Bridging the Research Gap between Live Collections in Zoos and Preserved Collections in Natural History Museums.

Zoos and natural history museums are both collections-based institutions with important missions in biodiversity research and education. Animals in zoos are a repository and living record of the world's biodiversity, whereas natural history museums are a permanent historical record of snapshots of biodiversity in time. Surprisingly, despite significant overlap in institutional missions, formal partnerships between these institution types are infrequent. Life history information, pedigrees, and medical records maintained at zoos should be seen as complementary to historical records of morphology, genetics, and distribution kept at museums. Through examining both institution types, we synthesize the benefits and challenges of cross-institutional exchanges and propose actions to increase the dialog between zoos and museums. With a growing recognition of the importance of collections to the advancement of scientific research and discovery, a transformational impact could be made with long-term investments in connecting the institutions that are caretakers of living and preserved animals.

Chromosome-Level Genome Assembly Reveals Dynamic Sex Chromosomes in Neotropical Leaf-Litter Geckos (Sphaerodactylidae: Sphaerodactylus).

Sex determination is a critical element of successful vertebrate development, suggesting that sex chromosome systems might be evolutionarily stable across lineages. For example, mammals and birds have maintained conserved sex chromosome systems over long evolutionary time periods. Other vertebrates, in contrast, have undergone frequent sex chromosome transitions, which is even more amazing considering we still know comparatively little across large swaths of their respective phylogenies. One reptile group in particular, the gecko lizards (infraorder Gekkota), shows an exceptional lability with regard to sex chromosome transitions and may possess the majority of transitions within squamates (lizards and snakes). However, detailed genomic and cytogenetic information about sex chromosomes is lacking for most gecko species, leaving large gaps in our understanding of the evolutionary processes at play. To address this, we assembled a chromosome-level genome for a gecko (Sphaerodactylidae: Sphaerodactylus) and used this assembly to search for sex chromosomes among six closely related species using a variety of genomic data, including whole-genome re-sequencing, RADseq, and RNAseq. Previous work has identified XY systems in two species of Sphaerodactylus geckos. We expand upon that work to identify between two and four sex chromosome cis-transitions (XY to a new XY) within the genus. Interestingly, we confirmed two different linkage groups as XY sex chromosome systems that were previously unknown to act as sex chromosomes in tetrapods (syntenic with Gallus chromosome 3 and Gallus chromosomes 18/30/33), further highlighting a unique and fascinating trend that most linkage groups have the potential to act as sex chromosomes in squamates.

Embryonic development of a parthenogenetic vertebrate, the mourning gecko (Lepidodactylus lugubris).

BACKGROUND: One goal of evolutionary developmental biology is to understand the role of development in the origin of phenotypic novelty and convergent evolution. Geckos are an ideal system to study this topic, as they are species-rich and exhibit a suite of diverse morphologies-many of which have independently evolved multiple times within geckos. RESULTS: We characterized and discretized the embryonic development of Lepidodactylus lugubris-an all-female, parthenogenetic gecko species. We also used soft-tissue µCT to characterize the development of the brain and central nervous system, which is difficult to visualize using traditional microscopy techniques. Additionally, we sequenced and assembled a de novo transcriptome for a late-stage embryo as a resource for generating future developmental tools. Herein, we describe the derived and conserved patterns of L. lugubris development in the context of squamate evolution and development. CONCLUSIONS: This embryonic staging series, µCT data, and transcriptome together serve as critical enabling resources to study morphological evolution and development, the evolution and development of parthenogenesis, and other questions concerning vertebrate evolution and development in an emerging gecko model.

ZZ/ZW Sex Chromosomes in the Endemic Puerto Rican Leaf-Toed Gecko (Phyllodactylus wirshingi).

