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USGS2001

Cruise Report; RV Moana Wave cruise M1-01-GM; the bathymetry and acoustic backscatter of the mid shelf to upper slope off Panama City, Florida, northeastern Gulf of Mexico; September 3, through October 12, 2001, Panama City, FL to Panama City, FL

A zone of deep-water reefs is thought to extend from the mid and outer shelf south of Mississippi and Alabama to at least the northwestern Florida shelf off Panama City, Florida (Figure 1, 67kb). The reefs off Mississippi and Alabama are found in water depths of 60 to 120 m (Ludwick and Walton, 1957; Gardner et al., in press) and were the focus of a multibeam echosounder (MBES) mapping survey by the U.S. Geological Survey (USGS) in 2000 (Gardner et al., 2000; in press). If this deep-water-reef trend does exist along the northwestern Florida shelf, then it is critical to determine the accurate geomorphology and type of the reefs that occur because of their importance as benthic habitats for fisheries. Precisely georeferenced high-resolution mapping of bathymetry is a fundamental first step in the study of areas suspected to be critical habitats. Morphology is thought to be critical to defining the distribution of dominant demersal plankton/planktivores communities. Fish faunas of shallow hermatypic reefs have been well studied, but those of deep ahermatypic reefs have been relatively ignored. The ecology of deep-water ahermatypic reefs is fundamentally different from hermatypic reefs because autochthonous intracellular symbiotic zooxanthellae (the carbon source for hermatypic corals) do not form the base of the trophic web in ahermatypic reefs. Instead, exogenous plankton, transported to the reef by currents, serves as the primary carbon source. Thus, one of the principle uses of the morphology data will be to identify whether any reefs found are hermatypic or ahermatypic in origin. Community structure and trophodynamics of demersal fishes of the outer continental of the northeastern Gulf of Mexico presently are the focus of a major USGS reseach project. A goal of the project is to answer questions concerning the relative roles played by morphology and surficial geology in controling biological differentiation. Deep-water reefs are important because they are fish havens, key spawning sites, and are critical early larval and juvenile habitats for economically important sport/food fishes. It is known that deep-water reefs function as a key source for re-population (via seasonal and ontogenetic migration) of heavily impacted inshore reefs. The deep-water reefs south of Mississippi and Alabama support a lush fauna of ahermatypic hard corals, soft corals, black corals, sessile crinoids and sponges, that together form a living habitat for a well-developed fish fauna. The fish fauna comprises typical Caribbean reef fishes and Carolinian shelf fishes, plus epipelagic fishes, and a few deep-sea fishes. The base of the megafaunal invertebrate food web is plankton, borne by essentially continuous semi-laminar currents generated by eddies, spawned off the Loop Current, that periodically travel across the shelf edge. A few, sidescan-sonar surveys have been made of areas locally identified as Destin Pinnacles, Steamboat Lumps Marine Reserve (Koenig et al., 2000; Scanlon, et al., 2000; 2001), Twin Ridges (Briere, et al., 2000; Scanlon, et al., 2000), and Madison-Swanson Marine Reserve (Koenig et al., 2000; Scanlon, et al., 2000; 2001). However, no quantitative and little qualitative information about the geomorphology and surficial geology can be gained from these data. Existing bathymetry along the northwestern Florida shelf suggests the existence of areas of possible isolated deep-water reefs. NOAA bathymetric maps NOS NH16-9 and NG16-12 show geomorphic expressions that hint of the presence of reefs in isolated areas rather than in a continuous zone. There has been no systematic, high-resolution bathymetry collected in this area, prior to this cruise. After the successful mapping of the deep-water reefs on the Mississippi and Alabama shelf (Gardner et al., 2000; in press), a partnership composed of the USGS, Minerals Management Service, and NOAA was formed to continue the deep-reef mapping to the northwest Florida mid shelf and upper slope. This cruise is the first fruit of that partnership.

