Cytonuclear genetic structure of a hybrid zone in lizards of the Sceloporus grammicus complex (Sauria, Phrynosomatidae)

Lizards of the Sceloporus grammicus complex are comprised of multiple chromosome races that form several zones of parapatric hybridization in central Mexico. We scored diagnostic mitochondrial DNA (mtDNA) haplotypes and autosomal chromosome markers in a sample of 342 lizards from one well-defined zone between 2n = 34 and 2n = 46 races. A two-part analysis was performed on this data set in an attempt to infer the predominant evolutionary forces shaping the cytonuclear structure of this zone. The complications posed by its spatial structure were addressed by analysing a hierarchical series of smaller subsamples chosen to approximate single mating units. Two critical conclusions were drawn from this first-stage analysis. First and foremost, the three chromosomes have largely concordant cytonuclear disequilibrium patterns within each subsample with adequate numbers of individuals for detecting nonrandom cytonuclear associations. This suggests that the cytonuclear structure of this zone is predominantly a result of deterministic genome-wide forces rather than genetic drift or deterministic forces specific to individual chromosomes or loci. Second, the fit of a series of migration models to the data shows that the cytonuclear structure of the subsamples is well accounted for by continued gene flow from the two parental races alone, with random mating with respect to cytonuclear genotype and no other evolutionary forces. These results motivate several further empirical and theoretical investigations to refine our understanding of the relative roles of migration and other potentially important forces such as natural selection and genetic drift, in this and other hybrid zones.     

Reproduction and sexual dimorphism in the viviparous lizard Sceloporus palaciosi (Squamata: Phrynosomatidae) from the Trans‐Mexican Volcanic Belt,Mexico

In this study, sexual dimorphism, reproductive cycles, litter size and offspring size of a population of the little‐known species Sceloporus palaciosi in central Mexico were analysed. Significant male‐biased sexual size dimorphism was recorded in snout–vent length (SVL), head length, head width, forearm length and tibia length. Both sexes showed asynchronous reproductive cycles, and males reached sexual maturity at a smaller SVL (33 mm) than females (37 mm). Testes volumes were small from January to February, testicular recrudescence began from March to June, and decreased in July, but increased again in August and September, followed by a second decrease from October to December. In females, vitellogenesis began from May until ovulation in December. Embryonic development extended from November to March, and a small number of females carried embryos through July. Mean litter size was 4.0 and was positively correlated with female SVL. The length of the reproductive period in S. palaciosi recorded in this study is longer than that recorded for other populations in other parts of this species range. Further studies are needed to clarify reproductive cycles in the other isolated populations of S. palaciosi, and then extended to other species and chromosome races in the Sceloporus grammicus complex.     

Placentation in the Mexican lizard Sceloporus mucronatus (Squamata: Phrynosomatidae)

We used light microscopy to study placental structure of the lizard Sceloporus mucronatus throughout 6 months of embryonic development. Three stages of placental development could be assigned to embryos based on the arrangement of the extraembryonic membranes. A highly vascular choriovitelline placenta was present in the embryonic hemisphere and a nonvascular bilaminar omphalopleure covered most of the abembryonic hemisphere of the egg during embryonic Stages 10-28. A chorioallantoic placenta replaced the choriovitelline placenta by embryonic Stage 29 and an omphaloplacenta covered the abembryonic hemisphere at this stage. The combination of these two placental types occurred in Stage 29-36 embryos. The final stage of placentation, embryonic Stages 37-40, was characterized by an omphalallantoic placenta in the abembryonic hemisphere and a chorioallantoic placenta in the embryonic hemisphere of the egg. The choriovitelline and chorioallantoic placentae are well vascularized, with closely apposed maternal and embryonic blood vessels. These structures are the most likely sites of respiratory exchange. In contrast, the omphaloplacenta and omphalallantoic placentae contain cuboidal or columnar epithelia and these structures may function in histotrophic exchange. Placentation of S. mucronatus is similar to that of predominantly lecithotrophic species in other squamate lineages suggesting that the evolution of this placental morphology is a response to similar factors and is independent of phylogeny.     

