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Abstract The lungs of squamate reptiles (lizards and snakes) are highly diverse, exhibiting single chambers, multiple chambers, transitional forms with two to three chambers, along with a suite of other anatomical features, including finger-like epithelial projections into the body cavity known as diverticulae. During embryonic development of the simple, sac-like lungs of anoles, the epithelium is pushed through the openings of a pulmonary smooth muscle mesh by the forces of luminal fluid pressure. This process of stress ball morphogenesis generates the faveolar epithelium typical of squamate lungs. Here, we compared embryonic lung development in brown anoles, leopard geckos, and veiled chameleons to determine if stress ball morphogenesis is conserved across squamates and to understand the physical processes that generate transitional-chambered lungs with diverticulae. We found that epithelial protrusion through the holes in a pulmonary smooth muscle mesh is conserved across squamates. Surprisingly, however, we found that luminal inflation is not conserved. Instead, leopard geckos and veiled chameleons appear to generate their faveolae via epithelial folding downstream of epithelial proliferation. We also found experimental and computational evidence suggesting that the transitional chambers and diverticulae of veiled chameleon lungs develop via apical constriction, a process known to be crucial for airway branching in the bird lung. Thus, distinct morphogenetic mechanisms generate epithelial diversity in squamate lungs, which may underpin their species-specific physiological and ecological adaptations. 

Abstract Among squamates, hemipenes are known to evolve rapidly and exhibit diverse shapes, sizes, and ornamentation. Croaking geckos (Aristelliger) are unique among geckos in exhibiting mineralized structures (hemibacula) in their hemipenes. We here describe the gross morphology of the hemibacula of each currently recognized species ofAristelliger, document hemibacular histology, and report on hemibaculum development. We confirm the presence of hemibacula in all currently recognized species and demonstrate that three distinct morphologies correspond to three putative clades in the genus. Histology revealed that hemibacula are superficially similar to chondroid bone and composed of mineralized dense connective tissue covered in a thin layer of epidermis with alcian‐positive cells embedded within a mineralized matrix. Additionally, we demonstrate that hemibacula do not develop until past the onset of sexual maturity and that hemibaculum length scales isometrically with body size. We hypothesize that hemibacula ofAristelligerdevelop via peramorphosis, a phenomenon also expressed in the cranial morphology of this genus. Additionally, we speculate on the functional significance of these enigmatic structures. 

Summary Pluripotency, the ability of cells to self-renew and differentiate into all the cell types in an animal’s body, is vital for mammalian early development. This study presented a comprehensive comparative transcriptomic analysis of embryonic stem cells across multiple mammalian species, defining their progression through expanded/extended, naïve, formative, and primed pluripotency states. Our findings revealed both conserved and species-specific mechanisms underlying pluripotency regulation. We also emphasized the limitations of existing state-specific markers and their limited cross-species applicability, while identifyingde novopluripotency markers that can inform future research. Despite variability in gene expression dynamics, gene co-expression networks showed remarkable conservation across species. Among pluripotency states, the primed state demonstrated the highest conservation, evidenced by shared markers, preserved gene networks, and stronger selective pressures acting on its genes. These findings provide critical insights into the evolution and regulation of pluripotency, laying a foundation for refining stem cell models to enhance their translational potential in regenerative medicine, agriculture, and conservation biology. 

Abstract Transposable elements (TEs) are repetitive DNA sequences which create mutations and generate genetic diversity across the tree of life. In amniote vertebrates, TEs have been mainly studied in mammals and birds, whose genomes generally display low TE diversity. Squamates (Order Squamata; including ∼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 genome dynamics have evolved over the course of squamate evolution. To understand the interplay between TEs and host genomes, we analyzed the evolutionary history of the chicken repeat 1 (CR1) retrotransposon, a TE family found in most tetrapod genomes which is the dominant TE in most reptiles. 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. 

Several species of geckos have independently evolved patagia, membranous features that facilitate gliding.Detailed morphological investigations of gecko patagia have largely been limited to gliding members of the genus Gekko(formerly in the genus Ptychozoon). Herein we describe the morphology of gliding patagia of the Flat-tailed HouseGecko (Hemidactylus platyurus), a species with an independent evolutionary origin of gliding patagia from Gekko andan important species for researching gliding biomechanics. We compared morphology of H. platyurus with a closelyrelated non-gliding species, the Common House Gecko (Hemidactylus frenatus). Using external examination and histologicaltechniques, we compared and contrasted three regions that exhibit patagia (trunk, femoral region, and tail)in H. platyurus but not in H. frenatus. We find that patagia in a gliding Hemidactylus, like patagia in gliding membersof the genus Gekko, are derived from expansion of lateral fat bodies, suggesting analogous processes to achieve similarphenotypic outcomes. 

Synopsis 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. 

Abstract 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.