FLOwPER v3 user’s guide supplement: Field application for collection of FLOw PERmanence field observations
No abstract available.
Report↗
Geology topics
Nathan Chelgren
Publications and source records attributed to Nathan Chelgren.
A streamflow permanence classification model for forested streams that explicitly accounts for uncertainty and extrapolation
Accurate mapping of headwater streams and their flow status has important implications for understanding and managing water resources and land uses. However, accurate information is rare, especially in rugged, forested terrain. We developed a streamflow permanence classification model for forested lands in western Oregon using the latest light detection and ranging-derived hydrography published in the National Hydrography Dataset. Models were trained using 2,518 flow/no flow field observations collected in late summer 2019–2021 across headwaters of 129 sub-watersheds. The final model, the Western Oregon WeT DRy model, used Random Forest and 13 environmental covariates for classifying every 5-m stream sub-reach across 426 sub-watersheds. The most important covariates were annual precipitation and drainage area. Model output included probabilities of late summer surface flow presence and were subsequently categorized into three streamflow permanence classes—Wet, Dry, and Ambiguous. Ambiguous denoted model probabilities and associated prediction intervals that extended over the 50% classification threshold between wet and dry. Model accuracy was 0.83 for sub-watersheds that contained training data and decreased to 0.67 for sub-watersheds that did not have observations of late summer surface flow. The model identified where predictions extrapolated beyond the domain characterized by the training data. The combination of spatially continuous estimates of late summer streamflow status along with uncertainty and extrapolation estimates provide critical information for strategic project planning and designing additional field data collection.
Oregon↗
Combining expert knowledge of a threatened trout distribution with sparse occupancy data for climate-related projection
Objective To evaluate the vulnerability of Bull Trout Salvelinus confluentus to potential climate changes across its range in Oregon, we compiled disparate expert knowledge of the distribution of spawning and rearing and combined these probabilistic statements as data along with documented records of breeding and rearing in a joint occupancy model. Methods The joint expert knowledge–occupancy model, which was based on discrete patches of cold water (≤13°C) suitable for spawning and rearing, permitted the association of true occupancy with climate and other explanatory variables while accounting for variation in detection probability. We then applied estimated relationships of patch occupancy with explanatory variables to projected coldwater patch configurations in the years 2040 and 2080. Result Projections of the kilometers of occupied coldwater patch in future decades suggest precipitous declines if current relationships of occupancy with environmental variables are maintained. Impacts of climate changes in future decades manifest directly through the outright loss of coldwater patches and increases in winter high flows but also indirectly by increased isolation. Conclusion Combining probabilistic statements of species distributions from knowledgeable experts with sparse occupancy data may be a robust and timely alternative when large numbers of repeated occupancy surveys are infeasible.
Oregon↗
Adjacent and downstream effects of forest harvest on the distribution and abundance of larval headwater stream amphibians in the Oregon Coast Range
Forest harvest is a primary landscape-scale management action affecting riparian forests. Although concerns about impacts of forest harvest on stream amphibians is generally limited to areas adjacent to harvest, there is a paucity of information regarding potential downstream effects of forest harvest on these species. We designed a before-after, control-impact (BACI) experiment to quantify potential impacts of clearcut logging that included 12-m buffers or smaller variable-width buffers on the distribution and abundance of headwater stream amphibians in adjacent and downstream areas. We sampled larval coastal tailed frogs ( Ascaphus truei ), coastal giant salamanders ( Dicamptodon tenebrosus ), and Columbia torrent salamanders ( Rhyacotriton kezeri ) across 3,915 sampling occasions that spanned 13 study reaches in 2008–2011 (pre-harvest) and 2013–2016 (post-harvest) as part of the Trask River Watershed Study in the Oregon Coast Range, U.S.A. We analyzed these data using occupancy models to estimate occupancy and (when possible) relative abundance, while accounting for various sources of imperfect detection. All species exhibited reduced occupancy adjacent to clearcuts with variable-width buffers (odds ratios [ORs] ranged = 0.24–0.48), and these negative impacts were not always diminished when increasing the buffer size to 12 m (ORs ranged = 0.20–3.56). Dicamptodon tenebrosus was the only species to have occupancy impacted in downstream areas, and this negative impact was related to clearcut logging with uniform 12-m buffers (OR = 0.60). This species was also the only species to have abundance negatively impacted by forest harvest in downstream areas (OR = 0.41 with uniform 12-m buffers, OR = 0.38 with variable-width buffers), albeit impacts to abundance were not evaluated for R. kezeri . Ascaphus truei abundance increased in areas downstream of clearcut logging with uniform 12-m buffers (OR = 2.92). Although we found the direction and magnitude of responses varied by species, our study confirms that clearcut logging can have negative impacts on amphibians that inhabit the adjacent stream areas. Perhaps more importantly, we also found that forest harvest can have negative effects on stream amphibians downstream of the harvested area and that increasing the buffer size to 12 m did not necessarily diminish these impacts in adjacent and downstream areas. Altogether, our study provides a nuanced picture of adjacent and downstream effects of forest harvest on three endemic headwater stream amphibians, and our findings demonstrate that forest management practices should consider downstream effects on aquatic taxa when assessing the impact of harvesting trees near headwater streams.
