Related Experiment Video
Updated: Jun 30, 2025
04:52
Following the Dynamics of Structural Variants in Experimentally Evolved Populations
Published on: February 3, 2023
962
Investigating structural variant, indel and single nucleotide polymorphism differentiation between locally adapted
Laurie Lecomte1,2, Mariann Árnyasi3, Anne-Laure Ferchaud1,2,4
1Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Canada.
Evolutionary Applications
|March 18, 2024
Summary
Genomic structural variants (SVs) are crucial for evolution but hard to study in wild populations. This study successfully characterized SVs in Atlantic salmon, revealing their role in local adaptation and potential links to neural development.
Area of Science:
- Population Genomics
- Evolutionary Biology
- Genetics
Background:
- Genomic structural variants (SVs) are key to intraspecific polymorphism and evolution but are challenging to detect in wild populations using short-read sequencing.
- Atlantic salmon (Salmo salar) populations exhibit significant variation in life history and habitat, making them ideal for studying adaptive polymorphism.
- The contribution of SVs to fine-scale local adaptation in salmonids remains largely unexplored.
Purpose of the Study:
- To comparatively analyze structural variants (SVs), single nucleotide polymorphisms (SNPs), and small indels in two putatively locally adapted Atlantic salmon populations (Romaine and Puyjalon).
- To investigate the role of SVs in local adaptation by examining their distribution and association with phenotypic variation in growth, fecundity, and age at maturity/smoltification.
- To demonstrate the feasibility of large-scale SV characterization in wild salmonid populations.
Main Methods:
- Employed a hybrid sequencing approach combining short-read (16X) and long-read (20X) data for comprehensive variant discovery.
- Utilized graph-based genotyping to characterize SVs across 60 Atlantic salmon genomes.
- Performed comparative analysis of SVs, SNPs, and small indels, including population structure, FST, and outlier detection using Redundancy Analysis (RDA).
Main Results:
- Identified a substantial number of variants: 115,907 SVs, 8,777,832 SNPs, and 1,089,321 small indels, with SVs covering significantly more base pairs than SNPs.
- Observed congruent population structures and similar patterns of FST and variant density across all three variant types (SVs, SNPs, indels).
- Identified candidate variants associated with local adaptation, with nearby genes enriched for nervous system functions, suggesting a role in neural development and life history variation.
Conclusions:
- Large-scale SV characterization is feasible and highly relevant for understanding population genomics in salmonids.
- SVs contribute to local adaptation in Atlantic salmon, potentially influencing key life history traits through mechanisms like altered neural development.
- This study provides a foundation for future research on the evolutionary impact of structural variation in wild populations.
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