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Global climatic fluctuation has significantly impacted biodiversity by shaping adaptations across numerous species. Pleistocene climate changes notably affected species’ geographic distributions and population sizes, especially fostering post-glacial expansions in temperate regions. Evolutionary theory suggests spatial sorting of morphological traits associated with dispersal in recently expanded species. However, evidence of predicted intraspecific trait variation is scant. We investigated intraspecific trait variation in five lizard species along a forest-savanna gradient affected by Pleistocene climate. Lizards serve as an ideal group to test these ideas due to climate’s known influence on their morphological traits linked to essential functions like feeding and locomotion. We assessed two hypotheses: (i) niche variation and (ii) spatial sorting. For the niche variation hypothesis, we predicted increased intraspecific variability in head dimensions with distance from stable areas. For spatial sorting, we anticipated larger hind limb sizes with increased distance from stable areas. We gathered data on five quantitative traits from 663 samples across species. There was no evidence supporting either hypothesis across the five species. Limited sample sizes, challenges in habitat modeling, or other factors might explain this lack of support. Nonetheless, our study illuminates complexities in exploring trait variation within species. The data collected here, although inconclusive, represent a crucial test for evolutionary theory. 

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. 

Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit spectacular innovations in locomotion, feeding, and sensory processing. However, the evolutionary drivers of this radiation remain poorly known. We infer potential causes and ultimate consequences of squamate macroevolution by combining individual-based natural history observations (>60,000 animals) with a comprehensive time-calibrated phylogeny that we anchored with genomic data (5400 loci) from 1018 species. Due to shifts in the dynamics of speciation and phenotypic evolution, snakes have transformed the trophic structure of animal communities through the recurrent origin and diversification of specialized predatory strategies. Squamate biodiversity reflects a legacy of singular events that occurred during the early history of snakes and reveals the impact of historical contingency on vertebrate biodiversity. 

Abstract The discipline of phylogeography has evolved rapidly in terms of the analytical toolkit used to analyse large genomic data sets. Despite substantial advances, analytical tools that could potentially address the challenges posed by increased model complexity have not been fully explored. For example, deep learning techniques are underutilized for phylogeographic model selection. In non‐model organisms, the lack of information about their ecology and evolution can lead to uncertainty about which demographic models are appropriate. Here, we assess the utility of convolutional neural networks (CNNs) for assessing demographic models in South American lizards in the genusNorops. Three demographic scenarios (constant, expansion, and bottleneck) were considered for each of four inferred population‐level lineages, and we found that the overall model accuracy was higher than 98% for all lineages. We then evaluated a set of 26 models that accounted for evolutionary relationships, gene flow, and changes in effective population size among the four lineages, identifying a single model with an estimated overall accuracy of 87% when using CNNs. The inferred demography of the lizard system suggests that gene flow between non‐sister populations and changes in effective population sizes through time, probably in response to Pleistocene climatic oscillations, have shaped genetic diversity in this system. Approximate Bayesian computation (ABC) was applied to provide a comparison to the performance of CNNs. ABC was unable to identify a single model among the larger set of 26 models in the subsequent analysis. Our results demonstrate that CNNs can be easily and usefully incorporated into the phylogeographer's toolkit. 

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. 

Abstract 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).] 

Abstract AimSquamate fitness is affected by body temperature, which in turn is influenced by environmental temperatures and, in many species, by exposure to solar radiation. The biophysical drivers of body temperature have been widely studied, but we lack an integrative synthesis of actual body temperatures experienced in the field, and their relationships to environmental temperatures, across phylogeny, behaviour and climate. LocationGlobal (25 countries on six continents). TaxaSquamates (210 species, representing 25 families). MethodsWe measured the body temperatures of 20,231 individuals of squamates in the field while they were active. We examined how body temperatures vary with substrate and air temperatures across taxa, climates and behaviours (basking and diel activity). ResultsHeliothermic lizards had the highest body temperatures. Their body temperatures were the most weakly correlated with substrate and air temperatures. Body temperatures of non‐heliothermic diurnal lizards were similar to heliotherms in relation to air temperature, but similar to nocturnal species in relation to substrate temperatures. The correlation of body temperature with air and substrate temperatures was stronger in diurnal snakes and non‐heliothermic lizards than in heliotherms. Body‐substrate and body‐air temperature correlations varied with mean annual temperatures in all diurnal squamates, especially in heliotherms. Thermal relations vary with behaviour (heliothermy, nocturnality) in cold climates but converge towards the same relation in warm climates. Non‐heliotherms and nocturnal species body temperatures are better explained by substrate temperature than by air temperature. Body temperature distributions become left‐skewed in warmer‐bodied species, especially in colder climates. Main ConclusionsSquamate body temperatures, their frequency distributions and their relation to environmental temperature, are globally influenced by behavioural and climatic factors. For all temperatures and climates, heliothermic species' body temperatures are consistently higher and more stable than in other species, but in regions with warmer climate these differences become less pronounced. A comparable variation was found in non‐heliotherms, but in not nocturnal species whose body temperatures were similar to air and substrate irrespective of the macroclimatic context. 

Abstract AimSpecies adapt differently to contrasting environments, such as open habitats with sparse vegetation and forested habitats with dense forest cover. We investigated colonization patterns in the open and forested environments in the diagonal of open formations and surrounding rain forests (i.e. Amazonia and Atlantic Forest) in Brazil, tested whether the diversification rates were affected by the environmental conditions and identified traits that enabled species to persist in those environments. LocationSouth America, Brazil. TaxonSquamata, Lizards. MethodsWe used phylogenetic information and the current distribution of species in open and forested habitats to estimate ancestral ranges and identify range shifts relative to the current habitats. To evaluate whether these environments influenced species diversification, we tested 12 models using a Hidden Geographic State Speciation and Extinction analysis. Finally, we combined phylogenetic relatedness and species traits in a machine learning framework to identify the traits permitting adaptation in those contrasting environments. ResultsWe identified 41 total transitions between open and forested habitats, of which 80% were from the forested habitats to the open habitats. Widely distributed species had higher speciation, turnover, extinction, and extinction fraction rates than species in forested or open habitats, but had also the lower net diversification rate. Mean body temperature, microhabitat, female snout–vent length and diet were identified as putative traits that enabled adaptation to different environments, and phylogenetic relatedness was an important predictor of species occurrence. Main conclusionsTransitions from forested to open habitats are most common, highlighting the importance of habitat shift in current patterns of biodiversity. The combination of phylogenetic reconstruction of ancestral distributions and the machine learning framework enables us to integrate organismal trait data, environmental data and evolutionary history in a manner that could be applied on a global scale.