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1. Differential Conservation and Loss of Chicken Repeat 1 (CR1) Retrotransposons in Squamates Reveal Lineage-Specific Genome Dynamics Across Reptiles

   https://doi.org/10.1093/gbe/evae157  

   Gable, Simone M; Bushroe, Nicholas A; Mendez, Jasmine M; Wilson, Adam; Pinto, Brendan J; Gamble, Tony; Tollis, Marc (July 2024, Genome Biology and Evolution)

   Mueller, Rachel (Ed.)

   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. 

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2. Taphonomic megabiases constrain phylogenetic information in the squamate fossil record

   https://doi.org/10.1017/pab.2025.10060  

   Woolley, C Henrik; Bottjer, David J; Smith, Nathan D (August 2025, Paleobiology)

   Abstract Fossil data are subject to inherent biological, geologic, and anthropogenic filters that can distort our interpretations of ancient life and environments. The inevitable presence of incomplete fossils thus requires a holistic assessment of how to navigate the downstream effects of bias on our ability to accurately reconstruct aspects of biology in deep time. In particular, we must assess how biases affect our capacity to infer evolutionary relationships, which are essential to analyses of diversification, paleobiogeography, and biostratigraphy in Earth history. In this study, we use an established completeness metric to quantify the effects of taphonomic filters on the amount of phylogenetic information available in the fossil record of 795 extinct squamate (e.g., lizards, snakes, amphisbaenians, and mosasaurs) species spanning 242 Myr of geologic time. This study found no meaningful relationship between spatiotemporal sampling intensity and fossil record completeness. Instead, major differences in squamate fossil record completeness stem from a combination of anatomy/body size and affinities of different squamate groups to specific lithologies and depositional environments. These results reveal that naturally occurring processes create structural megabiases that filter anatomical and phylogenetic data in the squamate fossil record, while anthropogenic processes play a secondary role. 

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3. Origin and Early Evolution of Squamates and Their Kin: From Fossils to Genomes

   https://doi.org/10.1146/annurev-ecolsys-102723-050400  

   Simões, Tiago R; Tollis, Marc; Burbrink, Frank T (November 2025, Annual Review of Ecology, Evolution, and Systematics)

   Squamates (lizards, including snakes) are the most diverse group of terrestrial vertebrates on Earth today and have an evolutionary history dating back to at least the Middle Triassic (ca. 242 Mya). Despite their vast taxonomic, morphological, and ecological diversity, understanding their origin has remained a challenging and controversial topic for over a century. Initial studies focused on their patchy early fossil record using morphological data, yielding strongly contrasting hypotheses on squamate early evolutionary trajectories. The past decade has seen a massive overhaul of the subject, due to rapid advances in the areas studying phylogenomics, comparative genomics, phenotypic evolution, and new fossil discoveries. Here, we review advances across all of these fields and how they have been bridging hypotheses previously considered irreconcilable, providing a renewed and synthetic understanding of early squamate evolution. We conclude by discussing new datasets and methods behind these advances and perspectives on how the field will move forward for the next decade. 

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4. Maximizing Molecular Data From Low-Quality Fluid-Preserved Specimens in Natural History Collections

   https://doi.org/10.3389/fevo.2022.893088  

   Bernstein, Justin M.; Ruane, Sara (June 2022, Frontiers in Ecology and Evolution)

   Over the past decade, museum genomics studies have focused on obtaining DNA of sufficient quality and quantity for sequencing from fluid-preserved natural history specimens, primarily to be used in systematic studies. While these studies have opened windows to evolutionary and biodiversity knowledge of many species worldwide, published works often focus on the success of these DNA sequencing efforts, which is undoubtedly less common than obtaining minimal or sometimes no DNA or unusable sequence data from specimens in natural history collections. Here, we attempt to obtain and sequence DNA extracts from 115 fresh and 41 degraded samples of homalopsid snakes, as well as from two degraded samples of a poorly known snake, Hydrablabes periops . Hydrablabes has been suggested to belong to at least two different families (Natricidae and Homalopsidae) and with no fresh tissues known to be available, intractable museum specimens currently provide the only opportunity to determine this snake’s taxonomic affinity. Although our aim was to generate a target-capture dataset for these samples, to be included in a broader phylogenetic study, results were less than ideal due to large amounts of missing data, especially using the same downstream methods as with standard, high-quality samples. However, rather than discount results entirely, we used mapping methods with references and pseudoreferences, along with phylogenetic analyses, to maximize any usable molecular data from our sequencing efforts, identify the taxonomic affinity of H. periops , and compare sequencing success between fresh and degraded tissue samples. This resulted in largely complete mitochondrial genomes for five specimens and hundreds to thousands of nuclear loci (ultra-conserved loci, anchored-hybrid enrichment loci, and a variety of loci frequently used in squamate phylogenetic studies) from fluid-preserved snakes, including a specimen of H. periops from the Field Museum of Natural History collection. We combined our H. periops data with previously published genomic and Sanger-sequenced datasets to confirm the familial designation of this taxon, reject previous taxonomic hypotheses, and make biogeographic inferences for Hydrablabes . A second H. periops specimen, despite being seemingly similar for initial raw sequencing results and after being put through the same protocols, resulted in little usable molecular data. We discuss the successes and failures of using different pipelines and methods to maximize the products from these data and provide expectations for others who are looking to use DNA sequencing efforts on specimens that likely have degraded DNA. Life Science Identifier ( Hydrablabes periops ) urn:lsid:zoobank.org :pub:F2AA44 E2-D2EF-4747-972A-652C34C2C09D. 

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5. Biophysical mechanisms of morphogenesis in lizard lungs

   https://doi.org/10.1101/2025.09.01.673487  

   Hill, Kaleb; Griffing, Aaron H; Palmer, Michael A; Lemma, Bezia; Lupo, Aria; Gamble, Tony; Shylo, Natalia A; Košmrlj, Andrej; Trainor, Paul A; Nelson, Celeste M (September 2025, bioRxiv)

   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. 

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