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USGS2024

Streams, springs, and volcanic lakes for volcano monitoring

Introduction Volcanic unrest can trigger appreciable change to surface waters such as streams, springs, and volcanic lakes. Magma degassing produces gases and soluble salts that are absorbed into groundwater that feeds streams and lakes. As magma ascends, the amount of heat and degassing will increase, and so will any related geochemical and thermal signal. Subsurface magma movement can cause pressurization that alters hydrostatic head and may induce groundwater discharge. Fluid-pressure changes have been linked to distal volcano-tectonic earthquakes (White and McCausland, 2016; Coulon and others, 2017) and phreatic eruptions (for example, Yamaoka and others, 2016). Clearly, changes in groundwater and surface waters are both indicators of unrest and clues to how and where magma is rising toward the surface. Where possible, it is prudent to incorporate real-time hydrologic data into multiparameter monitoring of restless volcanoes. Hydrologic dynamics can also be tracked by changes in groundwater levels that are commonly measured in shallow boreholes (see of Flinders, A.F., Lowenstern, J.B., Coombs, M.L., and Poland, M.P., eds., Recommended capabilities and instrumentation for volcano monitoring in the United States: U.S. Geological Survey Scientific Investigations Report 2024–5062–K, 5 p., https://doi.org/10.3133/sir20245062k. ">chapter K , this volume, on boreholes; Hurwitz and Lowenstern, 2024). Although inferred to be common, relatively few volcano-hydrology anomalies are well documented, and many are essentially anecdotal (Newhall and others, 2001), reflecting the fact that high-resolution time series remain rare. Extreme examples include the 2008 eruption of Nevado del Huila, Colombia, where relatively minor phreatomagmatic eruptions were accompanied by expulsion of as much as 300 million cubic meters of groundwater from fissures high on the volcano (Worni and others, 2011), generating large lahars. Substantial decreases in flow rate from springs about 8 kilometers from the summit of Mayon Volcano, Philippines, have been noted before most eruptions in the 20th century (Newhall and others, 2001). Stream monitoring at Redoubt Volcano in 2009 allowed Werner and others (2012) to recognize that groundwater was unable to absorb (or scrub) the high flux of volcanic gas and that a high CO 2 /SO 2 precursor signal had been evident for 5 months prior to the eruption. A key to better interpreting hydrologic anomalies—or even identifying them—is therefore obtaining adequate baseline data. Most hydrologic monitoring at U.S. volcanoes has been accomplished by intermittent sampling surveys with annual or less frequent sampling (for example, https://hotspringchem.wr.usgs.gov/index.php ). More frequent sampling, however, generally is needed to establish reliable baselines. A recent hydrologic and hydrothermal monitoring experiment at 25 sites and 10 of the 12 level 4 (very high threat) volcanoes in the U.S. portion of the Cascade Range demonstrated that there is sufficient temporal variability in hydrothermal fluxes, even during quiescent periods, that one-time measurements will commonly have limited interpretive value (Crankshaw and others, 2018). Thus, surveys are best augmented with data from streamgages (for example, Evans and others, 2004; Bergfeld and others, 2008). Streamflow (water discharge) data allow measured temperature and specific conductance to be converted to heat and solute mass fluxes, which could be insightful parameters for detecting anomalous activity (McCleskey and others, 2012). At the Yellowstone Caldera, long-term monitoring of river solutes has allowed calculation of the chloride flux, a proxy for heat discharge (Hurwitz and others, 2007; McCleskey and others, 2016) from the subsurface magma. This is readily accomplished because data from streamgages are continuously recorded and archived by the U.S. Geological Survey (USGS) National Water Information System (NWIS) (USGS, 2024). Similar studies on stratovolcanoes or shield volcanoes would be scientifically useful, and yet are logistically challenging, requiring streamgages on numerous radial drainages complemented by either frequent manual sampling or numerous deployments of equipment to measure water temperature and specific conductance as a proxy for water chemistry. Another challenge is that some volcanic areas, especially shield volcanoes, are characterized by near-surface porous rocks and soils, such that surface streams are rare and replaced by distant, dilute large-volume springs with only a trace of any original volcanically sourced water (Manga, 2001; Hurwitz and others, 2021). Volcanic lakes are worthy of special attention for monitoring efforts, as their temperature and composition can provide evidence of increased flux of volatile-rich fluids from below. Quantifying changes in volatile and heat release from magma can be simpler in lakes than for volcanoes with radial drainages and no major lakes. Moreover, volcanic lakes pose a range of hazards themselves, including phreatomagmatic eruptions, debris flows, flank collapse, tsunamis, and toxic gas release (Mastin and Witter, 2000; Delmelle and others, 2015; Manville, 2015; Rouwet and others, 2015)—hazards that have historically been responsible for substantial loss of life at many volcanoes worldwide (Manville, 2015). Catastrophic CO 2 release at Lake Nyos, Cameroon, in 1986 suffocated about 1,750 people and about 3,500 livestock and was probably triggered by a large landslide into the gas-saturated lake (Kling and others, 1987; Evans and others, 1993). Gas-charged springs in Soda Bay within Clear Lake (California) have caused almost a dozen deaths to bathers in the