ArticleG3 (Bethesda, Md.)2020
Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon.
Article in G3 (Bethesda, Md.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 33 citations in OpenAlex.
- Surviving the Squeeze: Genomic Analysis of a Successful Invasion by European Common Wall Lizards (Podarcis muralis) in North America (Ohio, USA).Molecular ecology · 2026Article
- The Potential Role of Haploblocks in the Persistence of Small, Isolated Populations of Brook Trout (Ecology and evolution · 2025Article
- Sex Differentiation and Long-Distance Gene Flow in the Elusive Antarctic FishEcology and evolution · 2025Article
- Genomic Signals of Local Adaptation Associated With Environmental Variables inEcology and evolution · 2025Article
- Connections Across Open Water: A Bi-Organelle, Genomics-Scale Assessment of Atlantic-Wide Population Dynamics in a Pelagic, Endangered Apex Predator Shark (Evolutionary applications · 2025Article
- Characterization and distribution of a 14-Mb chromosomal inversion in native populations of rainbow trout (Oncorhynchus mykiss).G3 (Bethesda, Md.) · 2024Article
- Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function.G3 (Bethesda, Md.) · 2023Article
- High-density genomic data reveal fine-scale population structure and pronounced islands of adaptive divergence in lake whitefish (Evolutionary applications · 2022Article
- Neutral and adaptive loci reveal fine-scale population structure inEcology and evolution · 2022Article
- A chromosomal inversion may facilitate adaptation despite periodic gene flow in a freshwater fish.Ecology and evolution · 2022Article
- Contrasting population differentiation in two sympatricFrontiers in genetics · 2022Article
- Whole-genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self-incompatibility.Molecular ecology · 2021Article
- Population structure of chum salmon and selection on the markers collected for stock identification.Ecology and evolution · 2021Article
- A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques.G3 (Bethesda, Md.) · 2021Article
- Y-chromosome haplotypes are associated with variation in size and age at maturity in male Chinook salmon.Evolutionary applications · 2020Article
- Power of a dual-use SNP panel for pedigree reconstruction and population assignment.Ecology and evolution · 2020Article
- The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome.PloS one · 2020Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many studies exclude loci that exhibit linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the effect of the sex-determining region on population structure was only obvious after restricting analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. Our results highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of excluding or ignoring loci exhibiting LD. Blindly excluding loci in LD would have prevented detection of the sex-determining region and chromosome inversion while failing to understand the genomic features leading to high-LD could have resulted in false interpretations of population structure.
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