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 ultrastructural features of the infundibulum of the green iguana, Iguana iguana

The purpose of this study is to describe, in detail, the ultrastructure of the infundibulum of the sexually mature and active female green iguana, Iguana iguana. The infundibulum of five iguanas was remarkably distinct from the uterus, and was also clearly demarcated into cranial (expanded v-shaped) and caudal (tubular) divisions. Tissue samples obtained from five portions (three from the cranial division and two from the caudal division) of the infundibulum were processed conventionally for light and electron microscopy. The epithelial lining of the most anterior, middle, and posterior, parts of the cranial division displayed nonciliated cells predominantly, and occasionally ciliated cells. The numerous secretory granules in nonciliated type 1 cell found in the fimbrial aspect of the infundibulum were homogenous and deeply electron-dense, but those in the other two regions were variants of this cell type because they contained variably electron-dense secretory granules. Two main types of nonciliated cells (type 2 and its variant, type 3, as well as type 4) occurred in the epithelial lining of the caudal division of the infundibulum, but they, clearly, showed no dense secretory granules. Whereas the nonciliated type 2 cell and its variant (type 3 cell) contained large glycogen deposits, the type 4 cell lacked these deposits but its apical part contained large lipid-like droplets and, remarkably, blebbed into the duct lumen. The nonciliated cells lining the mucosal tubular glands contained highly electron-dense secretory granules, which were similar to those found in the nonciliated type 1 cell in the epithelial lining of the fimbrial part of the cranial division of the infundibulum.

A landmarking protocol for geometric morphometric analysis of squamate endocasts

Landmark-based geometric morphometrics is widely used to study the morphology of the endocast, or internal mold of the braincase, and the diversity associated with this structure across vertebrates. Landmarks, as the basic unit of such methods, are intended to be points of correspondence, selected depending on the question at hand, whose proper definition is essential to guarantee robustness and reproducibility of results. In this study, 20 landmarks are defined to provide a framework to analyze the morphological variability in squamate endocasts. Ten species representing a cross-section of the diversity of Squamata from both phylogenetic and ecological (i.e., habitat) perspectives were considered, to select landmarks replicable throughout the entire clade, regardless of the degree of neuroanatomical resolution of the endocast. To assess the precision, accuracy, and repeatability of these newly defined landmarks, both intraobserver and interobserver error were investigated. Estimates of measurement error show that most of the landmarks established here are highly replicable, and preliminary results suggest that they capture aspects of endocast shape related to both phylogenetic and ecologic signals. This study provides a basis for further examinations of squamate endocast disparity using landmark-based geometric morphometrics.

Endocast, brain, and bones: Correspondences and spatial relationships in squamates

Vertebrate endocasts are widely used in the fields of paleoneurology and comparative neuroanatomy. The validity of endocranial studies is dependent upon the extent to which an endocast reflects brain morphology. Due to the variable neuroanatomical resolution of vertebrate endocasts, direct information about the brain morphology can be sometimes difficult to assess and needs to be investigated across lineages. Here, we employ X-ray computed tomography (CT), including diffusible iodine-based contrast-enhanced CT, to qualitatively compare brains and endocasts in different species of squamates. The relative position of the squamate brain within the skull, as well as the variability that may exist in such spatial relationships, was examined to help clarify the neurological regions evidence on their endocasts. Our results indicate that squamate endocasts provide variable representation of the brain, depending on species and neuroanatomical regions. The olfactory bulbs and peduncles, cerebral hemispheres, as well as the medulla oblongata represent the most easily discernable brain regions from squamate endocasts. In contrast, the position of the optic lobes, the ventral diencephalon and the pituitary may be difficult to determine depending on species. Finally, squamate endocasts provide very limited or no information about the cerebellum. The spatial relationships revealed here between the brain and the surrounding bones may help to identify each of the endocranial region. However, as one-to-one correspondences between a bone and a specific region appear limited, the exact delimitation of these regions may remain challenging according to species. This study provides a basis for further examination and interpretation of squamate endocast disparity.