Delimiting species: comparing methods for Mendelian characters using lizards of the Sceloporus grammicus (Squamata: Phrynosomatidae) complex

Species form the fundamental units of analysis in many areas of biology and, therefore, rigorous delimitation of this unit is important to a broad array of researchers. Recently, many new empirical methods have been proposed to delimit species in nature, and a large literature exists on the theoretical merit and superiority of each method. However, few empirical studies actually compare the results of these methods applied in the same study system. We used a large allozyme and chromosome dataset to apply a number of genetic-distance, character-based, and tree-based methods to a well-studied, data-rich system: the Sceloporus grammicus lizard complex of central Mexico. We hypothesized species boundaries under a general lineage or evolutionary species conceptual framework in an a priori fashion using mapped restriction-site data (mitochondrial DNA and nuclear rDNA), allozymes, and morphology. We then compared the ability of different methods to recover the "hypothesized evolutionary species" (HES). Highton's genetic-distance method and a tree-based method consistently recovered all four HES, although sometimes with weak support. With two exceptions, other methods recovered the same HES, but additional groups were weakly delimited and nested within the HES. Given the apparent recent divergence of some of the chromosome races and distinct populations in this complex, these are encouraging results. We emphasize the value of specifying testable criteria as clearly as possible and testing these with methods that make use of different properties of a single dataset.     

A comparison of five hybrid zones of the weta Hemideina thoracica (Orthoptera: Anostostomatidae): degree of cytogenetic differentiation fails to predict zone width

Abstract Tension zones are maintained by the interaction between selection against hybrids and dispersal of individuals. Investigating multiple hybrid zones within a single species provides the opportunity to examine differences in zone structure on a background of differences in extrinsic factors (e.g., age of the zone, ecology) or intrinsic factors (e.g., chromosomes). The New Zealand tree weta Hemideina thoracica comprises at least eight distinct chromosomal races with diploid numbers ranging from 2n = 11 (XO) to 2n = 23 (XO). Five independent hybrid zones were located that involve races differing from one another by a variety of chromosomal rearrangements. The predicted negative correlation between extent of karyotypic differentiation (measured in terms of both percent of genome and number of rearrangements) and zone width was not found. Conversely, the widest zones were those characterized by two chromosome rearrangements involving up to 35% of the genome. The narrowest zone occurred where the two races differ by a single chromosome rearrangement involving approximately 2% of the genome. The five estimates of chromosomal cline width ranged from 0.5 km to 47 km. A comparative investigation of cline width for both chromosomal and mitochondrial markers revealed a complex pattern of zone characteristics. Three of the five zones in this study showed cline concordance for the nuclear and cytoplasmic markers, and at two of the zones the clines were also coincident. Zones with the widest chromosomal clines had the widest mitochondrial DNA clines. It appears that, even within a single species, the extent of karyotypic differentiation between pairs of races is not a good predictor of the level of disadvantage suffered by hybrids.     

Atypical reproductive cycles in a population of Sceloporus grammicus (Squamata: Phrynosomatidae) from the Mexican Plateau

The spiny lizard Sceloporus grammicus (Squamata: Phrynosomatidae) is a small reptile from central México and the southern United States, occurring in a wide geographic area characterized by extensive variation in topographic and climatic regimes. Genetic variation among lineages from central México is substantial, though the extent to which this variation corresponds with life-history traits remains obscure. To address part of this puzzle, we studied a population of S. grammicus from Tepeapulco, Hidalgo, México. Male-biased sexual dimorphism was extensive in this population; males were larger than females overall, and expressed proportionately larger heads and longer limbs. Minimum size at sexual maturity was similar in the sexes (males: 43 mm; females: 42 mm). In contrast to other populations from the Central Plateau, reproductive activity of males and females was synchronous. Testicular recrudescence of adult males was initiated in October-November, and maximum testis size maintained from December to July. Female reproductive activity showed no clear seasonal pattern: females had vitellogenic follicles from October to July, and pregnant females were found throughout the year. Female body size was not related to litter size. Neither male nor female gonadal mass was correlated with any abiotic environmental variable examined. Differences in reproductive characteristics among populations of S. grammicus might be indicative of plasticity in response to local environmental conditions, local adaptation, or complex gene × environment interactions. We consider these results in the context of previously studied populations of S. grammicus from the Central Plateau and elsewhere, and propose directions for future research.     

