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.
Little is known about local adaptations in marine fishes since population genetic surveys in these species have typically not applied genetic markers subject to selection. In this study, we used a ...candidate gene approach to investigate adaptive population divergence in the European flounder (Platichthys flesus L.) throughout the northeastern Atlantic. We contrasted patterns of genetic variation in a presumably neutral microsatellite baseline to patterns from a heat-shock cognate protein gene, Hsc70. Using two different neutrality tests we found that the microsatellite data set most likely represented a neutral baseline. In contrast, Hsc70 strongly deviated from neutral expectations. Importantly, when estimating standardized levels of population divergence (F(ST)'), we also found a large discrepancy in the patterns of structuring in the two data sets. Thus, samples grouped according to geographical or historical proximity with regards to microsatellites, but according to environmental similarities with regards to Hsc70. The differences between the data sets were particularly pronounced in pairwise comparisons involving populations in the western and central Baltic Sea. For instance, the genetic differentiation between geographically close Baltic Sea and North Sea populations was found to be 0.02 and 0.45 for microsatellites and Hsc70 respectively. Our results strongly suggest adaptive population divergence and indicate local adaptations at the DNA level in a background of high levels of gene flow, typically found in many marine fish species. Furthermore, this study highlights the usefulness of the candidate gene approach for demonstrating local selection in non-model organisms such as most marine fishes.
Changing environmental conditions can lead to population diversification through differential selection on standing genetic variation. Structural variant (SV) polymorphisms provide examples of ...ancient alleles that in time become associated with novel environmental gradients. The European plaice (Pleuronectes platessa) is a marine flatfish showing large allele-frequency differences at two putative SVs associated with environmental variation. In this study, we explored the contribution of these SVs to population structure across the North East Atlantic. We compared genome-wide population structure using sets of RAD-sequencing SNPs with the spatial structure of the SVs. We found that in contrast to the rest of the genome, the SVs were only weakly associated with an isolation-by-distance pattern. Indeed, both SVs showed important variation in haplogroup frequencies, with the same haplogroup increasing both along the salinity gradient of the Baltic Sea, and found in high frequency in the northern-range margin of the Atlantic. Phylogenetic analyses suggested that the SV alleles are much older than the age of the Baltic Sea itself. These results suggest that the SVs are older than the age of the environmental gradients with which they currently co-vary. Altogether, our results suggest that the plaice SVs were shaped by evolutionary processes occurring at two time frames, firstly following their origin, ancient spread and maintenance in the ancestral populations, and secondly related to their current association with more recently formed environmental gradients such as those found in the North Sea-Baltic Sea transition zone.
Coexistence in the same habitat of closely related yet genetically different populations is a phenomenon that challenges our understanding of local population structure and adaptation. Identifying ...the underlying mechanisms for such coexistence can yield new insight into adaptive evolution, diversification and the potential for organisms to adapt and persist in response to a changing environment. Recent studies have documented cryptic, sympatric populations of Atlantic cod (Gadus morhua) in coastal areas. We analysed genetic origin of 6,483 individual cod sampled annually over 14 years from 125 locations along the Norwegian Skagerrak coast and document stable coexistence of two genetically divergent Atlantic cod ecotypes throughout the study area and study period. A “fjord” ecotype dominated in numbers deep inside fjords while a “North Sea” ecotype was the only type found in offshore North Sea. Both ecotypes coexisted in similar proportions throughout coastal habitats at all spatial scales. The size‐at‐age of the North Sea ecotype on average exceeded that of the fjord ecotype by 20% in length and 80% in weight across all habitats. Different growth and size among individuals of the two types might be one of several ecologically significant variables that allow for stable coexistence of closely related populations within the same habitat. Management plans, biodiversity initiatives and other mitigation strategies that do not account for the mixture of species ecotypes are unlikely to meet objectives related to the sustainability of fish and fisheries.
Fish serve as transport hosts to a range of parasites, with potential negative effects on fish health. In the Baltic Sea, the grey seal Halichoerus grypus (Fabricius) population has increased ...markedly since the early 2000s. H. grypus is the main final host to the liver worm Contracaecum osculatum (Rudolphi, 1802), a parasitic nematode to which cod Gadus morhua (Linnaeus) is one of several transport hosts. Recent investigations have shown a marked increase in prevalence and abundance of infection of this parasite in livers of G. morhua inhabiting the central Baltic Sea. Yet no recent knowledge exists on levels of C. osculatum infection in G. morhua in adjacent areas. We investigated spatial differences in prevalence and abundance of this parasitic nematode in livers of G. morhua, covering a transect consisting of 9 areas from the Skagerrak to the eastern part of the central Baltic Sea. We further provide survey data of local abundances of H. grypus and harbour seal Phoca vitulina (Linnaeus) throughout this transect. Prevalence and abundance of C. osculatum sensu stricto in G. morhua livers differed significantly between east and west, with highest levels of infection occurring in the low-salinity central Baltic areas. Fish in the east had significantly lower condition than their westerly conspecifics. Spatial differences in local seal abundance and seal species, salinity and feeding ecology may explain the observed differences in C. osculatum infection between eastern and western G. morhua.
Factors such as oceanographic retention, isolation by distance and secondary contact zones have, among others, been suggested to explain the low, but statistically significant, neutral population ...structure observed in many marine fishes. European sprat Sprattus sprattus L. is not known to display philopatric spawning behaviour or to exhibit local retention of eggs and larvae. It thus constitutes a good model for studying population structure in a characteristic small pelagic fish with high dispersal potential and an opportunistic life history. We analysed 931 specimens of sprat from 9 spawning locations in and around the North Sea and Baltic Sea area and from a geographically distant population from the Adriatic Sea. Analyses of 9 microsatellite loci revealed a sharp genetic division separating samples from the northeastern Atlantic Ocean and the Baltic Sea (pairwise f = 0.019 to 0.035), concurring with a steep salinity gradient. We found, at most, weak structure among samples within the northeastern Atlantic region and within the Baltic Sea (pairwise f = 0.001 to 0.009). The Adriatic Sea population was highly differentiated from all northern samples (pairwise f = 0.071 to 0.092). Overall, the observed population structure resembles that of most other marine fishes studied in the North and Baltic Sea areas. Nevertheless, spatially explicit differences are observed among species, probably reflecting specific life histories. Such fine-scale population structures should be taken into account when considering complex ecosystem functions, e.g. in multispecies stock management.
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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