Developmental Patterns Underlying Variation in Form And Function Exhibited by House Gecko Toe Pads

Adhesive toe pads have evolved numerous times over lizard evolutionary history, most notably in geckos. Despite significant variation in adult toe pad morphology across independent origins of toe pads, early developmental patterns of toe pad morphogenesis are similar among distantly related species. In these distant phylogenetic comparisons, toe pad variation is achieved during the later stages of development. We aimed to understand how toe pad variation is generated among species sharing a single evolutionary origin of toe pads (house geckos-Hemidactylus). We investigated toe pad functional variation and developmental patterns in three species of Hemidactylus, ranging from highly scansorial (H. platyurus), to less scansorial (H. turcicus), to fully terrestrial (H. imbricatus). We found that H. platyurus generated significantly greater frictional adhesive force and exhibited much larger toe pad area relative to the other two species. Furthermore, differences in the offset of toe pad extension phase during embryonic development results in the variable morphologies seen in adults. Taken together, we demonstrate how morphological variation is generated in a complex structure during development and how that variation relates in important functional outcomes.

Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles

Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniotic vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; ~11,000 extant species of lizards and snakes) show as much variation in TE abundance and activity as they do in species and phenotypes. Despite this high TE activity, squamate genomes are remarkably uniform in size. We hypothesize that novel, lineage-specific dynamics have evolved over the course of squamate evolution to constrain genome size across the order. Thus, squamates may represent a prime model for investigations into TE diversity and evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the CR1 retrotransposon, a TE family found in most tetrapod genomes. We compared 113 squamate genomes to the genomes of turtles, crocodilians, and birds, and used ancestral state reconstruction to identify shifts in the rate of CR1 copy number evolution across reptiles. We analyzed the repeat landscapes of CR1 in squamate genomes and determined that shifts in the rate of CR1 copy number evolution are associated with lineage-specific variation in CR1 activity. We then used phylogenetic reconstruction of CR1 subfamilies across amniotes to reveal both recent and ancient CR1 subclades across the squamate tree of life. The patterns of CR1 evolution in squamates contrast other amniotes, suggesting key differences in how TEs interact with different host genomes and at different points across evolutionary history.

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.

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.

The revised reference genome of the leopard gecko (Eublepharis macularius) provides insight into the considerations of genome phasing and assembly

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.

A lizard is never late: Squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution

In 2011, the first high-quality genome assembly of a squamate reptile (lizard or snake) was published for the green anole. Dozens of genome assemblies were subsequently published over the next decade, yet these assemblies were largely inadequate for answering fundamental questions regarding genome evolution in squamates due to their lack of contiguity or annotation. As the "genomics age" was beginning to hit its stride in many organismal study systems, progress in squamates was largely stagnant following the publication of the green anole genome. In fact, zero high-quality (chromosome-level) squamate genomes were published between the years 2012 and 2017. However, since 2018, an exponential increase in high-quality genome assemblies has materialized with 24 additional high-quality genomes published for species across the squamate tree of life. As the field of squamate genomics is rapidly evolving, we provide a systematic review from an evolutionary genomics perspective. We collated a near-complete list of publicly available squamate genome assemblies from more than half-a-dozen international and third-party repositories and systematically evaluated them with regard to their overall quality, phylogenetic breadth, and usefulness for continuing to provide accurate and efficient insights into genome evolution across squamate reptiles. This review both highlights and catalogs the currently available genomic resources in squamates and their ability to address broader questions in vertebrates, specifically sex chromosome and microchromosome evolution, while addressing why squamates may have received less historical focus and has caused their progress in genomics to lag behind peer taxa.

