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USGS2017

Assessing the global distribution of river fisheries harvest: A systematic map protocol

Background Although surface freshwater comprises < 0.01% of the total water volume of earth, freshwater inland capture fisheries and aquaculture represent 40% of the global reported finfish harvest. While the social, economic, and ecological importance of inland fish and fisheries is difficult to overstate, they are often undervalued and underappreciated. Accurate information about these highly dispersed fisheries is inherently difficult to acquire, often unreported, and not collected in a standardized format globally. A standardized river fishery database is needed for managing aquatic systems as well as for defining relevant development policies. Here, we describe our methodology to search, identify, and describe available river fisheries information to create a harmonized global database of river fisheries harvest. This database will provide the first global database of spatially and temporally explicit river fisheries data. The database can be used to identify locations, hotspots of data collection, and gaps in existing knowledge and will be especially important to inform studies and management at larger spatial scales (i.e., watershed, regional, or global scales). This database will also be critical for developing fish biomass models for rivers, which can provide managers with information critical for decision-making, such as improved valuation methods for river fish and fisheries. Methods This systematic map protocol describes the methodology to search, identify, and describe available information on river fish and fisheries across the globe. We define river fisheries as “both capture and aquaculture of river finfish species for food, income, or recreation”. River fish species are those finfish that live part, or all of their lives in rivers. The searches will be conducted for the period from 1950 to present using bibliographic databases and grey literature sources. To identify relevant evidence, pre-defined inclusion and exclusion criteria will be used to screen articles at title, abstract, and full text. A searchable database containing extracted meta-data from relevant included studies will be developed and presented as a geodatabase. The final systematic map will consist of a descriptive narrative report of the distribution and content of river fish literature including a geodatabase of available information.

Environmental Evidence↗
USGS2017

An introduction to high-frequency nutrient and biogeochemical monitoring for the Sacramento–San Joaquin Delta, northern California

Executive Summary This report is the first in a series of three reports that provide information about high-frequency (HF) nutrient and biogeochemical monitoring in the Sacramento–San Joaquin Delta of northern California (Delta). This first report provides an introduction to the reasons for and fundamental concepts behind collecting HF measurements, and describes the benefits associated with a real-time, continuous, HF, multi-parameter water quality monitoring station network that is co-located with flow stations. It then provides examples of how HF nutrient measurements have improved our understating of nutrient sources and cycling in aquatic systems worldwide, followed by specific examples from the Delta. These examples describe the ways in which HF instrumentation may be used for both fixed-station and spatial assessments. The overall intent of this document is to describe how HF measurements currently (2017) are being used in the Delta to examine the relationship between nutrient concentrations, nutrient cycling, and aquatic habitat conditions. The second report in the series (Downing and others, 2017) summarizes information about HF nutrient and associated biogeochemical monitoring in the northern Delta. The report synthesizes data available from the nutrient and water quality monitoring network currently operated by the U.S. Geological Survey in this ecologically important region of the Delta. In the report, we present and discuss the available data at various timescales—first, at the monthly, seasonal, and inter-annual timescales; and, second, for comparison, at the tidal and event (for example, storms, reservoir releases, phytoplankton blooms) timescales. As expected, we determined that there is substantial variability in nitrate concentrations at short timescales within hours, but also significant variability at longer timescales such as months or years. This multi-scale, high variability affects calculation of fluxes and loads, indicating that HF monitoring is necessary for understanding and assessing flux-based processes and outcomes in tidal environments, such as the Delta. The third report in the series (Bergamaschi and others, 2017) provides information about how to design HF nutrient and biogeochemical monitoring for assessment of nutrient inputs and dynamics in the Delta. The report provides background, principles, and considerations for designing an HF nutrient-monitoring network for the Sacramento–San Joaquin Delta to address high-priority, nutrient-management questions. The report starts with high-priority management questions to be addressed, continues with questions and considerations that place demands and constraints on network design, discusses the principles applicable to network design, and concludes with the presentation of three example nutrient‑monitoring network designs for the Delta. For the three example networks, we assess how they would address high-priority questions identified by the Delta Regional Monitoring Program (Delta Regional Monitoring Program Technical Advisory Committee, 2015).