past hundred years (ABC News, 2000). A 2005 example of lake overturn and abundant gas release was documented at Mount Chiginagak in Alaska (Schaefer and others, 2008) but did not result in any human casualties. Although thermally stratified lakes, which promote trapping of exsolved magmatic gas, tend to develop in tropical regions, the phenomenon can also arise where salinity creates meromixis (a condition in which a lake does not mix completely), as occurs in Mono Lake, California (Jellison and Melack, 1993; Jellison and others, 1998). If magma erupts or flows into a lake, the interaction between hot magma and cold water can be explosive (Mastin and others, 2004; Zimanowski and others, 2015) and substantially expand the area affected by the eruption. Another hazard is the breaching of crater rims by landslides triggered by volcanic and (or) seismic activity. Under some circumstances, substantial volumes of water can be displaced, leading to large floods and lahars. Late Holocene lake flooding from Aniakchak Crater in the Alaska Peninsula (Waythomas, 2022) and from Paulina Lake in Newberry Crater, Oregon (Chitwood and Jensen, 2000), caused by the failure of outlet sills, testify to the substantial hazards at lake-filled calderas. Several volcanic systems in the United States host lakes known to receive heat and gas from underlying magma. These lakes vary widely in area, depth, and chemical composition. Lakes are present at level 4 volcanoes, including Crater Lake and Newberry Volcano in Oregon; Yellowstone Caldera in Wyoming; Long Valley Caldera, Clear Lake volcanic field, Medicine Lake, and Salton Buttes in California; and Aniakchak Crater, Mount Katmai, Fisher Caldera, Mount Okmok, and Kaguyak Crater, among others, in Alaska. A water lake was present in Halemaʻumaʻu, the crater of Kīlauea, Hawai‘i (fig. F1), from October 2019 to December 2020. Level 3 volcanoes with lakes include Mono Lake volcanic field (Calif.), Mount Bachelor (Ore.), Ukinrek Maars and Mount Chiginagak (Alaska), and Soda Lake (Nevada). In addition, there are lakes at many levels 1 and 2 volcanoes. In the United States, there are no strongly acidic lakes that receive abundant input of magmatic gas, such as those found at Mount Ruapehu (New Zealand), Ijen and Kelud (Indonesia), and Poás (Costa Rica). Nevertheless, many contain fluids that provide clues to magmatic processes below. Since publication of a previous report on recommended instrumentation for volcano monitoring (Moran and others, 2008), continuous hydrologic monitoring has become increasingly feasible. However, changes in water pressure, temperature, and chemistry remain, in general, poorly studied phenomena at volcanoes (Sparks, 2003; National Academies of Sciences, Engineering, and Medicine, 2017). Recent efforts by the USGS have included the temporary study of Cascade Range volcanoes, which included frequent (15 minute to hourly) temporal sampling of temperature, depth, and conductivity (Crankshaw and others, 2018; Ingebritsen and Evans, 2019). At Yellowstone Caldera, many streamgages have now added thermistors and specific conductance sensors, allowing estimation of time-dependent chloride flux as a proxy for variations in subsurface heat flux (McCleskey and others, 2012, 2016). Efforts to better understand lakes have also accelerated, with bathymetric mapping and sampling carried out at several locations in the United States. Especially thorough work was done at Yellowstone Lake thanks to the Hydrothermal Dynamics of Yellowstone Lake (HD-YLAKE, https://hdylake.org ) project, funded primarily by the National Science Foundation. In addition to geophysical surveys and recovery of cores and other samples, HD-YLAKE investigations included remotely operated vehicle (ROV) investigations of hydrothermal vents on the lake floor (fig. F2). Data collected by the ROV provided a better understanding of the thermal and chemical influx from lake-bottom hydrothermal systems (Sohn and others, 2017). In this chapter, we focus on detecting changes in the chemistry, temperature, discharge, or water levels of streams, springs, and lakes that can be caused by seismicity, volumetric strains, or increases in gas flux associated with ascending magma. There is unavoidable overlap with other chapters of this report. Samples of water and gas can also be obtained in boreholes ( of Flinders, A.F., Lowenstern, J.B., Coombs, M.L., and Poland, M.P., eds., Recommended capabilities and instrumentation for volcano monitoring in the United States: U.S. Geological Survey Scientific Investigations Report 2024–5062–K, 5 p., https://doi.org/10.3133/sir20245062k. ">chapter K , this volume; Hurwitz and Lowenstern, 2024), both shallow and deep. Gas monitoring ( of Flinders, A.F., Lowenstern, J.B., Coombs, M.L., and Poland, M.P., eds., Recommended capabilities and instrumentation for volcano monitoring in the United States: U.S. Geological Survey Scientific Investigations Report 2024–5062–E, 11 p., https://doi.org/10.3133/sir20245062e.">chapter E , this volume; Lewicki and others, 2024) relies in part on samples from springs and wells, particularly where measurable gas plumes are absent. Water acts as a trigger and lubricant for landslides and sediment-rich floods, and so hydrology has obvious relevance for lahar monitoring, as discussed in of Flinders, A.F., Lowenstern, J.B., Coombs, M.L., and Poland, M.P., eds., Recommended capabilities and instrumentation for volcano monitoring in the United States: U.S. Geological Survey Scientific Investigations Report 2024–5062–H, 6 p., https://doi.org/10.3133/sir20245062h. ">chapter H (this volume; Thelen and others, 2024). Shared situational awareness among scientists engaged in geophysical, gas, and hydrologic monitoring will improve overall understanding of the volcanic hazard.