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 lizard is never late: squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution

In 2011, the first high-quality genome assembly of a squamate reptile (lizard or snake) was published for the green anole. Dozens of genome assemblies were subsequently published over the next decade, yet these assemblies were largely inadequate for answering fundamental questions regarding genome evolution in squamates due to their lack of contiguity or annotation. As the "genomics age" was beginning to hit its stride in many organismal study systems, progress in squamates was largely stagnant following the publication of the green anole genome. In fact, zero high-quality (chromosome-level) squamate genomes were published between the years 2012-2017. However, since 2018, an exponential increase in high-quality genome assemblies has materialized with 24 additional high-quality genomes published for species across the squamate tree of life. As the field of squamate genomics is rapidly evolving, we provide a systematic review from an evolutionary genomics perspective. We collated a near-complete list of publicly available squamate genome assemblies from more than half-a-dozen international and third-party repositories and systematically evaluated them with regard to their overall quality, phylogenetic breadth, and usefulness for continuing to provide accurate and efficient insights into genome evolution across squamate reptiles. This review both highlights and catalogs the currently available genomic resources in squamates and their ability to address broader questions in vertebrates, specifically sex chromosome and microchromosome evolution, while addressing why squamates may have received less historical focus and has caused their progress in genomics to lag behind peer taxa.

The revised reference genome of the leopard gecko ( Eublepharis macularius ) provides insight into the considerations of genome phasing and assembly

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 that 9 of the 19 chromosomes were assembled as single contigs, while the other 10 chromosomes were each scaffolded together from two or more contigs. We qualitatively identified that 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 previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000. The genome version and its associated annotations are also available via this Figshare repository https://doi.org/10.6084/m9.figshare.20069273 .

Ontogeny of the paraphalanges and derived phalanges of Hemidactylus turcicus (Squamata: Gekkonidae)

Gekkotan lizards of the genus Hemidactylus exhibit 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 of Hemidactylus. 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 of Hemidactylus are the products of paedomorphosis. Furthermore, we found divergent developmental patterns between convergently evolved paraphalanges.

3D Visualization Processes for Recreating and Studying Organismal Form

The study of biological form is a vital goal of evolutionary biology and functional morphology. We review an emerging set of methods that allow scientists to create and study accurate 3D models of living organisms and animate those models for biomechanical and fluid dynamic analyses. The methods for creating such models include 3D photogrammetry, laser and CT scanning, and 3D software. New multi-camera devices can be used to create accurate 3D models of living animals in the wild and captivity. New websites and virtual reality/augmented reality devices now enable the visualization and sharing of these data. We provide examples of these approaches for animals ranging from large whales to lizards and show applications for several areas: Natural history collections; body condition/scaling, bioinspired robotics, computational fluids dynamics (CFD), machine learning, and education. We provide two datasets to demonstrate the efficacy of CFD and machine learning approaches and conclude with a prospectus.

Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC

DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6  ×  6  ×  6 m 3 liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019-2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7 m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties.

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-specific aging in animals: Perspective and future directions

Sex differences in aging occur in many animal species, and they include sex differences in lifespan, in the onset and progression of age-associated decline, and in physiological and molecular markers of aging. Sex differences in aging vary greatly across the animal kingdom. For example, there are species with longer-lived females, species where males live longer, and species lacking sex differences in lifespan. The underlying causes of sex differences in aging remain mostly unknown. Currently, we do not understand the molecular drivers of sex differences in aging, or whether they are related to the accepted hallmarks or pillars of aging or linked to other well-characterized processes. In particular, understanding the role of sex-determination mechanisms and sex differences in aging is relatively understudied. Here, we take a comparative, interdisciplinary approach to explore various hypotheses about how sex differences in aging arise. We discuss genomic, morphological, and environmental differences between the sexes and how these relate to sex differences in aging. Finally, we present some suggestions for future research in this area and provide recommendations for promising experimental designs.

