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USGS2017

Protected areas as social-ecological systems: perspectives from resilience and social-ecological systems theory

Conservation biology and applied ecology increasingly recognize that natural resource management is both an outcome and a driver of social, economic, and ecological dynamics. Protected areas offer a fundamental approach to conserving ecosystems, but they are also social-ecological systems whose ecological management and sustainability are heavily influenced by people. This editorial, and the papers in the invited feature that it introduces, discuss three emerging themes in social-ecological systems approaches to understanding protected areas: (1) the resilience and sustainability of protected areas, including analyses of their internal dynamics, their effectiveness, and the resilience of the landscapes within which they occur; (2) the relevance of spatial context and scale for protected areas, including such factors as geographic connectivity, context, exchanges between protected areas and their surrounding landscapes, and scale dependency in the provision of ecosystem services; and (3) efforts to reframe what protected areas are and how they both define and are defined by the relationships of people and nature. These emerging themes have the potential to transform management and policy approaches for protected areas and have important implications for conservation, in both theory and practice.

Ecological Applications↗

USGS2021

Establishing the foundation for the global observing system for marine life

Maintaining healthy, productive ecosystems in the face of pervasive and accelerating human impacts including climate change requires globally coordinated and sustained observations of marine biodiversity. Global coordination is predicated on an understanding of the scope and capacity of existing monitoring programs, and the extent to which they use standardized, interoperable practices for data management. Global coordination also requires identification of gaps in spatial and ecosystem coverage, and how these gaps correspond to management priorities and information needs. We undertook such an assessment by conducting an audit and gap analysis from global databases and structured surveys of experts. Of 371 survey respondents, 203 active, long-term (>5 years) observing programs systematically sampled marine life. These programs spanned about 7% of the ocean surface area, mostly concentrated in coastal regions of the United States, Canada, Europe, and Australia. Seagrasses, mangroves, hard corals, and macroalgae were sampled in 6% of the entire global coastal zone. Two-thirds of all observing programs offered accessible data, but methods and conditions for access were highly variable. Our assessment indicates that the global observing system is largely uncoordinated which results in a failure to deliver critical information required for informed decision-making such as, status and trends, for the conservation and sustainability of marine ecosystems and provision of ecosystem services. Based on our study, we suggest four key steps that can increase the sustainability, connectivity and spatial coverage of biological Essential Ocean Variables in the global ocean: (1) sustaining existing observing programs and encouraging coordination among these; (2) continuing to strive for data strategies that follow FAIR principles (findable, accessible, interoperable, and reusable); (3) utilizing existing ocean observing platforms and enhancing support to expand observing along coasts of developing countries, in deep ocean basins, and near the poles; and (4) targeting capacity building efforts. Following these suggestions could help create a coordinated marine biodiversity observing system enabling ecological forecasting and better planning for a sustainable use of ocean resources.

Frontiers in Marine Science↗

USGS2026

Unprecedented burning in tropical peatlands during the 20th century compared to the previous two millennia

Tropical peatland wildfire incidence has risen in recent decades, driven by drainage for land use and intensified by severe droughts with global climate change. These disturbances have altered vegetation structure, disrupted ecosystem functioning, and increased carbon emissions, particularly in Southeast Asia. However, the long-term history and characteristics of wildfires in tropical peatlands remain largely unknown. Here, we compiled fifty-eight macro-charcoal records from peatlands across the tropics, ranging from lowland forested to montane peatlands, to assess millennia-scale changes and controlling factors of tropical peatland burning. We divided the datasets into four main sub-regions: Neotropical, Afrotropical, Indomalayan and Australasian ecoregions to explore regional variability. Tropical peatlands had high burning levels between 0 and 850 ce , followed by a relatively low and stable period until a marked increase during the 20th century. The general trend in tropical peatland burning follows changes in global temperature, and climate variables that control the length and severity of drought events have a notable influence on peat burning before 1900 ce . During the 20th century, regional differences were observed, with declining fire trends in the Neotropical and Afrotropical regions and increasing fire trends in the Indomalayan and Australasian regions. This difference is likely attributable to human activities, and such intervention is also evident in palm swamps and hardwood swamps under similar wet, weakly seasonal climates. With the increase in anthropogenic pressures on peatlands and greater climate variability, future wildfires in peatlands are likely to become more frequent and widespread across all tropical ecoregions. Conservation and sustainable land-use practices could be used to mitigate and control peatland burning and protect these carbon-rich sinks.