Florida↗

USGS2020

Using advanced population genomics to better understand the relationship between offshore and spawning habitat use for Atlantic Sturgeon

Atlantic Sturgeon ( Acipenser oxyrinchus oxyrinchus ) are a large-bodied anadromous fish that historically supported important fisheries along the east coast of the United States. Following years of overharvest and habitat degradation, populations experienced severe declines. In 2012, the National Marine Fisheries Service listed Atlantic Sturgeon under the Endangered Species Act (ESA; 61 FR 4722). Their listing named five Distinct Population Segments (DPSs), predicated on genetic groups composed of geographically proximate populations. Federal management of Atlantic Sturgeon presents challenges, as sturgeon from each of the five DPSs mix extensively in coastal and marine habitats yet take and recovery progress must be evaluated separately for each unit. Genetic assignment testing based on mitochondrial and microsatellite markers allows individuals to be assigned back to their natal river and DPS. However, this approach is not perfect and some individuals may be incorrectly assigned. Recent advances in genomics offer the potential of a higher resolution approach to genetic assignment testing, and thus may reduce uncertainty associated with assignment testing. In addition, genomics allows a greater number of markers to be examined from across a broader portion of the sturgeon genome, thus may provide an enhanced perspective of population structure for the species, and potentially allow other previously intractable questions to be addressed (Bernatchez et al. 2017, Supple and Shapiro 2018). We used next-generation sequencing to develop a draft genome for Atlantic Sturgeon and identify single nucleotide polymorphisms (SNPs) that could be used to resolve the natal river and DPS of individual Atlantic Sturgeon. We identified 1,210 candidate SNPs within the nuclear genome as well as 49 SNPs within the mitochondrial genome. After filtering and review, we selected 161 nuclear SNPs and 39 mitochondrial SNPs for further testing and evaluation. We used genotyping-in-thousands by sequencing (GT-seq) to simultaneously sequence nuclear SNP loci, mitochondrial SNP loci, and the existing panel of twelve microsatellite loci. This effort required a pilot sequencing run on a single sturgeon sample to test marker amplification and refine primer strengths, followed by a series of sequencing runs to generate baseline data for 288 individuals representing nine populations of Atlantic Sturgeon in four DPSs. Using baseline data from the nine populations, we ran a series of genomic analyses to characterize diversity within and among populations, providing a benchmark for this species using the new SNP markers. Allelic richness was similar for all populations, although there was a general trend of more northern population containing greater levels of allelic richness. Interestingly, we observed linkage disequilibrium among many pairs of loci within many populations. This might be the result of physical linkage but could also suggest these populations are recovering from genetic bottlenecks and/or are effectively small, leading to specific haplotypes to be favored by chance. Pairwise differentiation among populations varied among the populations ( F ST range: 0.010-0.098) and was significantly correlated ( r = 0.771; P < 0.001) to pairwise F ST observed using microsatellite markers). Population clustering and ordination techniques using the new genomic data both support an overall population structure that is similar to the current DPS management units (which were developed primarily based on microsatellite genetic data). Overall, this suggests that existing microsatellite markers and the panel of SNP markers developed in this study provide similar information about the populations structure and ecology of Atlantic Sturgeon. Given the observed differences in allele frequencies among populations, our genomic baseline supports previous assertations that Atlantic Sturgeon show natal homing, despite mixing extensively in marine waters during non-breeding periods. Lower levels of differentiation between populations in the South Atlantic DPS suggest that populations in this region may have greater levels of gene flow relative to their more northerly conspecifics, which has also previously been suggested based on microsatellite data. The observed differentiation among populations provides the necessary foundation for determining the natal river and DPS of Atlantic Sturgeon using assignment testing. We tested the utility of our new genomic baseline for resolving the population and DPS of Atlantic Sturgeon. Our nuclear SNP markers showed utility for identifying the origin of unknown Atlantic Sturgeon samples, as 86.5% were assigned to the correct DPS and 66.3% were assigned to the correct natal river. However, since this study was funded the Conservation Genetics and Genomics Laboratory at Leetown Science Center has made significant improvements to their microsatellite genetic baseline, which now performs more effectively than our new genomic approach (the genetic baseline includes 12 populations and 5 DPSs, and correctly assigns 95.8% of individuals to DPS and 84.9% of individuals to their natal population using 12 microsatellite loci). We conducted an ad hoc exploration of how additional microsatellite or nuclear SNP loci may further improve the accuracy of assignment testing. We found that additional microsatellite markers are likely to result in greater improvements in assignment efficiency than additional nuclear SNPs. However, a much larger number of SNP loci (which if identified could be sequenced using other methods that are now available; e.g., the RAD-capture approach published by Ali et al. 2016) could produce assignment efficiencies that are greater than what is currently feasible using microsatellites. In the absence of further research and development of additional SNP markers for Atlantic Sturgeon (possibly using an approach other than GT-seq), the existing microsatellite loci are the most effective means available to determine the natal river and DPS of Atlantic Sturgeon encountered in offshore waters. Because our new genomic markers were less effective than the existing panel of 12 microsatellite markers, we chose to use the existing microsatellite markers to assign Atlantic Sturgeon captured in another BOEM-funded study (cooperative agreement M16AC00003; Monitoring endangered Atlantic Sturgeon and commercial finfish habitat use offshore New York) following consultation with our project officer. Using this approach, we genotyped and assigned 186 Atlantic Sturgeon captured in coastal waters off the Rockaway Peninsula, New York. The vast majority of these sturgeon were assigned to the New York Bight DPS (94.62%), and most appear to belong to the Hudson River population (87.10%) with smaller contributions from the Delaware River population (7.53%). Smaller contributions (2.15%) were observed from six other populations, including those from the James, York, Kennebec, Ogeechee, and Edisto rivers. Although most of the fish we assigned were assigned to the nearest spawning rivers (Hudson and Delaware), the contributions from distant rivers is consistent with the propensity of this species to move long distances and form mixed stock aggregations along the continental shelf. This finding indicates that spawning populations (and their corresponding DPS) from distant locations may potentially be impacted by offshore activities. In fact, activities in this region of the New York Bight could negatively impact Atlantic Sturgeon population from at least four different DPSs. Genetic or genomic assignment testing remains an essential tool to characterize potential impacts to Atlantic Sturgeon populations and should be applied more broadly to better characterize potential impacts of activities in other locations.