Oregon↗
Northwest Forest Plan — The first 25 years (1994–2018): Watershed condition status and trends
This report describes status and trends in watershed condition across the Northwest Forest Plan (NWFP) area over the first 25 years since its inception in 1994. The program charged with this task is the Aquatic and Riparian Effectiveness Monitoring Program (AREMP), which has assembled information from field data collection, spatial datasets, and a host of landscape models to evaluate the status and trends in aquatic resources in streams and watersheds. Field data included hydrologic measurements (stream wetted widths and temperatures), geomorphic responses (instream wood and sediment), and biological responses (macroinvertebrates and aquatic organism passage). Novel statistical models were used to estimate trends in these measured responses. A suite of complementary modeled results was also employed to describe hydrometeorological drivers (e.g., drought indices and stream discharge), forest cover (upslope and riparian vegetation), and geomorphic conditions (e.g., road-related estimates of chronic and shallow landslide sediment delivery risk). Collectively, information on these responses allowed us to rigorously evaluate instream responses and hypothesize watershed drivers of those responses across the NWFP area and over time. The majority of responses we observed indicated widespread and incremental improvements from active management of forests, forest roads, and road-stream crossings as envisioned by the aquatic conservation strategy of the NWFP. Additionally, many of the responses we observed were consistent with those expected under the influences of changing climates in the Pacific Northwest. Ultimately, the long-term, broad-scale information provided by AREMP is a critical foundation for evaluating the effectiveness of federal land management and the effects of changing climates on water resources that sustain the Pacific Northwest’s human and natural landscapes.
California, Oregon, Washington↗
Fish response to successive clearcuts in a second-growth forest from the central Coast range of Oregon
Research dating back to the 1950 s has documented negative effects from harvesting of primeval forests on stream ecosystems of the Pacific Northwest. By the early 1990 s, state and federal forest practice rules governing timber harvest were modified throughout North America to better protect aquatic habitats and biotic resources, principally salmonids. These rules inspired a generation of studies using a before-after-control-impact (BACI) design to document the capacity of contemporary timber harvest rules to protect salmonids in headwater streams of second-growth forests. One important unanswered question concerns the potential effects of successive clearcuts in second growth forests. Consequently, we used a paired watershed approach to evaluate the effects of two successive clearcut harvests in the Alsea Watershed, site of the seminal Alsea Watershed Study that was conducted from 1958 to 1973, on relative biomass, movement, survival, and distribution of coastal cutthroat trout ( Oncorhynchus clarkii clarkii ) and three physical habitat characteristics (pool area and depth, and water temperature). Although the total clearcut harvest encompassed 87% of the treatment catchment in six years, no negative effects of logging were detected for either age-1 + coastal cutthroat trout or habitat variables. Comparisons between the harvested and reference catchments suggested the survival of coastal cutthroat trout (>94 mm fork length) and total catchment relative biomass of age-1+ (i.e., > 80 mm) exhibited similar patterns, increasing from the pre-logging period (2006–2009) through the Phase I post-logging period (2009–2014), and decreasing to levels observed in the pre-logging period during the Phase II post-logging period (2014–2017). Additionally, there was no evidence for differences in movement of coastal cutthroat trout related to the harvesting treatment. In terms of habitat variables, there was a relative increase in annual total pool area in the harvested catchment during the Phase II post-logging period, but there was no evidence the 7-day moving mean maximum stream temperature changed after the Phase I and Phase II harvests. Moreover, stream water temperatures never exceeded the criterion designed to protect core coldwater habitat for salmonids (16 °C). As such, it is unlikely that cutthroat trout experienced thermal stress following either harvest. More generally, results from this and other recent studies suggest that forest practice rules developed in conjunction with current best management practices for logging in headwater catchments have substantially improved outcomes for stream biota relative to unregulated forest harvest, at least for short periods of time after logging (i.e., ≤ 8 years).
