The evolutionary history of an accidental model organism, the leopard gecko Eublepharis macularius (Squamata: Eublepharidae)

Untangling the Wallacean Shortfall: The herpetofauna of central-eastern Afghanistan including two snake species new for the reptiles list of the country

Afghanistan's herpetological diversity is not well studied due to limited access, environmental conditions, and historical socio-political instability. This study aims to address this gap by documenting the amphibians and reptiles found in central-eastern Afghanistan. Specifically, we focus on two new country records of colubrid snakes, Lycodon bicolor and Spalerosophis arenarius, presented in the study, provide updated provincial data on herpeto-diversity, and present an updated checklist of the family Colubridae for Afghanistan. The record of S. arenarius is further validated by sequences of two gene fragments of mitochondrial DNA, which also establish the phylogenetic context of the species within the genus. Our findings include records of four species of amphibians and 16 species of reptiles from the provinces of Kabul, Nangarhar, Paktia, and Wardak in central-eastern Afghanistan, representing two and nine families, respectively. In conclusion, this study highlights the potential for further significant herpetological discoveries in Afghanistan due to its biogeographic location between Central and South Asia. It also emphasizes the need for further systematic investigations using techniques of molecular taxonomy.

Does the pancreas of gekkotans differentiate similarly? Developmental structural and 3D studies of the mourning gecko (Lepidodactylus lugubris) and the leopard gecko (Eublepharis macularius)

This study investigated the pancreas differentiation of two species of gekkotan families-the mourning gecko Lepidodactylus lugubris (Gekkonidae) and the leopard gecko Eublepharis macularius (Eublepharidae)-based on two-dimensional (2D) histological samples and three-dimensional (3D) reconstructions of the position of the pancreatic buds and the surrounding organs. The results showed that at the moment of egg laying, the pancreas of L. lugubris is composed of three distinct primordia: one dorsal and two ventral. The dorsal primordium differentiates earlier than either ventral primordium. The right ventral primordium is more prominent and distinctive, starting to form earlier than the left one. Moreover, at this time, the pancreas of the leopard gecko is composed of the dorsal and right ventral primordium and the duct of the left ventral primordium. It means that the leopard gecko's left primordium is a transitional structure. These results indicate that the early development of the gekkotan pancreas is species specific. The pancreatic buds of the leopard and mourning gecko initially enter the duodenum by separate outlets, similar to the pancreas of other vertebrates. The pancreatic buds (3 of the mourning gecko and 2 of the leopard gecko) fuse quickly and form an embryonic pancreas. After that, the structure of this organ changes. After fusion, the pancreas of both gekkotans comprises four parts: the head of the pancreas (central region) and three lobes: upper, splenic, and lower. This organ develops gradually and is very well distinguished at hatching time. In both gekkotan species, cystic, hepatic, and pancreatic ducts enter the duodenum within the papilla. During gekkotan pancreas differentiation, the connection between the common bile duct and the dorsal pancreatic duct is associated with intestinal rotation, similar to other vertebrates.

The dynamic behavior of chromatophores marks the transition from bands to spots in leopard geckos

Reptilian skin coloration is spectacular and diverse, yet little is known about the ontogenetic processes that govern its establishment and the molecular signaling pathways that determine it. Here, we focus on the development of the banded pattern of leopard gecko hatchlings and the transition to black spots in the adult. With our histological analyses, we show that iridophores are present in the white and yellow bands of the hatchling and they gradually perish in the adult skin. Furthermore, we demonstrate that melanophores can autonomously form spots in the absence of the other chromatophores both on the regenerated skin of the tail and on the dorsal skin of the Mack Super Snow (MSS) leopard geckos. This color morph is characterized by uniform black coloration in hatchlings and black spots in adulthood; we establish that their skin is devoid of xanthophores and iridophores at both stages. Our genetic analyses identified a 13-nucleotide deletion in the PAX7 transcription factor of MSS geckos, affecting its protein coding sequence. With our single-cell transcriptomics analysis of embryonic skin, we confirm that PAX7 is expressed in iridophores and xanthophores, suggesting that it plays a key role in the differentiation of both chromatophores. Our in situ hybridizations on whole-mount embryos document the dynamics of the skin pattern formation and how it is impacted in the PAX7 mutants. We hypothesize that the melanophores-iridophores interactions give rise to the banded pattern of the hatchlings and black spot formation is an intrinsic capacity of melanophores in the postembryonic skin.

