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.

It's a trap?! Escape from an ancient, ancestral sex chromosome system and implication of Foxl2 as the putative primary sex-determining gene in a lizard (Anguimorpha; Shinisauridae).

Although sex determination is ubiquitous in vertebrates, mechanisms of sex determination vary from environmentally to genetically influenced. In vertebrates, genetic sex determination is typically accomplished with sex chromosomes. Groups like mammals maintain conserved sex chromosome systems, while sex chromosomes in most vertebrate clades are not conserved across similar evolutionary timescales. One group inferred to have an evolutionarily stable mode of sex determination is Anguimorpha, a clade of charismatic taxa including monitor lizards, Gila monsters, and crocodile lizards. The common ancestor of extant anguimorphs possessed a ZW system that has been retained across the clade. However, the sex chromosome system in the endangered, monotypic family of crocodile lizards (Shinisauridae) has remained elusive. Here, we analyze genomic data to demonstrate that Shinisaurus has replaced the ancestral anguimorph ZW system on LG7 with a novel ZW system on LG3. The linkage group, LG3, corresponds to chromosome 9 in chicken, and this is the first documented use of this syntenic block as a sex chromosome in amniotes. Additionally, this ~1 Mb region harbors approximately 10 genes, including a duplication of the sex-determining transcription factor, Foxl2, critical for the determination and maintenance of sexual differentiation in vertebrates, and thus a putative primary sex-determining gene for Shinisaurus.

It's a Trap?! Escape from an ancient, ancestral sex chromosome system and implication of Foxl2 as the putative primary sex determining gene in a lizard (Anguimorpha; Shinisauridae).

Although sex determination is ubiquitous in vertebrates, mechanisms of sex determination vary from environmentally- to genetically-influenced. In vertebrates, genetic sex determination is typically accomplished with sex chromosomes. Groups like mammals maintain conserved sex chromosome systems, while sex chromosomes in most vertebrate clades aren't conserved across similar evolutionary timescales. One group inferred to have an evolutionarily stable mode of sex determination is Anguimorpha, a clade of charismatic taxa including: monitor lizards, Gila monsters, and crocodile lizards. The common ancestor of extant anguimorphs possessed a ZW system that has been retained across the clade. However, the sex chromosome system in the endangered, monotypic family of crocodile lizards (Shinisauridae) has remained elusive. Here, we analyze genomic data to demonstrate that Shinisaurus has replaced the ancestral anguimorph ZW system on LG7 chromosome with a novel ZW system on LG3. The linkage group LG3 corresponds to chromosome 9 in chicken, and this is the first documented use of this syntenic block as a sex chromosome in amniotes. Additionally, this ~1Mb region harbors approximately 10 genes, including a duplication of the sex-determining transcription factor, Foxl2-critical for the determination and maintenance of sexual differentiation in vertebrates, and thus a putative primary sex determining gene for Shinisaurus.

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.

Clarifying a male color morph of Sphaerodactylus macrolepis Gnther, 1859 and resolving the taxonomic confusion on Saint Croix.

Many species of sphaerodactyl gecko exhibit sexual dichromatism. In particular, dichromatism plays an important role in intersexual signaling for Sphaerodactylus. Furthermore, some species exhibit polymorphism in male color and pattern. Here, we describe a regional male color morph of Sphaerodactylus macrolepis from St. Croix. After generating both mitochondrial and nuclear phylogenies, we found that individuals with the St. Croix-specific yellow/orange head morph are part of the S. macrolepis clade. This distinct color morph likely contributed to the turbulent taxonomic history of the S. macrolepis species group. Given the documented diversity of the color patterns in this group and that sexual signals evolve rapidly, we suggest S. macrolepis is an excellent group to study the ecological and evolutionary consequences of dichromatism and polymorphism.

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.

A comprehensive phylogeny of dwarf geckos of the genus Lygodactylus, with insights into their systematics and morphological variation.

