Mesohabitat modelling in fish ecology: A global synthesis Wegscheider, Bernhard; Linnansaari, Tommi; Curry, R. Allen
Fish and fisheries (Oxford, England),
September 2020, 2020-09-00, 20200901, Letnik:
21, Številka:
5
Journal Article
Recenzirano
Modelling the linkage between physical habitat and aquatic organisms on multiple spatial scales has become an important tool in the management of rivers. The mesoscale (100–102 m) represents an ...intermediate resolution in modelling that bridges the gap between available resources and conservation efforts for riverine species. However, existing mesohabitat classification schemes for lotic systems vary significantly in the definition of habitat types as well as in their application in the field. This article aims to provide an overview of current attempts to model the mesoscale pattern of physical habitats with a focus on fish. First, we outline descriptive, qualitative as well as objective, quantitative classification methods that are available in the literature. Next, the ecological relevance of the mesohabitat concept is being discussed, using single‐species and community‐level approaches as examples. Different modelling approaches that describe and quantify riverine mesohabitats are presented, and finally, limitations and uncertainties in the modelling process are discussed, followed by an outline of future perspectives in mesohabitat modelling.
Reservoir formation in a river system changes a lotic environment to more lacustrine conditions, with impacts throughout the ecosystem. In this study, a river reach containing typical salmonid ...riffle/run habitat was flooded to create a large, deep pool from June to September in each of 3 years. We test the hypothesis that juvenile Atlantic salmon (Salmo salar) with their preference for run/riffle habitats will respond to the transformation to a lentic environment by moving into adjacent lotic environments. Movements of juvenile Atlantic salmon were monitored using a combination of biotelemetry (radio‐ and passive integrated transponder‐tagging) and electrofishing. Results showed that no tracked fish moved away from the created pool habitat. Mass‐specific growth rates showed the created pool habitat resulted in net growth of juveniles. The results confirm that fish may not immediately (i.e., at least for an approximate 2 months) respond to rapid, large‐scale habitat alterations by moving to find similar habitat conditions outside the altered habitat. This is most probably related to plasticity of behavior and habitat use, and no change in biological conditions to a point that would negatively impact fish growth and survival, for example food availability, competition, or predation. The results also support the hypothesis that the relative importance of physical habitat variables is not universal among streams and populations, therefore limiting the value of applying standard habitat suitability criteria and use.
Water temperature is a key determinant of biological processes in rivers. Temperature in northern latitude rivers is expected to increase under climate change, with potentially adverse consequences ...for cold water-adapted species. In Canada, little is currently known about the timescales or magnitude of river temperature change, particularly in large (≥10
4
km
2
) watersheds. However, because Canadian watersheds are home to a large number of temperature-sensitive organisms, there is a pressing need to understand the potential impacts of climate change on thermal habitats. This paper presents the results of a study to simulate the effects of climate change on the thermal regime of the lower Saint John River (SJR), a large, heavily impounded, socio-economically important watershed in eastern Canada. The CEQUEAU hydrological-water temperature model was calibrated against river temperature observations and driven using meteorological projections from a series of regional climate models. Changes in water temperature were assessed for three future periods (2030–2034, 2070–2074 and 2095–2099). Results show that mean water temperature in the SJR will increase by approximately ~1 °C by 2070–2074 and a further ~1 °C by 2095–2099, with similar findings for the maximum, minimum and standard deviation. We calculated a range of temperature metrics pertaining to the Atlantic Salmon and Striped Bass, key species within the SJR. Results show that while the SJR will become increasingly thermally-limiting for Atlantic Salmon, the Striped Bass growth season may actually lengthen under climate change. These results provide an insight into how climate change may affect thermal habitats for fish in eastern Canadian rivers.
Chromosomal inversions have been implicated in facilitating adaptation in the face of high levels of gene flow, but whether chromosomal fusions also have similar potential remains poorly understood. ...Atlantic salmon are usually characterized by population structure at multiple spatial scales; however, this is not the case for tributaries of the Miramichi River in North America. To resolve genetic relationships between populations in this system and the potential for known chromosomal fusions to contribute to adaptation, we genotyped 728 juvenile salmon using a 50 K SNP array. Consistent with previous work, we report extremely weak overall population structuring (Global FST = 0.004) and failed to support hierarchical structure between the river's two main branches. We provide the first genomic characterization of a previously described polymorphic fusion between chromosomes 8 and 29. Fusion genomic characteristics included high LD, reduced heterozygosity in the fused homokaryotes, and strong divergence between the fused and the unfused rearrangement. Population structure based on fusion karyotype was five times stronger than neutral variation (FST = 0.019), and the frequency of the fusion was associated with summer precipitation supporting a hypothesis that this rearrangement may contribute local adaptation despite weak neutral differentiation. Additionally, both outlier variation among populations and a polygenic framework for characterizing adaptive variation in relation to climate identified a 250‐Kb region of chromosome 9, including the gene six6 that has previously been linked to age‐at‐maturity and run‐timing for this species. Overall, our results indicate that adaptive processes, independent of major river branching, are more important than neutral processes for structuring these populations.
