Climate change can disproportionately reduce habitats of stream fishes with restricted ranges in southern South America.

Freshwater fishes are among the most threatened taxa worldwide owing to changes in land use, species introductions, and climate change. Although more than half of the freshwater fishes in the Chilean Mediterranean ecoregion are considered vulnerable or endangered, still little is known about their biogeography. Fishes of the family Perciliidae are endemic of this region and ideal cases to study potential implications of global warming given their endangered conservation status, small size, restricted range, and limited dispersal capacity in fragmented habitats. Here, we model the spatial distribution of habitats for Percilia irwini and P. gillissi under current (1970-2000) and future (2050-2080) climatic scenarios (SSP245, SSP585). We implement maximum entropy (MaxEnt) models adapted for stream networks using high-resolution datasets of selected geophysical and climatic variables. At present, both species inhabit relatively low-quality habitats. In the future (SSP585), suitable habitats for P. irwini are predicted to be reduced drastically (99%) with potential local extirpations in its northern range. Similarly, up to 62% of suitable habitats for P. gillissi would also be reduced in the future. Our study provides insights about assessing future threats and vulnerability of endemic, endangered, range-restricted, and small-bodied freshwater species in this region and elsewhere.

Shrinking sizes of trout and salamanders are unexplained by climate warming alone.

Decreases in body sizes of animals related to recent climate warming can affect population persistence and stability. However, direct observations of average sizes over time and their interrelationships with underlying density-dependent and density-independent processes remain poorly understood owing to the lack of appropriate long-term datasets. We measured body size of two species common to headwater streams in coastal and Cascades ecoregions of the Pacific Northwest of North America over multiple decades, comparing old-growth and managed forests. We found consistent decreases in median length of Coastal Cutthroat Trout Oncorhynchus clarkii clarkii, but a coexisting species, the Coastal Giant Salamander Dicamptodon tenebrosus, appears to be more resilient to size changes over time. Based on observed trends, adult trout have decreased in length by 6-13% over the last 30 years. Length decreased more in larger compared to smaller animals, suggesting that these effects reflect changes in growth trajectories. Results from a model-selection approach that included hydroclimatic and biological information as covariates in one of our study ecoregions demonstrated that stream temperature alone did not explain observed length reductions. Rather, a combination of density-dependent (animal abundances) and local density-independent factors (temperature, habitat, and streamflow) explained observed patterns of size. Continued decreases in size could lead to trophic cascades, biodiversity loss, or in extreme cases, species extirpation. However, the intricate links between density-independent and density-dependent factors in controlling population-level processes in streams need further attention.

Evidence for infection influencing survival of the freshwater copepod Salmincola californiensis, a parasite of Pacific salmon and trout.

OBJECTIVE: We explore apparent infection of Salmincola californiensis arising during investigations involving this lernaeopodid copepod parasitic on Pacific salmon and trout Oncorhynchus spp. METHODS: We noted occasional unusual coloration of adult female copepods collected from the wild. These females were bright blue and pink in contrast to the cream white coloration characteristic of the copepod. We also observed that similar color patterns developed under laboratory settings when copepod eggs were held for hatching. In paired egg cases, we found consistent hatching failure of blue and pink eggs and patterns in apparent disease development that would be consistent with both vertical and horizontal transmission. RESULT: Attempts to identify the cause of the apparent infection using genetic methods and transmission electron microscopy were inconclusive. CONCLUSION: Iridovirus infection was initially suspected, but bacterial infection is also plausible. This apparent reduced hatching success of S. californiensis warrants further exploration as it could reduce local abundances. Given the potential importance of a disease impacting this copepod, a parasite that itself affects endangered and commercially important Pacific salmon and trout, future research would benefit from clarification of the apparent infection through additional sequencing, primer development, visualization, and exploration into specificity and transmission.

Habitat overlap among native and introduced cold-water fishes in the Himalayas.