Global Change Biology↗

USGS2020

Moving from decision to action in conservation science

Biodiversity loss is a major threat to the integrity of ecosystems and is projected to worsen, yet the path to successful conservation remains elusive. Decision support frameworks (DSFs) are increasingly applied by resource managers to navigate the complexity, uncertainty, and differing socio-ecological objectives inherent to conservation problems. Most published conservation research that uses DSFs focuses on analytical stages (e.g., identifying an optimal decision), making it difficult to assess and learn from previous examples in a conservation practice context. Here, we (1) evaluate the relationship between the application of decision science and the resulting conservation outcomes, and (2) identify and address existing barriers to the application of DSFs to conservation practice. To do this, we develop a framework for evaluating conservation initiatives using decision science that emphasizes setting attainable goals, building momentum, and obtaining partner buy-in. We apply this framework to a systematic review of amphibian conservation decision support projects, including a follow-up survey of the pertinent conservation practitioners, stakeholders, and scientists. We found that all projects identified optimal solutions to reach stated objectives, but positive conservation outcomes were limited when implementation challenges arose. Further, we identified multiple barriers (e.g., dynamic and hierarchical leadership, scale complexity, limited resource availability) that can inhibit the progression from decision identification to action implementation (i.e., ‘decision-implementation gap’), and to successful conservation outcomes. Based on these results, we provide potential actionable steps and avenues for future development of DSFs to facilitate the transition from decision to action and the realization of conservation successes.

Biological Conservation↗

USGS2021

Intended consequences statement

As the biodiversity crisis accelerates, the stakes are higher for threatened plants and animals. Rebuilding the health of our planet will require addressing underlying threats at many scales, including habitat loss and climate change. Conservation interventions such as habitat protection, management, restoration, predator control, translocation, genetic rescue, and biological control have the potential to help threatened or endangered species avert extinction. These existing, well-tested methods can be complemented and augmented by more frequent and faster adoption of new technologies, such as powerful new genetic tools. In addition, synthetic biology might offer solutions to currently intractable conservation problems. We believe that conservation needs to be bold and clear-eyed in this moment of great urgency.

Conservation Science and Practice↗

USGS2021

U.S. Geological Survey landscape science strategy 2020–2030

Across our Nation, multiple Federal, State, Tribal, and local governments are working with stakeholders and landowners to restore, conserve, and manage lands and resources to benefit fish, wildlife, and people. One of the largest Federal efforts is led by the U.S. Department of the Interior (DOI), with multiple DOI agencies working to conserve and manage public lands, resources, and cultural heritage for the benefit and enjoyment of current and future generations. As a science provider within the DOI, the U.S. Geological Survey (USGS) has an important role in developing actionable science products that can inform decision making on public lands and across all of our Nation’s landscapes. Our landscapes and resources are undergoing continual change from a complex and interacting suite of stressors that include traditional and nontraditional land uses, a changing climate, a dynamic economy, and a culturally diverse and ever-changing society. Landscape science seeks to understand how the physical, biological, and social components of ecosystems and landscapes interact with each other and are affected by these stressors across local to global scales. The USGS has developed this landscape science strategy to focus and strengthen the agency’s efforts to inform critical conservation, restoration, and management decisions for American landscapes. The strategy directly supports the overarching 21st-century science strategy of the USGS and expands our perspective and focus on partnerships, including with internal, external, traditional, and nontraditional partners. The vision for USGS landscape science is to integrate multiple disciplines and approaches to create and deliver relevant, timely, and scientifically sound products that enable our partners to make informed decisions about how to manage complex interacting natural and human systems across changing American landscapes. This strategy seeks to leverage the expertise, data, analytical capacity, and tools of the agency and to strengthen integration of science efforts across programs and scales. A cornerstone of the strategy is working closely with landowners and resource managers to identify the science that is needed to inform management actions, and then working collaboratively with those same partners to coproduce science and data products that are timely, practical, and useful for their decision making. Many individual efforts within the USGS already embrace landscape science ideas and practices. With the development of this strategy, we are seeking to build on these efforts and to focus agency attention and expertise on expanding, connecting, and institutionalizing core practices and approaches for landscape science that produces actionable science products and tools that decision makers can use to help conserve and manage American landscapes.