California↗
USGS1997

Zinc hazards to plants and animals with emphasis on fishery and wildlife resources

Ecological and toxicological aspects of zinc in the environment are reviewed with emphasis on natural resources. Subtopics include sources and uses; chemical and biochemical properties; carcinogenicity, mutagenicity, teratogenicity; background concentrations in biological and nonbiological compartments; effects of zinc deficiency; toxic and sublethal effects on terrestrial plants and invertebrates, aquatic organisms, birds, and mammals; and recommendations for the protection of sensitive resources.

Book chapter↗
USGS2002

Impacts of aquatic nonindigenous invasive species on the Lake Erie ecosystem

Lake Erie is particularly vulnerable to the introduction and establishment of aquatic nonindigenous invasive species (NIS) populations. A minimum of 144 aquatic NIS have been recorded in the Lake Erie basin including several species [e.g., Eurasian watermilfoil ( Myriophyllum spicatum ); zebra mussel ( Dreissena polymorpha ); quagga mussel (Dreissena bugensis); an amphipod (Echinogammarus ischnus); round goby (Neogobius melanostomus); and sea lamprey ( Petromyzon marinus )] that have had discernible impacts on the lake's ecology. NIS pose threats to the Lake Erie ecosystem for a variety of reasons including their ability to proliferate quickly, compete with native species, and transfer contaminants (e.g., PCBs) and disease through the food web. Six of the 14 beneficial use impairments listed in Annex 2 of the Great Lakes Water Quality Agreement are impaired in Lake Erie, in part as a result of the introduction of NIS. The Lake Erie Lakewide Management Plan (LaMP) has adopted an ecosystem approach to restore beneficial use impairments in the lake. Furthermore, a research consortium, known as the Lake Erie Millennium Network, is working alongside the LaMP, to address research problems regarding NIS, the loss of habitat, and the role of contaminants in the Lake Erie ecosystem.

Conference Paper↗
USGS2015

River corridor science: Hydrologic exchange and ecological consequences from bedforms to basins

Previously regarded as the passive drains of watersheds, over the past 50 years, rivers have progressively been recognized as being actively connected with off-channel environments. These connections prolong physical storage and enhance reactive processing to alter water chemistry and downstream transport of materials and energy. Here we propose river corridor science as a concept that integrates downstream transport with lateral and vertical exchange across interfaces. Thus, the river corridor, rather than the wetted river channel itself, is an increasingly common unit of study. Main channel exchange with recirculating marginal waters, hyporheic exchange, bank storage, and overbank flow onto floodplains are all included under a broad continuum of interactions known as “hydrologic exchange flows.” Hydrologists, geomorphologists, geochemists, and aquatic and terrestrial ecologists are cooperating in studies that reveal the dynamic interactions among hydrologic exchange flows and consequences for water quality improvement, modulation of river metabolism, habitat provision for vegetation, fish, and wildlife, and other valued ecosystem services. The need for better integration of science and management is keenly felt, from testing effectiveness of stream restoration and riparian buffers all the way to reevaluating the definition of the waters of the United States to clarify the regulatory authority under the Clean Water Act. A major challenge for scientists is linking the small-scale physical drivers with their larger-scale fluvial and geomorphic context and ecological consequences. Although the fine scales of field and laboratory studies are best suited to identifying the fundamental physical and biological processes, that understanding must be successfully linked to cumulative effects at watershed to regional and continental scales.

