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
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.
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.
•Identification of indicator genera for flow provides important ecological information for large river benthic macroinvertebrate assemblages.•Taxa Indicator Threshold Analysis was applied on benthic ...macroinvertebrate monitoring data in a large river in Eastern Canada•Flow velocity was strongly associated with the distribution and relative abundance of benthic macroinvertebrates.•Hydraulic-habitat thresholds and taxa associations were linked to alternative flow scenarios.
Holistic environmental flows frameworks are built on our understanding of key flow-ecology relationships that support sensitive taxa and critical ecosystem functions under different flow and water level scenarios. Most research on flow-ecology relationships has typically focused on small systems, with less known about flow associations, indicator taxa, and environmental thresholds of assemblage change along hydraulic gradients of large non-wadeable rivers. We assessed benthic macroinvertebrate assemblage structure and applied Taxa Indicator Threshold ANalysis (TITAN) on biomonitoring data collected during a six-year period in the Wolastoq | Saint John River in Atlantic Canada. Flow velocity was strongly associated with the distribution and relative abundance of benthic macroinvertebrates in the river, and taxon associations reflected functional adaptations to flow. We identified 33 genus-level indicator taxa that were either positively or negatively associated with flow velocity. Weaker taxa responses were shown for the gradient in median substrate particle size where 22 negatively and positively responding taxa were identified. We predicted changes in indicator taxon abundance under different flow scenarios using a hydrodynamic model, and characterised the distribution and availability of suitable hydraulic habitat patches within a 20 km reach downstream of a large hydropower generating station. These observations set the stage for the development of ecologically-based flow targets to support holistic environmental flow management in large rivers.
Broadening our understanding of river thermal variability is of paramount importance considering the role temperature plays in aquatic ecosystem health. At the catchment scale, spatial statistical ...river network models (SSN) are popular for analyses of river temperature, as these are less “data hungry” than other modeling methods, and have offered invaluable insights into how thermal habitats of salmonids may change with climate warming. However, recent work has demonstrated that hydrogeological complexity can disrupt river temperature spatial autocorrelation. We test the prediction that the non‐linearity of hydrological processes inherent in a hydrogeologically complex setting, such as the Miramichi River, invalidates the SSN approach, and a Random Forest (RF) model can overcome these complexities. In all instances, RFs outperformed SSNs when predicting average (TwA) and maximum (TwM) August river temperature during 2017, and were quite robust (TwA and TwM: R2 = 0.93; RMSE = 0.6°C; R2 = 0.91; RMSE = 1.0°C, respectively). We conclude that RF models can capture the inherent non‐linearity of hydrological processes in complex hydrogeologic settings. We examined thermal habitat change for adult and 1+/2+ Atlantic salmon—AS—(Salmo salar), and all age classes of brook trout—BKT—(Salvelinus fontinalis), during August 2017, with thresholds of behavioral thermoregulation specific to the catchment. We assumed a baseline = TwA and investigated river network contraction (km) for TwM. During TwA, all habitat was suggested to be thermally suitable for 1+/2+ AS (<23°C), but 4.2% was unsuitable for adult AS and BKT of all ages (>20°C). For TwM, ~80% of the catchment was predicted to be unsuitable for adult AS and BKT. We examined two boundaries for behavorial thermoregulation in 1+/2+ AS: >23°C and >27°C. For the >23°C boundary, ~27.7% of the catchment is thermally unsuitable during TwM, and 4.9% is thermally unsuitable for the >27°C boundary. TwA in August 2017 was identical to long‐term (1970–1999) July–August TwA, as such these thermal maps will be useful for resource managers.
The development of consumer hydroacoustic systems continues to advance, enabling the use of low-cost methods for professional mapping purposes. Information describing habitat characteristics produced ...with a combination of low-cost commercial echosounder (Lowrance HDS) and a cloud-based automated data processing tool (BioBase EcoSound) was tested. The combination frequently underestimated water depth, with a mean absolute error of 0.17 ± 0.13 m (avg ± 1SD). The average EcoSound bottom hardness value was high (0.37–0.5) for all the substrate types found in the study area and could not be used to differentiate between the substrate size classes that varied from silt to bedrock. Overall, the bottom hardness value is not informative in an alluvial river bed setting where the majority of the substrate is composed of hard sands, gravels, and stones. EcoSound separated vegetation presence/absence with 85–100% accuracy and assigned vegetation height (EcoSound biovolume) correctly in 55% of instances but often overestimated it in other instances. It was most accurate when the vegetation canopy was ≤25% or >75% of the water column. Overall, as a low-cost, easy-to-use application EcoSound offers rapid data collection and allows users with no specialized skill requirements to make more detailed bathymetry and vegetation maps than those typically available for many rivers, lakes, and estuaries.
Fish fin is a widely used, non-lethal sample material in studies using stable isotopes to assess the ecology of fishes. However, fish fin is composed of two distinct tissues (ray and membrane) which ...may have different stable isotope values and are not homogeneously distributed within a fin. As such, estimates of the stable isotope values of a fish may vary according to the section of fin sampled.