Circular↗

USGS2000

Viability of piping plover Charadrius melodus metapopulations

The metapopulation viability analysis package, VORTEX , was used to examine viability and recovery objectives for piping plovers Charadrius melodus , an endangered shorebird that breeds in three distinct regions of North America. Baseline models indicate that while Atlantic Coast populations, under current management practices, are at little risk of near-term extinction, Great Plains and Great Lakes populations require 36% higher mean fecundity for a significant probability of persisting for the next 100 years. Metapopulation structure (i.e. the delineation of populations within the metapopulation) and interpopulation dispersal rates had varying effects on model results; however, spatially-structured metapopulations exhibited lower viability than that reported for single-population models. The models were most sensitive to variation in survivorship; hence, additional mortality data will improve their accuracy. With this information, such models become useful tools in identifying successful management objectives; and sensitivity analyses, even in the absence of some data, may indicate which options are likely to be most effective. Metapopulation viability models are best suited for developing conservation strategies for achieving recovery objectives based on maintaining an externally derived, target population size and structure.

Biological Conservation↗

USGS2026

Watershed Continuum Monitoring Approach: Combining multiple water quality patterns along stream and river flowpaths to track sources, pathways, and processing of pollutants

There is a growing need to improve and expand water quality monitoring approaches to more accurately track the sources, fate, and transport of multiple chemicals and pollutants holistically and quantify the effects of best management practices (BMPs) at the watershed scale. An overarching question raised by scientists, environmental managers, and the general public is: how far can water quality impacts from disturbances or benefits from watershed management and restoration propagate along stream and river flowpaths? Many studies using the classic watershed approach focus on analyzing changes in water quality over time at one or a few sampling stations, whereas theories such as the River Continuum Concept focus on predicting shifts in energy sources and biological communities along rivers but have not been directly applied to water quality. We propose to merge these concepts to create a Watershed Continuum Monitoring Approach (WCMA) that combines both spatial and temporal monitoring in order to better detect and quantify trends and transitions in multiple water quality indicators along flowpaths. Specifically, an array of multiple water quality indicators are analyzed at multiple downstream points along a watershed flowpath over time. These multiple water quality indicators are analyzed together for making comparisons to infer hydrological, biological, and geochemical processes controlling sources, transport, and attenuation of pollutants ( e.g. , analagous to stream tracer studies at the watershed scale). The WCMA leverages the natural expansion of watershed areas along a flowpath, which reflect transitions in land use, land cover, and environmental management across spatial and temporal dimensions for making direct comparisons across different stream reaches and spatial trend analysis. WCMA facilitates monitoring of multiple water quality indicators together, and identifcation of hot spots in sources and attenuation of pollutants or mixtures of pollutants. We illustrate practical applications of the WCMA to analyze water quality trends, transitions, and tradeoffs ( i.e. , a tradeoff occurs when one pollutant is reduced but another is directly or indirectly increased downstream). We explore case studies that quantify: (1) downstream reductions in concentrations of multiple pollutants along a stream flowing to a major drinking water source due to engineered and nature-based solutions, (2) downstream reductions in multiple pollutants and water quality tradeoffs along streams experiencing stormwater BMPs and stream restoration, (3) comparisons in downstream reductions of multiple pollutants and nutrient uptake along streams draining into major drinking water sources based on types of stream restoration, (4) comparisons of downstream pollutant reductions along streams experiencing riparian forest conservation vs. stream restoration, and (5) mapping and visualizing hot spots of increasing water quality problems such as hypoxia, contaminant mobilization, and freshwater salinization that extend downstream to tidal rivers of the Chesapeake Bay. We explore future applications of WCMA for tracking decreasing trends in salinity, E. coli , and other pollutants of emerging concern. WCMA can holistically inform progress towards achieving multiple water quality goals and also be used as a screening tool for selecting monitoring sites and targeting management in strategic locations. Overall, WCMA enables the simultaneous quantification and comparison of sources and transport and attenuation rates for different chemicals and pollutants across a broader range of watershed sizes and flowpath lengths, which is critical for understanding ecological, hydrological, geochemical, and biogeochemical processes along human-impacted streams and rivers.

