Landscape Connectivity and Genetic Structure in a Mainstem and a Tributary Stonefly (Plecoptera) Species Using a Novel Reference Genome.

Understanding how environmental variation influences population genetic structure can help predict how environmental change influences population connectivity, genetic diversity, and evolutionary potential. We used riverscape genomics modeling to investigate how climatic and habitat variables relate to patterns of genetic variation in 2 stonefly species, one from mainstem river habitats (Sweltsa coloradensis) and one from tributaries (Sweltsa fidelis) in 40 sites in northwest Montana, USA. We produced a draft genome assembly for S. coloradensis (N50 = 0.251 Mbp, BUSCO > 95% using "insecta_ob9" reference genes). We genotyped 1930 SNPs in 372 individuals for S. coloradensis and 520 SNPs in 153 individuals for S. fidelis. We found higher genetic diversity for S. coloradensis compared to S. fidelis, but nearly identical genetic differentiation among sites within each species (both had global loci median FST = 0.000), despite differences in stream network location. For landscape genomics and testing for selection, we produced a less stringently filtered data set (3454 and 1070 SNPs for S. coloradensis and S. fidelis, respectively). Environmental variables (mean summer precipitation, slope, aspect, mean June stream temperature, land cover type) were correlated with 19 putative adaptive loci for S. coloradensis, but there was only one putative adaptive locus for S. fidelis (correlated with aspect). Interestingly, we also detected potential hybridization between multiple Sweltsa species which has never been previously detected. Studies like ours, that test for adaptive variation in multiple related species are needed to help assess landscape connectivity and the vulnerability of populations and communities to environmental change.

Tolerance of aquifer stoneflies to repeated hypoxia exposure and oxygen dynamics in an alluvial aquifer.

Aquatic insects cope with hypoxia and anoxia using a variety of behavioral and physiological responses. Most stoneflies (Plecoptera) occur in highly oxygenated surface waters, but some species live underground in alluvial aquifers containing heterogeneous oxygen concentrations. Aquifer stoneflies appear to be supported by methane-derived food resources, which they may exploit using anoxia-resistant behaviors. We documented dissolved oxygen dynamics and collected stoneflies over 5 years in floodplain wells of the Flathead River, Montana. Hypoxia regularly occurred in two wells, and nymphs of Paraperla frontalis were collected during hypoxic periods. We measured mass-specific metabolic rates (MSMRs) at different oxygen concentrations (12, 8, 6, 4, 2, 0.5 mg l-1, and during recovery) for 111 stonefly nymphs to determine whether aquifer and benthic taxa differed in hypoxia tolerance. Metabolic rates of aquifer taxa were similar across oxygen concentrations spanning 2 to 12 mg l-1 (P>0.437), but the MSMRs of benthic taxa dropped significantly with declining oxygen (P<0.0001; 2.9-times lower at 2 vs. 12 mg l-1). Aquifer taxa tolerated short-term repeated exposure to extreme hypoxia surprisingly well (100% survival), but repeated longer-term (>12 h) exposures resulted in lower survival (38-91%) and lower MSMRs during recovery. Our work suggests that aquifer stoneflies have evolved a remarkable set of behavioral and physiological adaptations that allow them to exploit the unique food resources available in hypoxic zones. These adaptations help to explain how large-bodied consumers might thrive in the underground aquifers of diverse and productive river floodplains.

Remarkable anoxia tolerance by stoneflies from a floodplain aquifer.

