The role of historical biogeography in shaping colour morph diversity in the common wall lizard.

The maintenance of polymorphisms often depends on multiple selective forces, but less is known on the role of stochastic or historical processes in maintaining variation. The common wall lizard (Podarcis muralis) is a colour polymorphic species in which local colour morph frequencies are thought to be modulated by natural and sexual selection. Here, we used genome-wide single-nucleotide polymorphism data to investigate the relationships between morph composition and population biogeography at a regional scale, by comparing morph composition with patterns of genetic variation of 54 populations sampled across the Pyrenees. We found that genetic divergence was explained by geographic distance but not by environmental features. Differences in morph composition were associated with genetic and environmental differentiation, as well as differences in sex ratio. Thus, variation in colour morph frequencies could have arisen via historical events and/or differences in the permeability to gene flow, possibly shaped by the complex topography and environment. In agreement with this hypothesis, colour morph diversity was positively correlated with genetic diversity and rates of gene flow and inversely correlated with the likelihood of the occurrence of bottlenecks. Concurrently, we did not find conclusive evidence for selection in the two colour loci. As an illustration of these effects, we observed that populations with higher proportions of the rarer yellow and yellow-orange morphs had higher genetic diversity. Our results suggest that processes involving a decay in overall genetic diversity, such as reduced gene flow and/or bottleneck events have an important role in shaping population-specific morph composition via non-selective processes.

The macroevolutionary singularity of snakes.

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.

Does thermal biology differ between two colour pattern morphs of a widespread Australian lizard?

Alternative phenotypes allow individuals to pursue different adaptive pathways in response to the same selective challenge. Colour polymorphic species with geographically varying morph frequencies may reflect multiple adaptations to spatial variables such as temperature and climate. We examined whether thermal biology differed between colour morphs of an Australian lizard, the delicate skink, Lampropholis delicata. The delicate skink has two colour pattern morphs, with frequencies varying across latitude and sex: plain (darker, more common at temperate latitudes, more common in males) or striped (lighter, more common at lower latitudes, more common in females). We tested heating and cooling rate, sprint speed, thermal preference, field body temperature and metabolic rate in both morphs and sexes to determine any link between colour and morph frequency distribution. Plain individuals heated more quickly, but other thermal traits showed little variation among morphs. Lampropholis delicata colour influences rates of heat exchange, but the relationship does not appear to be adaptive, suggesting that behavioural thermoregulation homogenises body temperature in the field. While we find no substantial evidence of thermal differences between the two colour morphs, morph-specific behaviour may buffer against differences in heat exchange. Latitudinal variation in species colour may be driven by selection pressures other than temperature.

A new species of naked-toed gecko Cyrtopodion sensu lato (Squamata: Sauria: Gekkonidae) from Gujarat, India.

We describe a new species of naked-toed gecko of the genus Cyrtopodion Fitzinger, 1843, from the Dahod and Panchmahal districts of Gujarat state, India. The new species is diagnosable by the following suite of characters: a medium-sized Cyrtopodion (adult, snout to vent length up to 50 mm); dorsal scalation on trunk granular, intermixed with enlarged, regularly arranged transverse rows of 15 trihedral tubercles; 6 transverse rows of tubercles on the second segment of the tail; midbody scale rows across belly 20-22; midventral scales 89-97; males with a continuous series of 29-33 precloacal-femoral pores. The new species, Cyrtopodion vindhya sp. nov. is the fifth endemic species of reptile described in the last 15 years from the state of Gujarat that highlights the rich and unique diversity of this understudied region.

The evolutionary network of whiptail lizards reveals predictable outcomes of hybridization.

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.

Generalizing Bayesian phylogenetics to infer shared evolutionary events.

Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a "super-spreading" event, and a geological event fragmenting whole communities of species. It is difficult to test for patterns of shared divergences predicted by such processes because all phylogenetic methods assume that lineages diverge independently. We introduce a Bayesian phylogenetic approach to relax the assumption of independent, bifurcating divergences by expanding the space of topologies to include trees with shared and multifurcating divergences. This allows us to jointly infer phylogenetic relationships, divergence times, and patterns of divergences predicted by processes of diversification that affect multiple evolutionary lineages simultaneously or lead to more than two descendant lineages. Using simulations, we find that the method accurately infers shared and multifurcating divergence events when they occur and performs as well as current phylogenetic methods when divergences are independent and bifurcating. We apply our approach to genomic data from two genera of geckos from across the Philippines to test if past changes to the islands' landscape caused bursts of speciation. Unlike previous analyses restricted to only pairs of gecko populations, we find evidence for patterns of shared divergences. By generalizing the space of phylogenetic trees in a way that is independent from the likelihood model, our approach opens many avenues for future research into processes of diversification across the life sciences.

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.

Revising the taxonomy of Darevskia valentini (Boettger, 1892) and Darevskia rudis (Bedriaga, 1886) (Squamata, Lacertidae): a Morpho-Phylogenetic integrated study in a complex Anatolian scenario.

Revealing biodiversity allows the accurate determination of the underlying causes of many biological processes such as speciation and hybridization. These processes contain many complex patterns, especially in areas with high species diversity. As two of the prominent zoogeographic areas, Anatolia and Caucasus are also home to the genus Darevskia, which has a complex morphological structure and parthenogenetic speciation. Darevskia valentini and D. rudis are two largely distributed taxa of this genus, both of which have a controversial taxonomic delimitation. Here we performed both a highly detailed morphological comparison and a molecular evaluation for the populations in both species groups. The most comprehensive taxonomic revision of this complex was carried out to determine the cases where the data obtained were compatible or not with each approach. As a result of the obtained outputs, it seems that D. spitzenbergerae stat. nov., D. mirabilis stat. nov. and D. obscura stat. nov. should be accepted as the species level, this later with subspecies D. o. bischoffi comb. nov. and D. o. macromaculata comb. nov.. Also, we propose two new taxa: D. josefschmidtleri sp. nov. and D. spitzenbergerae wernermayeri ssp. nov.. It has also been shown that "lantzicyreni" subspecies belong to D. rudis instead of D. valentini. The extensive revision has contributed to subsequent studies to more accurately understand the past histories of species in the genus Darevskia.

Goniurosaurus wangshu sp. nov., a new species of Tiger Gecko from Guangdong, China (Squamata: Eublepharidae).

A new species of Tiger Gecko in the genus Goniurosaurus is described from Guangdong, China. This new species, Goniurosaurus wangshu sp. nov. is the fifth species of Goniurosaurus found in karst topography of Guangdong. It is distinguished morphologically from congeners in this region by the combination of thirteen precloacal pores in male; dorsal ground color of head, body, and limbs in adults yellow; and iris orange. To validate our morphological inferences and support the description of Goniurosaurus wangshu sp. nov. as a new species, we sequenced 16S, CMOS, cytb, and RAG1 gene regions and performed molecular phylogenetic analyses. Phylogenetic analysis places the new species within the G. yingdeensis group and highlights the evolutionary distinction between this new species and other described congeners.

Altered fire regimes modify lizard communities in globally endangered Araucaria forests of the southern Andes.

Wildfire regimes are being altered in ecosystems worldwide. The density of reptiles responds to fires and changes to habitat structure. Some of the most vulnerable ecosystems to human-increased fire frequency are old-growth Araucaria araucana forests of the southern Andes. We investigated the effects of wildfires on the density and richness of a lizard community in these ecosystems, considering fire frequency and elapsed time since last fire. During the 2018/2019 southern summer season, we conducted 71 distance sampling transects to detect lizards in Araucaria forests of Chile in four fire "treatments": (1) unburned control, (2) long-term recovery, (3) short-term recovery, and (4) burned twice. We detected 713 lizards from 7 species. We found that the density and richness of lizards are impacted by wildfire frequency and time of recovery, mediated by the modification of habitat structure. The lizard community varied from a dominant arboreal species (L. pictus) in unburned and long-recovered stands, to a combination of ground-dwelling species (L. lemniscatus and L. araucaniensis) in areas affected by two fires. Araucaria forests provided key habitat features to forest reptiles after fires, but the persistence of these old-growth forests and associated biodiversity may be threatened given the increase in fire frequency.

Phylogenetic value of jaw elements of lacertid lizards (Squamata: Lacertoidea): a case study with Oligocene material from France.

