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.Funding provided by: Marine S & T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology*Crossref Funder Registry ID: Award Number: 2018SDKJ0501-2Funding provided by: National Natural Science Foundation of ChinaCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809Award Number: 31172411Funding provided by: Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery SciencesCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100012428Award Number: 2060302202000