The Turtle Project: Conservation epigenomics of endangered sea turtles with temperature-dependen...
Abstract
Species with temperature-dependent sex determination (TSD) face the risk of heavily skewed sex ratios under climate change, threatening population viability. Endangered sea turtles are particularly vulnerable, with many populations predicted to become entirely feminised by the century end. However, large-scale assessments of nest sex ratios are hindered by the lack of a reliable method for sexing hatchlings non-lethally, which must be rectified to guide conservation interventions as warming progresses. DNA methylation is an epigenetic mechanism involved in gene expression regulation, including of sex-related genes. High-quality genomic and epigenomic resources will therefore support efforts for identifying non-lethal biomarkers of sex in sea turtles. By leveraging Oxford Nanopore Technologies (ONT) sequencing, the Turtle Project simultaneously produced a chromosome-level genome assembly and methylome profile for loggerhead sea turtles (Caretta caretta) from the globally important Cabo Verde (Northeast Atlantic) rookery. We next performed epigenome-wide discovery scans that identified over 700 differentially methylated sites between the sexes of loggerhead hatchlings from minimally invasive blood samples. This set of sex-diagnostic molecular biomarkers offer a scalable solution that can now be applied to monitor sex ratios of wild sea turtle populations. Finally, we demonstrate the usage of an ONT P2 Solo platform as a portable tool for sequencing in the field, thus enabling the application of our biomarkers to inform real-time hatchery management decisions. This work represents a promising step towards a precision conservation approach for protecting the resilience of endangered species and populations under climate change.