Many domesticated species exhibit remarkable phenotypic diversity. In nature, selection produces not only divergence but also convergence when organisms experience similar selective pressures. Whether artificial selection during domestication also produces convergence has received little attention. Three-dimensional shape analysis of domestic cat and dog skulls demonstrated convergence at multiple levels. Most broadly, cats and dogs have both diversified greatly: equaling or exceeding the morphological disparity among all modern-day species of their respective families. Moreover, as a result of artificial selection, some breeds of these two phenotypically distinct species, evolutionarily separated for 50 My, have converged to such an extreme extent that they are more similar to each other than they are to many members of their own species or their ancestors, a phenomenon never previously observed in domesticated species. Remarkably, this convergence evolved not only between dogs and cats but also multiple times within each taxon.

Ancestral state reconstruction is a phylogenetic comparative method that involves estimating the unknown trait values of hypothetical ancestral taxa at internal nodes of a phylogenetic tree. Ancestral state reconstruction has long been, and continues to remain, among the most popular analyses in phylogenetic comparative research. In this review, I illustrate the theory and practice of ancestral state reconstruction for both discretely and continuously-valued phenotypic traits. For discrete characters, I focus on the Mk model and describe the distinction between marginal and joint reconstruction, as well as between local vs. global estimation. For continuous traits, I describe ancestral state reconstruction under a model of Brownian motion evolution. I highlight several use cases of ancestral state reconstruction via a set of empirical examples, ranging from diel activity pattern in primates, to environmental tolerance in lizards. Finally, I discuss and explore the statistical properties of ancestral state estimation as well as its limitations. By illustrating ancestral reconstruction under the hidden-rates and threshold models (for discrete traits), and bounded Brownian motion (for continuous characters), I demonstrate the considerable sensitivity of ancestral reconstruction to model misspecification. Although ancestral state reconstruction is virtually certain to retain its popularity into the future, I conclude by recommending considerable caution and circumspection in the use and interpretation of ancestral reconstruction in empirical evolutionary research.

Many hypotheses in the field of phylogenetic comparative biology involve specific changes in the rate or process of trait evolution. We present a method designed to test whether the rate of evolution of a discrete character has changed in one or more clades, lineages, or time periods. This method differs from other related approaches (such as the ‘covarion’ model) in that the ‘regimes’ in which the rate or process is postulated to have changed are specified a priori by the user, rather than inferred from the data. Similarly, it differs from methods designed to model a correlation between two binary traits in that the regimes mapped onto the tree are fixed. We apply our method to investigate the rate of dewlap color and/or caudal vertebra number evolution in Caribbean and mainland clades of the diverse lizard genus Anolis. We find little evidence to support any difference between mainland and island evolution in either character. We also examine the statistical properties of the method more generally and show that it has acceptable type I error, parameter estimation, and power. Finally, we discuss the relationship of our method to existing models of heterogeneity in the rate of discrete character evolution on phylogenies.

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 phytools R package has grown to become an important research tool for phylogenetic comparative analysis. phytools is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology. As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology. Here, I describe some significant features of and recent updates to phytools, while also illustrating several popular workflows of the phytools computational software.

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 Γ distribution. When the edge-wise rates of evolution are, in fact, Γ-distributed, we show via simulation that this model can be used to reliably estimate the shape parameter ( α ) 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 Γ-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)][1]. ### Competing Interest Statement The authors have declared no competing interest. This article was written in Rmarkdown ([Xie et al. 2018][2], [2020][3]; [Allaire et al. 2023][4]), and developed with the help of both bookdown ([Xie 2016][5], [2023][6]) and the posit Rstudio IDE ([RStudio Team 2020][7]). All data and markdown code necessary to exactly rebuild the submitted version of this article (including its analyses and figures) are available at . [1]: #ref-5 [2]: #ref-57 [3]: #ref-58 [4]: #ref-1 [5]: #ref-56 [6]: #ref-55 [7]: #ref-48

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. Little is known, however, about the genetic basis of adaptive phenotypic differentiation in urban populations nor the extent to which phenotypic parallelism is reflected at the genomic level with signatures of parallel selection. Here, we analyzed the genomic underpinnings of parallel urban-associated phenotypic change in Anolis cristatellus, a small-bodied neotropical lizard found abundantly in both urbanized and forested environments. We show that phenotypic parallelism in response to parallel urban environmental change is underlain by genomic parallelism and identify candidate loci across the Anolis genome associated with this adaptive morphological divergence. Our findings point to polygenic selection on standing genetic variation as a key process to effectuate rapid morphological adaptation. Identified candidate loci represent several functions associated with skeletomuscular development, morphology, and human disease. Taken together, these results shed light on the genomic basis of complex morphological adaptations, provide insight into the role of contingency and determinism in adaptation to novel environments, and underscore the value of urban environments to address fundamental evolutionary questions.