A hybrid zone revisited: molecular and morphological analysis of the maintenance, movement, and evolution of a Great Plains avian (Cardinalidae: Pheucticus) hybrid zone

Black-headed grosbeaks ( Pheucticus melanocephalus ) and rose-breasted grosbeaks ( Pheucticus ludovicianus ) are passerine bird species known to hybridize in the Great Plains of North America. Both extrinsic (environmental) and intrinsic factors (pre- and postzygotic reproductive isolation) have been credited for the generation and maintenance of the grosbeak hybrid zone, but little is known about the genetic characteristics of this hybrid zone. To investigate the stability and extent of the grosbeak hybrid zone, we constructed clines from both molecular sequence data (mtDNA, three autosomal intron loci, and one Z-linked locus) and morphological data (morphometric analyses and hybrid index scores) to determined zone centre and width. Hybrid zone centre and width were also determined for samples collected across the zone 40 years ago from morphological data. The present and past clines were compared and provided support for stability in hybrid zone location and width, and the evolutionary implications of this are discussed. Three models of hybrid zone maintenance were investigated to consider the influence of intrinsic and extrinsic factors on this zone. Our results suggest low hybrid frequencies, a stable zone location and narrow width, and reduced hybrid fitness over the past 40 years best categorize the grosbeak hybrid zone as a tension zone.     

The ultrastructure of spermatid development during spermiogenesis within the rosebelly lizard,Sceloporus variabilis (Reptilia,Squamata, Phrynosomatidae)

Several recent studies have mapped out the characters of spermiogenesis within several species of squamates. Many of these data have shown both conserved and possibly apomorphic morphological traits that could be important in future phylogenetic analysis within Reptilia. There, however, has not been a recent study that compares spermiogenesis and its similarities or differences between two species of reptile that reside in the same genus. Thus, the present analysis details the changes to spermiogenesis in Sceloporus variabilis and then compares spermatid morphologies to that of Sceloporus bicanthalis. Many of the morphological changes that the spermatids undergo in these two species are similar or conserved, which is similar to what has been reported in other squamates. There are six main character differences that can be observed during the development of the spermatids between these two sceloporid lizards. They include the presence (S. variabilis) or absence (S. bicanthalis) of a mitochondrial/endoplasmic reticulum complex near the Golgi apparatus during acrosome development, a shallow (S. variabilis) or deep (S. bicanthalis) nuclear indentation that accommodates the acrosomal vesicle, filamentous (S. variabilis) or granular (S. bicanthalis) chromatin condensation, no spiraling (S. variabilis) or spiraling (S. bicanthalis) of chromatin during condensation, absence (S. variabilis) or presence (S. bicanthalis) of the longitudinal manchette microtubules, and the lack of (S. variabilis) or presence (S. bicanthalis) of nuclear lacunae. This is the first study that compares spermiogenic ultrastructural characters between species within the same genus. The significance of the six character differences between two distantly related species within Sceloporus is still unknown, but these data do suggest that spermiogenesis might be a good model to study the hypothesis that spermatid ontogeny is species specific. J. Morphol. 275:258–268, 2014. © 2013 Wiley Periodicals, Inc.     

Plumage and mitochondrial DNA haplotype variation across a moving hybrid zone

We analyze variation in phenotypes and mitochondrial DNA (mtDNA) haplotypes over the breeding ranges of hermit and Townsend's warblers and across two of their three hybrid zones. Within these two hybrid zones, we demonstrate that the placement, shape, and width of transitions in seven plumage characters are remarkably similar, suggesting that a balance between dispersal and sexual selection keeps these hybrid zones narrow. A consistent asymmetry in these character transition curves suggests that Townsend's warblers have a selective advantage over hermit warblers, which is presumably due to the aggressive superiority of Townsend's over hermit males (Pearson and Rohwer 2000). An association between plumage and mtDNA haplotypes shows that pure Townsend's warblers, but not pure hermit warblers, immigrate into these hybrid zones, further supporting the competitive superiority of Townsend's warblers over hermit warblers. The mitochondrial haplotype transitions across these hybrid zones are much wider than the phenotypic transitions and provide no indication that the mtDNA haplotypes representing these two warblers are selectively maintained. More importantly, the phenotypically pure populations of Townsend's warblers throughout a 2,000-km coastal strip north of the Washington hybrid zones contain a preponderance of hermit warbler mtDNA haplotypes. This result suggests massive movement of the hybrid zone between these warblers during the 5,000 years since their most recent interglacial contact. We develop a model to explain the phenotypic and genetic divergence between these warblers and the evolution of their dramatic differences in aggressiveness; we also show how differences in male aggression, in combination with biased pairing patterns, can explain the haplotype footprint recording the historical movement of this hybrid zone.     