Investigating the evolutionary processes influencing the origin, evolution, and turnover of vertebrate sex chromosomes requires the classification of sex chromosome systems in a great diversity of species. Among amniotes, squamates (lizards and snakes) - and gecko lizards in particular - are worthy of additional study. Geckos possess all major vertebrate sex-determining systems, as well as multiple transitions among them, yet we still lack data on the sex-determining systems for the vast majority of species. We here utilize restriction-site associated DNA sequencing (RADseq) to identify the sex chromosome system of the Puerto Rican endemic leaf-toed gecko (Phyllodactylidae: Phyllodactylus wirshingi), in order to confirm a ZZ/ZW sex chromosome system within the genus, as well as to better categorize the diversity within this poorly characterized family. RADseq has proven an effective alternative to cytogenetic methods for determining whether a species has an XX/XY or ZZ/ZW sex chromosome system - particularly in taxa with non-differentiated sex chromosomes - but can also be used to identify which chromosomes in the genome are the sex chromosomes. We here identify a ZZ/ZW sex chromosome system in P. wirshingi. Furthermore, we show that 4 of the female-specific markers contain fragments of genes found on the avian Z and discuss homology with P. wirshingi sex chromosomes.

Persistence of a Geographically-Stable Hybrid Zone in Puerto Rican Dwarf Geckos.

Determining the mechanisms that create and maintain biodiversity is a central question in ecology and evolution. Speciation is the process that creates biodiversity. Speciation is mediated by incompatibilities that lead to reproductive isolation between divergent populations and these incompatibilities can be observed in hybrid zones. Gecko lizards are a speciose clade possessing an impressive diversity of behavioral and morphological traits. In geckos, however, our understanding of the speciation process is negligible. To address this gap, we used genetic sequence data (both mitochondrial and nuclear markers) to revisit a putative hybrid zone between Sphaerodactylus nicholsi and Sphaerodactylus townsendi in Puerto Rico, initially described in 1984. First, we addressed discrepancies in the literature on the validity of both species. Second, we sampled a 10-km-wide transect across the putative hybrid zone and tested explicit predictions about its dynamics using cline models. Third, we investigated potential causes for the hybrid zone using species distribution modeling and simulations; namely, whether unique climatic variables within the hybrid zone might elicit selection for intermediate phenotypes. We find strong support for the species-level status of each species and no evidence of movement, or unique climatic variables near the hybrid zone. We suggest that this narrow hybrid zone is geographically stable and is maintained by a combination of dispersal and selection. Thus, this work has identified an extant model system within geckos that that can be used for future investigations detailing genetic mechanisms of reproductive isolation in an understudied vertebrate group.

Diffusible iodine-based contrast-enhanced computed tomography (diceCT): an emerging tool for rapid, high-resolution, 3-D imaging of metazoan soft tissues.

Morphologists have historically had to rely on destructive procedures to visualize the three-dimensional (3-D) anatomy of animals. More recently, however, non-destructive techniques have come to the forefront. These include X-ray computed tomography (CT), which has been used most commonly to examine the mineralized, hard-tissue anatomy of living and fossil metazoans. One relatively new and potentially transformative aspect of current CT-based research is the use of chemical agents to render visible, and differentiate between, soft-tissue structures in X-ray images. Specifically, iodine has emerged as one of the most widely used of these contrast agents among animal morphologists due to its ease of handling, cost effectiveness, and differential affinities for major types of soft tissues. The rapid adoption of iodine-based contrast agents has resulted in a proliferation of distinct specimen preparations and scanning parameter choices, as well as an increasing variety of imaging hardware and software preferences. Here we provide a critical review of the recent contributions to iodine-based, contrast-enhanced CT research to enable researchers just beginning to employ contrast enhancement to make sense of this complex new landscape of methodologies. We provide a detailed summary of recent case studies, assess factors that govern success at each step of the specimen storage, preparation, and imaging processes, and make recommendations for standardizing both techniques and reporting practices. Finally, we discuss potential cutting-edge applications of diffusible iodine-based contrast-enhanced computed tomography (diceCT) and the issues that must still be overcome to facilitate the broader adoption of diceCT going forward.

New genus and species names for the Eocene lizard Cadurcogekko rugosus Augé, 2005.

Cadurcogekko rugosus Augé, 2005 was described as a gekkotan lizard from the Eocene of France. A revision of the material has revealed that the holotype, a nearly complete dentary, actually belongs to a scincid lizard, for which we erect the new genus Gekkomimus. The rest of material originally referred to C. rugosus is of undoubted gekkotan nature and is included in the new species Cadurcogekko verus, with the exception of a partial left dentary belonging to the iguanid lizard Cadurciguana hoffstetteri.

