Historical and recent genetic bottlenecks in European grayling, Thymallus thymallus

Sharp declines in population size, known as genetic bottlenecks, increase the level of inbreeding and reduce genetic diversity threatening population sustainability in both short- and long-term. We evaluated the presence, severity and approximate time of bottlenecks in 34 European grayling (Thymallus thymallus) populations covering the majority of the species distribution using microsatellite markers. We identified footprints of population decline in all grayling populations using the M ratio test. In contrast to earlier simulation studies assuming isolated populations, forward simulations allowing low levels of migration demonstrated that bottleneck footprints measured using the M ratio can persist within small populations much longer (up to thousands of generations) than previously anticipated. Using a coalescence approach, the beginning of population reduction was dated back to 1,000–10,000 years ago which suggests that the extremely low M ratio in European grayling is most likely caused by the last glaciation and subsequent post-glacial recolonization processes. In contrast to the M ratio, two alternative methods for bottleneck detection identified more recent bottlenecks in six populations and thus, from a conservation perspective, these populations warrant future monitoring. Based on a single time-point analysis using approximate Bayesian computation methodology, all grayling populations exhibited very small effective population sizes with the majority of N _e estimates below 50. Taken together, our results demonstrate the predominate role of genetic drift in European grayling populations in the short term but also emphasize the importance of gene flow counteracting the effects of genetic drift and loss of variation over longer evolutionary timescales.     

Expressed sequence tag-linked microsatellites as a source of gene-associated polymorphisms for detecting signatures of divergent selection in atlantic salmon (Salmo salar L.)

The prediction that selection affects the genome in a locus-specific way also affecting flanking neutral variation, known as genetic hitchhiking, enables the use of polymorphic markers in noncoding regions to detect the footprints of selection. However, as the strength of the selective footprint on a locus depends on the distance from the selected site and will decay with time due to recombination, the utilization of polymorphic markers closely linked to coding regions of the genome should increase the probability of detecting the footprints of selection as more gene-containing regions are covered. The occurrence of highly polymorphic microsatellites in the untranslated regions of expressed sequence tags (ESTs) is a potentially useful source of gene-associated polymorphisms which has thus far not been utilized for genome screens in natural populations. In this study, we searched for the genetic signatures of divergent selection by screening 95 genomic and EST-derived mini- and microsatellites in eight natural Atlantic salmon, Salmo salar L., populations from different spatial scales inhabiting contrasting natural environments (salt-, brackish, and freshwater habitat). Altogether, we identified nine EST-associated microsatellites, which exhibited highly significant deviations from the neutral expectations using different statistical methods at various spatial scales and showed similar trends in separate population samples from different environments (salt-, brackish, and freshwater habitats) and sea areas (Barents vs. White Sea). We consider these ESTs as the best candidate loci affected by divergent selection, and hence, they serve as promising genes associated with adaptive divergence in Atlantic salmon. Our results demonstrate that EST-linked microsatellite genome scans provide an efficient strategy for discovering functional polymorphisms, especially in nonmodel organisms.     

Use of differential expression data for identification of novel immune relevant expressed sequence tag-linked microsatellite markers in Atlantic salmon (Salmo salar L.)

Despite the large number of genes contributing to the immune response, wildlife immunogenetic studies have tended to focus mostly on the major histocompatibility complex-related genes. Here, we utilized previously published microarray and competitive RNA hybridization information to identify 3750 immune relevant Atlantic salmon (Salmo salar) expressed sequence tags. We then identified those expressed sequence tags containing microsatellites and subsequently designed 48 primer pairs and tested them for polymorphism in Atlantic salmon. Altogether, 16 polymorphic markers were characterized, with allele numbers ranging from two to 18, and these 16 loci were further tested in five other salmonid species.     