The 71 currently known species of dwarf geckos of the genus Lygodactylus are a clade of biogeographic interest due to their occurrence in continental Africa, Madagascar, and South America. Furthermore, because many species are morphologically cryptic, our knowledge of species-level diversity within this genus is incomplete, as indicated by numerous unnamed genetic lineages revealed in previous molecular studies. Here we provide an extensive multigene phylogeny covering 56 of the named Lygodactylus species, four named subspecies, and 34 candidate species of which 19 are newly identified in this study. Phylogenetic analyses, based on ∼10.1 kbp concatenated sequences of eight nuclear-encoded and five mitochondrial gene fragments, confirm the monophyly of 14 Lygodactylus species groups, arranged in four major clades. We recover two clades splitting from basal nodes, one comprising exclusively Malagasy species groups, and the other containing three clades. In the latter, there is a clade with only Madagascar species, which is followed by a clade containing three African and one South American species groups, and its sister clade containing six African and two Malagasy species groups. Relationships among species groups within these latter clades remain weakly supported. We reconstruct a Lygodactylus timetree based on a novel fossil-dated phylotranscriptomic tree of squamates, in which we included data from two newly sequenced Lygodactylus transcriptomes. We estimate the crown diversification of Lygodactylus started at 46 mya, and the dispersal of Lygodactylus among the main landmasses in the Oligocene and Miocene, 35-22 mya, but emphasize the wide confidence intervals of these estimates. The phylogeny suggests an initial out-of-Madagascar dispersal as most parsimonious, but accounting for poorly resolved nodes, an out-of-Africa scenario may only require one extra dispersal step. More accurate inferences into the biogeographic history of these geckos will likely require broader sampling of related genera and phylogenomic approaches to provide better topological support. A survey of morphological characters revealed that most of the major clades and species groups within Lygodactylus cannot be unambiguously characterized by external morphology alone, neither by unique character states nor by a diagnostic combination of character states. Thus, any future taxonomic work will likely benefit from integrative, phylogenomic approaches.

Do male and female heterogamety really differ in expression regulation? Lack of global dosage balance in pygopodid geckos.

Differentiation of sex chromosomes is thought to have evolved with cessation of recombination and subsequent loss of genes from the degenerated partner (Y and W) of sex chromosomes, which in turn leads to imbalance of gene dosage between sexes. Based on work with traditional model species, theory suggests that unequal gene copy numbers lead to the evolution of mechanisms to counter this imbalance. Dosage compensation, or at least achieving dosage balance in expression of sex-linked genes between sexes, has largely been documented in lineages with male heterogamety (XX/XY sex determination), while ZZ/ZW systems are assumed to be usually associated with the lack of chromosome-wide gene dose regulatory mechanisms. Here, we document that although the pygopodid geckos evolved male heterogamety with a degenerated Y chromosome 32-72 Ma, one species in particular, Burton's legless lizard (Lialis burtonis), does not possess dosage balance in the expression of genes in its X-specific region. We summarize studies on gene dose regulatory mechanisms in animals and conclude that there is in them no significant dichotomy between male and female heterogamety. We speculate that gene dose regulatory mechanisms are likely to be related to the general mechanisms of sex determination instead of type of heterogamety. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.

Rampant tooth loss across 200 million years of frog evolution.

Teeth are present in most clades of vertebrates but have been lost completely several times in actinopterygian fishes and amniotes. Using phenotypic data collected from over 500 genera via micro-computed tomography, we provide the first rigorous assessment of the evolutionary history of dentition across all major lineages of amphibians. We demonstrate that dentition is invariably present in caecilians and salamanders, but teeth have been lost completely more than 20 times in frogs, a much higher occurrence of edentulism than in any other vertebrate group. The repeated loss of teeth in anurans is associated with a specialized diet of small invertebrate prey as well as shortening of the lower jaw, but it is not correlated with a reduction in body size. Frogs provide an unparalleled opportunity for investigating the molecular and developmental mechanisms of convergent tooth loss on a large phylogenetic scale.