Alluvial aquifers are key components of river floodplains and biodiversity worldwide, but they contain extreme environmental conditions and have limited sources of carbon for sustaining food webs. Despite this, they support abundant populations of aquifer stoneflies that have large proportions of their biomass carbon derived from methane. Methane is typically produced in freshwater ecosystems in anoxic conditions, while stoneflies (Order: Plecoptera) are thought to require highly oxygenated water. The potential importance of methane-derived food resources raises the possibility that stonefly consumers have evolved anoxia-resistant behaviors and physiologies. Here we tested the anoxic and hypoxic responses of 2,445 stonefly individuals in three aquifer species and nine benthic species. We conducted experimental trials in which we reduced oxygen levels, documented locomotor activity, and measured survival rates. Compared to surface-dwelling benthic relatives, stoneflies from the alluvial aquifer on the Flathead River (Montana) performed better in hypoxic and anoxic conditions. Aquifer species sustained the ability to walk after 4-76 h of anoxia vs. 1 h for benthic species and survived on average three times longer than their benthic counterparts. Aquifer stoneflies also sustained aerobic respiration down to much lower levels of ambient oxygen. We show that aquifer taxa have gene sequences for hemocyanin, an oxygen transport respiratory protein, representing a possible mechanism for surviving low oxygen. This remarkable ability to perform well in low-oxygen conditions is unique within the entire order of stoneflies (Plecoptera) and uncommon in other freshwater invertebrates. These results show that aquifer stoneflies can exploit rich carbon resources available in anoxic zones, which may explain their extraordinarily high abundance in gravel-bed floodplain aquifers. These stoneflies are part of a novel food web contributing biodiversity to river floodplains.

Phenological tracking associated with increased salmon consumption by brown bears.

There is growing interest in the ecological significance of phenological diversity, particularly in how spatially variable resource phenologies (i.e. resource waves) prolong foraging opportunities for mobile consumers. While there is accumulating evidence of consumers moving across landscapes to surf resource waves, there is little data quantifying how phenological tracking influences resource consumption due to the challenge of documenting all the components of this ecological phenomenon (i.e., phenological variation, consumer movement, resource consumption, and consumer fitness). We examined the space use of GPS collared female brown bears to quantify the exploitation of a salmon resource wave by individual bears. We then estimated salmon consumption levels in the same individuals using stable isotope and mercury analyses of hair. We found strong positive relationships between time spent on salmon streams and percent salmon in assimilated diets (R2 = 0.70) and salmon mass consumed (R2 = 0.49). Salmon abundance varied 2.5-fold between study years, yet accounting for salmon abundance did not improve salmon consumption models. Resource abundance generally is viewed as the key variable controlling consumption levels and food web dynamics. However, our results suggest that in intact watersheds of coastal Alaska with abundant salmon runs, interannual variation in salmon abundance likely has less effect on salmon consumption than individual variation in bear foraging behavior. The results complement previous work to demonstrate the importance of phenological variation on bear foraging behavior and fitness.

Phenological synchronization disrupts trophic interactions between Kodiak brown bears and salmon.

Climate change is altering the seasonal timing of life cycle events in organisms across the planet, but the magnitude of change often varies among taxa [Thackeray SJ, et al. (2016) Nature 535:241-245]. This can cause the temporal relationships among species to change, altering the strength of interaction. A large body of work has explored what happens when coevolved species shift out of sync, but virtually no studies have documented the effects of climate-induced synchronization, which could remove temporal barriers between species and create novel interactions. We explored how a predator, the Kodiak brown bear (Ursus arctos middendorffi), responded to asymmetric phenological shifts between its primary trophic resources, sockeye salmon (Oncorhynchus nerka) and red elderberry (Sambucus racemosa). In years with anomalously high spring air temperatures, elderberry fruited several weeks earlier and became available during the period when salmon spawned in tributary streams. Bears departed salmon spawning streams, where they typically kill 25-75% of the salmon [Quinn TP, Cunningham CJ, Wirsing AJ (2016) Oecologia 183:415-429], to forage on berries on adjacent hillsides. This prey switching behavior attenuated an iconic predator-prey interaction and likely altered the many ecological functions that result from bears foraging on salmon [Helfield JM, Naiman RJ (2006) Ecosystems 9:167-180]. We document how climate-induced shifts in resource phenology can alter food webs through a mechanism other than trophic mismatch. The current emphasis on singular consumer-resource interactions fails to capture how climate-altered phenologies reschedule resource availability and alter how energy flows through ecosystems.

Ancient and methane-derived carbon subsidizes contemporary food webs.