Sensory Stimulation as a Means of Sustained Enhancement of Well-Being in Leopard Geckos, Eublepharis macularius (Eublepharidae, Squamata)

Although the private keeping of reptiles has boomed in most western countries since the millennium, studies dealing with the recognition and promotion of welfare in these reptiles seem to represent a blind spot of scientific attention. The vast majority of studies from the field of animal welfare science still concern mammals and birds. The leopard gecko is probably the most common lizard that is kept in domestic terrariums worldwide. Due to its characteristic as an ecological generalist, it is easy to keep and breed, and it is considered a good "starter reptile" for beginners as it "condones" husbandry mistakes, even for extended periods. However, being a mass species is not a second-class classification. They, too, have an equal claim to good well-being as all animals in human care. The aim of the study was to test the hypothesis of whether an increase in stimulus density leads to an increase in activity and behavioural diversity and, thus, an increase in welfare. For this purpose, 18 leopard geckos were fed insects that were ≤1 cm in size, and both the quantity and quality of behaviour was documented and analysed in the pre-intervention, intervention and post-intervention stages. In addition, it was of interest whether behavioural indicators could be identified that indicate a state of positive well-being. The results showed that this type of enrichment led to a quantitative doubling of the activity levels from the baseline (total of 12,519 behavioural elements) to the intervention (total of 25,366 behavioural elements). And even 11 months after the introduction of small insect feeding (post-intervention total of 23,267 behavioural elements), the activity level was still significantly increased. The behavioural diversity, as the absolute number of behavioural categories across all 18 leopard geckos, also increased, although less than the behavioural intensity, between the baseline (5507 behavioural categories) and intervention (6451 behavioural categories) and between the baseline and post-intervention (6079 behavioural categories). The results clearly show that feeding small insects to leopard geckos is a very efficient tool to increase the welfare of leopard geckos. Attractively, this feeding regime can be implemented by any leopard gecko keeper without significant additional cost or time, and therefore, these methods have a potentially high impact.

Melanistic coloration does not influence thermoregulation in the crepuscular gecko Eublepharis macularius

Body coloration in ectotherms serves multiple biological functions, including avoiding predators, communicating with conspecific individuals, and involvement in thermoregulation. As ectotherms rely on environmental sources of heat to regulate their internal body temperature, stable melanistic body coloration or color change can be used to increase or decrease heat absorption and heat exchange with the environment. While melanistic coloration for thermoregulation functions to increase solar radiation absorption and consequently heating in many diurnal ectotherms, research on crepuscular and nocturnal ectotherms is lacking. Since crepuscular and nocturnal ectotherms generally absorb heat from the substrate, in these organisms melanistic coloration may have other primary functions beside thermoregulation. As such, in this work we hypothesized that the proportion of dorsal melanistic body coloration would not influence heating and cooling rates in the crepuscular gecko, Eublepharis macularius, and that changes in environmental temperature would not trigger color changes in this species. Temperature measurements of the geckos and of the environment were taken using infrared thermography and temperature loggers. Color data were obtained using objective photography and a newly developed custom software package. We found that body temperature reflected substrate temperatures, and that the proportion of melanistic coloration has no influence on heating or cooling rates or on color changes. These findings support that melanistic coloration in E. macularius may not be used for thermoregulation and strengthen the hypothesis that in animals active in low light conditions, melanistic coloration may be used instead for camouflage or other functions.

