Can we rely on selected genetic markers for population identification? Evidence from coastal Atlantic cod

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.

Disparate movement behavior and feeding ecology in sympatric ecotypes of Atlantic cod

“…In total, 43% of cod tagged with acoustic transmitters belonged to be North Sea ecotype, while the remaining 57% belonged to the Fjord ecotype. The genetic origin analysis has some uncertainty (5%) in assigning fjord individuals correctly (Jorde, Synnes, et al, 2018) and a few individuals might have been misclassified in our data.…”

“…Twenty‐seven SNPs were previously developed to segregate between “Fjord‐” and “North Sea” individuals, and there were genotyped on a MassARRAY platform (Sequenom Inc.) at the IMR laboratory in Bergen, Norway. Genetic assignment of individual cod to ecotype was computed using the GeneClass2 software (Piry et al., 2004 ), using previously sampled reference populations of “Fjord” and “North Sea” cod (see Jorde, Synnes, et al., 2018 for additional information). The Bayesian method of (Rannala & Mountain, 1997 ) was used where a score >80% is needed in order to classify each individual either as a North Sea ecotype or Fjord ecotype.…”

“…Genetic assignment of individual cod to ecotype was computed using the GeneClass2 software (Piry et al, 2004), using previously sampled reference populations of "Fjord" and "North Sea" cod (see Jorde, Synnes, et al, 2018 for additional information). The Bayesian method of (Rannala & Mountain, 1997) was used where a score >80% is needed in order to classify each individual either as a North Sea ecotype or Fjord ecotype.…”

Single nucleotide polymorphisms reveal a genetic cline across the north‐east Atlantic and enable powerful population assignment in the European lobster

“…The development and use of SNP panels composed of high‐ranking loci has proven to be extremely informative for assignment studies (e.g. Nielsen et al, ; Storer et al, ) and appears to offer particular promise for marine organisms showing weak overall genetic differentiation (Jorde, Synnes, Espeland, Sodeland, & Knutsen, ). In this study, the predictive model built using the baseline data composed of 79 SNPs was able to correctly assign 871 out of 874 (99.7%) “unknown” lobsters to their correct basin of origin.…”

SNP genotyping reveals substructuring in weakly differentiated populations of Atlantic cod (Gadus morhua) from diverse environments in the Baltic Sea

“…Genotyping a significant number of SNP loci also provides an opportunity to identify 'outliers' (i.e. loci under selection 20,21 ), which can be more informative markers in defining conservation units in comparison with neutral SNP markers [22][23][24][25][26] .…”