Cryptic diversity in the Mexican highlands: Thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus).

With the continued adoption of genome-scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent-based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (>3,000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent-based methods. Unpartitioned and partitioned maximum likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp. ASTRAL analysis on a subset of the more variable loci also results in a tree consistent with concatenation and bpp, whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species tree inference using SVDquartets, warranting additional investigation on optimal data characteristics for this method. Species delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent-based species tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data.

The first riparian skink (Genus: Sphenomorphus Strauch, 1887) from Peninsular Malaysia and its relationship to other Indochinese and Sundaic species.

Recently discovered populations of skinks of the genus Sphenomorphus from central Peninsular Malaysia represent a new species, S. sungaicolus sp. nov., and the first riparian skink known from Peninsular Malaysia. Morphological analyses of an earlier specimen reported as S. tersus from the Forest Research Institute of Malaysia (FRIM), Selangor indicate that it too is the new riparian species S. sungaicolus sp. nov. Additionally, two specimens from the Tembat Forest Reserve, Hulu Terengganu, Kelantan and another from Ulu Gombak, Selangor have been diagnosed as new the species. The latter specimen remained unidentified in the Bernice Pauahi Bishop Museum, Honolulu, Hawaii since its collection in June 1962. Morphological and molecular analyses demonstrate that S. sungaicolus sp. nov. forms a clade with the Indochinese species S. maculatus, S. indicus, and S. tersus and is the sister species of the latter. Sphenomorphus sungaicolus sp. nov. can be differentiated from all other members of this clade by having a smaller SVL (66.5-89.6 mm); 39-44 midbody scale rows; 72-81 paravertebral scales; 74-86 ventral scales; a primitive plantar scale arrangement; and 20-22 scale rows around the tail at the position of the 10th subcaudal.

Additions to Philippine Slender Skinks of the Brachymeles bonitae Complex (Reptilia: Squamata: Scincidae) I: a new species from Lubang Island.

A new species of slender skink is described from the Philippines. The species is endemic to Lubang Island, and is assigned to the Brachymeles bonitae Complex based on phenotypic and genetic data. Specimens were collected from Lubang Island between 1991 and 2012, and were examined based on morphological data (qualitative traits, meristic counts, and mensural measurements). Published genetic sequence data from phylogenetic studies of the genus reveal the new species to be highly divergent from congeners. Brachymeles ligtas sp. nov. is differentiated from other members of the genus based on a number of distinct morphological features, including small body size (SVL 60.7-79.6 mm), bidactyl fore-limbs, digitless hind limbs, high number of presacral vertebrae (50), and the absence of auricular openings. Additionally, the new species has diagnostic, distinct dorsal head scale patterns. This new species becomes the only member of the genus known to occur on the deep-ocean island of Lubang.

The transfer of two clades of Malaysian Sphenomorphus Fitzinger (Squamata: Scincidae) into the genus Tytthoscincus Linkem, Diesmos, & Brown and the description of a new Malaysian swamp-dwelling species.

Phylogenetic analyses based on the mitochondrial gene ND2 and its flanking tRNAs indicate the diminutive upland and insular species Sphenomorphus bukitensis, S. butleri, S. langkawiensis, S. perhentianensis, and S. temengorensis form a monophyletic group that is phylogenetically embedded within the Southeast Asian genus Tytthoscincus. The analyses also indicate that a new swamp-dwelling skink from the Bukit Panchor State Park, Pulau Pinang, Peninsular Malaysia is the sister species to the swamp-dwelling species S. sibuensis from Pulau Sibu, Johor and Singapore and that these two are also embedded in the genus Tytthoscincus. By transferring the two Peninsular Malaysian clades of Sphenomorphus into the genus Tytthoscincus, the monophyly of the latter is maintained. The new species T. panchorensis sp. nov. can be distinguished from all other species of Tytthoscincus by having a unique combination of morphological and color pattern characteristics.

Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)?

