Genome-wide DNA methylation patterns harbor signatures of hatchling sex and past incubation temperature in a species with environmental sex determination

Abstract

Conservation of thermally sensitive species depends on monitoring organismal and population-level responses to environmental change in real time. Epigenetic processes are increasingly recognized as key integrators of environmental conditions into developmentally plastic responses, and attendant epigenomic datasets hold potential for revealing cryptic phenotypes relevant to conservation efforts. Here, we demonstrate the utility of genome-wide DNA methylation (DNAm) patterns in the face of climate change for a group of especially vulnerable species, those with temperature-dependent sex determination (TSD). Due to their reliance on thermal cues during development to determine sexual fate, contemporary shifts in temperature are predicted to skew offspring sex ratios and ultimately destabilize sensitive populations. Using reduced-representation bisulfite sequencing, we profiled the DNA methylome in blood cells of hatchling American alligator (Alligator mississippiensis), a TSD species lacking reliable markers of sexual dimorphism in early life-stages. We identified 120 sex-associated differentially methylated cytosines (DMCs; FDR < 0.1) in hatchlings incubated under a range of temperatures, as well as 707 unique temperature-associated DMCs. We further developed DNAm-based models capable of predicting hatchling sex with 100% accuracy and past incubation temperature with a mean absolute error of 1.2°C based on the methylation status of 20 and 24 loci, respectively. Though largely independent of epigenomic patterning occurring in the embryonic gonad during TSD, DNAm patterns in blood cells may serve as non-lethal markers of hatchling sex and past incubation conditions in conservation applications. These findings also raise intriguing questions regarding tissue-specific epigenomic patterning in the context of developmental plasticity.

Differential early-life survival underlies the adaptive significance of temperature-dependent sex determination in a long-lived reptile

“…Sex ratios of each size class were summarized across the species' geographic range by taking the mean sex ratio of studies from each state (North Carolina = NC, South Carolina = SC, Louisiana = LA, Florida = FL) weighted by the reported sample size. Sexing hatchlings remains challenging in this species due to the lack of sexually dimorphic morphology in early life stages (Bock et al, 2022), thus empirically derived hatchling sex ratios were supplemented with predicted sex ratios from nest temperatures. Nest temperatures were translated to predicted hatchling sex ratios using the established temperatureby-sex ratio reaction norm for the American alligator (Lang & Andrews, 1994) and mean nest temperatures measured during the thermosensitive period, the window of time during which sex responds to temperature (Bock et al, 2020).…”

Genome‐wide DNA methylation patterns harbour signatures of hatchling sex and past incubation temperature in a species with environmental sex determination

“…Additional related data are available via the Dryad Digital Repository: https://doi.org/10.5061/dryad.cfxpn vx7p (Bock et al, 2022).…”

“…The raw sequencing reads and associated metadata from reduced‐representation bisulphite sequencing libraries are available via the NCBI Sequence Read Archive (SRA) under the BioProject PRJNA857046 (whole blood) and PRJNA857084 (embryonic gonad). Additional related data are available via the Dryad Digital Repository: https://doi.org/10.5061/dryad.cfxpnvx7p (Bock et al, 2022 ).…”