Water Resources Research↗
USGS2013

Great Lakes rivermouth ecosystems: scientific synthesis and management implications

At the interface of the Great Lakes and their tributary rivers lies the rivermouths, a class of aquatic ecosystem where lake and lotic processes mix and distinct features emerge. Many rivermouths are the focal point of both human interaction with the Great Lakes and human impacts to the lakes; many cities, ports, and beaches are located in rivermouth ecosystems, and these human pressures often degrade key ecological functions that rivermouths provide. Despite their ecological uniqueness and apparent economic importance, there has been relatively little research on these ecosystems as a class relative to studies on upstream rivers or the open-lake waters. Here we present a synthesis of current knowledge about ecosystem structure and function in Great Lakes rivermouths based on studies in both Laurentian rivermouths, coastal wetlands, and marine estuarine systems. A conceptual model is presented that establishes a common semantic framework for discussing the characteristic spatial features of rivermouths. This model then is used to conceptually link ecosystem structure and function to ecological services provided by rivermouths. This synthesis helps identify the critical gaps in understanding rivermouth ecology. Specifically, additional information is needed on how rivermouths collectively influence the Great Lakes ecosystem, how human alterations influence rivermouth functions, and how ecosystem services provided by rivermouths can be managed to benefit the surrounding socioeconomic networks.

Great Lakes↗
USGS2010

Low genetic variation and evidence of limited dispersal in the regionally important Belize manatee

The Antillean subspecies of the West Indian manatee Trichechus manatus is found throughout Central and South America and the Caribbean. Because of severe hunting pressure during the 17th through 19th centuries, only small populations of the once widespread aquatic mammal remain. Fortunately, protections in Belize reduced hunting in the 1930s and allowed the country's manatee population to become the largest breeding population in the Wider Caribbean. However, increasing and emerging anthropogenic threats such as coastal development, pollution, watercraft collision and net entanglement represent challenges to this ecologically important population. To inform conservation and management decisions, a comprehensive molecular investigation of the genetic diversity, relatedness and population structure of the Belize manatee population was conducted using mitochondrial and microsatellite DNA. Compared with other mammal populations, a low degree of genetic diversity was detected ( H E =0.455; N A =3.4), corresponding to the small population size and long-term exploitation. Manatees from the Belize City Cayes and Southern Lagoon system were genetically different, with microsatellite and mitochondrial F ST values of 0.029 and 0.078, respectively ( P ≤0.05). This, along with the distinct habitats and threats, indicates that separate protection of these two groups would best preserve the region's diversity. The Belize population and Florida subspecies appear to be unrelated with microsatellite and mitochondrial F ST values of 0.141 and 0.63, respectively ( P ≤0.001), supporting the subspecies designations and suggesting low vagility throughout the northern Caribbean habitat. Further monitoring and protection may allow an increase in the Belize manatee genetic diversity and population size. A large and expanding Belize population could potentially assist in the recovery of other threatened or functionally extinct Central American Antillean manatee populations.

Animal Conservation↗
USGS2001

A preliminary survey of marine contamination from mining-related activities on Marinduque Island, Philippines: porewater toxicity and chemistry results from a field trip, October 14-19, 2000