A new, enigmatic species of black-eyed gecko (Reptilia: Diplodactylidae: Mokopirirakau/) from North Otago, New Zealand.

The New Zealand endemic gecko genus, Mokopirirakau, is notable for its ecology, with some species inhabiting extreme alpine environments, as well as for the large number of geographically circumscribed, species-level lineages awaiting formal description. In, 2018, a population superficially similar in colour and morphology to the black-eyed gecko (M. kahutarae) was discovered in alpine greywacke rock outcrops in the Oteake Conservation Park, North Otago, ~400 km south of the nearest M. kahutarae populations in the upper South Island. Genetic and morphological data indicate that this population is distinct, sister to a clade comprising M. granulatus and M. kahutarae. It can be distinguished from all but one Mokopirirakau species by colour pattern, and from M. kahutarae by smaller adult body size, eye and supraciliary characters, mouth and throat colour, ventral scale row count, tail length, toe shape, and lamellar count. Using an integrated taxonomic approach, we here formally describe this form as a new species, M. galaxias sp. nov., as well as discuss its ecology, likely distribution (particularly with respect to M. kahutarae), and potential conservation issues and requirements. Mokopirirakau galaxias sp. nov. should be considered "Threatened-Nationally Endangered" (qualifiers Data Poor) in the New Zealand Threat Classification System due to the low abundance and restricted known distribution, with potential threats from invasive predatory mammals and climate change. It should be considered Data Deficient in the IUCN Red List system.

A new species of Naultinus from the Te Paki area, northern New Zealand.

We describe a new species of the New Zealand diplodactylid gecko genus Naultinus. Molecular phylogenetics and distinctive morphological features support taxonomic separation of the populations on the northern half of Aupori Peninsula in the far north of the North Island as a new species, Naultinus flavirictus sp. nov. The specific epithet refers to the diagnostic yellow colour at the corners of the mouth. We discuss the conservation status of and threats to this novel taxon and to Te Paki, Northland-the unique area of New Zealand where it is found. We further discuss the distribution and possible function of bright mouth colour within Naultinus.

Sex Chromosome Turnover in Bent-Toed Geckos (Cyrtodactylus).

Lizards and snakes (squamates) are known for their varied sex determining systems, and gecko lizards are especially diverse, having evolved sex chromosomes independently multiple times. While sex chromosomes frequently turnover among gecko genera, intrageneric turnovers are known only from Gekko and Hemidactylus. Here, we used RADseq to identify sex-specific markers in two species of Burmese bent-toed geckos. We uncovered XX/XY sex chromosomes in Cyrtodactylus chaunghanakwaensis and ZZ/ZW sex chromosomes in Cyrtodactylus pharbaungensis. This is the third instance of intrageneric turnover of sex chromosomes in geckos. Additionally, Cyrtodactylus are closely related to another genus with intrageneric turnover, Hemidactylus. Together, these data suggest that sex chromosome turnover may be common in this clade, setting them apart as exceptionally diverse in a group already known for diverse sex determination systems.

Earning your stripes: a second species of striped gecko in the New Zealand gecko genus Toropuku (Gekkota: Diplodactylidae).

The New Zealand diplodactylid gecko genus Toropuku is currently monotypic, but the sole member of the genus, T. stephensi, is distributed in two disjunct, geographically distant regions of New Zealand - the islands of Cook Strait (which includes the type locality, Stephens Island), between New Zealand's North and South Islands, and the Coromandel Peninsula, in the northeastern North Island. Previously published phylogenetic results, based on three total individuals, recognized substantial-possibly species-level-diversity between these disparate localities, although no taxonomic decisions were made at that time. More recently, additional animals have been found on the Coromandel Peninsula. We here present phylogenetic and morphological evidence based on this expanded dataset to formally describe the populations on the Coromandel Peninsula as a new species, Toropuku inexpectatus sp. nov. The specific epithet refers to the species' surprise discovery in a herpetologically well-surveyed area. The recognition of T. inexpectatus sp. nov. as a distinct species has implications for the conservation status of T. stephensi, which is now considered restricted to three islands in Cook Strait.

