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Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. Our results strongly resolve most squamate relationships and reveal some surprising results. In contrast to most other recent studies, we find that dibamids and gekkotans are together the sister group to all other squamates. Remarkably, we find that the distinctive scolecophidians (blind snakes) are paraphyletic with respect to other snakes, suggesting that snakes were primitively burrowers and subsequently re-invaded surface habitats. Finally, we find that some clades remain poorly supported, despite our extensive data. Our analyses show that weakly supported clades are associated with relatively short branches for which individual genes often show conflicting relationships. These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets.

Investigates the major transformations in the body form of lizards over evolutionary time. List of evolutionary changes involved in the body transformations; Characteristics of snakelike lizards; Explanation for the dichotomy in the body form and habitat of the snakelike lizards; Factors which contribute to the evolution of lizards into a snakelike form.

Allozyme data are widely used to infer the phylogenies of populations and closely-related species. Numerous parsimony, distance, and likelihood methods have been proposed for phylogenetic analysis of these data; the relative merits of these methods have been debated vigorously, but their accuracy has not been well explored. In this study, I compare the performance of 13 phylogenetic methods (six parsimony, six distance, and continuous maximum likelihood) by applying a congruence approach to eight allozyme data sets from the literature. Clades are identified that are supported by multiple data sets other than allozymes (e.g. morphology, DNA sequences), and the ability of different methods to recover these «known» clades is compared. The results suggest that (1) distance and likelihood methods generally outperform parsimony methods, (2) methods that utilize frequency data tend to perform well, and (3) continuous maximum likelihood is among the most accurate methods, and appears to be robust to violations of its assumptions. These results are in agreement with those from recent simulation studies, and help provide a basis for empirical workers to choose among the many methods available for analysing allozyme characters.

A widespread trend in animals is the evolution of morphological ornaments and behaviours that are involved in aggressive and courtship displays. These display traits are important from the standpoint of communication, sexual selection, and speciation. Previous authors have suggested that the evolution of display morphology and display behaviour should be closely linked. In this study, I tested for this association with behavioural and morphological data for 59 taxa of phrynosomatid lizards using phylogenetic comparative methods (Maddison's concentrated changes test and Felsenstein's independent contrasts). The results showed little significant association between features of display morphology and behaviour, suggesting that the evolution of these traits is not tightly coupled. This decoupling is particularly evident in the genus Sceloporus, in which several species have lost the display coloration but retain unmodified display behaviour. The results also suggest that display morphology is more evolutionarily labile than display behaviour in this group.

Species are fundamental units in studies of systematics, biodiversity and ecology, but their delimitation has been relatively neglected methodologically. Species are typically circumscribed based on the presence of fixed (intraspecifically invariant or non–overlapping) diagnostic morphological characters which distinguish them from other species. In this paper, we argue that determining whether diagnostic characters are truly fixed with certainty is generally impossible with finite sample sizes and we show that sample sizes of hundreds or thousands of individuals may be necessary to have a reasonable probability of detecting polymorphisms in diagnostic characters at frequencies approaching zero. Instead, we suggest that using a non–zero frequency cut–off may be a more realistic and practical criterion for character–based species delimitation (for example, allowing polymorphisms in the diagnostic characters at frequencies of 5 or less). Given this argument, we then present a simple statistical method to evaluate whether at least one of a set of apparently diagnostic characters is below the frequency cut–off. This method allows testing of the strength of the evidence for species distinctness and is readily applicable to empirical studies.

Abstract Polymorphism, or variation within species, is common in all kinds of data and is the major focus of research on microevolution. However, polymorphism is often ignored by those who study macroevolution: systematists and comparative evolutionary biologists. Polymorphism may have a profound impact on phylogeny reconstruction, species-delimitation, and studies of character evolution. A variety of methods are used to deal with polymorphism in phylogeny reconstruction, and many of these methods have been extremely controversial for more than 20 years. Recent research has attempted to address the accuracy of these methods (their ability to estimate the true phylogeny) and to resolve these issues, using computer simulation, congruence, and statistical analyses. These studies suggest three things: that (a) the exclusion of polymorphic characters (as is commonly done in morphological phylogenetics) is unjustified and may greatly decrease accuracy relative to analyses that include these characters; (b) methods that incorporate frequency information on polymorphic characters tend to perform best, and (c) distance and likelihood methods designed for polymorphic data may often outperform parsimony methods. Although rarely discussed, polymorphism may also have a major impact on comparative studies of character evolution, such as the reconstruction of ancestral character states. Finally, polymorphism is an important issue in the delimitation of species, although this area has been somewhat neglected methodologically. The integration of within-species variation and microevolutionary processes into studies of systematics and comparative evolutionary biology is another example of the benefits of exchange of ideas between the fields of population genetics and systematics.

