Are Geckos Special in Sex Determination? Independently Evolved Differentiated ZZ/ZW Sex Chromosomes in Carphodactylid Geckos

Pivotal temperature is not for everyone: Evidence for temperature-dependent sex determination in three gecko species

The prevalence of environmental sex determination (ESD) in squamate reptiles is often overestimated in the literature. This is surprising because we have reliable data demonstrating ESD in only a few species. The documentation of ESD in three species of geckos presented here has significantly increased our knowledge, given that satisfactory evidence for ESD existed in only eight other gecko species. For the first time, we document the occurrence of ESD in the family Sphaerodactylidae. Our finding of unexpected variability in the shapes of reaction norms among geckos highlights that traditional descriptions using parameters such as pivotal temperature, that is, temperature producing a 50:50 sex ratio, are unsatisfactory. For example, the gecko Pachydactylus tigrinus lacks any pivotal temperature and its sex ratios are strongly female-biased across the entire range of viable temperatures. We argue for the effective capture of the relationship between temperature and sex ratio using specific nonlinear models rather than using classical simplistic descriptions and classifications of reaction norms.

Differentiated sex chromosomes, karyotype evolution, and spontaneous triploidy in carphodactylid geckos

Geckos exhibit derived karyotypes without a clear distinction between macrochromosomes and microchromosomes and intriguing diversity in sex determination mechanisms. We conducted cytogenetic analyses in six species from the genera Nephrurus, Phyllurus, and Saltuarius of the gecko family Carphodactylidae. We confirmed the presence of a female heterogametic system with markedly differentiated and heteromorphic sex chromosomes in all examined species, typically with the W chromosome notably larger than the Z chromosome. One species, Nephrurus cinctus, possesses unusual multiple Z1Z1Z2Z2/Z1Z2W sex chromosomes. The morphology of the sex chromosomes, along with repetitive DNA content, suggests that the differentiation or emergence of sex chromosomes occurred independently in the genus Phyllurus. Furthermore, our study unveils a case of spontaneous triploidy in a fully grown individual of Saltuarius cornutus (3n = 57) and explores its implications for reproduction in carphodactylid geckos. We revealed that most carphodactylids retain the putative ancestral gekkotan karyotype of 2n = 38, characterized by predominantly acrocentric chromosomes that gradually decrease in size. If present, biarmed chromosomes emerge through pericentric inversions, maintaining the chromosome (and centromere) numbers. However, Phyllurus platurus is a notable exception, with a karyotype of 2n = 22 chromosomes. Its eight pairs of biarmed chromosomes were probably formed by Robertsonian fusions of acrocentric chromosomes. The family underscores a remarkable instance of evolutionary stability in chromosome numbers, followed by a profound transformation through parallel interchromosomal rearrangements. Our study highlights the need to continue generating cytogenetic data in order to test long-standing ideas about reproductive biology and the evolution of genome and sex determination.

Environmental (and Random?) Sex Determination in Endangered and Invasive Phelsuma Geckos

INTRODUCTION

Sex is a fundamental characteristic of an individual. It is therefore puzzling why in some systems sex is precisely determined by a genotype, while in others it is influenced by the environment or even subtle, not to say random, factors. Some stochasticity in sex determination would be expected if environmental conditions did not have a large sex-specific effect on fitness. Although data are only available for a small fraction of species, geckos show exceptional variability in sex determination.

METHODS

We tested the effects of three incubation temperatures on sex ratio and adult body size in the invasive gecko Phelsuma laticauda and the vulnerable gecko Phelsuma nigristriata.

RESULTS

We document temperature-dependent sex determination (TSD) in both species. Only females hatched at a low temperature (24°C), whereas male production peaked at an intermediate temperature (28°C) and declined, at least in P. laticauda, again at the highest temperature (31°C). Interestingly, full siblings hatched from eggs glued together during the incubation at temperatures producing both sexes are often of the opposite sex. We found no significant effect of incubation temperature on adult body length.

CONCLUSIONS

Documentation of TSD in the day geckos has implications for conservation practice in environmental management of endangered species or eradication of invasive species. However, it appears that a very subtle (random?) factor may also be involved in their sex determination. In line with this, we found no significant effect of incubation temperature on adult body length.

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.

