High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Coregonus clupeaformis) from Lake Michigan

Understanding patterns of genetic structure and adaptive variation in
natural populations is crucial for informing conservation and management.
Past genetic research using 11 microsatellite loci identified six genetic
stocks of lake whitefish (Coregonus clupeaformis) within Lake Michigan,
USA. However, ambiguity in genetic stock assignments suggested those
neutral microsatellite markers did not provide adequate power for
delineating lake whitefish stocks in this system, prompting calls for a
genomics approach to investigate stock structure. Here, we generated a
dense genomic dataset to characterize population structure and investigate
patterns of neutral and adaptive genetic diversity among lake whitefish
populations in Lake Michigan. Using Rapture sequencing, we genotyped 829
individuals collected from 17 baseline populations at 197,588 SNP markers
after quality filtering. Although the overall pattern of genetic structure
was similar to the previous microsatellite study, our genomic data
provided several novel insights. Our results indicated a large genetic
break between the northwestern and eastern sides of Lake Michigan, and we
found a much greater level of population structure on the eastern side
compared to the northwestern side. Collectively, we observed five genomic
islands of adaptive divergence on five different chromosomes. Each island
displayed a different pattern of population structure, suggesting that
combinations of genotypes at these adaptive regions are facilitating local
adaptation to spatially heterogenous selection pressures. Additionally, we
identified a large linkage disequilibrium block of ~8.5 Mb on chromosome
20 that is suggestive of a putative inversion but with a low frequency of
the minor haplotype. Our study provides a comprehensive assessment of
population structure and adaptive variation that can help inform
management of Lake Michigan's lake whitefish fishery and highlights
the utility of incorporating adaptive loci into fisheries
management.