Atlantic Coast↗

USGS2022

Framework for the development of the Columbia River mainstem fish tissue and water quality monitoring program - Bonneville Dam to Canadian border

The Columbia River provides important cultural, economic, and ecological services to a significant portion of the United States. Anadromous and resident fish species and other wildlife are integrated into the cultural traditions of all Tribes in the Columbia River Basin. Salmon, lamprey, sturgeon, and resident fish are an integral part of Tribal religion, culture, and physical sustenance. Despite concerns about the effect of contaminants on the aquatic ecosystem, the disproportionate effects of contaminants on members of Tribal sovereignties, and the known effects of contaminants on species protected under the Endangered Species Act, efforts to address toxic chemical pollution in the Columbia River have been limited. The lack of a dedicated contaminant monitoring program impedes evaluation and decision making regarding the health of the Columbia River ecosystem, as well as human health for Tribal members and others that consume fish and other biota from the Columbia River. The purpose of this framework is to provide guidance for the development of a long-term program (Program) that provides the basis for assessing the status and trends of contaminants in fish, sediment, water, and invertebrates along the 962-kilometer length of the Columbia River from the Bonneville Dam upriver to the Canadian Border (Figure ES1). This framework will focus on four persistent and bioaccumulative classes of toxic contaminants: • Mercury • Polychlorinated biphenyls (PCBs) • Dichlorodiphenyltrichloroethane (DDT) • Polybrominated diphenyl ethers (PBDEs) Media of interest in this framework include anadromous and resident fish, sediment, invertebrates, biofilm, and surface water. Future consideration of additional contaminants could include pesticides, per or poly-fluoroalkyl substances, 6PPD-quinone, and contaminants of emerging concern (CECs), which comprises a diverse group of anthropogenic chemicals that include thousands of pharmaceuticals, hormones, illicit drugs, new pesticides, personal care products, flame retardants, artificial sweeteners, perfluorinated compounds, disinfection byproducts, ultraviolet filters, and other industrial chemicals. This framework includes the vision, goals, and objectives for the Program. The vision for the Program is that it will provide the basis for assessing the status and trends of contaminants in the Columbia River to guide ecosystem recovery resulting in clean, healthy fish for current and future generations . The goals of the Program are to 1) conduct long-term monitoring to assess the spatial and temporal status and trends of toxics in fish, water, sediment, and other potential media in the Columbia River mainstem, from Bonneville Dam to the Canadian Border in perpetuity, 2) stimulate conversion of science into action by providing information to facilitate future decision making that improves ecosystem function and reduces contaminants in all levels of the food chain, and 3) adaptively manage the Program to address new key questions, incorporate new and emerging science advancements, and respond to community information needs. To facilitate achieving these goals, this framework provides details on technical planning; community outreach and engagement; and adaptive management to promote understanding and improve future decision making over the long-term, including updating the Program with new and emerging science and community needs. Additionally, data associated with the Program will be made available to the public through the EPA Water Quality Exchange (https://www.epa.gov/waterdata/water-quality-data). Documents and other materials associated with the Program can be accessed via a website hosted by Yakama Nation Fisheries (https://yakamafish-nsn.gov/restore/projects/columbia-river-mainstem- water-quality-monitoring-program). Although the Program is limited to the Columbia River upstream of the Bonneville Dam, collaboration with other entities that monitor contaminants in the Columbia River Basin, including the Columbia River estuary below Bonneville Dam, are also an important component of outreach. Our goal is to encourage efforts to ensure data comparability across programs and recognize that the growth and adaptive management of the Program considers basin-wide monitoring developments.

Oregon, Washington↗

USGS2022

It’s complicated and it depends: A review of the effects of ecosystem changes on Walleye and Yellow Perch populations in North America

Walleye Sander vitreus and Yellow Perch Perca flavescens are culturally, economically, and ecologically significant fish species in North America that are affected by drivers of global change. Here, we review and synthesize the published literature documenting the effects of ecosystem changes on Walleye and Yellow Perch. We focus on four drivers: climate (including temperature and precipitation), aquatic invasive species, land use and nutrient loading, and water clarity. We identified 1,232 tests from 370 papers, split evenly between Walleye ( n = 613) and Yellow Perch ( n = 619). Climate was the most frequently studied driver ( n = 572), and growth or condition was the most frequently studied response ( n = 297). The most commonly reported relationship was “no effect” (42% of analyses), usually because multiple variables were tested and only a few were found to be significant. Overall responses varied among studies for most species-response–driver combinations. For example, the influence of invasive species on growth of both Walleye and Yellow Perch was approximately equally likely to be positive, negative, or have no effect. Even when results were variable, important patterns emerged; for example, growth responses of both species to temperature were variable, but very few negative responses were observed. A few relationships were relatively consistent across studies. Invasive species were negatively associated with Walleye recruitment and abundance, and higher water clarity was negatively associated with Walleye abundance, biomass, and production. Some variability in responses may be due to differences in methodology or the range of variables studied; others represent true context dependence, where the effect of a driver depends on the influence of other variables. Using common metrics of impact, publishing negative results, and robust analytical approaches could facilitate comparisons among systems and provide a more comprehensive understanding of the responses of Walleye and Yellow Perch to ecosystem change.