Heteromorphic ZZ/ZW sex chromosomes sharing gene content with mammalian XX/XY are conserved in Madagascan chameleons of the genus Furcifer

Chameleons are well-known lizards with unique morphology and physiology, but their sex determination has remained poorly studied. Madagascan chameleons of the genus Furcifer have cytogenetically distinct Z and W sex chromosomes and occasionally Z1Z1Z2Z2/Z1Z2W multiple neo-sex chromosomes. To identify the gene content of their sex chromosomes, we microdissected and sequenced the sex chromosomes of F. oustaleti (ZZ/ZW) and F. pardalis (Z1Z1Z2Z2/Z1Z2W). In addition, we sequenced the genomes of a male and a female of F. lateralis (ZZ/ZW) and F. pardalis and performed a comparative coverage analysis between the sexes. Despite the notable heteromorphy and distinctiveness in heterochromatin content, the Z and W sex chromosomes share approximately 90% of their gene content. This finding demonstrates poor correlation of the degree of differentiation of sex chromosomes at the cytogenetic and gene level. The test of homology based on the comparison of gene copy number variation revealed that female heterogamety with differentiated sex chromosomes remained stable in the genus Furcifer for at least 20 million years. These chameleons co-opted for the role of sex chromosomes the same genomic region as viviparous mammals, lacertids and geckos of the genus Paroedura, which makes these groups excellent model for studies of convergent and divergent evolution of sex chromosomes.

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.

Chromosome evolution in Iberolacerta, a genus that deviates from the standard karyotype formula of Lacertidae

This paper describes the preparation of flow-sorted chromosome paints from the Iberian Rock lizard Iberolacerta monticola, exemplifying their subsequent use in cross-species comparisons of chromosome painting. We carried out comparative analyses of chromosome evolution in the congeneric species I. galani and I. bonnali, as well as in two other species of Lacertini (Lacerta schreiberi and Timon lepidus) whose sex chromosomes were also studied through comparative genomic hybridization. Most species of Lacertini possess a diplod number of 2n = 38, with 36 acrocentric macrochromosomes and 2 microchromosomes. However, the nine species included in the genus Iberolacerta do not possess microchromosomes. Furthermore, very conspicuous differences from the standard Lacertini karyotype were observed in the three Pyrenean species of this genus, which included several biarmed metacentrics and a Z1Z2W multiple sex-chromosome system. With the possible exception of L. schreiberi, all the species of the family Lacertidae described to date appear to share homologous Z chromosomes, which date back to the last common ancestor of the whole group. We provide conclusive evidence that L. schreiberi should no longer be considered an exception to this rule, and demonstrate that the loss of microchromosomes in Iberolacerta was produced by their fusion to a middle-sized chromosome. Furthermore, we show that the multiple sex-chromosome system of the Pyrenean species of Iberolacerta originated from the fusion of the ancestral W chromosome with one of the shortest autosomes, and provide additional evidence of the fast evolution of DNA sequences linked to the W chromosome in Lacertini.

Robertsonian fusion triggers recombination suppression on sex chromosomes in Coleonyx geckos

The classical hypothesis proposes that the lack of recombination on sex chromosomes arises due to selection for linkage between a sex-determining locus and sexually antagonistic loci, primarily facilitated by inversions. However, cessation of recombination on sex chromosomes could be attributed also to neutral processes, connected with other chromosome rearrangements or can reflect sex-specific recombination patterns existing already before sex chromosome differentiation. Three Coleonyx gecko species share a complex X1X1X2X2/X1X2Y system of sex chromosomes evolved via a fusion of the Y chromosome with an autosome. We analyzed synaptonemal complexes and sequenced flow-sorted sex chromosomes to investigate the effect of chromosomal rearrangement on recombination and differentiation of these sex chromosomes. The gecko sex chromosomes evolved from syntenic regions that were also co-opted also for sex chromosomes in other reptiles. We showed that in male geckos, recombination is less prevalent in the proximal regions of chromosomes and is even further drastically reduced around the centromere of the neo-Y chromosome. We highlight that pre-existing recombination patterns and Robertsonian fusions can be responsible for the cessation of recombination on sex chromosomes and that such processes can be largely neutral.

