The efficacy of single mitochondrial genes at reconciling the complete mitogenome phylogeny-a case study on dwarf chameleons.

Although genome-scale data generation is becoming more tractable for phylogenetics, there are large quantities of single gene fragment data in public repositories and such data are still being generated. We therefore investigated whether single mitochondrial genes are suitable proxies for phylogenetic reconstruction as compared to the application of full mitogenomes. With near complete taxon sampling for the southern African dwarf chameleons (Bradypodion), we estimated and compared phylogenies for the complete mitogenome with topologies generated from individual mitochondrial genes and various combinations of these genes. Our results show that the topologies produced by single genes (ND2, ND4, ND5, COI, and COIII) were analogous to the complete mitogenome, suggesting that these genes may be reliable markers for generating mitochondrial phylogenies in lieu of generating entire mitogenomes. In contrast, the short fragment of 16S commonly used in herpetological systematics, produced a topology quite dissimilar to the complete mitogenome and its concatenation with ND2 weakened the resolution of ND2. We therefore recommend the avoidance of this 16S fragment in future phylogenetic work.

Fossil-informed biogeographic analysis suggests Eurasian regionalization in crown Squamata during the early Jurassic.

Background: Squamata (lizards, snakes, and amphisbaenians) is a Triassic lineage with an extensive and complex biogeographic history, yet no large-scale study has reconstructed the ancestral range of early squamate lineages. The fossil record indicates a broadly Pangaean distribution by the end- Cretaceous, though many lineages (e.g., Paramacellodidae, Mosasauria, Polyglyphanodontia) subsequently went extinct. Thus, the origin and occupancy of extant radiations is unclear and may have been localized within Pangaea to specific plates, with potential regionalization to distinct Laurasian and Gondwanan landmasses during the Mesozoic in some groups. Methods: We used recent tectonic models to code extant and fossil squamate distributions occurring on nine discrete plates for 9,755 species, with Jurassic and Cretaceous fossil constraints from three extinct lineages. We modeled ancestral ranges for crown Squamata from an extant-only molecular phylogeny using a suite of biogeographic models accommodating different evolutionary processes and fossil-based node constraints from known Jurassic and Cretaceous localities. We hypothesized that the best-fit models would not support a full Pangaean distribution (i.e., including all areas) for the origin of crown Squamata, but would instead show regionalization to specific areas within the fragmenting supercontinent, likely in the Northern Hemisphere where most early squamate fossils have been found. Results: Incorporating fossil data reconstructs a localized origin within Pangaea, with early regionalization of extant lineages to Eurasia and Laurasia, while Gondwanan regionalization did not occur until the middle Cretaceous for Alethinophidia, Scolecophidia, and some crown Gekkotan lineages. While the Mesozoic history of extant squamate biogeography can be summarized as a Eurasian origin with dispersal out of Laurasia into Gondwana, their Cenozoic history is complex with multiple events (including secondary and tertiary recolonizations) in several directions. As noted by previous authors, squamates have likely utilized over-land range expansion, land-bridge colonization, and trans-oceanic dispersal. Tropical Gondwana and Eurasia hold more ancient lineages than the Holarctic (Rhineuridae being a major exception), and some asymmetries in colonization (e.g., to North America from Eurasia during the Cenozoic through Beringia) deserve additional study. Future studies that incorporate fossil branches, rather than as node constraints, into the reconstruction can be used to explore this history further.

Plasticity of Gene Expression and Thermal Tolerance: Implications for Climate Change Vulnerability in a Tropical Forest Lizard.

AbstractTropical ectotherms are thought to be especially vulnerable to climate change because they have evolved in temporally stable thermal environments and therefore have decreased tolerance for thermal variability. Thus, they are expected to have narrow thermal tolerance ranges, live close to their upper thermal tolerance limits, and have decreased thermal acclimation capacity. Although models often predict that tropical forest ectotherms are especially vulnerable to rapid environmental shifts, these models rarely include the potential for plasticity of relevant traits. We measured phenotypic plasticity of thermal tolerance and thermal preference as well as multitissue transcriptome plasticity in response to warmer temperatures in a species that previous work has suggested is highly vulnerable to climate warming, the Panamanian slender anole lizard (Anolis apletophallus). We found that many genes, including heat shock proteins, were differentially expressed across tissues in response to short-term warming. Under long-term warming, the voluntary thermal maxima of lizards also increased, although thermal preference exhibited only limited plasticity. Using these data, we modeled changes in the activity time of slender anoles through the end of the century under climate change and found that plasticity should delay declines in activity time by at least two decades. Our results suggest that slender anoles, and possibly other tropical ectotherms, can alter the expression of genes and phenotypes when responding to shifting environmental temperatures and that plasticity should be considered when predicting the future of organisms under a changing climate.

