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The Pampas is a biologically rich South American biome, but is poorly represented in phylogeographic studies. While the Pleistocene glacial cycles may have affected the evolutionary history of species distributed in forested biomes, little is known about their effects on the habitats that remained stable through glacial cycles. The South American Pampas have been covered by grasslands during both glacial and interglacial periods and therefore represent an interesting system to test whether the genetic structure in such environments is less pronounced. In this study, we sampled Pampean populations of Homonota uruguayensis from Southern Brazil and Uruguay to assess the tempo and mode of population divergence, using both morphological measurements and molecular markers. Our results indicate that, in spite of its narrow geographic distribution, populations of H. uruguayensis show high levels of genetic structure. We found four major well-supported mtDNA clades with strong geographic associations. Estimates of their divergence times fell between 3.16 and 1.82 million years before the present. Populations from the central portion of the species distribution, on the border between Uruguay and Brazil, have high genetic diversity and may have undergone a population expansion approximately 250,000 years before the present. The high degree of genetic structure is reflected in the analyses of morphological characters, and most individuals could be correctly assigned to their parental population based on morphology alone. Finally, we discuss the biogeographic and conservation implications of these findings.

Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards, snakes, andamphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications usingDNAsequence data and reaching a consensus on the relationships among them has been highly problematic. In this study, we use high-throughput sequence data from 289 samples covering 75 families of squamates to address phylogenetic affinities, estimate divergence times, and characterize residual topological uncertainty in the presence of genome-scale data. Importantly, we address genomic support for the traditional taxonomic groupings Scleroglossa and Macrostomata using novel machine-learning techniques. We interrogate genes using various metrics inherent to these loci, including parsimony-informative sites (PIS),phylogenetic informativeness, length, gaps, number of substitutions, and site concordance to understand why certain loci fail to find previously wellsupported molecular clades and how they fail to support species-tree estimates. We show that both incomplete lineage sorting and poor gene-tree estimation (due to a fewundesirable gene properties, such as an insufficient number of PIS), may account for most gene and species-tree discordance. We find overwhelming signal for Toxicofera, and also show that none of the loci included in this study supports Scleroglossa or Macrostomata.We comment on the origins and diversification of Squamata throughout theMesozoic and underscore remaining uncertainties that persist in both deeper parts of the tree (e.g., relationships between Dibamia, Gekkota, and remaining squamates; among the three toxicoferan clades Iguania, Serpentes, and Anguiformes) and within specific clades (e.g., affinities among gekkotan, pleurodont iguanians, and colubroid families).

Most of Switzerland is inhabited by the nominotypical subspecies of the barred grass snake ( ), which is characterized by mitochondrial DNA lineage E. Only in the northeast of the country, the common grass snake ( ) occurs and hybridizes with in a narrow contact zone. However, we discovered that in southern and western Switzerland barred grass snakes representing another mtDNA lineage (lineage C) are widely distributed. Lineage C is typical for Alpine populations of the southern subspecies . Our microsatellite analyses of the Swiss samples revealed differences between the two subspecies and also a substructure with two clusters in each subspecies. Furthermore, we discovered a contact and hybrid zone of and along the northern shore of Lake Geneva and also confirm that interbreeding with alien common grass snakes ( , mtDNA lineage 7) occurs there. This finding is of concern for nature conservation and measures should be taken to prevent further genetic pollution. Using morphometrics, we found no differences between the two subspecies of , while was slightly distinct from .

Background The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. Results The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b , ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. Conclusions We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards, and boid, colubrid, and lamprophiid snakes.

Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.

Factors intrinsic and extrinsic to organisms dictate the course of morphological evolution but are seldom considered together in comparative analyses. Among vertebrates, squamates (lizards and snakes) exhibit remarkable morphological and developmental variations that parallel their incredible ecological spectrum. However, this exceptional diversity also makes systematic quantification and analysis of their morphological evolution challenging. We present a squamate-wide, high-density morphometric analysis of the skull across 181 modern and extinct species to identify the primary drivers of their cranial evolution within a unified, quantitative framework. Diet and habitat preferences, but not reproductive mode, are major influences on skull-shape evolution across squamates, with fossorial and aquatic taxa exhibiting convergent and rapid changes in skull shape. In lizards, diet is associated with the shape of the rostrum, reflecting its use in grasping prey, whereas snakes show a correlation between diet and the shape of posterior skull bones important for gape widening. Similarly, we observe the highest rates of evolution and greatest disparity in regions associated with jaw musculature in lizards, whereas those forming the jaw articulation evolve faster in snakes. In addition, high-resolution ancestral cranial reconstructions from these data support a terrestrial, nonfossorial origin for snakes. Despite their disparate evolutionary trends, lizards and snakes unexpectedly share a common pattern of trait integration, with the highest correlations in the occiput, jaw articulation, and palate. We thus demonstrate that highly diverse phenotypes, exemplified by lizards and snakes, can and do arise from differential selection acting on conserved patterns of phenotypic integration.