Maternal behavioral thermoregulation facilitated evolutionary transitions from egg laying to live birth

Live birth is a key innovation that has evolved from egg-laying ancestors over 100 times in reptiles. However, egg-laying lizards and snakes can have preferred body temperatures that are lethal to developing embryos, which should select against prolonged egg retention. Here, we demonstrate that thermal mismatches between mothers and offspring are widespread across the squamate phylogeny. This mismatch is resolved by gravid females adjusting their body temperature towards the thermal optimum of their embryos. We find that the same response occurs in both live-bearing and egg-laying species, despite the latter only retaining embryos during the early stages of development. Importantly, phylogenetic reconstructions suggest this thermoregulatory behavior in gravid females evolved in egg-laying species prior to the evolution of live birth. Maternal thermoregulatory behavior, therefore, bypasses the constraints imposed by a slowly evolving thermal physiology and has likely been a key facilitator in the repeated transition to live birth.

Incomplete dosage balance and 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.

Dermatomycosis Caused by Paranannizziopsis australasiensis in Nonnative Panther Chameleons (Furcifer pardalis) Captured in Central Florida, USA

Emergent fungal pathogens in herpetofauna are a concern in both wild and captive populations. We diagnosed dermatomycosis by Paranannizziopsis australasiensis in two panther chameleons (Furcifer pardalis) and suspected it in eight others captured from an established free-living nonnative population in Florida, USA. Chameleons developed skin lesions following recent exposure to cold weather conditions while housed in captivity, approximately 10 mo after capture and 12 wk after being placed in outdoor enclosures. Affected animals were treated with oral voriconazole and terbinafine until most cases resolved; however, medications were ultimately discontinued. Paranannizziopsis australasiensis has not previously been described in chameleons, nor in animals originating from a free-ranging population in the USA. Although the source of P. australasiensis infection is uncertain, we discuss several scenarios related to the pet trade and unique situation of chameleon "ranching" present in the USA.

Morphological and molecular diagnosis of two new species of Trypanosoma Gruby, 1843 infecting South African cordylid lizards (Squamata: Cordylidae: Cordylinae), Trypanosoma (Squamatrypanum) ndumoensis n. sp. and Trypanosoma (Trypanosoma) tokoloshi n. sp

Despite reptile trypanosomes forming a large group, the majority of species descriptions are data deficient, lacking key characteristic data and supporting molecular data. Reptile hosts show potential to facilitate transmission of zoonotic trypanosomiases and offer key information to understanding the genus of Trypanosoma. Several species of squamates from different localities in South Africa were screened molecularly and microscopically for trypanosomes in the present study. Based on the combination of morphological and molecular analyses, two new species of Trypanosoma, Trypanosoma (Squamatrypanum) ndumoensis n. sp. and Trypanosoma (Trypanosoma) tokoloshi n. sp., infecting South African cordylid lizards (Cordylidae: Cordylinae) are described in this study. The first molecular data for a South African reptile trypanosome is provided herewith.

Spontaneous neuronal regeneration in the forebrain of the leopard gecko (Eublepharis macularius) following neurochemical lesioning

BACKGROUND

Neurogenesis is the ability to generate new neurons from resident stem/progenitor populations. Although often understood as a homeostatic process, several species of teleost fish, salamanders, and lacertid lizards are also capable of reactive neurogenesis, spontaneously replacing lost or damaged neurons. Here, we demonstrate that reactive neurogenesis also occurs in a distantly related lizard species, Eublepharis macularius, the leopard gecko.

RESULTS

To initiate reactive neurogenesis, the antimetabolite 3-acetylpyridine (3-AP) was administered. Four days following 3-AP administration there is a surge in neuronal cell death within a region of the forebrain known as the medial cortex (homolog of the mammalian hippocampal formation). Neuronal cell death is accompanied by a shift in resident microglial morphology and an increase neural stem/progenitor cell proliferation. By 30 days following 3-AP administration, the medial cortex was entirely repopulated by NeuN+ neurons. At the same time, local microglia have reverted to a resting state and cell proliferation by neural stem/progenitors has returned to levels comparable with uninjured controls.

CONCLUSIONS

Together, these data provide compelling evidence of reactive neurogenesis in leopard geckos, and indicate that the ability of lizards to spontaneously replace lost or damaged forebrain neurons is more taxonomically widespread and evolutionarily conserved than previously considered.

