A global reptile assessment highlights shared conservation needs of tetrapods.

Comprehensive assessments of species' extinction risks have documented the extinction crisis1 and underpinned strategies for reducing those risks2. Global assessments reveal that, among tetrapods, 40.7% of amphibians, 25.4% of mammals and 13.6% of birds are threatened with extinction3. Because global assessments have been lacking, reptiles have been omitted from conservation-prioritization analyses that encompass other tetrapods4-7. Reptiles are unusually diverse in arid regions, suggesting that they may have different conservation needs6. Here we provide a comprehensive extinction-risk assessment of reptiles and show that at least 1,829 out of 10,196 species (21.1%) are threatened-confirming a previous extrapolation8 and representing 15.6 billion years of phylogenetic diversity. Reptiles are threatened by the same major factors that threaten other tetrapods-agriculture, logging, urban development and invasive species-although the threat posed by climate change remains uncertain. Reptiles inhabiting forests, where these threats are strongest, are more threatened than those in arid habitats, contrary to our prediction. Birds, mammals and amphibians are unexpectedly good surrogates for the conservation of reptiles, although threatened reptiles with the smallest ranges tend to be isolated from other threatened tetrapods. Although some reptiles-including most species of crocodiles and turtles-require urgent, targeted action to prevent extinctions, efforts to protect other tetrapods, such as habitat preservation and control of trade and invasive species, will probably also benefit many reptiles.

No link between population isolation and speciation rate in squamate reptiles.

Rates of species formation vary widely across the tree of life and contribute to massive disparities in species richness among clades. This variation can emerge from differences in metapopulation-level processes that affect the rates at which lineages diverge, persist, and evolve reproductive barriers and ecological differentiation. For example, populations that evolve reproductive barriers quickly should form new species at faster rates than populations that acquire reproductive barriers more slowly. This expectation implicitly links microevolutionary processes (the evolution of populations) and macroevolutionary patterns (the profound disparity in speciation rate across taxa). Here, leveraging extensive field sampling from the Neotropical Cerrado biome in a biogeographically controlled natural experiment, we test the role of an important microevolutionary process-the propensity for population isolation-as a control on speciation rate in lizards and snakes. By quantifying population genomic structure across a set of codistributed taxa with extensive and phylogenetically independent variation in speciation rate, we show that broad-scale patterns of species formation are decoupled from demographic and genetic processes that promote the formation of population isolates. Population isolation is likely a critical stage of speciation for many taxa, but our results suggest that interspecific variability in the propensity for isolation has little influence on speciation rates. These results suggest that other stages of speciation-including the rate at which reproductive barriers evolve and the extent to which newly formed populations persist-are likely to play a larger role than population isolation in controlling speciation rate variation in squamates.

Genetic structure and landscape effects on gene flow in the Neotropical lizard Norops brasiliensis (Squamata: Dactyloidae).

One key research goal of evolutionary biology is to understand the origin and maintenance of genetic variation. In the Cerrado, the South American savanna located primarily in the Central Brazilian Plateau, many hypotheses have been proposed to explain how landscape features (e.g., geographic distance, river barriers, topographic compartmentalization, and historical climatic fluctuations) have promoted genetic structure by mediating gene flow. Here, we asked whether these landscape features have influenced the genetic structure and differentiation in the lizard species Norops brasiliensis (Squamata: Dactyloidae). To achieve our goal, we used a genetic clustering analysis and estimate an effective migration surface to assess genetic structure in the focal species. Optimized isolation-by-resistance models and a simulation-based approach combined with machine learning (convolutional neural network; CNN) were then used to infer current and historical effects on population genetic structure through 12 unique landscape models. We recovered five geographically distributed populations that are separated by regions of lower-than-expected gene flow. The results of the CNN showed that geographic distance is the sole predictor of genetic variation in N. brasiliensis, and that slope, rivers, and historical climate had no discernible influence on gene flow. Our novel CNN approach was accurate (89.5%) in differentiating each landscape model. CNN and other machine learning approaches are still largely unexplored in landscape genetics studies, representing promising avenues for future research with increasingly accessible genomic datasets.