Ecological Engineering↗

USGS2021

Riverscape approaches in practice: Perspectives and applications

Landscape perspectives in riverine ecology have been undertaken increasingly in the last 30 years, leading aquatic ecologists to develop a diverse set of approaches for conceptualizing, mapping and understanding ‘riverscapes’. Spatiotemporally explicit perspectives of rivers and their biota nested within the socio-ecological landscape now provide guiding principles and approaches in inland fisheries and watershed management. During the last two decades, scientific literature on riverscapes has increased rapidly, indicating that the term and associated approaches are serving an important purpose in freshwater science and management. We trace the origins and theoretical foundations of riverscape perspectives and approaches and examine trends in the published literature to assess the state of the science and demonstrate how they are being applied to address recent challenges in the management of riverine ecosystems. We focus on approaches for studying and visualizing rivers and streams with remote sensing, modelling and sampling designs that enable pattern detection as seen from above (e.g. river channel, floodplain, and riparian areas) but also into the water itself (e.g. aquatic organisms and the aqueous environment). Key concepts from landscape ecology that are central to riverscape approaches are heterogeneity, scale (resolution, extent and scope) and connectivity (structural and functional), which underpin spatial and temporal aspects of study design, data collection and analysis. Mapping of physical and biological characteristics of rivers and floodplains with high-resolution, spatially intensive techniques improves understanding of the causes and ecological consequences of spatial patterns at multiple scales. This information is crucial for managing river ecosystems, especially for the successful implementation of conservation, restoration and monitoring programs. Recent advances in remote sensing, field-sampling approaches and geospatial technology are making it increasingly feasible to collect high-resolution data over larger scales in space and time. We highlight challenges and opportunities and discuss future avenues of research with emerging tools that can potentially help to overcome obstacles to collecting, analysing and displaying these data. This synthesis is intended to help researchers and resource managers understand and apply these concepts and approaches to address real-world problems in freshwater management.

Biological Reviews↗

USGS2019

Parallel signatures of selection at genomic islands of divergence and the major histocompatibility complex in ecotypes of sockeye salmon across Alaska

Understanding the genetic mechanisms that facilitate adaptive radiation is an important component of evolutionary biology. Here, we genotyped 82 neutral SNPs, seven SNPs in islands of divergence identified in a previous study (island SNPs), and a region of the major histocompatibility complex (MHC) in 32 populations of sockeye salmon to investigate whether conserved genes and genomic regions are involved in adaptive radiation. Populations representing three ecotypes were sampled from seven drainages with differing habitats and colonization histories spanning a range of 2,000 km. We found strong signatures of parallel selection across drainages at the island SNPs and MHC, suggesting that the same loci undergo divergent selection during adaptive radiation. However, patterns of differentiation at most island SNPs and the MHC were not associated with ecotypes, suggesting that these loci are responding differently to a mosaic of selective pressures. Our study provides some of the first evidence that conserved genomic islands may be involved in adaptive divergence of salmon populations. Additionally, our data provide further support for the hypothesis that sockeye salmon inhabiting rivers unconnected to lakes harbour similar genetic diversity across large distances, are likely the ancestral form of the species, and have repeatedly recolonized lake systems as they have become available after glacial recession. Finally, our results highlight the value and importance of validating outlier loci by screening additional populations and regions, a practice that will hopefully become more common in the future.

Alaska↗

USGS2002

Mexican native trouts: A review of their history and current systematic and conservation status

