Genomic landscape of among-subspecies divergence
The genic view of speciation has provided a schema for thinking about how genetic divergence across the genome evolves as speciation proceeds under the antagonistic forces of natural selection and gene flow (Feder et al., 2012; Wu, 2001; Wu & Ting, 2004). Initially gene flow is extensive across the genome, except at a few loci under strong divergent selection. These loci exhibiting excess of divergence are like islands emerging over sea. Genomic islands expand gradually via genetic hitchhiking. As genetic differentiation associated with reproductive isolation accumulates, genetic hitchhiking grades into genomic hitchhiking. Lastly, complete reproductive isolation is established and gene flow is impeded by various forms of behavioral, ecological, or genetic incompatibilities (Abbott, 2017; Abbott et al., 2013; Seehausen et al., 2014). With the establishment of full species, genomic islands with high divergence have expanded to a whole plateau, i.e. high divergence across most or all of the genome (Wu, 2001; Wu & Ting, 2004; Feder, Egan, & Nosil, 2012; Feder, Flaxman, Egan, Comeault, & Nosil, 2013).
We estimate that only about 10% of the genome shows excess genetic divergence among the three subspecies of A. marina. The proportion not affected by gene flow is around 3%. This pattern indicates a small portion of the genome belongs to genomic islands of speciation. Some degree of genetic differentiation may exist in the rest of the genome in one subspecies or some populations, or almost no differentiation among subspecies. At this stage, analyses using markers covering 10% of the genome may recognize the three taxa as full species, while those using markers sampled from the rest may indicate no more than structured populations.