Hot, dry, and salty: The present and future of an Extremophile model lizard from Argentina.

Global warming poses a threat to lizard populations by raising ambient temperatures above historical norms and reducing thermoregulation opportunities. Whereas the reptile fauna of desert systems is relatively well studied, the lizard fauna of saline environments has not received much attention and-to our knowledge-thermal ecology and the effects of global warming on lizards from saline environments have not been yet addressed. This pioneer study investigates the thermal ecology, locomotor performance and potential effects of climate warming on Liolaemus ditadai, a lizard endemic to one of the largest salt flats on Earth. We sampled L. ditadai using traps and active searches along its known distribution, as well as in other areas within Salinas Grandes and Salinas de Ambargasta, where the species had not been previously recorded. Using ensemble models (GAM, MARS, RandomForest), we modeled climatically suitable habitats for L. ditadai in the present and under a pessimistic future scenario (SSP585, 2070). L. ditadai emerges as an efficient thermoregulator, tolerating temperatures near its upper thermal limits. Our ecophysiological model suggests that available activity hours predict its distribution, and the projected temperature increase due to global climate change should minimally impact its persistence or may even have a positive effect on suitable thermal habitat. However, this theoretical increase in habitat could be linked to the distribution of halophilous scrub in the future. Our surveys reveal widespread distribution along the borders of Salinas Grandes and Salinas de Ambargasta, suggesting a potential presence along the entire border of both salt plains wherever halophytic vegetation exists. Optimistic model results, extended distribution, and no evidence of flood-related adverse effects offer insights into assessing the conservation status of L. ditadai, making it and the Salinas Grandes system suitable models for studying lizard ecophysiology in largely unknown saline environments.

Species limits and diversification of the Dendropsophus rubicundulus subgroup (Anura, Hylidae) in Neotropical savannas.

Understanding the processes that generate and maintain biodiversity at and below the species level is a central goal of evolutionary biology. Here we explore the spatial and temporal drivers of diversification of the treefrog subgroup Dendropsophus rubicundulus, a subgroup of the D. microcephalus species group, over periods of pronounced geological and climatic changes in the Neotropical savannas that they inhabit. This subgroup currently comprises 11 recognized species distributed across the Brazilian and Bolivian savannas, but the taxonomy has been in a state of flux, necessitating reexamination. Using newly generated single nucleotide polymorphism (SNP) data from restriction-site associated DNA sequencing (RADseq) and mitochondrial 16S sequence data for ∼150 specimens, we inferred phylogenetic relationships, tested species limits using a model-based approach, and estimated divergence times to gain insights into the geographic and climatic events that affected the diversification of this subgroup. Our results recognized at least nine species: D. anataliasiasi, D. araguaya, D. cerradensis, D. elianeae, D. jimi, D. rubicundulus, D. tritaeniatus, D. rozenmani, and D. sanborni. Although we did not collect SNP data for the latter two species, they are likely distinct based on mitochondrial data. In addition, we found genetic structure within the widespread species D. rubicundulus, which comprises three allopatric lineages connected by gene flow upon secondary contact. We also found evidence of population structure and perhaps undescribed diversity in D. elianeae, which warrants further study. The D. rubicundulus subgroup is estimated to have originated in the Late Miocene (∼5.45 million years ago), with diversification continuing through the Pliocene and Early Pleistocene, followed by the most recent divergence of D. rubicundulus lineages in the Middle Pleistocene. The epeirogenic uplift followed by erosion and denudation of the central Brazilian plateau throughout the Pliocene and Pleistocene, in combination with the increasing frequency and amplitude of climatic fluctuations during the Pleistocene, was important for generating and structuring diversity at or below the species level in the D. rubicundulus subgroup.

Comparative and predictive phylogeography in the South American diagonal of open formations: Unravelling the biological and environmental influences on multitaxon demography.