Oregon↗
FLOwPER user guide—For collection of FLOw PERmanence field observations
The accurate mapping of streams and their streamflow conditions in terms of presence or absence of surface water is important to both understanding physical, chemical, and biological processes in streams and to managing land, water, and ecological resources. This document describes a field form, FLOwPER (FLOw PERmanence), available within a mobile application (app), for standardized data collection of the presence or absence of surface flow in streams. The FLOwPER Database is a publicly available geodataset that can be used for research and management applications. This document provides instructions on how to (1) access and download the FLOwPER field form within the mobile app service, (2) use and complete a FLOwPER field form, and (3) view and download data from the FLOwPER Database.
Open-File Report↗
Application of multiple-population viability analysis to evaluate species recovery alternatives
Population viability analysis (PVA) is a powerful conservation tool, but one that remains unapproachable for many species. This is particularly true for species with multiple, broadly-distributed populations for which collecting suitable data can be challenging. A recently-developed method of multiple population viability analysis (MPVA), however, addresses many limitations of traditional PVA. We build on previous development of MPVA for Lahontan cutthroat trout (LCT), a species listed under the US Endangered Species Act which is distributed broadly across habitat fragments in the Great Basin, USA. We simulated potential management scenarios and assessed their effects on population sizes and extinction risks in 211 streams where LCT exist or may be reintroduced.
Conservation Biology↗
Hierarchical multi-population viability analysis
Population viability analysis (PVA) uses concepts from theoretical ecology to provide a powerful tool for quantitative estimates of population dynamics and extinction risks. However, conventional statistical PVA requires long-term data from every population of interest, whereas many species of concern exist in multiple isolated populations that are only monitored occasionally. We present a hierarchical multi-population viability analysis model that increases inference power from sparse data by sharing information among populations to assess extinction risks while accounting for incomplete detection and sampling biases with explicit observation and sampling sub-models. We present a case study in which we customized this model for historical population monitoring data (1985–2015) from federally threatened Lahontan cutthroat trout populations in the Great Basin, USA. Data were counts of fish captured during backpack electrofishing surveys from locations associated with 155 isolated populations. Some surveys (25%) included multi-pass removal sampling, which provided valuable information about capture efficiency. GIS and remote sensing were used to estimate August stream temperatures, peak flows, and riparian vegetation condition in each population each year. Field data were used to derive an annual index of nonnative trout densities. Results indicated that population growth rates were higher in colder streams and that nonnative trout reduced carrying capacities of native trout. Extinction risks increased with more environmental stochasticity and were also related to population extent, water temperatures, and nonnative densities. We developed a graphical user interface to interact with the fitted model results and to simulate future habitat scenarios and management actions to assess their influence on extinction risks in each population. Hierarchical multi-population viability analysis bridges the gap between site-level field observations and population-level processes, making effective use of existing datasets to support management decisions with robust estimates of population dynamics, extinction risks, and uncertainties.
Ecology↗
Viability analysis for multiple populations
Many species of conservation interest exist solely or largely in isolated populations. Ideally, prioritization of management actions among such populations would be guided by quantitative estimates of extinction risk, but conventional methods of demographic population viability analysis (PVA) model each population separately and require temporally extensive datasets that are rarely available in practice. We introduce a general class of statistical PVA that can be applied to many populations at once, which we term multiple population viability analysis or MPVA. The approach combines models of abundance at multiple spatial locations with temporal models of population dynamics, effectively borrowing information from more data-rich populations to inform inferences for data-poor populations. Covariates are used to explain population variability in space and time. Using Bayesian analysis, we illustrate the method with a dataset of Lahontan cutthroat trout ( Oncorhynchus clarkii henshawi ) observations that previously had been analyzed with conventional PVA. We find that MPVA predictions are similar in bias and higher in precision than predictions from simple PVA models that treat each population individually; moreover, the use of covariates in MPVA allows for predictions in minimally-sampled and unsampled populations. The basic MPVA model can be extended in multiple ways, such as by linking to a sampling and observation model to provide a full accounting of uncertainty. We conclude that the approach has great potential to expand the use of PVA for species that exist in multiple, isolated populations.
