| Summary: | Speciation in the ocean could differ from terrestrial environments due to fewer barriers to gene flow. Hence, sympatric speciation might be common, with American and European eel being candidates for exemplifying this. They show disjunct continental distributions on both sides of the Atlantic, but spawn in overlapping regions of the Sargasso Sea from where juveniles are advected to North American, European and North African coasts. Hybridization and introgression is known to occur, with hybrids almost exclusively observed in Iceland. Different speciation scenarios have been suggested, involving either vicariance or sympatric ecological speciation. Using RAD sequencing and whole-genome sequencing data from parental species and F1 hybrids, we analyzed speciation history based on the Joint Allele Frequency Spectrum (JAFS) and PSMC (pairwise sequentially Markovian coalescent) plot. JAFS supported a model involving a split without gene flow 150,000 – 160,000 generations ago, followed by secondary contact 87,000 – 92,000 generations ago, with 64% of the genome experiencing restricted gene flow. This supports vicariance rather than sympatric speciation, likely associated with Pleistocene Glaciation cycles and ocean current changes. Whole genome PSMC analysis of F1 hybrids from Iceland suggested divergence 200,000 generations ago and indicated subsequent gene flow rather than strict isolation. Finally, simulations showed that results from both approaches (JAFS and PSMC) were congruent. Hence, there is strong evidence against sympatric speciation in North Atlantic eels. These results reiterate the need for careful consideration of cases of possible sympatric speciation, as even in seemingly barrier-free oceanic environments palaeoceanographic factors may have promoted vicariance and allopatric speciation. In the SNP dataset (Genepop and VCF files) the following individuals are European eel: LEG11 LEG9 RHG12 RHG13 RHG14 RHG16 RHG17 RHG3 RHG5 RHG6 RHG8 LEG12 RHG9 VG11 VG12 VG13 VG14 VG15 VG16 VG17 VG18 VG19 LEG13 VG20 ...
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