Peter A. Scott

The transition from terrestrial to marine environments represents one of the most fundamental evolutionary shifts in vertebrate history, requiring radical physiological and genomic remodeling. We investigated the genomic signatures of saltwater adaptation in the green sea turtle (Chelonia mydas), the leatherback turtle (Dermochelys coriacea), and the independently evolved estuarine diamondback terrapin (Malaclemys terrapin). Our analyses reveal that the marine transition is characterized by rapid evolution and expansion in gene families linked to iron metabolism, organ morphogenesis, and sensory perception-patterns that mirror those seen in other secondarily marine tetrapods. Notably, while we identified shared targets of positive selection across these independent lineages, we found no evidence of repeated evolution at the nucleotide level, reinforcing that functional convergence often arises through distinct molecular trajectories. Furthermore, demographic reconstructions reveal that saltwater-adapted turtles share a history of deep-time population declines; however, the delayed recovery of M. terrapin underscores the specific susceptibility of estuarine specialists to Pleistocene sea-level volatility. By bridging comparative genomics and historical demography, this study provides new insights into the genomic basis of marine adaptations in turtles and a comprehensive framework for understanding the molecular and ecological mechanisms that facilitate major vertebrate transitions into the marine realm.

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•Salamanders of the genus Lyciasalamandra were sampled comprehensively throughout Mediterranean coast of Turkey and a handful of Aegean Islands.•DdRADseq was used to generate > 220,000 SNPs from > 110,000 RAD-loci for 110 specimens of Lyciasalamandra.•Multiple methods of lineage discovery were used to infer putative operational taxonomic units in the genus.•Multiple Bayesian species delimitation methods are used to infer species limits and infer interspecific relationships for the genus and a new taxonomy is provided.
Salamanders of the genus Lyciasalamandra are represented by as many as 20 narrow-range endemic taxa inhabiting the Mediterranean coast of Turkey and a handful of Aegean Islands. Despite recent molecular phylogenetic studies, the genus is rife with uncertainty about the number of contained species and their phylogenetic relationships, both of which can interfere with needed conservation actions. To test species limits and infer interrelationships we generated as many as 113,176 RAD loci containing 229,427 single nucleotide polymorphisms (SNPs), for 110 specimens of Lyciasalamandra representing 19 of the 20 described taxa. Through a conservative species delimitation approach, we found support for eight species in the genus which broadly agree with currently described species-level diversity. We then use multiple coalescent-based species tree methods to resolve relationships in this relatively old, synchronous species radiation. We recommend synonymization of the largely over-split subspecific taxa, and the elevation of L. luschani finikensis to full species status as L. finikensis. Our hope is that this revised taxonomic framework provides a stable foundation for conservation management in these fragile, microendemic taxa.

Urosaurus nigricaudus is a phrynosomatid lizard endemic to the Baja California Peninsula in Mexico. This work presents a chromosome-level genome assembly and annotation from a male individual. We used PacBio long reads and HiRise scaffolding to generate a high-quality genomic assembly of 1.87 Gb distributed in 327 scaffolds, with an N50 of 279 Mb and an L50 of 3. Approximately 98.4% of the genome is contained in 14 scaffolds, with 6 large scaffolds (334-127 Mb) representing macrochromosomes and 8 small scaffolds (63-22 Mb) representing microchromosomes. Using standard gene modeling and transcriptomic data, we predicted 17,902 protein-coding genes on the genome. The repeat content is characterized by a large proportion of long interspersed nuclear elements that are relatively old. Synteny analysis revealed some microchromosomes with high repeat content are more prone to rearrangements but that both macro- and microchromosomes are well conserved across reptiles. We identified scaffold 14 as the X chromosome. This microchromosome presents perfect dosage compensation where the single X of males has the same expression levels as two X chromosomes in females. Finally, we estimated the effective population size for U. nigricaudus was extremely low, which may reflect a reduction in polymorphism related to it becoming a peninsular endemic.

