Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP.

Adaptive capacity can present challenges for modelling as it encompasses multiple ecological and evolutionary processes such as natural selection, genetic drift, gene flow and phenotypic plasticity. Spatially explicit, individual-based models provide an outlet for simulating these complex interacting eco-evolutionary processes. We expanded the existing Cost-Distance Meta-POPulation (CDMetaPOP) framework with inducible plasticity modelled as a habitat selection behaviour, using temperature or habitat quality variables, with a genetically based selection threshold conditioned on past individual experience. To demonstrate expected results in the new module, we simulated hypothetical populations and then evaluated model performance in populations of redband trout (Oncorhynchus mykiss gairdneri) across three watersheds where temperatures induce physiological stress in parts of the stream network. We ran simulations using projected warming stream temperature data under four scenarios for alleles that: (1) confer thermal tolerance, (2) bestow plastic habitat selection, (3) give both thermal tolerance and habitat selection preference and (4) do not provide either thermal tolerance or habitat selection. Inclusion of an adaptive allele decreased declines in population sizes, but this impact was greatly reduced in the relatively cool stream networks. As anticipated with the new module, high-temperature patches remained unoccupied by individuals with the allele operating plastically after exposure to warm temperatures. Using complete habitat avoidance above the stressful temperature threshold, habitat selection reduced the overall population size due to the opportunity cost of avoiding areas with increased, but not guaranteed, mortality. Inclusion of plasticity within CDMetaPOP will provide the potential for genetic or plastic traits and 'rescue' to affect eco-evolutionary dynamics for research questions and conservation applications.

Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout.

Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low-coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids (GREB1L, ROCK1, SIX6). Genotype-environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high-elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high-elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change.

Technical fishway passage structures provide high passage efficiency and effective passage for adult Pacific salmonids at eight large dams.

Fishways have been widely used for upstream passage around human-built structures, but 'success' has varied dramatically. Evaluation of fishway success has typically been conducted at local scales using metrics such as fish passage efficiency and passage time, but evaluations are increasingly used in broader assessments of whether passage facilities meet population-specific conservation and management objectives. Over 15 years, we monitored passage effectiveness at eight dams on the Columbia and Snake rivers for 26,886 radio-tagged spring-summer and fall Chinook Salmon O. tshwaytscha, Sockeye Salmon O. nerka, and summer steelhead O. mykiss during their migrations to spawning sites. Almost all fish that entered dam tailraces eventually approached and entered fishways. Tailrace-to-forebay passage efficiency estimates at individual dams were consistently high, averaging 0.966 (SD = 0.035) across 245 run×year×dam combinations. These estimates are among the highest recorded for any migratory species, which we attribute to the scale of evaluation, salmonid life history traits (e.g., philopatry), and a sustained adaptive management approach to fishway design, maintenance, and improvement. Full-dam fish passage times were considerably more variable, with run×year×dam medians ranging from 5-65 h. Evaluation at larger scales provided evidence that fishways were biologically effective, e.g., we observed rapid migration rates (medians = 28-40 km/d) through river reaches with multiple dams and estimated fisheries-adjusted upstream migration survival of 67-69%. However, there were substantive uncertainties regarding effectiveness. Uncertainty about natal origins confounded estimation of population-specific survival and interpretation of apparent dam passage 'failure', while lack of post-migration reproductive data precluded analyses of delayed or cumulative effects of passing the impounded system on fish fitness. Although the technical fishways are effective for salmonids in the Columbia-Snake River system, other co-migrating species have lower passage rates, highlighting the need for species-specific design and evaluation wherever passage facilities impact fish management and conservation goals.

Building a bridge between adaptive capacity and adaptive potential to understand responses to environmental change.