Genomic variation in cline shape across a hybrid zone

Hybrid zones are unique biological interfaces that reveal both population level and species level evolutionary processes. A genome‐scale approach to assess gene flow across hybrid zones is vital, and now possible. In Mexican towhees (genus Pipilo), several morphological hybrid gradients exist. We completed a genome survey across one such gradient (9 populations, 140 birds) using mitochondrial DNA, 28 isozyme, and 377 AFLP markers. To assess variation in introgression among loci, cline parameters (i.e., width, center) for the 61 clinally varying loci were estimated and compiled into genomic distributions for tests against three empirical models spanning the range of observed cline shape. No single model accounts for observed variation in cline shape among loci. Numerous backcross individuals near the gradient center confirm a hybrid origin for these populations, contrary to a previous hypothesis based on social mimicry and character displacement. In addition, the observed variation does not bin into well‐defined categories of locus types (e.g., neutral vs. highly selected). Our multi‐locus analysis reveals cross‐genomic variation in selective constraints on gene flow and locus‐specific flexibility in the permeability of the interspecies membrane.     

Allozyme and mitochondrial DNA analysis of a hybrid zone between white-tailed deer and mule deer (Odocoileus) in west texas

Thirty allozyme loci and 35 mitochondrial DNA (mtDNA) restriction sites were examined in 24 white-tailed deer and 46 mule deer from a hybrid zone in West Texas. A common mtDNA genotype is shared by all of the mule deer with 67% of the white-tailed deer. At the albumin locus, 13% of the white-tailed deer and 24% of the mule deer are heterozygous, sharing alleles that are otherwise species-specific in allopatric populations; 7% of the mule deer are homozygous for the allele that is characteristic of allopatric white-tailed deer. Gene flow appears to have been bidirectional, with greater genetic introgression into mule deer. The mtDNA data suggest that matings between white-tailed and mule deer have occurred in the past. Despite evidence of genetic introgression, analysis of multilocus genotypes indicates that none of the deer examined is an F₁ hybrid. Production of such hybrids appears to be generally uncommon in North American deer; management plans that assume otherwise should be reconsidered.This work was supported by an NIH Biomedical Research Support Grant, Texas Agricultural Experiment Station Program Development and Expanded Research Awards, the Caesar Kleberg Research Program in Wildlife Ecology, and a Natural Sciences and Engineering Research Council Operating Grant.     

Staggered clines in a hybrid zone between two chromosome races of the harvestman Gagrellopsis nodulifera (Arachnida: Opiliones)

We analyzed a hybrid zone between two chromosome races (2n = 16 and 2n = 22) of a Japanese harvestman, Gagrellopsis nodulifera Sato and Suzuki (Arachnida: Opiliones: Phalangiidae). The hybrid zone is located in the eastern part of Tottori Prefecture, western Honshu. The width of the zone is approximately 5 to 15 km. Three independent tandem fusions/fissions seem to be the main cause of the karyotypic differences between the parental races. Ten karyotypic variants were found in the hybrid zone. They differed by numbers of diploid chromosomes and trivalents detected in meiosis. In most of the collecting sites, karyotypic heterozygotes were less common than expected. A positive correlation was found between number of trivalents in a karyotype and its deficiency rate. In some sites, the deficit of heterozygous individuals was accompanied by an excess of the intermediate homozygotes. One of the three transects across the zone was studied in detail. We found that three types of single heterozygotes (2n = 17, 2n = 19 and 2n = 21) formed a series of successive, spatially separated peaks along the transect. Two types of intermediate homozygotes (2n = 18 and 2n = 20) were also spatially separated. The most parsimonious explanation of such a structure is the staggering of clines of three tandem (or Robertsonian) fusion/fission variants that differentiate the parental races caused by selection against multiple heterozygotes. Analysis of nondisjunction in single heterozygotes demonstrated that there was a strong interindividual variation in nondisjunction rate. The mean frequency of aneuploid MII in single heterozygotes was 0.10 +/- 0.03. Crossover exchanges in some critical regions of trivalents result in abnormal chromosomal configurations: chromosomes with unequal chromatids and dicentric chromosomes. Frequency of crossover-induced chromosomal abnormalities was low in single heterozygotes (approximately equal to 4%), and was unexpectedly high in the double heterozygotes (approximately equal to 15%). Selection against karyotypic heterozygotes is considered as a main evolutionary force responsible for the structuring of the hybrid zone. A positive association between diploid chromosome number and altitude was found. The race 2n = 16 tended to occupy lower altitudes than the 2n = 22 parental race. Differences in ecological preferences may be a result of previous adaptations to different environments in allopatry. A hypothesis concerning the origin and evolution of the hybrid zone is proposed.     