The embryology of the retinal pigmented epithelium in dwarf geckos (Gekkota: Sphaerodactylinae): a unique developmental pattern.

BACKGROUND: The retinal pigmented epithelium (RPE) is a rounded shaped structure in almost all lizards. In the New World dwarf geckos, this structure shows an unusual morphology. In addition to this ocular character, we describe notable differences in the development of these geckos in comparison with available developmental staging tables for other geckos and squamate reptiles. RESULTS: We identified two main patterns of development of the RPE for squamates. These patterns were mapped onto a metatree of concordant hypotheses of squamates based on molecular data. During post-ovopositional stages the representative species of sphaerodactyls exhibit a RPE layer that transforms gradually from an ovoid form into the generalized spherical form. Sphaerodactyls are the only group of squamates in which this pattern is known. CONCLUSIONS: This transition might be circumstantial evidence that the accessory RPE plays a role in providing additional protection for their apomorphic concaviclivate temporal fovea. We also report the presence of conjunctival papillae in a developmental stage prior to the formation of scleral ossicles. This developmental progression is similar to that of birds and turtles.

Variation in the cranial osteology of the amphisbaenian genus Zygaspis based on high-resolution x-ray computed tomography.

Amphisbaenians are a specialized fossorial group of reptiles, having developed head-first burrowing, a specialized skull architecture, and an elongated body. This group is generally small-bodied, with some species possessing skulls only a few millimeters long. In this study, we used high-resolution x-ray computed tomography to compare the skulls of 15 specimens from seven of the eight species in the amphisbaenian genus Zygaspis (Zygaspis dolichomenta, Zygaspis ferox, Zygaspis quadrifrons, Zygaspis kafuensis, Zygaspis nigra, Zygaspis vandami, and Zygaspis violacea). Both interspecific and intraspecific variation, including asymmetry, is observed among the cranial bones of the specimens. There are unique morphological features on some cranial bones, including the premaxilla and ectopterygoid of Z. quadrifrons, the pterygoid and vomer of Z. kafuensis, and the extracolumella of Z. nigra. Sexual dimorphism has been previously reported for the species Z. quadrifrons and is observed here as well.

Toe pad morphology and adhesion in the miniaturized gecko, Chatogekko amazonicus (Gekkota: Sphaerodactylidae).

Chatogekko amazonicus is a miniaturized gecko from northern South America and is among the smallest of toe pad bearing lizards. The toe pads of C. amazonicus are miniscule, between 18% and 27% of the plantar surface area. We aimed to investigate the relationship between adhesive toe pad morphology, body size, and adhesive capabilities. Using scanning electron microscopy, we determine that the adhesive pads of C. amazonicus exhibit branched setae similar to those of other geckos, but that are generally much smaller. When compared with other gecko taxa, we show that C. amazonicus setae occupy a similar range of seta length: snout-vent length ratio and aspect ratio as other gekkonoid species (i.e. Gekkonidae, Phyllodactylidae, and Sphaerodactylidae). We demonstrate that C. amazonicus-even with its relatively small toe pads-is capable of climbing a smooth glass surface at a nearly vertical angle. We suggest that sphaerodactylids like C. amazonicus offer an excellent system for studying toe pad morphology and function in relation to miniaturization.

The skull of the semi-aquatic neotropical lizard Echinosaura horrida (Gymnophthalmidae: Cercosaurinae) reveals new synapomorphies within Gymnophthalmoidea.

The rough teiid or water cork lizard (Echinosaura horrida) is a small reptile from Colombia and Ecuador placed in a genus that contains eight species and well-known phylogenetic relationships. Here we provide a detailed description and illustrations, bone by bone, of its skull, while we discussed its intraspecific variation by comparing high-resolution computed tomography data from two specimens and the variation within the genus by including previously published data from Echinosaura fischerorum. This allowed to propose putative diagnostic character states for Echinosaura horrida and synapomorphies for Echinosaura. In addition, our discussion includes broader comparisons of new character transformations of the jugal, vomer, orbitosphenoid, and hyoid. These characters are important for diagnosing clades at different levels of the Gymnophthalmoidea phylogeny.