First evidence of hemiclitores in snakes

Female genitalia are conspicuously overlooked in comparison to their male counterparts, limiting our understanding of sexual reproduction across vertebrate lineages. This study is the first complete description of the clitoris (hemiclitores) in female snakes. We describe morphological variation in size and shape (n = 9 species, 4 families) that is potentially comparable to the male intromittent organs in squamate reptiles (hemipenes). Dissection, diffusible iodine contrast-enhanced micro-CT and histology revealed that, unlike lizard hemiclitores, the snake hemiclitores are non-eversible structures. The two individual hemiclitores are separated medially by connective tissue, forming a triangular structure that extends posteriorly. Histology of the hemiclitores in Australian death adders (Acanthophis antarcticus) showed erectile tissue and strands/bundles of nerves, but no spines (as is found in male hemipenes). These histological features suggest the snake hemiclitores have functional significance in mating and definitively show that the hemiclitores are not underdeveloped hemipenes or scent glands, which have been erroneously indicated in other studies. Our discovery supports that hemiclitores have been retained across squamates and provides preliminary evidence of differences in this structure among snake species, which can be used to further understand systematics, reproductive evolution and ecology across squamate reptiles.

Comparative development of limb musculature in phylogenetically and ecologically divergent lizards

BACKGROUND

Squamate reptiles (lizards, snakes, and amphisbaenians) exhibit incredible diversity in their locomotion, behavior, morphology, and ecological breadth. Although they often are used as models of locomotor diversity, surprisingly little attention has been given to muscle development in squamate reptiles. In fact, the most detailed examination was conducted almost 80 years ago and solely focused on the proximal limb regions. Herein, we present forelimb and hindlimb muscle morphogenesis data for three lizard species with different locomotion and feeding strategies: the desert grassland whiptail lizard, the central bearded dragon, and the veiled chameleon. This study fills critical gaps in our understanding of muscle morphogenesis in squamate reptiles and presents a comparative and temporospatial analysis of muscle development.

RESULTS

Our results reveal a conserved pattern of early muscle development among lizards with different adult morphologies and ecologies. The variations that exist are concentrated in distal regions, particularly the specialized autopodia of chameleons, where differentiation of muscles associated with the digits is delayed.

CONCLUSIONS

The chameleon autopod provides an example of major evolutionary modifications to the skeleton with only minor disruption of the conserved order and pattern of limb muscle development. This robustness of muscle patterning facilitates the evolution of extreme yet functional phenotypes.

A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology

Background

High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources.

Findings

We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length.

Conclusions

These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.

Integrative developmental biology in the age of anthropogenic change

Humans are changing and challenging nature in many ways. Conservation Biology seeks to limit human impacts on nature and preserve biological diversity. Traditionally, Developmental Biology and Conservation Biology have had nonoverlapping objectives, operating in distinct spheres of biological science. However, this chasm can and should be filled to help combat the emerging challenges of the 21st century. The means by which to accomplish this goal were already established within the conceptual framework of evo- and eco-devo and can be further expanded to address the ways that anthropogenic disturbance affect embryonic development. Herein, I describe ways that these approaches can be used to advance the study of reptilian embryos. More specifically, I explore the ways that a developmental perspective can advance ongoing studies of embryonic physiology in the context of global warming and chemical pollution, both of which are known stressors of reptilian embryos. I emphasize ways that these developmental perspectives can inform conservation biologists trying to develop management practices that will address the complexity of challenges facing reptilian embryos.

Tail autotomy works as a pre-capture defense by deflecting attacks

Caudal autotomy is a dramatic antipredator adaptation where prey shed their tail in order to escape capture by a predator. The mechanism underlying the effectiveness of caudal autotomy as a pre-capture defense has not been thoroughly investigated. We tested two nonexclusive hypotheses, that caudal autotomy works by providing the predator with a "consolation prize" that makes it break off the hunt to consume the shed tail, and the deflection hypothesis, where the autotomy event directs predator attacks to the autotomized tail enabling prey escape. Our experiment utilized domestic dogs Canis familiaris as model predator engaged to chase a snake-like stimulus with a detachable tail. The tail was manipulated to vary in length (long versus short) and conspicuousness (green versus blue), with the prediction that dog attacks on the tail should increase with length under the consolation-prize hypothesis and conspicuous color under the deflection hypothesis. The tail was attacked on 35% of trials, supporting the potential for pre-capture autotomy to offer antipredator benefits. Dogs were attracted to the tail when it was conspicuously colored, but not when it was longer. This supports the idea that deflection of predator attacks through visual effects is the prime antipredator mechanism underlying the effectiveness of caudal autotomy as opposed to provision of a consolation prize meal.

