Computational protocol: Historical changes in genotypic frequencies at the Pantophysin locus in Atlantic cod (Gadus morhua) in Icelandic waters: evidence of fisheries-induced selection?

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Protocol publication

[…] Changes in the age distribution between sampling years were tested using chi-square tests. In situations of low expected values (<5), samples from cod aged 6 years or younger, and eleven years or older, were pooled together. The changes in Pan I genotype frequencies between age groups and cohort classes were also tested using chi-square tests. For these tests, individuals aged 5 years or younger, and aged twelve years or older, were pooled, while all intermediate age classes were kept separate.To investigate the long-term consistency of genotypic change by age, we pooled the samples in three time periods. The earliest period consisted of samples collected in 1948, 1957, 1959 and 1966 when average fishing mortality is estimated to have been <0.3. The middle period, characterized by an average fishing mortality of 0.6, contained samples from 1972, 1973, 1976 and 1979. The latest period comprised samples collected in 1985, 1996, 2000 and 2002 and featured several peaks of very high fishing mortality (>0.8).We used a multinomial log-linear model () to explore changes in genotype frequencies with time. The purpose of the model was to describe the long-term changes in genotype frequencies of cohorts 1932–1999, after taking into account that some cohorts were only sampled at a younger age and other cohorts only at an older age. In a single model, we fitted the frequencies of Pan I genotypes Pan IAA, Pan IAB and Pan IBB as a smooth function of both cohort and age. The smooth functions for cohort and age were natural cubic splines, each with 3 degrees of freedom. The multinomial model ensures that the predicted relative frequencies of the three Pan I genotypes sum to one within each cohort-age stratum.Potential differences in growth between the Pan I genotypes were investigated by analysing length-at-age data, combined for all years. The analyses included cod aged 7–9 years only since those age classes contained sufficient individuals from all three Pan I genotypes in all time periods. To test whether differences in growth of Icelandic cod were related to their Pan I genotype, mean length was modelled using analysis of covariance (ANCOVA) with Pan I genotype as the categorical independent variable and age as continuous covariate.For the suite of six microsatellite loci, observed (HO) and expected (HE) heterozygosity were calculated in GENETIX 4.03 (). Tests for deviations from Hardy–Weinberg equilibrium (HWE) were conducted for both the Pan I locus and the suite of six microsatellite loci using the exact test in GENEPOP 3.1 (). Genetic differentiation between sampling sites and all pairs of populations was estimated with pairwise FST estimates following , and 95% confidence intervals were determined by bootstrapping over loci. The program FSTAT 2.9.2 () was used for this analysis. An analysis of molecular variance (AMOVA) was carried out for both the Pan I locus and the suite of six microsatellite loci in ARLEQUIN 3.0 () to assess hierarchical partitioning of genetic variance. The genetic relationships among samples were further analysed using principal component analysis and visualized with a multidimensional scaling (MDS) plot based on a matrix of pairwise FST′s. […]

Pipeline specifications

Software tools Genepop, Arlequin
Application Population genetic analysis
Organisms Gadus morhua