Several extinct species are known from the family Lacertidae, but due to poor preservation, many of them are based on single bones. Here, we compare phylogenetic signals of disarticulated premaxillae, maxillae and dentaries of lacertids from four French Oligocene localities (Coderet, La Colombière, Roqueprune 2, Mas de Got B). We identified five morphotypes among the premaxillae, six among the maxillae, and ten among the dentaries. These morphotypes were scored as individual taxa per locality into three separate character matrices with the same 246 characters, one matrix for each jaw element. Subsequently, the phylogenetic position of the morphotypes was tested using maximum parsimony. The consensus trees with the dentaries and the maxillae found a large polytomy including all taxa except the outgroup taxon Gekko gecko. The consensus tree with the premaxillae showed a considerably more resolved topology but found all morphotype taxa outside Lacertidae. In a second step, we compared the constitution of our three datasets and the morphotype taxa. Our results suggest that a combination of convergent characters and missing data led to the outgroup position of the premaxilla morphotype taxa. The poor resolution of the maxillae strict consensus is likely a consequence of their fragmentary preservation. For the dentaries, a high amount of missing data due to the high number of morphotype taxa most likely caused the poor tree resolution. Indeed, tests with fewer morphotypes found tree resolutions comparable to the premaxilla data. When linking the morphotypes, five possible lacertid "species" were found. Comparison with already known French Oligocene lacertid species points to a slightly higher species richness of Lacertidae at that time than known before. Reliable species classification based on phylogeny only seems possible when combining the jaw elements or in association with other cranial and postcranial material, putting some doubt on species identifications based on single bones.

When adaptive radiations collide: Different evolutionary trajectories between and within island and mainland lizard clades.

Oceanic islands are known as test tubes of evolution. Isolated and colonized by relatively few species, islands are home to many of nature's most renowned radiations from the finches of the Galápagos to the silverswords of the Hawaiian Islands. Despite the evolutionary exuberance of insular life, island occupation has long been thought to be irreversible. In particular, the presumed much tougher competitive and predatory milieu in continental settings prevents colonization, much less evolutionary diversification, from islands back to mainlands. To test these predictions, we examined the ecological and morphological diversity of neotropical Anolis lizards, which originated in South America, colonized and radiated on various islands in the Caribbean, and then returned and diversified on the mainland. We focus in particular on what happens when mainland and island evolutionary radiations collide. We show that extensive continental radiations can result from island ancestors and that the incumbent and invading mainland clades achieve their ecological and morphological disparity in very different ways. Moreover, we show that when a mainland radiation derived from island ancestors comes into contact with an incumbent mainland radiation the ensuing interactions favor the island-derived clade.

De novo Assembly, Annotation, and Analysis of Transcriptome Data of the Ladakh Ground Skink Provide Genetic Information on High-Altitude Adaptation.

The Himalayan Arc is recognized as a global biodiversity hotspot. Among its numerous cryptic and undiscovered organisms, this composite high-mountain ecosystem harbors many taxa with adaptations to life in high elevations. However, evolutionary patterns and genomic features have been relatively rarely studied in Himalayan vertebrates. Here, we provide the first well-annotated transcriptome of a Greater Himalayan reptile species, the Ladakh Ground skink Asymblepharus ladacensis (Squamata: Scincidae). Based on tissues from the brain, an embryonic disc, and pooled organ material, using pair-end Illumina NextSeq 500 RNAseq, we assembled ~77,000 transcripts, which were annotated using seven functional databases. We tested ~1600 genes, known to be under positive selection in anurans and reptiles adapted to high elevations, and potentially detected positive selection for 114 of these genes in Asymblepharus. Even though the strength of these results is limited due to the single-animal approach, our transcriptome resource may be valuable data for further studies on squamate reptile evolution in the Himalayas as a hotspot of biodiversity.

Diversifying on the Ark: multiple new endemic lineages of dwarf geckos from the Western Ghats provide insights into the systematics and biogeography of South Asian Cnemaspis (Reptilia: Squamata).

