Rare alleles increase genome-wide in a hybrid zone

In mutation-order speciation, different series of alleles are fixed in populations adapting to identical environments1,2. These may include gene pairs which are beneficial within each population, but cause reproductive isolation when combined in hybrids. It has been predicted (Ref. 3: p. 372) that the continuous generation of genotypes recombined for such loci in the centre of a hybrid zone will create a novel selection regime, favouring variants at speciation genes that reduce hybrid disadvantage, and any markers associated with them. This process may explain the frequent observation4-10 of unexpected gene variants in hybrid zones, the so-called “rare-allele phenomenon”. Here, we use Illumina sequencing in a snail hybrid zone to reveal that this pattern is indeed widespread throughout the genome, involving thousands of loci. This “rare-allele phenomenon” allows more direct assessment of the genomic architecture of speciation, and in particular could be employed as a quick method for finding speciation genes in non-model organisms.