As a follow-up of an initial overview of environmental problems caused by mining activities on Marinduque Island, Philippines, USGS and TAMU-CC scientists went to Marinduque in October 2000 to do a preliminary assessment of potential impacts of mining-related activities on the marine environment. Like the previous visit in May 2000, the marine assessment was conducted at the invitation of Philippine Congressman Edmund O. Reyes. In this report we present the results of sediment porewater toxicity tests and chemical analyses. Toxicity tests consist of laboratory analyses for the assessment of adverse effects caused by environmental contaminants to animals or plants. Sediments (sand or mud) are known to accumulate contaminants (e.g., copper and other heavy metals). Therefore, it is common to perform toxicity tests using different phases of the sedimentary environment in order to analyze adverse effects of contaminants accumulated in the sediment. Sediment pore water (or interstitial water, i.e., the water distributed among the sediment grains) is a sedimentary phase which controls the bioavailability of contaminants to bottom dwelling aquatic organisms (both plants and animals). There are several different kinds of organisms with which toxicity tests can be performed. Among those, tests with sea urchin early life stages (gametes and embryos) are very common due to their high sensitivity to contaminants, ease of maintenance under laboratory conditions, and ecological importance, particularly in coral reefs. The basis of these tests is the exposure of gametes or embryos to the pore water to be analyzed for toxicity. If the pore water contains contaminants in levels that can adversely affect a number of marine species, fertilization and/or embryological development of sea urchins is inhibited. Chemical analyses provide additional information and aid in the interpretation of the toxicity test results. For the current study, chemical analyses were performed for the measurement of porewater concentrations of several heavy metals associated with copper mining activities. Pore waters for toxicological and chemical analyses were collected at several stations on the coast of Marinduque, near the mouths of the Boac and Mogpog rivers, and near the causeways formed by mine tailings disposal. Porewater samples were also collected at the Tres Reyes Marine Reserve, so that these non-contaminated samples could serve as a reference for test performance. Sea urchin embryological development and fertilization were only significantly impaired by two porewater samples, suggesting the presence of contaminants in toxic amounts at those stations. The toxic samples were collected near the up current side of the Calancan (Marcopper) mine tailings causeway (stations 2 and 3 – see figure 10). The pore water from station 2 also had the highest levels of heavy metals, particularly cadmium, cobalt, copper, nickel, lead and zinc (Table 5). The concentrations of cobalt, nickel and zinc were also elevated 2 at station 3. Copper concentrations were also elevated at the two river mouth stations (8 and 9) and near the CMI tailings causeway (station 7). Visual observations also indicated biological degradation due to heavy siltation and smothered coral at a gradient off the Calancan causeway, suggesting that siltation might also be causing a physical impact. This preliminary survey suggests that effects related to past mining activities are still evident and warrant a more comprehensive study to assess their severity and areal extent.

Open-File Report↗
USGS2017

Designing a high-frequency nutrient and biogeochemical monitoring network for the Sacramento–San Joaquin Delta, northern California

Executive Summary This report is the third in a series of three reports that provide information about how high-frequency (HF) nutrient monitoring may be used to assess nutrient inputs and dynamics in the Sacramento–San Joaquin Delta, California (Delta). The purpose of this report is to provide the background, principles, and considerations for designing an HF nutrient-monitoring network for the Delta to address high-priority, nutrient-management questions. The report starts with discussion of the high-priority management questions to be addressed, continues through discussion of the questions and considerations that place demands and constraints on network design, discusses the principles applicable to network design, and concludes with the presentation of three example nutrient-monitoring network designs for the Delta. For three example network designs, we assess how they would address high-priority questions that have been identified by the Delta Regional Monitoring Program (Delta Regional Monitoring Program Technical Advisory Committee, 2015). This report, along with the other two reports of this series (Kraus and others, 2017; Downing and others, 2017), was drafted in cooperation with the Delta Regional Monitoring Program to help scientists, managers, and planners understand how HF data improve our understanding of nutrient sources and sinks, drivers, and effects in the Delta. The first report in the series (Kraus and others, 2017) provides an introduction to the reasons for and fundamental concepts behind using HF monitoring measurements, including a brief summary of nutrient status and trends in the Delta and an extensive literature review showing how and where other research and monitoring programs have used HF monitoring to improve our understanding of nutrient cycling. The report covers the various technologies available for HF nutrient monitoring and presents the different ways HF monitoring instrumentation may be used for both fixed station and spatial assessments. Finally, it presents numerous examples of how HF measurements are currently (2017) being used in the Delta to examine how nutrients and nutrient cycling are related to aquatic habitat conditions. The second report in the series (Downing and others, 2017) summarizes information about HF nutrient and associated biogeochemical monitoring in the north Delta. The report synthesizes data available from the nutrient and water quality monitoring network currently (2017) operated by the U.S. Geological Survey in this ecologically important region of the Delta. In the report, we present and discuss the available data at various timescales—first at the monthly, seasonal, and inter-annual timescales; and, second, for comparison, at the tidal and event timescales. As expected, we determined that there is substantial variability in nitrate concentrations at short timescales, such as within a few hours, but also significant variability at longer timescales such as months or years. This high variability affects calculation of fluxes and loads, indicating that HF monitoring is necessary for understanding and assessing flux-based processes and outcomes in Delta tidal environments.

