Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

Abstract

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 ( Dermochelys coriacea ) and green ( Chelonia mydas ) 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.

Effects of postovipositional hypoxia and hyperoxia on leatherback turtle reproductive success and hatchling performance

“…Bacterial or fungal infections have been suggested as a potential cause (Bell et al, 2003), but in a study of the Columbian nesting population, the authors found no impact of microorganisms on hatching success (Patino‐Martinez et al, 2012). Furthermore, Bentley et al (2023) recently found that leatherbacks exhibit extremely low genetic diversity and have a higher genetic load compared with other reptiles. The authors suggested these factors may contribute to the high levels of embryonic death exhibited in leatherback turtles.…”

Chromosome evolution in a genus that deviates from the standard karyotype formula of Lacertidae

“…Perhaps the most important ecological characteristic that these three taxa have in common is their independent conquest of cold environments (Garcia-Porta et al 2019). Taking into consideration the increasing evolutionary importance attributed to microchromosomes (Uno et al 2012; Srikulnath et al 2021;Waters et al 2021), and the apparently direct involvement of some of their gene contents in differential adaptations of other sqamate reptiles (Bentley et al 2023), it can not be discarded that their loss has been due to selection, in a still unspeci ed way.…”

Recent expansion of Penelope-like retrotransposons in the leatherback turtle Dermochelys coriacea

“…To identify potentially active copies of TEs, we analysed the long-read transcriptome (IsoSeq) data from 3 different tissues (brain, ovaries, and lungs) of D. coriacea available at the NCBI database under identi ers SRR9594996, SRR9594994, and SRR9594995, respectively (Bentley et al 2023). IsoSeq reads were mapped to the genome of D. coriacea (GCF_009764565.3) with minimap2 (Li 2018), applying the additional parameters -ax splice -uf -secondary = no -C5 -O6,24 -B4.…”