Adaptive capacity is a topic at the forefront of environmental change research with roots in both social, ecological, and evolutionary science. It is closely related to the evolutionary biology concept of adaptive potential. In this systematic literature review, we: (1) summarize the history of these topics and related fields; (2) assess relationship(s) between the concepts among disciplines and the use of the terms in climate change research, and evaluate methodologies, metrics, taxa biases, and the geographic scale of studies; and (3) provide a synthetic conceptual framework to clarify concepts. Bibliometric analyses revealed the terms have been used most frequently in conservation and evolutionary biology journals, respectively. There has been a greater growth in studies of adaptive potential than adaptive capacity since 2001, but a greater geographical extent of adaptive capacity studies. Few studies include both, and use is often superficial. Our synthesis considers adaptive potential as one process contributing to adaptive capacity of complex systems, notes "sociological" adaptive capacity definitions include actions aimed at desired outcome (i.e., policies) as a system driver whereas "biological" definitions exclude such drivers, and suggests models of adaptive capacity require integration of evolutionary and social-ecological system components.

Genomic islands of divergence infer a phenotypic landscape in Pacific lamprey.

High rates of dispersal can breakdown coadapted gene complexes. However, concentrated genomic architecture (i.e., genomic islands of divergence) can suppress recombination to allow evolution of local adaptations despite high gene flow. Pacific lamprey (Entosphenus tridentatus) is a highly dispersive anadromous fish. Observed trait diversity and evidence for genetic basis of traits suggests it may be locally adapted. We addressed whether concentrated genomic architecture could influence local adaptation for Pacific lamprey. Using two new whole genome assemblies and genotypes from 7,716 single nucleotide polymorphism (SNP) loci in 518 individuals from across the species range, we identified four genomic islands of divergence (on chromosomes 01, 02, 04, and 22). We determined robust phenotype-by-genotype relationships by testing multiple traits across geographic sites. These trait associations probably explain genomic divergence across the species' range. We genotyped a subset of 302 broadly distributed SNPs in 2,145 individuals for association testing for adult body size, sexual maturity, migration distance and timing, adult swimming ability, and larval growth. Body size traits were strongly associated with SNPs on chromosomes 02 and 04. Moderate associations also implicated SNPs on chromosome 01 as being associated with variation in female maturity. Finally, we used candidate SNPs to extrapolate a heterogeneous spatiotemporal distribution of these predicted phenotypes based on independent data sets of larval and adult collections. These maturity and body size results guide future elucidation of factors driving regional optimization of these traits for fitness. Pacific lamprey is culturally important and imperiled. This research addresses biological uncertainties that challenge restoration efforts.

Classifying and inferring behaviors using real-time acceleration biotelemetry in reproductive steelhead trout (Oncorhynchus mykiss).

Movement behaviors are central to ecology and conservation. Movement sensing technologies can monitor behaviors that are otherwise difficult to observe under field conditions and may enhance the ability to quantify behaviors at the population scale. We monitored steelhead trout (Oncorhynchus mykiss) spawning behaviors in a seminatural enclosure using accelerometer telemetry tags while simultaneously observing behaviors with underwater cameras. Behavioral assignments from visual observations were compared to acceleration histories to develop assignment criteria for acceleration data, including for a key behavior (oviposition). Behavioral events independently classified using acceleration data prior to reviewing video were compared to video scoring and 97% of holding behaviors, 93% of digging behaviors, and 86% of oviposition/covering behaviors were correctly assigned using acceleration data alone. We applied the method to at-liberty steelhead in spawning tributaries. Acceleration records revealed putative spawning and oviposition in at-liberty female steelhead, and time budgets for at-liberty steelhead were similar to those monitored within enclosures. The use of similar movement sensing tags and classification approaches offers a method for monitoring movement behavior, activity budgets, and habitat use in a broad array of aquatic and terrestrial taxa, and may be especially useful when behaviors are cryptic.

Temperature and depth profiles of Chinook salmon and the energetic costs of their long-distance homing migrations.