Fish invasions threaten native freshwater ecosystems worldwide, yet methods to map biodiversity in data-deficient regions are scarce. Rainbow trout (Oncorhynchus mykiss) and brown trout (Salmo trutta fario) have been introduced to the Himalayan ecoregion where they are sympatric with vulnerable native snow trout Schizothorax plagiostomus and Schizothorax richardsonii. We aim to evaluate potential habitat overlap among snow trout and non-native trout in the Indus and Ganges River basins, Himalayan ecoregion. We transferred maximum entropy (MaxEnt) models developed with spatially continuous freshwater-specific environmental variables to map the distribution of potentially suitable habitats for rainbow and brown trout in the Himalayas. We adopted a similar procedure to map suitable habitats for snow trout species. There were substantial habitat overlaps (up to 96%) among snow trout and non-native trout. Yet, the physiography of receiving basins could play a role minimizing the impacts of each non-native trout on native snow trout. We generate high-resolution classified stream suitability maps as decision support tools to help managers in habitat allocation and policy formation to balance recreational fisheries with conservation of snow trout. Our workflow can be transferred to other basins and species for mapping freshwater biodiversity patterns in species-rich yet data-poor regions of the world.

UPRLIMET: UPstream Regional LiDAR Model for Extent of Trout in stream networks.

Predicting the edges of species distributions is fundamental for species conservation, ecosystem services, and management decisions. In North America, the location of the upstream limit of fish in forested streams receives special attention, because fish-bearing portions of streams have more protections during forest management activities than fishless portions. We present a novel model development and evaluation framework, wherein we compare 26 models to predict upper distribution limits of trout in streams. The models used machine learning, logistic regression, and a sophisticated nested spatial cross-validation routine to evaluate predictive performance while accounting for spatial autocorrelation. The model resulting in the best predictive performance, termed UPstream Regional LiDAR Model for Extent of Trout (UPRLIMET), is a two-stage model that uses a logistic regression algorithm calibrated to observations of Coastal Cutthroat Trout (Oncorhynchus clarkii clarkii) occurrence and variables representing hydro-topographic characteristics of the landscape. We predict trout presence along reaches throughout a stream network, and include a stopping rule to identify a discrete upper limit point above which all stream reaches are classified as fishless. Although there is no simple explanation for the upper distribution limit identified in UPRLIMET, four factors, including upstream channel length above the point of uppermost fish, drainage area, slope, and elevation, had highest importance. Across our study region of western Oregon, we found that more of the fish-bearing network is on private lands than on state, US Bureau of Land Mangement (BLM), or USDA Forest Service (USFS) lands, highlighting the importance of using spatially consistent maps across a region and working across land ownerships. Our research underscores the value of using occurrence data to develop simple, but powerful, prediction tools to capture complex ecological processes that contribute to distribution limits of species.

Consumption of marine-derived nutrients from invasive Chinook salmon (Oncorhynchus tshawytscha) transfer ω-3 highly unsaturated fatty acids to invasive resident rainbow trout (O. mykiss).

Marine-derived nutrients (MDN) contained in gametes (mature eggs and sperm), carcasses and metabolic wastes from anadromous migratory salmon can transfer energy and materials to fresh water, thereby affecting the structure and function of stream ecosystems. This is crucial among ecosystems where humans have mediated biological invasions by propagating non-native species. Previous studies have demonstrated that consumption of MDN from salmon can benefit both native and invasive resident fishes. Yet, a more detailed understanding of the transfer of biomolecules with important physiological functions such as ω-3 highly unsaturated fatty acids (HUFAs) have received less attention among researchers. Here we demonstrate that consumption of MDN contained in invasive Chinook salmon eggs transfers ω-3 HUFAs (e.g., EPA and DHA) to resident invasive rainbow trout in a river food web. We conducted a field study in river sections previously identified as spawning areas for Chinook salmon in the Cisnes River, Patagonia. Rainbow trout were sampled around salmon spawning areas before, during, and after the salmon spawning season. Additionally, we collected tissue from different food web resources and components of different origin (e.g., primary producers, aquatic and terrestrial items) from the Cisnes River system. Analyses of stomach contents of trout were performed in conjunction with analyses of both lipid content and fatty acid profiles of trout tissue and food web components. Chinook salmon eggs showed higher content of ω-3 HUFAs, especially EPA (31.08 ± 23.08 mg g DW-1) and DHA (27.50 ± 14.11 mg g DW-1) than either freshwater or terrestrial components (0-6.10 mg g DW-1 both EPA and DHA). We detected marked shifts in the fatty acid profile (~six-fold increase in EPA and DHA) of trout following consumption of Chinook salmon eggs. Our findings suggest that MDN via consumption of salmon eggs by resident rainbow trout may positively influence resident trout and likely contribute to gauge synergistic interactions between invaders on receiving ecosystems of Patagonia.

Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in freshwaters.

Environmental DNA (eDNA) detection of aquatic invasive species is currently at the forefront of aquatic conservation efforts because the methodology provides a cost effective and sensitive means to detect animals at low densities. Developments in eDNA technologies have improved detection probabilities for rare, indicator, and invasive species over the past decade. However, standard lab analysis can take days or weeks before results are available and is prohibitive when rapid management decisions are required for mitigation. Here, we investigated the performance of a real-time quantitative PCR system for on-site eDNA detection of New Zealand mud snails (Potamopyrgus antipodarum). Six sites in western Washington, USA were sampled using the rapid eDNA technique and traditional methods, with five samples per site. On-site eDNA detection of mud snails resulted in a 10% increase in positive sites (16/30 = 53% positive) relative to visual surveys (13/30 = 43% positive). In addition, positive associations were observed between mud snail eDNA concentration (eDNA copies per reaction) and the number of mud snail individuals at each site (R 2 = 0.78). We show that the rapid on-site eDNA technology can be effective for detection and quantification of New Zealand mud snails in freshwaters. This on-site eDNA detection approach could possibly be used to initiate management protocols that allow for more rapid responses during the onset of biological invasions.

A method to evaluate body length of live aquatic vertebrates using digital images.

Traditional methods to measure body lengths of aquatic vertebrates rely on anesthetics, and extended handling times. These procedures can increase stress, potentially affecting the animal's welfare after its release. We developed a simple procedure using digital images to estimate body lengths of coastal cutthroat trout (Oncorhynchus clarkii clarkii) and larval coastal giant salamander (Dicamptodon tenebrosus). Images were postprocessed using ImageJ2. We measured more than 900 individuals of these two species from 200 pool habitats along 9.6 river kilometers. The percent error (mean ± SE) of our approach compared to the use of a traditional graded measuring board was relatively small for all length metrics of the two species. Total length of trout was -2.2% ± 1.0. Snout-vent length and total length of larval salamanders was 3.5% ± 3.3 and -0.6% ± 1.7, respectively. We cross-validated our results by two independent observers that followed our protocol to measure the same animals and found no significant differences (p > .7) in body size distributions for all length metrics of the two species. Our procedure provides reliable information of body size reducing stress and handling time in the field. The method is transferable across taxa and the inclusion of multiple animals per image increases sampling efficiency with stored images that can be reviewed multiple times. This practical tool can improve data collection of animal size over large sampling efforts and broad spatiotemporal contexts.

The importance of warm habitat to the growth regime of cold-water fishes.

A common goal of biological adaptation planning is to identify and prioritize locations that remain suitably cool during summer. This implicitly devalues areas that are ephemerally warm, even if they are suitable most of the year for mobile animals. Here we develop an alternative conceptual framework, the growth regime, which considers seasonal and landscape variation in physiological performance, focusing on riverine fish. Using temperature models for 14 river basins, we show that growth opportunities propagate up and down river networks on a seasonal basis, and that downstream habitats that are suboptimally warm in summer may actually provide the majority of growth potential expressed annually. We demonstrate with an agent-based simulation that shoulder-season use of warmer downstream habitats can fuel annual fish production. Our work reveals a synergy between cold and warm habitats that could be fundamental for supporting coldwater fisheries, highlighting the risk in conservation strategies that underappreciate warm habitats.

Introduced beaver improve growth of non-native trout in Tierra del Fuego, South America.