California↗
USGS2008

Tracking sea turtles in the Everglades

The U.S. Geological Survey (USGS) has a long history of conducting research on threatened, endangered, and at-risk species inhabiting both terrestrial and marine environments, particularly those found within national parks and protected areas. In the coastal Gulf of Mexico region, for example, USGS scientist Donna Shaver at Padre Island National Seashore in Texas has focused on “headstarting” hatchlings of the rare Kemp’s ridley sea turtle (Lepidochelys kempii). She is also analyzing trends in sea turtle strandings onshore and interactions with Gulf shrimp fisheries. Along south Florida’s Gulf coast, the USGS has focused on research and monitoring for managing the greater Everglades ecosystem. One novel project involves the endangered green sea turtle (Chelonia mydas). The ecology and movements of adult green turtles are reasonably well understood, largely due to decades of nesting beach monitoring by a network of researchers and volunteers. In contrast, relatively little is known about the habitat requirements and movements of juvenile and subadult sea turtles of any species in their aquatic environment.

Florida↗
USGS2001

Establishment of two invasive crustaceans (Copepoda: Harpacticoida) on the nearshore sands of Lake Michigan

Benthic copepods (Copepoda: Harpacticoida) in the nearshore sediments of southern Lake Michigan appear to be dominated by two new invasive species. We report the first occurrence in North America of Schizopera borutzkyi Montschenko, a native to the Danube River delta, and Heteropsyllus nr. nunni, likely a new species that is morphologically similar to the marine species Heteropsyllus nunni and represents the first occurrence of this genus in freshwater. Schizopera borutzkyi is a euryhaline species occurring in shallow sands in its native habitat and in deeper sands (6-15 m) in southern Lake Michigan. Based on the absence of these species from previous studies, we suggest that they are recent introductions. Heteropsyllus nr. nunni dominated (55-100%) the harpacticoid abundance to depths of 9 m, but S. borutzkyi comprised 75% of the harpacticoid abundance at 15 m. Native harpacticoids were always greatly outnumbered by invasive harpacticoids in our samples, which suggests that the natives are being replaced rapidly or that the invasive species are finding unused resources. The ecological implications of these introductions are not known, but these invasions may represent continued 'invasional meltdown' in Lake Michigan.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2022

Habitat-specific foraging by striped bass (Morone saxatilis) in the San Francisco Estuary, California: Implications for tidal restoration

Non-native predatory fish strongly impact aquatic communities, and their impacts can be exacerbated by anthropogenic habitat alterations. Loss of natural habitat and restoration actions reversing habitat loss can modify relationships between non-native predators and prey. Predicting how these relationships will change is often difficult because insufficient information exists on the habitat-specific feeding ecology of non-native predators. To address this information gap, we examined diets of non-native Striped Bass ( Morone saxatilis ; 63 to 671 mm standard length; estimated age 1-5 yrs) in the San Francisco Estuary during spring and summer in three habitat types – marsh, shoal, and channel – with the marsh habitat type serving as a model for ongoing and future restoration. Based on a prey-specific index of relative importance, Striped Bass diets were dominated by macroinvertebrates in spring and summer (amphipods in spring, decapods and isopods in summer). In spring, diets were relatively consistent across habitats. In summer, marsh diets were dominated by sphaeromatid isopods and shoal/channel diets by idoteid amphipods and decapods. Striped Bass consumed a variety of native and non-native fishes, primarily Prickly Sculpin ( Cottus asper ) and Gobiidae. The highest importance of fish prey was in the marsh in spring (~40% prey weight), and fish prey comprised less than 25% prey weight in all other season/habitat combinations. Linear discriminant analyses suggested that marsh foraging was prevalent in Striped Bass collected in other habitats, mostly due to the predominance of marsh-associated invertebrates found in the stomachs of individual Striped Bass collected outside of the marsh. Striped Bass diets differ across habitats, with marsh foraging important to Striped Bass regardless of collection location. This information can be used to forecast the potential utilization of restored habitats by this non-native piscivore.

