a set of land masses. Comparing these relationships across island systems globally is an extremely difficult task because gathering and processing a large amount of species occurrence data and island data often requires researchers to conduct lengthy literature searches and combine datasets from several different sources. Here we present SSARP (Species/Speciation-Area Relationship Projector), an R package that provides a simple workflow for creating SARs and SpARs. The SSARP workflow allows users to gather occurrence data from GBIF, use mapping tools to determine whether the GPS points in the occurrence data refer to valid land masses, associate those land masses with their areas using a built-in dataset of island names and areas, and create SARs using linear and segmented regression. SSARP also provides multiple functions for estimating speciation rates for use in creating a SpAR. Using SSARP allows researchers to dramatically increase the scope of their biodiversity research through the creation of SARs and SpARs with data from island systems across the globe.

evolutionary biology↗

bioRxiv2024

A discrete character evolution model for phylogenetic comparative biology with {Gamma}-distributed rate heterogeneity among branches of the tree

Phylogenetic comparative methods are now widely used to measure trait evolution on the tree of life. Often these methods involve fitting an explicit model of character evolution to trait data and then comparing the explanatory power of this model to alternative scenarios. In this article, we present a new model for discrete trait evolution in which the rate of character change in the tree varies from edge (i.e., "branch") to edge of the phylogeny according to a discretized {Gamma} distribution. When the edge-wise rates of evolution are, in fact, {Gamma}-distributed, we show via simulation that this model can be used to reliably estimate the shape parameter () of the distribution of rate variation among edges. We also describe how our model can be employed in ancestral state reconstruction, and demonstrate via simulation how doing so will tend to increase the accuracy of our estimated states when the generating edge rates are {Gamma}-distributed. We discuss how marginal edge rates are estimated under the model, and apply our method to a real dataset of digit number in squamate reptiles, modified from Brandley et al. (2008).

evolutionary biology↗

bioRxiv2022

Modeling the Evolution of Rates of Continuous Trait Evolution

AO_SCPLOWBSTRACTC_SCPLOWRates of phenotypic evolution vary markedly across the tree of life, from the accelerated evolution apparent in adaptive radiations to the remarkable evolutionary stasis exhibited by so-called "living fossils". Such rate variation has important consequences for large-scale evolutionary dynamics, generating vast disparities in phenotypic diversity across space, time, and taxa. Despite this, most methods for estimating trait evolution rates assume rates vary deterministically with respect to some variable of interest or change infrequently during a clades history. These assumptions may cause underfitting of trait evolution models and mislead hypothesis testing. Here, we develop a new trait evolution model that allows rates to vary gradually and stochastically across a clade. Further, we extend this model to accommodate generally decreasing or increasing rates over time, allowing for flexible modeling of "early/late bursts" of trait evolution. We implement a Bayesian method, termed "evolving rates" (evorates for short), to efficiently fit this model to comparative data. Through simulation, we demonstrate that evorates can reliably infer both how and in which lineages trait evolution rates varied during a clades history. We apply this method to body size evolution in cetaceans, recovering substantial support for an overall slowdown in body size evolution over time with recent bursts among some oceanic dolphins and relative stasis among beaked whales of the genus Mesoplodon. These results unify and expand on previous research, demonstrating the empirical utility of evorates.

evolutionary biology↗

bioRxiv2021

Frequent origins of traumatic insemination involve convergent shifts in sperm and genital morphology

Traumatic insemination is a mating behaviour during which the (sperm) donor uses a traumatic intromittent organ to inject an ejaculate through the epidermis of the (sperm) recipient, thereby frequently circumventing the female genitalia. Traumatic insemination occurs widely across animals, but the frequency of its evolution, the intermediate stages via which it originates, and the morphological changes that such shifts involve remain poorly understood. Based on observations in 145 species of the free-living flatworm genus Macrostomum, we identify at least nine independent evolutionary origins of traumatic insemination from reciprocal copulation, but no clear indication of reversals. These origins involve convergent shifts in multivariate morphospace of male and female reproductive traits, suggesting that traumatic insemination has a canalising effect on morphology. Signatures of male-female coevolution across the genus indicate that sexual selection and sexual conflict drive the evolution of traumatic insemination, because it allows donors to bypass postcopulatory control mechanisms of recipients.

evolutionary biology↗

bioRxiv2020

Reconstructing Squamate Biogeography in Afro-Arabia Reveals the Influence of a Complex and Dynamic Geologic Past

The geographic distribution of biodiversity is central to understanding evolutionary biology. Paleogeographic and paleoclimatic histories often help to explain how biogeographic patterns unfold through time. However, such patterns are also influenced by a variety of other factors, such as lineage diversification, that may affect the probability of certain types of biogeographic events. The complex and well-known geologic and climatic history of Afro-Arabia, together with the extensive research on reptile systematics in the region, makes Afro-Arabian squamate communities an ideal system to investigate biogeographic patterns and their drivers. Here we reconstruct the phylogenetic relationships and the ancestral geographic distributions of several Afro-Arabian reptile clades (totaling 430 species) to estimate the number of dispersal, vicariance and range contraction events. We then compare the observed biogeographic history to a distribution of simulated biogeographic events based on the empirical phylogeny and the best-fit model. This allows us to identify periods in the past where the observed biogeographic history was likely shaped by forces beyond the ones included in the model. We find an increase in vicariance following the Oligocene, most likely caused by the fragmentation of the Afro-Arabian plate. In contrast, we did not find differences between observed and expected dispersal and range contraction levels. This is consistent with diversification enhanced by environmental processes and with the establishment of a dispersal corridor connecting Africa, Arabia and Eurasia since the middle Miocene. Finally, here we show that our novel approach is useful to pinpoint events in the evolutionary history of lineages that might reflect external forces not predicted by the underlying biogeographic model.

evolutionary biology↗

bioRxiv2019

Hybridizing salamanders experience accelerated diversification

Whether hybridization generates or erodes species diversity has long been debated, but to date most studies have been conducted at small taxonomic scales. Salamanders (order Caudata) represent a taxonomic order in which hybridization plays a prevalent ecological and evolutionary role. We employed a recently developed model of trait-dependent diversification to test the hypothesis that hybridization impacts the diversification dynamics of species that are currently hybridizing. We find strong evidence supporting this hypothesis, showing that hybridizing salamander lineages have significantly greater net-diversification rates than non-hybridizing lineages. This pattern is driven by concurrently increased speciation rates and decreased extinction rates in hybridizing lineages. Our results support the hypothesis that hybridization can act as a generative force in macroevolutionary diversification.

evolutionary biology↗

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↗