While most global productivity is driven by modern photosynthesis, river ecosystems are supplied by locally fixed and imported carbon that spans a range of ages. Alluvial aquifers of gravel-bedded river floodplains present a conundrum: despite no possibility for photosynthesis in groundwater and extreme paucity of labile organic carbon, they support diverse and abundant large-bodied consumers (stoneflies, Insecta: Plecoptera). Here we show that up to a majority of the biomass carbon composition of these top consumers in four floodplain aquifers of Montana and Washington is methane-derived. The methane carbon ranges in age from modern to up to >50,000 years old and is mostly derived from biogenic sources, although a thermogenic contribution could not be excluded. We document one of the most expansive ecosystems to contain site-wide macroinvertebrate biomass comprised of methane-derived carbon and thereby advance contemporary understanding of basal resources supporting riverine productivity.

Do beaver dams reduce habitat connectivity and salmon productivity in expansive river floodplains?

Beaver have expanded in their native habitats throughout the northern hemisphere in recent decades following reductions in trapping and reintroduction efforts. Beaver have the potential to strongly influence salmon populations in the side channels of large alluvial rivers by building dams that create pond complexes. Pond habitat may improve salmon productivity or the presence of dams may reduce productivity if dams limit habitat connectivity and inhibit fish passage. Our intent in this paper is to contrast the habitat use and production of juvenile salmon on expansive floodplains of two geomorphically similar salmon rivers: the Kol River in Kamchatka, Russia (no beavers) and the Kwethluk River in Alaska (abundant beavers), and thereby provide a case study on how beavers may influence salmonids in large floodplain rivers. We examined important rearing habitats in each floodplain, including springbrooks, beaver ponds, beaver-influenced springbrooks, and shallow shorelines of the river channel. Juvenile coho salmon dominated fish assemblages in all habitats in both rivers but other species were present. Salmon density was similar in all habitat types in the Kol, but in the Kwethluk coho and Chinook densities were 3-12× lower in mid- and late-successional beaver ponds than in springbrook and main channel habitats. In the Kol, coho condition (length: weight ratios) was similar among habitats, but Chinook condition was highest in orthofluvial springbrooks. In the Kwethluk, Chinook condition was similar among habitats, but coho condition was lowest in main channel versus other habitats (0.89 vs. 0.99-1.10). Densities of juvenile salmon were extremely low in beaver ponds located behind numerous dams in the orthofluvial zone of the Kwethluk River floodplain, whereas juvenile salmon were abundant in habitats throughout the entire floodplain in the Kol River. If beavers were not present on the Kwethluk, floodplain habitats would be fully interconnected and theoretically could produce 2× the biomass (between June-August, 1,174 vs. 667 kg) and rear 3× the number of salmon (370,000 vs. 140,000) compared to the existing condition with dams present. The highly productive Kol river produces an order of magnitude more salmon biomass and rears 40× the individuals compared to the Kwethluk. If beavers were introduced to the Kol River, we estimate that off-channel habitats would produce half as much biomass (2,705 vs. 5,404 kg) and 3× fewer individuals (1,482,346 vs. 4,856,956) owing to conversion of inter-connected, productive springbrooks into inaccessible pond complexes. We concluded that beaver dams may limit the total amount of floodplain habitat available for salmon rearing in the Kwethluk river and that the introduction of beavers to the Kol river could be detrimental to salmon populations. The introduction of beavers to other large alluvial rivers like those found in Kamchatka could have negative consequences for salmon production.

A time-lapse photography method for monitoring salmon (Oncorhynchus spp.) passage and abundance in streams.

Accurately estimating population sizes is often a critical component of fisheries research and management. Although there is a growing appreciation of the importance of small-scale salmon population dynamics to the stability of salmon stock-complexes, our understanding of these populations is constrained by a lack of efficient and cost-effective monitoring tools for streams. Weirs are expensive, labor intensive, and can disrupt natural fish movements. While conventional video systems avoid some of these shortcomings, they are expensive and require excessive amounts of labor to review footage for data collection. Here, we present a novel method for quantifying salmon in small streams (<15 m wide, <1 m deep) that uses both time-lapse photography and video in a model-based double sampling scheme. This method produces an escapement estimate nearly as accurate as a video-only approach, but with substantially less labor, money, and effort. It requires servicing only every 14 days, detects salmon 24 h/day, is inexpensive, and produces escapement estimates with confidence intervals. In addition to escapement estimation, we present a method for estimating in-stream salmon abundance across time, data needed by researchers interested in predator--prey interactions or nutrient subsidies. We combined daily salmon passage estimates with stream specific estimates of daily mortality developed using previously published data. To demonstrate proof of concept for these methods, we present results from two streams in southwest Kodiak Island, Alaska in which high densities of sockeye salmon spawn.