Adaptive variation in the development of extraembryonic membranes of gekkotan embryos: A meta-analytical approach

Highly mineralized rigid-shelled eggs characterize one lineage of gekkotans. In contrast, poorly mineralized flexible-shelled eggs characterize basal lineages of gekkotans and all other squamates. Low oxygen permeability of rigid-shelled eggs is associated with small eggs and hatchlings, and long incubation lengths compared to flexible-shelled gekkotan eggs. These features represent a demographic cost for species with rigid-shelled eggs. This cost is offset, at least in part, because mortality due to desiccation and predation is reduced for rigid-shelled eggs relative to flexible-shelled eggs. Developmental traits may also compensate for the low oxygen permeability of rigid-shelled eggs. Oviposition, for example, occurs at earlier developmental stages for gekkotans with rigid- versus flexible-shelled eggs. Such early oviposition facilitates development because eggs move from the relatively hypoxic oviduct to the much better oxygenated nest environment. In this study, I tested the hypothesis that the growth of the yolk sac (YS) and chorioallantoic membrane (CAM) of gekkotans with rigid-shelled eggs is initiated and completed earlier than those of gekkotans with flexible-shelled eggs. I measured the surface area of eggs covered by the YS and CAM from oviposition to hatching and determined which of four nonlinear models provide the best fit for growth curves. I also compiled a data set on embryonic metabolism of gekkotans and other lizards in order to place growth of the YS and CAM in the context of energy utilization of lizard embryos overall. Growth of the YS and CAM of gekkotans with rigid-shelled eggs is accelerated relative to that of gekkotans with flexible-shelled eggs and may serve to separate the cost of YS and CAM development from that of the embryo itself. Adaptive variation in YS and CAM development may extend to birds, crocodilians, and turtles as they also exhibit life history variation that affects oxygen availability to embryos during development.

Glia-Mediated Regenerative Response Following Acute Excitotoxic Damage in the Postnatal Squamate Retina

The retina is a complex tissue responsible for both detection and primary processing of visual stimuli. Although all vertebrate retinas share a similar, multi-layered organization, the ability to regenerate individual retinal cells varies tremendously, being extremely limited in mammals and birds when compared to anamniotes such as fish and amphibians. However, little is yet known about damage response and regeneration of retinal tissues in "non-classical" squamate reptiles (lizards, snakes), which occupy a key phylogenetic position within amniotes and exhibit unique regenerative features in many tissues. Here, we address this gap by establishing and characterizing a model of excitotoxic retinal damage in bearded dragon lizard (Pogona vitticeps). We particularly focus on identifying, at the cellular and molecular level, a putative endogenous cellular source for retinal regeneration, as diverse self-repair strategies have been characterized in vertebrates using a variety of retinal injury and transgenic models. Our findings reveal for the first time that squamates hold the potential for postnatal retinal regeneration following acute injury. Although no changes occur in the activity of physiologically active progenitors recently identified at the peripheral retinal margin of bearded dragon, two distinct successive populations of proliferating cells at central retina respond to neurotoxin treatment. Following an initial microglia response, a second source of proliferating cells exhibit common hallmarks of vertebrate Müller glia (MG) activation, including cell cycle re-entry, dedifferentiation into a progenitor-like phenotype, and re-expression of proneural markers. The observed lizard glial responses, although not as substantial as in anamniotes, appear more robust than the absent or neonatal-limited regeneration reported without exogenous stimulation in other amniotes. Altogether, these results help to complete our evolutionary understanding of regenerative potential of the vertebrate retina, and further highlight the major importance of glial cells in retinal regeneration. Furthermore, our work offers a new powerful vertebrate model to elucidate the developmental and evolutionary bases of retinal regeneration within amniotes. Such new understanding of self-repair mechanisms in non-classical species endowed with regenerative properties may help designing therapeutic strategies for vertebrate retinal diseases.