Robertsonian fusion triggers recombination suppression on sex chromosomes in Coleonyx geckos

The classical hypothesis proposes that the lack of recombination on sex chromosomes arises due to selection for linkage between a sex-determining locus and sexually antagonistic loci, primarily facilitated by inversions. However, cessation of recombination on sex chromosomes could be attributed also to neutral processes, connected with other chromosome rearrangements or can reflect sex-specific recombination patterns existing already before sex chromosome differentiation. Three Coleonyx gecko species share a complex X1X1X2X2/X1X2Y system of sex chromosomes evolved via a fusion of the Y chromosome with an autosome. We analyzed synaptonemal complexes and sequenced flow-sorted sex chromosomes to investigate the effect of chromosomal rearrangement on recombination and differentiation of these sex chromosomes. The gecko sex chromosomes evolved from syntenic regions that were also co-opted also for sex chromosomes in other reptiles. We showed that in male geckos, recombination is less prevalent in the proximal regions of chromosomes and is even further drastically reduced around the centromere of the neo-Y chromosome. We highlight that pre-existing recombination patterns and Robertsonian fusions can be responsible for the cessation of recombination on sex chromosomes and that such processes can be largely neutral.

The revised reference genome of the leopard gecko (Eublepharis macularius) provides insight into the considerations of genome phasing and assembly

Genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems and high-quality reference genomes remain scarce. Of the 23 chromosome-scale reference genomes across the order, only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant families. Using the latest advances in genome sequencing and assembly methods, we generated one of the highest-quality squamate genomes to date for the leopard gecko, Eublepharis macularius (Eublepharidae). We compared this assembly to the previous, short-read only, E. macularius reference genome published in 2016 and examined potential factors within the assembly influencing contiguity of genome assemblies using PacBio HiFi data. Briefly, the read N50 of the PacBio HiFi reads generated for this study was equal to the contig N50 of the previous E. macularius reference genome at 20.4 kilobases. The HiFi reads were assembled into a total of 132 contigs, which was further scaffolded using HiC data into 75 total sequences representing all 19 chromosomes. We identified 9 of the 19 chromosomal scaffolds were assembled as a near-single contig, whereas the other 10 chromosomes were each scaffolded together from multiple contigs. We qualitatively identified that the percent repeat content within a chromosome broadly affects its assembly contiguity prior to scaffolding. This genome assembly signifies a new age for squamate genomics where high-quality reference genomes rivaling some of the best vertebrate genome assemblies can be generated for a fraction of previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000.

Kukri snakes Oligodon Fitzinger, 1826 of the Western Palearctic with the resurrection of Contia transcaspica Nikolsky, 1902 (Reptilia, Squamata, Colubridae)

The kukri snakes of the genus Oligodon Fitzinger, 1826 reach the westernmost limits of their distribution in Middle and Southwest Asia (Afghanistan, Iran, and Turkmenistan), and the Palearctic portions of Pakistan. In this article, we review the systematics and distribution of the two species native to this region, Oligodon arnensis (Shaw, 1802) and Oligodon taeniolatus (Jerdon, 1853) based on an integrative approach combining morphological, molecular, and species distribution modeling (SDM) data. Phylogenetic analyses recover O. taeniolatus populations from Iran and Turkmenistan in a clade with the O. arnensis species complex, rendering the former species paraphyletic relative to O. taeniolatus sensu stricto on the Indian subcontinent. To correct this, we resurrect the name Contia transcaspica Nikolsky, 1902 from the synonymy of O. taeniolatus and assign it to populations in Middle-Southwest Asia. So far, Oligodon transcaspicus comb. et stat. nov. is known only from the Köpet-Dag Mountain Range of northeast Iran and southern Turkmenistan, but SDM mapping suggests it may have a wider range. Genetic samples of O. "arnensis" from northern Pakistan are nested in a clade sister to the recently described Oligodon churahensis Mirza, Bhardwaj & Patel, 2021, and are phylogenetically separate from O. arnensis sensu stricto in south India and Sri Lanka. Based on morphological similarity, the Afghanistan and Pakistan populations are assigned to Oligodon russelius (Daudin, 1803) and we synonymize O. churahensis with this species. Our investigation leads us to remove O. taeniolatus from the snake fauna of Afghanistan, Iran, and Turkmenistan, with the consequence that only Oligodon transcaspicus comb. et stat. nov. and O. russelius are present in these countries. Additional studies are needed to resolve the taxonomy of the O. taeniolatus and O. arnensis species complexes on the Indian subcontinent, and an updated key for both groups is provided.