Modern squamates (lizards, snakes and amphisbaenians) are the world’s most diverse group of tetrapods along with birds 1 and have a long evolutionary history, with the oldest known fossils dating from the Middle Jurassic period—168 million years ago 2 – 4 . The evolutionary origin of squamates is contentious because of several issues: (1) a fossil gap of approximately 70 million years exists between the oldest known fossils and their estimated origin 5 – 7 ; (2) limited sampling of squamates in reptile phylogenies; and (3) conflicts between morphological and molecular hypotheses regarding the origin of crown squamates 6 , 8 , 9 . Here we shed light on these problems by using high-resolution microfocus X-ray computed tomography data from the articulated fossil reptile Megachirella wachtleri (Middle Triassic period, Italian Alps 10 ). We also present a phylogenetic dataset, combining fossils and extant taxa, and morphological and molecular data. We analysed this dataset under different optimality criteria to assess diapsid reptile relationships and the origins of squamates. Our results re-shape the diapsid phylogeny and present evidence that M. wachtleri is the oldest known stem squamate. Megachirella is 75 million years older than the previously known oldest squamate fossils, partially filling the fossil gap in the origin of lizards, and indicates a more gradual acquisition of squamatan features in diapsid evolution than previously thought. For the first time, to our knowledge, morphological and molecular data are in agreement regarding early squamate evolution, with geckoes—and not iguanians—as the earliest crown clade squamates. Divergence time estimates using relaxed combined morphological and molecular clocks show that lepidosaurs and most other diapsids originated before the Permian/Triassic extinction event, indicating that the Triassic was a period of radiation, not origin, for several diapsid lineages. Computed tomography scanning of the Triassic fossil Megachirella wachtleri combined with a broad morphological and molecular phylogenetic analysis of reptile relationships confirm it as the most primitive stem squamate.

Pereira et al discuss the distribution extension of Alopoglossus buckleyi (O'Shaughnessy, 1881) (Squamata: Alopoglossidae). On Sep 2018 an individual of Alopoglossus buckleyi was captured in a pitfall trap at the Cazumba-Iracema Extractive Reserve in the State of Acre, Brazil. Although knowledge on the taxonomic status of Alopoglossus has increased in recent years, many species still lack important information about natural history and distribution, which increases the need for further studies. This new record highlights our lack of knowledge on A. buckleyi, which is the result of poor sampling in many areas of the Amazon.

Phylogenetic and morphological analyses delimit and diagnose, respectively, a new population of a karst-dwelling from extreme northern Thailand. The new species, , of the group inhabits karst caves and outcroppings and karst vegetation in the vicinity of Pha Mi Village in Chiang Rai Province, Thailand. Within the group, is the earliest diverging species of a strongly supported clade composed of the granite-dwelling and the karst-dwelling sister species sp. 6 and . The nearly continuous karstic habitat between the type locality of and its close relatives sp. 6 and , extends for approximately 200 km along the border region of Thailand and the eastern limit of the Shan Plateau of Myanmar. Further exploration of this region, especially the entire eastern ~ 95% of the Shan Plateau, will undoubtably recover new populations whose species status will need evaluation. As in all other countries of Indochina and northern Sundaland, the continual discovery of new karst-dwelling populations of shows no signs of tapering off, even in relatively well-collected areas. This only highlights the conservation priority that these unique karstic landscapes still lack on a large scale across all of Asia.

Climate change represents a real threat to biodiversity conservation worldwide. Although the effects on several species of conservation priority are known, comprehensive information about the impact of climate change on reptile populations is lacking. In the present study, we analyze outcomes on the potential distribution of the black beaded lizard (Helodermaalvarezi Bogert & Martin del Campo, 1956) under global warming scenarios. Its potential distribution, at present and in projections for the years 2050 and 2070, under both optimistic and pessimistic climate change forecasts, were computed using current data records and seven bioclimatic variables. General results predict a shift in the future potential distribution of H.alvarezi due to temperature increase. The optimistic scenario (4.5 W/m2) for 2070 suggests an enlargement in the species' distribution as a response to the availability of new areas of suitable habitat. On the contrary, the worst-case scenario (7 W/m2) shows a distribution decrease by 65%. Moreover, the range distribution of H.alvarezi is directly related to the human footprint, which consequently could magnify negative outcomes for this species. Our research elucidates the importance of conservation strategies to prevent the extinction of the black beaded lizard, especially considering that this species is highly threatened by aversive hunting.Climate change represents a real threat to biodiversity conservation worldwide. Although the effects on several species of conservation priority are known, comprehensive information about the impact of climate change on reptile populations is lacking. In the present study, we analyze outcomes on the potential distribution of the black beaded lizard (Helodermaalvarezi Bogert & Martin del Campo, 1956) under global warming scenarios. Its potential distribution, at present and in projections for the years 2050 and 2070, under both optimistic and pessimistic climate change forecasts, were computed using current data records and seven bioclimatic variables. General results predict a shift in the future potential distribution of H.alvarezi due to temperature increase. The optimistic scenario (4.5 W/m2) for 2070 suggests an enlargement in the species' distribution as a response to the availability of new areas of suitable habitat. On the contrary, the worst-case scenario (7 W/m2) shows a distribution decrease by 65%. Moreover, the range distribution of H.alvarezi is directly related to the human footprint, which consequently could magnify negative outcomes for this species. Our research elucidates the importance of conservation strategies to prevent the extinction of the black beaded lizard, especially considering that this species is highly threatened by aversive hunting.