Facultative oviparity in a viviparous skink ( Saiphos equalis)

Facultative changes in parity mode (oviparity to viviparity and vice versa) are rare in vertebrates, yet offer fascinating opportunities to investigate the role of reproductive lability in parity mode evolution. Here, we report apparent facultative oviparity by a viviparous female of the bimodally reproductive skink Saiphos equalis-the first report of different parity modes within a vertebrate clutch. Eggs oviposited facultatively possess shell characteristics of both viviparous and oviparous S. equalis, demonstrating that egg coverings for viviparous embryos are produced by the same machinery as those for oviparous individuals. Since selection may act in either direction when viviparity has evolved recently, squamate reproductive lability may confer a selective advantage. We suggest that facultative oviparity is a viable reproductive strategy for S. equalis and that squamate reproductive lability is more evolutionarily significant than previously acknowledged.

Distinct telomere differences within a reproductively bimodal common lizard population

Different strategies of reproductive mode, either oviparity (egg-laying) or viviparity (live-bearing), will be associated with a range of other life-history differences that are expected to affect patterns of ageing and longevity. It is usually difficult to compare the effects of alternative reproductive modes because of evolutionary and ecological divergence. However, the very rare exemplars of reproductive bimodality, in which different modes exist within a single species, offer an opportunity for robust and controlled comparisons.One trait of interest that could be associated with life history, ageing and longevity is the length of the telomeres, which form protective caps at the chromosome ends and are generally considered a good indicator of cellular health. The shortening of these telomeres has been linked to stressful conditions; therefore, it is possible that differing reproductive costs will influence patterns of telomere loss. This is important because a number of studies have linked a shorter telomere length to reduced survival.Here, we have studied maternal and offspring telomere dynamics in the common lizard (Zootoca vivipara). Our study has focused on a population where oviparous and viviparous individuals co-occur in the same habitat and occasionally interbreed to form admixed individuals.While viviparity confers many advantages for offspring, it might also incur substantial costs for the mother, for example require more energy. Therefore, we predicted that viviparous mothers would have relatively shorter telomeres than oviparous mothers, with admixed mothers having intermediate telomere lengths. There is thought to be a heritable component to telomere length; therefore, we also hypothesized that offspring would follow the same pattern as the mothers.Contrary to our predictions, the viviparous mothers and offspring had the longest telomeres, and the oviparous mothers and offspring had the shortest telomeres. The differing telomere lengths may have evolved as an effect of the life-history divergence between the reproductive modes, for example due to the increased growth rate that viviparous individuals may undergo to reach a similar size at reproduction. A free http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.13408/suppinfo can be found within the Supporting Information of this article.

Retrospective review of neoplasms of captive lizards in the United Kingdom

BACKGROUND

Neoplasia has historically been regarded as an unusual occurrence in reptiles. The aim of the present study was to evaluate the prevalence of neoplasms in routine diagnostic samples submitted to a specialist exotic animal laboratory.

METHODS

Over a 10-year period, 690 lizard samples were submitted for histopathological or cytopathological examination by Royal College of Veterinary Surgeons specialists in Veterinary Pathology (Zoo and Wildlife). Records were reviewed retrospectively and non-neoplastic diagnoses excluded from further analysis.

RESULTS

158 neoplasms were diagnosed in 149 lizards, with 22.9% of submissions resulting in a diagnosis of neoplasia. The skin was the most commonly affected organ, and squamous cell carcinomas were the most common neoplasms identified (17.7% of all neoplastic diagnoses).Bearded dragons and panther chameleons had a statistically significant higher proportion of neoplasia diagnosis than the lizard population as a whole, and geckos had a statistically significantly lower proportion.Several neoplasms identified in this study have not been previously reported in lizards, including a testicular Sertoli cell tumour, testicular granulosa cell tumour, splenic haemangiosarcoma, gastric adenocarcinoma and basal cell carcinoma.

CONCLUSION

The results suggest that the prevalence of neoplasia in captive lizards may be higher than previously reported, and that there is variation in prevalence between different lizard species and families. It is unclear whether these differences relate to genetic or management factors.

