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Hoplodactylus delcourtiis 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 genusHoplodactylusbased 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 extantHoplodactylusor 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 betweenH. delcourtiand New ZealandHoplodactylus. Based on the phylogenetic results, we placeH. delcourtiin a new genus.

 

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

 

Gekkotan lizards of the genusHemidactylusexhibit derived digital morphologies. These include heavily reduced antepenultimate phalanges of digits III and IV of the manus and digits III–V of the pes, as well as enigmatic cartilaginous structures called paraphalanges. Despite this well‐known morphological derivation, no studies have investigated the development of these structures. We aimed to determine if heterochrony underlies the derived antepenultimate phalanges ofHemidactylus. Furthermore, we aimed to determine if convergently evolved paraphalanges exhibit similar or divergent developmental patterns. Herein we describe embryonic skeletal development in the hands and feet of four gekkonid species, exhibiting a range of digital morphologies. We determined that the derived antepenultimate phalanges ofHemidactylusare the products of paedomorphosis. Furthermore, we found divergent developmental patterns between convergently evolved paraphalanges.

 

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.

 

The veiled chameleon (Chamaeleo calyptratus) is an emerging model system for studying functional morphology and evolutionary developmental biology (evo‐devo). Chameleons possess body plans that are highly adapted to an arboreal life style, featuring laterally compressed bodies, split hands/ft for grasping, a projectile tongue, turreted independently moving eyes, and a prehensile tail. Despite being one of the most phenotypically divergent clades of tetrapods, genomic resources for chameleons are severely lacking.

To address this lack of resources, we used RNAseq to generate 288 million raw Illumina sequence reads from four adult tissues (male and female eyes and gonads) and whole embryos at three distinct developmental stages. We used these data to assemble a largely complete de novo transcriptome consisting of only 82 952 transcripts. In addition, a majority of assembled transcripts (67%) were successfully annotated.

We then demonstrated the utility of these data in the context of studying visual system evolution by examining the content of veiled chameleon opsin genes to show that chameleons possess all five ancestral tetrapod opsins.

We present this de novo, annotated, multi‐tissue transcriptome assembly for the Veiled Chameleon,Chamaeleo calyptratus, as a resource to address a range of evolutionary and developmental questions. The associated raw reads and final annotated transcriptome assembly are freely available for use on NCBI and Figshare, respectively.

 

Armored skin resulting from the presence of bony dermal structures, osteoderms, is an exceptional phenotype in gekkotans (geckos and flap‐footed lizards) only known to occur in three genera:Geckolepis,Gekko, andTarentola. The Tokay gecko (Gekko geckoLINNAEUS 1758) is among the best‐studied geckos due to its large size and wide range of occurrence, and although cranial dermal bone development has previously been investigated, details of osteoderm development along a size gradient remain less well‐known. Likewise, a comparative survey of additional species within the broaderGekkoclade to determine the uniqueness of this trait has not yet been completed. Here, we studied a large sample of gekkotans (38 spp.), including 18 specimens ofG. gecko, using X‐rays and high‐resolution computed tomography for visualizing and quantifying the dermal armorin situ. Results from this survey confirm the presence of osteoderms in a second species within this genus,GekkoreevesiiGRAY 1831, which exhibits discordance in timing and pattern of osteoderm development when compared with its sister taxon,G. gecko. We discuss the developmental sequence of osteoderms in these two species and explore in detail the formation and functionality of these enigmatic dermal ossifications. Finally, we conducted a comparative analysis of endolymphatic sacs in a wide array of gekkotans to explore previous ideas regarding the role of osteoderms as calcium reservoirs. We found thatG. geckoand other gecko species with osteoderms have highly enlarged endolymphatic sacs relative to their body size, when compared to species without osteoderms, which implies that these membranous structures might fulfill a major role of calcium storage even in species with osteoderms.

 

The auditory papilla of geckos contains two zones of sensory hair cells, one covered by a continuous tectorial membrane affixed to the hair bundles and the other by discrete tectorial sallets each surmounting a transverse row of bundles. Gecko papillae are thought to encode sound frequencies up to 5 kHz, but little is known about the hair cell electrical properties or their role in frequency tuning. We recorded from hair cells in the isolated auditory papilla of the crested gecko, Correlophus ciliatus , and found that in both the nonsalletal region and part of the salletal region, the cells displayed electrical tuning organized tonotopically. Along the salletal zone, occupying the apical two-thirds of the papilla, hair bundle length decreased threefold and stereociliary complement increased 1.5-fold. The two morphological variations predict a 13-fold gradient in bundle stiffness, confirmed experimentally, which, when coupled with salletal mass, could provide passive mechanical resonances from 1 to 6 kHz. Sinusoidal electrical currents injected across the papilla evoked hair bundle oscillations at twice the stimulation frequency, consistent with fast electromechanical responses from hair bundles of two opposing orientations across the papilla. Evoked bundle oscillations were diminished by reducing Ca 2+ influx, but not by blocking the mechanotransduction channels or inhibiting prestin action, thereby distinguishing them from known electromechanical mechanisms in hair cells. We suggest the phenomenon may be a manifestation of an electromechanical amplification that augments the passive mechanical tuning of the sallets over the high-frequency region. 

Abstract How developmental modifications produce key innovations, which subsequently allow for rapid diversification of a clade into new adaptive zones, has received much attention. However, few studies have used a robust comparative framework to investigate the influence of evolutionary and developmental constraints on the origin of key innovations, such as the adhesive toe pad of lizards. Adhesive toe pads evolved independently at least 16 times in lizards, allowing us to examine whether the patterns observed are general evolutionary phenomena or unique, lineage-specific events. We performed a high-resolution comparison of plantar scale development in 14 lizard species in Anolis and geckos, encompassing five independent origins of toe pads (one in Anolis, four in geckos). Despite substantial evolutionary divergence between Anolis and geckos, we find that these clades have undergone similar developmental modifications to generate their adhesive toe pads. Relative to the ancestral plantar scale development, in which scale ridges form synchronously along the digit, both padded geckos and Anolis exhibit scansor formation in a distal-to-proximal direction. Both clades have undergone developmental repatterning and, following their origin, modifications in toe pad morphology occurred through relatively minor developmental modifications, suggesting that developmental constraints governed the diversification of the adhesive toe pad in lizards.