A new species of Rain Frog (Brevicipitidae, Breviceps) endemic to Angola.

Recent molecular phylogenetic work has found that Breviceps Merrem, 1820 comprises two major clades, one of which, the B. mossambicus group, is widely distributed across southern sub-Saharan Africa. This group is notable for harboring abundant cryptic diversity. Of the four most recently described Breviceps species, three are members of this group, and at least five additional lineages await formal description. Although Breviceps has long been known to occur in Angola, no contemporary material has been collected until recently. The three most widespread taxa, B. adspersus, B. mossambicus, and B. poweri, may all occur in Angola, but accurate species assignment remains challenging given the rampant morphological similarity between these taxa, and, until recently, the lack of genetic resources. Phylogenetic, morphological, and acoustic analyses of recently collected samples from disparate localities within Angola provide evidence for an undescribed species that is sister to B. poweri. The new species can be diagnosed from its sister taxon by lacking pale spots along the flanks, a pale patch above the vent, and a short, dark band below the nares (all present in B. poweri). Additionally, the male advertisement call differs from the three other Breviceps that might occur in Angola in having both a longer interval between consecutive calls and a higher average dominant frequency. We here describe this lineage as a distinct species, currently only known from Angola, and discuss the presence of other Breviceps taxa within Angola.

ResumoInvestigações moleculares recentes revelaram que o género Breviceps Merrem, 1820, é composto por duas linhagens principais, uma das quais, o grupo B. mossambicus, é amplamente distribuído na região sul da África subsaariana. Este grupo é notável por albergar uma abundante diversidade críptica. Das quatro espécies de Breviceps recentemente descritas, três pertencem a este grupo, e pelo menos outras cinco linhagens adicionais aguardam a sua descrição formal. Apesar de o género ser conhecido de Angola desde há muito tempo, só muito recentemente foram colhidos novos espécimes. Os três taxa mais amplamente distribuídos, B. adspersus, B. mossambicus e B. poweri podem todos, porventura, ocorrer em Angola, no entanto a correta identificação destas espécies têm sido problemática devido às semelhanças morfológicas extremas entre este taxa, e, até muito recente, a completa ausência de material genético. Análises filogenéticas, morfológicas e acústicas dos espécimes recentemente colhidos em diferentes locais de Angola apontam para a existência de uma espécie nova para a ciência, irmã de B. poweri. A nova espécie pode ser diferenciada do seu táxon irmão pela falta de marcas pálidas nos flancos, mancha pálida acima do ventre e pequena banda negra abaixo do nariz (presentes em B. poweri). Para além destas características, o chamamento dos machos difere das outras três espécies de Breviceps que podem ocorrer em Angola por ter um maior intervalo entre chamamentos consecutivos e uma maior frequência média dominante. Descrevemos aqui esta linhagem como uma espécie distinta, atualmente apenas conhecida de Angola, e discutimos a presença de outras espécies de Breviceps em Angola.

Conserved ZZ/ZW sex chromosomes in Caribbean croaking geckos (Aristelliger: Sphaerodactylidae).

Current understanding of sex chromosome evolution is largely dependent on species with highly degenerated, heteromorphic sex chromosomes, but by studying species with recently evolved or morphologically indistinct sex chromosomes we can greatly increase our understanding of sex chromosome origins, degeneration and turnover. Here, we examine sex chromosome evolution and stability in the gecko genus Aristelliger. We used RADseq to identify sex-specific markers and show that four Aristelliger species, spanning the phylogenetic breadth of the genus, share a conserved ZZ/ZW system syntenic with avian chromosome 2. These conserved sex chromosomes contrast with many other gecko sex chromosome systems by showing a degree of stability among a group known for its dynamic sex-determining mechanisms. Cytogenetic data from A. expectatus revealed homomorphic sex chromosomes with an accumulation of repetitive elements on the W chromosome. Taken together, the large number of female-specific A. praesignis RAD markers and the accumulation of repetitive DNA on the A. expectatus W karyotype suggest that the Z and W chromosomes are highly differentiated despite their overall morphological similarity. We discuss this paradoxical situation and suggest that it may, in fact, be common in many animal species.