BACKGROUND: Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. We collected targeted sequence capture data from 585 nuclear loci (541 ultraconserved elements and 44 protein-coding genes) to estimate the phylogenetic relationships among iguanian lizards in the North American genus Sceloporus. We tested for diversification rate shifts to determine if rapid radiation in the genus is correlated with chromosomal evolution. RESULTS: The phylogenomic trees that we obtained for Sceloporus using concatenation and coalescent-based species tree inference provide strong support for the monophyly and interrelationships among nearly all major groups. The diversification analysis supported one rate shift on the Sceloporus phylogeny approximately 20-25 million years ago that is associated with the doubling of the speciation rate from 0.06 species/million years (Ma) to 0.15 species/Ma. The posterior probability for this rate shift occurring on the branch leading to the Sceloporus species groups exhibiting increased chromosomal diversity is high (posterior probability = 0.997). CONCLUSIONS: Despite high levels of gene tree discordance, we were able to estimate a phylogenomic tree for Sceloporus that solves some of the taxonomic problems caused by previous analyses of fewer loci. The taxonomic changes that we propose using this new phylogenomic tree help clarify the number and composition of the major species groups in the genus. Our study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of Sceloporus across North America.

Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).

The anomaly zone, defined by the presence of gene tree topologies that are more probable than the true species tree, presents a major challenge to the accurate resolution of many parts of the Tree of Life. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data via loci concatenation will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies often employ coalescent-based species tree methods to avoid the anomaly zone, but to this point these studies have not had a method for providing any direct evidence that the species tree is actually in the anomaly zone. In this study, we use 16 species of lizards in the family Scincidae to investigate whether nodes that are difficult to resolve place the species tree within the anomaly zone. We analyze new phylogenomic data (429 loci), using both concatenation and coalescent-based species tree estimation, to locate conflicting topological signal. We then use the unifying principle of the anomaly zone, together with estimates of ancestral population sizes and species persistence times, to determine whether the observed phylogenetic conflict is a result of the anomaly zone. We identify at least three regions of the Scincidae phylogeny that provide demographic signatures consistent with the anomaly zone, and this new information helps reconcile the phylogenetic conflict in previously published studies on these lizards. The anomaly zone presents a real problem in phylogenetics, and our new framework for identifying anomalous relationships will help empiricists leverage their resources appropriately for investigating and overcoming this challenge.

Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing.

Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas RADseq is designed for discovering single nucleotide polymorphisms (SNPs) suitable for population genetic or phylogeographic analyses. Phylogenetic questions that span both "recent" and "deep" timescales could benefit from either type of data, but studies that directly compare the two approaches are lacking. We compared phylogenies estimated from sequence capture and double digest RADseq (ddRADseq) data for North American phrynosomatid lizards, a species-rich and diverse group containing nine genera that began diversifying approximately 55 Ma. Sequence capture resulted in 584 loci that provided a consistent and strong phylogeny using concatenation and species tree inference. However, the phylogeny estimated from the ddRADseq data was sensitive to the bioinformatics steps used for determining homology, detecting paralogs, and filtering missing data. The topological conflicts among the SNP trees were not restricted to any particular timescale, but instead were associated with short internal branches. Species tree analysis of the largest SNP assembly, which also included the most missing data, supported a topology that matched the sequence capture tree. This preferred phylogeny provides strong support for the paraphyly of the earless lizard genera Holbrookia and Cophosaurus, suggesting that the earless morphology either evolved twice or evolved once and was subsequently lost in Callisaurus.

Implications of uniformly distributed, empirically informed priors for phylogeographical model selection: a reply to Hickerson et al.