Compound osteoderms preserved in amber reveal the oldest known skink.

Scincidae is one of the most species-rich and cosmopolitan clades of squamate reptiles. Abundant disarticulated fossil material has also been attributed to this group, however, no complete pre-Cenozoic crown-scincid specimens have been found. A specimen in Burmite (99 MYA) is the first fossil that can be unambiguously referred to this clade. Our analyses place it as nested within extant skinks, supported by the presence of compound osteoderms formed by articulated small ostedermites. The specimen has a combination of dorsal and ventral compound osteoderms and overlapping cycloid scales that is limited to skinks. We propose that this type of osteoderm evolved as a response to an increased overlap of scales, and to reduced stiffness of the dermal armour. Compound osteoderms could be a key innovation that facilitated diversification in this megadiverse family.

A preliminary phylogeny of the Palearctic naked-toed geckos (Reptilia: Squamata: Gekkonidae) with taxonomic implications.

Palearctic naked-toed geckos are a group of gekkonid geckos that range from North Africa to northern India and western China, with their greatest diversity in Iran and Pakistan. Relationships among the constituent genera remain incompletely resolved and the monophyly of key genera remains unverified. Further, competing classifications are in current use and many species have been allocated to different genera by different authors. We used both mitochondrial (ND2) and nuclear genes (RAG1, PDC) to explore relationships among representatives of all but one genus in the group (Rhinogecko), including four genera not previously included in phylogenetic analyses (Asiocolotes, Altigekko, Indogekko, and Siwaligekko). Siwaligekko (and presumably other Tibeto-Himalayan species often referred to Cyrtopodion) are more closely related to tropical Asian Cyrtodactylus than to Palearctic naked-toed geckos. Sampled species of Asiocolotes and Altigekko are sister taxa, but both genera are here considered junior subjective synonyms of Altiphylax. Cyrtopodion sensu lato is non-monophyletic; Mediodactylus and Tenuidactylus, which have variably been considered as subgenera or synonyms of Cyrtopodion are both valid genera. Indogekko is embedded within Cyrtopodion and is here treated as a subgenus. Bunopus and Crossobamon are closely related to one-another, and with Agamura are interdigitated among taxa previously assigned to Cyrtopodion. Our data confirm the previous identification of a Saharo-Arabian Stenodactylus/Tropiocolotes/Pseudoceramodactylus clade and verify that Microgecko and Alsophylax are not members of the main clade of Palearctic naked-toed geckos. Osteological differences between Tropiocolotes and Microgecko, formerly treated as congeneric, are discussed and illustrated. The divergence between Cyrtodactylus and the Palearctic naked-toed clade predates the initial collision of the Indian and Eurasian plates, but deeper divergences within both groups are consistent with mountain building in the Himalayas and adjacent ranges as promoting cladogenic events. Miocene divergences within Tenuidactylus are consistent with vicariant speciation caused by uplift events in the Iranian and Transcaspian regions. Taxonomic implications of our phylogenetic results are discussed and a preliminary allocation of all species of padless Palearctic gekkonids to genus is provided.

Reappraising the evolutionary history of the largest known gecko, the presumably extinct Hoplodactylus delcourti, via high-throughput sequencing of archival DNA.

Hoplodactylus delcourti is a presumably extinct species of diplodactylid gecko known only from a single specimen of unknown provenance. It is by far the largest known gekkotan, approximately 50% longer than the next largest-known species. It has been considered a member of the New Zealand endemic genus Hoplodactylus based on external morphological features including shared toe pad structure. We obtained DNA from a bone sample of the only known specimen to generate high-throughput sequence data suitable for phylogenetic analysis of its evolutionary history. Complementary sequence data were obtained from a broad sample of diplodactylid geckos. Our results indicate that the species is not most closely related to extant Hoplodactylus or any other New Zealand gecko. Instead, it is a member of a clade whose living species are endemic to New Caledonia. Phylogenetic comparative analyses indicate that the New Caledonian diplodactylid clade has evolved significantly more disparate body sizes than either the Australian or New Zealand clades. Toe pad structure has changed repeatedly across diplodactylids, including multiple times in the New Caledonia clade, partially explaining the convergence in form between H. delcourti and New Zealand Hoplodactylus. Based on the phylogenetic results, we place H. delcourti in a new genus.