North American Journal of Fisheries Management↗

USGS2014

The effect of adjusting model inputs to achieve mass balance on time-dynamic simulations in a food-web model of Lake Huron

Ecopath with Ecosim (EwE) is a widely used modeling tool in fishery research and management. Ecopath requires a mass-balanced snapshot of a food web at a particular point in time, which Ecosim then uses to simulate changes in biomass over time. Initial inputs to Ecopath, including estimates for biomasses, production to biomass ratios, consumption to biomass ratios, and diets, rarely produce mass balance, and thus ad hoc changes to inputs are required to balance the model. There has been little previous research of whether ad hoc changes to achieve mass balance affect Ecosim simulations. We constructed an EwE model for the offshore community of Lake Huron, and balanced the model using four contrasting but realistic methods. The four balancing methods were based on two contrasting approaches; in the first approach, production of unbalanced groups was increased by increasing either biomass or the production to biomass ratio, while in the second approach, consumption of predators on unbalanced groups was decreased by decreasing either biomass or the consumption to biomass ratio. We compared six simulation scenarios based on three alternative assumptions about the extent to which mortality rates of prey can change in response to changes in predator biomass (i.e., vulnerabilities) under perturbations to either fishing mortality or environmental production. Changes in simulated biomass values over time were used in a principal components analysis to assess the comparative effect of balancing method, vulnerabilities, and perturbation types. Vulnerabilities explained the most variation in biomass, followed by the type of perturbation. Choice of balancing method explained little of the overall variation in biomass. Under scenarios where changes in predator biomass caused large changes in mortality rates of prey (i.e., high vulnerabilities), variation in biomass was greater than when changes in predator biomass caused only small changes in mortality rates of prey (i.e., low vulnerabilities), and was amplified when environmental production was increased. When standardized to mean changes in biomass within each scenario, scenarios when vulnerabilities were low and when fishing mortality was increased explained the most variation in biomass. Our findings suggested that approaches to balancing Ecopath models have relatively little effect on changes in biomass over time, especially when compared to assumptions about how mortality rates of prey change in response to changes in predator biomass. We concluded that when constructing food-web models using EwE, determining the effect of changes in predator biomass on mortality rates of prey should be prioritized over determining the best way to balance the model.

Lake Huron↗

USGS2012

A brief history and summary of the effects of river engineering and dams on the Mississippi River system and delta

