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The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction‐site‐associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as FST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half‐ and full‐siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual‐level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual‐level genotype information, such as quantifying relatedness and individual‐level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity. We compared the performance of restriction‐site‐associated DNA sequencing (RADseq) and DNA microsatellite markers for estimating genetic diversity, relatedness, and genetic differentiation in brown trout (Salmo trutta) populations. The results indicate that moderately polymorphic microsatellites and SNPs from RADseq found similar genetic structure of moderately diverged, small populations, but RADseq outperformed microsatellites for quantifying relatedness and individual‐level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.

The migratory life history of anadromous salmonids requires successful migration between nursery, feeding, and spawning habitats. Smolting is the major transformation anadromous salmonids undergo before migration to feeding areas. It prepares juvenile fish for downstream migration and their entry to seawater. We reviewed the effects of climate change on smolt ecology from the growth of juveniles in fresh water to early post-smolts in the sea to identify the potential effects of climate change on migratory salmonid populations during this period in their life history. The focus was especially on Atlantic salmon. The shift in suitable thermal conditions caused by climate change results in Atlantic salmon expanding their range northward, while at the southern edge of their distribution, populations struggle with high temperatures and occasional droughts. Climatic conditions, particularly warmer temperatures, affect growth during the freshwater river phase. Better growth in northern latitudes leads to earlier smolting. Thermal refuges, the areas of cooler water in the river, are important for salmonids impacted by climate change. Restoring and maintaining connectivity and a suitably diverse mosaic habitat in rivers are important for survival and growth throughout the range. The start of the smolt migration has shifted earlier as a response to rising water temperatures, which has led to concerns about a mismatch with optimal conditions for post-smolts in the sea, decreasing their survival. A wide smolt window allowing all migrating phenotypes from early to late migrants’ safe access to the sea is important in changing environmental conditions. This is also true for regulated rivers, where flow regulation practices cause selection pressures on migrating salmonid phenotypes. The freshwater life history also affects marine survival, and better collaboration across life stages and habitats is necessary among researchers and managers to boost smolt production in rivers. Proactive measures are recommended against population declines, including sustainable land use in the catchment, maintaining a diverse mosaic of habitats for salmonids, restoring flow and connectivity, and conserving key habitats.

Carryover effects of environmental stressors occur when experiences of the environment in earlier life stages or seasons influence the performance of individuals later in life. These can be especially critical for species that have diverse developmental transition periods in their life cycle, such as salmonid fish. Sublethal changes in metabolism, size, or growth experienced in early life stages may have a long‐lasting effect on the subsequent life performance of these species, but very few studies have formally tested these changes in relation to environmental stressors. Here, we investigated whether different types of fine sediment result in carryover effects that change the life performance of migratory brown trout. First, we manipulated the early habitat conditions of brown trout through the life stages from egg to fry by incubating them in varying substrate treatments (i.e., gravel without added sediment, gravel with added fine sand, and gravel with added organic matter). Exposure to fine sediment during early development had serious effects on the metabolism, size, escape responses, timing of emergence, and potential survival of early life stages. These carryover effects were persistent and remained present over the critical life shift from relying on parentally provided resources as immobile eggs to independent exogenous feeding as parr. Second, fish were relocated as parr to either their original or different treatment environments and their metabolism, size, and growth were reanalyzed. The effects of environmental stress were observed later in their life cycle when fry from the gravel treatment were relocated to sand or organic‐rich treatments. These were found to be significantly smaller in size and had a higher metabolic rate than fry maintained in their original treatment environment. Together, our study experimentally demonstrated that the carryover effects of environmental stressors experienced in early stages may influence the fitness outcomes of migratory fish later in life. We suggest that sublethal environmental stressors should be better considered in restoration schemes and management strategies to reverse the current trend of declining salmonid populations.

An ability to understand and predict invasions is elemental for controlling the detrimental effects of introduced organisms on native biota. In eastern North America, European brown trout generally dominates over, and eventually replaces, the native brook trout. We show here that in northern Europe the pattern of replacement between these two species is reversed: when transferred to North European streams, brook trout spread extensively and partially replaced the native brown trout. The effect of brook trout on brown trout was habitat-specific: brook trout excluded the native species only in small tributary streams where the reproduction of brown trout was severely reduced, whereas in larger streams brown trout was largely unaffected. Thus, the pattern of coexistence among the two salmonids in our study area is approaching that typically observed in North American streams. In both areas, brook trout ultimately settles in small headwater streams, but the process of replacement differs profoundly: in North Europe, brook trout replaces brown trout in headwater streams, whereas in North America these same streams are the ultimate refuge area for brook trout under the invasion pressure by brown trout. Our results underline the importance of knowing species' niche characteristics to explain and predict biological invasions.

We combine evidence from small-scale experiments with a large-scale field survey to clarify the roles of biotic resistance and pre-adapted habitat niche segregation to the invasion success of the North American brook trout (Salvelinus fontinalis) in North European streams previously dominated by brown trout (Salmo trutta). Interspecific aggressions among the two species were negligible, yet there was distinct habitat niche segregation between them: brook trout occupied mainly pool habitats while brown trout tended to reside in fast-flowing riffles. Habitat niche segregation among brook trout and brown trout prevailed across a wide array of scales from experimental flumes to entire drainage systems, although the segregation pattern was weaker in the field. Habitat differentiation among the two species reflected their differential habitat requirements, suggesting that a match between a species' niche requirements in its native range and habitat availability in the new environment is a prerequisite for understanding invasion success.

