Data from: Genomic footprints of hybridization in North Atlantic eels (Anguilla anguilla and A. rostrata)

Understanding interspecific introgressive hybridization and the biological
significance of introgressed variation remains an important goal in
population genomics. European (Anguilla anguilla) and American eel (A.
rostrata) represent a remarkable case of hybridization. Both are 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 using
whole-genome sequences of 78 individuals, including 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. However, local ancestry
inference along individual chromosomes revealed that Icelandic hybrids
were primarily F1 or first-generation backcrosses toward European eel,
with some showing more complex backcrossing. All European eels outside
Iceland contained short chromosomal blocks from American eel, indicating a
porous genome. We found no evidence for previously hypothesized
geographical gradients of introgression in European eel outside Iceland.
Several chromosomal regions showed high interspecific divergence, but
haplotype blocks introgressed from American eel were identified both
within and outside these regions. There was little correspondence between
regions of high relative (FST) and absolute divergence (dXY), with the
former reflecting selective sweeps within species or reduced recombination
rather than barrier loci. A single genomic region showed evidence of
repeated introgression from American into European eel under positive
selection in both species. The study illustrates that species can maintain
genetic integrity despite porous genomes, and that standing variation in
one species can potentially be available for future adaptive responses in
the other species.