Phylogeography investigates historical drivers of the geographical distribution of intraspecific lineages. Particular attention has been given to ecological, climatic and geological processes in the diversification of the Neotropical biota. Several species sampled across the South American diagonal of open formations (DOF), comprising the Caatinga, Cerrado and Chaco biomes, experienced range shifts coincident with Quaternary climatic changes. However, comparative studies across different spatial, temporal and biological scales on DOF species are still meagre. Here, we combine phylogeographical model selection and machine learning predictive frameworks to investigate the influence of Pleistocene climatic changes on several plant and animal species from the DOF. We assembled mitochondrial/chloroplastic DNA sequences in public repositories and inferred the demographic responses of 44 species, comprising 70 intraspecific lineages of plants, lizards, frogs, spiders and insects. We then built a random forest model using biotic and abiotic information to identify the best predictors of demographic responses in the Pleistocene. Finally, we assessed the temporal synchrony of species demographic responses with hierarchical approximate Bayesian computation. Biotic variables related to population connectivity, gene flow and habitat preferences largely predicted how species responded to Pleistocene climatic changes, and demographic changes were synchronous primarily during the Middle Pleistocene. Although 22 (~31%) lineages underwent demographic expansion, presumably associated with the spread of aridity during the glacial Pleistocene periods, our findings suggest that nine lineages (~13%) exhibited the opposite response due to taxon-specific attributes.

Temporal and spatial diversification along the Amazonia-Cerrado transition in Neotropical treefrogs of the Boana albopunctata species group.

Despite extensive research on biodiversity in Neotropical forests, biodiversity in seasonally dry, open biomes in South America has been underestimated until recently. We leverage a widespread group, Boana albopunctata, to uncover cryptic lineages and investigate the timing of diversification in Neotropical anurans with a focus on dry diagonal biomes (Cerrado, Caatinga and Chaco) and the ecotone between Amazonia and the Cerrado. We inferred a multilocus phylogeny of the B. albopunctata species group that includes 15 of 18 described species, recovered two cryptic species, and reconstructed the timing of diversification among species distributed across multiple South American biomes. One new potential species (B. aff. steinbachi), sampled in the Amazonian state of Acre, clustered within the B. calcara-fasciata species complex and is close to B. steinbachi. A second putative new species (B. aff. multifasciata), sampled in the Amazonia-Cerrado ecotone, is closely related to B. multifasciata. Lastly, we place a recently identified Cerrado lineage (B. aff. albopuncata) into the B. albopunctata species group phylogeny for the first time. Our ancestral range reconstruction showed that species in the B. albopuctata group likely dispersed from Amazonia-Cerrado into the dry-diagonal and Atlantic Forest. Intraspecies demography showed, for both B. raniceps and B. albopunctata, signs of rapid expansion across the dry diagonal. Similarly, for one clade of B. multifasciata, our analyses support an invasion of the Cerrado from Amazonia, followed by a rapid expansion across the open diagonal biomes. Thus, our study recovers several recent divergences along the Amazonia-Cerrado ecotone in northern Brazil. Tectonic uplift and erosion in the late Miocene and climate oscillations in the Pleistocene corresponded with estimated divergence times in the dry diagonal and Amazonia-Cerrado ecotone. Our study highlights the importance of these threatened open formations in the generation of biodiversity in the Neotropics.

Congruence and Conflict in the Higher-Level Phylogenetics of Squamate Reptiles: An Expanded Phylogenomic Perspective.

Genome-scale data have the potential to clarify phylogenetic relationships across the tree of life but have also revealed extensive gene tree conflict. This seeming paradox, whereby larger data sets both increase statistical confidence and uncover significant discordance, suggests that understanding sources of conflict is important for accurate reconstruction of evolutionary history. We explore this paradox in squamate reptiles, the vertebrate clade comprising lizards, snakes, and amphisbaenians. We collected an average of 5103 loci for 91 species of squamates that span higher-level diversity within the clade, which we augmented with publicly available sequences for an additional 17 taxa. Using a locus-by-locus approach, we evaluated support for alternative topologies at 17 contentious nodes in the phylogeny. We identified shared properties of conflicting loci, finding that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes. Finally, by comparing our tests of nodal conflict to previous phylogenomic studies, we confidently resolve 9 of the 17 problematic nodes. We suggest this locus-by-locus and node-by-node approach can build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups. [Anchored hybrid enrichment (AHE); gene tree conflict; molecular evolution; phylogenomic concordance; target capture; ultraconserved elements (UCE).].