The evolutionary history of an accidental model organism, the leopard gecko Eublepharis macularius (Squamata: Eublepharidae)

The leopard gecko, Eublepharis macularius, is a widely used model organism in laboratory and experimental studies. The high phenotypic diversity in the pet trade, the fact that the provenance of different breeding lines is unknown, and that distinct Eublepharis species are known to hybridize, implies that the continued use of E. macularius as a model requires clarity on the origin of the lineages in the pet trade. We combine multi-locus sequence data and the first range-wide sampling of the genus Eublepharis to reconstruct the evolutionary history of the Eublepharidae and Eublepharis, with an updated time-tree for the Eublepharidae. Our sampling includes five of the six recognized species and additional nominal taxa of uncertain status comprising 43 samples from 34 localities plus 48 pet-trade samples. The Eublepharidae began diversifying in the Cretaceous. Eublepharis split from its sister genera in Africa in the Palaeocene-Eocene, and began diversifying in the Oligocene-Miocene, with late Miocene-Pliocene cladogenesis giving rise to extant species. The current species diversity within this group is moderately underestimated. Our species delimitation suggests 10 species with four potentially unnamed divergent lineages in Iran, India and Pakistan. All 30 individuals of E. macularius that we sampled from the pet trade, which include diverse morphotypes, come from a few shallow E. macularius clades, confirming that lab and pet trade strains are part of a single taxon. One of the wild-caught haplotypes of E. macularius, from near Karachi, Pakistan, is identical to (10) pet-trade samples and all other captive populations are closely related to wild-caught animals from central/southern Pakistan (0.1-0.5 % minimum pairwise uncorrected ND2 sequence divergence).

Convergent developmental patterns underlie the repeated evolution of adhesive toe pads among lizards

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.

Diversity of reptile sex chromosome evolution revealed by cytogenetic and linked-read sequencing

Reptile sex determination is attracting much attention because the great diversity of sex-determination and dosage compensation mechanisms permits us to approach fundamental questions about mechanisms of sex chromosome turnover. Recent studies have made significant progress in better understanding diversity and conservation of reptile sex chromosomes, with however no reptile master sex determination genes identified. Here we describe an integrated genomics and cytogenetics pipeline, combining probes generated from the microdissected sex chromosomes with transcriptome and genome sequencing to explore the sex chromosome diversity in non-model Australian reptiles. We tested our pipeline on a turtle, two species of geckos, and a monitor lizard. Genes identified on sex chromosomes were compared to the chicken genome to identify homologous regions among the four species. We identified candidate sex determining genes within these regions, including conserved vertebrate sex-determining genes pdgfa, pdgfraamh and wt1, and demonstrated their testis or ovary-specific expression. All four species showed gene-by-gene rather than chromosome-wide dosage compensation. Our results imply that reptile sex chromosomes originated by independent acquisition of sex-determining genes on different autosomes, as well as translocations between different ancestral macro- and microchromosomes. We discuss the evolutionary drivers of the slow differentiation and turnover of reptile sex chromosomes.

Comparative riverscape genomics of the rainbow darter (Etheostoma caeruleum) in glaciated and unglaciated environments

Periodic glaciation during the Quaternary period shaped the contemporary riverscape and distribution of freshwater fishes in the Mississippi River drainage of central North America. The rainbow darter (Etheostoma caeruleum) is a member of this ichthyofauna and has a disjunct distribution in glaciated and unglaciated environments west of the Mississippi River. Based on glacial history of the region, there are different expectations on the observed spatial genetic structure of populations in these environments. The aim of this study was to utilize genome-wide SNP data to compare the population genomic structure of the rainbow darter in river networks with disparate glacial histories; the Volga River in the glaciated upper Mississippi River basin and the Meramec River in the unglaciated Ozark Plateau. Individuals were sampled from localities within each river system at distances dictated by the organismal life history and habitat preferences. Riverscape analyses were performed on three datasets: total combined localities of both rivers and one for each river independently. The results revealed a lasting influence of historic glaciation on the population genomic structure of rainbow darter populations. There was evidence of population expansion into the glaciated northern region following glacial retreat. The population genetic signature within the Volga River did not fit expectations of the stream hierarchy model, but revealed a pattern of repeated colonization and extirpation due to cyclic glaciation. The population within the unglaciated Meramec River adhered to the stream hierarchy model, with a directional order of genetic diversity based on the life history and habitat preferences of the species. These results demonstrate the importance of considering the geologic and climatic history of a region as well as the life history of an organism when interpreting spatial genetic patterns.

