Trial Sequential Analysis (TSA) is a frequentist method to help researchers control the risks of random errors in meta‐analyses.1 Fisher et al.2 used TSA on cell therapy for heart diseases. The ...present article discusses the usefulness of TSA and its dependence on the choice of the parameters for calculation of the required information size and the adjacent monitoring boundaries, and comments on the approach by Fisher et al.2
Recent improvements in the speed, cost and accuracy of next generation sequencing are revolutionizing the discovery of single nucleotide polymorphisms (SNPs). SNPs are increasingly being used as an ...addition to the molecular ecology toolkit in nonmodel organisms, but their efficient use remains challenging. Here, we discuss common issues when employing SNP markers, including the high numbers of markers typically employed, the effects of ascertainment bias and the inclusion of nonneutral loci in a marker panel. We provide a critique of considerations specifically associated with the application and population genetic analysis of SNPs in nonmodel taxa, focusing specifically on some of the most commonly applied methods.
Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in aquaculture production. Consequently, more captive-bred fish are released ...into the wild through accidental escape or deliberate releases. The increased mixing of captive-bred and wild fish may affect the ecological and/or genetic integrity of wild fish populations. Unambiguous identification tools for captive-bred fish will be highly valuable to manage risks (fisheries management) and tracing of escapees and seafood products (wildlife forensics). Using single nucleotide polymorphism (SNP) data from captive-bred and wild populations of Atlantic cod Gadus morhua L. and sole Solea solea L., we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive-bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterized the broodstock and escapees originated from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive-bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case-by-case strategy when choosing the best method.
Genetic population structure of turbot (Scophthalmus maximus L.) in the Northeast Atlantic was investigated using eight highly variable microsatellite loci. In total 706 individuals from eight ...locations with temporal replicates were assayed, covering an area from the French Bay of Biscay to the Aaland archipelago in the Baltic Sea. In contrast to previous genetic studies of turbot, we found significant genetic differentiation among samples with a maximum pairwise FST of 0.032. Limited or no genetic differentiation was found among samples within the Atlantic/North Sea area and within the Baltic Sea, suggesting high gene flow among populations in these areas. In contrast, there was a sharp cline in genetic differentiation going from the low saline Baltic Sea to the high saline North Sea. The data were explained best by two divergent populations connected by a hybrid zone; however, a mechanical mixing model could not be ruled out. A significant part of the genetic variance could be ascribed to variation among years within locality. Nevertheless, the population structure was relatively stable over time, suggesting that the observed pattern of genetic differentiation is biologically significant. This study suggests that hybrid zones are a common phenomenon for marine fishes in the transition area between the North Sea and the Baltic Sea and highlights the importance of using interspecific comparisons for inferring population structure in high gene flow species such as most marine fishes.
In recent years, variation in gene expression has been recognized as an important component of environmental adaptation in multiple model species, including a few fish species. There is, however, ...still little known about the genetic basis of adaptation in gene expression resulting from variation in the aquatic environment (e.g. temperature, salinity and oxygen) and the physiological effect and costs of such differences in gene expression. This review presents and discusses progress and pitfalls of applying gene expression analyses to fishes and suggests simple frameworks to get started with gene expression analysis. It is emphasized that well‐planned gene expression studies can serve as an important tool for the identification of selection in local populations of fishes, even for non‐traditional model species where limited genomic information is available. Recent studies focusing on gene expression variation among natural fish populations are reviewed, highlighting the latest applications that combine genetic evidence from neutral markers and gene expression data.
The study of hybrid zones is central to our understanding of the genetic basis of reproductive isolation and speciation, yet very little is known about the extent and significance of hybrid zones in ...marine fishes. We examined the population structure of cod in the transition area between the North Sea and the Baltic Sea employing nine microsatellite loci. Genetic differentiation between the North Sea sample and the rest increased along a transect to the Baltic proper, with a large increase in level of differentiation occurring in the Western Baltic area. Our objective was to determine whether this pattern was caused purely by varying degrees of mechanical mixing of North Sea and Baltic Sea cod or by interbreeding and formation of a hybrid swarm. Simulation studies revealed that traditional Hardy–Weinberg analysis did not have sufficient power for detection of a Wahlund effect. However, using a model‐based clustering method for individual admixture analysis, we were able to demonstrate the existence of intermediate genotypes in all samples from the transition area. Accordingly, our data were explained best by a model of a hybrid swarm flanked by pure nonadmixed populations in the North Sea and the Baltic Sea proper. Significant correlation of gene identities across loci (gametic phase disequilibrium) was found only in a sample from the Western Baltic, suggesting this area as the centre of the apparent hybrid zone. A hybrid zone for cod in the ecotone between the high‐saline North Sea and the low‐saline Baltic Sea is discussed in relation to its possible origin and maintenance, and in relation to a classical study of haemoglobin variation in cod from the Baltic Sea/Danish Belt Sea, suggesting mixing of two divergent populations without interbreeding.