Synopsis Evidence suggests that hurricanes can influence the evolution of organisms, with phenotypic traits involved in adhesion, such as the toepads of arboreal lizards, being particularly susceptible to natural selection imposed by hurricanes. To investigate this idea, we quantified trait variation before and after Hurricanes Irma and Maria (2017) in forest and urban populations of the Puerto Rican lizard Anolis cristatellus. We found that the hurricanes affected toe morphology differently between forest and urban sites. In particular, toepads of the forefeet were longer and narrower in forest, but wider in urban populations, compared to pre-hurricane measures. Toepads of the hind feet were larger in area following the hurricanes. Fore and rear toes increased in length following the hurricane. There were no changes in the number of lamellae scales or lamellae spacing, but lamellae 6–11 of the forefeet shifted proximally following the hurricane. We also measured clinging performance and toe shape. We found that toepad area and toe lengths were stronger predictors of adhesive forces than toepad shape. Our results highlight an interaction between urbanization and hurricanes, demonstrating the importance to consider how urban species will respond to extreme weather events. Additionally, our different results for fore and rear feet highlight the importance of evaluating both of these traits when measuring the morphological response to hurricanes in arboreal lizards.

Determining 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 (Anolis sagrei) to test hypotheses about the predictability of evolution. We manipulated the presence/absence of predators and competitors of A. sagrei across 16 islands in the Bahamas that had preexisting brown anole populations. Before the experiment and again after roughly five generations, we measured traits related to locomotor performance and habitat use by brown anoles and used double-digest restriction enzyme–associated DNA sequencing to estimate genome-wide changes in allele frequencies. Although previous work showed that predators and competitors had characteristic effects on brown anole behavior, diet, and population sizes, we found that evolutionary change at both phenotypic and genomic levels was difficult to forecast. Phenotypic changes were contingent on sex and habitat use, whereas genetic change was unpredictable and not measurably correlated with phenotypic changes, experimental treatments, or other environmental factors. Our work shows how differences in ecological context can alter evolutionary outcomes over short timescales and underscores the difficulty of forecasting evolutionary responses to multispecies interactions in natural conditions, even in a well-studied system with ample supporting ecological information.

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. Likewise, the specific mechanism underlying plasticity expression may affect null expectations under neutral evolution. We used macroevolutionary numerical simulations to examine both of these important issues and their interaction, varying whether plasticity evolves, the evolutionary mechanism, trait measurement error, and experimental design. We also modified an existing reaction norm correction method to account for phylogenetic nonindependence. We found (1) regression to the mean is pervasive and can generate spurious support for genetic assimilation; (2) experimental design and post hoc correction can minimize this spurious effect; and (3) neutral evolution can produce patterns consistent with genetic assimilation without constraint or selection, depending on the mechanism of plasticity expression. Additionally, we reanalyzed published macroevolutionary data supporting genetic assimilation, and found that support was reduced after proper correction. Considerable caution is thus required whenever investigating genetic assimilation and reaction norm evolution at macroevolutionary scales.

Urbanization, the process whereby natural environments are modified for human habitation, is increasing worldwide. Many species are extirpated from urban settings, but others can survive and thrive in this environment. Few studies have compared population densities between urban and natural sites and none have investigated how hurricanes might interact with urbanization to affect animal species population dynamics in cities, which is crucial in evaluating population persistence in urban habitats. We quantified post-hurricane population dynamics between urban and forest populations of the tropical lizard Anolis cristatellus in paired urban and forest sites across the island of Puerto Rico at 4, 11, and 16 months following Hurricane Maria. Though we lacked pre-hurricane population density data, we expected lower than normal densities after the hurricane and a gradual increase through time. We found that urban population density was lower compared to natural areas across all pairs of sites. In forested areas, we found increases in perch density, likely associated with post-disturbance succession, but urban structural habitats remained relatively constant through time, with most hurricane-damaged vegetation being rapidly removed by humans. The two sites in our study that were most heavily impacted by the hurricane initially doubled in population density, and density continued to increase through our sampling period. Our findings suggest that hurricanes and urbanization can interact to shape population dynamics in lizards. Moreover, urban sites experience constant human modifications. As such, understanding population dynamics of urban species will require careful consideration of the effect of human intervention in these habitats.