Lack of spermatogenic variation in a polymorphic lizard,Sceloporus aeneus (Squamata: Phrynosomatidae)

Although different mechanisms exist to explain the presence of polymorphism in lizards, one model suggests that multiple morphotypes display the same level of fitness. Three male morphs (grey, yellow and orange) coexist in Sceloporus aeneus, a Mexican endemic oviparous lizard. Using a histological perspective, we test the hypothesis that spermatogenic output does not vary across morphotypes of S. aeneus during its maximum testicular activity. Males of S. aeneus (five grey, five yellow and five orange) were collected in Calimaya, Estado de México, Mexico. Snout-vent length (SVL), testis mass, diameter and epithelial heights for the seminiferous tubules and epididymis, and the number of layers of germ cells did not vary among morphs; moreover, according to principal component analysis, a high overlap among lateral colour morphs exists. Our results suggest strongly that the lateral colour morphs in S. aeneus have the same spermatogenic output, and natural selection may be a stronger driving force than sexual selection within this species. Further studies into other lizard species with multiple morphotypes are required to determine whether the lack of variation in spermatogenic output observed in this endemic lizard is consistent across polymorphic species which will provide a greater understanding of the selective mechanisms acting on an individual’s fitness.     

Estimation of the dispersal of a major pest of maize by cline analysis of a temporary contact zone between two invasive outbreaks

Dispersal is a key factor in invasion and in the persistence and evolution of species. Despite the importance of estimates of dispersal distance, dispersal measurement remains a real methodological challenge. In this study, we characterized dispersal by exploiting a specific case of biological invasion, in which multiple introductions in disconnected areas lead to secondary contact between two differentiated expanding outbreaks. By applying cline theory to this ecological setting, we estimated σ, the standard deviation of the parent–offspring distance distribution, of the western corn rootworm, Diabrotica virgifera virgifera, one of the most destructive pests of maize. This species is currently invading Europe, and the two largest invasive outbreaks, in northern Italy and Central Europe, have recently formed a secondary contact zone in northern Italy. We identified vanishing clines at 12 microsatellite loci throughout the contact zone. By analysing both the rate of change of cline slope and the spatial variation of linkage disequilibrium at these markers, we obtained two σ estimates of about 20 km/generation^1/2. Simulations indicated that these estimates were robust to changes in dispersal kernels and differences in population density between the two outbreaks, despite a systematic weak bias. These estimates are consistent with the results of direct methods for measuring dispersal applied to the same species. We conclude that secondary contact resulting from multiple introductions is very useful for the inference of dispersal parameters and should be more widely used in other species.     

Genetic panmixia within a narrow contact zone between chromosomally and ecologically distinct black fly sibling species (Diptera: Simuliidae)

Hybrid zones are windows into the speciation process, and their study can give clues into the maintenance and breakdown of species boundaries. Using both genetic and ecological tools, we investigate lineage diversification across a contact zone characterized by chromosome rearrangements. We show that black fly sibling species, Simulium arcticum sensu stricto (s.s.) and Simulium saxosum, lack genetic differentiation at both microsatellite and mtDNA loci in allopatry and sympatry, as well as exhibit high levels of gene flow and continuous chromosome variation in sympatry. Furthermore, hybrid frequencies at the contact zone are similar to those seen between races, rather than species. In contrast, S. arcticum s.s. and S. saxosum maintain ecological differences and distinct habitat associations ‐ the contact zone situated at the margin of suitable habitat for each sibling species. Moreover, gene flow occurs only in a narrow band along an ecological transition. Except for the contact zone, S. arcticum s.s. and S. saxosum hybrids do not occur elsewhere within the sibling species' ranges. Although S. arcticum s.s. and S. saxosum maintain the potential to interbreed freely, we conclude that habitat associations and, perhaps, chromosome systems prevent expansion of ranges and assimilation of lineages.     

Genome evolution in a Mediterranean species complex: phylogeny and cytogenetics of Helictotrichon (Poaceae) allopolyploids based on nuclear DNA sequences (rDNA,topoisomerase gene) and FISH

