Deviation from Hardy–Weinberg equilibrium, and temporal instability in allele frequencies at microsatellite loci in a local population of Atlantic cod

Abstract

A total of 1455 spawning cod, sampled from a local spawning area in Trondheimsfjord (Norway) between 1985 and 2002, was screened at the microsatellite loci Gmo132 and Gmo2. Samples from 15 spawning years comprising 29 consecutive cohorts were analysed. At the Gmo132 locus, but not at Gmo2, allele frequencies varied significantly among sampling years as well as cohorts, corresponding to FST-values of 0.004 and 0.006, respectively. Both loci showed examples of significant deviations from Hardy–Weinberg expectation within sampling years as well as cohorts, manifested as deficiencies of heterozygotes. Combining the p-values from the single tests (Fisher's method) revealed an overall significant p-value for deviation from the Hardy–Weinberg expectations at Gmo132 but not at Gmo2. Trend tests showed significant HW deficiencies at both loci for annual samples but not for cohorts. Possible reasons for the deficiencies were discussed; inter alia the existence of null alleles, or a form of pseudo Wahlund effect due to a patchy distribution of habitats for settling O-group cod in the Trondheimsfjord. It was noted that there might be a relationship between the relatively high temporal within-population variability of allele frequencies at Gmo132 and the fact that among microsatellite loci studied so far, Gmo132 is the one that usually shows the highest genetic differentiation geographically in cod.

A Roadmap for Bridging Basic and Applied Research in Forensic Entomology

“…It is routinely done in conservation genetics (reviewed in Reference 12), in many gene-mapping experiments when population structure correlates with a phenotype (156), and within the forensic sciences, as human populations have different frequencies of the same alleles, requiring the use of population-specific databases to more accurately identify individuals that belong to those groups (92). Tests of deviation from Hardy-Weinberg (HW) equilibrium (76), inbreeding coefficients/ fixation indices such as Wright's F st (68,155), and isolation by distance (3,42,111) can all be used to identify differentiated populations. F st can also be compared to quantitative trait divergence among populations (Q st ) to identify the effects of selection on a trait (83).…”

Atlantic cod (Gadus morhua L.) in inner and outer coastal zones of northern Norway display divergent genetic signature at non-neutral loci

“…Thus, the microsatellite data would also allow a possible discrimination of coastal cod samples that are genetically homogeneous in terms of Pan I allele frequencies. The neutrality of particularly one of the loci used herein (GMO 132) has recently been questioned (Karlsson and Mork, 2005;Nielsen et al, 2006). Whether this would detract it from being a supportive marker for discriminating between NEAC and NCC, or among populations within the NCC group, will be discussed.…”

Are low but statistically significant levels of genetic differentiation in marine fishes ‘biologically meaningful’? A case study of coastal Atlantic cod

“…Evidence has also been presented for selective effects on microsatellites (e.g. the Gmo132 locus), most likely through hitchhiking with linked genomic regions (Karlsson & Mork 2005; Nielsen et al. 2006).…”