While biologists have been aware of the existence of native Mexican trouts for over a century, they have received little study. The few early studies that did much more than mention their existence began in the 1930s and continued into the early 1960s, focusing primarily on distributional surveys and taxonomic analyses. Starting in the 1980s the Baja California rainbow trout became the subject of more detailed studies, but very little remains known of mainland trouts of the Sierra Madre Occidental. We review earlier studies and report on our own collections and observations made between 1975 and 2000. We present newly discovered historical evidence that leads us to conclude that a "lost" cutthroat trout, a lineage not previously known from Mexico, was collected more than a century ago from headwaters of the Ri??o Conchos (a major tributary of the Rio Grande (= Ri??o Bravo)), a basin not previously considered to harbor a native trout. We review the last century of regional natural resource management and discuss our own observations of trout habitats. Impacts of logging, road building and overgrazing are widespread and expanding. Many streams suffer from heavy erosion, siltation and contamination, and though long-term hydrologic data are generally not available, there is evidence of decreased discharge in many streams. These problems appear related to region-wide land management practices as well as recent regional drought. Trout culture operations using exotic rainbow trout have rapidly proliferated throughout the region, threatening genetic introgression and/or competition with native forms and predation on them. Knowledge of distribution, abundance, relationships and taxonomy, not to mention ecology and population biology, of native trouts of the Sierra Madre Occidental remains inadequate. Vast areas of most mainland drainages are still unexplored by fish collectors, and even rudimentary information regarding basic biology, ecology and population structure of stocks remains lacking. Concentrated exploration, research and management of this long overlooked and undervalued resource are all urgently needed. The history of natural resources exploitation that placed so many native trouts of the western United States on threatened and endangered species lists is repeating itself in the Sierra Madre Occidental. Without concentrated action and development of region-wide socio-economic solutions for current, largely non-sustainable resource management practices, native Mexican trout gene pools will soon be in grave danger of extinction.

Reviews in Fish Biology and Fisheries↗

USGS2004

Hydrologic, ecologic, and geomorphic responses of Brewery Creek to construction of a residential subdivision, Dane County, Wisconsin, 1999-2002

The U.S. Geological Survey (USGS), in cooperation with the Dane County Land Conservation Department (LCD) and the Wisconsin Department of Natural Resources (DNR), investigated the instream effects from construction of a residential subdivision on Brewery Creek in Dane County, Wisconsin. The purpose of the investigation was to determine whether a variety of storm-runoff and erosion-control best-management practices (BMPs) would effectively control the overall sediment load, as well as minimize any hydrologic, ecologic, and geomorphic stresses to Brewery Creek. Stormwater volumes decreased 60 percent from the preconstruction phase to the land-disturbance phase and slightly increased (9 percent) from the land-disturbance phase to the home-construction phase. The stormwater volumes were applied to total solids and total suspended solids concentrations to compute a solids load for each contaminant. Total and suspended solids load indicated a similar trend from preconstruction to land-disturbance phases with decreases of 52 and 72 percent, respectively. Both total and suspended solids load continued to decrease in the transition from land-disturbance to home-construction phases, by 22 and 37 percent, respectively. However, because of variability in the data, statistically there was no change in the magnitude of difference between the upstream and downstream solids load from one phase of construction to the next at the 90-percent confidence level. Other physical, biological, and ecological surveys including macroinvertebrates, fish, habitat, and geomorphology were done on segments of Brewery Creek affected by the study area. Macroinvertebrate sampling results (Hilsenhoff Biotic Index value, or HBI), on Brewery Creek ranged from 'very good' to 'good' water-quality with no appreciable differences during any phase of construction activity. Results for fish-community composition, however, were within the 'poor' range (Index of Biotic Integrity value, or IBI) during each year of testing. A general absence of intolerant species, with the exception of brown trout, reflects the low IBI values. Habitat values did not change significantly from preconstruction to postconstruction phases. Although installation of a double-celled culvert in Brewery Creek most likely altered the width-to-depth ratio in that reach, the overall habitat rating remained 'fair'. Fluvial geomorphology classifications including channel cross sections, bed- and bank-erosion surveys, and pebble counts did not indicate that stream geomorphic characteristics were altered by home-construction activity in the study area. Increases in fine-grained sediment at various cross sections were attributed to instream erosion processes, such as bank slumping, rather than increases in sediment delivery from the nearby construction site.

Wisconsin↗

USGS2024

Resilient riverine social–ecological systems: A new paradigm to meet global conservation targets