Scientific Investigations Report↗

USGS2014

Evaluating the predictive performance of empirical estimators of natural mortality rate using information on over 200 fish species

Many methods have been developed in the last 70 years to predict the natural mortality rate, M , of a stock based on empirical evidence from comparative life history studies. These indirect or empirical methods are used in most stock assessments to (i) obtain estimates of M in the absence of direct information, (ii) check on the reasonableness of a direct estimate of M , (iii) examine the range of plausible M estimates for the stock under consideration, and (iv) define prior distributions for Bayesian analyses. The two most cited empirical methods have appeared in the literature over 2500 times to date. Despite the importance of these methods, there is no consensus in the literature on how well these methods work in terms of prediction error or how their performance may be ranked. We evaluate estimators based on various combinations of maximum age ( t max ), growth parameters, and water temperature by seeing how well they reproduce >200 independent, direct estimates of M . We use tenfold cross-validation to estimate the prediction error of the estimators and to rank their performance. With updated and carefully reviewed data, we conclude that a t max -based estimator performs the best among all estimators evaluated. The t max -based estimators in turn perform better than the Alverson–Carney method based on t max and the von Bertalanffy K coefficient, Pauly’s method based on growth parameters and water temperature and methods based just on K . It is possible to combine two independent methods by computing a weighted mean but the improvement over the t max -based methods is slight. Based on cross-validation prediction error, model residual patterns, model parsimony, and biological considerations, we recommend the use of a t max -based estimator ( M = 4.899 t max − 0.916 "> M = 4.899 t − 0.916 max M=4.899tmax−0.916 , prediction error = 0.32) when possible and a growth-based method ( M = 4.118 K 0.73 L ∞ − 0.33 "> M = 4.118 K 0.73 L − 0.33 ∞ M=4.118K0.73L∞−0.33 , prediction error = 0.6, length in cm) otherwise.

