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At least 19 recordsLinked to original sources

PubMed2026

Chromosome-Level Reference Genome of the Desert Night Lizard Xantusia vigilis.

We present a reference-quality genome assembly for the desert night lizard (Xantusia vigilis). The night lizards (Xantusiidae) are a family of small-bodied lizards found in North America (Xantusia), Central America (Lepidophyma), and Cuba (Cricosaura). The night lizard family has an independent evolutionary history of at least 80 million years from its sister taxa within Scincoidea. The Xantusiids have several unique ecological, behavioral and evolutionary characteristics. For instance, the family contains the only squamate species that form diploid, unisexual, parthenogenic lineages. In addition, most night lizards are viviparous and form stable kin groups that are maintained over multiple years, an unusual life history strategy among lizards. Combining PacBio long-read sequencing, Hi-C, and RNAseq data we developed a reference-quality genome for the desert night lizard, X. vigilis. We assembled a complete mitochondrion and ~ 2.2 Gb nuclear genome, with 20 scaffolds that correlate in size to the X. vigilis karyotype. In addition, we found that X. vigilis chromosome 1 aligns with gene content of both of macrochromosome 1 and microchromosome 9 from a genome assembly of a species in the sister family Cordylidae (Hemicordylus capensis).

Xantusia↗

PubMed2026

Genome-wide barriers to gene flow reveal the genetic basis of viviparity evolution in a lizard.

Viviparity (live-bearing) is a major evolutionary transition repeatedly linked with ecological and evolutionary diversification throughout vertebrates. Live-bearing reproduction entails a novel suite of phenotypes and life history traits, but the genetic processes by which such a reproductive innovation evolves are unknown. Remarkable among amniotes, the common lizard (Zootoca vivipara) has extant oviparous (egg-laying) and viviparous lineages and a to-date unresolved history of parity mode emergence. This species represents an ideal model to reconstruct the evolutionary and genetic mechanisms of how viviparity arises. By analyzing whole genomes of individuals from across the species' distribution, we robustly show that viviparity evolved once. However, gene flow from oviparous to viviparous populations is found to be long-term and extensive, causing pronounced gene tree discordance. We inferred signals of selection for viviparity in many independent regions across the genome, and these were recruited over considerable time. Genomic barriers to gene flow between oviparity and viviparity were found genome wide. These are enriched for regions under selection for parity mode and for genes known to be involved in pregnancy and parturition in squamates and mammals. Further implicating their functional role in viviparity, we show that genes in genomic regions under selection and resisting gene flow are more highly expressed in the uterus of viviparous lizards during pregnancy. Our study demonstrates that viviparity in an amniote evolved by selection in the face of gene flow and primarily by the genome-wide accumulation of functional regulatory variants. These results reveal how complex adaptive innovations can arise and be maintained.

Animals↗

PubMed2025

Global Environmental Factors Impact the Evolution of Adult Hemoglobins in Squamata Reptiles (Lizards and Snakes) and Terrestrial Turtles.

Convergent evolution of oxygen transport mechanisms arises from respiratory proteins adapting to similar environmental pressures. We examined this relationship between adult hemoglobin subunits (Hbs: HBA1, HBAD, HBB1, and HBB2) found in land reptiles (lizards, snakes, and turtles) with their global distribution variables: Altitude, latitude, ambient temperature, and biomass production. We found that biomass was positively associated with the synonymous substitution rate (dS) of HBAD, while it showed the opposite trend for HBB2 in snakes. Additionally, latitude was negatively related to the dS of HBB2 in snakes, but nonsignificant with other Hbs. Altitude was negatively associated with ω = dN/dS of HBA1 and HBAD, whereas temperature showed a similar negative trend with the ω of HBAD across reptiles and in HBB2 of snakes. At amino acid sites, we found most were conserved except for 11 (two near the heme-binding pocket) across Hbs. These fast-changing sites shifted from polar to nonpolar residues, showing a pattern seen in high-altitude mammals. Our results highlight that in reptiles (i) Hbs are diversifying at individual amino acid sites while generally some subunits exhibiting lower ω rates at higher altitudes and hotter temperatures, with the later and higher biomass ecosystems also linked to increases in dS; (ii) HBBs are the most conserved of the Hbs; (iii) latitudinal gradients only show a significant association with the dS of HBB2 in snakes; and (iv) gene conversion events occurred across HBBs in reptiles, which confound their homology assignation, except for snakes that evidenced a single major duplication in their HBBs.