A new gecko from the earliest Eocene of Dormaal, Belgium: a thermophilic element of the 'greenhouse world'.

We here describe a new gekkotan lizard from the earliest Eocene (MP 7) of the Dormaal locality in Belgium, from the time of the warmest global climates of the past 66 million years (Myr). This new taxon, with an age of 56 Myr, together with indeterminate gekkotan material reported from Silveirinha (Portugal, MP 7) represent the oldest Cenozoic gekkotans known from Europe. Today gekkotan lizards are distributed worldwide in mainly warm temperate to tropical areas and the new gecko from Dormaal represents a thermophilic faunal element. Given the Palaeocene-Eocene thermal maximum at that time, the distribution of this group in such northern latitudes (above 50° North - the latitude of southern England) is not surprising. Although this new gekkotan is represented only by a frontal (further, dentaries and a mandibular fragment are described here as Gekkota indet. 1 and 2-at least two gekkotan species occurred in Dormaal), it provides a new record for squamate diversity from the earliest Eocene 'greenhouse world'. Together with the Baltic amber gekkotan Yantarogekko balticus, they document the northern distribution of gekkotans in Europe during the Eocene. The increase in temperature during the early Eocene led to a rise in sea level, and many areas of Eurasia were submerged. Thus, the importance of this period is magnified by understanding future global climate change.

A new Early Cretaceous lizard in Myanmar amber with exceptionally preserved integument.

We here report on a well-preserved juvenile lizard specimen in Albian amber (ca. 110 mya) from the Hkamti site (Myanmar). This new taxon is represented by an articulated skull and the anterior portion of the trunk, including the pectoral girdle and forelimbs. The scleral ossicles and eyelid are also visible, and the specimen exhibits pristine detail of the integument (of both head and body). In a combined molecular and morphological analysis, it was consistently recovered as a scincoid lizard (Scinciformata), as sister to Tepexisaurus + Xantusiidae. However, the phylogenetic position of the new taxon should be interpreted with caution as the holotype is an immature individual. We explored the possibility of miscoding ontogenetically variable characters by running alternative analyses in which these characters were scored as missing data for our taxon. With the exception of one tree, in which it was sister to Amphisbaenia, the specimen was recovered as a Pan-xantusiid. Moreover, we cannot rule out the possibility that it represents a separate lineage of uncertain phylogenetic position, as it is the case for many Jurassic and Cretaceous taxa. Nonetheless, this fossil offers a rare opportunity to glimpse the external appearance of one group of lizards during the Early Cretaceous.

Blind snakes beneath the surface: Continuing the legacy of Richard Thomas.

Blind snakes (Scolecophidia) are small-bodied, enigmatic burrowing reptiles with members found on all continents except Antarctica. This Special Issue on blind snakes honors and advances the foundational studies by a remarkable anatomist, Richard Thomas. Richard is currently one of the living herpetologists to have described the greatest number of herpetofauna species, including many blind snake taxa. Recent interest in scolecophidian research at several conferences led to the development of this Special Issue on blind snake anatomy. This issue spans a diversity of papers, from biographical accounts of Richard's life and works, to a brief history of scolecophidian anatomical studies and the benefits of computed tomography (CT) technology, to a variety of studies on the skull and post-cranial osteology, cranial and jaw biomechanics related to subterranean lifestyles, evolution, and systematics of blind snake taxa from around the globe. This Special Issue will hopefully serve as a valuable resource and contribution to the field of blind snake anatomy research, and a joyful reflection on the life and career of a herpetologist who mentored and inspired a new generation of researchers in this area.

Comparative anatomy of the middle ear in some lizard species with comments on the evolutionary changes within Squamata.