River warming poses an existential threat to many Pacific salmon (Oncorhynchus spp) populations. However, temperature-mediated risks to salmon are often complex and addressing them requires species- and population-specific data collected over large spatial and temporal scales. In this study, we combined radiotelemetry with archival depth and temperature sensors to collect continuous thermal exposure histories of 21 adult spring- and summer-run Chinook salmon (O. tshawytscha) as they migrated hundreds of kilometers upstream in the Columbia River basin. Salmon thermal histories in impounded reaches of the Columbia and Snake rivers were characterized by low daily temperature variation but frequent and extensive vertical movements. Dives were associated with slightly cooler salmon body temperatures (~ 0.01 to 0.02 °C/m), but there was no evidence for use of cool-water thermal refuges deep in reservoirs or at tributary confluences along the migration route. In tributaries, salmon were constrained to relatively shallow water, and they experienced ~ 2-5 °C diel temperature fluctuations. Differences in migration timing and among route-specific thermal regimes resulted in substantial among-individual variation in migration temperature exposure. Bioenergetics models using the collected thermal histories and swim speeds ranging from 1.0 to 1.5 body-lengths/s predicted median energetic costs of ~ 24-40% (spring-run) and ~ 37-60% (summer-run) of initial reserves. Median declines in total mass were ~ 16-24% for spring-run salmon and ~ 19-29% for summer-run salmon. A simulated + 2 °C increase in water temperatures resulted in 4.0% (spring-run) and 6.3% (summer-run) more energy used per fish, on average. The biotelemetry data provided remarkable spatial and temporal resolution on thermal exposure. Nonetheless, substantial information gaps remain for the development of robust bioenergetics and climate effects models for adult Chinook salmon.

Positioning Methods and the Use of Location and Activity Data in Forests.

In this paper, we provide an overview of positioning systems for moving resources in forest and fire management and review the related literature. Emphasis is placed on the accuracy and range of different localization and location-sharing methods, particularly in forested environments and in the absence of conventional cellular or internet connectivity. We then conduct a second review of literature and concepts related to several emerging, broad themes in data science, including the terms location-based services (LBS), geofences, wearable technology, activity recognition, mesh networking, the Internet of Things (IoT), and big data. Our objective in this second review is to inform how these broader concepts, with implications for networking and analytics, may help to advance natural resource management and science in the future. Based on methods, themes, and concepts that arose in our systematic reviews, we then augmented the paper with additional literature from wildlife and fisheries management, as well as concepts from video object detection, relative positioning, and inventory-tracking that are also used as forms of localization. Based on our reviews of positioning technologies and emerging data science themes, we present a hierarchical model for collecting and sharing data in forest and fire management, and more broadly in the field of natural resources. The model reflects tradeoffs in range and bandwidth when recording, processing, and communicating large quantities of data in time and space to support resource management, science, and public safety in remote areas. In the hierarchical approach, wearable devices and other sensors typically transmit data at short distances using Bluetooth, Bluetooth Low Energy (BLE), or ANT wireless, and smartphones and tablets serve as intermediate data collection and processing hubs for information that can be subsequently transmitted using radio networking systems or satellite communication. Data with greater spatial and temporal complexity is typically processed incrementally at lower tiers, then fused and summarized at higher levels of incident command or resource management. Lastly, we outline several priority areas for future research to advance big data analytics in natural resources.

Thermal exposure of adult Chinook salmon and steelhead: Diverse behavioral strategies in a large and warming river system.

Rising river temperatures in western North America have increased the energetic costs of migration and the risk of premature mortality in many Pacific salmon (Oncorhynchus spp.) populations. Predicting and managing risks for these populations requires data on acute and cumulative thermal exposure, the spatio-temporal distribution of adverse conditions, and the potentially mitigating effects of cool-water refuges. In this study, we paired radiotelemetry with archival temperature loggers to construct continuous, spatially-explicit thermal histories for 212 adult Chinook salmon (O. tshawytscha) and 200 adult steelhead (O. mykiss). The fish amassed ~500,000 temperature records (30-min intervals) while migrating through 470 kilometers of the Columbia and Snake rivers en route to spawning sites in Idaho, Oregon, and Washington. Spring- and most summer-run Chinook salmon migrated before river temperatures reached annual highs; their body temperatures closely matched ambient temperatures and most had thermal maxima in the lower Snake River. In contrast, many individual fall-run Chinook salmon and most steelhead had maxima near thermal tolerance limits (20-22 °C) in the lower Columbia River. High temperatures elicited extensive use of thermal refuges near tributary confluences, where body temperatures were ~2-10 °C cooler than the adjacent migration corridor. Many steelhead used refuges for weeks or more whereas salmon use was typically hours to days, reflecting differences in spawn timing. Almost no refuge use was detected in a ~260-km reach where a thermal migration barrier may more frequently develop in future warmer years. Within population, cumulative thermal exposure was strongly positively correlated (0.88 ≤ r ≤ 0.98) with migration duration and inconsistently associated (-0.28 ≤ r ≤ 0.09) with migration date. All four populations have likely experienced historically high mean and maximum temperatures in recent years. Expected responses include population-specific shifts in migration phenology, increased reliance on patchily-distributed thermal refuges, and natural selection favoring temperature-tolerant phenotypes.