Animals↗

PubMed2026

Understanding Genomic Landscapes of Differentiation in Round-Tailed Horned Lizards (Phrynosoma modestum).

Population divergence is promoted by divergent selection and inhibited by gene flow, but the mechanisms of and relationship between these two processes remain poorly understood. Developing a well-informed hypothesis of the selective pressures underlying divergence in a natural population requires a thorough understanding of both species structure and demographic history. In this study, we assess whole-genome sequences of round-tailed horned lizards (Phrynosoma modestum) from throughout the species range and combine phylogenetic analyses with genomic landscape scans to understand how current genetic diversity has been influenced by demographic histories and evolutionary pressures. Maximum likelihood (ML) phylogenetic analysis supports two lineages within the species, corresponding to a North/South population divide that developed around 7 million years ago (Ma) and displays little migration. However, intermediate genealogical divergence index values between the two lineages ultimately leave us unable to recommend a full taxonomic distinction. Genome-wide scans of population genetic statistics identified islands of divergence exhibiting differentiation patterns linked to models of reproductive isolation and within-population selection. Significantly negative values of Tajima's D and positive selection statistics in these islands offer support for selection acting on P. modestum, but patterns may also stem from recent population expansions. We posit that selection within populations has played a large role in shaping genomic divergence across the species' range. Taken together, our results provide perspective into how variable selective pressures shape the genomics of two divergent populations currently maintaining species integrity, despite significant signatures of geographic structure and divergence.

Animals↗

PubMed2026

Weak but repeated patterns of co-introgression of nuclear OXPHOS genes and mitochondrial DNA in Iberian wall lizards.

In this study, we took advantage of the previously reported instances of mitochondrial DNA capture in the Podarcis Iberian group, a speciose group of Iberian wall lizards, to test the hypothesis that nuclear genes from the OXPHOS (Oxidative phosphorylation) chain can co-introgress with the mitochondria as an evolutionary response to mitigate the costs of mitonuclear incompatibilities. Using dense population sampling and transcriptome data, we generated capture-sequence datasets for nuclear OXPHOS chain genes (nucOXPHOS), random nuclear loci (nucControl) and the complete mitochondrial genome. Phylogenetic analyses of nuclear and mitochondrial genes confirmed two previously identified events of mitochondrial introgression in the Podarcis Iberian group and revealed two new cases. Three of these cases have led to complete local mitochondrial DNA replacements, where the introgressed mitotypes have replaced the native ones in several populations, and involve a currently unknown and presumably extinct donor species, so-called "ghost lineage". Detecting introgression from ghost lineages, whose genomes are not accessible, remains challenging. To overcome this issue, we designed or adapted several tests aimed at detecting differential signals of introgression between our nucOXPHOS and nucControl gene sets. One of these tests, based on the effects of introgression on branch lengths in phylogenetic trees, uncovered a weak but consistently significant signal of partial co-introgression of nucOXPHOS genes compared to the genomic background (represented by the nucControl gene set) in three out of four cases of mtDNA introgression.

mitochondrial introgression↗

PubMed2025

Ancient Introgression Explains Mitochondrial Genome Capture and Mitonuclear Discordance Among South American Collared Tropidurus Lizards.