Two new species of Hypostomus suckermouth-armoured catfishes (Teleostei: Loricariidae) from central Brazil.

This study describes two new endemic Hypostomus species from central Brazil, which were previously identified as genetically distinct lineages in a recent genomic study that recommended their testing and potential description based on morphological data. A machine learning classification procedure (random forest) was used to investigate morphological variation and identify putatively diagnostic characters for these candidate species and revealed that each is morphologically distinct. The new species Hypostomus cafuringa is characterized by small size, dark spots under a light background, deeper caudal peduncle and shorter first ray of the pectoral fin and base of the dorsal fin when compared to congeneric species from the region. H. cafuringa is known from the headwaters of the Maranhão River, upper Tocantins River basin, Distrito Federal, Brazil. The second new species, Hypostomus crulsi, is characterized by dark spots under a light background, absence of plates along the abdomen region, shorter first ray of the pelvic fin, shorter first ray of the pectoral fin and smaller body size. H. crulsi is known from the headwaters of the São Bartolomeu River, upper Paraná River basin, Distrito Federal, Brazil. The rapid conversion of natural habitats for agricultural development and the isolation of protected areas represent a serious threat to the continued existence of these two newly described endemic species, which warrant conservation assessment.

Isolation by instability: Historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna.

Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present-day tropical biota. Using genome-wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the late Quaternary until the present, we evaluate the effect of paleoclimatic shifts on the genetic structure and population differentiation of Hypsiboas lundii, a treefrog endemic to the South American Cerrado savanna. Our results show a recent and strong genetic divergence in H. lundii across the Cerrado landscape, yielding four genetic clusters that do not seem congruent with any current physical barrier to gene flow. Isolation by distance (IBD) explains some of the population differentiation, but we also find strong support for past climate changes promoting range shifts and structuring populations even in the presence of IBD. Post-Pleistocene population persistence in four main areas of historical stable climate in the Cerrado seems to have played a major role establishing the present genetic structure of this treefrog. This pattern is consistent with a model of reduced gene flow in areas with high climatic instability promoting isolation of populations, defined here as "isolation by instability," highlighting the effects of Pleistocene climatic fluctuations structuring populations in tropical savannas.

Population genetic structure and species delimitation of a widespread, Neotropical dwarf gecko.

Amazonia harbors the greatest biological diversity on Earth. One trend that spans Amazonian taxa is that most taxonomic groups either exhibit broad geographic ranges or small restricted ranges. This is likely because many traits that determine a species range size, such as dispersal ability or body size, are autocorrelated. As such, it is rare to find groups that exhibit both large and small ranges. Once identified, however, these groups provide a powerful system for isolating specific traits that influence species distributions. One group of terrestrial vertebrates, gecko lizards, tends to exhibit small geographic ranges. Despite one exception, this applies to the Neotropical dwarf geckos of the genus Gonatodes. This exception, Gonatodes humeralis, has a geographic distribution almost 1,000,000 km2 larger than the combined ranges of its 30 congeners. As the smallest member of its genus and a gecko lizard more generally, G. humeralis is an unlikely candidate to be a wide-ranged Amazonian taxon. To test whether or not G. humeralis is one or more species, we generated molecular genetic data using restriction-site associated sequencing (RADseq) and traditional Sanger methods for samples from across its range and conducted a phylogeographic study. We conclude that G. humeralis is, in fact, a single species across its contiguous range in South America. Thus, Gonatodes is a unique clade among Neotropical taxa, containing both wide-ranged and range-restricted taxa, which provides empiricists with a powerful model system to correlate complex species traits and distributions. Additionally, we provide evidence to support species-level divergence of the allopatric population from Trinidad and we resurrect the name Gonatodes ferrugineus from synonymy for this population.

DNA barcode and minibarcode identification of freshwater fishes from Cerrado headwater streams in Central Brazil.