Species introductions threaten ecosystem function worldwide, and interactions among introduced species may amplify their impacts. Effects of multiple invasions are still poorly studied, and often, the mechanisms underlying potential interactions among invaders are unknown. Despite being a remote and well-conserved area, the southern portion of South America has been greatly impacted by invasions of both the American beaver (Castor canadensis) and Brown Trout (Salmo trutta fario). Here, we compared growth, condition, diet, and stable isotopes of sulfur δ34S, nitrogen δ15N, and carbon δ13C for stream-living Brown Trout from streams with (n = 6) and without (n = 6) beaver in Tierra del Fuego, Chile. We show that beaver may facilitate the success of trout by positively influencing fish growth. Beaver indirectly provide greater food subsidies (i.e., macroinvertebrate abundances) by modifying the local aquatic environment through active dam and lodge building suggesting a one-way positive interaction. Trout in beaver-influenced streams occupied a slightly higher trophic level with more depleted sulfur and carbon isotopic ratios suggesting that food web pathways rely on secondary production from autochthonous origin. Trout in beaver-influenced streams had a wider dietary breadth with diptera and amphipoda as the prey items providing most of the energy, whereas in streams without beaver, trichoptera were the main source of energy for trout. Ultimately, we find that these two species, which have never co-occurred naturally, bring about the same ecosystem function and the beneficial influences in their native ranges as in invaded systems.

Hatching and survival of the salmon 'gill maggot' Salmincola californiensis (Copepoda: Lernaeopodidae) reveals thermal dependence and undocumented naupliar stage.

Salmincola californiensis is a Lernaeopodid copepod parasitizing Pacific salmon and trout of the genus Oncorhynchus. Salmincola californiensis is of increasing concern in both native and introduced ranges because of its potential fish health impacts and high infection prevalence and intensity in some systems. Discrepancies in the documented life history phenology of S. californiensis with the sister species Salmincola edwardsii, as well as our laboratory observations, led us to question the existing literature. We documented a naupliar stage, thought lost for S. californiensis. In addition, we found a high degree of thermal sensitivity in egg development, with eggs developing faster under warmer conditions. Survival of copepodids was also highly dependent on temperature, with warmer conditions reducing lifespan. The longest lived copepodid survived 18 days at 4°C in stark contrast to the generally accepted <48 h survival for that life stage. We also note a consistent relationship between egg sac size and the number of eggs contained. However, egg sac sizes were highly variable. Our findings demonstrate that revisiting old assumptions for S. californiensis and related taxa will be a necessary step to improving our knowledge of the parasite life history and development that will be critical to disease management.

Short-term reservoir draining to streambed for juvenile salmon passage and non-native fish removal.

Fish passage out of reservoirs is a critical issue for downstream movement of juvenile salmonids and other migratory species. Reservoirs can delay downstream migrations by juvenile salmon for months or years. Here, we examine whether a novel management activity implementing annual short-term draining of a reservoir to streambed improves timely downstream migration of juvenile salmonids. We analyse 12 years of fish capture data from a screw trap located downstream of Fall Creek Reservoir (Oregon, USA) to examine changes in timing of passage out of the reservoir and to compare fish species composition pre- and post-draining. We observed a contraction in the timing of downstream migration for juvenile Chinook Salmon and reduction of yearlings in years following draining. We suggest that briefly draining the reservoir to streambed leads to reduced abundance of warm-water invasive fishes in the reservoir after it refills. These changes could decrease predation and shift competition between invasive and resident riverine-adapted native fishes in the reservoir. Collectively, our findings suggest that this low-cost reservoir management option may improve passage and connectivity for juvenile Chinook Salmon while also decreasing the abundance of invasive fish species in the reservoir. This case study underscores the crucial need for further evaluations of reservoir draining in other systems and contexts.

Examining the influence of human stressors on benthic algae, macroinvertebrate, and fish assemblages in Mediterranean streams of Chile.