ICES Journal of Marine Science↗

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↗

USGS2022

The developing zebrafish kidney is impaired by Deepwater Horizon crude oil early-life stage exposure: A molecular to whole-organism perspective

Crude oil is known to induce developmental defects in teleost fish exposed during early life stages (ELSs). While most studies in recent years have focused on cardiac endpoints, evidence from whole-animal transcriptomic analyses and studies with individual polycyclic aromatic hydrocarbons (PAHs) indicate that the developing kidney (i.e., pronephros) is also at risk. Considering the role of the pronephros in osmoregulation, and the common observance of edema in oil-exposed ELS fish, surprisingly little is known regarding the effects of oil exposure on pronephros development and function. Using zebrafish ( Danio rerio ) ELSs, we assessed the transcriptional and morphological responses to two dilutions of high-energy water accommodated fractions (HEWAF) of oil from the Deepwater Horizon oil spill using a combination of qPCR and whole-mount in situ hybridization (WM-ISH) of candidate genes involved in pronephros development and function, and immunohistochemistry (WM-IHC). To assess potential functional impacts on the pronephros, three 24 h osmotic challenges (2 hypo-osmotic, 1 near iso‐osmotic) were implemented at two developmental time points (48 and 96 h post fertilization; hpf) following exposure to HEWAF. Changes in transcript expression level and location specific to different regions of the pronephros were observed by qPCR and WM-ISH. Further, pronephros morphology was altered in crude oil exposed larvae, characterized by failed glomerulus and neck segment formation, and straightening of the pronephric tubules. The osmotic challenges at 96 hpf greatly exacerbated edema in both HEWAF-exposed groups regardless of osmolarity. By contrast, larvae at 48 hpf exhibited no edema prior to the osmotic challenge, but previous HEWAF exposure elicited a concentration-response increase in edema at hypo-osmotic conditions that appeared to have been largely alleviated under near iso‐osmotic conditions. In summary, ELS HEWAF exposure impaired proper pronephros development in zebrafish, which coupled with cardiotoxic effects, most likely reduced or inhibited pronephros fluid clearance capacity and increased edema formation.

Science of the Total Environment↗

USGS1955

Development of the hydrosphere and atmosphere, with special reference to probable composition of the early atmosphere