The highly speciose gekkonid genus Cnemaspis Strauch, 1887 is polyphyletic, with three distantly related and geographically isolated clades from Africa, South Asia (SA), and Southeast Asia. At present, there are 85 known species within SA Cnemaspis, although the number continues to increase rapidly with focused surveys and rigorous taxonomic work. Recent studies have provided valuable insights into the diversity and evolutionary history of SA Cnemaspis; however, most of these studies lack sufficient sampling in the Western Ghats (WG), where the genus has its greatest diversity. We addressed this research gap by conducting extensive sampling across the WG and re-examining museum specimens, thus providing a systematic account of various extant Cnemaspis species along with their distribution and natural history. We described 12 new species and a southern WG endemic clade of SA Cnemaspis. Ten of the newly described species are endemic to the forests of the southern WG. We also identified 10 well-supported subclades that can be separated across morphological, geographic, and phylogenetic axes. A time-calibrated phylogeny and ancestral area reconstructions confirmed the Paleocene origin of SA Cnemaspis in the WG and provide insights into its evolutionary history and biogeography. The discovery of multiple endemic and deeply divergent lineages further highlights the evolutionary significance of the WG for lizards.

Keratin intermediate filament chains in the European common wall lizard (Podarcis muralis) and a potential keratin filament crosslinker.

On the basis of sequence homology with mammalian α-keratins, and on the criteria that the coiled-coil segments and central linker in the rod domain of these molecules must have conserved lengths if they are to assemble into viable intermediate filaments, a total of 28 Type I and Type II keratin intermediate filament chains (KIF) have been identified from the genome of the European common wall lizard (Podarcis muralis). Using the same criteria this number may be compared to 33 found here in the green anole lizard (Anole carolinensis) and 25 in the tuatara (Sphenodon punctatus). The Type I and Type II KIF genes in the wall lizard fall in clusters on chromosomes 13 and 2 respectively. Although some differences occur in the terminal domains in the KIF chains of the two lizards and tuatara, the similarities between key indicator residues - cysteine, glycine and proline - are significant. The terminal domains of the KIF chains in the wall lizard also contain sequence repeats commonly based on glycine and large apolar residues and would permit the fine tuning of physical properties when incorporated within the intermediate filaments. The H1 domain in the Type II chain is conserved across the lizards, tuatara and mammals, and has been related to its role in assembly at the 2-4 molecule level. A KIF-like chain (K80) with an extensive tail domain comprised of multiple tandem repeats has been identified as having a potential filament-crosslinking role.

Cytogenetically Elusive Sex Chromosomes in Scincoidean Lizards.

The lizards of the species-rich clade Scincoidea including cordylids, gerrhosaurids, skinks, and xantusiids, show an almost cosmopolitan geographical distribution and a remarkable ecological and morphological divergence. However, previous studies revealed limited variability in cytogenetic traits. The sex determination mode was revealed only in a handful of gerrhosaurid, skink, and xantusiid species, which demonstrated either ZZ/ZW or XX/XY sex chromosomes. In this study, we explored the karyotypes of six species of skinks, two species of cordylids, and one gerrhosaurid. We applied conventional and molecular cytogenetic methods, including C-banding, fluorescence in situ hybridization with probes specific for telomeric motifs and rDNA loci, and comparative genomic hybridization. The diploid chromosome numbers are rather conserved among these species, but the chromosome morphology, the presence of interstitial telomeric sequences, and the topology of rDNA loci vary significantly. Notably, XX/XY sex chromosomes were identified only in Tiliqua scincoides, where, in contrast to the X chromosome, the Y chromosome lacks accumulations of rDNA loci. We confirm that within the lizards of the scincoidean clade, sex chromosomes remained in a generally poor stage of differentiation.

Nuclear phylogenies and genomics of a contact zone establish the species rank of Podarcis lusitanicus (Squamata, Lacertidae).