The extraordinary species diversity of the Neotropical freshwater fish fauna is world renown. Yet, despite rich species diversity, taxonomic and genetic resources for its Cerrado ichthyofauna remain poorly developed. We provide a reference library of 149 DNA barcodes for 39 species/lineages of Cerrado headwater stream fishes from the Brazilian Distrito Federal and nearby areas and test the utility of distance-based criteria, tree-based criteria and minibarcodes for specimen identification. Mean Kimura 2-parameter genetic distances within species to orders ranged 1·8-12·1%. However, mean intraspecific v. congeneric-interspecific distances (0·9-1·3%) overlapped extensively and distance-based barcoding failed to achieve correct identifications due to c. 4-12·1% error rates and 19·5% ambiguous identifications related to the presence of singletons. Overlap was reduced and best-match success rates improved drastically to 83·5% when Characidium barcodes representing potential misidentifications or undescribed species were removed. Tree-based monophyly criteria generally performed similarly to distance methods, correctly differentiating up to c. 85% of species/lineages despite neighbour-joining and Bayesian tree errors (random lineage-branching events, long-branch attraction). Five clusters (Ancistrus aguaboensis, Characidium spp., Eigenmannia trilineata, Hasemania hanseni and Hypostomus sp. 2) exhibited deep intraspecific divergences or para-/polyphyly and multiple Barcode Index Number assignments indicative of putative candidate species needing taxonomic re-examination. Sliding-window analyses also indicated that a 200 bp minibarcode region performed just as well at specimen identification as the entire barcode gene. Future DNA barcoding studies of Distrito Federal-Cerrado freshwater fishes will benefit from increased sampling coverage, as well as consideration of minibarcode targets for degraded samples and next-generation sequencing.

The evolutionary history of Lygodactylus lizards in the South American open diagonal.

The Pleistocenic Arc Hypothesis (PAH) posits that South American Seasonally Dry Tropical Forests (SDTF) were interconnected during Pleistocene glacial periods, enabling the expansion of species ranges that were subsequently fragmented in interglacial periods, promoting speciation. The lizard genus Lygodactylus occurs in Africa, Madagascar, and South America. Compared to the high diversity of African Lygodactylus, only two species are known to occur in South America, L. klugei and L. wetzeli, distributed in SDTFs and the Chaco, respectively. We use a phylogenetic approach based on mitochondrial (ND2) and nuclear (RAG-1) markers covering the known range of South American Lygodactylus to investigate (i) if they are monophyletic relative to their African congeners, (ii) if their divergence is congruent with the fragmentation of the PAH, and (iii) if cryptic diversity exists within currently recognized species. Maximum likelihood and Bayesian phylogenetic analyses recovered a well-supported monophyletic South American Lygodactylus, presumably resulting from a single trans-Atlantic dispersal event 29 Mya. Species delimitation analyses supported the existence of five putative species, three of them undescribed. Divergence times among L. klugei and the three putative undescribed species, all endemic to the SDTFs, are not congruent with the fragmentation of the PAH. However, fragmentation of the once broader and continuous SDTFs likely influenced the divergence of L. wetzeli in the Chaco and Lygodactylus sp. 3 (in a SDTF enclave in the Cerrado).

Extinction risks forced by climatic change and intraspecific variation in the thermal physiology of a tropical lizard.

Temperature increases can impact biodiversity and predicting their effects is one of the main challenges facing global climate-change research. Ectotherms are sensitive to temperature change and, although predictions indicate that tropical species are highly vulnerable to global warming, they remain one of the least studied groups with respect to the extent of physiological variation and local extinction risks. We model the extinction risks for a tropical heliothermic teiid lizard (Kentropyx calcarata) integrating previously obtained information on intraspecific phylogeographic structure, eco-physiological traits and contemporary species distributions in the Amazon rainforest and its ecotone to the Cerrado savannah. We also investigated how thermal-biology traits vary throughout the species' geographic range and the consequences of such variation for lineage vulnerability. We show substantial variation in thermal tolerance of individuals among thermally distinct sites. Thermal critical limits were highly correlated with operative environmental temperatures. Our physiological/climatic model predicted relative extinction risks for local populations within clades of K. calcarata for 2050 ranging between 26.1% and 70.8%, while for 2070, extinction risks ranged from 52.8% to 92.8%. Our results support the hypothesis that tropical-lizard taxa are at high risk of local extinction caused by increasing temperatures. However, the thermo-physiological differences found across the species' distribution suggest that local adaptation may allow persistence of this tropical ectotherm in global warming scenarios. These results will serve as basis to further research to investigate the strength of local adaptation to climate change. Persistence of Kentropyx calcarata also depends on forest preservation, but the Amazon rainforest is currently under high deforestation rates. We argue that higher conservation priority is necessary so the Amazon rainforest can fulfill its capacity to absorb the impacts of temperature increase on tropical ectotherms during climate change.

Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil.

Many studies propose that Quaternary climatic cycles contracted and/or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes. Using available single-locus data, we can now perform large-scale analyses, both in terms of number of species and geographic scope. Here, we first compared the power of four alternative hABC models for a collection of single-locus data. We found that the model incorporating an a priori hypothesis about the timing of simultaneous demographic change had the best performance. Second, we applied the hABC models to a data set of seven squamate and four amphibian species occurring in the Seasonally Dry Tropical Forests (Caatinga) in northeastern Brazil, which, according to paleoclimatic evidence, experienced an increase in aridity during the Pleistocene. If this increase was important for the diversification of associated xeric-adapted species, simultaneous population expansions should be evident at the community level. We found a strong signal of synchronous population expansion in the Late Pleistocene, supporting the increase of the Caatinga during this time. This expansion likely enhanced the formation of communities adapted to high aridity and seasonality and caused regional extirpation of taxa adapted to wet forest.

In the shadows: Phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus).

The recognition of cryptic diversity within geographically widespread species is gradually becoming a trend in the highly speciose Neotropical biomes. The statistical methods to recognise such cryptic lineages are rapidly advancing, but have rarely been applied to genomic-scale datasets. Herein, we used phylogenomic data to investigate phylogenetic history and cryptic diversity within Tropidurus itambere, a lizard endemic to the Cerrado biodiversity hotspot. We applied a series of phylogenetic methods to reconstruct evolutionary relationships and a coalescent Bayesian species delimitation approach (BPP) to clarify species limits. The BPP results suggest that the widespread nominal taxon comprises a complex of 5 highly supported and geographically structured cryptic species. We highlight and discuss the different topological patterns recovered by concatenated and coalescent species tree methods for these closely related lineages. Finally, we suggest that the existence of cryptic lineages in the Cerrado is much more common than traditionally thought, highlighting the value of using NGS data and coalescent techniques to investigate patterns of species diversity.

Life-History Patterns of Lizards of the World.

Identification of mechanisms that promote variation in life-history traits is critical to understand the evolution of divergent reproductive strategies. Here we compiled a large life-history data set (674 lizard populations, representing 297 species from 263 sites globally) to test a number of hypotheses regarding the evolution of life-history traits in lizards. We found significant phylogenetic signal in most life-history traits, although phylogenetic signal was not particularly high. Climatic variables influenced the evolution of many traits, with clutch frequency being positively related to precipitation and clutches of tropical lizards being smaller than those of temperate species. This result supports the hypothesis that in tropical and less seasonal climates, many lizards tend to reproduce repeatedly throughout the season, producing smaller clutches during each reproductive episode. Our analysis also supported the hypothesis that viviparity has evolved in lizards as a response to cooler climates. Finally, we also found that variation in trait values explained by clade membership is unevenly distributed among lizard clades, with basal clades and a few younger clades showing the most variation. Our global analyses are largely consistent with life-history theory and previous results based on smaller and scattered data sets, suggesting that these patterns are remarkably consistent across geographic and taxonomic scales.

Methodological congruence in phylogenomic analyses with morphological support for teiid lizards (Sauria: Teiidae).

