European (Anguilla anguilla) and American eel (A. rostrata) represent a remarkable case of interspecific hybridization. They are both panmictic and spawn in partial sympatry in the Sargasso Sea, occasionally producing viable, fertile hybrids, primarily found in Iceland. We studied introgressive hybridization from American into European eel based on whole-genome sequences of 78 individuals, encompassing European, American and 21 putative hybrid eels. Previous studies using few genetic markers could not resolve whether hybridization involved simple unidirectional backcrossing or a more complex hybrid swarm scenario. However, local ancestry inference along individual chromosomes revealed Icelandic hybrids were primarily F1 hybrids or first-generation backcrosses toward European eel, with a few showing more complex backcrossing histories. All European eels outside Iceland contained short chromosomal blocks from American eel, indicating a porous genome. We found no evidence for previously stated hypotheses about geographical gradients of introgression in European eel outside Iceland. Several chromosomal regions showed high divergence between the species, but haplotype blocks introgressed from American eel were identified both within and outside these regions. There was little correspondence between regions of high relative and high absolute divergence (dXY), and they presumably reflect selective sweeps within species or regions of reduced recombination rather than barrier loci. We identified a single genomic region with evidence of introgression from American into European eel at multiple occasions, under positive selection in both species. Thus, although the two species maintain genetic integrity, their gene pools are not independent and represent a common pool of standing variation for future adaptive responses.

The role of methylation in adaptive, developmental and speciation processes has attracted considerable interest, but interpretation of results is complicated by diffuse boundaries between genetic and non-genetic variation. We studied whole genome genetic and methylation variation in the European eel, distributed from subarctic to subtropical environments, but with panmixia precluding genetically based local adaptation beyond single-generation responses. Overall methylation was 70.9%, with hypomethylation predominantly found in promoters and first exons. Redundancy analyses involving juvenile glass eels showed 0.06% and 0.03% of the variance at SNPs to be explained by localities and environmental variables, respectively, with GO terms of genes associated with outliers primarily involving neural system functioning. For CpGs 2.98% and 1.36% of variance was explained by localities and environmental variables. Differentially methylated regions particularly included genes involved in developmental processes, with hox clusters featuring prominently. Life stage (adult versus glass eels) was the most important source of inter-individual variation in methylation, likely reflecting both ageing and developmental processes. Demethylation of transposable elements was observed in European X American eel hybrids, possibly representing postzygotic barriers in this system characterized by prolonged speciation and ongoing gene flow. Whereas the genetic data are consistent with a role of single-generation selective responses, the methylation results underpin the importance of epigenetics in the life cycle of eels and suggests interactions between local environments, development and phenotypic variation mediated by methylation variation. Eels are remarkable by having retained eight hox clusters, and the results suggest important roles of methylation at hox genes for adaptive processes.