Effects of substrate color on intraspecific body color variation in the toad-headed lizard, Phrynocephalus versicolor

Diversity in animal coloration is generally associated with adaptation to their living habitats, ranging from territorial display and sexual selection to predation or predation avoidance, and thermoregulation. However, the mechanism underlying color variation in toad-headed Phrynocephalus lizards remains poorly understood. In this study, we investigated the population color variation of Phrynocephalus versicolor. We found that lizards distributed in dark substrate have darker dorsal coloration (melanic lizards) than populations living in light substrates. This characteristic may improve their camouflage effectiveness. A reciprocal substrate translocation experiment was conducted to clarify the potential role of morphological adaptation and physiological plasticity of this variation. Spectrometry technology and digital photography were used to quantify the color variation of the above-mentioned melanic and nonmelanic P. versicolor populations and their native substrate. Additionally, substrate color preference in both populations was investigated with choice experiments. Our results indicate that the melanic and nonmelanic populations with remarkable habitat color difference were significantly different on measured reflectance, luminance, and RGB values. Twenty-four hours, 30 days, and 60 days of substrate translocation treatment had little effects on dorsal color change. We also found that melanic lizards choose to live in dark substrate, while nonmelanic lizards have no preference for substrate color. In conclusion, our results support that the dorsal coloration of P. versicolor, associated with substrate color, is likely a morphological adaptation rather than phenotypic plasticity.

The alternative regenerative strategy of bearded dragon unveils the key processes underlying vertebrate tooth renewal

Deep understanding of tooth regeneration is hampered by the lack of lifelong replacing oral dentition in most conventional models. Here, we show that the bearded dragon, one of the rare vertebrate species with both polyphyodont and monophyodont teeth, constitutes a key model for filling this gap, allowing direct comparison of extreme dentition types. Our developmental and high-throughput transcriptomic data of microdissected dental cells unveils the critical importance of successional dental lamina patterning, in addition to maintenance, for vertebrate tooth renewal. This patterning process happens at various levels, including directional growth but also gene expression levels, dynamics, and regionalization, and involves a large number of yet uncharacterized dental genes. Furthermore, the alternative renewal mechanism of bearded dragon dentition, with dual location of slow-cycling cells, demonstrates the importance of cell migration and functional specialization of putative epithelial stem/progenitor niches in tissue regeneration, while expanding the diversity of dental replacement strategies in vertebrates.

All multicellular organisms, from lizards to humans, must be able to repair and regrow damaged tissue. This includes not only healing after an injury, but also replacing parts of the body that suffer wear and tear. For example, many animals shed and replace worn out teeth throughout their life, but the number of times this occurs varies greatly between species.

Much of the understanding about how teeth grow and develop has come from researching mice. However, mice only develop one set of teeth, making them a poor ‘model’ for studying how species such as fish and reptiles can re-grow and replace their teeth. Recent studies of these species has shown that regenerating teeth relies on a specialised structure known as the dental lamina. In mice, the dental lamina forms but then quickly disappears, preventing new sets of teeth from developing. In most animals that regrow their teeth, however, the dental lamina keeps growing beyond the most recently produced tooth to create an area where its replacement will emerge. Now, Salomies et al. have identified other strategies involved in tooth replacement from studying the bearded dragon lizard, a rare example of an animal that continuously regenerates some, but not all, of its teeth.

Analysing the cells in different parts of the re-growing teeth from bearded dragon lizards revealed new features of the dental lamina. Specifically, Salomies et al. found that a previously uncharacterized set of genes within the dental lamina could determine whether or not a tooth will be replaced. Further experiments using microscope imaging revealed that bearded dragon lizards use two distinct groups of stem cells – specialised cells that have the potential to develop into various cell types in the body – to re-grow their teeth. These experiments demonstrate how the bearded dragon lizard uses a previously unknown mechanism to regenerate its teeth, combining elements used by gecko lizards and sharks.

These findings are an important step towards understanding the different strategies animals can use to maintain and regenerate their teeth. The knowledge gained could one day help design better therapies for patients suffering from inherited dental disorders or tooth loss.

Improving Terrestrial Squamate Surveys with Camera-Trap Programming and Hardware Modifications

Simple Summary

Camera-traps are a useful tool in wildlife research and management, as they allow researchers to observe wildlife with minimal intrusion. However, despite their utility, the rapid pace of technological change and the relative novelty of camera-traps in wildlife research mean that many aspects of their use have not been resolved. Put simply, it may be possible to use camera-traps far more effectively than they are currently being used. Here, we examined whether detections of terrestrial snakes and lizards could be improved with camera-traps by using both time-lapse and passive infrared triggers, which are present on most camera-traps, and by adjusting the focal length of the camera to improve image clarity. Additionally, we examined whether increasing the sensitivity of passive infrared sensors is of benefit. We found that using both types of trigger simultaneously improves detections of terrestrial snakes and lizards, and users can modify the focal length to improve image clarity of fauna that occur close to the lens. These minor adjustments in the use of camera-traps result in major improvements for detecting terrestrial snakes and lizards.