Cytogenetic Analysis of Seven Species of Gekkonid and Phyllodactylid Geckos

Geckos (Gekkota), the species-rich clade of reptiles with more than 2200 currently recognized species, demonstrate a remarkable variability in diploid chromosome numbers (2n = 16-48) and mode of sex determination. However, only a small fraction of gekkotan species have been studied with cytogenetic methods. Here, we applied both conventional (karyotype reconstruction and C-banding) and molecular (fluorescence in situ hybridization with probes for rDNA loci and telomeric repeats) cytogenetic analyses in seven species of geckos, namely Blaesodactylus boivini, Chondrodactylus laevigatus, Gekko badenii, Gekko cf. lionotum, Hemidactylus sahgali, Homopholis wahlbergii (Gekkonidae) and Ptyodactylus togoensis (Phyllodactylidae), in order to provide further insights into the evolution of karyotypes in geckos. Our analysis revealed the presence of interstitial telomeric repeats in four species, but we were not able to conclude if they are remnants of previous chromosome rearrangements or were formed by an accumulation of telomeric-like satellite motifs. Even though sex chromosomes were previously identified in several species from the genera Hemidactylus and Gekko by cytogenetic and/or genomic methods, they were not detected by us in any examined species. Our examined species either have poorly differentiated sex chromosomes or, possibly, environmental sex determination. Future studies should explore the effect of temperature and conduct genome-wide analyses in order to identify the mode of sex determination in these species.

Madagascar Leaf-Tail Geckos (Uroplatus spp.) Share Independently Evolved Differentiated ZZ/ZW Sex Chromosomes

Geckos are an excellent group to study the evolution of sex determination, as they possess a remarkable variability ranging from a complete absence of sex chromosomes to highly differentiated sex chromosomes. We explored sex determination in the Madagascar leaf-tail geckos of the genus Uroplatus. The cytogenetic analyses revealed highly heterochromatic W chromosomes in all three examined species (Uroplatus henkeli, U. alluaudi, U. sikorae). The comparative gene coverage analysis between sexes in U. henkeli uncovered an extensive Z-specific region, with a gene content shared with the chicken chromosomes 8, 20, 26 and 28. The genomic region homologous to chicken chromosome 28 has been independently co-opted for the role of sex chromosomes in several vertebrate lineages, including monitors, beaded lizards and monotremes, perhaps because it contains the amh gene, whose homologs were repeatedly recruited as a sex-determining locus. We demonstrate that all tested species of leaf-tail geckos share homologous sex chromosomes despite the differences in shape and size of their W chromosomes, which are not homologous to the sex chromosomes of other closely related genera. The rather old (at least 40 million years), highly differentiated sex chromosomes of Uroplatus geckos can serve as a great system to study the convergence of sex chromosomes evolved from the same genomic region.

ZZ/ZW Sex Chromosomes in the Madagascar Girdled Lizard, Zonosaurus madagascariensis (Squamata: Gerrhosauridae)

Scincoidea, the reptilian clade that includes girdled lizards, night lizards, plated lizards and skinks, are considered as a lineage with diversity in sex-determining systems. Recently, the hypothesis on the variability in sex determination in skinks and even more the absence of sex chromosomes in some of them has been rivalling. Homologous, evolutionary stable XX/XY sex chromosomes were documented to be widespread across skinks. However, sex determination in the other scincoidean families is highly understudied. ZZ/ZW sex chromosomes have been identified only in night lizards and a single species of plated lizards. It seems that although there are different sex chromosome systems among scincoidean lineages, they share one common trait: they are mostly poorly differentiated and often undetectable by cytogenetic methods. Here, we report one of the exceptions, demonstrating for the first time ZZ/ZW sex chromosomes in the plated lizard Zonosaurus madagascariensis. Its sex chromosomes are morphologically similar, but the W is clearly detectable by comparative genomic hybridization (CGH), suggesting that the Z and W chromosomes highly differ in sequence content. Our findings confirm the presence of female heterogamety in plated lizards and provides novel insights to expand our understanding of sex chromosome evolution in scincoidean lizards.

Identification of a cis-sex chromosome transition in banded geckos (Coleonyx, Eublepharidae, Gekkota)

Sex-determination systems are highly variable amongst vertebrate groups, and the prevalence of genomic data has greatly expanded our knowledge of how diverse some groups truly are. Gecko lizards are known to possess a variety of sex-determination systems, and each new study increases our knowledge of this diversity. Here, we used RADseq to identify male-specific markers in the banded gecko Coleonyx brevis, indicating this species has a XX/XY sex-determination system. Furthermore, we show that these sex-linked regions are not homologous to the XX/XY sex chromosomes of two related Coleonyx species, C. elegans and C. mitratus, suggesting that a cis-sex chromosome turnover-a change in sex chromosomes without a concomitant change in heterogamety-has occurred within the genus. These findings demonstrate the utility of genome-scale data to uncover novel sex chromosomes and further highlight the diversity of gecko sex chromosomes.

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.

Sex Chromosomes and Master Sex-Determining Genes in Turtles and Other Reptiles

Among tetrapods, the well differentiated heteromorphic sex chromosomes of birds and mammals have been highly investigated and their master sex-determining (MSD) gene, Dmrt1 and SRY, respectively, have been identified. The homomorphic sex chromosomes of reptiles have been the least studied, but the gap with birds and mammals has begun to fill. This review describes our current knowledge of reptilian sex chromosomes at the cytogenetic and molecular level. Most of it arose recently from various studies comparing male to female gene content. This includes restriction site-associated DNA sequencing (RAD-Seq) experiments in several male and female samples, RNA sequencing and identification of Z- or X-linked genes by male/female comparative transcriptome coverage, and male/female transcriptomic or transcriptome/genome substraction approaches allowing the identification of Y- or W-linked transcripts. A few putative master sex-determining (MSD) genes have been proposed, but none has been demonstrated yet. Lastly, future directions in the field of reptilian sex chromosomes and their MSD gene studies are considered.

Remnant of Unrelated Amniote Sex Chromosomal Linkage Sharing on the Same Chromosome in House Gecko Lizards, Providing a Better Understanding of the Ancestral Super-Sex Chromosome

Comparative chromosome maps investigating sex chromosomal linkage groups in amniotes and microsatellite repeat motifs of a male house gecko lizard (Hemidactylus frenatus, HFR) and a flat-tailed house gecko lizard (H. platyurus, HPL) of unknown sex were examined using 75 bacterial artificial chromosomes (BACs) from chicken and zebra finch genomes. No massive accumulations of microsatellite repeat motifs were found in either of the gecko lizards, but 10 out of 13 BACs mapped on HPL chromosomes were associated with other amniote sex chromosomes. Hybridization of the same BACs onto multiple different chromosome pairs suggested transitions to sex chromosomes across amniotes. No BAC hybridization signals were found on HFR chromosomes. However, HFR diverged from HPL about 30 million years ago, possibly due to intrachromosomal rearrangements occurring in the HFR lineage. By contrast, heterochromatin likely reshuffled patterns between HPL and HFR, as observed from C-positive heterochromatin distribution. Six out of ten BACs showed partial homology with squamate reptile chromosome 2 (SR2) and snake Z and/or W sex chromosomes. The gecko lizard showed shared unrelated sex chromosomal linkages-the remnants of a super-sex chromosome. A large ancestral super-sex chromosome showed a correlation between SR2 and snake W sex chromosomes.

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)'.

Lizards as Model Organisms of Sex Chromosome Evolution: What We Really Know from a Systematic Distribution of Available Data?

Lizards represent unique model organisms in the study of sex determination and sex chromosome evolution. Among tetrapods, they are characterized by an unparalleled diversity of sex determination systems, including temperature-dependent sex determination (TSD) and genetic sex determination (GSD) under either male or female heterogamety. Sex chromosome systems are also extremely variable in lizards. They include simple (XY and ZW) and multiple (X1X2Y and Z1Z2W) sex chromosome systems and encompass all the different hypothesized stages of diversification of heterogametic chromosomes, from homomorphic to heteromorphic and completely heterochromatic sex chromosomes. The co-occurrence of TSD, GSD and different sex chromosome systems also characterizes different lizard taxa, which represent ideal models to study the emergence and the evolutionary drivers of sex reversal and sex chromosome turnover. In this review, we present a synthesis of general genome and karyotype features of non-snakes squamates and discuss the main theories and evidences on the evolution and diversification of their different sex determination and sex chromosome systems. We here provide a systematic assessment of the available data on lizard sex chromosome systems and an overview of the main cytogenetic and molecular methods used for their identification, using a qualitative and quantitative approach.