Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata)

The importance of speciation-with-gene-flow scenarios is increasingly appreciated. However, the specific processes and the resulting genomic footprints of selection are subject to much discussion. We studied the genomics of speciation between the two panmictic, sympatrically spawning sister-species; European (Anguilla anguilla) and American eel (A. rostrata). Divergence is assumed to have initiated more than 3 million years ago, and although low gene flow still occurs strong postzygotic barriers are present. Restriction-site Associated DNA (RAD) sequencing identified 328,300 SNPs for subsequent analysis. However, despite the presence of 3,757 strongly differentiated SNPs (FST > 0.8), sliding window analyses of FST showed no larger genomic regions (i.e. hundreds of thousands to millions of bases) of elevated differentiation. Overall FST was 0.041 and linkage disequilibrium was virtually absent for SNPs separated by more than 1000 bp. We suggest this to reflect a case of genomic hitchh...