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. The first suggests an increasing diversification rate after the Cretaceous-Paleogene extinction event (K-Pg) as consequence of empty habitats left by the ammonites and belemnites. The second hypothesis proposes a mid-Cenozoic increase in diversification rate related to distributional changes during ice ages and biotic interactions. To test these hypotheses, we estimated a lineage through time (LTT) and the gamma-statistic along with model-based diversification rates. These analyses were conducted on a dated molecular phylogeny for coleoids that we reconstructed using five molecular markers (cytochrome b, 16S rRNA, cytochrome oxidase I, rhodopsin, and PAX-6). Our divergence time estimation suggests that coleoids originated in the Mesozoic Era (Middle Triassic) and that both main clades (Decapodiformes and Octopodiformes) diverged in the Cretaceous/Jurassic Period. The LTT, gamma statistic, and diversification rates inferred with the Bayesian Analysis of Macro-evolutionary Mixtures (BAMM), indicate an acceleration in diversification rate over time since the origin of coleoids. Additionally, BAMM allowed us to detect abrupt increases in diversification rate before and after the K-Pg boundary. Our results partially support both hypotheses as all analyses indicate that the coleoid diversification rate was increasing during the Cenozoic. However, our results also indicate increasing diversification rates before the K-Pg boundary. We propose that the radiation of coleoids has been shaped by an acceleration in diversification rate over time, including exceptional episodes of abrupt increases before and after the K-Pg boundary.

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. Here, we present a method designed to fit a hierarchical series of models for heterogeneity in the evolutionary rates and correlation of two quantitative traits on a phylogenetic tree. We apply the method to two datasets: one for different attributes of the buccal morphology in sunfishes (Centrarchidae); and a second for overall body length and relative body depth in rock- and non-rock-dwelling South American iguanian lizards. We also examine the performance of the method for parameter estimation and model selection using a small set of numerical simulations.

The genus Sphaerodactylus is a very species-rich assemblage of sphaerodactylid lizards that has undergone a level of speciation in parallel to that of the well-known Anolis lizards. Nevertheless, molecular phylogenetic research on this group consists of a handful of smaller studies of regional focus (e.g., western Puerto Rico, the Lesser Antilles) or large-scale analyses based on relatively limited sequence data. Few medium-scale multi-locus studies exist— for example, studies that encompass an entire radiation on an island group. Building upon previous work done in Puerto Rican Sphaerodactylus , we performed multi-locus sampling of Sphaerodactylus geckos from across the Puerto Rico Bank. We then used these data for phylogeny estimation with near-complete taxon sampling. We focused on sampling the widespread nominal species S. macrolepis and in so doing, we uncovered a highly divergent and morphologically distinct lineage of Sphaerodactylus macrolepis from Puerto Rico, Culebra, and Vieques islands, which we recognize as S. grandisquamis ([Stejneger, 1904][1]) on the basis of molecular and morphological characters. S. grandisquamis co-occurs with S. macrolepis only on Culebra Island but is highly genetically differentiated and morphologically distinct. Sphaerodactylus macrolepis is now restricted to the eastern Puerto Rico Bank, from Culebra east through the Virgin Islands and including the topotypic population on St. Croix. We include additional discussion of the evolutionary history and historical biogeography of the Sphaerodactylus of the Puerto Rican Bank in the context of these new discoveries.### Competing Interest StatementThe authors have declared no competing interest. [1]: #ref-62

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. Herein, I present a tool (the covid19.Explorer R package and web application) that has been designed to explore and analyze publicly available United States COVID-19 infection and death data from the 2020/21 U.S. SARS-CoV-2 pandemic. The analyses and visualizations that this R package and web application facilitate can help users better comprehend the geographic progress of the pandemic, the effectiveness of non-pharmaceutical interventions (such as lockdowns and other measures, which have varied widely among U.S. states), and the relative risks posed by COVID-19 to different age groups within the U.S. population. The end result is an interactive tool that will help its users develop an improved understanding of the temporal and geographic dynamics of the SARS-CoV-2 pandemic, accessible to lay people and scientists alike.

Little is known about the synergistic impacts of urbanization and hurricanes on synanthropes. We compared morphological traits of the lizard Anolis cristatellus on Puerto Rico sampled before the 2017 category 5 Hurricane Maria and 4 and 11 months after the hurricane. We measured limb lengths, toepad size and the number of subdigital scales, termed lamellae, that facilitate adhesion. We hypothesized that the hurricane should have selected for longer limbs and larger toepads with more lamellae, which are traits that other research has suggested to increase clinging performance. Given prior work demonstrating that urban lizards of this species tend to share this phenotype, we also predicted increased phenotypic overlap between post-hurricane urban–forest pairs. Instead, we found that forest and urban populations alike had smaller body sizes, along with a small size-adjusted decrease in most traits, at 4 months after the hurricane event. Many traits returned to prehurricane values by 11 months post-hurricane. Toe morphology differed in the response to the hurricane between urban and forest populations, with significantly decreased trait values in forest but not in urban populations. This difference could be attributable to the different biomechanical demands of adhesion to anthropogenic substrates compared with natural substrates during intense winds. Overall, more research will be required to understand the impacts of hurricanes on urban species and whether differential natural selection can result.