Mitonuclear discordance-evolutionary discrepancies between mitochondrial and nuclear DNA phylogenies-can arise from various factors, including introgression, incomplete lineage sorting, recent or ancient demographic fluctuations, sex-biased dispersal asymmetries, among others. Understanding this phenomenon is crucial for accurately reconstructing evolutionary histories, as failing to account for discordance can lead to misinterpretations of species boundaries, phylogenetic relationships, and historical biogeographic patterns. We investigate the evolutionary drivers of mitonuclear discordance in the Tropidurus spinulosus species group, which contains nine species of lizards inhabiting open tropical and subtropical environments in South America. Using a combination of population genetic and phylogenomic approaches applied to mitochondrial and nuclear data, we identified different instances of gene flow that occurred in ancestral lineages of extant species. Our results point to a complex evolutionary history marked by prolonged isolation between species, demographic fluctuations, and potential episodes of secondary contact with genetic admixture. These conditions likely facilitated mitochondrial genome capture while diluting signals of nuclear introgression. Furthermore, we found no strong evidence supporting incomplete lineage sorting or natural selection as primary drivers of the observed mitonuclear discordance. Therefore, the unveiled patterns are most consistent with neutral demographic processes, coupled with ancient mitochondrial introgression, as the main factors underlying the mismatch between nuclear and mitochondrial phylogenies in this system. Future research could further explore the role of other demographic processes, such as asymmetric sex-biased dispersal, in shaping these complex evolutionary patterns.

Animals↗

PubMed2025

The genome sequence of the Tyrrhenian Wall Lizard, Podarcis tiliguerta (Gmelin, 1789) (Squamata: Lacertidae).

We present a genome assembly from an individual female Podarcis tiliguerta (Tyrrhenian Wall Lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1 462.31 megabases and 1 394.94 megabases. Most of haplotype 1 (99.26%) is scaffolded into 20 chromosomal pseudomolecules, including the W and Z sex chromosomes. Most of haplotype 2 (99.2%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.19 kilobases.

Podarcis tiliguerta; Tyrrhenian Wall Lizard; genom↗

PubMed2026

The genome sequence of the Eurasian common lizard, Zootoca vivipara (von Jacquin, 1787) (Squamata: Lacertidae).

We present a genome assembly from an individual male Zootoca vivipara (Eurasian common lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1 424.51 megabases and 1 423.70 megabases. Most of the haplotype 1 assembly (99.49%) and the haplotype 2 assembly (99.42%) are each scaffolded into 18 chromosomal pseudomolecules, including the Z 1 and Z 2 sex chromosomes. The mitochondrial genome has also been assembled, with a length of 17.09 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland.

Eurasian common lizard↗

PubMed2026

Genome-wide SNP data reveal geographic structure and landscape-associated genomic differentiation in a widespread lizard in arid Eastern Central Asia.

Arid landscapes provide important systems for examining how geographic structure and environmental heterogeneity shape genomic differentiation. In topographically complex desert regions, however, it remains challenging to determine whether population structure primarily reflects landscape resistance, geographic distance, or contemporary environmental variation. Here, we use genome-wide SNP data to investigate population structure, phylogenetic relationships, historical gene flow, demographic history, and landscape correlates of genomic differentiation in the variegated racerunner (Eremias vermiculata), a widespread lacertid lizard across arid Eastern Central Asia. Analyses of 164 individuals recovered six geographically structured nuclear clusters associated with major desert basins and mountain-bounded regions. Nuclear phylogenies resolved two broad regional clades corresponding to northeastern and southwestern parts of the species' range, while PCA and ADMIXTURE analyses recovered six finer-scale genetic clusters. Mitochondrial phylogenies, based on combined NCBI-derived Cyt b and COI sequences from the same individuals, recovered four deeper maternal lineages. These patterns indicate overall phylogeographic agreement between nuclear and mitochondrial datasets, with genome-wide SNPs providing finer-scale resolution of population structure. Demographic reconstructions further uncovered regionally heterogeneous Late Pleistocene histories among clusters, including signals of expansion, stability, and decline. Landscape genomic analyses revealed that genomic differentiation is primarily associated with landscape resistance, particularly elevation and land cover, as well as geographic distance, whereas contemporary environmental variables explained comparatively little variation after controlling for spatial structure. Together, our results suggest that genomic differentiation in E. vermiculata reflects the interplay of persistent landscape configuration, historical connectivity, and region-specific demographic histories across arid Eastern Central Asia. More broadly, this study highlights the value of integrating phylogeographic and landscape genomic approaches for understanding population differentiation and evolutionary history in topographically heterogeneous desert ecosystems.