California↗
USGS2001

Planned flooding and Colorado River riparian trade-offs downstream from Glen Canyon Dam, Arizona

Regulated river restoration through planned flooding involves trade-offs between aquatic and terrestrial components, between relict pre-dam and novel post-dam resources and processes, and between management of individual resources and ecosystem characteristics. We review the terrestrial (wetland and riparian) impacts of a 1274 m 3 /s test flood conducted by the U.S. Bureau of Reclamation in March/April 1996, which was designed to improve understanding of sediment transport and management downstream from Glen Canyon Dam in the Colorado River ecosystem. The test flood successfully restored sandbars throughout the river corridor and was timed to prevent direct impacts to species of concern. A total of 1275 endangered Kanab ambersnail ( Oxyloma haydeni kanabensis ) were translocated above the flood zone at Vaseys Paradise spring, and an estimated 10.7% of the total snail habitat and 7.7% of the total snail population were lost to the flood. The test flood scoured channel margin wetlands, including potential foraging habitats of endangered Southwestern Willow Flycatcher ( Empidonax traillii extimus ). It also buried ground-covering riparian vegetation under >1 m of fine sand but only slightly altered woody sandbar vegetation and some return-current channel marshes. Pre-flood control efforts and appropriate flood timing limited recruitment of four common nonnative perennial plant species. Slight impacts on ethnobotanical resources were detected >430 km downstream, but those plant assemblages recovered rapidly. Careful design of planned flood hydrograph shape and seasonal timing is required to mitigate terrestrial impacts during efforts to restore essential fluvial geomorphic and aquatic habitats in regulated river ecosystems.

Arizona↗
USGS2010

Streamflow characteristics and benthic invertebrate assemblages in streams across the western United States

Hydrographic characteristics of streamflow, such as high-flow pulses, base flow (background discharge between floods), extreme low flows, and floods, significantly influence aquatic organisms. Streamflow can be described in terms of magnitude, timing, duration, frequency, and variation (hydrologic regime). These characteristics have broad effects on ecosystem productivity, habitat structure, and ultimately on resident fish, invertebrate, and algae communities. Increasing human use of limited water resources has modified hydrologic regimes worldwide. Identifying the most ecologically significant hydrographic characteristics would facilitate the development of water-management strategies. Benthic invertebrates include insects, mollusks (snails and clams), worms, and crustaceans (shrimp) that live on the streambed. Invertebrates play an important role in the food web, consuming other invertebrates and algae and being consumed by fish and birds. Hydrologic alteration associated with land and water use can change the natural hydrologic regime and may affect benthic invertebrate assemblage composition and structure through changes in density of invertebrates or taxa richness (number of different species). This study examined associations between the hydrologic regime and characteristics of benthic invertebrate assemblages across the western United States and developed tools to identify streamflow characteristics that are likely to affect benthic invertebrate assemblages.

Fact Sheet↗
USGS2022

Monitoring framework to evaluate effectiveness of aquatic and floodplain habitat restoration activities for native fish along the Willamette River, northwestern Oregon

