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Hybridization between diverging lineages is associated with the generation and loss of species diversity, introgression, adaptation, and changes in reproductive mode, but it is unknown when and why it results in these divergent outcomes. We estimate a comprehensive evolutionary network for the largest group of unisexual vertebrates and use it to understand the evolutionary outcomes of hybridization. Our results show that rates of introgression between species decrease with time since divergence and suggest that species must attain a threshold of evolutionary divergence before hybridization results in transitions to unisexuality. Rates of hybridization also predict genome-wide patterns of genetic diversity in whiptail lizards. These results distinguish among models for hybridization that have not previously been tested and suggest that the evolutionary outcomes can be predictable.

Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and provide a time frame for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum likelihood (ML) and Bayesian analyses provided highly congruent results, with differences limited to poorly supported nodes. Similar topologies were inferred from coalescent analyses in Bayesian Phylogenetics and Phylogeography and SVDquartets, albeit with lower support for some nodes. All divergence times fell within the Miocene, linking speciation to local Neogene vicariance and/or global cooling trends following the mid-Miocene Climatic Optimum. We detected a high level of genomic divergence for a morphologically distinct species restricted to the arid mountains of north-eastern Mexico, and erected a new genus to better reflect evolutionary history. In summary, our results further advocate leveraging the strengths and weaknesses of concatenation and coalescent methods, provide evidence for old divergences for alligator lizards, and indicate that the MTZ continues to harbour substantial unrecognized diversity.

Palacios-Aguilar, Ricardo, Colín-Martínez, Víctor H., Hernández-Rubio, Salvador, Canseco-Márquez, Luis, Nieto-Montes de Oca, Adrián, Ochoa-Ochoa, Leticia M. (2022): Another case of colour pattern polymorphism in Earth Snakes of the genus Geophis (Dipsadidae) from southern Mexico. Journal of Natural History 55 (47-48): 2985-2997, DOI: 10.1080/00222933.2021.2024906, URL: http://dx.doi.org/10.1080/00222933.2021.2024906

Transitions between sexual and unisexual reproductive modes have significant consequences for the evolutionary trajectories of species. These transitions have occurred numerous times in vertebrates and are frequently mediated by hybridization events. Triploid unisexual vertebrates are thought to arise through hybridization between individuals of a diploid unisexual lineage and a sexual species, although additional evidence that confirms this mechanism is needed in numerous groups. North American whiptail lizards (Aspidoscelis) are notable for being one of the largest radiations of unisexual vertebrates, and the most diverse group of Aspidoscelis includes numerous triploid lineages that have no known diploid unisexual ancestors. This pattern of "missing" ancestors may result from the short evolutionary life span of unisexual lineages or the selective advantages of polyploidy, or it could suggest that alternative mechanisms of triploid formation are operating in nature. We leverage genomic, morphological, and karyotypic data to describe a new diploid unisexual whiptail and show that it is likely the unisexual progenitor of an extant triploid lineage, A. opatae. We also resolve patterns of polyploidization within the A. sexlineatus species group and test predictions about the phenotypic outcomes of hybridization.

Introgression is now commonly reported in studies across the Tree of Life, aided by recent advancements in data collection and analysis. Nevertheless, researchers working with nonmodel species lacking reference genomes may be stymied by a mismatch between available resources and methodological demands. In this study, we demonstrate a fast and simple approach for inferring introgression using RADseq data, and apply it to a case study involving spiny lizards (Sceloporus) from northeastern Mexico. First, we find evidence for recurrent mtDNA introgression between the two focal species based on patterns of mito-nuclear discordance. We then test for nuclear introgression by exhaustively applying the "five-taxon" D-statistic (DFOIL ) to all relevant individuals sampled for RADseq data. In our case, this exhaustive approach (dubbed "ExDFOIL ") entails testing up to ~250,000 unique four-taxon combinations of individuals across species. To facilitate use of this ExDFOIL approach, we provide scripts for many relevant tasks, including the selection of appropriate four-taxon combinations, execution of DFOIL tests in parallel and visualization of introgression results in phylogenetic and geographic space. Using ExDFOIL , we find evidence for ancient introgression between the focal species. Furthermore, we reveal geographic variation in patterns of introgression that is consistent with patterns of mito-nuclear discordance and with recurrent introgression. Overall, our study demonstrates that the combination of DFOIL and RADseq data can effectively detect introgression under a variety of sampling conditions (for individuals, populations and loci). Importantly, we also find evidence that batch-specific error and linkage in RADseq data may mislead inferences of introgression under certain conditions.