A satisfactory hypothesis of the development of the hydrosphere and atmosphere depends upon evidence from many sciences and the solution of many other fundamental problems of earth history. But because it is so closely related to many other problems, any progress toward unravelling the history of the hydrosphere and atmosphere limits the range of permissible speculation about such distantly related questions as the origin of the solar system, continents, mountains, and living organisms. Several hypotheses of the source of the earth’s air and waters are examined for their consistency with established principles and observed geologic evidence, and special attention is given to the probable composition of the early atmosphere. Hypotheses of the origin of the atmosphere and hydrosphere fall into two chief categories: (1) that all air and water of the earth are residual from a dense primitive atmosphere that once enveloped a molten globe; or (2) that they have accumulated at the earth’s surface by leakage from the interior. The quantities of water, carbon dioxide, organic carbon, nitrogen, sulfur, etc., that have been or are now part of the earth’s atmosphere and hydrosphere may be estimated within reasonable limits of uncertainty and these “excess” volatiles afford a basis for testing chemical consequences of the alternative hypotheses. Several writers have suggested that the primitive atmosphere may have been composed largely of CH 4 and NH 3 . However, the equilibrium constants for reactions of these and other gases, combined with the evidence of the “excess” volatiles, indicate that CO 2 and N 2 are much more likely. The stabilities of methane and ammonia depend upon the presence of free hydrogen; and the escape rate of hydrogen from the earth is such that methane probably could have persisted in significant amounts in the early atmosphere no more than 10 6 to 10 8 years. For all but a relatively brief period at the very beginning of earth history, the atmosphere probably contained CO 2 and N 2 rather than CH 4 and NH 3 . When the consequences of a dense atmosphere of CO 2 and N 2 (but with almost no free O 2 or H 2 ) are examined, it is found that several chemical effects (such as the quantity of rocks that would have to be weathered, of sodium dissolved in sea water, and of CaCO 3 deposited on the sea floor very early in early history) are not borne out by the observed geologic record. From this and other lines of evidence it seems extremely improbable that the present atmosphere and hydrosphere are residual from any such dense primitive atmosphere. Instead, it seems likely that the atmosphere and hydrosphere have accumulated gradually during geologic time by the escape of water vapor, CO 2 , CO, N 2 , and other volatiles from intrusive and extrusive rocks that have risen more or less continuously from the deep interior of the earth. The amount of free oxygen in the early atmosphere is a separate problem that cannot be solved until the evidence of the earliest rocks has been appraised more fully. Current hypotheses of the origin of life appear to require a reducing atmosphere, yet it seems likely that oxygen has been accumulating from the photodissociation of water vapor ever since the earth was formed. The oxidation of ferrous iron and sulfides in the earliest sediments may have kept the oxygen content very low, and life may have begun in local reducing environments.

GSA Special Papers↗

USGS2003

Geothermal energy: clean power from the Earth's heat

Societies in the 21st century require enormous amounts of energy to drive the machines of commerce and to sustain the lifestyles that many people have come to expect. Today, most of this energy is derived from oil, natural gas, and coal, supplemented by nuclear power. Local exceptions exist, but oil is by far the most common source of energy worldwide. Oil resources, however, are nonrenewable and concentrated in only a few places around the globe, creating uncertainty in long-term supply for many nations. At the time of the Middle East oil embargo of the 1970s, about a third of the United States oil supply was imported, mostly from that region. An interruption in the flow of this import disrupted nearly every citizen’s daily life, as well as the Nation’s economy. In response, the Federal Government launched substantial programs to accelerate development of means to increasingly harness “alternative energies”—primarily biomass, geothermal, solar, and wind. The new emphasis on simultaneously pursuing development of several sources of energy recognized the timeless wisdom found in the proverb of “not putting all eggs in one basket.” This book helps explain the role that geothermal resources can play in helping promote such diversity and in satisfying our Nation’s vast energy needs as we enter a new millennium. For centuries, people have enjoyed the benefits of geothermal energy available at hot springs, but it is only through technological advances made during the 20th century that we can tap this energy source in the subsurface and use it in a variety of ways, including the generation of electricity. Geothermal resources are simply exploitable concentrations of the Earth’s natural heat (thermal energy). The Earth is a bountiful source of thermal energy, continuously producing heat at depth, primarily by the decay of naturally occurring radioactive isotopes—principally of uranium, thorium, and potassium—that occur in small amounts in all rocks. This heat then rises to and through the Earth’s surface, where it escapes into the atmosphere. The amount of heat that flows annually from the Earth into the atmosphere is enormous—equivalent to ten times the annual energy consumption of the United States and more than that needed to power all nations of the world, if it could be fully harnessed. Even if only 1 percent of the thermal energy contained within the uppermost 10 kilometers of our planet could be tapped, this amount would be 500 times that contained in all oil and gas resources of the world. How might we benefit from this vast amount of thermal energy beneath our feet? Where, by what means, and how much of the Earth’s natural heat can be usefully harnessed? These are especially important questions to contemplate, because global population is expected to soon exceed seven billion and many scientists believe that the world’s fossilfuel resources may be substantially depleted within this century. Faced with such prospects, both the public and private sectors are working toward more fully utilizing the Earth’s abundant thermal energy and other alternative energy resources. A skeptic might question the wisdom of devoting much national effort to geothermal energy development, especially because many experts think that geothermal heat can contribute at most about 10 percent to the Nation’s energy supply using current technologies. However, ongoing advances in exploration and heat-extraction technologies are improving our ability to use the resource and may substantially increase the geothermal contribution to the Nation’s energy supply. In an attempt to help national planners and average citizens alike understand the nature and energy potential of geothermal resources, this book (1) describes the distribution and nature of geothermal energy, (2) reviews the common types of geothermal systems that provide useful energy with current technology, (3) considers potential geothermal resources that might someday be tapped with developing technologies, and (4) summarizes the role of earth-science information in assessing and harnessing geothermal resources wherever they occur worldwide. The predecessor to this book (Tapping the Earth’s Natural Heat, U.S. Geological Survey Circular 1125, published in 1994) summarized the situation in the early 1990s. In an effort to support national energy planners, this new circular incorporates more recent advances in geothermal science and technology.