Since 2008, large-scale restoration programs have been implemented along the Willamette River, Oregon, to address historical losses of floodplain habitats caused by dam construction, bank protection, large wood removal, land conversion, and other anthropogenic influences. The Willamette Focused Investment Partnership (WFIP) restoration initiative brings together more than 16 organizations to improve floodplain habitats on more than 35,000 hectares upstream from Willamette Falls with the overarching goal to expand and enhance native fish habitats through the following restoration activities implemented along the floodplains and off-channel areas of the Willamette River: (A) modify floodplain topography and human-made barriers to inundation; (B) enhance gravel pits; (C) remove revetments; (D) construct off-channel features; (E) increase and enhance floodplain forest vegetation; and (F) treat aquatic invasive plant species (AIS). The WFIP Effectiveness Monitoring Program was initiated to inform future refinement of Willamette River restoration program goals and activities and has three goals: (1) evaluate the effectiveness of different restoration activities at increasing and enhancing native fish habitat, (2) improve overall understanding of the physical and ecological responses associated with different restoration activities undertaken by the WFIP, and (3) relate site-scale responses to restoration with broader patterns of fish communities, hydrogeomorphology, stream temperature, and vegetation across the Willamette River floodplain, so that the relative importance of restoration activities on habitat availability for native fish can be assessed. A monitoring framework was developed to evaluate effectiveness of floodplain restoration activities at increasing and enhancing habitat for native fish in the Willamette River corridor, northwestern Oregon. This framework describes monitoring indicators, metrics, and approaches for evaluating responses in native fish communities and physical habitat conditions to restoration activities and determining effectiveness of restoration activities at improving habitats for native fish. The monitoring indicators and approaches are grouped into five restoration monitoring categories that are useful for characterizing ecological and physical habitat responses to restoration activities: fish, hydrogeomorphology, floodplain forest vegetation, birds, and AIS. This monitoring framework provides a common science foundation to support collaborative decisions on future interdisciplinary effectiveness monitoring activities for Willamette River restoration programs. To evaluate restoration effectiveness, data must be evaluated according to metrics and thresholds that permit direct comparison between habitat conditions at the restoration site and restoration program goals; this framework provides examples of metrics and thresholds for evaluating data, recognizing that the precise evaluation criteria for a particular site or program will need to be tailored to meet program questions and available resources. Refining restoration goals and activities as part of an adaptively managed process requires addressing critical uncertainties between restoration goals, restoration activities, and outcomes for habitats used by native fish. Although the monitoring activities of this framework will generate important datasets useful for evaluating restoration effectiveness, additional research, syntheses, and reporting is ultimately necessary to provide a common science foundation to support adaptively managed restoration programs. This report is intended as a resource for restoration program managers, practitioners, scientists, and contractors as they develop detailed annual monitoring plans for data collection and identify the monitoring indicators, metrics, and approaches that are appropriate for evaluating effectiveness of different restoration activities.

Oregon↗
USGS2021

Bayesian change point quantile regression approach to enhance the understanding of shifting phytoplankton-dimethyl sulfide relationships in aquatic ecosystems

Dimethyl sulfide (DMS) serves as an anti-greenhouse gas, plays multiple roles 7 in aquatic ecosystems, and contributes to the global sulfur cycle. The chlorophyll 8 a (CHL, an indicator of phytoplankton biomass)-DMS relationship is critical for 9 estimating DMS emissions from aquatic ecosystems. Importantly, recent research has 10 identified that the CHL-DMS relationship has a breakpoint, where the relationship 11 is positive below a CHL threshold and negative at higher CHL concentrations. 12 Conventionally, mean regression methods are employed to characterize the CHL-DMS 13 relationship. However, these approaches focus on the response of mean conditions 14 and cannot illustrate responses of other parts of the DMS distribution, which could 15 be important in order to obtain a complete view of the CHL-DMS relationship. In 16 this study, for the first time, we proposed a novel Bayesian change point quantile 17 regression (BCPQR) model that integrates and inherits advantages of Bayesian change 18 point models and Bayesian quantile regression models. Our objective was to examine 19 whether or not the BCPQR approach could enhance the understanding of shifting 20 CHL-DMS relationships in aquatic ecosystems. We fitted BCPQR models at five 21 regression quantiles for freshwater lakes and for seas. We found that BCPQR models 22 could provide a relatively complete view on the CHL-DMS relationship. In particular, 23 it quantified the upper boundary of the relationship, representing the limiting effect of 24 CHL on DMS. Based on the results of paired parameter comparisons, we revealed the 25 inequality of regression slopes in BCPQR models for seas, indicating that applying 26 the mean regression method to develop the CHL-DMS relationship in seas might not 27 be appropriate. We also confirmed relationship differences between lakes and seas at 28 multiple regression quantiles. Further, by introducing the concept of DMS emission 29 potential, we found that pH was not likely a key factor leading to the change of the 30 CHL-DMS relationship in lakes. These findings cannot be revealed using piecewise 31 linear regression. We thereby concluded that the BCPQR model does indeed enhance 32 the understanding of shifting CHL-DMS relationships in aquatic ecosystems and is 33 expected to benefit efforts aimed at estimating DMS emissions. Considering that 34 shifting (threshold) relationships are not rare and that the BCPQR model can easily 35 be adapted to different systems, the BCPQR approach is expected to have great 36 potential for generalization in other environmental and ecological studies.