Genetic biodiversity in the Baltic Sea: species-specific patterns challenge management

Information on spatial and temporal patterns of genetic diversity is a prerequisite to understanding the demography of populations, and is fundamental to successful management and conservation of species. In the sea, it has been observed that oceanographic and other physical forces can constitute barriers to gene flow that may result in similar population genetic structures in different species. Such similarities among species would greatly simplify management of genetic biodiversity. Here, we tested for shared genetic patterns in a complex marine area, the Baltic Sea. We assessed spatial patterns of intraspecific genetic diversity and differentiation in seven ecologically important species of the Baltic ecosystem—Atlantic herring (Clupea harengus), northern pike (Esox lucius), European whitefish (Coregonus lavaretus), three-spined stickleback (Gasterosteus aculeatus), nine-spined stickleback (Pungitius pungitius), blue mussel (Mytilus spp.), and bladderwrack (Fucus vesiculosus). We used nuclear genetic data of putatively neutral microsatellite and SNP loci from samples collected from seven regions throughout the Baltic Sea, and reference samples from North Atlantic areas. Overall, patterns of genetic diversity and differentiation among sampling regions were unique for each species, although all six species with Atlantic samples indicated strong resistence to Atlantic-Baltic gene-flow. Major genetic barriers were not shared among species within the Baltic Sea; most species show genetic heterogeneity, but significant isolation by distance was only detected in pike and whitefish. These species-specific patterns of genetic structure preclude generalizations and emphasize the need to undertake genetic surveys for species separately, and to design management plans taking into consideration the specific structures of each species.     

Is telomere length a molecular marker of past thermal stress in wild fish?

Telomeres protect eukaryotic chromosomes; variation in telomere length has been linked (primarily in homoeothermic animals) to variation in stress, cellular ageing and disease risk. Moreover, telomeres have been suggested to function as biomarker for quantifying past environmental stress, but studies in wild animals remain rare. Environmental stress, such as extreme environmental temperatures in poikilothermic animals, may result in oxidative stress that accelerates telomere attrition. However, growth, which may depend on temperature, can also contribute to telomere attrition. To test for associations between multitissue telomere length and past water temperature while accounting for the previous individual growth, we used quantitative PCR to analyse samples from 112 young‐of‐the‐year brown trout from 10 natural rivers with average water temperature differences of up to 6°C (and an absolute maximum of 23°C). We found negative associations between relative telomere length (RTL) and both average river temperature and individual body size. We found no indication of RTL–temperature association differences among six tissues, but we did find indications for differences among the tissues for associations between RTL and body size; size trends, albeit nonsignificant in their differences, were strongest in muscle and weakest in fin. Although causal relationships among temperature, growth, oxidative stress, and cross‐sectional telomere length remain largely unknown, our results indicate that telomere‐length variation in a poikilothermic wild animal is associated with both past temperature and growth.     

High Gyrodactylus salaris infection rate in triploid Atlantic salmon Salmo salar

We describe an unusually high infection rate of Gyrodactylus salaris Malmberg in juvenile Atlantic salmon Salmo salar L. of Baltic Sea origin, which are generally believed to be more resistant to G. salaris than East Atlantic salmon populations. Based on analyses of mitochondrial (complete cytochrome oxidase 1 [CO1] gene, 1548 bp) and nuclear (ADNAM1, 435 bp; internal transcribed spacer [ITS] rDNA region, 1232 bp) DNA fragments, the closest relatives of the characterized Estonian G. salaris strain were parasites found off the Swedish west coast and in Raasakka hatchery, Iijoki (Baltic Sea, Finland). Analyses of 14 microsatellite loci of the host S. salarrevealed that approximately 40% of studied fish were triploids. We subsequently identified triploid Atlantic salmon of Baltic origin as more susceptible to G. salaris infection than their diploid counterparts, possibly due to compromised complement-dependent immune pathways in triploid salmon. This is in accordance with earlier studies that have shown elevated susceptibility of triploids to various viral or bacterial pathogens, and represents one of the first reports of increased susceptibility of triploid salmonid fish to an ectoparasite. However, further experimental work is needed to determine whether triploid Atlantic salmon is generally more susceptible to G. salaris compared to their diploid counterparts, irrespective of the particular triploidization method and population of origin.     