Thermal exposure of adult Chinook salmon in the Willamette River basin.

Radiotelemetry and archival temperature loggers were used to reconstruct the thermal experience of adult spring Chinook salmon (Oncorhynchus tshawytscha) in the highly regulated Willamette River system in Oregon. The study population is threatened and recovery efforts have been hampered by episodically high prespawn mortality that is likely temperature mediated. Over three years, 310 salmon were released with thermal loggers and 68 were recovered in spawning tributaries, primarily at hatchery trapping facilities downstream from high-head dams. More than 190,000 internal body temperature records were collected (mean ~2800 per fish) and associated with 14 main stem and tributary reaches. Most salmon experienced a wide temperature range (minima ~8-10 °C; maxima ~13-22 °C) and 65% encountered potentially stressful conditions (≥18 °C). The warmest salmon temperatures were in lower Willamette River reaches, where some fish exhibited short-duration behavioral thermoregulation. Cumulative temperature exposure, measured by degree days (DD) above 0 °C, varied more than seven-fold among individuals (range=208-1498 DDs) and more than two-fold among sub-basin populations, on average. Overall, ~72% of DDs accrued in tributaries and ~28% were in the Willamette River main stem. DD differences among individuals and populations were related to migration distance, migration duration, and salmon trapping protocols (i.e., extended pre-collection holding in tributaries versus hatchery collection shortly after tributary entry). The combined data provide spatially- and temporally-referenced information on both short-duration stressful temperature exposure and the biologically important total exposure. Thermal exposure in this population complex proximately influences adult salmon physiology, maturation, and disease processes and ultimately affects prespawn mortality and fitness. The results should help managers develop more effective salmon recovery plans in basins with marginal thermal conditions.

Genes predict long distance migration and large body size in a migratory fish, Pacific lamprey.

Elucidation of genetic mechanisms underpinning migratory behavior could help predict how changes in genetic diversity may affect future spatiotemporal distribution of a migratory species. This ability would benefit conservation of one such declining species, anadromous Pacific lamprey (Entosphenus tridentatus). Nonphilopatric migration of adult Pacific lamprey has homogenized population-level neutral variation but has maintained adaptive variation that differentiates groups based on geography, run-timing and adult body form. To investigate causes for this adaptive divergence, we examined 647 adult lamprey sampled at a fixed location on the Columbia River and radiotracked during their subsequent upstream migration. We tested whether genetic variation [94 neutral and adaptive single nucleotide polymorphisms (SNPs) previously identified from a genomewide association study] was associated with phenotypes of migration distance, migration timing, or morphology. Three adaptive markers were strongly associated with morphology, and one marker also correlated with upstream migration distance and timing. Genes physically linked with these markers plausibly influence differences in body size, which is also consistently associated with migration distance in Pacific lamprey. Pacific lamprey conservation implications include the potential to predict an individual's upstream destination based on its genotype. More broadly, the results suggest a genetic basis for intrapopulation variation in migration distance in migratory species.

Indirect effects of impoundment on migrating fish: temperature gradients in fish ladders slow dam passage by adult Chinook salmon and steelhead.

