An epigenetic toolbox for conservation biologists

BackgroundCharacterising genetic and epigenetic diversity is crucial for assessing the adaptive potential of populations and species. Slow-reproducing and already threatened species, including endangered sea turtles, are particularly at risk. Those species with temperature-dependent sex determination (TSD) have heightened climate vulnerability, with sea turtle populations facing feminisation and extinction under future climate change. High- quality genomic and epigenomic resources will therefore support conservation efforts for these flagship species with such plastic traits.FindingsWe generated a chromosome-level genome assembly for the loggerhead sea turtle (Caretta caretta) from the globally important Cabo Verde rookery. Using Oxford Nanopore Technology (ONT) and Illumina reads followed by homology-guided scaffolding, we achieved a contiguous (N50: 129.7 Mbp) and complete (BUSCO: 97.1%) assembly, with 98.9% of the genome scaffolded into 28 chromosomes and 29,883 annotated genes. We then extracted the ONT-derived methylome and validated it via whole genome bisulfite sequencing of ten loggerheads from the same population. Applying our novel resources, we reconstructed population size fluctuations and matched them with major climatic events and niche availability. We identified microchromosomes as key regions for monitoring genetic diversity and epigenetic flexibility. Isolating 191 TSD-linked genes, we further built the largest network of functional associations and methylation patterns for sea turtles to date.ConclusionsWe present a high-quality loggerhead sea turtle genome and methylome from the globally significant East Atlantic population. By leveraging ONT sequencing to create genomic and epigenomic resources simultaneously, we showcase this dual strategy for driving conservation insights into endangered sea turtles.

show abstract

Epigenetic Diversity and the Evolutionary Potential of Wild Populations

Baltazar‐Soares,

Balard,

Heckwolf

2024

Evolutionary Applications

View full text Add to dashboard Cite

Fast‐paced selective pressures imposed by climate change and anthropogenic activities call for adaptive evolutionary responses to emerge at ecological timescales. However, the evolution and heritability of genomic variation underlie mechanistic constraints, which dictate a slower pace of adaptation exclusively relying on standing genetic variation and novel mutations. Environmentally responsive epigenetic mechanisms can allow acclimatisation and adaptive phenotypes to arise faster than DNA sequence‐based mechanisms alone. Nevertheless, the knowledge gap between identifying epigenetic marks and effectively deeming them functional is still wide in a natural context and often outside the scope of model organisms. With this Special Issue, we aimed to narrow this gap by presenting a compilation of original research articles, reviews and opinions on the topic of epigenetics in wild populations. We contextualised this collection within the overarching topic of conservation biology, as we firmly propose that epigenetic research can significantly enhance the effectiveness of conservation measures. Contributions highlighted the putative role of epigenetic variation in the acclimatisation and adaptive potential of species and populations directly and indirectly affected by climatic shifts and anthropogenic actions. They further exemplified how epigenetic variation can be used as biomarkers for monitoring variations in physiology, phenology and behaviour. Lastly, reviews and perspective articles illustrated the past and present of epigenetic research in wild populations while suggesting future research avenues.

show abstract

An epigenetic toolbox for conservation biologists

Cited by 3 publications

References 243 publications

Approaching the mystery of aging by the epigenetic clock

Approaching the mystery of aging by the epigenetic clock

Chromosome-level genome assembly and methylome profile enables insights for the conservation of endangered loggerhead sea turtles

Epigenetic Diversity and the Evolutionary Potential of Wild Populations

Contact Info

Product

Resources

About