A primary challenge for modern phylogeography is understanding how ecology and geography, both contemporary and historical, shape the spatial distribution and evolutionary histories of species. Phylogeographic patterns are the result of many factors, including geology, climate, habitat, colonization history and lineage-specific constraints. Assessing the relative influences of these factors is difficult because few species, regions and environments are sampled in enough detail to compare competing hypotheses rigorously and because a particular phylogeographic pattern can potentially result from different evolutionary scenarios. The silky anoles (Anolis sericeus complex) of Central America and Mexico are abundant and found in all types of lowland terrestrial habitat, offering an excellent opportunity to test the relative influences of the factors affecting diversification. Here, we performed a range-wide statistical phylogeographic analysis on restriction site-associated DNA (RAD) markers from silky anoles and compared the phylogeographic patterns we recovered to historical and contemporary environmental and topographic data. We constructed niche models to compare niche overlap between sister lineages and conducted coalescent simulations to characterize how the major lineages of silky anoles have diverged. Our results revealed that the mode of divergence for major lineage diversification events was geographic isolation, resulting in ecological divergence between lineages, followed by secondary contact. Moreover, comparisons of parapatric sister lineages suggest that ecological niche divergence contributed to isolation by environment in this system, reflecting the natural history differences among populations in divergent environments.

Integrative taxonomy has been generally considered as a goal in systematics for more than a decade. Here, we employed environmental, molecular, and morphological data to evaluate the species boundaries within the short-nosed skink Plestiodon brevirostris from south-central Mexico, one member of the morphologically conservative P. brevirostris group. Our molecular dataset includes one mitochondrial and two nuclear loci. The mitochondrial fragment includes the full length of the gene coding for the NADH dehydrogenase subunit 1 protein, a segment of the gene coding for 16S ribosomal RNA, and flanking tRNAs. The nuclear dataset includes fragments of the genes coding for the megakaryoblastic leukemia 1 and RNA fingerprint 35 proteins. We employed phylogenetic reconstruction, analyses of population structure and morphological variation, and species delimitation methods (including the integration of the three kinds of data in a unified probabilistic framework) to evaluate species limits. Our results suggest that P. brevirostris represents four distinct species. The information provided by each kind of data allowed us to discern between alternative explanations for the observed patterns of geographic structure. Two of the newly recognized lineages are poorly differentiated morphologically but apparently differ in environmental preferences and are allopatric. Additionally, one lineage is microendemic and parapatric with respect to another one. Moreover, our phylogenetic analyses suggest that other taxa within the P. brevirostris group may represent species complexes. We discuss our results in the context of integrative species delimitation.

Recent studies on the systematics and phylogeny of the blue-tailed skinks in the Plestiodon brevirostris group identified a population from the Sierra Madre del Sur of eastern Guerrero, Mexico, that appeared to represent an undescribed species. Here, we formally describe this lineage as a new species, compare it with the other species in the P. brevirostris group, identify a specimen from western Oaxaca that belongs to the new species, and provide an updated key to the group. The new species is morphologically similar and closely related to P. ochoterenae, but molecular and morphological data support its evolutionary independence. The new species is distinguished from the other species in the P. brevirostris group, except for P. ochoterenae, by the presence of a primary temporal, a well-defined lateral pale line on the neck, and a well-defined dorsolateral pale line that extends posteriorly to the level of the hind limbs. It differs from P. ochoterenae by having longer limbs and a well-defined lateral pale line on the neck. The present study further highlights the relevance of the Sierra Madre del Sur as a hotspot of endemism and undescribed diversity.

A new species of Gerrhonotus, previously confused with G. infernalis, is described from the Cuatro Cienegas Basin, Coahuila, Mexico. The new species is known from the type locality only and is characterized by the following combination of characters: a cantholoreal scale usually present, a dark mark extending anteriorly from the lower temporal scales through the lower border of the orbit to the preocular or cantholoreal scales, keeled dorsal scales, dorsal body pattern usually composed of cross-bands mostly interrupted or barely discernible on middorsum, usually indiscernible vertical dark bars on the lateral fold (few, faint bars occasionally present), and black flecks scattered on the venter. The new species is geographically closest to G. lugoi and G. infernalis but morphologically most similar to G. infernalis.