Establishing that a set of population-splitting events occurred at the same time can be a potentially persuasive argument that a common process affected the populations. Recently, Oaks et al. () assessed the ability of an approximate-Bayesian model-choice method (msBayes) to estimate such a pattern of simultaneous divergence across taxa, to which Hickerson et al. () responded. Both papers agree that the primary inference enabled by the method is very sensitive to prior assumptions and often erroneously supports shared divergences across taxa when prior uncertainty about divergence times is represented by a uniform distribution. However, the papers differ about the best explanation and solution for this problem. Oaks et al. () suggested the method's behavior was caused by the strong weight of uniformly distributed priors on divergence times leading to smaller marginal likelihoods (and thus smaller posterior probabilities) of models with more divergence-time parameters (Hypothesis 1); they proposed alternative prior probability distributions to avoid such strongly weighted posteriors. Hickerson et al. () suggested numerical-approximation error causes msBayes analyses to be biased toward models of clustered divergences because the method's rejection algorithm is unable to adequately sample the parameter space of richer models within reasonable computational limits when using broad uniform priors on divergence times (Hypothesis 2). As a potential solution, they proposed a model-averaging approach that uses narrow, empirically informed uniform priors. Here, we use analyses of simulated and empirical data to demonstrate that the approach of Hickerson et al. () does not mitigate the method's tendency to erroneously support models of highly clustered divergences, and is dangerous in the sense that the empirically derived uniform priors often exclude from consideration the true values of the divergence-time parameters. Our results also show that the tendency of msBayes analyses to support models of shared divergences is primarily due to Hypothesis 1, whereas Hypothesis 2 is an untenable explanation for the bias. Overall, this series of papers demonstrates that if our prior assumptions place too much weight in unlikely regions of parameter space such that the exact posterior supports the wrong model of evolutionary history, no amount of computation can rescue our inference. Fortunately, as predicted by fundamental principles of Bayesian model choice, more flexible distributions that accommodate prior uncertainty about parameters without placing excessive weight in vast regions of parameter space with low likelihood increase the method's robustness and power to detect temporal variation in divergences.

Taxonomic revision of the semi-aquatic skink Parvoscincus leucospilos (Reptilia: Squamata: Scincidae), with description of three new species.

We review the recent discovery of multiple populations of the enigmatic, semi-aquatic Sphenomorphus Group skink, Parvoscincus leucospilos Peters, and investigate the morphological and genetic diversity of isolated, allopatric populations of this unique skink. Our investigations support the recognition of four unique evolutionary lineages distributed across Luzon Island in the Philippines, three of which are herein described as new species (P. tikbalangi sp. nov., P. manananggalae sp. nov., and P. duwendorum sp. nov.). All four recognized species are genetically divergent in both mitochondrial and nuclear DNA sequences, and morphologically distinct. The description of three new Luzon Island endemic species adds to the growing body of literature suggesting that mechanisms driving the accumulation of vertebrate diversity in the Philippines may vary regionally across the archipelago. 

Multilocus species delimitation in the Crotalus triseriatus species group (Serpentes: Viperidae: Crotalinae), with the description of two new species.

Members of the Crotalus triseriatus species group of montane rattlesnakes are widely distributed across the highlands of Mexico and southwestern USA. Although five species are currently recognized within the group, species limits remain to be tested. Genetic studies suggest that species may be paraphyletic and that at least one cryptic species may be present. We generate 3,346 base pairs of DNA sequence data from seven nuclear loci to test competing models of species delimitation in the C. triseriatus group using Bayes factor delimitation. We also examine museum specimens from the Trans-Mexican Volcanic Belt for evidence of cryptic species. We find strong support for a nine-species model and genetic and morphological evidence for recognizing two new species within the group, which we formally describe here. Our results suggest that the current taxonomy of the C. triseriatus species group does not reflect evolutionary history. We suggest several conservative taxonomic changes to the group, but future studies are needed to better clarify relationships among species and examine genetic patterns and structure within wide-ranging lineages.

A hybrid phylogenetic-phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification.