Cross-Species BAC Mapping Highlights Conservation of Chromosome Synteny across Dragon Lizards (Squamata: Agamidae).

Dragon lizards (Squamata: Agamidae) comprise about 520 species in six subfamilies distributed across Asia, Australasia and Africa. Only five species are known to have sex chromosomes. All of them possess ZZ/ZW sex chromosomes, which are microchromosomes in four species from the subfamily Amphibolurinae, but much larger in Phrynocephalus vlangalii from the subfamily Agaminae. In most previous studies of these sex chromosomes, the focus has been on Australian species from the subfamily Amphibolurinae, but only the sex chromosomes of the Australian central bearded dragon (Pogona vitticeps) are well-characterized cytogenetically. To determine the level of synteny of the sex chromosomes of P. vitticeps across agamid subfamilies, we performed cross-species two-colour FISH using two bacterial artificial chromosome (BAC) clones from the pseudo-autosomal regions of P. vitticeps. We mapped these two BACs across representative species from all six subfamilies as well as two species of chameleons, the sister group to agamids. We found that one of these BAC sequences is conserved in macrochromosomes and the other in microchromosomes across the agamid lineages. However, within the Amphibolurinae, there is evidence of multiple chromosomal rearrangements with one of the BACs mapping to the second-largest chromosome pair and to the microchromosomes in multiple species including the sex chromosomes of P. vitticeps. Intriguingly, no hybridization signal was observed in chameleons for either of these BACs, suggesting a likely agamid origin of these sequences. Our study shows lineage-specific evolution of sequences/syntenic blocks and successive rearrangements and reveals a complex history of sequences leading to their association with important biological processes such as the evolution of sex chromosomes and sex determination.

Cryptic diversity among Yazoo Darters (Percidae: Etheostoma raneyi) in disjunct watersheds of northern Mississippi.

The Yazoo Darter, Etheostoma raneyi (Percidae), is an imperiled freshwater fish species endemic to tributaries of the Yocona and Little Tallahatchie rivers of the upper Yazoo River basin, in northern Mississippi, USA. The two populations are allopatric, isolated by unsuitable lowland habitat between the two river drainages. Relevant literature suggests that populations in the Yocona River represent an undescribed species, but a lack of data prevents a thorough evaluation of possible diversity throughout the range of the species. Our goals were to estimate phylogenetic relationships of the Yazoo Darter across its distribution and identify cryptic diversity for conservation management purposes. Maximum likelihood (ML) phylogenetic analyses of the mitochondrial cytochrome b (cytb) gene returned two reciprocally monophyletic clades representing the two river drainages with high support. Bayesian analysis of cytb was consistent with the ML analysis but with low support for the Yocona River clade. Analyses of the nuclear S7 gene yielded unresolved relationships among individuals in the Little Tallahatchie River drainage with mostly low support, but returned a monophyletic clade for individuals from the Yocona River drainage with high support. No haplotypes were shared between the drainages for either gene. Additional cryptic diversity within the two drainages was not indicated. Estimated divergence between Yazoo Darters in the two drainages occurred during the Pleistocene (<1 million years ago) and was likely linked to repeated spatial shifts in suitable habitat and changes in watershed configurations during glacial cycles. Individuals from the Yocona River drainage had lower genetic diversity consistent with the literature. Our results indicate that Yazoo Darters in the Yocona River drainage are genetically distinct and that there is support for recognizing Yazoo Darter populations in the Yocona River drainage as a new species under the unified species concept.