Adaptive radiation is a widely recognized pattern of evolution wherein substantial phenotypic change accompanies rapid speciation. Adaptive radiation may be triggered by environmental opportunities resulting from dispersal to new areas or via the evolution of traits, called key innovations, that allow for invasion of new niches. Species sampling is a known source of bias in many comparative analyses, yet classic adaptive radiations have not been studied comparatively with comprehensively sampled phylogenies. In this study, we use unprecedented comprehensive phylogenetic sampling of Anolis lizard species to examine comparative evolution in this well-studied adaptive radiation. We compare adaptive radiation models within Anolis and in the Anolis clade and a potential sister lineage, the Corytophanidae. We find evidence for island (i.e., opportunity) effects and no evidence for trait (i.e., key innovation) effects causing accelerated body size evolution within Anolis. However, island effects are scale dependent: when Anolis and Corytophanidae are analyzed together, no island effect is evident. We find no evidence for an island effect on speciation rate and tenuous evidence for greater speciation rate due to trait effects. These results suggest the need for precision in treatments of classic adaptive radiations such as Anolis and further refinement of the concept of adaptive radiation.

The genus Sarcohyla is composed by 24 species endemic to México. Despite the large number of phylogenetic studies focusing on the family Hylidae, the relationships among the species of Sarcohyla are still poorly known, and the scarce numbers of specimens and tissue samples available for some of the species has hampered an appropriate phylogenetic analysis. We present the most comprehensive molecular phylogenetic study of Sarcohyla to date. We included 17 species of the genus Sarcohyla using data from two mitochondrial (ND1 and 12S) and three nuclear genes (Rag-1, Rhod, and POMc). We performed phylogenetic analyses using Bayesian inference, and the absence of conflicts with strong support between the separate gene trees indicates that incomplete lineage sorting and/or introgressive hybridization are negligible. A coalescent-based species-tree analysis of the four independent loci (three nuclear genes+mtDNA) mostly supports the same species-level relationships as the analysis of the concatenated data. By including new samples from additional species and localities, we find that: (1) the widely distributed species S. bistincta is a complex of at least three species, (2) another undescribed species exists in the group, (3) the species S. ephemera is not valid and it corresponds to a junior synonym of S. calthula. In addition, we conducted marginal likelihood estimation and used Bayes factors to test alternative species delimitation models for S. bistincta, the most widespread nominal species in the group. Our findings support three independent lineages of S. bistincta group, which are paraphyletic with respect to S. pentheter and S. calthula.

Koprowski, John L, Nieto-Montes de Oca, Adrián, Palmer, Geoffrey H, Ramos-Lara, Nicolás, Timm, Robert M. (2017): Sciurus aureogaster (Rodentia: Sciuridae). Mammalian Species 49 (951): 81-92, DOI: 10.1093/mspecies/sex009, URL: http://dx.doi.org/10.1093/mspecies/sex009

The spiny lizard Sceloporus minor exhibits substantial variation in a variety of life history traits, but the factors promoting this variation remain unclear. We analyzed within- and between-population variation in morphological traits in two populations (El Enzuelado and La Manzana, Hidalgo, Central Mexico), and estimated the genetic distance between populations on the basis of sequence variation of the mitochondrial genes encoding a fragment of the ND4 gene, all of tRNA-His and tRNA-Ser, and a fragment of tRNA-Leu. Consistent with earlier reports, males and females exhibited marked sexual dimorphism in body size and coloration. The genetic distance between the two populations was 0.024, slightly greater than the distance measured within each population (0.015 for La Manzana and 0.003 for El Enzuelado). Maximum likelihood analysis indicated that these populations were indeed conspecific, along with other studied populations of S. minor. The morphological differences and the previously described variation in reproductive traits contrast with the limited genetic variation between populations reported herein. This suggests that a combination of both phenotypic plasticity and genes of large effect may be contributing to variation in anatomical and physiological traits in Sceloporus minor.