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.

Species divergence in valleys: the phylogeny of Phrynocephalus forsythii complex and description of a new species.

Background: Geographic isolation caused by high-altitude valleys promotes the formation of geographic segregation of species, leading to species differentiation. The subgenus Oreosaura contains viviparous species from the Tibetan Plateau and the vicinity of the Tarim Basin, which can be divided into three species complexes according to their geographical distribution: Phrynocephalus vlangalii, Phrynocephalus theobaldi, and Phrynocephalus forsythii. However, molecular data for the P. forsythii complex are limited and the diversity of this species complex has been greatly underestimated. Therefore, this study aimed to explore the species diversity of Oreosaura and species differentiation within the P. forsythii complex. Methods: We analysed the species diversity of Oreosaura by combining previous data, constructed a phylogenetic tree of the subgenus based on cytochrome c oxidase subunit I and 16S sequences, and estimated the divergence time. Results: The results suggest significant genetic differences between the Tarim Basin populations and adjacent mountain valley populations of the P. forsythii complex and that the combination of deep valley landscapes in the high mountains and ice-age events have contributed to the differentiation of the viviparous toad-headed agama lizard, which is a key factor in the phylogenetics of the P. forsythii complex. Furthermore, we identified a population collected from Wuqia County, Xinjiang, as a new species, Phrynocephalus kangsuensis sp. nov. The results will provide data for phylogenetic studies following the P. forsythii complex and help demonstrate that valleys promote the formation of Phrynocephalus species.

Adaptive introgression reveals the genetic basis of a sexually selected syndrome in wall lizards.

The joint expression of particular colors, morphologies, and behaviors is a common feature of adaptation, but the genetic basis for such "phenotypic syndromes" remains poorly understood. Here, we identified a complex genetic architecture associated with a sexually selected syndrome in common wall lizards, by capitalizing on the adaptive introgression of coloration and morphology into a distantly related lineage. Consistent with the hypothesis that the evolution of phenotypic syndromes in vertebrates is facilitated by developmental linkage through neural crest cells, most of the genes associated with the syndrome are involved in neural crest cell regulation. A major locus was a ~400-kb region, characterized by standing structural genetic variation and previously implied in the evolutionary innovation of coloration and beak size in birds. We conclude that features of the developmental and genetic architecture contribute to maintaining trait integration, facilitating the extensive and rapid introgressive spread of suites of sexually selected characters.

Cytogenetic Analysis of Satellitome of Madagascar Leaf-Tailed Geckos.

Satellite DNA (satDNA) consists of sequences of DNA that form tandem repetitions across the genome, and it is notorious for its diversity and fast evolutionary rate. Despite its importance, satDNA has been only sporadically studied in reptile lineages. Here, we sequenced genomic DNA and PCR-amplified microdissected W chromosomes on the Illumina platform in order to characterize the monomers of satDNA from the Henkel's leaf-tailed gecko U. henkeli and to compare their topology by in situ hybridization in the karyotypes of the closely related Günther's flat-tail gecko U. guentheri and gold dust day gecko P. laticauda. We identified seventeen different satDNAs; twelve of them seem to accumulate in centromeres, telomeres and/or the W chromosome. Notably, centromeric and telomeric regions seem to share similar types of satDNAs, and we found two that seem to accumulate at both edges of all chromosomes in all three species. We speculate that the long-term stability of all-acrocentric karyotypes in geckos might be explained from the presence of specific satDNAs at the centromeric regions that are strong meiotic drivers, a hypothesis that should be further tested.

Morphometric dataset of Varanus salvator for non-invasive sex identification using machine learning.

Reliable sex identification in Varanus salvator traditionally relied on invasive methods like genetic analysis or dissection, as less invasive techniques such as hemipenes inversion are unreliable. Given the ecological importance of this species and skewed sex ratios in disturbed habitats, a dataset that allows ecologists or zoologists to study the sex determination of the lizard is crucial. We present a new dataset containing morphometric measurements of V. salvator individuals from the skin trade, with sex confirmed by dissection post- measurement. The dataset consists of a mixture of primary and secondary data such as weight, skull size, tail length, condition etc. and can be used in modelling studies for ecological and conservation research to monitor the sex ratio of this species. Validity was demonstrated by training and testing six machine learning models. This dataset has the potential to streamline sex determination, offering a non-invasive alternative to complement existing methods in V. salvator research, mitigating the need for invasive procedures.

