Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes

Area of Science:

• Evolutionary biology
• Population genomics
• Speciation research

Background:

• Population genomic studies offer insights into genome-scale evolutionary processes.
• Genomic architecture, including islands of divergence, is crucial for adaptive population differentiation and speciation.
• Threespine stickleback is a model organism for evolutionary and speciation studies.

Purpose of the Study:

• To investigate linkage disequilibrium (LD) patterns in oceanic and freshwater threespine stickleback populations using next-generation sequencing data.
• To identify associations between LD and signatures of divergent selection.
• To assess the influence of recombination rate variation on LD patterns.

Main Methods:

• Analysis of next-generation sequencing data.
• Examination of local and long-distance linkage disequilibrium (LD).
• Assessment of divergent selection signatures and recombination rate variation.

Main Results:

• Extensive local and long-distance LD was observed in freshwater stickleback populations, consistent with unidirectional gene flow.
• Surprisingly, oceanic populations also exhibited elevated LD, particularly in regions linked to freshwater adaptation.
• These findings challenge the traditional biogeographic model.

Conclusions:

• Results support an alternative metapopulation model for stickleback radiation, involving bidirectional gene flow and strong divergent selection.
• Linkage disequilibrium is maintained within genomic islands of divergence by these processes.
• Oceanic stickleback genomic architecture may facilitate rapid evolution of multi-locus genotypes in new habitats, explaining parallel phenotypic variation.