Adaptation to Freshwater in Allis Shad Involved a Combination of Genomic and Epigenomic Changes

TL;DR

This study shows that Allis shad adapted to freshwater by combining genetic and epigenetic changes, with DNA methylation playing a key role.

Contribution

The study reveals that DNA methylation and genetic selection work together in adaptation, with methylation generating polymorphism for evolution.

Findings

227 differentially methylated regions were identified in freshwater Allis shad, overlapping genes important for adaptation.

DMRs are largely outside genomic regions under natural selection but are linked to CpG deamination events.

Both genetic and epigenetic mechanisms are crucial during early stages of freshwater adaptation in Allis shad.

Abstract

Epigenetic modifications are one of the evolutionary mechanisms that allow individuals and populations to adapt to environmental changes. However, the relative importance of epigenetic versus genetic changes in adaptation and how they may interact remains poorly understood. Here, we investigate the role of DNA methylation in adaptation by studying a population of Allis shad (Alosa alosa) that evolved a completely freshwater life history approximately 70 years ago and the anadromous one that founded it. Using reduced representation bisulfite sequencing, we identified 227 differentially methylated regions (DMRs) between them, overlapping known important genes for freshwater adaptation, such as ATP2B4, PRLH2, and KCNF1A. Enrichment analysis of GO terms suggested that genes in the identified DMRs play key roles in neural, growth, and developmental functions, which is concordant with previous studies on adaptation to freshwater in this species and genus. Using pool-seq data from an earlier study, we then tested if the DMRs for freshwater shad found here overlapped genomic outlier regions that may be under genetic selection in three independently evolved, freshwater populations (including the one studied here). Our analysis showed that the DMRs identified here fall broadly outside genomic regions under natural selection. However, 45% of these were associated with CpG > TpG deamination events in DMRs, a mutation tightly linked with DNA methylation. Our study illustrates that both genetic and epigenetic mechanisms are important during the initial stages of adaptation in this system. It also supports the hypothesis that methylation may generate polymorphism that fuels adaptive evolution.

The online version contains supplementary material available at 10.1007/s00239-025-10253-9.

Figures