Allochrony is a form of reproductive isolation characterized by differences in the timing of breeding and may play a crucial role in the genetic and phenotypic divergence within species. This study explores the genetic and phenotypic divergence in Atlantic lumpfish (Cyclopterus lumpus), focusing on spring and autumn spawners along the Norwegian coast. Through genomic analysis and otolith morphology, we identified pronounced genetic and morphologic differences between the two spawning groups. Notably, chromosomes 13 and 14 exhibited local adaptations, while chromosome 1 showed parallel evolution across different localities, suggesting broader evolutionary processes influencing reproductive isolation and adaptive divergence. Functional analysis revealed genes on chromosome 1 associated with responses to environmental stressors, possibly adaptations to seasonal variations at high latitudes. Morphological analysis of otoliths supported these findings, showing differences that may be adaptations to seasonal light availability. The presence of genomic islands of divergence, alongside a general lack of differentiation across the mitochondrial genome, suggests recent and rapid selection processes potentially moderated by ongoing gene flow. This study underscores the importance of considering temporal genetic structures in conservation and management strategies, particularly for species with bimodal spawning time to prevent overexploitation and optimize breeding programs.

Genomic architecture is a key evolutionary trait for living organisms. Due to multiple complex adaptive and neutral forces which impose evolutionary pressures on genomes, there is a huge disparity of genomic features. However, existing genome architecture studies are taxon biased, and thus a wider picture should be obtained by expanding the taxonomic scope. Moreover, the extent to which genomic architecture determines the typology of loci recovered in reduced representation sequencing techniques with digestion enzymes is largely unexplored. Here, we observed that whereas plants mostly increase their genome size by expanding their intergenic regions, animals expand both intergenic and intronic regions, although the expansion patterns differ between deuterostomes and protostomes. We found positive correlations between the percentage of loci obtained with in-silico digestion using 2b-enzymes mapping in introns, exons and intergenic categories and the percentage of these regions in the genome. However, exonic regions showed a significant enrichment regardless of the enzyme used. Moreover, the percentage of loci retained after secondary reductions varied with selective-adaptors and genome GC content. In summary, we show that genome architecture has an impact on the markers obtained in reduced representation sequencing that should be considered in conservation genomics for correct wildlife management.