The Conservation Status of the World’s Reptiles

Effective and targeted conservation action requires detailed information about species, their distribution, systematics and ecology as well as the distribution of threat processes which affect them. Knowledge of reptilian diversity remains surprisingly disparate, and innovative means of gaining rapid insight into the status of reptiles are needed in order to highlight urgent conservation cases and inform environmental policy with appropriate biodiversity information in a timely manner. We present the first ever global analysis of extinction risk in reptiles, based on a random representative sample of 1500 species (16% of all currently known species). To our knowledge, our results provide the first analysis of the global conservation status and distribution patterns of reptiles and the threats affecting them, highlighting conservation priorities and knowledge gaps which need to be addressed urgently to ensure the continued survival of the world’s reptiles. Nearly one in five reptilian species are threatened with extinction, with another one in five species classed as Data Deficient. The proportion of threatened reptile species is highest in freshwater environments, tropical regions and on oceanic islands, while data deficiency was highest in tropical areas, such as Central Africa and Southeast Asia, and among fossorial reptiles. Our results emphasise the need for research attention to be focussed on tropical areas which are experiencing the most dramatic rates of habitat loss, on fossorial reptiles for which there is a chronic lack of data, and on certain taxa such as snakes for which extinction risk may currently be underestimated due to lack of population information. Conservation actions specifically need to mitigate the effects of human-induced habitat loss and harvesting, which are the predominant threats to reptiles

Using RAD‐seq to recognize sex‐specific markers and sex chromosome systems

Next‐generation sequencing methods have initiated a revolution in molecular ecology and evolution (Tautz et al. 2010). Among the most impressive of these sequencing innovations is restriction site‐associated DNA sequencing or RAD‐seq (Baird et al. 2008; Andrews et al. 2016). RAD‐seq uses the Illumina sequencing platform to sequence fragments of DNA cut by a specific restriction enzyme and can generate tens of thousands of molecular genetic markers for analysis. One of the many uses of RAD‐seq data has been to identify sex‐specific genetic markers, markers found in one sex but not the other (Baxter et al. 2011; Gamble & Zarkower 2014). Sex‐specific markers are a powerful tool for biologists. At their most basic, they can be used to identify the sex of an individual via PCR. This is useful in cases where a species lacks obvious sexual dimorphism at some or all life history stages. For example, such tests have been important for studying sex differences in life history (Sheldon 1998; Mossman & Waser 1999), the management and breeding of endangered species (Taberlet et al. 1993; Griffiths & Tiwari 1995; Robertson et al. 2006) and sexing embryonic material (Hacker et al. 1995; Smith et al. 1999). Furthermore, sex‐specific markers allow recognition of the sex chromosome system in cases where standard cytogenetic methods fail (Charlesworth & Mank 2010; Gamble & Zarkower 2014). Thus, species with male‐specific markers have male heterogamety (XY) while species with female‐specific markers have female heterogamety (ZW). In this issue, Fowler & Buonaccorsi (2016) illustrate the ease by which RAD‐seq data can generate sex‐specific genetic markers in rockfish (Sebastes). Moreover, by examining RAD‐seq data from two closely related rockfish species, Sebastes chrysomelas and Sebastes carnatus (Fig. 1), Fowler & Buonaccorsi (2016) uncover shared sex‐specific markers and a conserved sex chromosome system

Sex determination

Multicellular animals are a diverse lot, with widely varied body plans and lifestyles. One feature they share, however, is a nearly universal reliance on sexual reproduction for species propagation. Humans have long been fascinated by human sex differences and formal theories on how human sex is determined date at least to Aristotle (in De Generatione Animalium, ca. 335 BCE). However, it is only in the past couple of decades that the genetic and molecular programs responsible for generating the two sexes have been understood in any detail. Sex, it turns out, can be established by many very different and fast-evolving mechanisms, but often these involve a conserved class of transcriptional regulators, the DM domain proteins

Comparison of Harvested and Nonharvested Painted Turtle Populations

Painted turtles (Chrysemys picta) are commercially harvested in large numbers in Minnesota for sale to biological supply companies and the pet trade. We investigated the possible effects of this harvest by comparing size, demography, and catch rates of painted turtles in 12 harvested and 10 nonharvested painted turtle populations in 2001 and 2002. We correlated turtle catch rates to harvest status, and harvested lakes had a lower catch-per-unit-effort than nonharvested lakes. Harvest had minimal effect on the size of turtles captured, and we found no significant differences in the count of male:female:juvenile turtles among lakes of different harvest status. We suggest that painted turtle populations likely have been impacted by harvester activities, but it was unclear whether the current harvest is sustainable. Further work is needed to determine whether there are any long-term effects on painted turtle populations

A Review of Sex Determining Mechanisms in Geckos (Gekkota: Squamata)

Geckos are a species-rich clade of reptiles possessing diverse sex determining mechanisms. Some species possess genetic sex determination, with both male and female heterogamety, while other species have temperature-dependent sex determination. I compiled information from the literature on the taxonomic distribution of these sex determining mechanisms in geckos. Using phylogenetic data from the literature, I reconstructed the minimum number of transitions among these sex determining mechanisms with parsimony-based ancestral state reconstruction. While only a small number of gecko species have been characterized, numerous changes among sex determining mechanisms were inferred. This diversity, coupled with the high frequency of transitions, makes geckos excellent candidates as a model clade for the study of vertebrate sex determination and evolution