Biological Conservation↗
Mercury and drought along the lower Carson River, Nevada: IV. Snowy egret post-fledging dispersal, timing of migration and survival, 2002–2004
This telemetry study is an extension of our 1997–2006 research on historical mercury contamination on snowy egrets ( Egretta thula ) up to ~ 20 days of age. Findings from initial studies at the mercury-contaminated Carson River colony at Lahontan Reservoir (LR) and a similar-sized reference (REF) colony on the Humboldt River included mercury-related physiological, biochemical, histopathological and reproductive effects up to ~20 days of age; with poor water years (2000–04), i.e., reduced prey availability, exacerbating effects. Herein, we compare timing of dispersal and migration at LR vs. REF, but the primary question now addressed is “whether survival of young mercury-exposed snowy egrets from LR would be further compromised beyond ~20 days of age? ” Based upon telemetry signals until 90–110 days of age (including dead bird counts and survival rate estimates), we conclude that mercury did not further compromise survival. Dead bird counts and survival rate estimates included time in the colony when fed by adults, plus the critical period when young dispersed from the colony to forage independently. The extended drought during this 3-year study was most critical in 2002 when production of ~20 d old egrets at LR was only 0.24 young/nest. In 2002, survival rates were low at both colonies and we documented the highest counts of dead egrets for both colonies. We suggest the losses in 2002 beyond 20 days of age were more a function of prey availability influenced by drought than exposure to mercury, especially at LR, because higher mercury concentrations, higher survival rates and fewer dead birds were documented at LR in 2003 when water conditions improved. Furthermore, total mercury (THg) in blood in 2003 was more than double 2002 (geometric mean, 3.39 vs 1.47 µg/g wet weight (ww). This higher THg exposure at LR in 2003 was associated with a redistribution of parent and post-dispersal feeding activities upstream (where there was higher mercury from historic mining) related to slightly improved water levels. When comparing the 3-year telemetry findings based upon ~20 d old young at LR (blood THg, geo. means 1.47, 3.39 and 1.89 µg/g ww), we found no evidence that age at dispersal, Julian date at dispersal, timing of migration, or pre-migration survival (~20 to ~100 days post-hatch) were adversely affected by elevated mercury.
Nevada↗
Inference of timber harvest effects on survival of stream amphibians is complicated by movement
The effects of contemporary logging practices on headwater stream amphibians have received considerable study but with conflicting or ambiguous results. We posit that focusing inference on demographic rates of aquatic life stages may help refine understanding, as aquatic and terrestrial impacts may differ considerably. We investigated in-stream survival and movement of two stream-breeding amphibian species within a before-after timber harvest experiment in the Oregon Coast Range. We used recaptures of marked individuals and a joint probability model of survival, movement, and capture probability, to measure variation in these rates attributed to stream reach, stream gradient, pre- and post-harvest periods, and the timber harvest intensity. Downstream biased movement occurred in both species but was greater for Coastal Tailed Frog ( Ascaphus truei ) larvae than aquatic Coastal Giant Salamanders ( Dicamptodon tenebrosus ). For D. tenebrosus , downstream biased movement occurred early in life, soon after an individual's first summer. Increasing timber harvest intensity reduced downstream movement bias and reduced survival of D. tenebrosus , but neither of these effects were detected for larvae of A. truei . Our findings provide insight into the demographic mechanisms underlying previous nuanced studies of amphibian responses to timber harvest based on biomass or counts of larvae.