Circular↗

USGS2024

Toxicity of crude oil-derived polar unresolved complex mixtures to Pacific herring embryos: Insights beyond polycyclic aromatic hydrocarbons

Crude oil toxicity to early life stage fish is commonly attributed to polycyclic aromatic hydrocarbons (PAHs). However, it remains unclear how the polar unresolved complex mixture (UCM), which constitutes the bulk of the water-soluble fraction of crude oil, contributes to crude oil toxicity. Additionally, the role of photomodification-induced toxicity in relation to the polar UCM is not well understood. This study addresses these knowledge gaps by assessing the toxicity of two laboratory generated polar UCMs from Cook Inlet crude oil, representing the readily water-soluble fraction of crude oil and photoproduced hydrocarbon oxidation products (HOPs), to Pacific herring ( Clupea pallasii ) embryos. A small-scale semi-static exposure design was utilized with a range of polar UCM concentrations (0.5–14 mg/L) in nonvolatile dissolved organic carbon (NVDOC) units, quantifying the entire polar UCM. Compositional analyses revealed a photochemical-driven shift toward more complex aromatic compositions, naphthenic acids, and no detectable levels of PAHs (above 0.3 μg/L). Exposure to the dark polar UCM resulted in higher mortality than exposure to the light polar UCM. Both dark and light polar UCMs induced developmental abnormalities commonly attributed to the PAH fraction, including edema, reduced heart rate, body axis defects, and decreased body lengths, with these effects observed at the lowest dose group (0.5 mg/L NVDOC). These responses suggest photomodification-induced toxicity is driven by exposure to increased concentrations of dissolved HOPs rather than photochemical induced compositional changes. Gene expression analyses focusing on xenobiotic metabolism and cardiac morphogenesis yielded results consistent with previous studies examining the biological mechanisms of crude oil toxicity. In summary, these phenotypic and genotypic responses in Pacific herring embryos indicate that the polar UCM is a significant driver of crude oil toxicity. These findings emphasize the importance of considering the polar UCM in future studies, metric reporting, and risk assessments related to crude oil toxicity.

Science of the Total Environment↗

USGS2023

Identifying invertebrate indicators for streamflow duration assessments in forested headwater streams