Egg Removal via Cloacoscopy in Three Dystocic Leopard Geckos (Eublepharis macularius)

Dystocia is a multifactorial, life-threatening condition commonly affecting pet reptiles. Treatment for dystocia can be either medical or surgical. Medical treatment usually involves the administration of oxytocin, but in some species or, in some cases, this treatment does not work as expected. Surgical treatments such as ovariectomy or ovariosalpingectomy are resolutive, but invasive in small-sized reptiles. In this paper, we describe three cases of post ovulatory egg retention in three leopard geckos (Eublepharis macularius) successfully treated through a cloacoscopic removal of the retained eggs, after a non resolutive medical treatment. The intervention was fast, non-invasive, and no procedure-related adverse effects were noted. The problem relapsed six months later in one animal, and a successful bilateral ovariosalpingectomy was performed. Cloacoscopy should be considered a valuable, non-invasive tool for egg removal in dystocic leopard geckos when the egg is accessible to manipulation. Recrudescence or complications such as adhesions, oviductal rupture, or the presence of ectopic eggs should recommend surgical intervention.

The revised reference genome of the leopard gecko ( Eublepharis macularius ) provides insight into the considerations of genome phasing and assembly

Genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems and high-quality reference genomes remain scarce. Of the 23 chromosome-scale reference genomes across the order, only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant families. Using the latest advances in genome sequencing and assembly methods, we generated one of the highest quality squamate genomes to date for the leopard gecko, Eublepharis macularius (Eublepharidae). We compared this assembly to the previous, short-read only, E. macularius reference genome published in 2016 and examined potential factors within the assembly influencing contiguity of genome assemblies using PacBio HiFi data. Briefly, the read N50 of the PacBio HiFi reads generated for this study was equal to the contig N50 of the previous E. macularius reference genome at 20.4 kilobases. The HiFi reads were assembled into a total of 132 contigs, which was further scaffolded using HiC data into 75 total sequences representing all 19 chromosomes. We identified that 9 of the 19 chromosomes were assembled as single contigs, while the other 10 chromosomes were each scaffolded together from two or more contigs. We qualitatively identified that percent repeat content within a chromosome broadly affects its assembly contiguity prior to scaffolding. This genome assembly signifies a new age for squamate genomics where high-quality reference genomes rivaling some of the best vertebrate genome assemblies can be generated for a fraction previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000. The genome version and its associated annotations are also available via this Figshare repository https://doi.org/10.6084/m9.figshare.20069273 .

Identification of a cis-sex chromosome transition in banded geckos (Coleonyx, Eublepharidae, Gekkota)

Sex-determination systems are highly variable amongst vertebrate groups, and the prevalence of genomic data has greatly expanded our knowledge of how diverse some groups truly are. Gecko lizards are known to possess a variety of sex-determination systems, and each new study increases our knowledge of this diversity. Here, we used RADseq to identify male-specific markers in the banded gecko Coleonyx brevis, indicating this species has a XX/XY sex-determination system. Furthermore, we show that these sex-linked regions are not homologous to the XX/XY sex chromosomes of two related Coleonyx species, C. elegans and C. mitratus, suggesting that a cis-sex chromosome turnover-a change in sex chromosomes without a concomitant change in heterogamety-has occurred within the genus. These findings demonstrate the utility of genome-scale data to uncover novel sex chromosomes and further highlight the diversity of gecko sex chromosomes.

Description of a new species of leopard geckos, Eublepharis Gray, 1827 from Eastern Ghats, India with notes on Eublepharis hardwickii Gray, 1827

A recent molecular phylogenetic study of the genus Eublepharis Gray, 1827 revealed the presence of a genetically divergent lineage sister to Eublepharis hardwickii Gray, 1827. We re-assessed the taxonomy of Eublepharis hardwickii based on museum material in light of the molecular phylogenetic study and the results support the recognization of two species distributed on either sides of the Brahmani River. A redescription of E. hardwickii is presented based on the holotype and additional museum material along-with the description of a new species, Eublepharis pictussp. nov. from Andhra Pradesh and Odisha. The presence of yet another distinct lineage in such close geographical proximity in the northern Eastern Ghats highlights the significance of these relic forests and advocates the need for conservation prioritization.