High-Quality, Chromosome-Level Reference Genomes of the Viviparous Caribbean Skinks Spondylurus nitidus and S. culebrae.

New World mabuyine skinks are a diverse radiation of morphologically cryptic lizards with unique reproductive biologies. Recent studies examining population-level data (morphological, ecological, and genomic) have uncovered novel biodiversity and phenotypes, including the description of dozens of new species and insights into the evolution of their highly complex placental structures. Beyond the potential for this diverse group to serve as a model for the evolution of viviparity in lizards, much of the taxonomic diversity is concentrated in regions experiencing increasing environmental instability from climate and anthropogenic change. Consequently, a better understanding of genome structure and diversity will be an important tool in the adaptive management and conservation of this group. Skinks endemic to Caribbean islands are particularly vulnerable to global change with several species already considered likely extinct and several remaining species either endangered or threatened. Combining PacBio long-read sequencing, Hi-C, and RNAseq data, here we present the first genomic resources for this group by describing new chromosome-level reference genomes for the Puerto Rican Skink Spondylurus nitidus and the Culebra Skink S. culebrae. Results indicate two high quality genomes, both ∼1.4 Gb, assembled nearly telomere to telomere with complete mitochondrion assembly and annotation.

Genetic Basis and Evolutionary Forces of Sexually Dimorphic Color Variation in a Toad-Headed Agamid Lizard.

In the animal kingdom, sexually dimorphic color variation is a widespread phenomenon that significantly influences survival and reproductive success. However, the genetic underpinnings of this variation remain inadequately understood. Our investigation into sexually dimorphic color variation in the desert-dwelling Guinan population of the toad-headed agamid lizard (Phrynocephalus putjatai) utilized a multidisciplinary approach, encompassing phenotypic, ultrastructural, biochemical, genomic analyses, and behavioral experiments. Our findings unveil the association between distinct skin colorations and varying levels of carotenoid and pteridine pigments. The red coloration in males is determined by a genomic region on chromosome 14, housing four pigmentation genes: BCO2 and three 6-pyruvoyltetrahydropterin synthases. A Guinan population-specific nonsynonymous single nucleotide polymorphism in BCO2 is predicted to alter the electrostatic potential within the binding domain of the BCO2-ß-carotene complex, influencing their interaction. Additionally, the gene MAP7 on chromosome 2 emerges as a potential contributor to the blue coloration in subadults and adult females. Sex-specific expression patterns point to steroid hormone-associated genes (SULT2B1 and SRD5A2) as potential upstream regulators influencing sexually dimorphic coloration. Visual modeling and field experiments support the potential selective advantages of vibrant coloration in desert environments. This implies that natural selection, potentially coupled with assortative mating, might have played a role in fixing color alleles, contributing to prevalence in the local desert habitat. This study provides novel insights into the genetic basis of carotenoid and pteridine-based color variation, shedding light on the evolution of sexually dimorphic coloration in animals. Moreover, it advances our understanding of the driving forces behind such intricate coloration patterns.

Digest: Liolaemus lizards as an emerging model system to study hybridization as a driver of rapid radiations.

Recent perspectives on speciation genomics emphasize the pivotal role of hybridization in driving rapid radiations. The Liolaemus lizard genus displays impressive species richness with around 290 species widely distributed across southern South America. Sánchez et al. conducted a comprehensive study on the 5-million-year-old Liolaemus kingii group, which includes 14 species. The research provides new key insights to enhance our understanding of this rapid radiation, including its diversification in space and time and the consequences of hybridization in its morphological evolution and taxonomy.

Population genomics of flat-tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape.

Phrynosoma mcallii (flat-tailed horned lizards) is a species of conservation concern in the Colorado Desert of the United States and Mexico. We analysed ddRADseq data from 45 lizards to estimate population structure, infer phylogeny, identify migration barriers, map genetic diversity hotspots, and model demography. We identified the Colorado River as the main geographic feature contributing to population structure, with the populations west of this barrier further subdivided by the Salton Sea. Phylogenetic analysis confirms that northwestern populations are nested within southeastern populations. The best-fit demographic model indicates Pleistocene divergence across the Colorado River, with significant bidirectional gene flow, and a severe Holocene population bottleneck. These patterns suggest that management strategies should focus on maintaining genetic diversity on both sides of the Colorado River and the Salton Sea. We recommend additional lands in the United States and Mexico that should be considered for similar conservation goals as those in the Rangewide Management Strategy. We also recommend periodic rangewide genomic sampling to monitor ongoing attrition of diversity, hybridization, and changing structure due to habitat fragmentation, climate change, and other long-term impacts.