Anolis lizards (anoles) are textbook study organisms in evolution and ecology. Although several topics in evolutionary biology have been elucidated by the study of anoles, progress in some areas has been hampered by limited phylogenetic information on this group. Here, we present a phylogenetic analysis of all 379 extant species of Anolis, with new phylogenetic data for 139 species including new DNA data for 101 species. We use the resulting estimates as a basis for defining anole clade names under the principles of phylogenetic nomenclature and to examine the biogeographic history of anoles. Our new taxonomic treatment achieves the supposed advantages of recent subdivisions of anoles that employed ranked Linnaean-based nomenclature while avoiding the pitfalls of those approaches regarding artificial constraints imposed by ranks. Our biogeographic analyses demonstrate complexity in the dispersal history of anoles, including multiple crossings of the Isthmus of Panama, two invasions of the Caribbean, single invasions to Jamaica and Cuba, and a single evolutionary dispersal from the Caribbean to the mainland that resulted in substantial anole diversity. Our comprehensive phylogenetic estimate of anoles should prove useful for rigorous testing of many comparative evolutionary hypotheses. [Anoles; biogeography; lizards; Neotropics; phylogeny; taxonomy].

Middle American knob-scaled lizards of the genus Xenosaurus are a unique radiation of viviparous species that are generally characterized by a flattened body shape and a crevice-dwelling ecology. Only eight species of Xenosaurus, one of them with five subspecies (X. grandis), have been formally described. However, species limits within Xenosaurus have never been examined using molecular data, and no complete phylogeny of the genus has been published. Here, we used ddRADseq data from all of the described and potentially undescribed taxa of Xenosaurus to investigate species limits, and to obtain a phylogenetic hypothesis for the genus. We analyzed the data using a variety of phylogenetic models, and were able to reconstruct a well-resolved and generally well-supported phylogeny for this group. We found Xenosaurus to be composed of four major, allopatric clades concordant with geography. The first and second clades that branch off the tree are distributed on the Atlantic slopes of the Sierra Madre Oriental and are composed of X. mendozai, X. platyceps, and X. newmanorum, and X. tzacualtipantecus and an undescribed species from Puebla, respectively. The third clade is distributed from the Atlantic slopes of the Mexican Transvolcanic Belt in west-central Veracruz south to the Pacific slopes of the Sierra Madre del Sur in Guerrero and Oaxaca, and is composed of X. g. grandis, X. rectocollaris, X. phalaroanthereon, X. g. agrenon, X. penai, and four undescribed species from Oaxaca. The last clade is composed of the four taxa that are geographically closest to the Isthmus of Tehuantepec (X. g. arboreus, X. g. rackhami, X. g. sanmartinensis, and an undescribed species from Oaxaca). We also utilized a variety of molecular species delimitation approaches, including analyses with GMYC, PTP, BPP, and BFD∗, which suggested that species diversity in Xenosaurus is at least 30% higher than currently estimated.

Abronia and Mesaspis are two of the five anguid lizard genera in the subfamily Gerrhonotinae. Their members are restricted to Mesoamerica, and most have allopatric distributions. Species of Abronia are primarily arboreal and occur in cloud and seasonally dry pine-oak forests, whereas those of Mesaspis are terrestrial and inhabit mesic microhabitats of montane forests. Recent molecular studies suggest that although these genera together form a monophyletic group, neither genus is monophyletic. Here we performed a phylogenetic study of Abronia and Mesaspis based on the most comprehensive taxonomic sampling of these genera to date and double digest restriction site-associated (ddRADseq) data. Our reconstructed phylogeny differed considerably from all previously published topologies, consistently recovering multiple independent clades of arboreal and terrestrial species and Abronia and Mesaspis as non-monophyletic. Geography, rather than current taxonomy, provides the best explanation of their phylogenetic relationships. Our analyses consistently recovered two main clades, distributed on the highlands of Middle America east and west of the Isthmus of Tehuantepec, respectively, and each composed of subclades of Abronia and Mesaspis. In the former main clade, members of the subgenus Auriculabronia formed the sister taxon to the Mesaspis moreletii complex, whereas the main clade west of the Isthmus was composed of two clades with a subclade of Abronia and another of Mesaspis each (one clade on the Atlantic versant of the main mountain ranges of eastern Mexico and another one on the Sierra Madre del Sur exclusive of its Atlantic versant) and a third clade with species of the subgenera Abronia and Scopaeabronia. We discuss the taxonomic implications of our results for the classification of the examined taxa and list the morphological characters that diagnose the recovered clades. This study highlights the utility of ddRADseq data to reconstruct the evolutionary history of supraspecific vertebrate taxa.

