[Show abstract][Hide abstract] ABSTRACT: In recent years, biologists have increasingly recognized that evolutionary change can occur rapidly when natural selection is strong; thus, real-time studies of evolution can be used to test classic evolutionary hypotheses directly. One such hypothesis is that negative interactions between closely related species can drive phenotypic divergence. Such divergence is thought to be ubiquitous, though well-documented cases are surprisingly rare. On small islands in Florida, we found that the lizard Anolis carolinensis moved to higher perches following invasion by Anolis sagrei and, in response, adaptively evolved larger toepads after only 20 generations. These results illustrate that interspecific interactions between closely related species can drive evolutionary change on observable time scales.
[Show abstract][Hide abstract] ABSTRACT: 1. The phylogeny methods software package PHYLIP has long been among the most widely used packages for phylogeny inference and phylogenetic comparative biology. Numerous methods available in PHYLIP, including several new phylogenetic comparative analyses of considerable importance, are not implemented in any other software.2. Over the past decade, the popularity of the R statistical computing environment for many different types of phylogenetic analyses has soared, particularly in phylogenetic comparative biology. There are now numerous packages and methods developed for the R environment.3. In this article, we present Rphylip, a new R interface for the PHYLIP package. Functions of Rphylip interface seamlessly with all of the major analysis functions of the PHYLIP package. This new interface will enable the much easier use of PHYLIP programs in an integrated R workflow.4. In this paper we describe our motivation for developing Rphylip and present an illustration of how functions in the Rphylip package can be used for phylogenetic analysis in R.This article is protected by copyright. All rights reserved.
Methods in Ecology and Evolution 07/2014; · 5.92 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: 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. Here we show that transitions between suction-based and biting modes of prey capture, which require different degrees of coordination among skull components, are associated with shifts in the pattern of skull diversification in eels (Anguilliformes). Biting eels have experienced greater independence of the jaws, hyoid and operculum during evolution and exhibit more varied morphologies than closely related suction feeders, and this pattern reflects the weakened functional integration among skull components required for biting. Our results suggest that behavioural transitions can change the evolutionary potential of the vertebrate skeleton by altering functional relationships among structures.
[Show abstract][Hide abstract] ABSTRACT: 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. No previously published study has produced a species-level molecular phylogeny for more than 61% of boa species or 65% of python species. Using both novel and previously published sequence data, we have produced a species-level phylogeny for 84.5% of boid species and 82.5% of pythonid species, contextualized within a larger phylogeny of henophidian snakes. We obtained new sequence data for three boid, one pythonid, and two tropidophiid taxa which have never previously been included in a molecular study, in addition to generating novel sequences for seven genes across an additional 12 taxa. We compiled an 11-gene dataset for 127 taxa, consisting of the mitochondrial genes CYTB, 12S, and 16S, and the nuclear genes bdnf, bmp2, c-mos, gpr35, rag1, ntf3, odc, and slc30a1, totaling up to 7561 base pairs per taxon. We analyzed this dataset using both maximum likelihood and Bayesian inference and recovered a well-supported phylogeny for these species. We found significant evidence of discordance between taxonomy and evolutionary relationships in the genera Tropidophis, Morelia, Liasis, and Leiopython, and we found support for elevating two previously suggested boid species. We suggest a revised taxonomy for the boas (13 genera, 58 species) and pythons (8 genera, 40 species), review relationships between our study and the many other molecular phylogenetic studies of henophidian snakes, and present a taxonomic database and alignment which may be easily used and built upon by other researchers.
Molecular Phylogenetics and Evolution 12/2013; · 4.07 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: 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. In the present article I introduce a new approach for ancestral character estimation for discretely valued traits. This approach is based on the threshold model from evolutionary quantitative genetics. Under the threshold model, the value exhibited by an individual or species for a discrete character is determined by an underlying, unobserved continuous trait called 'liability.' In this new method for ancestral state reconstruction, I use Bayesian MCMC to sample the liabilities of ancestral and tip species, and the relative positions of two or more thresholds, from their joint posterior probability distribution. Using data simulated under the model, I find that the method has very good performance in ancestral character estimation. Use of the threshold model for ancestral state reconstruction relies on a priori specification of the order of the discrete character states along the liability axis. I test the use of a Bayesian MCMC information theoretic criterion (DIC) based approach to choose among different hypothesized orderings for the discrete character. Finally, I apply the method to the evolution of feeding mode in centrarchid fishes. This article is protected by copyright. All rights reserved.