Thermal layering in reservoirs upstream from hydroelectric dams can create temperature gradients in fishways used by upstream migrating adults. In the Snake River, Washington, federally-protected adult salmonids (Oncorhynchus spp.) often encounter relatively cool water in dam tailraces and lower ladder sections and warmer water in the upstream portions of ladders. Using radiotelemetry, we examined relationships between fish passage behavior and the temperature difference between the top and bottom of ladders (∆T) at four dams over four years. Some spring Chinook salmon (O. tshawytscha) experienced ∆T ≥ 0.5 °C. Many summer and fall Chinook salmon and summer steelhead (O. mykiss) experienced ∆T ≥ 1.0 °C, and some individuals encountered ΔT > 4.0°C. As ΔT increased, migrants were consistently more likely to move down fish ladders and exit into dam tailraces, resulting in upstream passage delays that ranged from hours to days. Fish body temperatures equilibrated to ladder temperatures and often exceeded 20°C, indicating potential negative physiological and fitness effects. Collectively, the results suggest that gradients in fishway water temperatures present a migration obstacle to many anadromous migrants. Unfavorable temperature gradients may be common at reservoir-fed fish passage facilities, especially those with seasonal thermal layering or stratification. Understanding and managing thermal heterogeneity at such sites may be important for ensuring efficient upstream passage and minimizing stress for migratory, temperature-sensitive species.

Transporting juvenile salmonids around dams impairs adult migration.

Mitigation and ecosystem-restoration efforts may have unintended consequences on both target and nontarget populations. Important effects can be displaced in space and time, making them difficult to detect without monitoring at appropriate scales. Here, we examined the effects of a mitigation program for juvenile salmonids on subsequent adult migration behaviors and survival. Juvenile chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) were collected and uniquely tagged with passive integrated transponder (PIT) tags at Lower Granite Dam (Washington State, USA) on the Snake River and were then either transported downstream in barges in an effort to reduce out-migration mortality or returned to the river as a control group. Returning adults were collected and radio-tagged at Bonneville Dam (Washington-Oregon, USA) on the Columbia River 1-3 years later and then monitored during approximately 460 km of their homing migrations. The proportion of adults successfully homing was significantly lower, and unaccounted loss and permanent straying into non-natal rivers was higher, for barged fish of both species. On average, barged fish homed to Lower Granite Dam at rates about 10% lower than for in-river migrants. Barged fish were also 1.7-3.4 times more likely than in-river fish to fall back downstream past dams as adults, a behavior strongly associated with lower survival. These results suggest that juvenile transport impaired adult orientation or homing abilities, perhaps by disrupting sequential imprinting processes during juvenile out-migration. While juvenile transportation has clear short-term juvenile-survival benefits, the delayed effects that manifest in adult stages illustrate the need to assess mitigation success throughout the life cycle of target organisms, i.e., the use of fitness-based measures. In the case of Snake River salmonids listed under the Endangered Species Act, the increased straying and potential associated genetic and demographic effects may represent significant risks to successful recovery for both target and nontarget populations.

Beaver herbivory on aquatic plants.

Herbivores have strong impacts on marine and terrestrial plant communities, but their impact is less well studied in benthic freshwater systems. For example, North American beavers (Castor canadensis) eat both woody and non-woody plants and focus almost exclusively on the latter in summer months, yet their impacts on non-woody plants are generally attributed to ecosystem engineering rather than herbivory. Here, we excluded beavers from areas of two beaver wetlands for over 2 years and demonstrated that beaver herbivory reduced aquatic plant biomass by 60%, plant litter by 75%, and dramatically shifted plant species composition. The perennial forb lizard's tail (Saururus cernuus) comprised less than 5% of plant biomass in areas open to beaver grazing but greater than 50% of plant biomass in beaver exclusions. This shift was likely due to direct herbivory, as beavers preferentially consumed lizard's tail over other plants in a field feeding assay. Beaver herbivory also reduced the abundance of the invasive aquatic plant Myriophyllum aquaticum by nearly 90%, consistent with recent evidence that native generalist herbivores provide biotic resistance against exotic plant invasions. Beaver herbivory also had indirect effects on plant interactions in this community. The palatable plant lizard's tail was 3 times more frequent and 10 times more abundant inside woolgrass (Scirpus cyperinus) tussocks than in spatially paired locations lacking tussocks. When the protective foliage of the woolgrass was removed without exclusion cages, beavers consumed nearly half of the lizard's tail leaves within 2 weeks. In contrast, leaf abundance increased by 73-93% in the treatments retaining woolgrass or protected by a cage. Thus, woolgrass tussocks were as effective as cages at excluding beaver foraging and provided lizard's tail plants an associational refuge from beaver herbivory. These results suggest that beaver herbivory has strong direct and indirect impacts on populations and communities of herbaceous aquatic plants and extends the consequences of beaver activities beyond ecosystem engineering.