The U.S. Geological Survey Forecast Mekong project is providing technical assistance and information to aid management decisions and build science capacity of institutions in the Mekong River Basin. A component of this effort is to produce a synthesis of the effects of dams and other engineering structures on large-river hydrology, sediment transport, geomorphology, ecology, water quality, and deltaic systems. The Mississippi River Basin (MRB) of the United States was used as the backdrop and context for this synthesis because it is a continental scale river system with a total annual water discharge proportional to the Mekong River, has been highly engineered over the past two centuries, and the effects of engineering have been widely studied and documented by scientists and engineers. The MRB is controlled and regulated by dams and river-engineering structures. These modifications have resulted in multiple benefits including navigation, flood control, hydropower, bank stabilization, and recreation. Dams and other river-engineering structures in the MRB have afforded the United States substantial socioeconomic benefits; however, these benefits also have transformed the hydrologic, sediment transport, geomorphic, water-quality, and ecologic characteristics of the river and its delta. Large dams on the middle Missouri River have substantially reduced the magnitude of peak floods, increased base discharges, and reduced the overall variability of intraannual discharges. The extensive system of levees and wing dikes throughout the MRB, although providing protection from intermediate magnitude floods, have reduced overall channel capacity and increased flood stage by up to 4 meters for higher magnitude floods. Prior to major river engineering, the estimated average annual sediment yield of the Mississippi River Basin was approximately 400 million metric tons. The construction of large main-channel reservoirs on the Missouri and Arkansas Rivers, sedimentation in dike fields, and protection of channel banks by revetments throughout the basin, have reduced the overall sediment yield of the MRB by more than 60 percent. The primary alterations to channel morphology by dams and other engineering projects have been (1) channel simplification and reduced dynamism; (2) lowering of channel-bed elevation; and (3) disconnection of the river channel from the flood plain, except during extreme flood events. Freshwater discharge from the Mississippi River and its associated sediment and nutrient loads strongly influence the physical and biological components in the northern Gulf of Mexico. Ninety percent of the nitrogen load reaching the Gulf of Mexico is from nonpoint sources with about 60 percent coming from fertilizer and mineralized soil nitrogen. Much of the phosphorus is from animal manure from pasture and rangelands followed by fertilizer applied to corn and soybeans. Increased nutrient enrichment in the northern Gulf of Mexico has resulted in the degradation of water quality as more phytoplankton grow, which increases turbidity and depletes oxygen in the lower depths creating what is known as the "dead zone." In 2002, the dead zone was 22,000 square kilometers (km2), an area similar to the size of the State of Massachusetts. Changes in the flow regime from engineered structures have had direct and indirect effects on the fish communities. The navigation pools in the upper Mississippi River have aged, and these overwintering habitats, which were created when the pools filled, have declined as sedimentation reduces water depth. Reproduction of paddlefish may have been adversely affected by dams, which impede access to suitable spawning habitats. Fishes that inhabit swift-current habitats in the unimpounded lower Mississippi River have not declined as much as in the upper Mississippi River. The decline of the pallid sturgeon may be attributable to channelization of the Missouri River above St. Louis, Missouri. The Missouri River supports a rich fish community