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)'.

Sex chromosome evolution among amniotes: is the origin of sex chromosomes non-random?

Sex chromosomes are a great example of a convergent evolution at the genomic level, having evolved dozens of times just within amniotes. An intriguing question is whether this repeated evolution was random, or whether some ancestral syntenic blocks have significantly higher chance to be co-opted for the role of sex chromosomes owing to their gene content related to gonad development. Here, we summarize current knowledge on the evolutionary history of sex determination and sex chromosomes in amniotes and evaluate the hypothesis of non-random emergence of sex chromosomes. The current data on the origin of sex chromosomes in amniotes suggest that their evolution is indeed non-random. However, this non-random pattern is not very strong, and many syntenic blocks representing putatively independently evolved sex chromosomes are unique. Still, repeatedly co-opted chromosomes are an excellent model system, as independent co-option of the same genomic region for the role of sex chromosome offers a great opportunity for testing evolutionary scenarios on the sex chromosome evolution under the explicit control for the genomic background and gene identity. Future studies should use these systems more to explore the convergent/divergent evolution of sex chromosomes. 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)'.

A brief review of vertebrate sex evolution with a pledge for integrative research: towards 'sexomics'

Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue a sexomics integrative research initiative across vertebrates. The vertebrate sexome comprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. The sexome also includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of the sexomes of many key vertebrate species. 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 I)'.

And thereby hangs a tail: morphology, developmental patterns and biomechanics of the adhesive tails of crested geckos (Correlophus ciliatus)

Among the most specialized integumentary outgrowths in amniotes are the adhesive, scale-like scansors and lamellae on the digits of anoles and geckos. Less well-known are adhesive tail pads exhibited by 21 gecko genera. While described over 120 years ago, no studies have quantified their possible adhesive function or described their embryonic development. Here, we characterize adult and embryonic morphology and adhesive performance of crested gecko (Correlophus ciliatus) tail pads. Additionally, we use embryonic data to test whether tail pads are serial homologues to toe pads. External morphology and histology of C. ciliatus tail pads are largely similar to tail pads of closely related geckos. Functionally, C. ciliatus tail pads exhibit impressive adhesive ability, hypothetically capable of holding up to five times their own mass. Tail pads develop at approximately the same time during embryogenesis as toe pads. Further, tail pads exhibit similar developmental patterns to toe pads, which are markedly different from non-adhesive gecko toes and tails. Our data provide support for the serial homology of adhesive tail pads with toe pads.

A chromosome-level genome assembly of the parasitoid wasp, Cotesia glomerata (Hymenoptera: Braconidae)

Hymenopterans make up about 20% of all animal species, but most are poorly known and lack high-quality genomic resources. One group of important, yet under-studied hymenopterans, are parasitoid wasps in the family Braconidae. Among this under-studied group are braconid wasps in the genus Cotesia; a clade of ~1,000 species routinely used in studies of physiology, ecology, biological control, and genetics. However, our ability to understand these organisms has been hindered by a lack of genomic resources. We helped bridge this gap by generating a high-quality genome assembly for the parasitoid wasp, Cotesia glomerata (Braconidae; Microgastrinae). We generated this assembly using multiple sequencing technologies, including Oxford Nanopore, whole-genome shotgun sequencing, and 3-D chromatin contact information (Hi-C). Our assembly is one of the most contiguous, complete, and publicly available hymenopteran genomes, represented by 3,355 scaffolds with a scaffold N50 of ~28Mb and a BUSCO score of ~99%. Given the genome sizes found in closely related species, our genome assembly was ~50% larger than expected, which was apparently induced by runaway amplification of three types of repetitive elements: simple repeats, Long Terminal Repeats (LTRs), and Long Interspersed Nuclear Elements (LINEs). This assembly is another step forward for genomics across this hyper-diverse, yet understudied, order of insects. The assembled genomic data and metadata files are publicly available via Figshare (https://doi.org/10.6084/m9.figshare.13010549).