Hydrologic and behavioral constraints on oviposition of stream insects: implications for adult dispersal.

The supply of recruits plays an important role in plant and animal population dynamics, and may be governed by environmental and behavioral constraints on animals. Mated females of the mayfly genus Baetis alight on rocks protruding from streams, crawl under water and deposit a single egg mass under a rock. We surveyed oviposition and emergence of a bivoltine population of B. bicaudatus in multiple stream reaches in one high-altitude watershed in western Colorado over 3 years to establish qualitative patterns at a regional scale (entire watershed), and quantitative patterns over six generations at a local scale (one stream reach). We also measured characteristics of preferred oviposition substrates, performed experiments to test hypotheses about cues used by females to select oviposition sites, and measured mortality of egg masses in the field. Our goals were to determine whether: (1) hydrologic variation necessitated dispersal of females to find suitable oviposition sites; (2) the local supply of females could provide the supply of local recruits; and (3) local recruitment determined the local production of adults. The onset of oviposition corresponded with the decline of spring run-off, which differed dramatically among years and among sites within years. However, eggs appeared before any adults had emerged in 8 of 22 site-years, and adults emerged 2-3 weeks before any eggs were oviposited in 3 site-years. Furthermore, the size distribution of egg masses differed from that predicted by the size distribution of females that emerged from seven of nine stream reaches. Protruding rocks and eggs appeared earlier each summer in smaller tributaries than in larger mainstream reaches, suggesting that hydrologic and behavioral constraints on oviposition may force females to disperse away from their natal reach to oviposit, and possibly explain the predominantly upstream flight of Baetis females reported in other studies. Local oviposition rates in one third-order stream-reach increased rapidly as soon as substrates protruded from the water surface, and females preferred large rocks that became available early in the flight season. However, females oviposited on <10% of all available rocks, and <65% of preferred rocks as determined by an empirical model. These data indicated that the timing of appearance of suitable oviposition sites determined the phenology of local recruitment, but that preferred oviposition sites were not saturated. Thus, the magnitude of local recruitment was not limited by the absolute abundance of preferred oviposition sites. Only 22% of egg masses observed in the field suffered mortality during their embryonic development, and per capita Baetis egg mass mortality was significantly lower on rocks with higher densities of egg masses. Thus, we suspect that specialized oviposition behavior may reduce the probability of egg mortality, potentially compensating for the costs of dispersal necessary to locate suitable oviposition sites. Finally, the number of adults that emerged at one stream reach was independent of the number of egg masses oviposited over six generations of Baetis; and local recruitment was not a function of the number of adults of the previous generation that emerged locally. The patterns of oviposition and emergence of Baetis found in this study are consistent with the following hypotheses. Recruitment of eggs in a stream reach is not limited by the local supply of adults, but is a function of the regional supply of dispersing adults, which are constrained by the spatial and temporal distribution of preferred oviposition habitat. Furthermore, subsequent local production of adults is not a function of the supply of recruits, arguing for post-recruitment control of local populations by processes operating in the larval stage (e.g., predation, competition, dispersal, disturbance). Processes affecting larval and adult stages of Baetis act independently and at different scales, thereby decoupling local population dynamics of successive generations.