Changes in land-uses and cover are strong drivers of stream degradation worldwide. In Mediterranean ecoregions, land conversion from forest with native species to tree plantations, agricultural, and urban areas have drastically increased in recent years. Here, we examined the influence of land-use types on water quality (physical and chemical variables) and biota (benthic algae, macroinvertebrates, and fishes). We conducted field surveys between December-March 2016 (dry season) in 24 sites located across four land-use types including native vegetation (NV), tree plantation (TP), agriculture (Ag), and urban (Ur) within the Chilean Mediterranean ecoregion. We calculated metrics and multivariate statistics to assess correlations between biological and environmental variables. Significant differences between land-uses were found for environmental/physicochemical variables and the three biotic groups (i.e., benthic algae, macroinvertebrates, and fishes). We found higher chlorophyll-a biomass for TP, Ag, and Ur compared to NV streams. The macroinvertebrate diversity of sensitive taxa (i.e., Ephemeroptera, Plecoptera, and Trichoptera) and water quality were lower in land draining streams with human uses, other than NV, with the most evident impact found in Ag and Ur streams. NV and TP streams had a lower Diptera density and lower percentage of non-insect taxa. Fish richness and diversity were not affected by land-use. However, cold-water fishes (both native and introduced) were closely associated with NV and TP streams whereas warm-water fishes (mostly introduced) were closely associated with Ag and Ur streams. Multivariate analysis revealed that both local habitat and catchment-scale variables influenced each biological assemblage. Our findings suggest that benthic algae, macroinvertebrates, and fish populations are good indicators of human land-use disturbances, with Ag and Ur areas being the most detrimental for freshwater biota.

Climate-Altered Wetlands Challenge Waterbird Use and Migratory Connectivity in Arid Landscapes.

Wetlands in arid landscapes provide critical habitat for millions of migratory waterbirds across the world and throughout their annual cycle. The scope and scale of understanding avian use of these wetlands in conjunction with changes in climate are daunting yet critical to address lest we lose continent-wide migratory pathways. Here, we assess changes in waterbird use of North America's Pacific Flyway in the Great Basin by examining water availability and climate trends over the past 100 years. We found recent (1980-2015) climate warming has significantly reduced the amount and shifted seasonality of water flowing into wetlands. Further, we found remarkable changes in waterbird species composition over time. We propose that a reduced hydroperiod and lower water quality from reduction in water level and flow limits sites used by waterbirds. These factors reduce chick survivorship as they cannot metabolize saline water, which makes suitable freshwater conditions a limiting resource. Collectively, climate-induced changes in Great Basin wetlands suggest a major shift in freshwater ecosystems, resulting in degradation of a continental migratory route. This work illustrates the importance of examining multi-scale changes in critical regional resources to understand their impact across a hemispheric flyway and provides a model to examine other flyways.

Evidence for lasting alterations to aquatic food webs with short-duration reservoir draining.

Large dams and their respective reservoirs provide renewable energy and water security, but also can profoundly alter riverine ecosystems. Here, we present evidence of changing aquatic food web structure in the seasons following short-duration, extreme manipulation of water levels in a reservoir (i.e., draining of the reservoir to the original riverbed during fall to assist outmigration of juvenile Chinook Salmon). We find unintended and lagged consequences of transitioning from a lake to a river, even temporarily, that resulted in trophic shifts away from piscivory and towards feeding at lower trophic levels for two common piscivorous fishes in reservoirs. Using natural abundances of nitrogen stable isotopes, we observed lower trophic level of feeding for invasive Largemouth Bass (Micropterus salmoides) and native Rainbow Trout (Oncorhynchus mykiss) during the summers following reservoir refilling than in nearby reference reservoirs that were not temporarily drained during fall. Declines in trophic levels of aquatic top predators have been rarely documented outside of controlled laboratory conditions. While useful for assisting outmigration of juvenile salmonids, the temporary draining of a reservoir to riverbed can also result in novel shifts in foodweb dynamics including reduced piscivory. As large dams continue to be operated and constructed worldwide, increased understanding of the community and ecosystem-level effects of reservoir management will be critical to evaluating trade-offs between human water needs, conservation of high value species, and ecosystem services impacted by river fragmentation.

A novel approach for examining downstream thermal responses of streams to contemporary forestry.