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment: DUNE Collaboration

The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE's sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.

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.

Distinct patterns of pigment development underlie convergent hyperpigmentation between nocturnal and diurnal geckos (Squamata: Gekkota)

BACKGROUND

Evolutionary transitions in temporal niche necessitates specialized morphology, physiology, and behaviors. Diurnal, heliothermic squamates (lizards and snakes) that bask require protection from ultraviolet radiation (UV) that can damage internal organs such as the brain, viscera, and gonads. Many smaller squamates have accomplished this protection by hyperpigmentation of the peritoneum and subcutaneous dorsum. Typically, nocturnal species do not require these protections from ultraviolet light. However, some nocturnal species that exhibit extreme crypsis may be exposed to sunlight and UV and require some means of mediating that damage. One such species is Gekko (Ptychozoon) kuhli, a nocturnal, arboreal gecko that uses extreme crypsis to blend in with tree bark. Hiding motionless on tree trunks leaves geckos exposed to sunlight during the day. Thus, we predict that G. kuhli will have independently evolved a hyperpigmented phenotype. To investigate this hypothesized association between temporal niche, behavior, and morphology, we characterized adult subcutaneous pigment for eight gecko species and embryonic pigment accumulation for a subset of four of these species, exhibiting diverse temporal niche and thermoregulatory behaviors. We predicted that nocturnal/potentially-heliothermic G. kuhli would exhibit hyperpigmentation of internal structures like that of diurnal/heliothermic geckos. We further predicted that embryonic pigment accumulation of G. kuhli would resemble that of diurnal/heliothermic as opposed to nocturnal/thigmothermic geckos.

RESULTS

We found that temporal niche and thermoregulatory behavior predicted the degree of subcutaneous pigment in the eight gecko species examined. We demonstrate that G. kuhli accumulates pigment extremely early in embryonic development, unlike a diurnal/heliothermic gecko species, despite having a similar adult phenotype.

CONCLUSIONS

The evolution of hyperpigmentation in G. kuhli is likely an adaptation to limit damage from occasional daytime UV exposure caused by crypsis-associated basking behavior. Gekko kuhli achieves its hyperpigmented phenotype through a derived developmental pattern, not seen in any other lizard species investigated to date, suggesting novel temporal differences in the migration and/or differentiation of reptilian neural crest derivatives.

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (>1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC data set to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of 10 snakes and 7 lizards. The RELEC data set (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.

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.

Ecological, behavioral, and phylogenetic influences on the evolution of dorsal color pattern in geckos

The dorsal surfaces of many taxonomic groups often feature repetitive pattern elements consisting of stripes, spots, or bands. Here, we investigate how distinct categories of camouflage pattern work by relating them to ecological and behavioral traits in 439 species of gecko. We use phylogenetic comparative methods to test outstanding hypotheses based on camouflage theory and research in other taxa. We found that bands are associated with nocturnal activity, suggesting bands provide effective camouflage for motionless geckos resting in refugia during the day. A predicted association between stripes and diurnal activity was not supported, suggesting that stripes do not work via dazzle camouflage mechanisms in geckos. This, along with a lack of support for our prediction that plain patterning should be associated with open habitats, suggests that similar camouflage patterns do not work in consistent ways across taxa. We also found that plain and striped lineages frequently switched between using open or closed habitats, whereas spotted lineages rarely transitioned. This suggests that pattern categories differ in how specialized or generalized their camouflage is. This result has ramifications for theory on how camouflage compromises to background heterogeneity and how camouflage pattern might influence evolutionary trajectories.