Abstract
An epigenetic basis for transgenerational plasticity in animals is widely theorized, but convincing empirical support is limited by taxa-specific differences in the presence and role of ...epigenetic mechanisms. In teleost fishes, DNA methylation generally does not undergo extensive reprogramming and has been linked with environmentally induced intergenerational effects, but solely in the context of early life environmental differences. Using whole-genome bisulfite sequencing, we demonstrate that differential methylation of sperm occurs in response to captivity during the maturation of Atlantic Salmon (Salmo salar), a species of major economic and conservation significance. We show that adult captive exposure further induces differential methylation in an F1 generation that is associated with fitness-related phenotypic differences. Some genes targeted with differential methylation were consistent with genes differential methylated in other salmonid fishes experiencing early-life hatchery rearing, as well as genes under selection in domesticated species. Our results support a mechanism of transgenerational plasticity mediated by intergenerational inheritance of DNA methylation acquired late in life for salmon. To our knowledge, this is the first-time environmental variation experienced later in life has been directly demonstrated to influence gamete DNA methylation in fish.
Regolith, or unconsolidated materials overlying bedrock, exists as an active zone for many geological, geomorphological, hydrological and ecological processes. This zone and its processes are ...foundational to wide-ranging human needs and activities such as water supply, mineral exploration, forest harvesting, agriculture, and engineered structures. Regolith thickness, or depth-to-bedrock (DTB), is typically unavailable or restricted to finer scale assessments because of the technical and cost limitations of traditional drilling, seismic, and ground-penetrating radar surveys. The objective of this study was to derive a high-resolution (10 m2) DTB model for the province of New Brunswick, Canada as a case study. This was accomplished by developing a DTB database from publicly available soil profiles, boreholes, drill holes, well logs, and outcrop transects (n = 203,238). A Random Forest model was produced by modeling the relationships between DTB measurements in the database to gridded datasets derived from both a LiDAR-derived digital elevation model and photo-interpreted surficial geology delineations. In developing the Random Forest model, DTB measurements were split 70:30 for model development and validation, respectively. The DTB model produced an R2 = 92.8%, MAE = 0.18 m, and RMSE = 0.61 m for the training, and an R2 = 80.3%, MAE = 0.18 m, and RMSE = 0.66 m for the validation data. This model provides an unprecedented resolution of DTB variance at a landscape scale. Additionally, the presented framework provides a fundamental understanding of regolith thickness across a post-glacial terrain, with potential application at the global scale.
River temperature exerts a critical control on habitat for aquatic biota. As the climate warms in eastern Canada, threats to habitats of cold‐water species will increase, underpinning the necessity ...to develop an understanding of landscape‐scale, thermal regimes of flowing waters. We assessed the performance of spatial statistical network (SSN) models of river temperature using high‐resolution thermal infrared imagery (0.6 m) and LiDAR (1 m) compared to NASA's Shuttle Radar Topography Mission (SRTM—30 m) topographic data and interrogate LiDAR derived fine‐scale models (3 ha) to describe groundwater connectivity to surface waters in catchments with shallow overburden and varied bedrock geology. LiDAR improved model performance in a catchment underlain by a homogeneous, high hydraulic conductance bedrock (Cains River) but did not improve model performance in a catchment with heterogeneous bedrock and variable hydraulic conductance (North Pole Stream). We hypothesize that differences in bedrock conductance modified topographic controls on subsurface flows and discharge patterns to the rivers and thus produced the mixed performance of the SSN models. At finer scales, river reaches in steep valleys incising high conductance bedrock produced groundwater discharge, which was absent in incised valleys with low conductance bedrock. These findings indicate that while topography exerts an important control on landscape‐scale hydrological processes, geologic setting is a similarly important influence on hydrological processes. We suggest the inclusion of a third dimension of spatial autocorrelation, representative of the vertical plane that captures the geologic setting, would broaden the geographic applicability of spatial statistical models for river temperature studies.