AbstractThe genusSphaerodactylusis a very species-rich assemblage of sphaerodactylid lizards that has undergone a level of speciation in parallel to that of the well-knownAnolislizards. Nevertheless, molecular phylogenetic research on this group consists of a handful of smaller studies of regional focus (e.g., western Puerto Rico, the Lesser Antilles) or large-scale analyses based on relatively limited sequence data. Few medium-scale multi-locus studies exist— for example, studies that encompass an entire radiation on an island group. Building upon previous work done in Puerto RicanSphaerodactylus, we performed multi-locus sampling ofSphaerodactylusgeckos from across the Puerto Rico Bank. We then used these data for phylogeny estimation with near-complete taxon sampling. We focused on sampling the widespread nominal speciesS. macrolepisand in so doing, we uncovered a highly divergent and morphologically distinct lineage ofSphaerodactylus macrolepisfrom Puerto Rico, Culebra, and Vieques islands, which we recognize asS. grandisquamis(Stejneger, 1904) on the basis of molecular and morphological characters.S. grandisquamisco-occurs withS. macrolepisonly on Culebra Island but is highly genetically differentiated and morphologically distinct.Sphaerodactylus macrolepisis now restricted to the eastern Puerto Rico Bank, from Culebra east through the Virgin Islands and including the topotypic population on St. Croix. We include additional discussion of the evolutionary history and historical biogeography of theSphaerodactylusof the Puerto Rican Bank in the context of these new discoveries.

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 2 ) also evolves by Brownian motion on a logarithmic scale. Unfortunately, it’s not possible to simultaneously estimate the rates of evolution along each edge of the tree and the rate of evolution of σ 2 itself using Maximum Likelihood. As such, I propose a penalized-likelihood method in which the penalty term is equal to the log-transformed probability density of the rates under a Brownian model, multiplied by a ‘smoothing’ coefficient, λ, selected by the user. λ determines the magnitude of penalty that’s applied to rate variation between edges. Lower values of λ penalize rate variation relatively little; whereas larger λ values result in minimal rate variation among edges of the tree in the fitted model, eventually converging on a single value of σ 2 for all of the branches of the tree. In addition to presenting this model here, I have also implemented it as part of my phytools R package in the function multirateBM . Using different values of the penalty coefficient, λ, I fit the model to simulated data with: Brownian rate variation among edges (the model assumption); uncorrelated rate variation; rate changes that occur in discrete places on the tree; and no rate variation at all among the branches of the phylogeny. I then compare the estimated values of σ 2 to their known true values. In addition, I use the method to analyze a simple empirical dataset of body mass evolution in mammals. Finally, I discuss the relationship between the method of this article and other models from the phylogenetic comparative methods and finance literature, as well as some applications and limitations of the approach.

Relatively little is known about the dynamics of tropical urban forests, their phylogenetic diversity, as well as the socioeconomic and ecological factors that influence overall diversity across the urban landscape. However, permanent forest inventory and monitoring plot networks are increasingly being established across forests and cities of the world to monitor structural and functional attributes of urban forests, as well as ecosystem services. We analyzed a tropical, coastal urban forest in San Juan, Puerto Rico using metrics of phylogenetic diversity (PD), plant diversity, and available permanent plot data from an urban forest inventory and monitoring system. In total, we found 152 species belonging to 119 genera and 44 families in San Juan. PD tended to be highest in forest remnant areas. We also explored correlations between socioeconomic factors and taxonomic diversity and found that plant species richness was correlated with population density and housing price. We found marginally significant relationships between housing price, population density, and several PD metrics. Our results further suggest mixed evidence of luxury and legacy effects, two factors that have been linked to the plant diversity of anthropogenic ecosystems in other research. Overall, despite centuries of human influence, the existing urban forest diversity in San Juan - although perhaps not the particular species composition - is likely to be primarily the result of climate, biome, and multi-scale socioeconomic contexts and not legacy effects. The approach used and findings from this study could be used to better understand the application of PD metrics for assessing urban biodiversity and other beneficial attributes and traits of urban forests.