[Show abstract][Hide abstract] ABSTRACT: The tropical island Puerto Rico is potentially vulnerable to invasion by some species of exotic snakes; however, until now no established populations had been reported. Here we report and genetically characterize the nascent invasion of Puerto Rico by an exotic constricting snake of the family Boidae (Boa constrictor) using mtDNA and microsatellite data. Over 150 individual B. constrictor have been removed from Mayagüez municipality since May 2011, and our results from the genetic analysis of 32 individuals suggest that this population was recently founded by individuals of one subspecies from a genetic lineage common to zoo and breeding collections, but that the potential propagule pool consists of two subspecies. We also suggest that anthropogenic long-distance dispersal within the island of Puerto Rico may be occurring from the established population, with implications for further establishment across the island. This study represents the first report of the naturalization of an invasive species of boid snake in Puerto Rico and will be important in determining mitigation strategies for this invasion as well as providing a basis for comparison to other on-going studies of invasive snakes.
[Show abstract][Hide abstract] ABSTRACT: 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. We show that for Caribbean Anolis lizards, diversification on similar Simpsonian landscapes leads to striking convergence of entire faunas on four islands. Parallel radiations unfolding at large temporal scales shed light on the process of adaptive diversification, indicating that the adaptive landscape may give rise to predictable evolutionary patterns in nature, that adaptive peaks may be stable over macroevolutionary time, and that available geographic area influences the ability of lineages to discover new adaptive peaks.
[Show abstract][Hide abstract] ABSTRACT: The evolutionary and biogeographic history of West Indian boid snakes (Epicrates), a group of nine species and 14 subspecies, was once thought to be well understood; however, new research has indicated that we are missing a clear understanding of the evolutionary relationships of this group. Here, we present the first multilocus, species-tree based analyses of the evolutionary relationships, divergence times, and historical biogeography of this clade with data from 10 genes and 6,256 bp. We find evidence for a single colonization of the Caribbean from mainland South America in the Oligocene or early Miocene, followed by a radiation throughout the Greater Antilles and Bahamas. These findings support the previous suggestion that Epicrates sensu lato Wagler is paraphyletic with respect to the anacondas (Eunectes Wagler), and hence we restrict Epicrates to the mainland clade and use the available name Chilabothrus Duméril and Bibron for the West Indian clade. Our results suggest some diversification occurred within island banks, though most species divergence events seem to have occurred in allopatry. We also find evidence for a remarkable diversification within the Bahamian archipelago suggesting that the recognition of another Bahamian endemic species C. strigilatus is warranted.
Molecular Phylogenetics and Evolution 05/2013; · 4.07 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Adaptive divergence in coloration is expected to produce reproductive isolation in species that use colourful signals in mate choice and species recognition. Indeed, many adaptive radiations are characterized by differentiation in colourful signals, suggesting that divergent selection acting on coloration may be an important component of speciation. Populations in the Anolis marmoratus species complex from the Caribbean island of Guadeloupe display striking divergence in the colour and pattern of adult males that occurs over small geographic distances, suggesting strong divergent selection. Here we test the hypothesis that divergence in coloration results in reduced gene flow among populations. We quantify variation in adult male coloration across a habitat gradient between mesic and xeric habitats, use a multilocus coalescent approach to infer historical demographic parameters of divergence, and examine gene flow and population structure using microsatellite variation. We find that colour variation evolved without geographic isolation and in the face of gene flow, consistent with strong divergent selection and that both ecological and sexual selection are implicated. However, we find no significant differentiation at microsatellite loci across populations, suggesting little reproductive isolation and high levels of contemporary gene exchange. Strong divergent selection on loci affecting coloration probably maintains clinal phenotypic variation despite high gene flow at neutral loci, supporting the notion of a porous genome in which adaptive portions of the genome remain fixed whereas neutral portions are homogenized by gene flow and recombination. We discuss the impact of these findings for studies of colour evolution and ecological speciation.