Arid Eastern Central Asia↗

PubMed2026

Genomic consequences of admixture in an experimentally founded sand lizard population.

Conservation interventions are increasingly required for species threatened by population declines and isolation due to anthropogenic pressures. Small, isolated populations are particularly vulnerable to the loss of genetic diversity, increased inbreeding, and the accumulation of deleterious mutations. Translocations or supplementation of allopatric individuals for genetic rescue may be the only way to increase genetic diversity and increase population persistence via increased adaptive potential. Here, we use an experimentally admixed population of sand lizards on a small island in Sweden as a valuable model of genetic rescue. This population was established approximately 20 years ago (5-6 generations), resulting in increased fecundity and hatchling viability. This population was founded from crossings between individuals from an inbred population from the nearby mainland and individuals sourced from populations in southern Sweden. Low-coverage whole-genome sequencing revealed elevated genetic diversity and reduced realized genetic load in this admixed population relative to the source populations. Ancestry analyses indicated a greater contribution of southern Swedish genetic variation, potentially reflecting the contribution of beneficial adaptive variation from this region that may underlie the positive population effects. This system provides valuable empirical insights into the long-term genomic consequences of genetic rescue in this model vertebrate population.

Journal Article↗

PubMed2026

The evolutionary origins of the parthenogenetic lizard Aspidoscelis tesselatus.

Most vertebrate species reproduce sexually. The whiptail lizards (Aspidoscelis) are a notable exception; at least 11 of the 45 recognized species are parthenogenetic. Here, we focus on one such species (Aspidoscelis tesselatus) as a case study to understand how parthenogenetic species originate and evolve. Using genome-wide sequence data and ecological niche modelling, we find that A. tesselatus likely arose from a single hybrid speciation event between A. scalaris and A. marmoratus less than 500,000 years ago. The geographic ranges of A. tesselatus and its parental species overlap currently, and niche modelling shows this zone of sympatry was even broader during the period when A. tesselatus likely formed. We additionally show evidence that A. tesselatus has a dynamic genome post-formation, with de novo mutations, introgression, and double-strand break associated events all contributing to variation within the species. These results show that asexual lineages can continue to be shaped by ongoing genomic and ecological dynamics, illuminating the processes that influence transitions in reproductive mode.

asexuality↗

PubMed2026

Chromosome-Level Genome Assembly and Annotation of the Chinese Lizard Gudgeon (Saurogobio dabryi).

The Chinese lizard gudgeon (Saurogobio dabryi) is an economically important freshwater species within the Cyprinidae family, abundant in the middle and lower reaches of the Yangtze River and its adjacent basins. As a promising species suitable for aquaculture in China, the lack of genomic resources has rendered the genetic breeding and conservation research. Here, we present the first chromosome-level genome assembly of S. dabryi using PacBio HiFi long reads, short reads, and Hi-C sequencing data. The final assembly reaches a total size of 1.09 Gb and Hi-C scaffolding anchors 99.55% of the assembled contigs onto 25 chromosomes, with a scaffold N50 reaching 43.15 Mb. The final genome assembly shows a BUSCO completeness of 98.39%. We annotated 659.55 Mb repetitive sequences and 26,036 protein-coding genes, 99.47% of which are functionally annotated. Comparative phylogenomic analysis clarifies the phylogenetic position of Saurogobio within Gobioninae. This high-quality genome provides a critical genetic basis for exploring cyprinid phylogeny, benthic adaptive evolution, genetic improvement, and conservation efforts of S. dabryi.

Saurogobio dabryi↗

PubMed2025

Genome-Wide Mining of lncRNAs Reveals Their Potential Regulatory Role in the Evolution of Viviparity.

