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

Abstract

A key question in many genetic studies on marine organisms is how to interpret a low but statistically significant level of genetic differentiation. Do such observations reflect a real phenomenon, or are they caused by confounding factors such as unrepresentative sampling or selective forces acting on the marker loci? Further, are low levels of differentiation biologically trivial, or can they represent a meaningful and perhaps important finding? We explored these issues in an empirical study on coastal Atlantic cod, combining temporally replicated genetic samples over a 10-year period with an extensive capture-mark-recapture study of individual mobility and population size. The genetic analyses revealed a pattern of differentiation between the inner part of the fjord and the open skerries area at the fjord entrance. Overall, genetic differentiation was weak (average F(ST) = 0.0037), but nevertheless highly statistical significant and did not depend on particular loci that could be subject to selection. This spatial component dominated over temporal change, and temporal replicates clustered together throughout the 10-year period. Consistent with genetic results, the majority of the recaptured fish were found close to the point of release, with <1% of recaptured individuals dispersing between the inner fjord and outer skerries. We conclude that low levels of genetic differentiation in this marine fish can indeed be biologically meaningful, corresponding to separate, temporally persistent, local populations. We estimated the genetically effective sizes (N(e) ) of the two coastal cod populations to 198 and 542 and found a N(e) /N (spawner) ratio of 0.14.

Theory, consequences and evidence of eroding population spatial structure in harvested marine fishes: a review

“…The lack of genetic separation does not necessarily preclude the existence of a sympatric complex. Many factors can blur the genetic signature of demographically isolated populations, such as markers used for examining the separation, population sizes, and the isolation time (Palumbi 2003, Hutchings et al 2007, Knutsen et al 2011. In contrast to this pattern of isolation, a metapopulation is defined by the presence of several locally breeding subpopulations linked to each other by individual dispersal and each having equal potential for independent extinction and re-colonization (Smedbol et al 2002).…”

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany

“…In particular, the genome-wide analysis of 1,000s or more single nucleotide polymorphisms (SNPs) allows the determination of an individual's geographic origin with accuracy and precision, even when limited genetic differentiation exists among regions (20)(21)(22). Since low levels of genetic differentiation are typical for marine species with high dispersal capabilities like Atlantic cod (23,24), such genome-wide approaches are essential to increase the assignment power of modern (22) and ancient samples of these species (25). So far, however, aDNA studies using genome-wide approaches are lacking for marine fishes.…”

Development of gene-associated single nucleotide polymorphisms for Japanese anchovy Engraulis japonicus through cross-species amplification

“…This drawback is especially remarkable in fish species, which are typically characterized by high mutation rates [44]. Consequently, only a few examples of cross-species SNP amplification are available in fish species (see Table 3).…”