[Show abstract][Hide abstract] ABSTRACT: The endemic Puerto Rican boa (Epicrates inornatus) has spent 42 years on the Endangered Species List with little evidence for recovery. One significant impediment to effective conservation planning has been a lack of knowledge of the distribution of genetic variability in the species. It has previously been suggested that boas might best be protected around caves that harbor large populations of bats. Prior study has found Puerto Rican boas at relatively high densities in and around bat caves, which they use both to feed and seek shelter. However, it is unknown whether these behaviorally distinctive populations represent a distinct evolutionary lineage, or (conversely) whether caves harbor representative genetic diversity for the species across the island. We provide the first genetic study of the Puerto Rican boa, and we examine and compare genetic diversity and divergence among two cave populations and two surface populations of boas. We find three haplogroups and an apparent lack of phylogeographic structure across the island. In addition, we find that the two cave populations appear no less diverse than the two surface populations, and harbor multiple mtDNA lineages. We discuss the conservation implications of these findings, including a call for the immediate protection of the remaining cave-associated populations of boas.
PLoS ONE 01/2013; 8(5):e63899. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Modern phylogenetic comparative biology uses data from the relationships between species (phylogeny) combined with comparative information for phenotypic traits to draw model‐based statistical inferences about the evolutionary past. Recent years have seen phylogeny methods for evolutionary inference become central in the study of organic evolution.Here, I present two different graphical methods for visualizing phenotypic evolution on the tree. Method 1 is a new approach for plotting the posterior density of stochastically mapped character histories for a binary (two‐state) phenotypic trait on a phylogeny. Method 2 is a closely related technique that uses ancestral character estimation to visualize historical character states for a continuous trait along the branches of a tree.One shortcoming of Method 2 is that by mapping the point estimates of ancestral states along the branches of the tree, we have effectively ignored the uncertainty associated with ancestral character estimation of continuous traits. To alleviate this issue, I propose a new method for visualizing ancestral state uncertainty using a type of projection of the tree into morphospace called a ‘traitgram.’All of these approaches should prove useful in summarizing complex comparative inferences about ancestral character reconstruction. They are implemented in the freely available and open‐source R phylogenetics package ‘phytools.’
Methods in Ecology and Evolution 01/2013; 4(8). · 5.92 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Phylogenetic comparative methods that incorporate intraspecific variability are relatively new and, so far, not especially widely used in empirical studies. In the present short article we will describe a new Bayesian method for fitting evolutionary models to comparative data that incorporates intraspecific variability. This method differs from an existing likelihood-based approach in that it requires no a priori inference about species means and variances; rather it takes phenotypic values from individuals and a phylogenetic tree as input, and then samples species means and variances, along with the parameters of the evolutionary model, from their joint posterior probability distribution. One of the most novel and intriguing attributes of this approach is that jointly sampling the species means with the evolutionary model parameters means that the model and tree can influence our estimates of species mean trait values, not just the reverse. In the present implementation, we first apply this method to the most widely used evolutionary model for continuously valued phenotypic trait data (Brownian motion). However, the general approach has broad applicability, which we illustrate by also fitting the λ model, another simple model for quantitative trait evolution on a phylogeny. We test our approach via simulation and by analyzing two empirical datasets obtained from the literature. Finally, we have implemented the methods described herein in a new function for the R statistical computing environment, and this function will be distributed as part of the 'phytools' R library.
[Show abstract][Hide abstract] ABSTRACT: In recent years, a suite of methods has been developed to fit multiple rate models to phylogenetic comparative data. However, most methods have limited utility at broad phylogenetic scales because they typically require complete sampling of both the tree and the associated phenotypic data. Here, we develop and implement a new, tree-based method called MECCA (Modeling Evolution of Continuous Characters using ABC) that uses a hybrid likelihood/approximate Bayesian computation (ABC)-Markov-Chain Monte Carlo approach to simultaneously infer rates of diversification and trait evolution from incompletely sampled phylogenies and trait data. We demonstrate via simulation that MECCA has considerable power to choose among single versus multiple evolutionary rate models, and thus can be used to test hypotheses about changes in the rate of trait evolution across an incomplete tree of life. We finally apply MECCA to an empirical example of body size evolution in carnivores, and show that there is no evidence for an elevated rate of body size evolution in the pinnipeds relative to terrestrial carnivores. ABC approaches can provide a useful alternative set of tools for future macroevolutionary studies where likelihood-dependent approaches are lacking.