Temporal coherence or spatial synchrony refers to the tendency of population, community or ecosystem dynamics to behave similarly among locations through time as a result of spatially‐correlated environmental stochasticity (Moran effect), dispersal or trophic interactions. While terrestrial studies have treated synchrony mainly as a population‐level concept, the majority of freshwater studies have focused on community‐level patterns, particularly in lake planktonic communities. We used spatially and temporally hierarchical data on benthic stream invertebrates across six years, with three seasonal samples a year, in 11 boreal streams to assess temporal coherence at three spatial extents: 1) among regions (watersheds), 2) among streams within a region, and 3) among riffles within a stream, using the average of correlation coefficients for stream/riffle pairs across years. Our results revealed the primacy of strongly synchronized climatic factors (precipitation, air temperature) in inducing temporal coherence of macroinvertebrate assemblages across geographically distinct sites (i.e. Moran effect). Coherence tended to decrease with increasing spatial extent, but positive coherence was detected for most biological variables even at the largest extent (about 350 km). The generally high level of coherence reflected the strong seasonality of boreal freshwater communities. A hydrologically exceptional year enhanced the synchrony of biological variables, particularly total macroinvertebrate abundance. Regionally low precipitation in that year led to a substantial decrease in benthic densities across a broad spatial extent, followed by a rapid post‐drought recovery. Coherence at the among‐riffle (within‐stream) extent was lower than expected, implying that local‐scale habitat filters determine community dynamics at smaller spatial extents. Thus, temporal coherence of stream benthic communities appears to be controlled by partly different processes at different spatial scales.

The nonnative rainbow trout Oncorhynchus mykiss has been an unsuccessful invader in North European streams, although it has been widely introduced. Here we studied whether early life history stages (egg incubation and hatching, first overwintering) act as filters for the establishment of hatchery rainbow trout. Survival of hatched alevins was approximately 80%, whereas only 47% of the embryos survived. However, the latter value was impacted by the high number of unfertilized eggs. Correlation coefficients with embryo survival rate and environmental variables (pH and temperature) were statistically insignificant. In the overwintering experiments, the survival of rainbow trout was 93%. The growth was generally slowed during the winter, but in the spring the growth of rainbow trout exceeded that of the native brown trout. Our data demonstrated that the survival and growth of rainbow trout during early life-history stages were relatively high and comparable to those of the native brown trout. Based on the variables considered in our study, our results suggest that environmental conditions during early life-history stages are not detrimental for rainbow trout in the study streams.

We studied the ecological niche relations of native stream fish and an alien invader, brook trout (Salvelinus fontinalis), to examine if brook trout had located an underused environmental niche in our boreal study system. In both study years (1994 versus 2004), we found brook trout to have the most marginal niche position of all the fish species examined. The most important environmental variable affecting the distribution of brook trout was pH, with acid headwater sites being dominated by this species. Brown trout, in contrast, had relatively nonmarginal niche, occurring in average conditions across the sampled sites. Other fish species had niche positions between the two salmonids. Our results show that fish invasions may be strongly facilitated by the presence of suboptimally occupied environmental niche space in the recipient river system.

The effects of anthropogenic stressors on community structure and ecosystem functioning can be strongly influenced by local habitat structure and dispersal from source communities. Catchment land uses increase the input of fine sediments into stream channels, clogging the interstitial spaces of benthic habitats. Aquatic macrophytes enhance habitat heterogeneity and mediate important ecosystem functions, being thus a key component of habitat structure in many streams. Therefore, the recovery of macrophytes following in-stream habitat modification may be prerequisite for successful stream restoration. Restoration success is also affected by dispersal of organisms from the source community, with potentially the strongest responses in relatively isolated headwater sites that receive a limited amount of dispersing individuals. We used a factorial design in a set of stream mesocosms to study the independent and combined effects of an anthropogenic stressor (sand sedimentation), local habitat (macrophytes, i.e., moss transplants), and enhanced dispersal (two levels: high vs. low) on organic matter retention, algal accrual rate, leaf decomposition, and macroinvertebrate community structure. Overall, all responses were simple additive effects with no interactions between treatments. Sand reduced algal accumulation, total invertebrate density, and density of a few individual taxa. Mosses reduced algal accrual rate and algae-grazing invertebrates, but enhanced organic matter retention and the number of detritus and filter feeders. Mosses also reduced macroinvertebrate diversity by increasing the dominance by a few taxa. Mosses reduced leaf mass loss, possibly because the organic matter retained by mosses provided an additional food source for leaf-shredding invertebrates and thus reduced shredder aggregation into leaf packs. The effect of mosses on macroinvertebrate communities and ecosystem functioning was distinct irrespective of the level of dispersal, suggesting strong environmental control of community structure. The strong environmental control of macroinvertebrate community composition even under enhanced dispersal suggests that re-establishing key habitat features, such as natural stream vegetation, could aid ecosystem recovery in boreal streams.

We constructed generalized habitat criteria for juvenile Atlantic salmon (Salmo salar) based on four river-specific suitability indices for depth, water velocity, and substrate to assess whether habitat criteria for juvenile Atlantic salmon are transferable across rivers. We first tested whether salmon are more likely to occupy higher-quality habitats than generally available in a stream reach based on these composite criteria. We then repeated the same procedure using the river-specific criteria of this study and the generalized habitat suitability criteria of Heggenes. As expected, the river-specific criteria were generally the most effective ones in predicting fish habitat use. However, both of the two generalized criteria also transferred fairly well to the test sites. Viewed across salmon size-classes (<9 cm and >9 cm), the river-specific criteria passed the test in ten of eleven cases (91%), and the two generalized criteria passed in nine (82%) of eleven. Thus, it appears that with respect to summertime habitat criteria for juvenile Atlantic salmon, criteria transference is conceivable at least on a regional scale, and perhaps even on a more \"universal\" scale.