Squamate reptiles (lizards and snakes) are the most diverse group of terrestrial vertebrates, with more than 10 000 species. Despite considerable effort to resolve relationships among major squamates clades, some branches have remained difficult. Among the most vexing has been the placement of snakes among lizard families, with most studies yielding only weak support for the position of snakes. Furthermore, the placement of iguanian lizards has remained controversial. Here we used targeted sequence capture to obtain data from 4178 nuclear loci from ultraconserved elements from 32 squamate taxa (and five outgroups) including representatives of all major squamate groups. Using both concatenated and species-tree methods, we recover strong support for a sister relationship between iguanian and anguimorph lizards, with snakes strongly supported as the sister group of these two clades. These analyses strongly resolve the difficult placement of snakes within squamates and show overwhelming support for the contentious position of iguanians. More generally, we provide a strongly supported hypothesis of higher-level relationships in the most species-rich tetrapod clade using coalescent-based species-tree methods and approximately 100 times more loci than previous estimates.

Climate change may soon threaten much of global biodiversity, especially if species cannot adapt to changing climatic conditions quickly enough. A critical question is how quickly climatic niches change, and if this speed is sufficient to prevent extinction as climates warm. Here, we address this question in the grass family (Poaceae). Grasses are fundamental to one of Earth's most widespread biomes (grasslands), and provide roughly half of all calories consumed by humans (including wheat, rice, corn and sorghum). We estimate rates of climatic niche change in 236 species and compare these with rates of projected climate change by 2070. Our results show that projected climate change is consistently faster than rates of niche change in grasses, typically by more than 5000-fold for temperature-related variables. Although these results do not show directly what will happen under global warming, they have troubling implications for a major biome and for human food resources.

The major clades of vertebrates differ dramatically in their current species richness, from 2 to more than 32 000 species each, but the causes of this variation remain poorly understood. For example, a previous study noted that vertebrate clades differ in their diversification rates, but did not explain why they differ. Using a time-calibrated phylogeny and phylogenetic comparative methods, I show that most variation in diversification rates among 12 major vertebrate clades has a simple ecological explanation: predominantly terrestrial clades (i.e. birds, mammals, and lizards and snakes) have higher net diversification rates than predominantly aquatic clades (i.e. amphibians, crocodilians, turtles and all fish clades). These differences in diversification rates are then strongly related to patterns of species richness. Habitat may be more important than other potential explanations for richness patterns in vertebrates (such as climate and metabolic rates) and may also help explain patterns of species richness in many other groups of organisms.

The use of discrete, intraspecifically variable characters in parsimony analysis is reviewed. Seven data sets (two from morphology and five from allozymes) were analyzed to (1) compare different methods for treating polymorphic characters, (2) test for phylogenetic information in polymorphic characters, and (3) determine if there is a relationship between homoplasy and intraspecific variability. The performance of eight methods was compared using five criteria (number of characters treated as informative, number of shortest trees, phylogenetic signal, number of nodes supported by bootstrapping, and sensitivity to reduced sample size). Approaches that incorporate explicit frequency information perform best overall for all the criteria, although the “majority” method ties for best for the bootstrapping criterion. Levels of phylogenetic information in the polymorphic characters differed greatly among data sets and methods. Polymorphic characters in most data sets contained significant phylogenetic structure using most methods, but only one, the frequency method, extracted significant signal from the polymorphic characters in all seven data sets. Fixed characters appear to contain more signal than polymorphic characters, and homoplasy is significantly and positively correlated with intraspecific variability. This study supports the traditional view that polymorphic characters are less reliable ininferring phylogeny but does not necessarily support their exclusion. Systematists working with morphological data often do not report intraspecific variation, the frequencies ofdifferent traits, or how polymorphic characters are screened and analyzed; this situationshould change.

Intraspecific variation is ubiquitous in systematic characters, yet systematists often do not deal with polymorphism explicity. For example, morphological systematists typically exclude characters in which any or “too much” polymorphism is observed, and molecular systematists often avoid intraspecific variation by sampling a single individual per species. Recent empirical studies have suggested that polymorphic characters contain significant phylogenetic information but are more homoplastic than fixed characters. Given these two observations, should including polymorphic characters increase or decrease accuracy? We addressed this question using simulated data sets that also show a strong relationship between homoplasy and intraspecific variability. Data sets were generated with eight species, two alleles per locus, and a variety of branch lengths, number of loci, and sample sizes (individuals sampled per species). The data sets were analyzed using eight parsimony coding methods (with and without a priori and successive weighting) and different variability thresholds for excluding polymorphic characters. Excluding polymorphic characters decreased accuracy under almost all conditions examined, even when only the more variable characters were excluded. Sampling a single individual per species also consistently decreased accuracy. Thus, two common approaches for dealing with intraspecific variation in morphological and molecular systematics can give relatively poor estimates of phylogeny. In contrast, the unweighted frequency method, including polymorphic characters and sampling a reasonable number of individuals per species (n ≥ 5), can give accurate results under a variety of conditions.