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We conducted whole genome sequencing of samples collected across its range. While both Gulf of Maine GoM and Canadian CAN populations exhibit the size polymorphism, we detected a significant deficit of heterozygotes at the supergene and longer stretches of homozygosity in GoM population.
Coalescent-based demographic modelling reveals strong migration between regions maintaining genetic variability in the recombining genome, preventing speciation between morphs. This study highlights short-term context-dependent evolutionary consequences of a size-determining supergene providing new insights for the management of vulnerable species. Chromosomal inversions prevent recombination, thereby maintaining the specific allelic arrangement within the genes they encompass, leading to enhanced fitness 1 , 2 , 3 , 4 , 5.
Suites of genes in inversions are often referred to as supergenes, as they can lead to the Mendelian inheritance of complex phenotypes 6 , 7. While the existence of supergene systems has long been acknowledged 8 , the accessibility of whole genome sequencing WGS data has significantly amplified their detection.
The presence of supergene-associated traits has been shown in several systems including sociality in ants 9 , 10 , 11 , 12 , 13 , migratory behavior and adaptation to salinity and temperature in Atlantic cod 14 , 15 , 16 , and wing morphology and pattern coloration in butterflies 17 , Supergenes are maintained in populations by an interplay between demographic and selective processes 6 , the relative contributions of which can be difficult to disentangle without careful reconstruction of the demographic history of populations based on neutral markers.
