Richard E. Glor

GEIGER: investigating evolutionary radiations

SUMMARY GEIGER is a new software package, written in the R language, to describe evolutionary radiations. GEIGER can carry out simulations, parameter estimation and statistical hypothesis testing. Additionally, GEIGERs simulation algorithms can be used to analyze the statistical power of comparative approaches. AVAILABILITY This open source software is written entirely in the R language and is freely available through the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/.

Environmental Niche Equivalency versus Conservatism: Quantitative Approaches to Niche Evolution

Abstract Environmental niche models, which are generated by combining species occurrence data with environmental GIS data layers, are increasingly used to answer fundamental questions about niche evolution, speciation, and the accumulation of ecological diversity within clades. The question of whether environmental niches are conserved over evolutionary time scales has attracted considerable attention, but often produced conflicting conclusions. This conflict, however, may result from differences in how niche similarity is measured and the specific null hypothesis being tested. We develop new methods for quantifying niche overlap that rely on a traditional ecological measure and a metric from mathematical statistics. We reexamine a classic study of niche conservatism between sister species in several groups of Mexican animals, and, for the first time, address alternative definitions of “niche conservatism” within a single framework using consistent methods. As expected, we find that environmental niches of sister species are more similar than expected under three distinct null hypotheses, but that they are rarely identical. We demonstrate how our measures can be used in phylogenetic comparative analyses by reexamining niche divergence in an adaptive radiation of Cuban anoles. Our results show that environmental niche overlap is closely tied to geographic overlap, but not to phylogenetic distances, suggesting that niche conservatism has not constrained local communities in this group to consist of closely related species. We suggest various randomization tests that may prove useful in other areas of ecology and evolutionary biology.

Genetic variation increases during biological invasion by a Cuban lizard

A genetic paradox exists in invasion biology: how do introduced populations, whose genetic variation has probably been depleted by population bottlenecks, persist and adapt to new conditions? Lessons from conservation genetics show that reduced genetic variation due to genetic drift and founder effects limits the ability of a population to adapt, and small population size increases the risk of extinction. Nonetheless, many introduced species experiencing these same conditions during initial introductions persist, expand their ranges, evolve rapidly and become invasive. To address this issue, we studied the brown anole, a worldwide invasive lizard. Genetic analyses indicate that at least eight introductions have occurred in Florida from across this lizards native range, blending genetic variation from different geographic source populations and producing populations that contain substantially more, not less, genetic variation than native populations. Moreover, recently introduced brown anole populations around the world originate from Florida, and some have maintained these elevated levels of genetic variation. Here we show that one key to invasion success may be the occurrence of multiple introductions that transform among-population variation in native ranges to within-population variation in introduced areas. Furthermore, these genetically variable populations may be particularly potent sources for introductions elsewhere. The growing problem of invasive species introductions brings considerable economic and biological costs. If these costs are to be mitigated, a greater understanding of the causes, progression and consequences of biological invasions is needed.

The genome of the green anole lizard and a comparative analysis with birds and mammals

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse—more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.

Phylogenetic comparative methods and the geography of speciation

The geography of speciation has long been contentious. In recent years, phylogenetic approaches have been proposed to determine the geographical mode of speciation. If reliable, these methods not only provide a means of settling the debate about the geography of speciation, but also indicate that sympatric speciation is surprisingly common and that peripatric speciation is relatively rare. Similar to any phylogenetic inference, reconstructions of speciation mode are only useful if the underlying assumptions of the method are met. In this case, the key assumption is that the geographical range of both extant and ancestral species at the time of speciation can be inferred from present-day distributions. We discuss whether, and under what circumstances, such assumptions could be met. We conclude that interspecific phylogenies are unable to test alternative hypotheses concerning the geography of speciation rigorously because of the lability of geographical ranges and the lack of correlation between the role of adaptive processes and geographical mode of speciation.

