Testing for heterogeneous rates of discrete character evolution on phylogenies.

Many hypotheses in the field of phylogenetic comparative biology involve specific changes in the rate or process of trait evolution. This is particularly true of approaches designed to connect macroevolutionary pattern to microevolutionary process. We present a method to test whether the rate of evolution of a discrete character has changed in one or more clades, lineages, or time periods.

phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things).

Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. Over the past ten years or so, the R package has grown to become an important research tool for phylogenetic comparative analysis. is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology.

The Difficulty of Predicting Evolutionary Change in Response to Novel Ecological Interactions: A Field Experiment with Lizards.

AbstractDetermining whether and how evolution is predictable is an important goal, particularly as anthropogenic disturbances lead to novel species interactions that could modify selective pressures. Here, we use a multigeneration field experiment with brown anole lizards () to test hypotheses about the predictability of evolution. We manipulated the presence/absence of predators and competitors of across 16 islands in the Bahamas that had preexisting brown anole populations.

Genome-wide parallelism underlies contemporary adaptation in urban lizards.

Urbanization drastically transforms landscapes, resulting in fragmentation, degradation, and the loss of local biodiversity. Yet, urban environments also offer opportunities to observe rapid evolutionary change in wild populations that survive and even thrive in these novel habitats. In many ways, cities represent replicated "natural experiments" in which geographically separated populations adaptively respond to similar selection pressures over rapid evolutionary timescales.

A simple hierarchical model for heterogeneity in the evolutionary correlation on a phylogenetic tree.

Numerous questions in phylogenetic comparative biology revolve around the correlated evolution of two or more phenotypic traits on a phylogeny. In many cases, it may be sufficient to assume a constant value for the evolutionary correlation between characters across all the clades and branches of the tree. Under other circumstances, however, it is desirable or necessary to account for the possibility that the evolutionary correlation differs through time or in different sections of the phylogeny.

Testing for genetic assimilation with phylogenetic comparative analysis: Conceptual, methodological, and statistical considerations.

Genetic assimilation is a process that leads to reduced phenotypic plasticity during adaptation to novel conditions, a potentially important phenomenon under global environmental change. Null expectations when testing for genetic assimilation, however, are not always clear. For instance, the statistical artifact of regression to the mean could bias us toward detecting genetic assimilation when it has not occurred.

Early giant reveals faster evolution of large body size in ichthyosaurs than in cetaceans.

Body sizes of marine amniotes span six orders of magnitude, yet the factors that governed the evolution of this diversity are largely unknown. High primary production of modern oceans is considered a prerequisite for the emergence of cetacean giants, but that condition cannot explain gigantism in Triassic ichthyosaurs. We describe the new giant ichthyosaur sp.

Mesozoic origin of coleoid cephalopods and their abrupt shifts of diversification patterns.

Coleoids are the most diverse group of cephalopod mollusks. While their origin is date during the Mesozoic, the diversification pattern is unknown. However, two hypotheses have been proposed.

: a web application and R package to explore United States COVID-19 data.

Appearing at the end of 2019, a novel virus (later identified as SARS-CoV-2) was characterized in the city of Wuhan in Hubei Province, China. As of the time of writing, the disease caused by this virus (known as COVID-19) has already resulted in over three million deaths worldwide. SARS-CoV-2 infections and deaths, however, have been highly unevenly distributed among age groups, sexes, countries, and jurisdictions over the course of the pandemic.

A variable-rate quantitative trait evolution model using penalized-likelihood.

In recent years it has become increasingly popular to use phylogenetic comparative methods to investigate heterogeneity in the rate or process of quantitative trait evolution across the branches or clades of a phylogenetic tree. Here, I present a new method for modeling variability in the rate of evolution of a continuously-valued character trait on a reconstructed phylogeny. The underlying model of evolution is stochastic diffusion (Brownian motion), but in which the instantaneous diffusion rate (σ) evolves by Brownian motion on a logarithmic scale.

Phylogenetic signal and evolutionary correlates of urban tolerance in a widespread neotropical lizard clade.

Urbanization is intensifying worldwide, and while some species tolerate and even exploit urban environments, many others are excluded entirely from this new habitat. Understanding the factors that underlie tolerance of urbanization is thus of rapidly growing importance. Here, we examine urban tolerance across a diverse group of lizards: Caribbean members of the neotropical genus Anolis.

Phylogeographic and phenotypic outcomes of brown anole colonization across the Caribbean provide insight into the beginning stages of an adaptive radiation.

Some of the most important insights into the ecological and evolutionary processes of diversification and speciation have come from studies of island adaptive radiations, yet relatively little research has examined how these radiations initiate. We suggest that Anolis sagrei is a candidate for understanding the origins of the Caribbean Anolis adaptive radiation and how a colonizing anole species begins to undergo allopatric diversification, phenotypic divergence and, potentially, speciation. We undertook a genomic and morphological analysis of representative populations across the entire native range of A.

: An R package for population genetic simulation and numerical analysis.