and remains relatively intact. Nevertheless, the widespread and long history of human intervention in river discharge has contributed to the declines of about 25 percent of the species. The Mississippi River Delta Plain is built from six delta complexes composed of a massive area of coastal wetlands that support the largest commercial fishery in the conterminous United States. Since the early 20th century, approximately 4,900 km2 of coastal lands have been lost in Louisiana. One of the primary mechanisms of wetland loss on the Plaquemines-Balize complex is believed to be the disconnection of the river distributary network from the delta plain by the massive system of levees on the delta top, which prevent overbank flooding and replenishment of the delta top by sediment and nutrient deliveries. Efforts by Federal and State agencies to conserve and restore the Mississippi River Delta Plain began over three decades ago and have accelerated over the past decade. Regardless of these efforts, however, land losses are expected to continue because the reduced upstream sediment supplies are not sufficient to keep up with the projected depositional space being created by the combined forces of delta plain subsidence and global sea-level rise.

Alabama;Alberta;Arkansas;Colorado;Georgia;Illinois↗

USGS2023

Adult Sea Lamprey approach and passage at the Milford Dam fishway, Penobscot River, Maine, United States

Objective Sea Lamprey Petromyzon marinus provide important ecological services within their native range, such as nutrient cycling, and can also act as a prey source for other species. Adult Sea Lamprey must access freshwater rivers to spawn, and because of this they are susceptible to changes in river connectivity. Human-made structures, such as dams, can exclude them from usable habitat. Sea Lamprey dam passage has not been extensively studied in Maine, despite Maine being within the native range of this species. The goals of this study were to evaluate upstream passage efficiency at the Milford Dam on the Penobscot River, Maine, and to provide comprehensive information about adult Sea Lamprey passage at five other dams throughout the Penobscot River watershed. Methods In 2020–2021 we captured and tagged 150 Sea Lamprey at the Milford Dam, the lowest dam in the Penobscot River, Maine, and displaced them downstream to assess passage efficiency at this dam and five upstream dams. In 2020, 50 Sea Lamprey were released on the east shore of the river downstream of Milford Dam; in 2021, the east shore release was repeated with an additional 50 fish and another 50 fish were released on the west shore. Result Between 70–82% of Sea Lamprey were observed passing Milford Dam again after mean delay times of 9–11 days. The release location did not affect dam passage success or the amount of time that was required to locate and use the passage structures. Sea Lampreys from both release groups were equally likely to approach the entrance to the fishway upon returning to Milford Dam, despite the fishway being located against the eastern shore of the river. However, high flows shortly after release may have resulted in higher attraction to the fishway in 2020. Passage success at dams upstream of Milford was highly variable. All Sea Lamprey were able to successfully navigate past West Enfield Dam (100% passage, n = 63), whereas Brownsmill Dam apparently acted as a complete barrier to further migration (0% passage, n = 7). Fish from all years and release groups together had a median upstream migration distance of 38.8 km after fish had passed Milford Dam, and a maximum observed upstream travel distance of approximately 100 km, indicating that most tagged Sea Lamprey ended their migration in the vicinity of a dam. Conclusion The results of this study indicate that Sea Lamprey have high passage efficiency at the Milford Dam and highlight areas within the Penobscot River basin—such as the Brownsmill Dam—where passage facilities are currently inadequate for Sea Lamprey.