Worldwide, many commercial fish stocks have experienced dramatic declines due to overfishing. Such fisheries-induced population reductions could potentially erode the genetic diversity of marine fish ...populations. Based on analyses of DNA extracted from archived and contemporary samples, this paper compares the genetic variability at nine microsatellite loci in a Canadian population of Atlantic cod (
Gadus morhua
) over 80 years, spanning from before the fishery intensified to now when the population is at historically low abundance. Extensively validated genetic data from the temporally spaced samples were used to estimate the effective population size. Over the period, we observed no loss of either heterozygosity or allelic diversity. Several of the estimation methods applied could not distinguish the effective population size from infinity, and the lower 95% confidence limit on estimates was generally >500, suggesting that the effective population size is probably considerably larger than this. Hence, it appears that the southern Gulf of St. Lawrence cod stock has maintained genetic variability to sustain future evolution despite a dramatic population decline.
DNA from archived otoliths was used to explore the temporal stability of the genetic composition of two cod populations, the Moray Firth (North Sea) sampled in 1965 and 2002, and the Bornholm Basin ...(Baltic Sea) sampled in 1928 and 1997. We found no significant changes in the allele frequencies for the Moray Firth population, while subtle but significant genetic changes over time were detected for the Bornholm Basin population. Estimates of the effective population size (Ne) generally exceeded 500 for both populations when employing a number of varieties of the temporal genetic method. However, confidence intervals were very wide and Ne's most likely range in the thousands. There was no apparent loss of genetic variability and no evidence of a genetic bottleneck for either of the populations. Calculations of the expected levels of genetic variability under different scenarios of Ne showed that the number of alleles commonly reported at microsatellite loci in Atlantic cod is best explained by Ne's exceeding thousand. Recent fishery‐induced bottlenecks can, however, not be ruled out as an explanation for the apparent discrepancy between high levels of variability and recently reported estimates of Ne << 1000. From life history traits and estimates of survival rates in the wild, we evaluate the compatibility of the species’ biology and extremely low Ne/N ratios. Our data suggest that very small Ne's are not likely to be of general concern for cod populations and, accordingly, most populations do not face any severe threat of losing evolutionary potential due to genetic drift.
Recent technical advances have stimulated studies on spatial scales of adaptive genetic variation in marine fishes. However, very few studies have combined spatial and temporal sampling to ...investigate adaptive genetic structuring at local and microgeographical scales, i.e. scales at which neutral genetic markers have typically revealed very limited levels of population structure. In the present study we analyzed 92 gene-associated single-nucleotide polymorphism (SNP) markers in Atlantic codGadus morhuafrom several sampling sites within the North Sea and adjacent areas. To test for temporal stability, we included long- and short-term (i.e. from 24 to 38 and from 8 to 11 yr, respectively) temporally replicated samples from a subset of populations. As expected, we found very low levels of neutral genetic population structure (FST= 0.003). Three specific loci, however, showed highly elevated levels of genetic differentiation. Interestingly, these loci were identical to loci previously found to display signals of adaptive evolution on larger spatial scales. Analysis of historical samples revealed long-term temporally stable patterns of both neutral and adaptive divergence between some populations, indicating long-term temporal adaptive stability driven by strong local selection. In an environmentally dynamic area, on the other hand, patterns of genetic structuring were more variable. Overall, our results not only suggest separation of populations under both evolutionary and ecological paradigms, but also illustrate the usefulness of the spatio-temporal approach for making inferences about the dynamics and geographical distribution of adaptive genetic variation in natural populations.
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