A well-known issue in phylogenetics is discordance among gene trees, species trees, morphology, and other data types. Gene-tree discordance is often caused by incomplete lineage sorting, lateral gene transfer, and gene duplication. Multispecies-coalescent methods can account for incomplete lineage sorting and are believed by many to be more accurate than concatenation. However, simulation studies and empirical data have demonstrated that concatenation and species tree methods often recover similar topologies. We use three popular methods of phylogenetic reconstruction (one concatenation, two species tree) to evaluate relationships within Teiidae. These lizards are distributed across the United States to Argentina and the West Indies, and their classification has been controversial due to incomplete sampling and the discordance among various character types (chromosomes, DNA, musculature, osteology, etc.) used to reconstruct phylogenetic relationships. Recent morphological and molecular analyses of the group resurrected three genera and created five new genera to resolve non-monophyly in three historically ill-defined genera: Ameiva, Cnemidophorus, and Tupinambis. Here, we assess the phylogenetic relationships of the Teiidae using "next-generation" anchored-phylogenomics sequencing. Our final alignment includes 316 loci (488,656bp DNA) for 244 individuals (56 species of teiids, representing all currently recognized genera) and all three methods (ExaML, MP-EST, and ASTRAL-II) recovered essentially identical topologies. Our results are basically in agreement with recent results from morphology and smaller molecular datasets, showing support for monophyly of the eight new genera. Interestingly, even with hundreds of loci, the relationships among some genera in Tupinambinae remain ambiguous (i.e. low nodal support for the position of Salvator and Dracaena).

Cryptic lineages and diversification of an endemic anole lizard (Squamata, Dactyloidae) of the Cerrado hotspot.

The Cerrado is a wide Neotropical savanna with tremendously high endemic diversity. Yet, it is not clear what the prevalent processes leading to such diversification are. We used the Cerrado-endemic lizard Norops meridionalis to investigate the main abiotic factors that promoted genetic divergence, the timings of these divergence events, and how these relate to cryptic diversity in the group. We sequenced mitochondrial and nuclear genes from 21 sites of N. meridionalis to generate species tree, divergence time estimations, and estimate species limits. We also performed population-level analysis and estimated distribution models to test the roles of niche conservatism and divergence in the group diversification. We found that N. meridionalis is composed by at least five cryptic species. Divergence time estimations suggest that the deepest branches split back into the early-mid Miocene, when most of the geophysical activity of the Cerrado took place. The deep divergences found in N. meridionalis suggest that beta anoles invaded South America much earlier than previously thought. Recent published evidence supports this view, indicating that the Panama gap closed as early as 15 mya, allowing for an early invasion of Norops into South America. The spatial pattern of diversification within N. meridionalis follows a northwest-southeast direction, which is consistent across several species of vertebrates endemic to the Cerrado. Also, we found evidence for non-stationary isolation by distance, which occurs when genetic differentiation depends on space. Our preliminary data in two out of five lineages suggest that niche conservatism is an important mechanism that promoted geographic fragmentation in the group.

Speciation with gene flow in whiptail lizards from a Neotropical xeric biome.

Two main hypotheses have been proposed to explain the diversification of the Caatinga biota. The riverine barrier hypothesis (RBH) claims that the São Francisco River (SFR) is a major biogeographic barrier to gene flow. The Pleistocene climatic fluctuation hypothesis (PCH) states that gene flow, geographic genetic structure and demographic signatures on endemic Caatinga taxa were influenced by Quaternary climate fluctuation cycles. Herein, we analyse genetic diversity and structure, phylogeographic history, and diversification of a widespread Caatinga lizard (Cnemidophorus ocellifer) based on large geographical sampling for multiple loci to test the predictions derived from the RBH and PCH. We inferred two well-delimited lineages (Northeast and Southwest) that have diverged along the Cerrado-Caatinga border during the Mid-Late Miocene (6-14 Ma) despite the presence of gene flow. We reject both major hypotheses proposed to explain diversification in the Caatinga. Surprisingly, our results revealed a striking complex diversification pattern where the Northeast lineage originated as a founder effect from a few individuals located along the edge of the Southwest lineage that eventually expanded throughout the Caatinga. The Southwest lineage is more diverse, older and associated with the Cerrado-Caatinga boundaries. Finally, we suggest that C. ocellifer from the Caatinga is composed of two distinct species. Our data support speciation in the presence of gene flow and highlight the role of environmental gradients in the diversification process.