Maine↗

USGS2014

Guidelines for monitoring and adaptively managing restoration of Chinook salmon ( Oncorhynchus tshawytscha ) and steelhead ( O. mykiss ) on the Elwha River

As of January, 2014, the removal of the Elwha and Glines Canyon dams on the Elwha River, Washington, represents the largest dam decommissioning to date in the United States. Dam removal is the single largest step in meeting the goals of the Elwha River Ecosystem and Fisheries Restoration Act of 1992 (The Elwha Act) — full restoration of the Elwha River ecosystem and its native anadromous fisheries (Section 3(a)). However, there is uncertainty about project outcomes with regards to salmon populations, as well as what the ‘best’ management strategy is to fully restore each salmon stock. This uncertainty is due to the magnitude of the action, the large volumes of sediment expected to be released during dam removal, and the duration of the sediment impact period following dam removal. Our task is further complicated by the depleted state of the native salmonid populations remaining in the Elwha, including four federally listed species. This situation lends itself to a monitoring and adaptive management approach to resource management, which allows for flexibility in decision-making processes in the face of uncertain outcomes. The Elwha Monitoring and Adaptive Management (EMAM) guidelines presented in this document provide a framework for developing goals that define project success and for monitoring project implementation and responses, focused upon two federally listed salmon species — Puget Sound Chinook salmon (Oncorhynchus tshawytscha) and Puget Sound steelhead (O. mykiss). The framework also should serve as a guide to help managers adaptively manage fish restoration actions during and following dam removal. The document is organized into seven sections, including an introduction (Section 1), a description of the adaptive management approach (Section 2), suggested modifications to the existing restoration strategy developed in previous Elwha River restoration documents (section 3), specific descriptions of an adaptive management framework, including establishment of goals, performance indicators, and potential adaptive management responses to monitoring information (section 4), monitoring tools and methods for use in evaluating performance and project outcomes (section 5), and brief sections on data record keeping and reporting (Section 6) and an estimated budget (section 7). The purpose of the EMAM guidelines is to propose (1) refinement of existing goals established in previous documents (e.g., Ward et al. (2008), U.S. Department of the Interior, Department of Commerce, and Lower Elwha S’Klallam Tribe (1994)); (2) an adaptive management framework, (3) specific trigger values for relevant performance indicators that guide the adaptive management approach, (4) a specific monitoring strategy for evaluating outcomes of restoration activities; (5) a data management strategy, (6) information needed for adjusting goals when observations indicate conditions are different from anticipated. When taken together, our proposed adaptive management guidelines rely upon setting goals and objectives for each species of interest, which are monitored by relevant performance indicators and measurable trigger values that define success within each phase of the project. The guidelines themselves are arranged in a hierarchy for each species of interest. The levels of this hierarchy are goals, objectives, performance indicators, decision rules, triggers, and decisions (i.e., management/policy response). The monitoring and adaptive management approach provided is based on monitoring several categories of performance indicators, each containing associated ‘trigger’ values which, when met, alters restoration activities (e.g., hatchery releases and/or strategies) through four successive restoration phases. Performance indicators proposed in these EMAM guidelines are based upon Viable Salmon Population (VSP) metrics, including abundance, productivity, distribution, and diversity (McElhany et al. 2000). Trigger values for each performance indicator are developed for four different restoration phases: Preservation, Recolonization, Local Adaptation, and Viable Natural Population. These biologically-based phases each have a set of objectives that are based on resource management scenarios, including the dam removal project itself, which change largely based on the level of active management required and the degree, if any, of resource utilization. Thus, details of prescribed management actions for each phase are based upon different needs specific to that phase. The creation of biologically-based phases is one of the major differences between our proposed EMAM guidelines and previously presented plans for Elwha River Restoration Project management. Changed largely in response to the recommendations of the most recent of