The sprightly little sphaerodactyl: Systematics and biogeography of <br />the Puerto Rican dwarf geckos Sphaerodactylus (Gekkota, Sphaerodactylidae)

Studies of the Caribbean herpetofauna (amphibians and reptiles) have made significant contributions to our knowledge of evolutionary patterns and processes. A prerequisite for these studies are accurate taxonomies and robust phylogenetic hypotheses. One notable Caribbean radiation lacking such data are dwarf geckos of the genus Sphaerodactylus. Systematics of the Puerto Rican Sphaerodactylus have been turbulent since the initial species descriptions and no molecular phylogenies exist that include complete or near-complete taxon sampling. Here, we combine a multi-locus molecular phylogeny with extensive morphological information to investigate the current diversity of Sphaerodactylus geckos from the Puerto Rican Bank, with a large number of species from Hispaniola as an outgroup. In particular, we focus our efforts on resolving the taxonomy of the Sphaerodactylus macrolepis Günther species complex. We find S. macrolepis sensu lato (currently two nominal species with nine subspecies) is made up of at least four diagnosable species within two clades: (1) the sister species Sphaerodactylus macrolepis sensu stricto from the Virgin Islands (including St. Croix) and Culebra, and S. parvus King from islands in the northern Lesser Antilles; and (2) all other Sphaerodactylus macrolepis subspecies from Puerto Rico, Vieques, and Culebra. We resurrect Sphaerodactylus grandisquamis Stejneger from synonymy to refer to all subspecies from Puerto Rico and elevate the subspecies Sphaerodactylus inigoi Thomas Schwartz for geckos from Vieques and western Culebra. The resulting phylogeny and revised taxonomy will be a useful tool for subsequent research into Sphaerodactylus conservation and evolution.

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.

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.

A11 Evaluation of phylogenetic inference methods to determine direction of HIV transmission

It has been postulated that the direction of HIV transmission between two individuals can be determined by phylogenetic analysis of HIV sequences. This approach may be problematic, since HIV sequences from newly infected individuals are often more similar to index sequences from samples collected years before transmission, compared to those from samples collected at the time of transmission. We evaluated the accuracy of phylogenetic methods for determining the direction of HIV transmission by analyzing next-generation sequencing (NGS) data from index–partner pairs enrolled in the HIV Prevention Trials Network (HPTN) 052 trial. HIV-infected index and HIV-uninfected partner participants were enrolled as serodiscordant couples; samples were analyzed from couples with index-to-partner HIV transmission that was confirmed by genetic linkage studies. NGS for HIV gp41 (HXB2 coordinates: 7691–8374) was performed using plasma samples from thirty-nine index–partner pairs (seventy-eight samples collected within 3 months of partner seroconversion). Maximum likelihood trees were generated using the entire dataset using FastTree v.2. Topological patterns of HIV from each index–partner pair were analyzed. The analysis included 9,368 consensus sequences and 521,145 total sequence reads for the seventy-eight samples analyzed. In 10 per cent (four out of thirty-nine) of couples, the phylogeny was inconsistent with the known direction of transmission. In 26 per cent (ten out of thirty-nine) of couples, the phylogeny results could not discern directionality. In 64 per cent (twenty-five out of thirty-nine) of couples, the results correctly indicated index-to-partner transmission; in two of these twenty-five cases, only one index sequence was closest to the most recent common ancestor. Phylogenetic analysis of NGS data obtained from samples collected within 3 months of transmission correctly determined the direction of transmission in 64 per cent of the cases analyzed. In 36 per cent of the cases, the phylogenetic topology did not support the known direction of infection, and in one-third of these cases the observed topology was opposite to the known direction of transmission. This demonstrates that phylogenetic topology alone may not be sufficient to accurately determine the direction of HIV transmission.

Evolution of the Gekkotan Adhesive System: Does Digit Anatomy Point to One or More Origins?

