Abstract
The use of genetic markers under putative selection in population studies carries the potential for erroneous identification of populations and misassignment of individuals to population of origin. Selected markers are nevertheless attractive, especially in marine organisms that are characterized by weak population structure at neutral loci. Highly fecund species may tolerate the cost of strong selective mortality during early life stages, potentially leading to a shift in offspring genotypes away from the parental proportions. In Atlantic cod, recent genetic studies have uncovered different genotype clusters apparently representing phenotypically cryptic populations that coexist in coastal waters. Here, we tested if a high‐graded SNP panel specifically designed to classify individual cod to population of origin may be unreliable because of natural selection acting on the SNPs or their linked background. Temporal samples of cod were collected from two fjords, starting at the earliest life stage (pelagic eggs) and carried on until late autumn (bottom‐settled juveniles), covering the period during summer of high natural mortality. Despite the potential for selective mortality during the study period, we found no evidence for selection, as both cod types occurred throughout the season, already in the earliest egg samples, and there was no evidence for a shift during the season in the proportions of one or the other type. We conclude that high‐graded marker panels under putative natural selection represent a valid and useful tool for identifying biological population structure in this highly fecund species and presumably in others.
Highlights
IntroductionIn order to increase statistical power to resolve weak population genetic structure, a select panel of loci with higher than average level of genetic differentiation is often employed (André et al, 2011; Banks, Eichert, & Olsen, 2003; Henriques et al, 2018; Johansen et al, 2018; Jorde, Kleiven, et al, 2018; Larson, Seeb, Pascal, Templin, & Seeb, 2014; Nielsen et al, 2012; Russello, Kirk, Frazer, & Askey, 2012)
Strong selection acting on standing genetic variation could in principle lead to different clusters of genotypes, predominating in different environments, that could be mistaken for genetically differentiated biological populations
If selective survival of members from a common gene pool was responsible for generating genetic clusters of Atlantic cod in Skagerrak coastal waters, the shift in genotypic composition would be expected to take place during a period of strong natural mortality
Summary
In order to increase statistical power to resolve weak population genetic structure, a select panel of loci with higher than average level of genetic differentiation is often employed (André et al, 2011; Banks, Eichert, & Olsen, 2003; Henriques et al, 2018; Johansen et al, 2018; Jorde, Kleiven, et al, 2018; Larson, Seeb, Pascal, Templin, & Seeb, 2014; Nielsen et al, 2012; Russello, Kirk, Frazer, & Askey, 2012). Individuals and genotypes sampled after an episode of selective mortality may poorly represent the parental generation and could lead to false impressions of population structuring Such a scenario is illustrated, depicting the outcome of hypothetical selective mortality on genotype composition following transport of juveniles to different nursery areas.
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