Kodiak brown bears surf the salmon red wave: direct evidence from GPS collared individuals.

A key constraint faced by consumers is achieving a positive energy balance in the face of temporal variation in foraging opportunities. Recent work has shown that spatial heterogeneity in resource phenology can buffer mobile consumers from this constraint by allowing them to track changes in resource availability across space. For example, salmon populations spawn asynchronously across watersheds, causing high-quality foraging opportunities to propagate across the landscape, prolonging the availability of salmon at the regional scale. However, we know little about how individual consumers integrate across phenological variation or the benefits they receive by doing so. Here, we present direct evidence that individual brown bears track spatial variation in salmon phenology. Data from 40 GPS collared brown bears show that bears visited multiple spawning sites in synchrony with the order of spawning phenology. The number of sites used was correlated with the number of days a bear exploited salmon, suggesting the phenological variation in the study area influenced bear access to salmon, a resource which strongly influences bear fitness. Fisheries managers attempting to maximize harvest while maintaining ecosystem function should strive to protect the population diversity that underlies the phenological variation used by wildlife consumers.

Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics.

Understanding how environmental variation influences population genetic structure is important for conservation management because it can reveal how human stressors influence population connectivity, genetic diversity and persistence. We used riverscape genetics modelling to assess whether climatic and habitat variables were related to neutral and adaptive patterns of genetic differentiation (population-specific and pairwise FST ) within five metapopulations (79 populations, 4583 individuals) of steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, USA. Using 151 putatively neutral and 29 candidate adaptive SNP loci, we found that climate-related variables (winter precipitation, summer maximum temperature, winter highest 5% flow events and summer mean flow) best explained neutral and adaptive patterns of genetic differentiation within metapopulations, suggesting that climatic variation likely influences both demography (neutral variation) and local adaptation (adaptive variation). However, we did not observe consistent relationships between climate variables and FST across all metapopulations, underscoring the need for replication when extrapolating results from one scale to another (e.g. basin-wide to the metapopulation scale). Sensitivity analysis (leave-one-population-out) revealed consistent relationships between climate variables and FST within three metapopulations; however, these patterns were not consistent in two metapopulations likely due to small sample sizes (N = 10). These results provide correlative evidence that climatic variation has shaped the genetic structure of steelhead populations and highlight the need for replication and sensitivity analyses in land and riverscape genetics.

Long-term atmospheric deposition of nitrogen, phosphorus and sulfate in a large oligotrophic lake.

We documented significantly increasing trends in atmospheric loading of ammonium (NH4) and nitrate/nitrite (NO2/3) and decreasing trends in total phosphorus (P) and sulfate (SO4) to Flathead Lake, Montana, from 1985 to 2004. Atmospheric loading of NO2/3 and NH4 increased by 48 and 198% and total P and SO4 decreased by 135 and 39%. The molar ratio of TN:TP also increased significantly. Severe air inversions occurred periodically year-round and increased the potential for substantial nutrient loading from even small local sources. Correlations between our loading data and various measures of air quality in the basin (e.g., particulate matter <10 µm in size, aerosol fine soil mass, aerosol nutrient species, aerosol index, hectares burned) suggest that dust and smoke are important sources. Ammonium was the primary form of N in atmospheric deposition, whereas NO3 was the primary N form in tributary inputs. Atmospheric loading of NH4 to Flathead Lake averaged 44% of the total load and on some years exceeded tributary loading. Primary productivity in the lake is colimited by both N and P most of the year; and in years of high atmospheric loading of inorganic N, deposition may account for up to 6.9% of carbon converted to biomass.