Recently-developed, molecularly-based phylogenies of geckos have provided the basis for reassessing the number of times adhesive toe-pads have arisen within the Gekkota. At present both a single origin and multiple origin hypotheses prevail, each of which has consequences that relate to explanations about digit form and evolutionary transitions underlying the enormous variation in adhesive toe pad structure among extant, limbed geckos (pygopods lack pertinent features). These competing hypotheses result from mapping the distribution of toe pads onto a phylogenetic framework employing the simple binary expedient of whether such toe pads are present or absent. It is evident, however, that adhesive toe pads are functional complexes that consist of a suite of integrated structural components that interact to bring about adhesive contact with the substratum and release from it. We evaluated the competing hypotheses about toe pad origins using 34 features associated with digit structure (drawn from the overall form of the digits; the presence and form of adhesive scansors; the proportions and structure of the phalanges; aspects of digital muscular and tendon morphology; presence and form of paraphalangeal elements; and the presence and form of substrate compliance-enhancing structures). We mapped these onto a well-supported phylogeny to reconstruct their evolution. Nineteen of these characters proved to be informative for all extant, limbed geckos, allowing us to assess which of them exhibit co-occurrence and/or clade-specificity. We found the absence of adhesive toe pads to be the ancestral state for the extant Gekkota as a whole, and our data to be consistent with independent origins of adhesive toe pads in the Diplodactylidae, Sphaerodactylidae, Phyllodactylidae, and Gekkonidae, with a strong likelihood of multiple origins in the latter three families. These findings are consistent with recently-published evidence of the presence of adhesively-competent digits in geckos generally regarded as lacking toe pads. Based upon morphology we identify other taxa at various locations within the gekkotan tree that are promising candidates for the expression of the early phases of adhesively-assisted locomotion. Investigation of functionally transitional forms will be valuable for enhancing our understanding of what is necessary and sufficient for the transition to adhesively-assisted locomotion, and for those whose objectives are to develop simulacra of the gekkotan adhesive system for biotechnological applications.

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

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

Isolating and quantifying the role of developmental noise in generating phenotypic variation

Genotypic variation, environmental variation, and their interaction may produce variation in the developmental process and cause phenotypic differences among individuals. Developmental noise, which arises during development from stochasticity in cellular and molecular processes when genotype and environment are fixed, also contributes to phenotypic variation. While evolutionary biology has long focused on teasing apart the relative contribution of genes and environment to phenotypic variation, our understanding of the role of developmental noise has lagged due to technical difficulties in directly measuring the contribution of developmental noise. The influence of developmental noise is likely underestimated in studies of phenotypic variation due to intrinsic mechanisms within organisms that stabilize phenotypes and decrease variation. Since we are just beginning to appreciate the extent to which phenotypic variation due to stochasticity is potentially adaptive, the contribution of developmental noise to phenotypic variation must be separated and measured to fully understand its role in evolution. Here, we show that variation in the component of the developmental process corresponding to environmental and genetic factors (here treated together as a unit called the LALI-type) versus the contribution of developmental noise, can be distinguished for leopard gecko (Eublepharis macularius) head color patterns using mathematical simulations that model the role of random variation (corresponding to developmental noise) in patterning. Specifically, we modified the parameters of simulations corresponding to variation in the LALI-type to generate the full range of phenotypic variation in color pattern seen on the heads of eight leopard geckos. We observed that over the range of these parameters, variation in color pattern due to LALI-type variation exceeds that due to developmental noise in the studied gecko cohort. However, the effect of developmental noise on patterning is also substantial. Our approach addresses one of the major goals of evolutionary biology: to quantify the role of stochasticity in shaping phenotypic variation.

The transcriptome of the veiled chameleon (Chamaeleo calyptratus): A resource for studying the evolution and development of vertebrates

PURPOSE

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.

METHODS

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.

RESULTS

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.

CONCLUSION

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.

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.

Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome

Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes.