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USGS2015

Stable carbon and nitrogen isotope trophic enrichment factors for Steller sea lion vibrissae relative to milk and fish/invertebrate diets

Nutritional constraints have been proposed as a contributor to population declines in the endangered Steller sea lion Eumetopias jubatus in some regions of the North Pacific. Isotopic analysis of vibrissae (whiskers) is a potentially useful approach to resolving the nutritional ecology of this species because long-term (up to 8 yr) dietary information is sequentially recorded and metabolically inert once formed. Additionally, vibrissae are grown in utero , potentially offering indirect inference on maternal diet. However, diet reconstruction using isotopic techniques requires a priori knowledge of trophic enrichment factors (TEFs), which can vary relative to diet quality and among animal species. In this study, we provide new TEF estimates for (1) maternal relative to pup vibrissae during both gestation and nursing and (2) adult vibrissae relative to a complex diet. Further, we refine vibrissa-milk TEFs based on an additional 76 animals with an age distribution ranging from 1 to 20 mo. Mother-pup vibrissae TEF values during gestation and nursing were near zero for δ 13 C and averaged 0.8 and 1.6&permil;, respectively, for δ 15 N. In contrast, vibrissa-fish/invertebrate TEFs averaged 3.3 (± 0.3 SD) and 3.7&permil; (±0.3) for lipid-free δ 13 C and δ 15 N, respectively. Average lipid-free δ 13 C and δ 15 N vibrissa-milk TEFs were 2.5 (±0.9) and 1.8&permil; (±0.8), respectively, and did not differ among metapopulations. Empirically determined TEFs are critical for accurate retrospective diet modeling, particularly for evaluating the hypothesis of nutritional deficiency contributing to the lack of Steller sea lion population recovery in some regions of Alaska.

Marine Ecology Progress Series↗

USGS2014

A quantitative life history of endangered humpback chub that spawn in the Little Colorado River: variation in movement, growth, and survival

While the ecology and evolution of partial migratory systems (defined broadly to include skip spawning) have been well studied, we are only beginning to understand how partial migratory populations are responding to ongoing environmental change. Environmental change can lead to differences in the fitness of residents and migrants, which could eventually lead to changes in the frequency of the strategies in the overall population. Here, we address questions concerning the life history of the endangered Gila cypha (humpback chub) in the regulated Colorado River and the unregulated tributary and primary spawning area, the Little Colorado River. We develop eight multistate models for the population based on three movement hypotheses, in which states are defined in terms of fish size classes and river locations. We fit these models to mark–recapture data collected in 2009–2012. We compare survival and growth estimates between the Colorado River and Little Colorado River and calculate abundances for all size classes. The best model supports the hypotheses that larger adults spawn more frequently than smaller adults, that there are residents in the spawning grounds, and that juveniles move out of the Little Colorado River in large numbers during the monsoon season (July–September). Monthly survival rates for G. cypha in the Colorado River are higher than in the Little Colorado River in all size classes; however, growth is slower. While the hypothetical life histories of life-long residents in the Little Colorado River and partial migrants spending most of its time in the Colorado River are very different, they lead to roughly similar fitness expectations when we used expected number of spawns as a proxy. However, more research is needed because our study period covers a period of years when conditions in the Colorado River for G. cypha are likely to have been better than has been typical over the last few decades.

Colorado River;Little Colorado River↗

USGS2011

Effects of climate change on nutrition and genetics of White-tailed Ptarmigan

White-tailed Ptarmigan ( Lagopus leucura ) are well suited as a focal species for the study of climate change because they are adapted to cool, alpine environments that are expected to undergo unusually rapid climate change. We compared samples collected in the late 1930s, the late 1960s, and the late 2000s using molecular genetic and stable isotope methods in an effort to determine whether White-tailed Ptarmigan on Mt. Evans, Colorado, have experiences recent environmental changes resulting in shifts in genetic diversity, gene frequency, and nutritional ecology. We genotyped 115 individuals spanning the three time periods, using nine polymorphic microsatellite loci in our genetic analysis. These samples were also analyzed for stable carbon and nitrogen isotopic composition. We found a slight trend of lower heterozygosity through time, and allelic richness values were significantly lower in more recent times, but not significantly using an alpha of 0.05 ( P < 0.1). We found no changes in allele frequencies across time periods, suggesting that population sizes have not changed dramatically. Feather δ 13 C and δ 15 N values decreased significantly across time periods, whereas the range in isotope values increased consistently from the late 1930s to the late time periods. Inferred changes in the nutritional ecology of White-tailed Ptarmigan on Mt. Evans relate primarily to increased atmospheric deposition of nutrients that likely influenced foraging habits and tundra plant composition and nutritional quality. Future work seeks to integrate genetic and isotopic data with long-term demographics to develop a detailed understanding of the interaction among environmental stressors on the long-term viability of ptarmigan populations.

Studies in Avian Biology↗

USGS2021

Toward improved decision-support tools for Delta Smelt management actions

The Collaborative Science and Adaptive Management Program (CSAMP) has endorsed a goal of reversing the recent downward trajectory of the Delta Smelt population within 5-10 generations, with the long-term aim of establishing a self-sustaining population. An ambitious agenda of management actions is planned, and more management actions are being considered. This White Paper furthers one of the recommendations in the 2019 Delta Smelt Science Plan – the need to predict the potential ecological effects of taking a management action. Existing statistical models can be highly informative in assessing the response of Delta Smelt to changing system conditions and management actions. However, management actions can shift or alter conditions in ways that models based on analysis of historical data may not be able to represent, and short-term or localized effects may be missed with models designed to assess effects at the population level. Decision support tools (DSTs) are computer-based tools developed to assist decision-making, often combining computationally intensive analysis and spatial mapping of environmental relationships. DSTs can be used in planning processes that evaluate an array of actions, such as in Structured Decision Making (SDM), where DSTs are needed to compare among alternatives. DSTs can also be used to explore the potential effects of different approaches to implementing management actions. The goal of this White Paper is to identify plausible options for DSTs that could be developed for future use to evaluate management actions that seek to either reverse the decline of Delta Smelt or minimize or mitigate the effects of other water management actions. Different types of management actions lead to different needs for DSTs. This White Paper was developed using three types of actions currently being considered to enhance the Delta Smelt population: Supplementation with Hatchery Fish, Summer-Fall Habitat, and Food Enhancement actions. These three management actions target different parts of the estuary and different processes, with a variety of possible metrics to gauge performance. Three DSTs are proposed that collectively address management questions related to the management actions considered, with each requiring a slightly different set of processes to be included and producing an array of outputs at varying spatial and temporal scales: DST 1. Modeling Fish Movement, Survival, and Reproduction Across Their Range. This DST can address management questions that require information about Delta Smelt spatial distribution and movement. • DST 1 could be used to compare conditions with and without management actions in place, how the management action performs among different types of water years (with varied flow and associated abiotic conditions), and to assess relative change with different variations and strategies of the management actions. • DST 2. Changes in Habitat Conditions and Delta Smelt Response. This DST is intended to evaluate combinations of conditions that are considered to provide suitable habitat for Delta Smelt, and Delta Smelt response. Delta Smelt habitat is generally described as open water with low salinity (0 to 6), turbidity of at least 12 NTU, suitable temperature conditions, and sufficient food availability to support growth. • DST 3. Regional Effects of Food Subsidy. This DSTs seeks to evaluate effectiveness of food enhancement actions by providing information on responses of the immediate targets of the action (i.e., phytoplankton or zooplankton) and tracing those to projected growth responses of Delta Smelt. There is not a single DST that adequately addresses management questions relevant to all management actions, although there is some overlap in the management questions each of the three DSTs can address. For each of the DSTs a substantial foundation of models and approaches already exists and modeling has already been applied to several of the management actions described. However, a number of outstanding issues remain for further development of the proposed DSTs. These are summarized in this White Paper together with potential approaches that could be applied or tested. Some components for the DSTs are already available and thus development could be relatively easy. However, for several of the topics identified there are gaps in knowledge that currently limit formulation of model structure and process representations. This presents challenges to readily incorporate some needed mechanisms into the models. Eleven next steps, aligned with relevant DSTs, are outlined. The next steps vary in their complexity or technical ‘lift’ required. Many build on existing work, or methods and approaches that have already been developed or are underway, while others require additional thinking to establish a viable approach. Some interim utility for decisions could be gained during initial development of the DSTs with further features added over time. Development of a DST requires engagement of both managers and scientists. Identifying the outputs and resolution needed for management purposes early in development of any DST is essential for effective pursuit of next steps and suitable approaches to address challenges. Dialog between managers and technical experts also informs what process-based simulation can do, and what tradeoffs are acceptable to meet a given purpose. To further develop the DSTs outlined here for application in the estuary requires: - Engagement of a committed group of technical experts with appropriate expertise. - The development of a coordinated workplan including appropriate project management and tracking. - Dialog between potential users (i.e., managers and policy makers) and technical experts. - Resources to pursue DST development including personnel and computational resources. This White Paper demonstrates the potential for moving toward DSTs for a variety of management actions in support of Delta Smelt that include mechanistic representations of physical and biological processes. Through focused effort from technical experts, managers and policy makers, DSTs can be developed to provide quantitative predictions of management effects on the ecosystem, targeting the changes the management actions seek to achieve, how these effects compare to ambient conditions, and how the effects vary among water year types or with timing and location of actions. Importantly, solid foundations exist which can be leveraged, refined, and built upon to specifically inform current and future management decisions.

White Paper↗

USGS2011

Mitigating amphibian disease: strategies to maintain wild populations and control chytridiomycosis

Background Rescuing amphibian diversity is an achievable conservation challenge. Disease mitigation is one essential component of population management. Here we assess existing disease mitigation strategies, some in early experimental stages, which focus on the globally emerging chytrid fungus Batrachochytrium dendrobatidis . We discuss the precedent for each strategy in systems ranging from agriculture to human medicine, and the outlook for each strategy in terms of research needs and long-term potential. Results We find that the effects of exposure to Batrachochytrium dendrobatidis occur on a spectrum from transient commensal to lethal pathogen. Management priorities are divided between (1) halting pathogen spread and developing survival assurance colonies, and (2) prophylactic or remedial disease treatment. Epidemiological models of chytridiomycosis suggest that mitigation strategies can control disease without eliminating the pathogen. Ecological ethics guide wildlife disease research, but several ethical questions remain for managing disease in the field. Conclusions Because sustainable conservation of amphibians in nature is dependent on long-term population persistence and co-evolution with potentially lethal pathogens, we suggest that disease mitigation not focus exclusively on the elimination or containment of the pathogen, or on the captive breeding of amphibian hosts. Rather, successful disease mitigation must be context specific with epidemiologically informed strategies to manage already infected populations by decreasing pathogenicity and host susceptibility. We propose population level treatments based on three steps: first, identify mechanisms of disease suppression; second, parameterize epizootiological models of disease and population dynamics for testing under semi-natural conditions; and third, begin a process of adaptive management in field trials with natural populations.

Frontiers in Zoology↗

USGS2002

A reservoir landscape for age-0 largemouth bass

Landscape ecology is concerned with how ecological processes are affected by spatial patterns. Identification of heterogeneity in littoral zones has expanded the conceptual framework of aquatic landscapes. Long-term study of a reservoir largemouth bass population indicated that the amount and arrangement of habitat regulated the population processes. The distribution of age-0 largemouth bass was quantified in relation to littoral habitat and relations between landscape features and population parameters on scales from embayment to microhabitat were determined. At the embayment scale, shoreline slope and amount of gravel substratum predicted fivefold variability in abundance among four reservoir embayments. Within an embayment, these habitat features explained between 37 and 88 percent of variation in shoreline distribution of age-0 largemouth bass. At the microhabitat scale, age-0 largemouth bass exhibited patchy distributions in relation to gravel substratum at 40 percent of sites. These results indicate that the landscape scale domain for young largemouth bass is large; whereas, specific patterns explained processes across multiple scales. Distributions of age-0 largemouth bass in relation to habitat, however, were apparent on a fine scale (10 m) and these data, coupled with limited movement behavior of young largemouth bass, indicate that the ecological neighborhood of this life stage is small. Our data also suggested that some habitats may be source habitats because embayments with hypothesized higher source/sink ratios were more productive. Although patch arrangement critical to young largemouth bass ecology was not quantified, it was apparent that embayments with more complex habitats likely provided the extent of the landscape for age-0 largemouth bass in Jordan Lake. Identification of scale of patchiness (of fish distributions and habitats) for this life stage will assist in making inferences regarding complex ecological processes that can affect year-class productivity on multiple scales. ?? 2002 by the American Fisheries Society.

American Fisheries Society Symposium↗

USGS2007

Assessment and management of dead-wood habitat

The Bureau of Land Management (BLM) is in the process of revising its resource management plans for six districts in western and southern Oregon as the result of the settlement of a lawsuit brought by the American Forest Resource Council. A range of management alternatives is being considered and evaluated including at least one that will minimize reserves on O&C lands. In order to develop the bases for evaluating management alternatives, the agency needs to derive a reasonable range of objectives for key issues and resources. Dead-wood habitat for wildlife has been identified as a key resource for which decision-making tools and techniques need to be refined and clarified. Under the Northwest Forest Plan, reserves were to play an important role in providing habitat for species associated with dead wood (U.S. Department of Agriculture Forest Service and U.S. Department of the Interior Bureau of Land Management, 1994). Thus, the BLM needs to: 1) address the question of how dead wood will be provided if reserves are not included as a management strategy in the revised Resource Management Plan, and 2) be able to evaluate the effects of alternative land management approaches. Dead wood has become an increasingly important conservation issue in managed forests, as awareness of its function in providing wildlife habitat and in basic ecological processes has dramatically increased over the last several decades (Laudenslayer et al., 2002). A major concern of forest managers is providing dead wood habitat for terrestrial wildlife. Wildlife in Pacific Northwest forests have evolved with disturbances that create large amounts of dead wood; so, it is not surprising that many species are closely associated with standing (snags) or down, dead wood. In general, the occurrence or abundance of one-quarter to one-third of forest-dwelling vertebrate wildlife species, is strongly associated with availability of suitable dead-wood habitat (Bunnell et al., 1999; Rose et al., 2001). In Oregon and Washington, approximately 150 species of wildlife are reported to use dead wood in forests (O’Neil et al., 2001). Forty-seven sensitive and special-status species are associated with dead wood (Appendix A). These are key species for management consideration because concern over small or declining populations is often related to loss of suitable dead-wood habitat (Marshall et al., 1996). Primary excavators (woodpeckers) also are often the focus of dead-wood management, because they perform keystone functions in forest ecosystems by creating cavities for secondary cavity-nesters (Martin and Eadie, 1999; Aubry and Raley, 2002). A diverse guild of secondary cavity-users (including swallows, bluebirds, several species of ducks and owls, ash-throated flycatcher, flying squirrel, bats, and many other species) is unable to excavate dead wood, and therefore relies on cavities created by woodpeckers for nesting sites. Suitable nest cavities are essential for reproduction, and their availability limits population size (Newton, 1994). Thus, populations of secondary cavity-nesters are tightly linked to the habitat requirements of primary excavators. Although managers often focus on decaying wood as habitat for wildlife, the integral role dead wood plays in ecological processes is an equally important consideration for management. Rose et al. (2001) provide a thorough review of the ecological functions of dead wood in Pacific Northwest forests, briefly summarized here. Decaying wood functions in: soil development and productivity, nutrient cycling, nitrogen fixation, and carbon storage. From ridge tops, to headwater streams, to estuaries and coastal marine ecosystems, decaying wood is fundamental to diverse terrestrial and aquatic food webs. Wildlife species that use dead wood for cover or feeding are linked to these ecosystem processes through a broad array of functional roles, including facilitation of decay and trophic interactions with other organisms (Marcot, 2002; Marcot, 2003). For example, by puncturing bark and fragmenting sapwood, woodpeckers create sites favorable for wood-decaying organisms (Farris et al., 2004), which in turn create habitat for other species and facilitate nutrient cycling. Small mammals that use down wood for cover function in the dispersal of plant seeds and fungal spores (Carey et al., 1999). Resident cavitynesting birds may regulate insect populations by preying on overwintering arthropods (Jackson, 1979; Kroll and Fleet, 1979). These examples illustrate how dead wood not only directly provides habitat for a large number of wildlife species, but also forms the foundation of functional webs that critically influence forest ecosystems (Marcot, 2002; Marcot, 2003). The important and far-reaching implications of management of decaying wood highlight the need for conservation of dead-wood resources in managed forests. Consideration of the key ecological functions of species associated with dead wood can help guide management of dead wood in a framework consistent with the paradigm of ecosystem management (Marcot and Vander Heyden, 2001; Marcot, 2002.) As more information is revealed about the ecological and habitat values of decaying wood, concern has increased over a reduction in the current amounts of dead wood relative to historic levels (Ohmann and Waddell, 2002). Past management practices have tended to severely reduce amounts of dead wood throughout all stages of forest development (Hansen et al., 1991). The large amounts of legacy wood that characterize young post-disturbance forests are not realized in managed stands, because most of the wood volume is removed at harvest for economic and safety reasons. Mid-rotation thinning is used to “salvage” some mortality that might otherwise occur due to suppression, so fewer snags are recruited in mid-seral stages. Harvest rotations of 80 years or less truncate tree size in managed stands, and thus limit the production of large-diameter wood. As a consequence of these practices, dead wood has been reduced by as much as 90% after two rotations of managed Douglas-fir (Rose et al., 2001). Large legacy deadwood is becoming a scarce, critical habitat that will take decades to centuries to replace. Furthermore, management continues to have important direct and indirect effects on the amount and distribution of dead wood in forests. Current guidelines for managing dead wood may be inadequate to maintain habitat for all associated species because they largely focus on a single use of dead wood (nesting habitat) by a small suite of species (cavity-nesting birds), and may under represent the sizes and amounts of dead wood used by many wildlife species (Rose et al., 2001, Wilhere, 2003).

Open-File Report↗

USGS2016

Misapplied survey data and model uncertainty result in incorrect conclusions about the role of predation on alewife population dynamics in Lake Huron: a comment on He et al. (2015)

Drastic recent and ongoing changes to fish populations and food webs in the Great Lakes have been well-described ( Riley et al. 2008 ; Barbiero et al. 2009 ; Nalepa et al. 2009 ; Fahnenstiel et al. 2010 ; Evans et al. 2011 ; Gobin et al. 2015 ), and uncertainty regarding their potential effects on fisheries has caused concern among scientists and fishery managers (e.g., Dettmers et al. 2012 ). In particular, the relative importance of “bottom-up” (e.g., lower trophic level changes) versus “top-down” (e.g., predation) factors to fish community changes in the Great Lakes have been widely debated (e.g., Barbiero et al. 2011 ; Eshenroder and Lantry 2012 ; Bunnell et al. 2014 ). In Lake Huron, recent ecosystem changes have been particularly profound, and populations of alewife ( Alosa pseudoharengus ), an offshore pelagic prey fish, collapsed in 2003 and have yet to recover ( Riley et al. 2008 , 2014 ). He et al. (2015) recently used a series of linked ecological models to assess the role of predation in the dynamics of the offshore prey fish community in Lake Huron. While we believe that they provide a novel method for combining bioenergetics and stock assessment modeling, we question the validity of their conclusions because of the misapplication of survey data and the lack of critical interpretation of their modeling efforts. Here we describe how He et al. (2015) have misapplied bottom trawl data from Lake Huron, and we provide examples of how this has resulted in erroneous conclusions regarding the importance of predation to the population dynamics and collapse of alewife in Lake Huron.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2010

Reproductive ecology and habitat use of pacific Black Scoters (Melanitta nigra americana) nesting on the Yukon-Kuskokwim Delta, Alaska

Abundance indices of Black Scoters (Melanitta nigra. americana) breeding in Alaska indicate a long-term population decline without obvious cause (s). However, few life history data are available for the species in North America. In 2001–2004, information was collected on nesting habitat and reproductive parameters (i.e. components of productivity) from a population of Black Scoters nesting on the Yukon-Kuskokwim Delta, Alaska. A total of 157 nests were found over four years. Primarily, nests were among dense vegetation in shrub edge habitat, predominantly dwarf birch (Betula glandulosa) and Alaska spiraea (Spiraea beauverdiana), an average of 58 m from water. Females initiated nests from 11 June and 17 July across years. Clutch size averaged 7.5 eggs and did not vary annually. Nest success was highly variable among years and ranged from 0.01 to 0.37. Duckling survival to 30 days old varied among years, and ranged from 0.09 – 0.35. Nest success was poor in three of four years, likely due to predation by Red Fox (Vulpes vulpes). Black Scoters appear to have low but variable productivity, consistent with life-history patterns of other sea duck species. Information gained will direct future demographic research on Black Scoters, and highlights knowledge gaps impeding management strategies needed for population recovery.

Alaska↗

USGS2002

Ecological and evolutionary conditions for fruit abortion to regulate pollinating seed-eaters and increase plant production

Coevolved mutualisms, such as those between senita cacti, yuccas, and their respective obligate pollinators, benefit both species involved in the interaction. However, in these pollination mutualisms the pollinator's larvae impose a cost on plants through consumption of developing seeds and fruit. The effects of pollinators on benefits and costs are expected to vary with the abundance of pollinators, because large population sizes result in more eggs and larval seed-eaters. Here, we develop the hypothesis that fruit abortion, which is common in yucca, senita, and plants in general, could in some cases have the function of limiting pollinator abundance and, thereby, increasing fruit production. Using a general steady-state model of fruit production and pollinator dynamics, we demonstrate that plants involved in pollinating seed-eater mutualisms can increase their fecundity by randomly aborting fruit. We show that the ecological conditions under which fruit abortion can improve plants fecundity are not unusual. They are best met when the plant is long-lived, the population dynamics of the pollinator are much faster than those of the plant, the loss of one fruit via abortion kills a larva that would have the expectation of destroying more than one fruit through its future egg laying as an adult moth, and the effects of fruit abortion on pollinator abundance are spatially localized. We then use the approach of adaptive dynamics to find conditions under which a fruit abortion strategy based on regulating the pollinator population could feasibly evolve in this type of plant–pollinator interaction.

Theoretical Population Biology↗

USGS2011

Swallows as a sentinel species for contaminant exposure and effect studies

Tree swallows are an important model species to study the effects of contaminants in wild bird populations and have been used extensively in studies across North America. The advantages of swallows compared to other avian species are detailed. Three case histories are provided where swallows have been successfully used in Natural Resource Damage and Ecological Risk Assessments. The final two sections of this chapter are for individuals who want more in-depth information and include a summary of the chemical classes for which there are swallow data, including effect levels when known. Information provided in this section can be used to put exposure to most classes of contaminants into context with other sites across North America. Finally, commonly used endpoints, ranging from population-level down to cellular and genetic endpoints, are discussed including considerations and pitfalls, and when further work is needed to more fully understand the role of environmental and biological variation in interpreting these endpoints.

Book chapter↗

USGS2014

An ecological response model for the Cache la Poudre River through Fort Collins

The Poudre River Ecological Response Model (ERM) is a collaborative effort initiated by the City of Fort Collins and a team of nine river scientists to provide the City with a tool to improve its understanding of the past, present, and likely future conditions of the Cache la Poudre River ecosystem. The overall ecosystem condition is described through the measurement of key ecological indicators such as shape and character of the stream channel and banks, streamside plant communities and floodplain wetlands, aquatic vegetation and insects, and fishes, both coolwater trout and warmwater native species. The 13- mile-long study area of the Poudre River flows through Fort Collins, Colorado, and is located in an ecological transition zone between the upstream, cold-water, steep-gradient system in the Front Range of the Southern Rocky Mountains and the downstream, warm-water, low-gradient reach in the Colorado high plains. The City wanted to better understand the ecological response of the Poudre River ecosystem to potential changes in stream flow and other physical parameters through the conceptual framework of a multivariable integrated model. This goal was met through the use of a probabilistic model based on Bayesian concepts. This construct allowed the integration of a wide range of data and expert opinion (as informed by local data) to predict potential changes to ecosystem conditions under various flow scenarios. Nine flow scenarios representing past, present, and possible future hydrology were developed as the primary model input. Both reach-scale drivers such as stream channel conditions and pollutant loads, as well as ecological conditions, including species composition, interactions, and habitat requirements influenced model-predicted ecosystem outcomes. Model output consisted of probability distributions for eight ecological indicators collectively representing the physical setting, aquatic life, and riparian habitats of the river ecosystem. We are confident in model predictions related to probable trends, relative magnitude of changes and potential ecosystem responses to changing flow conditions, though data availability and the process of converting diverse data types into a common unit (probabilities) limit precision of individual results. Key findings suggest that: The present ecological function of the Poudre River is altered as a result of more than 150 years of human influences that include highly managed flows, urbanization, gravel mining, channelization and urban and industrial encroachment in the floodplain, underscoring the vulnerable and complex character of the Poudre River; A continuation of today’s flow management will lead to ongoing changes in ecosystem condition, and additional water depletions will compromise ecological conditions; High flows play an essential role in maintaining and improving the aquatic and riparian condition of the river; Adequate flows in base-flow periods are critical to desirable water quality, and thriving fish and insect populations; Improvement of native aquatic life is possible if issues related to channel modifications, siltation, invasive species, and base and high flow conditions are managed properly; The present confined river channel and modified flows has reduced the potential for a keystone and iconic species, plains cottonwood, to be self-sustaining in the study area; The streamside corridor retains the potential to support a functioning riparian forest that provides important ecological services if periodic floodplain inundation occurs. Environmental flows that combine stable and adequate flows in base-flow periods with occasional rejuvenating high flows that meet target levels defined in this study are likely improve all biological indicators across the system. ERM test scenarios that include both stable base flows and rejuvenating high flows indicate that substantial improvements in the river ecosystem can be achieved with improved management of flow volumes similar to those observed in the river during the last half century of intensive water development. These results underscore the possibility of improving the river ecosystem through active management while still maintaining the Poudre’s diverse economic benefits and role as a working river. The ERM was designed to represent the multi-dimensional ecological character of the contemporary urban Poudre River. It provides a scientific foundation that can serve as a decision support tool and foster a more informed community discussion about the future of the river as it provides a better understanding of the likely response of the Poudre River ecosystem to environmental flow management and other stewardship activities. In particular, model results can assist managers in developing specific management actions to achieve desirable goals for key indicators of river health.

Colorado↗

USGS2006

Integrating human impacts and ecological integrity into a risk-based protocol for conservation planning

Conservation planning aims to protect biodiversity by sustainng the natural physical, chemical, and biological processes within representative ecosystems. Often data to measure these components are inadequate or unavailable. The impact of human activities on ecosystem processes complicates integrity assessments and might alter ecosystem organization at multiple spatial scales. Freshwater conservation targets, such as populations and communities, are influenced by both intrinsic aquatic properties and the surrounding landscape, and locally collected data might not accurately reflect potential impacts. We suggest that changes in five major biotic drivers—energy sources, physical habitat, flow regime, water quality, and biotic interactions—might be used as surrogates to inform conservation planners of the ecological integrity of freshwater ecosystems. Threats to freshwater systems might be evaluated based on their impact to these drivers to provide an overview of potential risk to conservation targets. We developed a risk-based protocol, the Ecological Risk Index (ERI), to identify watersheds with least/most risk to conservation targets. Our protocol combines risk-based components, specifically the frequency and severity of human-induced stressors, with biotic drivers and mappable land- and water-use data to provide a summary of relative risk to watersheds. We illustrate application of our protocol with a case study of the upper Tennessee River basin, USA. Differences in risk patterns among the major drainages in the basin reflect dominant land uses, such as mining and agriculture. A principal components analysis showed that localized, moderately severe threats accounted for most of the threat composition differences among our watersheds. We also found that the relative importance of threats is sensitive to the spatial grain of the analysis. Our case study demonstrates that the ERI is useful for evaluating the frequency and severity of ecosystemwide risk, which can inform local and regional conservation planning.

Tennessee↗

USGS2006

Ecology of bonytail and razorback sucker and the role of off-channel habitats in their recovery

The bonytail and razorback sucker are two of four endangered mainstem fishes found in the Colorado River. Unlike the Colorado pikeminnow and humpback chub, wild populations of the bonytail and razorback sucker are either extirpated from the mainstem river or are nearly so. Agencies are aggressively stocking these fish and while repatriated fish spawn, their young are rapidly eaten by introduced predators. A decade of predator removal efforts has proved ineffective in restoring natural recruitment. Today, the presence of these species is totally dependent on stocking, suggesting both species are worse off today than when recovery efforts began nearly two decades ago. In contrast, both species readily produce young in ponds where nonnative predators are absent. Evidence shows they evolved with the ability to spawn in both flowing and standing water, which suggests isolated oxbow communities may have been an essential feature in their evolution and survival strategy. Sustainable populations during the past few decades have only occurred in isolated ponds devoid of predatory nonnative fish. Efforts to force recovery in the main channel river continue to fail due to the presence of nonnative predators that may be economically important recreational species. Off-channel sanctuaries provide research and management opportunities on a scale that are both biologically and economically realistic. Effective management of these species in small habitats appears to be the most logical approach to advance recovery in larger river reaches. This report presents new findings, updates existing information, and describes what may well represent the only practical approach to these species’ conservation and recovery. Chapter 1 provides an overview of the Colorado River system from its origin to the Gulf of California and includes a description of propagation and stocking programs which have not been described elsewhere. The report also updates what is known or suspected on the life history and ecology of these two endangered fishes. Chapter 2 describes the successful recruitment of both species at an oxbow pond on the Cibola National Wildlife Refuge in Arizona, discusses factors that contribute to completion of the life cycle of both fishes, and provides recommendations for future management of the impoundment. Chapter 3 provides historical evidence that oxbow habitats were formed historically in years of high runoff and the importance of these habitats for survival and evolution of native fishes. It also summarizes key features of habitats that can serve as sanctuaries that enhance early survival of the endangered fishes and allow the fish to complete their entire life cycles.

Scientific Investigations Report↗

USGS2008

The human footprint in the west: a large-scale analysis of anthropogenic impacts.

Anthropogenic features such as urbanization, roads, and power lines, are increasing in western United States landscapes in response to rapidly growing human populations. However, their spatial effects have not been evaluated. Our goal was to model the human footprint across the western United States. We first delineated the actual area occupied by anthropogenic features, the physical effect area. Next, we developed the human footprint model based on the ecological effect area, the zone influenced by features beyond their physical presence, by combining seven input models: three models quantified top-down anthropogenic influences of synanthropic predators (avian predators, domestic dog and cat presence risk), and four models quantified bottom-up anthropogenic influences on habitat (invasion of exotic plants, human-caused fires, energy extraction, and anthropogenic wildland fragmentation). Using independent bird population data, we found bird abundance of four synanthropic species to correlate positively with human footprint intensity and negatively for three of the six species influenced by habitat fragmentation. We then evaluated the extent of the human footprint in relation to terrestrial (ecoregions) and aquatic systems (major rivers and lakes), regional management and conservation status, physical environment, and temporal changes in human actions. The physical effect area of anthropogenic features covered 13% of the western United States with agricultural land (9.8%) being most dominant. High-intensity human footprint areas (class 8 – 10) overlapped highly productive low-elevation private landholdings and covered 7% of the western United States compared to 48% for low-intensity areas (class 1 – 3), which were confined to low-productivity high-elevation federal landholdings. Areas within 1 km of rivers were more affected by the human footprint compared to lakes. Percentage human population growth was higher in low-intensity human footprint areas. The disproportional regional effects of the human footprint on landscapes in the western United States create a challenge to management of ecosystems and wildlife populations. Using footprint models, managers can plan land use actions, develop restoration scenarios, and identify areas of high conservation value at local landscapes within a regional context. Moreover, human footprint models serve as a tool to stratify landscapes for studies investigating floral and faunal response to human disturbance intensity gradients.

Ecological Applications↗

USGS2010

Kinetics of viral shedding provide insights into the epidemiology of viral hemorrhagic septicemia in Pacific herring

Losses from infectious diseases are an important component of natural mortality among marine fish species, but factors controlling the ecology of these diseases and their potential responses to anthropogenic changes are poorly understood. We used viral hemorrhagic septicemia virus (VHSV) and a laboratory stock of Pacific herring Clupea pallasii to investigate the kinetics of viral shedding and its effect on disease transmission and host mortality. Outbreaks of acute disease, accompanied by mortality and viral shedding, were initiated after waterborne exposure of herring to concentrations of VHSV as low as 101 plaque-forming units (pfu) ml–1. Shed virus in flow-through tanks was first detected 4 to 5 d post-exposure, peaked after 6 to 10 d, and was no longer detected after 16 d. Shedding rates, calculated from density, flow and waterborne virus titer reached 1.8 to 5.0 × 108 pfu fish–1 d–1. Onset of viral shedding was dose-dependent and preceded initial mortality by 2 d. At 21 d, cumulative mortality in treatment groups ranged from 81 to 100% and was dependent not on challenge dose, but on the kinetics and level of viral shedding by infected fish in the tank. Possible consequences of the viral shedding and disease kinetics are discussed in the context of epizootic initiation and perpetuation among populations of wild Pacific herring.

Marine Ecology Progress Series↗

USGS2005

Assessing uncertainty in ecological systems using global sensitivity analyses: A case example of simulated wolf reintroduction effects on elk

Often landmark conservation decisions are made despite an incomplete knowledge of system behavior and inexact predictions of how complex ecosystems will respond to management actions. For example, predicting the feasibility and likely effects of restoring top-level carnivores such as the gray wolf ( Canis lupus ) to North American wilderness areas is hampered by incomplete knowledge of the predator-prey system processes and properties. In such cases, global sensitivity measures, such as Sobol’ indices, allow one to quantify the effect of these uncertainties on model predictions. Sobol’ indices are calculated by decomposing the variance in model predictions (due to parameter uncertainty) into main effects of model parameters and their higher order interactions. Model parameters with large sensitivity indices can then be identified for further study in order to improve predictive capabilities. Here, we illustrate the use of Sobol’ sensitivity indices to examine the effect of parameter uncertainty on the predicted decline of elk ( Cervus elaphus ) population sizes following a hypothetical reintroduction of wolves to Olympic National Park, Washington, USA. The strength of density dependence acting on survival of adult elk and magnitude of predation were the most influential factors controlling elk population size following a simulated wolf reintroduction. In particular, the form of density dependence in natural survival rates and the per-capita predation rate together accounted for over 90% of variation in simulated elk population trends. Additional research on wolf predation rates on elk and natural compensations in prey populations is needed to reliably predict the outcome of predator–prey system behavior following wolf reintroductions.

Ecological Modelling↗

USGS2025

3D habitat complexity and coral morphology modulate reef fish functional structure in a marine national park

The ongoing degradation of coral reef habitats is widely acknowledged to have adverse effects on the abundance and diversity of reef fish populations, yet the direct effects on ecosystem functions remain uncertain. This study used a quantitative approach to determine the mechanistic links between fish assemblages and ecological function. We investigated the effects of 3D habitat structure and coral morphology on the ecological, behavioral, and morphological functional traits of reef fish within a protected marine national park. Fish traits such as Gregariousness, Water Column Position, and Body Shape were identified to be highly influential in shaping the multidimensional fish functional space, which was categorized into 10 Fish Functional Groups (FFG). Furthermore, habitat complexity and coral morphology significantly explained the abundances of eight out of 10 FFG. Notably, the habitat complexity metrics of Slope and Surface Complexity, along with coral morphologies of Branching and Mounding types, emerged as the most influential habitat features across FFG. Pairing Compressiform species and Schooling Short/Deep species, for example, significantly increased in abundance on substrate with higher Slopes and increased percentages of branching coral cover. Additionally, Cryptic and Nocturnal species exhibited statistically significant associations with all coral morphologies and substrates with high trait values of Slope and Curvature. Elucidating ecological drivers of specific functional groups of reef fish is critical for determining how changes in reef composition and structure will alter fish assemblages. Broad scale patterns were also detected, suggesting that although structural complexity is important, live coral morphologies have a greater positive impact on reef fish functional groups. These findings have direct implications for conservation and monitoring efforts, offering valuable insights for predicting the impacts of environmental change on community dynamics and ecosystem functioning.

Hawaii↗