Duplications in Corneous Beta Protein Genes and the Evolution of Gecko Adhesion

Corneous proteins are an important component of the tetrapod integument. Duplication and diversification of keratins and associated proteins are linked with the origin of most novel integumentary structures like mammalian hair, avian feathers, and scutes covering turtle shells. Accordingly, the loss of integumentary structures often coincides with the loss of genes encoding keratin and associated proteins. For example, many hair keratins in dolphins and whales have become pseudogenes. The adhesive setae of geckos and anoles are composed of both intermediate filament keratins (IF-keratins, formerly known as alpha-keratins) and corneous beta‐proteins (CBPs, formerly known as beta-keratins) and recent whole genome assemblies of two gecko species and an anole uncovered duplications in seta-specific CBPs in each of these lineages. While anoles evolved adhesive toepads just once, there are two competing hypotheses about the origin(s) of digital adhesion in geckos involving either a single origin or multiple origins. Using data from three published gecko genomes, I examine CBP gene evolution in geckos and find support for a hypothesis where CBP gene duplications are associated with the repeated evolution of digital adhesion. Although these results are preliminary, I discuss how additional gecko genome assemblies, combined with phylogenies of keratin and associated protein genes and gene duplication models, can provide rigorous tests of several hypotheses related to gecko CBP evolution. This includes a taxon sampling strategy for sequencing and assembly of gecko genomes that could help resolve competing hypotheses surrounding the origin(s) of digital adhesion

On the Origin of Frictional Adhesion in Geckos: Small Morphological Changes Lead to a Major Biomechanical Transition in the Genus \u3cem\u3eGonatodes\u3c/em\u3e

The evolutionary history of vertebrate locomotion is punctuated by innovations that have permitted expansion into novel ecological niches. Frictional adhesion of geckos is an innovation renowned for enabling locomotion on vertical and inverted smooth surfaces. Much is known about the microstructure and function of the fully-expressed gekkotan adhesive apparatus, although how it originated is poorly understood. Therefore, identifying species that exhibit the earliest stages of expression of frictional adhesion will provide significant insights into the evolution of this trait. Our previous investigation of digital proportions, shape, scalation, skeletal form, and subdigital epidermal micro-ornamentation in the genus Gonatodes led us to hypothesize that Gonatodes humeralisexpresses incipient frictional adhesion. To test this, we first conducted a phylogenetic analysis of Gonatodes and related sphaerodactyl genera to clarify the historical context of the evolution of frictional adhesive capability in the genus. We then measured the ability of G. humeralis and its close relatives to generate frictional adhesive force, examined their locomotor capabilities on low-friction surfaces, and observed animals in their natural habitat. After accounting for body mass and phylogenetic relationships, we found that G. humeralis generates frictional adhesive force essentially equivalent to that of Anolis, and can scale vertical smooth surfaces. Gonatodes vittatus, a species that lacks elaborated epidermal setae, generates negligible frictional adhesive force and can only ascend smooth inclined surfaces with a pitch of ≤ 40°. We conclude that the ostensibly padless G. humeralis, with feet lacking the musculoskeletal, tendinous, and vascular modifications typical of pad-bearing geckos, nevertheless can employ frictional adhesive contact to assist locomotion. As in Anolis, the release of frictional adhesive contact occurs when the foot is plantar flexed after the heel has lifted from the surface. Our findings indicate that the origin of frictional adhesion was likely gradual but that, ultimately, this led to major shifts in ecology and function

Cryptic Diversity in the Neotropical Gecko Genus \u3cem\u3ePhyllopezus\u3c/em\u3e Peters, 1878 (Reptilia: Squamata: Phyllodactylidae): A New Species from Paraguay

The gecko genus Phyllopezus is distributed mainly along South America’s “Dry Diagonal” (Caatinga, Cerrado, and Chaco). The genus has been the subject of recent taxonomic analyses and includes four described species and seven candidate species referred to here as Phyllopezus pollicaris sensu lato. In Paraguay, Phyllopezus is known from the Chaco and Cerrado where it is abundant, and also from a small isolated population from a rocky hill formation named “Cordillera de Los Altos” (Los Altos mountain range). Here we analyzed genetic samples from across its range, including new samples from Paraguay, using DNA barcoding analysis of the mitochondrial 16S gene and phylogenetic analyses using both Bayesian and Maximum Likelihood methods. We found genetic and morphological differences among geckos from the Los Altos mountain range and the remaining Phyllopezus populations. Using both molecular and morphological evidence we describe a new Phyllopezus species, sister toP. przewalskii. Genetic differentiation among described and putative Phyllopezus species is greater than their morphological differences, which likely accounts for these cryptic taxa remaining undescribed for so long

Identification of Sex‐specific Molecular Markers Using Restriction Site‐associated DNA Sequencing

A major barrier to evolutionary studies of sex determination and sex chromosomes has been a lack of information on the types of sex‐determining mechanisms that occur among different species. This is particularly problematic in groups where most species lack visually heteromorphic sex chromosomes, such as fish, amphibians and reptiles, because cytogenetic analyses will fail to identify the sex chromosomes in these species. We describe the use of restriction site‐associated DNA (RAD) sequencing, or RAD‐seq, to identify sex‐specific molecular markers and subsequently determine whether a species has male or female heterogamety. To test the accuracy of this technique, we examined the lizard Anolis carolinensis. We performed RAD‐seq on seven male and ten female A. carolinensis and found one male‐specific molecular marker. Anolis carolinensis has previously been shown to possess male heterogamety and the recently published A. carolinensis genome facilitated the characterization of the sex‐specific RAD‐seq marker. We validated the male specificity of the new marker using PCR on additional individuals and also found that it is conserved in some other Anolis species. We discuss the utility of using RAD‐seq to identify sex‐determining mechanisms in other species with cryptic or homomorphic sex chromosomes and the implications for the evolution of male heterogamety in Anolis