Epigenetic aging in a self-fertilizing vertebrate, the mangrove rivulus Kryptolebias marmoratus

Abstract

DNA methylation changes predictably with age across taxa, but in most species these patterns are confounded by genetic variation. As a result, age-predictive methylation models have mostly been developed in genetically heterogeneous, cross-fertilizing organisms, limiting inference about epigenetic aging per se. Disentangling epigenetic and genetic effects is therefore essential for understanding aging, adaptation, and evolution. Here, we exploit the mangrove rivulus (Kryptolebias marmoratus), one of only two known self-fertilizing vertebrates (together with K. hermaphroditus), to examine epigenetic aging in a system of naturally occurring near-isogenic individuals. Using reduced-representation bisulfite sequencing of 90 brain samples spanning 60-1100 days of age, we identified 40 CpG sites whose methylation levels predict chronological age with high accuracy (R2 > 0.96, Median Absolute Error of 28.7 days). These 40 age-associated CpG sites were linked to nearby genes with known roles in cellular maintenance and neurodegeneration. These include genes implicated in aging and neurodegenerative processes across vertebrates, such as lamin-A, the aryl hydrocarbon receptor, and genes associated with Alzheimers disease in humans. By leveraging a self-fertilizing vertebrate, this study demonstrates that DNA methylation undergoes consistent, age-associated changes across the lifespan in the near absence of genetic variation. Our results establish self-fertilizing vertebrates as powerful models for disentangling epigenetic aging from genetic effects and provide a foundation for comparative and evolutionary studies of aging. STATEMENTSO_ST_ABSData availabilityC_ST_ABSThe datasets generated and/or analyzed during the current study are available in the NCBI repository, under the ID BioProject ID PRJNA1331489. Funding statementThis work was supported by the FNRS project J.0189.24 "Epigenome Stability in Mangrove Rivulus". Ethics approvalAll research reported in this manuscript was conducted in accordance with institutional and national ethical standards for animal care and use. Experimental procedures involving Kryptolebias marmoratus were approved by the Animal Experimentation Ethics Committee (UN PM KE 23/020). Authors contributionsJB designed the experimental process, conceptualized the article, generated and analyzed the data and wrote the manuscript. FS designed the experimental process, reviewed and edited the manuscript and did validation and supervision. All authors read and approved of the final manuscript. Conflict of interestThe authors declare that they have no competing interests. Patient consent statementNot applicable. Permission to reproduce material from other sourcesNot applicable. Clinical trial registrationNot applicable.