Linked selection, differential introgression and recombination rate variation promote heterogeneous divergence in a pair of yellow croakers

Understanding the mechanisms underlying heterogeneous genomic divergence
is of particular interest in evolutionary biology. Highly differentiated
genomic regions, known as genomic islands, often evolve between diverging
lineages. These genomic islands may be related to selection promoting
adaptation or reproductive isolation. Based on whole genome assembly and
genome-wide RAD sequencing in a pair of yellow croakers (genus:
Larimichthys), we investigated the evolutionary processes shaping genomic
landscapes of divergence. Demographic modelling indicated that the two
species diverged following a secondary contact scenario, where
differential introgression and linked selection were suggested to be
involved in heterogeneous genomic divergence. We identified reduced
recombination rate in genomic islands and a relatively good conservation
of both genetic diversity and recombination landscapes between species,
which highlight the roles of linked selection and recombination rate
variation in promoting heterogeneous divergence in the common ancestral
lineage of the two species. In addition, we found a positive correlation
between differentiation (FST) and absolute sequence divergence (Dxy), and
elevated Dxy in genomic islands, which were different from the patterns
under linked selection. Restricted gene flow in highly differentiated
regions has likely remodeled the landscape of heterogeneous genomic
divergence. Moreover, genomic islands showed little evidence of
overlapping within and between species, implying that high gene flow and
divergent selection when colonizing new habitats have reshaped the
patterns of intraspecific divergence. This study highlights that highly
differentiated genomic regions can also be from linked selection and
variation of recombination rate, and thus are not necessarily related to
speciation islands or local adaptation.