Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes

Area of Science:

• Population genetics
• Evolutionary biology
• Conservation genetics

Background:

• Quantifying evolutionary processes like genetic drift and selection on genome-wide allele frequencies in natural populations is challenging.
• Steelhead trout (Oncorhynchus mykiss) populations have experienced declines due to anthropogenic impacts, making their genetic variation a key conservation concern.

Purpose of the Study:

• To investigate genetic variation at major effect loci in steelhead populations.
• To contrast patterns of selection at key loci with neutral genetic drift.
• To understand the influence of evolutionary processes, including anthropogenic impacts, on allele frequencies.

Main Methods:

• Whole-genome resequencing of 74 steelhead populations.
• Analysis of approximately 8 million single nucleotide polymorphisms (SNPs).
• Comparison of genome-wide patterns with variation at major effect loci associated with migration timing and age at maturity.

Main Results:

• Genome-wide SNP patterns were consistent with neutral population structure.
• Allelic variation at major effect loci (e.g., GREB1L/ROCK1, SIX6) showed signals of selection, differing between Coastal and Inland lineages.
• Local natural selection and anthropogenic influences, including artificial selection in hatcheries and gene flow, affected allele frequencies in the Inland lineage.

Conclusions:

• Evolutionary processes, including selection and anthropogenic effects, significantly influence allele frequencies at major effect loci in steelhead.
• Understanding these mechanisms is critical for conserving phenotypic traits and life history variation in this protected species.
• Genetic variation at key loci reflects adaptation and human impacts, providing insights for effective conservation strategies.