Africa is renowned for its biodiversity and endemicity, yet little is known about the factors shaping them across the continent. African Agama lizards (45 species) have a pan-continental distribution, making them an ideal model for investigating biogeography. Many species have evolved conspicuous sexually dimorphic traits, including extravagant breeding coloration in adult males, large adult male body sizes, and variability in social systems among colorful versus drab species. We present a comprehensive time-calibrated species tree for Agama, and their close relatives, using a hybrid phylogenetic-phylogenomic approach that combines traditional Sanger sequence data from five loci for 57 species (146 samples) with anchored phylogenomic data from 215 nuclear genes for 23 species. The Sanger data are analyzed using coalescent-based species tree inference using (*)BEAST, and the resulting posterior distribution of species trees is attenuated using the phylogenomic tree as a backbone constraint. The result is a time-calibrated species tree for Agama that includes 95% of all species, multiple samples for most species, strong support for the major clades, and strong support for most of the initial divergence events. Diversification within Agama began approximately 23 million years ago (Ma), and separate radiations in Southern, East, West, and Northern Africa have been diversifying for >10Myr. A suite of traits (morphological, coloration, and sociality) are tightly correlated and show a strong signal of high morphological disparity within clades, whereby the subsequent evolution of convergent phenotypes has accompanied diversification into new biogeographic areas.

Comparative species divergence across eight triplets of spiny lizards (Sceloporus) using genomic sequence data.

Species divergence is typically thought to occur in the absence of gene flow, but many empirical studies are discovering that gene flow may be more pervasive during species formation. Although many examples of divergence with gene flow have been identified, few clades have been investigated in a comparative manner, and fewer have been studied using genome-wide sequence data. We contrast species divergence genetic histories across eight triplets of North American Sceloporus lizards using a maximum likelihood implementation of the isolation-migration (IM) model. Gene flow at the time of species divergence is modeled indirectly as variation in species divergence time across the genome or explicitly using a migration rate parameter. Likelihood ratio tests (LRTs) are used to test the null model of no gene flow at speciation against these two alternative gene flow models. We also use the Akaike information criterion to rank the models. Hundreds of loci are needed for the LRTs to have statistical power, and we use genome sequencing of reduced representation libraries to obtain DNA sequence alignments at many loci (between 340 and 3,478; mean = 1,678) for each triplet. We find that current species distributions are a poor predictor of whether a species pair diverged with gene flow. Interrogating the genome using the triplet method expedites the comparative study of species divergence history and the estimation of genetic parameters associated with speciation.

Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events.

Approximate Bayesian computation (ABC) is rapidly gaining popularity in population genetics. One example, msBayes, infers the distribution of divergence times among pairs of taxa, allowing phylogeographers to test hypotheses about historical causes of diversification in co-distributed groups of organisms. Using msBayes, we infer the distribution of divergence times among 22 pairs of populations of vertebrates distributed across the Philippine Archipelago. Our objective was to test whether sea-level oscillations during the Pleistocene caused diversification across the islands. To guide interpretation of our results, we perform a suite of simulation-based power analyses. Our empirical results strongly support a recent simultaneous divergence event for all 22 taxon pairs, consistent with the prediction of the Pleistocene-driven diversification hypothesis. However, our empirical estimates are sensitive to changes in prior distributions, and our simulations reveal low power of the method to detect random variation in divergence times and bias toward supporting clustered divergences. Our results demonstrate that analyses exploring power and prior sensitivity should accompany ABC model selection inferences. The problems we identify are potentially mitigable with uniform priors over divergence models (rather than classes of models) and more flexible prior distributions on demographic and divergence-time parameters.

Systematic revision of the Parvoscincus decipiens (Boulenger, 1894) complex of Philippine forest skinks (Squamata: Scincidae: Lygosominae) with descriptions of seven new species.

Analysis of external morphological characters, color pattern, and DNA sequence data, plus consideration of biogeographical patterns, leads us to the hypothesis that the Parvoscincus decipiens complex of Philippine forest skinks consists of a minimum of eight highly divergent, phenotypically distinct, cohesive evolutionary lineages. We rectify this taxonomic underestimation of species diversity with formal descriptions of seven new species (P. abstrusus sp. nov., P. agtorum sp. nov., P. arvindiesmosi sp. nov., P aurorus sp. nov., P banahaoensis sp. nov., P. jimmymcguirei sp. nov., and P. palaliensis sp. nov.) and highlight geographical sampling deficiencies, which, if addressed with additional fieldwork, should lead to additional new species discoveries. Due to the difficulty of identifying non-overlapping differences in scalation on similarly sized, small-bodied skinks, species level diversity in diminutive Philippine forest skinks is undoubtedly substantially underestimated.