Transcriptomic profiling revealed immune-related signaling pathways in response to experimental infection of Leishmania donovani in two desert lizards from Northwest China.

Little is known about the immune response of lizards to Leishmania parasties. In this study, we conducted the first liver transcriptome analysis of two lizards (Phrynocephalus przewalskii and Eremias multiocellata) challenged with L. donovani, endemic to the steppe desert region of northwestern China. Our results revealed that multiple biological processes and immune-related signaling pathways are closely associated with the immune response to experimental L. donovani infection in the two lizards, and that both lizards show similar changes to mammals in terms of immunity to Leishmania. However, the interspecific divergence of the two lizards leads to different transcriptomic changes. In particular, in contrast to P. przewalskii, the challenged E. mutltiocellata was characterized by the induction of down-regulation of most DEGs. These findings will contribute to the scarce resources on lizard immunity and provide a reference for further research on immune mechanisms in reptiles.

Lack of Dosage Balance and Incomplete Dosage Compensation in the ZZ/ZW Gila Monster (Heloderma suspectum) Revealed by De Novo Genome Assembly.

Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and this system is likely homologous to the ZZ/ZW system in the Komodo dragon (Varanus komodoensis), but little else is known about their sex chromosomes. Here, we report the assembly and analysis of the Gila monster genome. We generated a de novo draft genome assembly for a male using 10X Genomics technology. We further generated and analyzed short-read whole genome sequencing and whole transcriptome sequencing data for three males and three females. By comparing female and male genomic data, we identified four putative Z chromosome scaffolds. These putative Z chromosome scaffolds are homologous to Z-linked scaffolds identified in the Komodo dragon. Further, by analyzing RNAseq data, we observed evidence of incomplete dosage compensation between the Gila monster Z chromosome and autosomes and a lack of balance in Z-linked expression between the sexes. In particular, we observe lower expression of the Z in females (ZW) than males (ZZ) on a global basis, though we find evidence suggesting local gene-by-gene compensation. This pattern has been observed in most other ZZ/ZW systems studied to date and may represent a general pattern for female heterogamety in vertebrates.

The genetic architecture of dewlap pattern in Hispaniola anoles (Anolis distichus).

Color and pattern are often critical to survival and fitness, but we know little about their genetic architecture and heritability in groups like reptiles. We investigated the genetic architecture for the pattern of the dewlap-an extensible throat fan important for communication-in anole lizards. We studied the Hispaniolan bark anole (Anolis distichus)-a species that exhibits impressive intraspecific dewlap polymorphism across its range-by conducting multigenerational experimental crosses with 2 populations, one with a solid pale yellow dewlap and another with an orange dewlap surrounded by a yellow margin. Upon rejecting the hypothesis that the extent of the orange pattern is a quantitative trait resulting from many loci of minor effect, we used a maximum likelihood model-fitting framework to show that it is better explained as a simple Mendelian trait, with the solid yellow morph being dominant over the blush orange. The relatively simple genetic architecture underlying this important trait helps explain the complex distribution of dewlap color variation across the range of A. distichus and suggests that changes in dewlap color and pattern may evolve rapidly in response to natural selection.

Convergent genomic signatures associated with vertebrate viviparity.

BACKGROUND: Viviparity-live birth-is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree of Life. Viviparous species exhibit remarkable levels of reproductive diversity, both in the amount of care provided by the parent during gestation, and the ways in which that care is delivered. The genetic basis of viviparity has garnered increasing interest over recent years; however, such studies are often undertaken on small evolutionary timelines, and thus are not able to address changes occurring on a broader scale. Using whole genome data, we investigated the molecular basis of this innovation across the diversity of vertebrates to answer a long held question in evolutionary biology: is the evolution of convergent traits driven by convergent genomic changes? RESULTS: We reveal convergent changes in protein family sizes, protein-coding regions, introns, and untranslated regions (UTRs) in a number of distantly related viviparous lineages. Specifically, we identify 15 protein families showing evidence of contraction or expansion associated with viviparity. We additionally identify elevated substitution rates in both coding and noncoding sequences in several viviparous lineages. However, we did not find any convergent changes-be it at the nucleotide or protein level-common to all viviparous lineages. CONCLUSIONS: Our results highlight the value of macroevolutionary comparative genomics in determining the genomic basis of complex evolutionary transitions. While we identify a number of convergent genomic changes that may be associated with the evolution of viviparity in vertebrates, there does not appear to be a convergent molecular signature shared by all viviparous vertebrates. Ultimately, our findings indicate that a complex trait such as viviparity likely evolves with changes occurring in multiple different pathways.