Key Points
Spatial statistical river network models had mixed success in predicting river temperature in differing geologic and topographic settings
Valley incision in shallow, high hydraulic conductance bedrock facilitated groundwater discharge associated with cool river temperatures
Valley incision in shallow, low hydraulic conductance bedrock limited groundwater discharge and was associated with warm river temperatures
Tracking 47 post‐spawned adult Atlantic salmon Salmo salar L. in a hydropower‐regulated river through autumn, winter and spring revealed that winter survival was 56% and 75% in two study years, ...respectively, with higher mortality of males than females (50% vs. 33% and 100% vs. 13%, respectively). Some kelts (n = 7) displayed nondirected movements that were interpreted as a reconditioning period for an average of 9–17 days prior to directed downstream movements indicating the initiation of migration. Survival after the initiation of migration in spring was 83% and 94% to the hydropower dam in the first and second study years, and decreased to 60 and 63%, respectively, after dam passage. There were no further losses in the downriver reach in the second year, with the first year having a cumulative survival estimate of 53% to the river mouth. Kelts approached the dam when the spillway gates were available as a passage option most of the time (64%–75%), but some kelts arrived at the dam or had not yet passed when spillways were closed (n = 6) and the only remaining passage option was restricted to the turbines. However, all but one kelt that must have passed via turbine were successful in reaching the river mouth. Migratory delay presumably due to searching behaviour caused by low water flow was estimated at approximately 6 days as migration rates were significantly slower in the reservoir (median ± s.e. 8.5 ± 2.5 km day−1) than up‐ (29.7 ± 5.0 km day−1) or downriver (22.1 ± 3.1 km day−1). The proportion of time (median 30%) that kelts spent swimming upstream (searching behaviour) in the reservoir was a significant variable for migration success.
Anthropogenic influences, including climate change, are increasing river temperatures in northern and temperate regions and threatening the thermal habitats of native salmonids. When river ...temperatures exceed the tolerance levels of brook trout and Atlantic salmon, individuals exhibit behavioural thermoregulation by seeking out cold‐water refugia – often created by tributaries and groundwater discharge. Thermal infrared (TIR) imagery was used to map cold‐water anomalies along a 53 km reach of the Cains River, New Brunswick. Trout and salmon parr did not use all identified thermal anomalies as refugia during higher river temperature periods (>21°C). Most small‐bodied trout (8–30 cm) were observed in 80% of the thermal anomalies sampled. Large‐bodied trout (>35 cm) required a more specific set of physical habitat conditions for suitable refugia, that is, 100% of observed large trout used 30% of the anomalies sampled and required water depths >65 cm within or adjacent to the anomaly. Densities of trout were significantly higher within anomalies compared with areas of ambient river temperature. Salmon parr were less aligned with thermal anomalies at the observed temperatures, that is, 59% were found in 65% of the sampled anomalies; and densities were not significantly different within/ outside anomalies. Salmon parr appeared to aggregate at 27°C, and after several events over 27°C variability in aggregation behaviour was observed – some fish aggregated at 25°C, others did not. We stipulate this is due to variances of thermal fatigue. Habitat suitability curves were developed for velocity, temperature, depth, substrate, and deep water availability to characterize conditions preferred by fish during high‐temperature events. These findings are useful for managers as our climate warms, and can potentially be used as a tool to help conserve and enhance thermal refugia for brook trout and Atlantic salmon in similar systems.
We aimed to determine which processes drive patterns of α and β diversity in Arctic river benthic macrofauna across a broad latitudinal gradient spanning the low to high Arctic of eastern Canada (58 ...to 81oN). Further, we examined whether latitudinal differences in taxonomic composition resulted from species replacement with organisms better adapted to northerly conditions or from the loss of taxa unable to tolerate the harsh environments of higher latitudes. We used the bioclimatic envelope concept to provide a first approximation forecast of how climate warming may modify α and β diversity of Arctic rivers and to identify potential changes in environmental variables that will drive future assemblage structure. Benthic macroinvertebrates, environmental supporting variables, and geospatial catchment data were collected to assess drivers of ecological pattern. We compared α diversity (i.e., taxonomic richness) across latitudes and partitioned β diversity into components of nestedness and species turnover to assess their relative contributions to compositional differences. We found sharp declines in taxonomic richness along a latitudinal gradient. This α diversity pattern was not associated with a change in numerical abundance. β diversity was highest when the most distant latitudes were compared, and pairwise latitudinal comparisons indicated that nestedness (loss of species) was the dominant contributor to compositional differences. Biotic–abiotic associations reflected both large-scale climatic drivers, including air temperature and prevalence of vegetated tundra, and small-scale secondary abiotic drivers of assemblage composition (e.g., substrate composition, water chemistry). The importance of nestedness to β diversity across latitudes supports the physiological tolerance hypothesis that a change in environmental tolerance is a key driver of species richness declines with increasing latitude. Distinct taxonomic assemblages among low and high Arctic latitude sites were associated with large-scale, climate-related drivers (e.g., temperature trends, terrestrial vegetation), reflecting the primary structuring of assemblages by bioclimatic envelopes. The abiotic environment was the strongest driver of assemblage structure at high latitudes because of the extreme conditions. With continued warming, biodiversity differences along latitudinal gradients are expected to become less pronounced as temperatures and vegetation become more similar from south to north, with local-scale variables becoming dominant biotic drivers.
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