Reproduction in vertebrates usually involves egg-laying (oviparity) or live-bearing (viviparity). Oviparity is the ancestral trait from which viviparity has independently evolved more than 100 times in squamate reptiles. This transition involves a series of physiological and structural changes, including the degeneration of eggshell and the evolution of a placenta and differences in the temporal and spatial expression patterns of some functional genes that drive the structural transformation. Long non-coding RNAs (lncRNAs) play important roles in the regulation of gene expression, yet it remains unclear whether they participate in gene expression shifts during the transition from oviparity to viviparity, and if so how. Therefore, we employ deep mining to identify novel lncRNAs of a closely related oviparous-viviparous pair of lizards (Phrynocephalus przewalskii and P. vlangalii). We construct cis- and trans-regulatory networks between lncRNAs and target genes using the transcriptomic data of oviduct or uteri tissues across reproductive periods. Results show that lncRNAs that regulate eggshell gland developmental genes in the oviparous lizard are lost or less expressed in the viviparous lizard. A number of lncRNAs involved in the regulation of placental development and embryo attachment in viviparous species have no orthologs in oviparous species, and others show little or no expression. Accordingly, lncRNAs may play important regulatory roles in the physiological and structural changes in the transition from oviparity to viviparity. These results open doors to the further elucidation of genetic regulatory networks.

Animals↗

PubMed2026

Evolutionary Conservation and Reproductive Expression of ABC Transporter Genes in Two Sphenomorphus Skinks.

ATP-binding cassette (ABC) transporters represent one of the largest membrane protein superfamilies in vertebrates, playing essential roles in translocating diverse substrates across membranes. However, knowledge of ABC transporter genes in reptiles remains limited. In this study, we conducted a comprehensive genome-wide identification and characterization of the ABC gene family in oviparous Sphenomorphus incognitus and viviparous Sphenomorphus indicus. A total of 45 ABC genes were identified in each species and classified into seven subfamilies (ABCA-ABCG). Comparative and phylogenetic analyses revealed a generally conserved gene repertoire, with limited duplication events observed mainly in the ABCA and ABCG subfamilies, whereas other subfamilies (e.g., ABCE, ABCF, and ABCD) remained highly conserved. Interestingly, a lineage-specific duplication of ABCC2 was identified in lizards. Oviductal expression profiling revealed distinct temporal patterns of ABC gene expression across reproductive stages. Several genes, including ABCG1, ABCC3, and ABCD4, exhibited conserved expression trajectories across both species, suggesting shared transcriptional regulation. In contrast, ABCA1, ABCB1, and ABCG2 showed species-specific expression patterns, indicating regulatory divergence between the two lizard species. Overall, ABC gene expression was more dynamic in S. incognitus than in S. indicus. In summary, although the ABC transporter family is structurally conserved, it exhibits lineage-specific evolutionary changes and divergent transcriptional regulation in lizard oviducts. This study provides a foundation for understanding the diversity and regulation of ABC transporter genes in reptiles.

Animals↗

PubMed2025

Oogenesis and germinal bed morphology of the brown anole (A. sagrei).

BACKGROUND: The brown anole is a model species of the genus Anolis, a squamate (encompassing lizards and snakes) group widely studied in evolutionary, behavioral, and developmental biology. Full genome annotation, the establishment of gene editing techniques, and comprehensive description of reproductive tract morphology and embryogenesis in this species, has laid the foundation for functional studies. However, analysis of brown anole oogenesis is still required and vital to optimize genome modification, mutant line establishment, and analyses of the evolution of reproductive developmental mechanisms. RESULTS: Here, we characterize ovary morphology and gametogenesis in the female brown anole, A. sagrei using brightfield imaging, microCT, histology staining, electron microscopy, and confocal imaging. We define 10 stages of oocyte maturation which commences inside the oogonial nest within the germinal bed and concludes with the mature follicle ready to ovulate based on follicle size, yolk-acquisition, and follicular, cellular, and basement membrane architecture. CONCLUSIONS: We describe the complete oogenesis of the brown anole in 10 stages and report that oogenesis is highly conserved within iguanids, a suborder of lizards. With our staging framework, we lay the foundation for functional studies of oogenesis and optimized gene-editing.

Journal Article↗

PubMed2026

Mutation accumulation in a hybrid parthenogenetic vertebrate.