Water Research↗
USGS2007

Restoration of waterbird habitats in Chesapeake Bay: Great expectations or Sisyphus revisited?

In the past half century, many waterbird populations in Chesapeake Bay have declined or shifted ranges, indicating major ecological changes have occurred. While many studies have focused on the problems associated with environmental degradation such as the losses of coastal wetlands and submerged vegetation, a number of restoration efforts have been launched in the past few decades to reverse the "sea of despair." Most pertinent to waterbirds, restoration of submerged aquatic vegetation (SAV) beds, tidal wetland restoration, oyster reef restoration, and island creation/restoration have benefited a number of species. State and federal agencies and non-government agencies have formed partnerships to spawn many projects ranging in size from less than 0.5 ha to ca. 1,000 ha. While most SAV, wetland, and oyster reef projects have struggled to different degrees over the past ten to twenty years with inconsistent methods, irregular monitoring, and unknown reasons for failures, recent improvements in techniques and application of adaptive management have been made. The large dredge-material island projects at Hart-Miller Island near Baltimore, Poplar Island west of Tilghman Island, Maryland, and Craney Island in Portsmouth, Virginia have provided large outdoor "laboratories" for wildlife, fishery, and wetland habitat creation. All three have proven to be important for nesting waterbirds and migrant shorebirds and waterfowl; however nesting populations at all three islands have been compromised to different degrees by predators. Restoration success for waterbirds and other natural resources depends on: (1) establishing realistic, quantifiable objectives and performance criteria, (2) continued monitoring and management (e.g., predator control), (3) targeted research to determine causality, and (4) careful evaluation under an adaptive management regime.

Waterbirds↗
USGS2018

Distribution and seasonal differences in Pacific Lamprey and Lampetra spp eDNA across 18 Puget Sound watersheds

Lampreys have a worldwide distribution, are functionally important to ecological communities and serve significant roles in many cultures. In Pacific coast drainages of North America, lamprey populations have suffered large declines. However, lamprey population status and trends within many areas of this region are unknown and such information is needed for advancing conservation goals. We developed two quantitative PCR-based, aquatic environmental DNA (eDNA) assays for detection of Pacific Lamprey ( Entosphenus tridentatus ) and Lampetra spp, using locked nucleic acids (LNAs) in the probe design. We used these assays to characterize the spatial distribution of lamprey in 18 watersheds of Puget Sound, Washington, by collecting water samples in spring and fall. Pacific Lamprey and Lampetra spp were each detected in 14 watersheds and co-occurred in 10 watersheds. Lamprey eDNA detection rates were much higher in spring compared to fall. Specifically, the Pacific Lamprey eDNA detection rate was 3.5 times higher in spring and the Lampetra spp eDNA detection rate was 1.5 times higher in spring even though larval lamprey are present in streams year-round. This significant finding highlights the importance of seasonality on eDNA detection. Higher stream discharge in the fall likely contributed to reduced eDNA detection rates, although seasonal life history events may have also contributed. These eDNA assays differentiate Pacific Lamprey and Lampetra spp across much of their range along the west coast of North America. Sequence analysis indicates the Pacific Lamprey assay also targets other Entosphenus spp and indicates the Lampetra spp assay may have limited or no capability of detecting Lampetra in some locations south of the Columbia River Basin. Nevertheless, these assays will serve as a valuable tool for resource managers and have direct application to lamprey conservation efforts, such as mapping species distributions, occupancy modeling, and monitoring translocations and reintroductions.

Puget Sound↗