High level of population genetic structuring in lake-run brown trout, Salmo trutta, of the Inari Basin, northern Finland

Rivers draining into (Lake) Inarijärvi, northern Finland, sustain a number of lake‐run brown trout, Salmo trutta, populations but, as with most lake‐run S. trutta systems, the level of population genetic structuring among populations is unknown. To address this and to assist fish stock management in the region, the population genetic structure of S. trutta collected from 28 sampling sites in rivers flowing into Inarijärvi was studied using 13 microsatellite loci. Populations were clustered into three separate groups, largely corresponding to geographic regions, with between‐region F_ST values ranging from 0·11 to 0·16. The significant differentiation observed between most populations within each region also implies that individual populations should be recognized as separate management units and actions to improve, and subsequently maintain, conditions for natural spawning should be prioritized. The results of this study further indicate that the trout from each of these regions may have different biological characteristics, such as local‐lake feeding behaviour among the western populations and strong isolation among the northern stocks. As a consequence, further research is warranted to better understand the level of ecological uniqueness of lake‐run S. trutta populations.     

Generation of a neutral FST baseline for testing local adaptation on gill raker number within and between European whitefish ecotypes in the Baltic Sea basin

Divergent selection at ecologically important traits is thought to be a major factor driving phenotypic differentiation between populations. To elucidate the role of different evolutionary processes shaping the variation in gill raker number of European whitefish (Coregonus lavaretus sensu lato) in the Baltic Sea basin, we assessed the relationships between genetic and phenotypic variation among and within three whitefish ecotypes (sea spawners, river spawners and lake spawners). To generate expected neutral distribution of F_ST and to evaluate whether highly variable microsatellite loci resulted in deflated F_ST estimates compared to less variable markers, we performed population genetic simulations under finite island and hierarchical island models. The genetic divergence observed among (F_CT = 0.010) and within (F_ST = 0.014–0.041) ecotypes was rather low. The divergence in gill raker number, however, was substantially higher between sea and river spawners compared to observed microsatellite data and simulated neutral baseline (P_CT > F_CT). This suggests that the differences in gill raker number between sea and river spawners are likely driven by divergent natural selection. We also found strong support for divergent selection on gill raker number among different populations of sea spawners (P_ST > F_ST), most likely caused by highly variable habitat use and diverse diet. The putative role of divergent selection within lake spawners initially inferred from empirical microsatellite data was not supported by simulated F_ST distributions. This work provides a first formal test of divergent selection on gill raker number in Baltic whitefish, and demonstrates the usefulness of population genetic simulations to generate informative neutral baselines for P_ST–F_ST analyses helping to disentangle the effects of stochastic evolutionary processes from natural selection.     

Molecular identification of cryptic bumblebee species from degraded samples using PCR–RFLP approach

The worldwide decline and local extinctions of bumblebees have raised a need for fast and accurate tools for species identification. Morphological characters are often not sufficient, and molecular methods have been increasingly used for reliable identification of bumblebee species. Molecular methods often require high‐quality DNA which makes them less suitable for analysis of low‐quality or older samples. We modified the PCR–RFLP protocol for an efficient and cost‐effective identification of four bumblebee species in the subgenus Bombus s. str. (B. lucorum, B. terrestris, B. magnus and B. cryptarum). We used a short partial mitochondrial COI fragment (446 bp) and three diagnostic restriction enzymes (Hinf I, Hinc II and Hae III) to identify species from degraded DNA material. This approach allowed us to efficiently determine the correct species from all degraded DNA samples, while only a subset of samples 64.6% (31 of 48) resulted in successful amplification of a longer COI fragment (1064 bp) using the previously described method. This protocol can be applied for conservation and management of bumblebees within this subgenus and is especially useful for fast species identification from degraded samples.