The skeleton of the middle ear of lizards is composed of three anatomical elements: columella, extracolumella, and tympanic membrane, with some exceptions that show modifications of this anatomy. The main function of the middle ear is transforming sound waves into vibrations and transmitting these to the inner ear. Most middle ear studies mainly focus on its functional aspects, while few describe the anatomy in detail. In lizards, the morphology of the columella is highly conservative, while the extracolumella shows variation in its presence/absence, size, and the number of processes present on the structure. In this work, we used diaphanized and double-stained specimens of 38 species of lizards belonging to 24 genera to study the middle ear's morphology in a comparative framework. Results presented here indicate more variation in the morphology of the extracolumella than previously known. This variation in the extracolumella is found mainly in the pars superior and anterior processes, while the pars inferior and the posterior process are more constant in morphology. We also provide new information about the shape of gekkotan extracolumella, including traits that are diagnostic for the iguanid and gekkonid middle ear types. The data collected in this study were combined with information from published descriptive works. The new data included here refers to the length of the columella relative to the extracolumella central axis length, the general structure of the extracolumella, and the presence of the internal process. These characters were included in ancestral reconstruction analysis using Bayesian and parsimony approaches. The results indicate high levels of homoplasy in the variation of the columella-extracolumella ratio, providing a better understanding of the ratio variation among lizards. Additionally, the presence of four processes in the extracolumella is the ancestral state for Gekkota, Pleurodonta, and Xantusiidae, and the absence of the internal processes is the ancestral state for Gekkota, Gymnophthalmidae, and Scincidae; despite the fact that these groups convergently develop these character states, they could be used in combination with other characters to diagnose these clades. The posterior extension in the pars superior and an anterior process with some small and sharp projections is also a diagnostic trait for Gekkota. A more accurate description of each process of the extracolumella and its variation needs to be evaluated in a comprehensive analysis, including a greater number of species. Although the number of taxa sampled in this study is small considering the vast diversity of lizards, the results provide an overall idea of the amount of variation of the middle ear while helping to infer the evolutionary history of the lizard middle ear.

A biographical account of John Paul Richard Thomas, the man who leaves no stone unturned.

This biographical account summarizes the professional career and scientific contributions of John Paul Richard Thomas, a contemporary leading figure in the systematics of West Indian amphibians and non-avian reptiles, especially of blind snakes of the families Typhlopidae and Leptotyphlopidae. Since his first expedition to the West Indies in 1957, Richard's vast field experience (including three trips to Peru between 1968 and 1974), impressive collecting skills, and remarkable ability to detect phenotypic variation among natural populations have resulted in the description of more than 70 species of snakes (24 typhlopids, 4 leptotyphlopids), lizards, and frogs in 16 genera and 11 taxonomic families. Richard joined the faculty of the Department of Biology, University of Puerto Rico, Río Piedras, in 1976 and ever since his efforts significantly advanced organismal biology research at the institution. Although primarily a systematist, his desire to understand multiple aspects of an organism's biology and contagious passion for becoming intimately familiar with animals in their natural environments provided his students the opportunity to conduct research in fields such as behavioral and evolutionary ecology. Richard's mentoring fostered the scientific interests of his graduate students, who were exposed first-hand to every aspect of research, an invaluable experience that served as a springboard for the development of their professional careers inside and outside academia. This Commentary is a fitting tribute to an influential, unassuming scientist whose passion for turning over rocks has led to the discovery of many interesting species.

Underground Down Under: Skull anatomy of the southern blind snake Anilios australis Gray, 1845 (Typhlopidae: Serpentes: Squamata).

The cranial anatomy of blindsnakes has been markedly understudied, with the small size and relative rarity of encountering these subterranean reptiles being significant limiting factors. In this article, we re-visit the skull anatomy of the Australian southern blind snake Anilios australis Gray, 1845 using microCT data, and produce the first complete atlas for the cranial anatomy of a representative of this speciose typhlopid genus. The skull is formed by 18 paired and four unpaired elements. We here produce a bone-by-bone description of each element as well as an inner ear endocast for each of two specimens differing in skull size. This approach has revealed the presence of a highly perforated dorsal plate on the septomaxilla-a structure convergent with the cribriform plate of the mammalian ethmoid bone-and a feature previously unknown for typhlopid snakes. This detailed anatomical study will facilitate ongoing taxonomic and systematic studies in the genus Anilios as well as provide comparative data for future studies on blindsnake anatomy more broadly.