Here, I briefly present a new R package called that has been designed primarily for the purposes of teaching evolutionary biology, population genetics, and evolutionary theory. Functions of the package can be used to conduct simulations and numerical analyses of a wide range of evolutionary phenomena that would typically be covered in advanced undergraduate through graduate-level curricula in population genetics or evolution. For instance, functions can be used to visualize gene frequency changes through time under multiple deterministic and stochastic processes, to compute and animate the changes in phenotypic trait values or distributions under natural selection, to numerically analyze and graph the outcome of simple game theory models, and to plot coalescence within a population experiencing genetic drift, along with a number of other things.

Correlated evolution of flower size and seed number in flowering plants (monocotyledons).

Background And Aims: Kin selection theory predicts that a parent may minimize deleterious effects of competition among seeds developing within ovaries by increasing the genetic relatedness of seeds within an ovary. Alternatively, the number of developing seeds could be reduced to one or a few. It has also been suggested that single or few seeded fruits may be correlated with small flowers, and multi-ovulate ovaries or many seeded fruits may be associated with large flowers with specialized pollination mechanisms.

Comparing the rates of speciation and extinction between phylogenetic trees.

Over the past decade or so it has become increasingly popular to use reconstructed evolutionary trees to investigate questions about the rates of speciation and extinction. Although the methodology of this field has grown substantially in its sophistication in recent years, here I will take a step back to present a very simple model that is designed to investigate the relatively straightforward question of whether the tempo of diversification (speciation and extinction) differs between two or more phylogenetic trees, without attempting to attribute a causal basis to this difference. It is a likelihood method, and I demonstrate that it generally shows type I error that is close to the nominal level.

Linking locomotor performance to morphological shifts in urban lizards.

Urban habitats are drastically modified from their natural state, creating unique challenges and selection pressures for organisms that reside in them. We compared locomotor performance of lizards from urban and forest habitats on tracks differing in angle and substrate, and found that using artificial substrates came at a cost: lizards ran substantially slower and frequently lost traction on man-made surfaces compared to bark. We found that various morphological traits were positively correlated with sprint speed and that these same traits were significantly larger in urban compared to forest lizards.

Divergent habitat use of two urban lizard species.

Faunal responses to anthropogenic habitat modification represent an important aspect of global change. In Puerto Rico, two species of arboreal lizard, and , are commonly encountered in urban areas, yet seem to use the urban habitat in different ways. In this study, we quantified differences in habitat use between these two species in an urban setting.

Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life.

Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation (Otophysi) based on newly generated DNA sequences for 1,051 loci from 225 species.

Ecological specialization and morphological diversification in Greater Antillean boas.

Colonization of islands can dramatically influence the evolutionary trajectories of organisms, with both deterministic and stochastic processes driving adaptation and diversification. Some island colonists evolve extremely large or small body sizes, presumably in response to unique ecological circumstances present on islands. One example of this phenomenon, the Greater Antillean boas, includes both small (<90 cm) and large (4 m) species occurring on the Greater Antilles and Bahamas, with some islands supporting pairs or trios of body-size divergent species.

Phenotypic shifts in urban areas in the tropical lizard Anolis cristatellus.

Urbanization is an increasingly important dimension of global change, and urban areas likely impose significant natural selection on the species that reside within them. Although many species of plants and animals can survive in urban areas, so far relatively little research has investigated whether such populations have adapted (in an evolutionary sense) to their newfound milieu. Even less of this work has taken place in tropical regions, many of which have experienced dramatic growth and intensification of urbanization in recent decades.

Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: a case study with the lizard Anolis roosevelti.

In recent years, enormous effort and investment has been put into assembling the tree of life: a phylogenetic history for all species on Earth. Overwhelmingly, this progress toward building an ever increasingly complete phylogeny of living things has been accomplished through sophisticated analysis of molecular data. In the modern genomic age, molecular genetic data have become very easy and inexpensive to obtain for many species.

Biting disrupts integration to spur skull evolution in eels.

The demand that anatomical structures work together to perform biological functions is thought to impose strong limits on morphological evolution. Breakthroughs in diversification can occur, however, when functional integration among structures is relaxed. Although such transitions are expected to generate variation in morphological diversification across the tree of life, empirical tests of this hypothesis are rare.

Toward a Tree-of-Life for the boas and pythons: multilocus species-level phylogeny with unprecedented taxon sampling.

Snakes in the families Boidae and Pythonidae constitute some of the most spectacular reptiles and comprise an enormous diversity of morphology, behavior, and ecology. While many species of boas and pythons are familiar, taxonomy and evolutionary relationships within these families remain contentious and fluid. A major effort in evolutionary and conservation biology is to assemble a comprehensive Tree-of-Life, or a macro-scale phylogenetic hypothesis, for all known life on Earth.

Ancestral character estimation under the threshold model from quantitative genetics.

Evolutionary biology is a study of life's history on Earth. In researching this history, biologists are often interested in attempting to reconstruct phenotypes for the long extinct ancestors of living species. Various methods have been developed to do this on a phylogeny from the data for extant taxa.

Exceptional convergence on the macroevolutionary landscape in island lizard radiations.

G. G. Simpson, one of the chief architects of evolutionary biology's modern synthesis, proposed that diversification occurs on a macroevolutionary adaptive landscape, but landscape models are seldom used to study adaptive divergence in large radiations.