Speciation entails a reduction in gene flow between lineages. The rates at which genomic regions become isolated varies across space and time. Barrier markers are linked to putative genes involved in (processes of) reproductive isolation, and, when observed over two transects, indicate species-wide processes. In contrast, transect-specific putative barrier markers suggest local processes. We studied two widely separated transects along the 900 km hybrid zone between Bufo bufo and B. spinosus, in northern and southern France, for ~1200 RADseq markers. We used genomic and geographic cline analyses to identify barrier markers based on their restricted introgression, and found that some markers are transect-specific, while others are shared between transects. Twenty-six barrier markers were shared across both transects, of which some are clustered in the same chromosomal region, suggesting that their associated genes are involved in reduced gene flow across the entire hybrid zone. Transect-specific barrier markers were twice as numerous in the southern than in the northern transect, suggesting that the overall barrier effect is weaker in northern France. We hypothesize that this is consistent with a longer period of secondary contact in southern France. The smaller number of introgressed genes in the northern transect shows considerably more gene flow towards the southern (B. spinosus) than the northern species (B. bufo). We hypothesize that hybrid zone movement in northern France and hybrid zone stability in southern France explain this pattern. The Bufo hybrid zone provides an excellent opportunity to separate a general barrier effect from localized gene flow-reducing conditions.

Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in diverse marine habitats remains largely unknown. Additionally, many populations have drastically declined due to anthropogenic activities over the past two centuries, and their recovery is a high global conservation priority. We generated and analyzed high-quality reference genomes for the leatherback (
) and green (
) turtles, representing the two extant sea turtle families. These genomes are highly syntenic and homologous, but localized regions of noncollinearity were associated with higher copy numbers of immune, zinc-finger, and olfactory receptor (OR) genes in green turtles, with ORs related to waterborne odorants greatly expanded in green turtles. Our findings suggest that divergent evolution of these key gene families may underlie immunological and sensory adaptations assisting navigation, occupancy of neritic versus pelagic environments, and diet specialization. Reduced collinearity was especially prevalent in microchromosomes, with greater gene content, heterozygosity, and genetic distances between species, supporting their critical role in vertebrate evolutionary adaptation. Finally, diversity and demographic histories starkly contrasted between species, indicating that leatherback turtles have had a low yet stable effective population size, exhibit extremely low diversity compared with other reptiles, and harbor a higher genetic load compared with green turtles, reinforcing concern over their persistence under future climate scenarios. These genomes provide invaluable resources for advancing our understanding of evolution and conservation best practices in an imperiled vertebrate lineage.

The mountains of southern California represent unique, isolated ecosystems that support distinct high-elevation habitats found nowhere else in the area. Analyses of several moisture-dependent species across these sky-islands indicate they exist as locally endemic lineages that are distributed across these fragmented mountains ranges. The Rubber Boa is a semi-fossorial snake species that is widely distributed in the cooler and more moist ecoregions regions of western North America, including isolated populations across southern California mountain ranges. We developed a genomic and ecological dataset to examine genetic diversity within Rubber Boas and to determine if the endemic Southern Rubber Boa represents a distinct lineage. We quantified current and future habitat suitability under a range of climate change scenarios, and discuss the possible environmental threats facing these unique montane isolates. Our results support four major lineages within Rubber Boas, with genetic breaks that are consistent with biogeographic boundaries observed in other co-distributed, cool-temperature, moisture adapted species. Our data support previous studies that the Southern Rubber Boa is an independent evolutionary unit and now includes multiple locally endemic sky-island populations, restricted to isolated mountain tops and ranges across southern California. Analyses of future habitat suitability indicate that many of these sky-island populations will lose most of their suitable habitat over the next 70 years given predicted increases in drought, rising temperatures, and wildfires. Collectively these data emphasize the critical conservation needs of these montane ecosystems in southern California under current and projected climate change conditions.

The northwestern pond turtle,
Actinemys marmorata
, and its recently recognized sister species, the southwestern pond turtle,
A. pallida
, are the sole aquatic testudines occurring over most of western North America and the only living representatives of the genus
Actinemys.
Although it historically ranged from Washington state through central California, USA, populations of the northwestern pond turtle have been in decline for decades and the species is afforded state-level protection across its range; it is currently being considered for protection under the US Endangered Species Act. Here, we report a new, chromosome-level assembly of
A. marmorata
as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises 198 scaffolds spanning 2,319,339,408 base pairs, has a contig N50 of 75 Mb, a scaffold N50 of 146Mb, and BUSCO complete score of 96.7%, making it the most complete testudine assembly of the 24 species from 13 families that are currently available. In combination with the
A. pallida
reference genome that is currently under construction through the CCGP, the
A. marmorata
genome will be a powerful tool for documenting landscape genomic diversity, the basis of adaptations to salt tolerance and thermal capacity, and hybridization dynamics between these recently diverged species.