Abstract

Camera-traps are used widely around the world to census a range of vertebrate fauna, particularly mammals but also other groups including birds, as well as snakes and lizards (squamates). In an attempt to improve the reliability of camera-traps for censusing squamates, we examined whether programming options involving time lapse capture of images increased detections. This was compared to detections by camera-traps set to trigger by the standard passive infrared sensor setting (PIR), and camera-traps set to take images using time lapse in combination with PIR. We also examined the effect of camera trap focal length on the ability to tell different species of small squamate apart. In a series of side-by-side field comparisons, camera-traps programmed to take images at standard intervals, as well as through routine triggering of the PIR, captured more images of squamates than camera-traps using the PIR sensor setting alone or time lapse alone. Similarly, camera traps with their lens focal length set at closer distances improved our ability to discriminate species of small squamates. With these minor alterations to camera-trap programming and hardware, the quantity and quality of squamate detections was markedly better. These gains provide a platform for exploring other aspects of camera-trapping for squamates that might to lead to even greater survey advances, bridging the gap in knowledge of this otherwise poorly known faunal group.

Species Identification of Fragmented or Faded Shed Snake Skins by Light Microscopy

Few convenient/expeditious methods for identifying the species of shed snake skins in specific areas have been developed. The scales on shed snake skins are permeable to light and can be examined by light microscopy (LM), which is of higher availability-especially for wild animal researchers and citizen scientists-than conventional approach which examines the scale microstructures by scanning electron microscopy. We collected and examined a total of 801 shed samples or scale specimens from 53 snake species in Taiwan and adjacent islands, and developed the first guide to identify the fragmented or faded shed skins of most snake species by LM. Morphological characters of scales can be examined by LM include the apical notch, apical pits, apical lobes, keels, scale symmetry, unpigmented spots (mechanoreceptor-like organs), interscale follicles, cross/longitudinal micro-ridge, oberhautchen cells, rows of spines, light/tiny dots, and other microstructures. The microstructures on the scale specimens prepared by the stripped method and the impression method were similar to those on shed skins when examined by LM. We investigated the variations of scale morphology associated with ontogeny, body region, and position on scales, discussed the character evolution of snake scale morphology, and certified that the interscale follicles and the unpigmented spots could also be useful characters for shed skin identification. The methods and results of this study could be applied to identify squamate skins/sloughs and even fecal remnants.

Skull Development, Ossification Pattern, and Adult Shape in the Emerging Lizard Model Organism Pogona vitticeps: A Comparative Analysis With Other Squamates

The rise of the Evo-Devo field and the development of multidisciplinary research tools at various levels of biological organization have led to a growing interest in researching for new non-model organisms. Squamates (lizards and snakes) are particularly important for understanding fundamental questions about the evolution of vertebrates because of their high diversity and evolutionary innovations and adaptations that portrait a striking body plan change that reached its extreme in snakes. Yet, little is known about the intricate connection between phenotype and genotype in squamates, partly due to limited developmental knowledge and incomplete characterization of embryonic development. Surprisingly, squamate models have received limited attention in comparative developmental studies, and only a few species examined so far can be considered as representative and appropriate model organism for mechanistic Evo-Devo studies. Fortunately, the agamid lizard Pogona vitticeps (central bearded dragon) is one of the most popular, domesticated reptile species with both a well-established history in captivity and key advantages for research, thus forming an ideal laboratory model system and justifying his recent use in reptile biology research. We first report here the complete post-oviposition embryonic development for P. vitticeps based on standardized staging systems and external morphological characters previously defined for squamates. Whereas the overall morphological development follows the general trends observed in other squamates, our comparisons indicate major differences in the developmental sequence of several tissues, including early craniofacial characters. Detailed analysis of both embryonic skull development and adult skull shape, using a comparative approach integrating CT-scans and gene expression studies in P. vitticeps as well as comparative embryology and 3D geometric morphometrics in a large dataset of lizards and snakes, highlights the extreme adult skull shape of P. vitticeps and further indicates that heterochrony has played a key role in the early development and ossification of squamate skull bones. Such detailed studies of embryonic character development, craniofacial patterning, and bone formation are essential for the establishment of well-selected squamate species as Evo-Devo model organisms. We expect that P. vitticeps will continue to emerge as a new attractive model organism for understanding developmental and molecular processes underlying tissue formation, morphology, and evolution.