We examined the molecular phylogeny and chromosomal features of European Helictotrichon species to explore the relationships within the genus and to investigate the origin of several polyploids. Using both approaches, molecular and cytogenetic, revealed the strong impact of allopolyploidization on genome organization from chromosome structure to sequence level. Our research focused on Mediterranean and endemic species of the Alps. Altogether, the molecular phylogenetic analyses include a sample of 17 Helictotrichon species and subspecies, used DNA sequences from the nuclear ribosomal (nr) internal transcribed spacer region (ITS) and the single copy gene topoisomerase 6 (Topo6), and were analysed by maximum parsimony and Bayesian methods. Karyotype structures were investigated by fluorescence in situ hybridization (FISH) and fluorochrome banding. Cytogenetic characters were mapped on the combined phylogenetic tree. The absence or comparatively rare occurrence of different ITS sequence types in some (allo-) polyploid species of Helictotrichon suggests frequent intergenomic homogenization of ribosomal DNA (rDNA) loci due to the phenomenon of concerted evolution. This result implies that the ITS region is not an ideal marker to study polyploid evolution of these grasses. The phylogenetic analysis of the Topo6 region revealed three major clades that concur with three different copy types (termed SAR, SET, PAR), representing the major genome groups in Helictotrichon. A comparison of the molecular phylogenetic trees with the chromosome and karyotype structure supports allopolyploidy of several Helictotrichon species and identifies potential genome donors. A correlation between molecular phylogenetic/cytogenetic results and geographic distribution is expressed by a west-east disjunction, in the narrower or wider sense, of the analysed species. While SAR represents a geographically narrowly distributed southwest Mediterranean genome group, PAR and SET are very widespread (Mediterranean to Asia) and encompass several instances of west-east disjunctions.     

Scanning electron microscopy of the placental interface in the viviparous lizard Sceloporus jarrovi (Squamata: Phrynosomatidae)

Placental membranes mediate maternal‐fetal exchange in all viviparous reptilian sauropsids. We used scanning electron microscopy to examine the placental interface in the mountain spiny lizard, Sceloporus jarrovi (Phrynosomatidae). From the late limb bud stage until birth, the conceptus is surrounded by placental membranes formed from the chorioallantois and yolk sac omphalopleure. The chorioallantois lies directly apposed to the uterine lining with no intervening shell membrane. Both fetal and maternal sides of the chorioallantoic placenta are lined by continuous layers of flattened epithelial cells that overlie dense capillary networks. The chorioallantoic placenta shows specializations that enhance respiratory exchange, as well as ultrastructural evidence of maternal secretion and fetal absorption. The yolk sac placenta contains enlarged fetal and maternal epithelia with specializations for histotrophic nutrient transfer. This placenta lacks intrinsic vascularity, although the vascular allantois lies against its inner face, contributing to an omphallantoic placenta. In a specialized region at the abembryonic pole, uterine and fetal tissues are separated by a compact mass of shed shell membrane, yolk droplets, and cellular debris. The omphalopleure in this region develops elongate folds that may contribute to sequestration and absorption of this material. Fetal membrane morphogenesis and composition in S. jarrovi are consistent with those of typical squamates. However, this species exhibits unusual placental specializations characteristic of highly placentotrophic lizards. J. Morphol., 2011. © 2011 Wiley‐Liss, Inc.     

Phylogenetic relationships in the Sceloporus variabilis (Squamata: Phrynosomatidae) complex based on three molecular markers,continuous characters and geometric morphometric data

The monophyly of the Sceloporus variabilis group is well established with five species and two species complexes, but phylogenetic relationships within species complexes are still uncertain. We studied 278 specimens in 20 terminals to sample all taxa in the “variabilis group,” including three subspecies in the “variabilis complex,” and two outgroups (Sceloporus grammicus and Sceloporus megalepidurus). We assembled an extensive morphological data set with discrete and continuous characters (distances and scale counts), including geometric morphometric data (landmark coordinates of three shapes), and a three‐marker molecular data set as well (ND4, 12S and RAG1). We conducted parsimony and Bayesian phylogenetic inferences on these data, including several partitioning and weighting schemes. We suggest elevating three subspecies to full species status. Therefore, we recommend recognition of nine species in the “variabilis group.” First, S. variabilis is sister to Sceloporus teapensis. In turn, Sceloporus cozumelae is sister to Sceloporus olloporus. These four species are a monophyletic group, which is sister to Sceloporus smithi. Finally, Sceloporus marmoratus is sister of the clade of five species. The other species in the “variabilis group” (Sceloporus chrysostictus, Sceloporus couchii and Sceloporus parvus) are a paraphyletic grade at the base of the tree. Our analyses reject the existence of the “variabilis complex.” We conducted a parsimony‐based ancestral reconstruction on body size (snout–vent length), femoral pores and dorsal scales and related morphological changes to geographic distribution of the species. Our phylogenetic hypothesis will allow best designs of comparative studies with species in the “variabilis group,” one of the earliest divergent lineages in the genus.