Copeia↗
Occupancy patterns of mammals and lentic amphibians in the Elwha River riparian zone before dam removal
The downstream transport of sediments and organics and upstream migration of anadromous fishes are key ecological processes in unregulated riverine ecosystems of the North Pacific coast, but their influence on wildlife habitats and populations is poorly documented. Removal of two large hydroelectric dams in Washington’s Elwha Valley provides an unprecedented opportunity to study long-term responses of wildlife populations to dam removal and restoration of these key ecological processes. We compared pre-dam removal patterns in the relative abundance and occupancy of mesocarnivores, small mammals and lentic amphibians of the Elwha River riparian zone above, between and below the dams. Occupancy of riparian habitats by three mesocarnivore species diminished upriver but did not appear to be closely linked with the absence of salmon in the upper river. Although the importance of salmon in the lower river cannot be discounted, other gradients in food resources also likely contributed to observed distribution patterns of mesocarnivores. Abundance and occupancy patterns within congeneric pairs of new world mice (Peromyscus spp.) and shrews (Sorex spp.) indicated that closely related species were negatively associated with each other and responded to habitat gradients in the riparian zone. The availability of lentic habitats of amphibians was highly variable, and occupancy was low as a result of rapidly changing flows during the larval development period. We speculate that long-term changes in habitat conditions and salmon availability following dam removal will elicit long-term changes in distribution of mesocarnivores, small mammals and amphibians. Long-term monitoring will enhance understanding of the role of fish and restored ecosystem processes on wildlife communities along salmon-bearing rivers in the region.
Washington↗
Effects of El Niño on distribution and reproductive performance of Black Brant
Climate in low-latitude wintering areas may influence temperate and high-latitude breeding populations of birds, but demonstrations of such relationships have been rare because of difficulties in linking wintering with breeding populations. We used long-term aerial surveys in Mexican wintering areas and breeding areas in Alaska, USA, to assess numbers of Black Brant ( Branta bernicla nigricans ; hereafter brant) on their principal wintering and breeding area in El Niño and non-El Niño years. We used Pollock's robust design to directly estimate probability of breeding and apparent annual survival of individually marked brant at the Tutakoke River (TR) colony, Alaska, in each year between 1988 and 2001. Fewer brant wintered in Mexico during every El Niño event since 1965. Fewer brant were observed on the principal breeding area following each El Niño since surveys began in 1985. Probability of breeding was negatively related to January sea surface temperature along the subtropical coast of North America during the preceding winter. Between 23% (five-year-olds or older) and 30% (three-year-olds) fewer brant nested in 1998 following the strong El Niño event in the winter of 1997–1998 than in non-El Niño years. This finding is consistent with life history theory, which predicts that longer-lived species preserve adult survival at the expense of reproduction. Oceanographic conditions off Baja California, apparently by their effect on Zostera marina (eelgrass), strongly influence winter distribution of brant geese and their reproduction (but not survival), which in turn affects ecosystem dynamics in Alaska.
Alaska↗
Testing for handling bias in survival estimation for black brant
We used an ultrastructure approach in program SURVIV to test for, and remove, bias in survival estimates for the year following mass banding of female black brant ( Branta bernicla nigricans ). We used relative banding-drive size as the independent variable to control for handling effects in our ultrastructure models, which took the form: S = S 0 (1 - α D), where α was handling effect and D was the ratio of banding-drive size to the largest banding drive. Brant were divided into 3 classes: goslings, initial captures, and recaptures, based on their state at the time of banding, because we anticipated the potential for heterogeneity in model parameters among classes of brant. Among models examined, for which α was not constrained, a model with α constant across classes of brant and years, constant survival rates among years for initially captured brant but year-specific survival rates for goslings and recaptures, and year- and class-specific detection probabilities had the lowest Akaike Information Criterion (AIC). Handling effect, α , was -0.47 ± 0.13 SE, -0.14 ± 0.057, and -0.12 ± 0.049 for goslings, initially released adults, and recaptured adults. Gosling annual survival in the first year ranged from 0.738 ± 0.072 for the 1986 cohort to 0.260 ± 0.025 for the 1991 cohort. Inclusion of winter observations increased estimates of first-year survival rates by an average of 30%, suggesting that permanent emigration had an important influence on apparent survival, especially for later cohorts. We estimated annual survival for initially captured brant as 0.782 ± 0.013, while that for recaptures varied from 0.726 ± 0.034 to 0.900 ± 0.062. Our analyses failed to detect a negative effect of handling on survival of brant, which is consistent with an hypothesis of substantial inherent heterogeneity in post-fledging survival rates, such that individuals most likely to die as a result of handling also have lower inherent survival probabilities.
Alaska, California↗