Unravelling when divergent lineages constitute distinct species can be challenging, particularly in complex scenarios combining cryptic diversity and phylogenetic discordances between different types of molecular markers. Combining a phylogenetic approach with the study of contact zones can help to overcome such difficulties. The Podarcis hispanicus species complex has proven to be prosperous in independent evolutionary units, sometimes associated with cryptic diversity. Previous studies have revealed that one of the species of this complex, P. guadarramae, comprises two deeply divergent yet morphologically indistinguishable evolutionary units, currently regarded as subspecies (P. g. guadarramae and P. g. lusitanicus). In this study we used molecular data to address the systematics of the two lineages of Podarcis guadarramae and the closely related P. bocagei. Firstly, we reconstructed the species tree of these three and two additional taxa based on 30 nuclear loci using the multispecies coalescent with and without gene flow. Secondly, we used SNPs obtained from RADseq data to analyze the population structure across the distribution limits P. g. lusitanicus and P. g. guadarramae, and for comparison, a contact zone between P. bocagei and P. g. lusitanicus. Nuclear phylogenetic relationships between these three taxa are clearly difficult to determine due to the influence of gene flow, but our results give little support to the monophyly of P. guadarramae, potentially due to a nearly simultaneous divergence between them. Genetic structure and geographic cline analysis revealed that the two lineages of P. guadarramae replace each other abruptly across the sampled region and that gene flow is geographically restricted, implying the existence of strong reproductive isolation. Podarcis bocagei and P. g. lusitanicus show a similar degree of genetic differentiation and reproductive isolation, with very low levels of admixture in syntopy. These results support that all three forms are equally differentiated and reproductively isolated. In consequence, we conclude that the two former subspecies of Podarcis guadarramae constitute valid, yet cryptic species, that should be referred to as P. lusitanicus and P. guadarramae.

Neotype designation and redescription of Tropidophorus guangxiensis Wen, 1992 (Squamata: Sauria: Scincidae), with description of a new subspecies from central South China.

The genus Tropidophorus consists of small semi-aquatic lizards that dwell in lowland forest steams (Barbour, 1921; Bauer & Jackman, 2008). Here, we designate the neotype and re-describe T. guangxiensis Wen, 1992 based on newly collected topotypic specimens. We also describe a new subspecies from Xuefeng Mountain, Hongjiang County, Hunan Province, central South China. Based on two mitochondrial genes (12S rRNA and 16S rRNA), the phylogenetic position of T. guangxiensis is allocated for the first time. Additionally, our data strongly support that the new subspecies is phylogenetically closely related to T. g. guangxiensis. We also present a morphological identification key for known species and subspecies of Tropidophorus in China.

Gekko phuyenensis sp. nov. (Squamata: Gekkonidae), a new species from southern Vietnam.

A new species of the genus Gekko Laurenti, 1768 is described from Phu Yen Province, southern Vietnam based on morphological and molecular evidence. Gekko phuyenensis sp. nov. differs from other congeners by its moderate size, with a snout-vent length of 90.292.8 mm; nares in contact with rostral; internasal 1; interorbitals 35 or 36; ventrals 3032; dorsal tubercle rows 9 or 10; precloacal pores 12 or 13 in males and precloacal pits 13 in female; subdigital lamellae under first finger 1821, fourth finger 19 or 20, first toe 1820, and fourth toe 2123; subcaudals median enlarged; no webbing between toes; and the absence of tubercles on hind limbs. Molecular phylogenetic analyses of mitochondrial gene COI (681 bp) using the geckos from Phu Yen and its congeners in southern Vietnam resolve the new species as the sister lineage to G. cf. grossmanni from Khanh Hoa Province. Genetic distances between G. phuyenensis sp. nov. and its congeners in southern Vietnam range from 16.924.2%. The discovery of this new species raises the number of known species of Gekko in Vietnam to 14.

Taxonomy and predicted distribution of a rare Indian skink, Eutropis innotata (Blanford, 1870) (Reptilia: Scincidae) with the redescription of its holotype.

We examined the holotype of Euprepes innotatus Blanford, 1870 which was presented to the Natural History Museum, London (NHMUK) by Blanford himself, and is redescribed herein. Based on the morphological similarity, we placed Eutropis innotata within the E. carinata group (contra Blanford, 1870), as it is closely allied to E. dissimilis and E. carinata in morphological and morphometric traits. Based on the current distribution pattern, we conducted Species Distribution Modelling using the Maximum Entropy algorithm and the distribution range of this species was predicted to be wider than the currently known limits within the south-central parts of the Deccan plateau. Furthermore, we updated the conservation status of E. innotata using the criteria of the IUCN Red List, and suggested it be considered as a species of Least Concern.