Performance of salmon fishery portfolios across western North America.

Quantifying the variability in the delivery of ecosystem services across the landscape can be used to set appropriate management targets, evaluate resilience and target conservation efforts. Ecosystem functions and services may exhibit portfolio-type dynamics, whereby diversity within lower levels promotes stability at more aggregated levels. Portfolio theory provides a framework to characterize the relative performance among ecosystems and the processes that drive differences in performance. We assessed Pacific salmon Oncorhynchus spp. portfolio performance across their native latitudinal range focusing on the reliability of salmon returns as a metric with which to assess the function of salmon ecosystems and their services to humans. We used the Sharpe ratio (e.g. the size of the total salmon return to the portfolio relative to its variability (risk)) to evaluate the performance of Chinook and sockeye salmon portfolios across the west coast of North America. We evaluated the effects on portfolio performance from the variance of and covariance among salmon returns within each portfolio, and the association between portfolio performance and watershed attributes. We found a positive latitudinal trend in the risk-adjusted performance of Chinook and sockeye salmon portfolios that also correlated negatively with anthropogenic impact on watersheds (e.g. dams and land-use change). High-latitude Chinook salmon portfolios were on average 2·5 times more reliable, and their portfolio risk was mainly due to low variance in the individual assets. Sockeye salmon portfolios were also more reliable at higher latitudes, but sources of risk varied among the highest performing portfolios. Synthesis and applications. Portfolio theory provides a straightforward method for characterizing the resilience of salmon ecosystems and their services. Natural variability in portfolio performance among undeveloped watersheds provides a benchmark for restoration efforts. Locally and regionally, assessing the sources of portfolio risk can guide actions to maintain existing resilience (protect habitat and disturbance regimes that maintain response diversity; employ harvest strategies sensitive to different portfolio components) or improve restoration activities. Improving our understanding of portfolio reliability may allow for management of natural resources that is robust to ongoing environmental change. Portfolio theory provides a straightforward method for characterizing the resilience of salmon ecosystems and their services. Natural variability in portfolio performance among undeveloped watersheds provides a benchmark for restoration efforts. Locally and regionally, assessing the sources of portfolio risk can guide actions to maintain existing resilience (protect habitat and disturbance regimes that maintain response diversity; employ harvest strategies sensitive to different portfolio components) or improve restoration activities. Improving our understanding of portfolio reliability may allow for management of natural resources that is robust to ongoing environmental change.

Long-term effects of a trophic cascade in a large lake ecosystem.

Introductions or invasions of nonnative organisms can mediate major changes in the trophic structure of aquatic ecosystems. Here we document multitrophic level impacts in a spatially extensive system that played out over more than a century. Positive interactions among exotic vertebrate and invertebrate predators caused a substantial and abrupt shift in community composition resulting in a trophic cascade that extended to primary producers and to a nonaquatic species, the bald eagle. The opossum shrimp, Mysis diluviana, invaded Flathead Lake, Montana, the largest freshwater lake in the western United States. Lake trout had been introduced 80 y prior but remained at low densities until nonnative Mysis became established. The bottom-dwelling mysids eliminated a recruitment bottleneck for lake trout by providing a deep water source of food where little was available previously. Lake trout subsequently flourished on mysids and this voracious piscivore now dominates the lake fishery; formerly abundant kokanee were extirpated, and native bull and westslope cutthroat trout are imperiled. Predation by Mysis shifted zooplankton and phytoplankton community size structure. Bayesian change point analysis of primary productivity (27-y time series) showed a significant step increase of 55 mg C m(-2) d(-1) (i.e., 21% rise) concurrent with the mysid invasion, but little trend before or after despite increasing nutrient loading. Mysis facilitated predation by lake trout and indirectly caused the collapse of kokanee, redirecting energy flow through the ecosystem that would otherwise have been available to other top predators (bald eagles).

Habitat heterogeneity and associated microbial community structure in a small-scale floodplain hyporheic flow path.

