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

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.

Good from far, but far from good: The impact of a reference genome on evolutionary inference.

Genomic diversity and past population histories are key considerations in the fields of conservation and evolutionary biology. In this issue of Molecular Ecology Resources, Prasad et al. (Mol. Ecol. Resour., 2021) examine how the quality and phylogenetic divergence of reference genomes influences the outcomes of downstream analyses such as diversity and demographic history inference. Using the beluga whale and rowi kiwi as examples (Figure 1), they systematically estimate heterozygosity, runs of homozygosity (ROH), and demographic history (PSMC) using reference genomes of varying quality and phylogenetic divergence from the target species. They show that demographic history analyses are impacted by phylogenetic distance, although this is not pronounced until divergence exceeds 3% from the target species. Similarly, their results imply that heterozygosity estimates are dependent on phylogenetic distance and the method used to perform the estimates, and ROHs are potentially undetectable when a nonconspecific reference is used. This investigation into the role of divergence and quality of reference genomes highlights the impact and potential biases generated by genome selection on downstream analyses, and provides a possible alternative in cross-species scaffolding in instances where a conspecific reference genome is not available.

No evidence of selection against anomalous scute arrangements between juvenile and adult sea turtles in Florida.

Variations in the number and arrangement of scutes often are used for species identification in hard-shelled sea turtles. Despite the conserved nature of scute arrangements, anomalous arrangements have been noted in the literature for over a century, with anomalies linked to sub-optimal environmental conditions in the nest during development. Long-held assumptions suggest that anomalous scute arrangements are indicative of underlying physiological or morphological anomalies, with presumed long-term survival costs to the individual. Here, we examined a 25-year photo database of two species of sea turtle (Caretta caretta and Chelonia mydas) captured incidentally and non-selectively on the eastern coast of Florida. Our results suggest that C. mydas is substantially more variable with respect to the arrangement of carapacial scutes, while C. caretta had a relatively higher proportion of individuals with anomalous plastron scute arrangements. We also show evidence that (a) the forms and patterns of anomalous scutes are stable throughout growth; (b) there is limited evidence for selection against non-modal arrangements in the size classes that were examined; and (c) that their frequency has remained stable in juvenile cohorts from 1994 until present. These findings indicate that there may not be a survival cost associated with anomalous scute arrangements once the turtles reach juvenile size classes, and that variation in scute arrangements within populations is relatively common.

Microclimate modelling of beach sand temperatures reveals high spatial and temporal variation at sea turtle rookeries.

The continual development of ecological models and availability of high-resolution gridded climate surfaces have stimulated studies that link climate variables to functional traits of organisms. A primary constraint of these studies is the ability to reliably predict the microclimate that an organism experiences using macroscale climate inputs. This is particularly important in regions where access to empirical information is limited. Here, we contrast correlative models based on both ambient and sea surface temperatures to mechanistic modelling approaches to predict beach sand temperatures at depths relevant to sea turtle nesting. We show that mechanistic models are congruent with correlative models at predicting sand temperatures. We used these predictions to explore thermal variation across 46 mainland and island beaches that span the geographical range of sea turtle nesting in Western Australia. Using high resolution gridded climate surfaces and site-specific soil reflectance, we predict almost 9 °C variation in average annual temperatures between beaches, and nearly 10 °C variation in average temperatures during turtle nesting seasons. Validation of models demonstrated that predictions were typically within 2 °C of observations and, although most sites had high correlations (r2 > 0.7), predictive capacity varied between sites. An advantage of the mechanistic model demonstrated here is that it can be used to explore the impacts of climate change on sea turtle nesting beach temperatures as, unlike correlative models, it can be forced with novel combinations of environmental variables.

Environmental Causation of Turtle Scute Anomalies in ovo and in silico.

The turtle shell is often described as an evolutionary novelty that facilitated the radiation of the clade Testudines. The scutes, or keratinous plates, of the turtle shell are hypothesized to be patterned by reaction-diffusion dynamics, and this property of their development provides explanatory power to mechanisms of anomalous variation. A mathematical model of scute development predicts that anomalous variation in the phylogenetically stable pattern of scutes is achieved by environmental influence on the developmental program. We test this prediction with data on patterns of scute variation from natural nests and controlled incubation of sea turtle eggs in Florida and Western Australia. We find that high temperatures are sufficient to produce anomalous patterns in turtle scutes, and that this correlation is even stronger when conditions are dry. Furthermore, we find that the patterns of variation are not random; greater anomalous variation is found in the midline vertebral scutes and during a critical period of turtle development.

Loggerhead sea turtle embryos (Caretta caretta) regulate expression of stress response and developmental genes when exposed to a biologically realistic heat stress.

Oviparous reptile embryos are expected to breach their critical thermal maxima if temperatures reach those predicted under current climate change models due to the lack of the maternal buffering processes and parental care. Heat-shock proteins (HSPs) are integral in the molecular response to thermal stress, and their expression is heritable, but the roles of other candidate families such as the heat-shock factors (HSFs) have not been determined in reptiles. Here, we subject embryonic sea turtles (Caretta caretta) to a biologically realistic thermal stress and employ de novo transcriptomic profiling of brain tissue to investigate the underlying molecular response. From a reference transcriptome of 302 293 transcripts, 179 were identified as differentially expressed between treatments. As anticipated, genes enriched in the heat-shock treatment were primarily associated with the Hsp families, or were genes whose products play similar protein editing and chaperone functions (e.g. bag3, MYOC and serpinh1). Unexpectedly, genes encoding the HSFs were not significantly upregulated under thermal stress, indicating their presence in unstressed cells in an inactive state. Genes that were downregulated under thermal stress were less well functionally defined but were associated with stress response, development and cellular organization, suggesting that developmental processes may be compromised at realistically high temperatures. These results confirm that genes from the Hsp families play vital roles in the thermal tolerance of developing reptile embryos and, in addition with a number of other genes, should be targets for evaluating the capacity of oviparous reptiles to respond adaptively to the effects of climate change.