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Most fish species undergo ontogenetic niche shifts from feeding on pelagic zooplankton, to larger benthic invertebrates and in some cases also to fish. These ontogenetic niche shifts have strong impact on the interactions within and between species, with effects on individual growth, population abundance and food web dynamics. The productivity of northern lakes is mainly controlled by light-limited primary production in benthic habitats, highlighting the importance of lake bathymetry for the abundance of benthic algae feeding macroinvertebrates, which is an important resource for fish. Theory predicts that variation in fish size structure and biomass can arise due to size-dependent differences in competitive abilities between juvenile and adults in each of their niches and by variation in niche- and habitat-specific resource production i.e. pelagic zooplankton and benthic macroinvertebrates.

In this thesis, using gradient studies in mountain lakes, I studied how habitat-specific production and lake bathymetry variation affect growth, size structure and biomass in Arctic char and brown trout populations. Results showed that lake bathymetry determine the benthic contribution to whole lake primary production and the degree of ontogenetic niche shift from zooplankton to macroinvertebrates. In correspondence with theory, production of Arctic char and brown trout were related to stage- and habitat-specific gross primary production (GPP) as an increased benthic contribution to whole lake GPP in general increased individual size, population production and biomasses. Lake bathymetry also influenced the niche shift to piscivory in brown trout as reliance on piscivory were higher in relatively deep lakes more dominated by Arctic char. Finally, in a model approach, responses to different size selective harvest regulations showed that the size structure of Arctic char were more sensitive to fishing in shallow than in deep lakes. Size regulations protecting both smaller and the largest adults were shown to best preserve size structure, especially in shallower lakes. Collectively, these results contribute to the understanding of how variation in productivity and availability of stage- and habitat-specific resources and the presence of ontogenetic niche shifts affect the growth, size structure and biomass of fish. Specifically, the results highlighted the importance of shallow benthic habitats for individual size and biomass of salmonids in mountain lakes and suggests that management strategies based on relationships between lake bathymetry and population size structure and biomass could be a simple approach for sustainable management of lake salmonid population.

Benthic gross primary production (GPP) is often the most important part of aquatic food webs in northern lakes, which are gradually warming and receiving increased terrestrial colored dissolved organic carbon loadings due to global change. Yet, measurements of benthic GPP are fairly uncommon, and methods and unit dimensions of benthic GPP are unstandardized and rarely compared. In this study, we measured benthic GPP in 27 headwater lakes from three regions in northern Sweden and analyzed potential constraining drivers of benthic GPPz rates at discrete depths and estimates of benthic GPP averages across the whole lake, as well as across the littoral zone. We also compared in situ measurements of benthic GPP averages across the whole lake with modeled values using the “autotrophic structuring model.” We found that benthic GPPz rates were best explained by, and positively related to, available light (i.e., a function of depth and water color) and temperature. Benthic GPP averages across the whole lake, on the contrary, were best explained by the relative size of the littoral area, which is a measure that combines lake bathymetry and water color. The comparison between in situ measured and modeled estimates of benthic GPP averages across the whole lake revealed that (1) the autotrophic structuring model underestimates GPP at low values and overestimates GPP at high values compared with measured data, and that (2) measured values were related to temperature, which is not included as a variable in the autotrophic structuring model. Considering future predicted changes impacting northern latitude lakes, our results suggest that increased lake water temperatures can to some extent mitigate the negative impacts of reduced light availability from lake browning on benthic GPPz rates. The combined impact of these changes on benthic GPP averages across the whole lake will depend on, and be moderated by, lake bathymetry determining the relative size of the littoral area.