The United Nations' Convention on Biological Diversity set forth the 30 × 30 target, an agenda for countries to protect at least 30% of their terrestrial, inland water, and coastal and marine areas by 2030. With <6 years to reach that goal, riverine conservation professionals are faced with the difficult decision of prioritizing which rivers or river segments should be conserved (protected and/or restored). While incorporating resilience into conservation planning is essential for enhancing, restoring, and maintaining the vital riverine ecosystem services (ES) most threatened by climate change and other environmental and human stresses, this paradigm is at odds with traditional conservation approaches that are either opportunistic or reactionary, where only unique and highly visible ecosystems have been prioritized. Barriers to implementing resilience-based riverine conservation planning include: (1) difficulties in conceptualizing and quantifying resilience; (2) insufficient consideration of the social components of riverine systems; (3) the inapplicability of terrestrial-only conservation models to aquatic systems; and (4) the traditional ad hoc and opportunistic approach to conservation. To overcome these barriers, we propose a resilience-based riverine conservation framework that includes: (1) assessing riverine resilience using indicator frameworks; (2) considering rivers as dynamically coupled social–ecological systems; (3) explicitly incorporating terrestrial–aquatic network connectivity into conservation decision-making; and (4) strategic systems planning using a novel resilience–conservation matrix as a tool. This framework has the potential to transform conservation practices around the globe to more effectively protect river systems and enhance their resilience to climate change and human development.

WIREs Water↗

USGS2016

Integrating subsistence practice and species distribution modeling: assessing invasive elodea’s potential impact on Native Alaskan subsistence of Chinook salmon and whitefish

Alaska has one of the most rapidly changing climates on earth and is experiencing an accelerated rate of human disturbance, including resource extraction and transportation infrastructure development. Combined, these factors increase the state’s vulnerability to biological invasion, which can have acute negative impacts on ecological integrity and subsistence practices. Of growing concern is the spread of Alaska’s first documented freshwater aquatic invasive plant Elodea spp. (elodea). In this study, we modeled the suitable habitat of elodea using global and state-specific species occurrence records and environmental variables, in concert with an ensemble of model algorithms. Furthermore, we sought to incorporate local subsistence concerns by using Native Alaskan knowledge and available statewide subsistence harvest data to assess the potential threat posed by elodea to Chinook salmon ( Oncorhynchus tshawytscha ) and whitefish ( Coregonus nelsonii ) subsistence. State models were applied to future climate (2040–2059) using five general circulation models best suited for Alaska. Model evaluations indicated that our results had moderate to strong predictability, with area under the receiver-operating characteristic curve values above 0.80 and classification accuracies ranging from 66 to 89 %. State models provided a more robust assessment of elodea habitat suitability. These ensembles revealed different levels of management concern statewide, based on the interaction of fish subsistence patterns, known spawning and rearing sites, and elodea habitat suitability, thus highlighting regions with additional need for targeted monitoring. Our results suggest that this approach can hold great utility for invasion risk assessments and better facilitate the inclusion of local stakeholder concerns in conservation planning and management.

Alaska↗

USGS2007

Habitat classification modeling with incomplete data: Pushing the habitat envelope

Habitat classification models (HCMs) are invaluable tools for species conservation, land-use planning, reserve design, and metapopulation assessments, particularly at broad spatial scales. However, species occurrence data are often lacking and typically limited to presence points at broad scales. This lack of absence data precludes the use of many statistical techniques for HCMs. One option is to generate pseudo-absence points so that the many available statistical modeling tools can be used. Traditional techniques generate pseudoabsence points at random across broadly defined species ranges, often failing to include biological knowledge concerning the species-habitat relationship. We incorporated biological knowledge of the species-habitat relationship into pseudo-absence points by creating habitat envelopes that constrain the region from which points were randomly selected. We define a habitat envelope as an ecological representation of a species, or species feature's (e.g., nest) observed distribution (i.e., realized niche) based on a single attribute, or the spatial intersection of multiple attributes. We created HCMs for Northern Goshawk (Accipiter gentilis atricapillus) nest habitat during the breeding season across Utah forests with extant nest presence points and ecologically based pseudo-absence points using logistic regression. Predictor variables were derived from 30-m USDA Landfire and 250-m Forest Inventory and Analysis (FIA) map products. These habitat-envelope-based models were then compared to null envelope models which use traditional practices for generating pseudo-absences. Models were assessed for fit and predictive capability using metrics such as kappa, thresholdindependent receiver operating characteristic (ROC) plots, adjusted deviance (Dadj2), and cross-validation, and were also assessed for ecological relevance. For all cases, habitat envelope-based models outperformed null envelope models and were more ecologically relevant, suggesting that incorporating biological knowledge into pseudo-absence point generation is a powerful tool for species habitat assessments. Furthermore, given some a priori knowledge of the species-habitat relationship, ecologically based pseudo-absence points can be applied to any species, ecosystem, data resolution, and spatial extent. ?? 2007 by the Ecological Society of America.