Niche lability in the evolution of a Caribbean lizard community

Niche conservatism—the tendency for closely related species to be ecologically similar—is widespread. However, most studies compare closely related taxa that occur in allopatry; in sympatry, the stabilizing forces that promote niche conservatism, and thus inhibit niche shifts, may be countered by natural selection favouring ecological divergence to minimize the intensity of interspecific interactions. Consequently, the relative importance of niche conservatism versus niche divergence in determining community structure has received little attention. Here, we examine a tropical lizard community in which species have a long evolutionary history of ecological interaction. We find that evolutionary divergence overcomes niche conservatism: closely related species are no more ecologically similar than expected by random divergence and some distantly related species are ecologically similar, leading to a community in which the relationship between ecological similarity and phylogenetic relatedness is very weak. Despite this lack of niche conservatism, the ecological structuring of the community has a phylogenetic component: niche complementarity only occurs among distantly related species, which suggests that the strength of ecological interactions among species may be related to phylogeny, but it is not necessarily the most closely related species that interact most strongly.

Ecological opportunity and the rate of morphological evolution in the diversification of Greater Antillean anoles.

The pace of phenotypic diversification during adaptive radiation should decrease as ecological opportunity declines. We test this prediction using phylogenetic comparative analyses of a wide range of morphological traits in Greater Antillean Anolis lizards. We find that the rate of diversification along two important axes of Anolis radiation—body size and limb dimensions—decreased as opportunity declined, with opportunity quantified either as time elapsed in the radiation or as the diversity of competing anole lineages inferred to have been present on an island at different times in the past. Most previous studies of the ecological opportunity hypothesis have focused on the rate of species diversification; our results provide a complementary perspective, indicating that the rate of phenotypic diversification declines with decreasing opportunity in an adaptive radiation.

Equilibrium speciation dynamics in a model adaptive radiation of island lizards

The relative importance of equilibrium and nonequilibrium processes in shaping patterns of species richness is one of the most fundamental questions in biodiversity studies. If equilibrium processes predominate, then ecological interactions presumably limit species diversity, potentially through diversity dependence of immigration, speciation, and extinction rates. Alternatively, species richness may be limited by the rate at which diversity arises or by the amount of time available for diversification. These latter explanations constitute nonequilibrium processes and can apply only to biotas that are unsaturated or far from diversity equilibria. Recent studies have challenged whether equilibrium models apply to biotas assembled through in situ speciation, as this process may be too slow to achieve steady-state diversities. Here we demonstrate that speciation rates in replicate Caribbean lizard radiations have undergone parallel declines to equilibrium conditions on three of four major islands. Our results suggest that feedback between total island diversity and per-capita speciation rates scales inversely with island area, with proportionately greater declines occurring on smaller islands. These results are consistent with strong ecological controls on species richness and suggest that the iconic adaptive radiation of Caribbean anoles may have reached an endpoint.

Quantifying the roles of ecology and geography in spatial genetic divergence

Investigating the properties of ecological landscapes that influence gene flow among populations can provide key insights into the earliest stages of biological divergence. Both ecological and geographical factors can reduce gene flow, which can lead to population divergence, but we know little of the relative strengths of these phenomena in nature. Here, we use a novel application of structural equation modelling to quantify the contributions of ecological and geographical isolation to spatial genetic divergence in 17 species of Anolis lizards. Our comparative analysis shows that although both processes contributed significantly, geographical isolation explained substantially more genetic divergence than ecological isolation (36.3 vs. 17.9% of variance respectively), suggesting that despite the proposed ubiquity of ecological divergence, non-ecological factors play the dominant role in the evolution of spatial genetic divergence.

POOR STATISTICAL PERFORMANCE OF THE MANTEL TEST IN PHYLOGENETIC COMPARATIVE ANALYSES

The Mantel test, based on comparisons of distance matrices, is commonly employed in comparative biology, but its statistical properties in this context are unknown. Here, we evaluate the performance of the Mantel test for two applications in comparative biology: testing for phylogenetic signal, and testing for an evolutionary correlation between two characters. We find that the Mantel test has poor performance compared to alternative methods, including low power and, under some circumstances, inflated type‐I error. We identify a remedy for the inflated type‐I error of three‐way Mantel tests using phylogenetic permutations; however, this test still has considerably lower power than independent contrasts. We recommend that use of the Mantel test should be restricted to cases in which data can only be expressed as pairwise distances among taxa.