Ecological theory predicts that the relative distribution of primary production across habitats influence fish size structure and biomass production. In this study, we assessed individual, population, and community-level consequences for brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) of variation in estimated habitat specific (benthic and pelagic) and total whole lake (GPP_whole) gross primary production in 27 northern oligotrophic lakes. We found that higher contribution of benthic primary production to GPP_whole was associated with higher community biomass and larger maximum and mean sizes of fish. At the population level, species-specific responses differed. Increased benthic primary production (GPP_Benthic) correlated to higher population biomass of brown trout regardless of being alone or in sympatry, while Arctic char responded positively to pelagic primary production (GPP_Pelagic) in sympatric populations. In sympatric lakes, the maximum size of both species was positively related to both GPP_Benthic and the benthic contribution to GPP_Whole. In allopatric lakes, brown trout mean and maximum size and Arctic char mean size were positively related to the benthic proportion of GPP_Whole. Our results highlight the importance of light-controlled benthic primary production for fish biomass production in oligotrophic northern lakes. Our results further suggest that consequences of ontogenetic asymmetry and niche shifts may cause the distribution of primary production across habitats to be more important than the total ecosystem primary production for fish size, population biomass, and production. Awareness of the relationships between light availability and asymmetric resource production favoring large fish and fish production may allow for cost-efficient and more informed management actions in northern oligotrophic lakes.

The littoral zone varies in size among lakes from ∼3% to 100% of lake surface area. In this paper, we derive a simple theoretical scaling relationship that explains this variation, and test this theory using bathymetric data across the size spectra of freshwater lakes (surface area = 0.01–82,103 km2, maximum depth = 2–1,741 m). Littoral area primarily reflects the ratio of the maximum depth of photosynthesis to maximum lake depth. However, lakes that are similar in these characteristics can have different relative littoral areas because of variation in basin shape. Hypsometric (area-elevation) models that describe these patterns for individual lakes can be generalized among lakes to accurately predict the relative size of littoral habitat when there is incomplete bathymetric information. Collectively, our results provide simple rules for understanding patterns of littoral habitat size at the regional and global scales.

Classical methods for estimating the abundance of fish populations are often both expensive, time-consuming and destructive. Analyses of the environmental DNA (eDNA) present in water samples could alleviate such constraints. Here, we developed protocols to detect and quantify brown trout (Salmo trutta) and Arctic char (Salvelinus alpinus) populations by applying the droplet digital PCR (ddPCR) method to eDNA molecules extracted from water samples collected in 28 Swedish mountain lakes. Overall, contemporary fish CPUE (catch per unit effort) estimates from standardized survey gill nettings were not correlated to eDNA concentrations for either of the species. In addition, the measured environmental variables (e.g. dissolved organic carbon concentrations, temperature, and pH) appear to not influence water eDNA concentrations of the studied fish species. Detection probabilities via eDNA analysis showed moderate success (less than 70% for both species) while the presence of eDNA from Arctic char (in six lakes) and brown trout (in one lake) was also indicated in lakes where the species were not detected with the gillnetting method. Such findings highlight the limits of one or both methods to reliably detect fish species presence in natural systems. Additional analysis showed that the filtration of water samples through 1.2 mu m glass fiber filters and 0.45 mu m mixed cellulose ester filters was more efficient in recovering DNA than using 0.22 mu m enclosed polyethersulfone filters, probably due to differential efficiencies of DNA extraction. Altogether, this work showed the potentials and limits of the approach for the detection and the quantification of fish abundance in natural systems while providing new insights in the application of the ddPCR method applied to environmental DNA.

The temperature dependence of predation rates is a key issue for understanding and predicting the responses of ecosystems to climate change. Using a simple mechanistic model, we demonstrate that differences in the relative performances of predator and prey can cause strong threshold effects in the temperature dependence of attack rates. Empirical data on the attack rate of northern pike (Esox lucius) feeding on brown trout (Salmo trutta) confirm this result. Attack rates fell sharply below a threshold temperature of +11 degrees C, which corresponded to a shift in relative performance of pike and brown trout with respect to maximum attack and escape swimming speeds. The average attack speed of pike was an order of magnitude lower than the escape speed of brown trout at 5 degrees C, but approximately equal at temperatures above 11 degrees C. Thresholds in the temperature dependence of ecological rates can create tipping points in the responses of ecosystems to increasing temperatures. Thus, identifying thresholds is crucial when predicting future effects of climate warming.