Asexual lineages are thought to experience elevated extinction rates compared with sexual species, yet direct evidence for the underlying genetic causes remains scarce. Muller's ratchet predicts that the absence of recombination in asexual organisms facilitates the accumulation of deleterious mutations, thereby reducing long-term fitness. Here, we test this hypothesis in the hybrid-origin, parthenogenetic whiptail lizard Aspidoscelis tesselatus by integrating short-read RNAseq and long-read IsoSeq data from both the asexual lineage and its parental sexual species. We reconstructed phased transcripts for A. tesselatus to quantify mutation accumulation relative to the parental sexual species. Comparative analyses revealed elevated ω ratios in both parental genomic complements (subgenomes) of the parthenogenetic lineage, consistent with accelerated accumulation of nonsynonymous mutations. Structural variant analyses identified multiple indels in expressed transcripts predicted to disrupt protein domains. Functional annotation indicated that genes affected by both single-nucleotide variants and indels were enriched for roles in chromatin organization, apoptosis regulation, and transcriptional control. While both parental subgenomes showed similar evolutionary patterns, the maternal complement exhibited more structural and missense mutations than the paternal complement. Together, these results provide evidence that mutations accumulate in asexual A. tesselatus in genes involved in core cellular functions, supporting theoretical predictions that Muller's ratchet contributes to mutation accumulation in asexual lineages.

Animals↗

PubMed2024

Adaptive or non-adaptive? Cranial evolution in a radiation of miniaturized day geckos.

Lygodactylus geckos represent a well-documented radiation of miniaturized lizards with diverse life-history traits that are widely distributed in Africa, Madagascar, and South America. The group has diversified into numerous species with high levels of morphological similarity. The evolutionary processes underlying such diversification remain enigmatic, because species live in different ecological biomes, ecoregions and microhabitats, while suggesting strikingly high levels of homoplasy. To underscore this evolutionary pattern, here we explore the shape variation of skull elements (i.e., cranium, jaw and inner ear) using 3D geometric morphometrics and phylogenetic comparative methods on computed tomography scans (CT-scan) of a sample encompassing almost all recognized taxa within Lygodactylus. The results of this work show that skull and inner ear shape variation is low (i.e., there is high overlapping on the morphospace) across geographic regions, macrohabitats and lifestyles, implying extensive homoplasy. Furthermore, we also found a strong influence of allometry shaping cranial variation both at intra and interspecific levels, suggesting a major constraint underlying skull architecture, probably as a consequence of its miniaturization. The remaining variation that is not allometric is independent of phylogeny and ecological adaptation and can probably be interpreted as the result of intrinsic developmental plasticity. This, in turn, supports the interpretation that speciation in this group is largely concordant with a non-adaptive hypothesis, which results mainly from vicariant processes.

Animals↗

PubMed2026

Interplay between the role of DNA methylation in regulating gene expression and TE-silencing in a reptilian methylome.

DNA methylation is a major component of eukaryotic genomes with an important role in the defence against transposable elements, to transcriptionally silence their activity and prevent transposition. DNA methylation also plays a major role in the regulation of gene expression. This dual role can come into conflict, where DNA methylation in gene regulatory regions becomes perturbed due to transposable element transposition, leading to disruption of gene expression. Here, we describe how this conflict is reflected in DNA methylation patterns in the sand lizard genome where there is recent transposable element activity. Using long-read sequencing technology we show that CpG islands in gene transcriptional start sites are typically hypomethylated and associated with higher gene expression. Outside transcriptional start sites, a majority of CpG islands overlapped transposable elements and were associated with hypermethylation, consistent with a host-defence role in suppressing transposition activity. We identify 605 instances where transcriptional start sites were associated with transposable elements (4.3% of all genes). These instances were far rarer in conjunction with a CpG island, when methylation signatures would be in conflict. Transposable elements were found to be closer to and at higher density the more hypermethylated a transcriptional start site was, suggesting strong selection against selfish genetic elements transposing into hypomethylated transcriptional start sites.

CpG islands↗