Temperature is a fundamental driver of aquatic environments. Changes in thermal regimes due to timber harvest may be detrimental for cold-water instream biota. Although it is understood that stream temperature may increase immediately below timber harvest operations, the understanding of how thermal responses propagate downstream is less clear. Here, we examine the effects of timber harvest on stream temperature pre- (2-3 years) and post-harvest (5 years) at 16 sites (average annual streamflow rates <0.283 m3 s-1) located in the Coast Range, Oregon, USA. At each site, an array of temperature sensors were deployed on the extremes of three consecutive reaches: an upstream unharvested reference reach, a treatment reach, and a downstream unharvested reach. We used several metrics to describe and evaluate changes over time and space focusing on the responses of downstream reaches. Primarily, we evaluated the differences over time in daily maximum temperature between the two sensors located at the downstream unharvested reach. Furthermore, using a statistical ordination technique, we examined the spatial and temporal variability of an array of sensors for daily maximum temperature. Moreover, we assessed distributional shifts (statistical moments) of hourly temperature differences between the two sensors at the downstream unharvested reach over time. Lastly, we used a combination of statistical moments and the ordination technique to provide an index that describes the behavior of site-specific thermal disturbance over time. We found that stream reaches responded differently to upstream timber harvest operations between pre and post-harvest summer seasons. In addition, we showed distinct patterns of longitudinal variability of temperature across sites and summer seasons with increases, decreases or mixed responses including no change downstream. Overall, the net change of daily maximum temperature at the downstream reach revealed that the highest difference occurred during the first and second year post-harvest and, in some cases, a distinctive shift in stream warming and cooling occurred between the day and the night. Observed temperature patterns in downstream reaches were most similar to the pre-harvest conditions at the fifth year post-harvest. Collectively, we offer a novel approach for assessing stream temperature regime change using multiple metrics that can improve our understanding of thermal effects downstream of timber harvest, taking in consideration idiosyncratic responses across sites and time.

Rising synchrony controls western North American ecosystems.

Along the western margin of North America, the winter expression of the North Pacific High (NPH) strongly influences interannual variability in coastal upwelling, storm track position, precipitation, and river discharge. Coherence among these factors induces covariance among physical and biological processes across adjacent marine and terrestrial ecosystems. Here, we show that over the past century the degree and spatial extent of this covariance (synchrony) has substantially increased, and is coincident with rising variance in the winter NPH. Furthermore, centuries-long blue oak (Quercus douglasii) growth chronologies sensitive to the winter NPH provide robust evidence that modern levels of synchrony are among the highest observed in the context of the last 250 years. These trends may ultimately be linked to changing impacts of the El Niño Southern Oscillation on midlatitude ecosystems of North America. Such a rise in synchrony may destabilize ecosystems, expose populations to higher risks of extinction, and is thus a concern given the broad biological relevance of winter climate to biological systems.

Contrasting genetic metrics and patterns among naturalized rainbow trout (Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture.

Different pathways of propagation and dispersal of non-native species into new environments may have contrasting demographic and genetic impacts on established populations. Repeated introductions of rainbow trout (Oncorhynchus mykiss) to Chile in South America, initially through stocking and later through aquaculture escapes, provide a unique setting to contrast these two pathways. Using a panel of single nucleotide polymorphisms, we found contrasting genetic metrics and patterns among naturalized trout in Lake Llanquihue, Chile's largest producer of salmonid smolts for nearly 50 years, and Lake Todos Los Santos (TLS), a reference lake where aquaculture has been prohibited by law. Trout from Lake Llanquihue showed higher genetic diversity, weaker genetic structure, and larger estimates for the effective number of breeders (Nb) than trout from Lake TLS. Trout from Lake TLS were divergent from Lake Llanquihue and showed marked genetic structure and a significant isolation-by-distance pattern consistent with secondary contact between documented and undocumented stocking events in opposite shores of the lake. Multiple factors, including differences in propagule pressure, origin of donor populations, lake geomorphology, habitat quality or quantity, and life history, may help explain contrasting genetic metrics and patterns for trout between lakes. We contend that high propagule pressure from aquaculture may not only increase genetic diversity and Nb via demographic effects and admixture, but also may impact the evolution of genetic structure and increase gene flow, consistent with findings from artificially propagated salmonid populations in their native and naturalized ranges.