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.