[Show abstract][Hide abstract] ABSTRACT: Currently available phylogenetic methods for studying the rate of evolution in a continuously valued character assume that the rate is constant throughout the tree or that it changes along specific branches according to an a priori hypothesis of rate variation provided by the user. Herein, we describe a new method for studying evolutionary rate variation in continuously valued characters given an estimate of the phylogenetic history of the species in our study. According to this method, we propose no specific prior hypothesis for how the variation in evolutionary rate is structured throughout the history of the species in our study. Instead, we use a bayesian Markov Chain Monte Carlo approach to estimate evolutionary rates and the shift point between rates on the tree. We do this by simultaneously sampling rates and shift points in proportion to their posterior probability, and then collapsing the posterior sample into an estimate of the parameters of interest. We use simulation to show that the method is quite successful at identifying the phylogenetic position of a shift in the rate of evolution, and that estimated rates are asymptotically unbiased. We also provide an empirical example of the method using data for Anolis lizards.
[Show abstract][Hide abstract] ABSTRACT: The adaptive landscape and the G-matrix are keys concepts for understanding how quantitative characters evolve during adaptive radiation. In particular, whether the adaptive landscape can drive convergence of phenotypic integration (i.e., the pattern of phenotypic variation and covariation summarized in the P-matrix) is not well studied. We estimated and compared P for 19 morphological traits in eight species of Caribbean Anolis lizards, finding that similarity in P among species was not correlated with phylogenetic distance. However, greater similarity in P among ecologically similar Anolis species (i.e., the trunk-ground ecomorph) suggests the role of convergent natural selection. Despite this convergence and relatively deep phylogenetic divergence, a large portion of eigenstructure of P is retained among our eight focal species. We also analyzed P as an approximation of G to test for correspondence with the pattern of phenotypic divergence in 21 Caribbean Anolis species. These patterns of covariation were coincident, suggesting that either genetic constraint has influenced the pattern of among-species divergence or, alternatively, that the adaptive landscape has influenced both G and the pattern of phenotypic divergence among species. We provide evidence for convergent evolution of phenotypic integration for one class of Anolis ecomorph, revealing yet another important dimension of evolutionary convergence in this group.
[Show abstract][Hide abstract] ABSTRACT: The independent evolution of similar morphologies has long been a subject of considerable interest to biologists. Does phenotypic convergence reflect the primacy of natural selection, or does development set the course of evolution by channelling variation in certain directions? Here, we examine the ontogenetic origins of relative limb length variation among Anolis lizard habitat specialists to address whether convergent phenotypes have arisen through convergent developmental trajectories. Despite the numerous developmental processes that could potentially contribute to variation in adult limb length, our analyses reveal that, in Anolis lizards, such variation is repeatedly the result of changes occurring very early in development, prior to formation of the cartilaginous long bone anlagen.
Proceedings of the Royal Society B: Biological Sciences 08/2011; 279(1729):739-48. · 5.68 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: 1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment.2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks.3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples.4. Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.
Methods in Ecology and Evolution 01/2011; 3(2):217-223. · 5.92 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Summary1. A common procedure in the regression analysis of interspecies data is to first test the independent and dependent variables X and Y for phylogenetic signal, and then use the presence of signal in one or both traits to justify regression analysis using phylogenetic methods such as independent contrasts or phylogenetic generalized least squares.2. This is incorrect, because phylogenetic regression assumes that the residual error in the regression model (not in the original traits) is distributed according to a multivariate normal distribution with variances and covariances proportional to the historical relations of the species in the sample.3. Here, I examine the consequences of justifying and applying the phylogenetic regression incorrectly. I find that when used improperly the phylogenetic regression can have poor statistical performance, even under some circumstances in which the type I error rate of the method is not inflated over its nominal level.4. I also find, however, that when tests of phylogenetic signal in phylogenetic regression are applied properly, and in particular when phylogenetic signal in the residual error is simultaneously estimated with the regression parameters, the phylogenetic regression outperforms equivalent non-phylogenetic procedures.
Methods in Ecology and Evolution 11/2010; 1(4):319 - 329. · 5.92 Impact Factor