To assess the magnitude of this variation, we analysed carbon (δ13C), nitrogen (δ15N), hydrogen (δ2H) and oxygen (δ18O) stable isotopes of caudal fin from juvenile, riverine stages of Atlantic salmon (Salmo salar) and brown trout (Salmo trutta). Individual fins were sub-sectioned into tip, mid and base, of which a further subset were divided into ray and membrane.
Isotope variation between fin sections, evident in all four elements, was primarily related to differences between ray and membrane. Base sections were13C depleted relative to tip (~1‰) with equivalent variation evident between ray and membrane. A similar trend was evident in δ2H, though the degree of variation was far greater (~10‰). Base and ray sections were 18O enriched (~2‰) relative to tip and membrane, respectively. Ray and membrane sections displayed longitudinal variation in 15N mirroring that of composite fin (~1‰), indicating that variation in15N values was likely related to ontogenetic variation.
To account for the effects of intra-fin variability in stable isotope analyses we suggest that researchers sampling fish fin, in increasing priority, 1) also analyse muscle (or liver) tissue from a subsample of fish to calibrate their data, or 2) standardize sampling by selecting tissue only from the extreme tip of a fin, or 3) homogenize fins prior to analysis.
In 1979, the Shortnose Sturgeon (Acipenser brevirostrum) population of the Saint John River, New Brunswick, was estimated at 18,000 ± 5400 individuals. More recently, an estimate of 4836 ± 69 ...individuals in 2005, and between 3852 and 5222 individuals in 2009 and 2011, was made based on a single Shortnose Sturgeon winter aggregation in the Kennebecasis Bay of the Saint John River, a location thought to contain a large proportion of the population. These data, in combination with the Saint John River serving as the sole spawning location for Shortnose Sturgeon in Canada prompted a species designation of “Special Concern” in 2015 under Canada’s Species at Risk Act (SARA). A three-decade span of scientific observations amplified by the traditional knowledge and concerns of local indigenous groups have pointed to a declining population. However, the endemic Shortnose Sturgeon population of the Saint John River has not been comprehensively assessed in recent years. To help update the population estimate, we tested a rapid, low-cost side-scan sonar mapping method coupled with supervised image classification to enumerate individual Sturgeon in a previously undescribed critical winter location in the Saint John River. We then conducted an underwater video camera survey of the area, in which we did not identify any fish species other than Shortnose Sturgeon. These data were then synchronized with four years of continuous acoustic tracking of 18 Shortnose Sturgeon to produce a population estimate in each of the five identified winter habitats and the Saint John River as a whole. Using a side-scan sonar, we identified > 12,000 Shortnose Sturgeon in a single key winter location and estimated the full river population as > 20,000 individuals > ~40 cm fork length. We conclude that the combined sonar/image processing method presented herein provides an effective and rapid assessment of large fish such as Sturgeon when occurring in winter aggregation. Our results also indicate that the Shortnose Sturgeon population of the Saint John River could be similar to the last survey estimate conducted in the late 1970s, but more comprehensive and regular surveys are needed to more accurately assess the state of the population.
•Automated imaging sonar fish counts are desired but currently not common.•Echoview software and postprocessing was used for automated fish counts.•Good agreement for upstream counts, larger ...differences in downstream counts.•Filtering removed dynamic noise and milling fish from the fish tracks.•A model predicted if a downstream moving object was a fish or not.
Imaging sonars, such as the Adaptive Resolution Imaging Sonar (ARIS; Sound Metrics Corp.) produce continuous stream of sonar video footage, and they are commonly used for counting and sizing migrating fish in rivers. Although automated methods have been developed for processing imaging sonar data, manual analysis of the data is still common in fish population monitoring projects. In this study, we used Echoview software to automatically produce fish counts from long-range (up to 30 m) imaging sonar data in a prominent Atlantic salmon (Salmo salar) river; the Little Southwest Miramichi River, New Brunswick, Canada. We added postprocessing steps to address sources of error that have been reported in previous studies: 1) Major Axis Distance was used to filter out erroneous fish tracks (89 % of dynamic noise and 67 % of milling fish in the test-set) and to calculate the swimming direction (96 % correct), and 2) a logistic regression (target length, average speed, and absolute fish track change in range) was used to predict downstream moving fish from other objects with a test-set accuracy of 84 %. When 15-min tally counts were compared between computer-generated data and multiple human-generated counts, the mean of differences varied between -39 % and 65 % in the upstream counts in different datasets, and different analysis methods were in a good agreement between each other (ICC = 0.79). There were larger differences in the downstream counts where the mean of differences varied between 14 % and 115 % and there was no agreement between the datasets (ICC = 0.03). With a double-tracking method where the fish were tracked twice, the computer analysed the 24 -h datasets in 500−600 min and was slower than human-generated counts that required 200−600 min, however, computer generated-counts can be derived in the background without the presence of a technician and may produce significant savings in personnel cost.
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