Disentangling sex allocation in a viviparous reptile with temperature-dependent sex determination: a multifactorial approach

Females are predicted to alter sex allocation when ecological, physiological and behavioural variables have different consequences on the fitness of male and female offspring. Traditionally, tests of sex allocation have examined single causative factors, often ignoring possible interactions between multiple factors. Here, we used a multifactorial approach to examine sex allocation in the viviparous skink, Niveoscincus ocellatus. We integrated a 16-year observational field study with a manipulative laboratory experiment to explore whether the effects of the maternal thermal environment interact with the resources available to females for reproduction to affect sex allocation decisions. We found strong effects of temperature on sex allocation in the field, with females born in warm conditions and males in cold conditions; however, this was not replicated in the laboratory. In contrast, we found no effect of female resource availability on sex allocation, either independently, or in interaction with temperature. These results corresponded with an overall lack of an effect of resource availability on any of the life history traits that we predicted would mediate the benefits of differential sex allocation in this system, suggesting that selection for sex allocation in response to resource availability may be relatively weak. Combined, these results suggest that temperature may be the predominant factor driving sex allocation in this system.

Appendages and gene regulatory networks: Lessons from the limbless

Among squamate reptiles, dozens of lineages have independently evolved complete or partial limb reduction. This remarkable convergence of limbless and limb-reduced phenotypes provides multiple natural replicates of different ages to explore the evolution and development of the vertebrate limb and the gene regulatory network that controls its formation. The most successful and best known of the limb-reduced squamates are snakes, which evolved a limb-reduced body form more than 100 million years ago. Recent studies have revealed the unexpected finding that many ancient limb enhancers are conserved in the genomes of snakes. Analyses in limbed animals show that many of these limb enhancers are also active during development of the phallus, suggesting that these enhancers may have been retained in snakes due their importance in regulating transcription in the external genitalia. This hypothesis is substantiated by functional tests of snake enhancers, which demonstrate that snake enhancer elements have lost limb function while retaining genital enhancer function. The large degree of overlap in the gene regulatory networks deployed during limb and phallus development may act to constrain the divergence of shared gene network components and the evolution of appendage morphology. Future studies will reveal whether limb regulatory elements have undergone similar functional changes in other lineages of limb-reduced squamates.

Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia

In reptiles, sex-determining mechanisms have evolved repeatedly and reversibly between genotypic and temperature-dependent sex determination. The gene Dmrt1 directs male determination in chicken (and presumably other birds), and regulates sex differentiation in animals as distantly related as fruit flies, nematodes and humans. Here, we show a consistent molecular difference in Dmrt1 between reptiles with genotypic and temperature-dependent sex determination. Among 34 non-avian reptiles, a convergently evolved pair of amino acids encoded by sequence within exon 2 near the DM-binding domain of Dmrt1 distinguishes species with either type of sex determination. We suggest that this amino acid shift accompanied the evolution of genotypic sex determination from an ancestral condition of temperature-dependent sex determination at least three times among reptiles, as evident in turtles, birds and squamates. This novel hypothesis describes the evolution of sex-determining mechanisms as turnover events accompanied by one or two small mutations.

A central role for venom in predation by Varanus komodoensis (Komodo Dragon) and the extinct giant Varanus (Megalania) priscus

The predatory ecology of Varanus komodoensis (Komodo Dragon) has been a subject of long-standing interest and considerable conjecture. Here, we investigate the roles and potential interplay between cranial mechanics, toxic bacteria, and venom. Our analyses point to the presence of a sophisticated combined-arsenal killing apparatus. We find that the lightweight skull is relatively poorly adapted to generate high bite forces but better adapted to resist high pulling loads. We reject the popular notion regarding toxic bacteria utilization. Instead, we demonstrate that the effects of deep wounds inflicted are potentiated through venom with toxic activities including anticoagulation and shock induction. Anatomical comparisons of V. komodoensis with V. (Megalania) priscus fossils suggest that the closely related extinct giant was the largest venomous animal to have ever lived.