Ecological Applications↗

USGS2024

Restoring Pacific Lamprey in the Umpqua River Basin of Oregon: A workshop summary

The Umpqua River Basin in southwestern Oregon (Figure 1) is part of the lands inhabited by the Cow Creek Band of Umpqua Tribe of Indians and an area of active co-management authority. This Basin supports a unique fish fauna, including important populations of Pacific salmon ( Oncorhynchus spp.) and steelhead ( O. mykiss ), and other native fishes that are endemic to the region (Mims et al. 2018). Among these species, the Pacific Lamprey ( Entosphenus tridentatus ) is one of the most unique, representing an ancient lineage of jawless fishes that long predates the evolution of any other species of fish in the basin (Clemens et al. 2017, 2021a). The Pacific Lamprey also represents an important cultural and food resource that features prominently in the indigenous practices of the Cow Creek Band of Umpqua Tribe of Indians. This report provides a select summary of topics related to the conservation of Pacific Lamprey in the Umpqua River Basin. Many of the topics addressed herein were discussed in a workshop co-hosted by the Cow Creek Band of Umpqua Tribe of Indians and the U.S. Geological Survey in April of 2022. This workshop was focused on threats to Pacific Lamprey in fresh waters of the basin. The workshop highlighted science conducted over the past 15 years by local managers and researchers to understand and address these threats and provide new information relevant to the conservation and restoration of Pacific Lamprey. Attendees included staff from the Coquille Indian Tribe, Yakama Nation, Columbia River Inter-Tribal Fish Commission, Partnership for Umpqua Rivers, Rogue River Watershed Council, Curry Watersheds Council, PacifiCorp, Trout Unlimited, Jackson Soil and Water Conservation District, Oregon Department of Fish and Wildlife, Bureau of Land Management, U.S. Fish and Wildlife Service, and U.S. Forest Service. This report provides an overview of this workshop and recent science and provides an overview of potential future efforts that could inform restoration of Pacific Lamprey. This summary is organized into four sections that relate to the main topics of the workshop: 1) The physical habitat template (stream flow, instream wood, sediment, and water temperature), 2) movement barriers and reservoirs, 3) biological invasions, and 4) climate adaptation. These do not represent an exhaustive list of topics related to conservation of Pacific Lamprey in the Umpqua Basin.

Oregon↗

USGS2022

Global genetic diversity status and trends: Towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition

Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well-being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within-species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: ( i ) Genetic Diversity; ( ii ) Genetic Differentiation; ( iii ) Inbreeding; and ( iv ) Effective Population Size ( N e ). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large-scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long-term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.

Biological Reviews↗

USGS2016

Developing population models with data from marked individuals

Population viability analysis (PVA) is a powerful tool for biodiversity assessments, but its use has been limited because of the requirements for fully specified population models such as demographic structure, density-dependence, environmental stochasticity, and specification of uncertainties. Developing a fully specified population model from commonly available data sources – notably, mark–recapture studies – remains complicated due to lack of practical methods for estimating fecundity, true survival (as opposed to apparent survival), natural temporal variability in both survival and fecundity, density-dependence in the demographic parameters, and uncertainty in model parameters. We present a general method that estimates all the key parameters required to specify a stochastic, matrix-based population model, constructed using a long-term mark–recapture dataset. Unlike standard mark–recapture analyses, our approach provides estimates of true survival rates and fecundities, their respective natural temporal variabilities, and density-dependence functions, making it possible to construct a population model for long-term projection of population dynamics. Furthermore, our method includes a formal quantification of parameter uncertainty for global (multivariate) sensitivity analysis. We apply this approach to 9 bird species and demonstrate the feasibility of using data from the Monitoring Avian Productivity and Survivorship (MAPS) program. Bias-correction factors for raw estimates of survival and fecundity derived from mark–recapture data (apparent survival and juvenile:adult ratio, respectively) were non-negligible, and corrected parameters were generally more biologically reasonable than their uncorrected counterparts. Our method allows the development of fully specified stochastic population models using a single, widely available data source, substantially reducing the barriers that have until now limited the widespread application of PVA. This method is expected to greatly enhance our understanding of the processes underlying population dynamics and our ability to analyze viability and project trends for species of conservation concern.

Biological Conservation↗