We describe a new species of anguid lizard of the genus Mesaspis from the Sierra de los Cuchumatanes of northwestern Guatemala. This species reaches a maximum snout–vent length of about 72 mm, making it much smaller than Mesaspis moreletii. In the Sierra de los Cuchumatanes it occurs sympatrically with Mesaspis moreletii temporalis, the only such instance of congeneric sympatry known in Nuclear Central America. The new species appears most similar to the widely distributed species M. moreletii, which may be polytypic. Mesaspis cuchumatanus may be distinguished from M. moreletii by usually having expanded supranasals, 16 longitudinal scale rows, small and granular scales covering the side of the neck from about the level of upper edge of auricular opening to ventrolateral fold, and smaller body size.

We describe a new species of the genus Abronia from the La Sepultura Biosphere Reserve in western Chiapas, Mexico. The new species is known only from the vicinity of the type locality in the Sierra Madre de Chiapas. It is readily distinguished from all congeners by the following combination of characters: lack of protuberant or spine-like supra-auricular scales, lack of protuberant or casque-like posterolateral head scales, 30–35 transverse dorsal scale rows, lateralmost row of ventral scales enlarged relative to adjacent medial row, dorsum brown with 8–10 transverse dark crossbands, and dark lateral bar on the neck extending from the shoulder to near the auricular opening. We tentatively assign the new species to the subgenus Lissabronia pending the availability of a robust, comprehensive molecular phylogeny for the genus. We discuss regional Abronia biogeography and comment on the conservation implications of our discovery for the imperiled highland forests of the Sierra Madre de Chiapas, a globally important center of endemism.

Identifying patterns of introgression across the tree of life is foundational to understanding general mechanisms that govern the impacts of gene flow on the speciation process. There are few vertebrate groups in which hybridization is associated with as large a diversity of outcomes as in North American whiptail lizards (Aspidoscelis). Of particular interest is that hybridization among divergent whiptail species has repeatedly led to the formation of unisexual (parthenogenetic) lineages. Understanding the hybrid origin of these unisexual lineages requires an accurate understanding of species boundaries among gonochoristic whiptails. Doing so has historically been an extremely challenging problem which, in part, may be a consequence of widespread hybridization and incomplete reproductive isolation among lineages. The lack of a robust phylogenetic framework and uncertainty in species boundaries precludes studies of general patterns and mechanisms of introgression among whiptail species. Here, we use genomic data to reconstruct a robust estimate of evolutionary history in the largest clade of whiptail lizards (A. sexlineatus species group) and use it to identify patterns of introgression. Our results indicate substantial introgressive hybridization and admixture has occurred among multiple lineages of whiptails across diverse evolutionary time scales, and illustrate their impact on phylogenetic inference. Thus, hybridization among whiptail species appears to have been a prominent feature throughout their evolutionary history, which could, in part, explain why parthenogenesis has evolved so many times in whiptails in comparison to other vertebrate groups.

A new species of hylid frog is described from the southwestern edge of the Mexican Plateau from the states of Morelos and Mexico through Michoacan and Jalisco, reaching the Sierra Madre Occidental in Sinaloa and western Durango. The new species is part of the widespread Mexican hylid Sarcohyla bistincta ( sensu amplo ) complex, comprised of S. bistincta , S. pentheter , S. calthula , and S. ephemera . One subspecies of S. bistincta ( labeculata ) was proposed for an isolated population in Oaxaca. We restrict the group’s nominal species, S. bistincta ( sensu stricto ), to the Sierra Madre Oriental of Mexico and southward into the Sierra Madre del Sur of Guerrero and Oaxaca. Examination of type material places S. calthula and S. ephemera in the synonymy of S. labeculata (new combination). The species allied to S. bistincta, namely , S. bistincta , S. labeculata , S. pentheter , and the new species described herein, are diagnosed and described following recent suggested taxonomic changes and new available material.

Introgression is now commonly reported in studies across the Tree of Life, aided by recent advancements in data collection and analysis. Nevertheless, researchers working with nonmodel species lacking reference genomes may be stymied by a mismatch between available resources and methodological demands. In this study, we demonstrate a fast and simple approach for inferring introgression using RADseq data, and apply it to a case study involving spiny lizards (Sceloporus) from northeastern México. First, we find evidence for recurrent mtDNA introgression between the two focal species based on patterns of mito-nuclear discordance. We then test for nuclear introgression by exhaustively applying the "five-taxon" D-statistic (D