The natural and human-mediated expansion of a human-commensal lizard into the fringes of Southeast Asia.

BACKGROUND: Human-commensal species often display deep ancestral genetic structure within their native range and founder-effects and/or evidence of multiple introductions and admixture in newly established areas. We investigated the phylogeography of Eutropis multifasciata, an abundant human-commensal scincid lizard that occurs across Southeast Asia, to determine the extent of its native range and to assess the sources and signatures of human introduction outside of the native range. We sequenced over 350 samples of E. multifasciata for the mitochondrial ND2 gene and reanalyzed a previous RADseq population genetic dataset in a phylogenetic framework. RESULTS: Nuclear and mitochondrial trees are concordant and show that E. multifasciata has retained high levels of genetic structure across Southeast Asia despite being frequently moved by humans. Lineage boundaries in the native range roughly correspond to several major biogeographic barriers, including Wallace's Line and the Isthmus of Kra. Islands at the outer fringe of the range show evidence of founder-effects and multiple introductions. CONCLUSIONS: Most of enormous range of E. multifasciata across Southeast Asia is native and it only displays signs of human-introduction or recent expansion along the eastern and northern fringe of its range. There were at least three events of human-introductions to Taiwan and offshore islands, and several oceanic islands in eastern Indonesia show a similar pattern. In Myanmar and Hainan, there is a founder-effect consistent with post-warming expansion after the last glacial maxima or human introduction.

Heteromorphic ZZ/ZW sex chromosomes sharing gene content with mammalian XX/XY are conserved in Madagascan chameleons of the genus Furcifer.

Chameleons are well-known lizards with unique morphology and physiology, but their sex determination has remained poorly studied. Madagascan chameleons of the genus Furcifer have cytogenetically distinct Z and W sex chromosomes and occasionally Z1Z1Z2Z2/Z1Z2W multiple neo-sex chromosomes. To identify the gene content of their sex chromosomes, we microdissected and sequenced the sex chromosomes of F. oustaleti (ZZ/ZW) and F. pardalis (Z1Z1Z2Z2/Z1Z2W). In addition, we sequenced the genomes of a male and a female of F. lateralis (ZZ/ZW) and F. pardalis and performed a comparative coverage analysis between the sexes. Despite the notable heteromorphy and distinctiveness in heterochromatin content, the Z and W sex chromosomes share approximately 90% of their gene content. This finding demonstrates poor correlation of the degree of differentiation of sex chromosomes at the cytogenetic and gene level. The test of homology based on the comparison of gene copy number variation revealed that female heterogamety with differentiated sex chromosomes remained stable in the genus Furcifer for at least 20 million years. These chameleons co-opted for the role of sex chromosomes the same genomic region as viviparous mammals, lacertids and geckos of the genus Paroedura, which makes these groups excellent model for studies of convergent and divergent evolution of sex chromosomes.

Differentiated sex chromosomes, karyotype evolution, and spontaneous triploidy in carphodactylid geckos.

Geckos exhibit derived karyotypes without a clear distinction between macrochromosomes and microchromosomes and intriguing diversity in sex determination mechanisms. We conducted cytogenetic analyses in six species from the genera Nephrurus, Phyllurus, and Saltuarius of the gecko family Carphodactylidae. We confirmed the presence of a female heterogametic system with markedly differentiated and heteromorphic sex chromosomes in all examined species, typically with the W chromosome notably larger than the Z chromosome. One species, Nephrurus cinctus, possesses unusual multiple Z1Z1Z2Z2/Z1Z2W sex chromosomes. The morphology of the sex chromosomes, along with repetitive DNA content, suggests that the differentiation or emergence of sex chromosomes occurred independently in the genus Phyllurus. Furthermore, our study unveils a case of spontaneous triploidy in a fully grown individual of Saltuarius cornutus (3n = 57) and explores its implications for reproduction in carphodactylid geckos. We revealed that most carphodactylids retain the putative ancestral gekkotan karyotype of 2n = 38, characterized by predominantly acrocentric chromosomes that gradually decrease in size. If present, biarmed chromosomes emerge through pericentric inversions, maintaining the chromosome (and centromere) numbers. However, Phyllurus platurus is a notable exception, with a karyotype of 2n = 22 chromosomes. Its eight pairs of biarmed chromosomes were probably formed by Robertsonian fusions of acrocentric chromosomes. The family underscores a remarkable instance of evolutionary stability in chromosome numbers, followed by a profound transformation through parallel interchromosomal rearrangements. Our study highlights the need to continue generating cytogenetic data in order to test long-standing ideas about reproductive biology and the evolution of genome and sex determination.