three Hatchery Scientific Review Group project reviews (HSRG 2012), the goal-oriented phases replaced the previous system of temporal changes centered around the decommissioning of the dams (i.e., before, during, and after dam removal). By focusing on outcomes associated with rebuilding salmon populations instead of an engineering schedule, the guidelines are more amenable to an adaptive management framework and the ability for management actions to influence outcomes, particularly in the periods during and following dam removal. Trigger values for each performance indicator were generally developed using existing data from the Elwha River watershed, the Puget Sound region, or other Pacific Northwest rivers (i.e., elsewhere in Washington State, Oregon, British Columbia) modified to be relevant for Chinook salmon and steelhead recovery in the Elwha River. By meeting all of the trigger value levels for all performance indicators for a set amount of time within a management phase, the guidelines call for moving to the next phase. This next phase has a new set of trigger values for the same performance indicators. For example, upon moving from the Preservation phase to the Recolonization phase, the trigger value for intrinsic potential increases. Intrinsic potential is a pre-defined estimate of the total extent of available habitat within a watershed for adult and juvenile fish, specific to the target species and is therefore a performance indicator of spatial distribution. By the final Viable Natural Population phase, the entire intrinsic potential of the watershed is being occupied by the species of interest. For those cases when a performance indicator is not exceeding the target value for a particular phase after a certain time period, the trigger values provided in this document, as well as a series of exogenous variables, are explored that may help explain why the performance indicator is not being met. These exogenous variables include variables that are not part of the suite of performance indicators, such as hatchery production, harvest, habitat, and ecosystem indicators. In these cases where the program is stuck in a particular recovery phase, the situation could be caused by the selection of inappropriate trigger values or unforeseen environmental conditions. If the former, adaptive management would call for existing monitoring data to be used for modifying trigger values to an appropriate level. If one of the exogenous variables is found to be preventing the program moving to the next phase, then appropriate changes to management would be advised. For each performance indicator and many of the exogenous variables, a set of monitoring tools were proposed. Data standards were also proposed for data generated by each monitoring tool. Data management, record keeping, and reporting of monitoring and adaptive management activities and results are also outlined. Management of data from the focused monitoring program and documenting the outcomes of trigger value evaluations and associated decisions from the adaptive management approach are key components of the EMAM guidelines. Without a clear history of data generated and adaptive management decisions taken by managers, the ability to learn through adaptive management breaks down. In addition to the long time period involved, another complication is the fact that the data will likely be collected by different federal and state agencies, tribal staff, and others. Having a system of reporting developed should help alleviate potential problems. The restoration of the migration route to spawning and rearing habitats upstream of the former Glines Canyon Dam represents a great opportunity for salmon on the Olympic Peninsula. By removing two aging structures, it will be possible for all 5 species of salmon and steelhead to return to wild stretches of the Elwha River and major floodplain habitat characterized by multiple channels, as well as significant portions of numerous tributaries. Measuring the progress of restoration, from the perspective of both salmon populations and the ecosystem upon which they depend, is a great test for a collaborative team of scientists. The normally challenging conditions of working in a steep gradient, high velocity wilderness river are exacerbated by the release of millions of cubic yards of sediment that had accumulated in the reservoirs. After the first two years of the dam decommissioning process, this release has changed the ecology of the river, estuary, and nearshore habitats downstream of the dams. Our goal in developing the guidelines described is to provide a roadmap for tracking what hopefully will become a successful outcome. If successfully implemented, this information should prove useful as others begin planning for the removal, alteration, or reconstruction of dams throughout North America and elsewhere, an inevitable outcome of an aging dam infrastructure.

Washington↗