The Nyack floodplain is located on the Middle Fork of the Flathead River, an unregulated, pristine, fifth-order stream in Montana, USA, bordering Glacier National Park. The hyporheic zone is a nutritionally heterogeneous floodplain component harboring a diverse array of microbial assemblages essential in fluvial biogeochemical cycling, riverine ecosystem productivity, and trophic interactions. Despite these functions, microbial community structure in pristine hyporheic systems is not well characterized. The current study was designed to assess whether physical habitat heterogeneity within the hyporheic zone of the Nyack floodplain was sufficient to drive bacterial beta diversity between three different hyporheic flow path locations. Habitat heterogeneity was assessed by measuring soluble reactive phosphorous, nitrate, dissolved organic carbon, dissolved oxygen, and soluble total nitrogen levels seasonally at surface water infiltration, advection, and exfiltration zones. Significant spatial differences were detected in dissolved oxygen and nitrate levels, and seasonal differences were detected in dissolved oxygen, nitrate, and dissolved organic carbon levels. Denaturing gradient gel electrophoresis (DGGE) and cell counts indicated that bacterial diversity increased with abundance, and DGGE fingerprints covaried with nitrate levels where water infiltrated the hyporheic zone. The ribosomal gene phylogeny revealed that hyporheic habitat heterogeneity was sufficient to drive beta diversity between bacterial assemblages. Phylogenetic (P) tests detected sequence disparity between the flow path locations. Small distinct lineages of Firmicutes, Actinomycetes, Planctomycetes, and Acidobacteria defined the infiltration zone and alpha- and beta-proteobacterial lineages delineated the exfiltration and advection zone communities. These data suggest that spatial habitat heterogeneity drives hyporheic microbial community development and that attempts to understand functional differences between bacteria inhabiting nutritionally heterogeneous hyporheic environments might begin by focusing on the biology of these taxa.

Climate, hydrologic disturbance, and succession: drivers of floodplain pattern.

Floodplains are among the world's most threatened ecosystems due to the pervasiveness of dams, levee systems, and other modifications to rivers. Few unaltered floodplains remain where we may examine their dynamics over decadal time scales. Our study provides a detailed examination of landscape change over a 60-year period (1945-2004) on the Nyack floodplain of the Middle Fork of the Flathead River, a free-flowing, gravel-bed river in northwest Montana, USA. We used historical aerial photographs and airborne and satellite imagery to delineate habitats (i.e., mature forest, regenerative forest, water, cobble) within the floodplain. We related changes in the distribution and size of these habitats to hydrologic disturbance and regional climate. Results show a relationship between changes in floodplain habitats and annual flood magnitude, as well as between hydrology and the cooling and warming phases of the Pacific Decadal Oscillation (PDO). Large magnitude floods and greater frequency of moderate floods were associated with the cooling phases of the PDO, resulting in a floodplain environment dominated by extensive restructuring and regeneration of floodplain habitats. Conversely, warming phases of the PDO corresponded with decreases in magnitude, duration, and frequency of critical flows, creating a floodplain environment dominated by late successional vegetation and low levels of physical restructuring. Over the 60-year time series, habitat change was widespread throughout the floodplain, though the relative abundances of the habitats did not change greatly. We conclude that the long- and short-term interactions of climate, floods, and plant succession produce a shifting habitat mosaic that is a fundamental attribute of natural floodplain ecosystems.

Effects of stocking-up freshwater food webs.

The establishment of exotic game fishes to enhance recreational fisheries through authorized and unauthorized stocking into freshwater systems is a global phenomenon. Stocked fishes are often top predators that either replace native top predators or increase the species richness of top predators. Many direct effects of stocking have been documented, but the ecosystem consequences are seldom quantified. New studies increasingly document how species and community shifts influence ecosystem processes. We discuss here how predator stocking might increase top-down effects, alter nutrient cycles and decrease links between aquatic and surrounding terrestrial ecosystems. As fisheries management moves beyond species-specific utilitarian objectives to incorporate ecosystem and conservation goals, ecologists must address how common management practices alter food-web structure and subsequent ecosystem-level effects.