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

Autor: Shi Y; College of Fisheries and Ocean Sciences University of Alaska Fairbanks Juneau Alaska USA.; Wisconsin Cooperative Fishery Research Unit, College of Natural Resources University of Wisconsin-Stevens Point Stevens Point Wisconsin USA., Homola JJ; U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, College of Natural Resources University of Wisconsin-Stevens Point Stevens Point Wisconsin USA., Euclide PT; Wisconsin Cooperative Fishery Research Unit, College of Natural Resources University of Wisconsin-Stevens Point Stevens Point Wisconsin USA., Isermann DA; U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, College of Natural Resources University of Wisconsin-Stevens Point Stevens Point Wisconsin USA., Caroffino DC; Michigan Department of Natural Resources Charlevoix Research Station Charlevoix Michigan USA., McPhee MV; College of Fisheries and Ocean Sciences University of Alaska Fairbanks Juneau Alaska USA., Larson WA; U.S. Geological Survey, Wisconsin Cooperative Fishery Research Unit, College of Natural Resources University of Wisconsin-Stevens Point Stevens Point Wisconsin USA.; National Marine Fisheries Service, Alaska Fisheries Science Center, Auke Bay Laboratories National Oceanic and Atmospheric Administration Juneau Alaska USA.
Jazyk: angličtina
Zdroj: Evolutionary applications [Evol Appl] 2022 Sep 20; Vol. 15 (11), pp. 1776-1791. Date of Electronic Publication: 2022 Sep 20 (Print Publication: 2022).
DOI: 10.1111/eva.13475
Abstrakt: 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 the management of Lake Michigan's lake whitefish fishery and highlights the utility of incorporating adaptive loci into fisheries management.
Competing Interests: The authors declare no conflict of interest.
(© 2022 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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