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Abstract Although the publication of high-quality reference genomes is steadily increasing, many clades remain chronically neglected. Skinks (order, Squamata; family, Scincidae) are one of the most diverse lizard families (1,785 species), yet there are currently just six published chromosome-level skink genomes. Here, we present the first telomere-to-telomere, chromosome-level reference genome for one of the most abundant lizards in the eastern United States, the common five-lined skink (Plestiodon fasciatus). Through the sequencing of RNA, long-read DNA, and Hi-C chromatin interactions, we produced an annotated reference genome (N50 = 227MB, L50 = 3) consisting of 6 macrochromosome pairs and 7 microchromosome pairs with 98% of BUSCO genes represented (lineage, Sauropsida; 7480 BUSCO markers), providing one of the most complete skink genomes to date: rPleFas1.1. Functional annotation predicts 32,520 protein-coding genes (16,100 unique, named genes) with an average gene length of 9,372 bp. Repeat annotations estimate that transposable elements comprise 46.7% of the genome, for which we show the amount and content is remarkably conserved across Scincidae. 

The distributions of species radiations reflect environmental changes driven by both Earth history (geological processes) and the evolution of biological traits (critical to survival and adaptation), which profoundly drive biodiversity yet are rarely studied together. Modern toads (Bufonidae, Amphibia), an iconic radiation with global distribution and high phenotypic diversity, are an ideal group for exploring these dynamics. Using phylogenomic data from 124 species across six continents, we reconstruct their evolutionary history. Biogeographic analyses suggest modern toads originated in South America approximately 61 million years ago (Ma), later dispersing to Africa and Asia, thereby challenging hypotheses of dispersal via North America. Species diversification rates increased after leaving South America, linked to Cenozoic geological events and key innovations like toxic parotoid glands for predator defence. The emergence of parotoid glands coincided with the South American dispersal, promoting diversification and enabling toads to dominate both Old and New Worlds. In contrast, the evolution of other traits, despite being crucial to adaptation, did not promote species diversification (e.g. large body size) or were ambiguously associated with expansion into the Old World (e.g. developmental modes). These findings highlight the adaptability of modern toads and reveal the interplay between Earth’s history and phenotypic innovation in shaping biodiversity. 

The subgenus Ochthomantis is an obligate forest and stream-dwelling group of mantellid frogs, endemic to Madagascar, with six species currently recognized. However, this group suffers from ongoing taxonomic confusion due to low numbers of examined specimens, and failure to consider morphological variation from development and sexual dimorphism. Here, we examined the morphology of 637 sexed adult specimens collected by us in the field and from other museum collections. We also sequenced a DNA fragment of the 16S mtDNA gene for each lineage to determine congruence between morphological and molecular data sets and to help delimit species. Our results demonstrate that the subgenus Ochthomantis includes eleven valid species: five already recognized, M. catalai and M. poissoni that we resurrect from synonymy, and four new species which we describe for the first time here. In some analyses, Mantidactylus majori groups with other Mantidactylus subgenera, so we do not consider it a member of the subgenus Ochthomantis in this study. All species have restricted distributions and elevational ranges in the humid forests of Madagascar. This study demonstrates the utility of assessing cryptic species using both diagnostic morphological characters and molecular data. The discovery of this new cryptic biodiversity, and the taxonomic revision herein, will likely require conservation activities for those species with the most restricted distributions. 

Abstract Speciation rates vary substantially across the tree of life. These rates should be linked to the rate at which population structure forms if a continuum between micro and macroevolutionary patterns exists. Previous studies examining the link between speciation rates and the degree of population formation in clades have been shown to be either correlated or uncorrelated depending on the group, but no study has yet examined the relationship between speciation rates and population structure in a young group that is constrained spatially to a single‐island system. We examine this correlation in 109 gemsnakes (Pseudoxyrhophiidae) endemic to Madagascar and originating in the early Miocene, which helps control for extinction variation across time and space. We find no relationship between rates of speciation and the formation rates of population structure over space in 33 species of gemsnakes. Rates of speciation show low variation, yet population structure varies widely across species, indicating that speciation rates and population structure are disconnected. We suspect this is largely due to the persistence of some lineages not susceptible to extinction. Importantly, we discuss how delimiting populations versus species may contribute to problems understanding the continuum between shallow and deep evolutionary processes. 

ABSTRACT Optimal preservation of tissues from the field to long‐term cryo‐storage is paramount to securing genetic resources for research needs. DNA preservation techniques vary, with flash freezing currently considered the gold standard in tissue preservation. However, flash freezing tissue samples in the field presents challenges, necessitating a more comprehensive understanding of the quantity and quality of preserved DNA from different techniques in archival collections. We compared metrics from DNA extractions from field‐collected amphibian, squamate and bird tissues from archival collections that were flash‐frozen in liquid nitrogen or fixed in either ethanol or tissue lysis buffer prior to archival cryopreservation. We also included DNA extracted from tissues of known liquid nitrogen tank failures to provide a baseline of DNA degradation under the very worst‐case scenario. Flash‐frozen tissues often preserved higher yields of DNA, but peak fragment size, the percentage of fragments larger than 10 kb and DNA integrity numbers were all significantly reduced compared to tissues first preserved in fixative buffers. This pattern was observed across independent samples and between flash‐frozen and buffer‐preserved pair replicates. Degradation seen in flash‐frozen tissues was also distinct to tissues from known tank failures. We suggest that degradation in flash‐frozen tissues occurred during shipping, sample sorting/accession or during subsequent subsampling when tissues may partially or fully thaw, exposing DNA to damaging freeze–thaw processes. By contrast, tissues in fixative buffers were likely protected from freeze–thaw damage. This study highlights that using multiple field preservation methods and minimising freeze–thaw cycles for flash‐frozen tissues may provide the most robust protection against the DNA degradation sources encountered by field collections. 

Abstract A fundamental assumption of evolutionary biology is that phylogeny follows a bifurcating process. However, hybrid speciation and introgression are becoming more widely documented in many groups. Hybrid inference studies have been historically limited to small sets of taxa, while exploration of the prevalence and trends of reticulation at deep time scales remains unexplored. We study the evolutionary history of an adaptive radiation of 109 gemsnakes in Madagascar (Pseudoxyrhophiinae) to identify potential instances of introgression. Using several network inference methods, we find 12 reticulation events within the 22-million-year evolutionary history of gemsnakes, producing 28% of the diversity for the group, including one reticulation that resulted in the diversification of an 18 species radiation. These reticulations are found at nodes with high gene tree discordance and occurred among parental lineages distributed along a north-south axis that share similar ecologies. Younger hybrids occupy intermediate contact zones between the parent lineages showing that post-speciation dispersal in this group has not eroded the spatial signatures of introgression. Reticulations accumulated consistently over time, despite drops in overall speciation rates during the Pleistocene. This suggests that while bifurcating speciation rates may decline as the result of species accumulation and environmental change, speciation by hybridization may be more robust to these processes.