Molecular systematics of the Philippine forest skinks (Squamata: Scincidae: Sphenomorphus): testing morphological hypotheses of interspecific relationships.

Skinks of the genus Sphenomorphus are the most diverse clade of squamates in the Philippine Archipelago. Morphological examination of these species has defined six phenotypic groups that are commonly used in characterizations of taxonomic hypotheses. We used a molecular phylogeny based on four mitochondrial and two nuclear genes to assess the group's biogeographical history in the archipelago and examine the phylogenetic validity of the currently recognized Philippine species groups. We re-examined traditional characters used to define species groups and used multivariate statistics to quantitatively evaluate group structure in morphometric space. Clustering analyses of phenotypic similarity indicate that some (but not all) members of previously defined species groups are phenotypically most similar to other members of the same group. However, when species group membership was mapped on our partitioned Bayesian phylogenetic hypothesis, only one species group corresponds to a clade; all other species group arrangements are strongly rejected by our phylogeny. Our results demonstrate that (1) previously recognized species group relationships were misled by phenotypic convergence; (2) Sphenomorphus is widely paraphyletic; and (3) multiple lineages have independently invaded the Philippines. Based on this new perspective on the phylogenetic relationships of Philippine Sphenomorphus, we revise the archipelago's diverse assemblage of species at the generic level, and resurrect and/or expand four previously recognized genera, and describe two new genera to accommodate the diversity of Philippine skinks of the Sphenomorphus group. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163, 1217-1243.

Phylogeography and historical demography of Polypedates leucomystax in the islands of Indonesia and the Philippines: evidence for recent human-mediated range expansion?

Southeast Asia's widespread species offer unique opportunities to explore the effects of geographical barriers to dispersal on patterns of vertebrate lineage diversification. We analyzed mitochondrial gene sequences (16S rDNA) from a geographically widespread sample of 266 Southeast Asian tree frogs, including 244 individuals of Polypedates leucomystax and its close relatives. Our expectation was that lineages on island archipelagos would exhibit more substantial geographic structure, corresponding to the geological history of terrestrial connectivity in this region, compared to the Asian mainland. Contrary to predictions, we found evidence of numerous highly divergent lineages from a limited area on the Asian mainland, but fewer lineages with shallower divergences throughout oceanic islands of the Philippines and Indonesia. Surprisingly and in numerous instances, lineages in the archipelagos span distinct biogeographical provinces. Phylogeographic analyses identified four major haplotype clades; summary statistics, mismatch distributions, and Bayesian coalescent inference of demography provide support for recent range expansion, population growth, and/or admixture in the Philippine and some Sulawesi populations. We speculate that the current range of P. leucomystax in Southeast Asia is much larger now than in the recent past. Conversion of forested areas to monoculture agriculture and transportation of agricultural products between islands may have facilitated unprecedented population and range expansion in P. leucomystax throughout thousands of islands in the Philippine and Indonesian archipelagos.

Species boundaries and cryptic lineage diversity in a Philippine forest skink complex (Reptilia; Squamata; Scincidae: Lygosominae).

In the megadiverse conservation hotspot of the Philippines, biodiversity is not uniformly distributed throughout the archipelago, but hierarchically partitioned into islands and island groups that were conjoined during the mid- to late-Pleistocene. Few species groups are widely distributed throughout the archipelago, but some exceptions exist, such as the common scincid lizards of the Sphenomorphus jagori complex (including S. jagori, S. coxi, and S. abdictus). Using mtDNA haplotype data we test biogeographic and taxonomic predictions in these abundant, large-bodied, forest floor lizards and arrive at conclusions that differ significantly from both past, and current, appraisals of species diversity. In contrast to expectations based on existing taxonomy (three species, each with two subspecies), we find evidence of at least eleven highly divergent species lineages diagnosed by haplotypic variation. Each lineage corresponds to a biogeographically circumscribed distribution (i.e., isolated islands or geological components of islands), suggesting lineage cohesion and allopatric differentiation. Parametric bootstrapping tests reject taxonomic and biogeographic hypotheses and suggest a complex pattern of unpredicted relationships. Only one of the former species (S. jagori) appears as a monophyletic entity (including four allopatric, highly divergent lineages that we suspect may represent evolutionary species), and the remaining species are paraphyletic, necessitating a comprehensive future taxonomic revision. The pattern of biogeographic provincialism and hidden cryptic species diversity detected here leads us to suspect that even the most common, presumably well-studied, and widespread species complexes in the Philippines are in need of thorough analysis with modern genetic and phylogenetic techniques. Such studies of speciation genetics in these common, widely distributed groups may lead to a better understanding of the genetic underpinnings of biodiversity, allow for an enhanced appreciation of the evolutionary history of this model island archipelago, and enable more informed conservation planning in a global biodiversity hotspot.

Choice of topology estimators in Bayesian phylogenetic analysis.

Wheeler WC and Pickett KM (2008. Topology-Bayes versus clade-Bayes in phylogenetic analysis. Mol Biol Evol. 25:447-453.) discuss two ways of summarizing the posterior probability distribution of a Bayesian phylogenetic analysis, which they refer to as "topology-Bayes" and "clade-Bayes." They claim that the clade-Bayes approach leads to problems such as "exaggerated clade support, inconsistently biased priors, and the impossibility of topology hypothesis testing," which are not problems for the topology-Bayes approach. However, their argument for topology-Bayes over clade-Bayes is based on errors in the interpretation of summary statistics associated with Bayesian phylogenetic analysis. Although there is a well-documented difference between the maximum posterior probability topology and the majority-rule consensus topology (the established terms for topology-Bayes and clade-Bayes summaries, respectively), both have a place in phylogenetic analysis. Choice of summarization strategy should be driven by choice of parameters that need to be estimated versus those to be marginalized given the evolutionary questions being asked or hypotheses being tested.

Mitochondrial introgression and incomplete lineage sorting through space and time: phylogenetics of crotaphytid lizards.

We investigate the roles of mitochondrial introgression and incomplete lineage sorting during the phylogenetic history of crotaphytid lizards. Our Bayesian phylogenetic estimate for Crotaphytidae is based on analysis of mitochondrial DNA sequence data for 408 individuals representing the 12 extant species of Crotaphytus and Gambelia. The mitochondrial phylogeny disagrees in several respects with a previously published morphological tree, as well as with conventional species designations, and we conclude that some of this disagreement stems from hybridization-mediated mitochondrial introgression, as well as from incomplete lineage sorting. Unidirectional introgression of Crotaphytus collaris (western collared lizard) mitochondria into C. reticulatus (reticulate collared lizard) populations in the Rio Grande Valley of Texas has resulted in the replacement of ancestral C. reticulatus mitochondria over approximately two-thirds of the total range of the species, a linear distance of approximately 270 km. Introgression of C. collaris mitochondria into C. bicinctores (Great Basin collared lizard) populations in southwestern Arizona requires a more complex scenario because at least three temporally separated and superimposed introgression events appear to have occurred in this region. We propose an "introgression conveyor" model to explain this unique pattern of mitochondrial variation in this region. We show with ecological niche modeling that the predicted geographical ranges of C. collaris, C. bicinctores, and C. reticulatus during glacial maxima could have provided enhanced opportunities for past hybridization. Our analyses suggest that incomplete lineage sorting and/or introgression has further confounded the phylogenetic placements of additional species including C. nebrius, C. vestigium, C. insularis, C. grismeri, and perhaps G. copei. Despite many independent instances of interspecific hybridization among crotaphytid lizards, the species continue to maintain morphological and geographic cohesiveness throughout their ranges.