First Report of Sex Chromosomes in Night Lizards (Scincoidea: Xantusiidae).

Squamate reptiles (lizards, snakes, and amphibians) are an outstanding group for studying sex chromosome evolution-they are old, speciose, geographically widespread, and exhibit myriad sex-determining modes. Yet, the vast majority of squamate species lack heteromorphic sex chromosomes. Cataloging the sex chromosome systems of species lacking easily identifiable, heteromorphic sex chromosomes, therefore, is essential before we are to fully understand the evolution of vertebrate sex chromosomes. Here, we use restriction site-associated DNA sequencing (RADseq) to classify the sex chromosome system of the granite night lizard, Xantusia henshawi. RADseq is an effective alternative to traditional cytogenetic methods for determining a species' sex chromosome system (i.e., XX/XY or ZZ/ZW), particularly in taxa with non-differentiated sex chromosomes. Although many xantusiid lineages have been karyotyped, none possess heteromorphic sex chromosomes. We identified a ZZ/ZW sex chromosome system in X. henshawi-the first such data for this family. Furthermore, we report that the X. henshawi sex chromosome contains fragments of genes found on Gallus gallus chromosomes 7, 12, and 18 (which are homologous to Anolis carolinensis chromosome 2), the first vertebrate sex chromosomes to utilize this linkage group.

Escaping the evolutionary trap? Sex chromosome turnover in basilisks and related lizards (Corytophanidae: Squamata).

Most pleurodont lizard families (anoles, iguanas and their relatives), with the exception of the basilisks and casquehead lizards (family Corytophanidae), share homologous XX/XY sex chromosomes, syntenic with chicken chromosome 15. Here, we used a suite of methods (i.e. RADseq, RNAseq and qPCR) to identify corytophanid sex chromosomes for the first time. We reveal that all examined corytophanid species have partially degenerated XX/XY sex chromosomes, syntenic with chicken chromosome 17. Transcriptomic analyses showed that the expression of X-linked genes in the corytophanid, Basiliscus vittatus, is not balanced between the sexes, which is rather exceptional under male heterogamety, and unlike the dosage-balanced sex chromosomes in other well-studied XX/XY systems, including the green anole, Anolis carolinensis. Corytophanid sex chromosomes may represent a rare example of a turnover away from stable, differentiated sex chromosomes. However, because of poor phylogenetic resolution among pleurodont families, we cannot reject the alternative hypothesis that corytophanid sex chromosomes evolved independently from an unknown ancestral system.

Transcriptomic data support a nocturnal bottleneck in the ancestor of gecko lizards.

Gecko lizards are a species-rich clade of primarily-nocturnal squamate reptiles. In geckos, adaptations to nocturnality have dramatically reshaped the eye. Perhaps the most notable change is the loss of rod cells in the retina and subsequent "transmutation" of cones into a rod-like morphology and physiology. While many studies have noted the absence of some rod-specific genes, such as the visual pigment Rhodopsin (RH1), these studies have focused on just a handful of species that are nested deep in the gecko phylogeny. Thus, it is not clear whether these changes arose through convergence, are homologous and ubiquitous across geckos, or restricted to a subset of species. Here, we used de novo eye transcriptomes from five gecko species, and genomes from two additional gecko species, representing the breadth of extant gecko diversity (i.e. 4 of the 7 gecko families, spanning the deepest divergence of crown Gekkota), to show that geckos lost expression of almost the entire suite of necessary rod-cell phototransduction genes in the eye, distinct from all other squamate reptiles. Geckos are the first vertebrate group to have lost their complete rod-cell expression pathway, not just the visual pigment. In addition, all sampled species have also lost expression of the cone-opsin SWS2 visual pigment. These results strongly suggest a single loss of rod cells and subsequent cone-to-rod transmutation that occurred prior to the diversification of extant geckos.