Streamflow-duration assessment methods (SDAMs) are rapid, indicator-based tools for classifying streamflow duration (e.g., intermittent vs perennial flow) at the reach scale. Indicators are easily assessed stream properties used as surrogates of flow duration, which is too resource intensive to measure directly for many reaches. Invertebrates are commonly used as SDAM indicators because many are not highly mobile, and different species have life stages that require flow for different durations and times of the year. The objectives of this study were to 1) identify invertebrate taxa that can be used as SDAM indicators to distinguish between stream reaches having intermittent and perennial flow, 2) to compare indicator strength across different taxonomic and numeric resolutions, and 3) to assess the relative importance of season and habitat type on the ability of invertebrates to predict streamflow-duration class. We used 2 methods, random forest models and indicator species analysis, to analyze aquatic and terrestrial invertebrate data (presence/absence, density, and biomass) at the family and genus levels from 370 samples collected from both erosional and depositional habitats during both wet and dry seasons. In total, 36 intermittent and 53 perennial reaches were sampled along 31 forested headwater streams in 4 level II ecoregions across the United States. Random forest models for family- and genus-level datasets had stream classification accuracy ranging from 88.9 to 93.2%, with slightly higher accuracy for density than for presence/absence and biomass datasets. Season (wet/dry) tended to be a stronger predictor of streamflow-duration class than habitat (erosional/depositional). Many taxa at the family (58.8%) and genus level (61.6%) were collected from both intermittent and perennial reaches, and most taxa that were exclusive to 1 streamflow-duration class were rarely collected. However, 23 family-level or higher taxa (20 aquatic and 3 terrestrial) and 44 aquatic genera were identified as potential indicators of streamflow-duration class for forested headwater streams. The utility of the potential indicators varied across level II ecoregions in part because of representation of intermittent and perennial reaches in the dataset but also because of variable ecological responses to drying among species. Aquatic invertebrates have been an important field indicator of perennial reaches in existing SDAMs, but our findings highlight how including aquatic and terrestrial invertebrates as indicators of intermittent reaches can further maximize the data collected for streamflow-duration classifications.

Freshwater Science↗

USGS2022

Assessing the distribution and habitat needs of the Least Darter and sympatric species of the Ozark and Arbuckle Mountain ecoregions

Limited information is known about factors driving the distribution of Least Darter in Oklahaoma. The Least Darter occurs in the Ozark Highland and Arbuckle Uplift ecoregions of Oklahoma which represent the southern extent of its range. Least Darter was historically recorded in Oklahoma from groundwater-fed streams. Our study objectives were to determine the distribution of Least Darter and a subset of congeners across the two ecoregions of Oklahoma and assess factors driving patch occupancy of Least Darter at a fine spatial scale. We used temporally replicated snorkel surveys conducted in July through October 2018-2019 to determine occupany by Least Darter. We snorkeled and seined for four species in each reach including two life stages of Smallmouth Bass (subadult and adult). We sampled 153 sites (i.e., riffle-pool complexes) nested within 61 stream reaches (i.e., 200-500-m long) in the Arbuckle Uplift and Ozark Highland ecoregions. Detection probability was similar between ecoregions. Least Darter was detected at more sites when snorkeling compared to seining (24 versus 18). Smallmouth Bass, Redspot Chub and Southern Redbelly Dace were typically 2-3 times more likely to be detected by snorkeling than by seining. We found relationships between occupancy and habitat parameters that were both shared among species but also species-specific. Least Darter occurrence probability in the Ozark Highlands was lower than in the Arbuckle Uplift. Occurrence probability was higher for subadult Smallmouth Bass and Southern Redbelly Dace in 2018 compared to 2019. Occurrence probabilities of both Least Darter and Southern Redbelly Dace were higher in cooler habitat patches. Southern Redbelly Dace was negatively associated with a higher proportion of pool habitat across a reach. Lastly, subadult Smallmouth Bass and Redspot Chub were more likely to occur in deeper pools and in larger streams (i.e., drainage area). We sampled one study reach (~150-m long with shallow riffles or a waterfall on each end) in the Arbuckle Uplift (winter and summer sampling) and Ozark Highland (winter sampling) ecoregions to determine fine-scale habitat selection during the thermally harsh seasons. We developed transects across the reaches to quantify depth, velocity, substrate, cover and water temperature. We found Least Darter used higher water column velocities and shallower water depths with little vegetation during the winter. The average water depth used was similar during summer and winter (~ 20 cm deep). Least Darter used denser vegetation during the summer and tended to avoid coarse substrates in both seasons. If the conservation of Least Darter is a management goal, actions to mitigate increasing stream water temperatures (e.g., protection of springs and riparian corridors) and protecting stream morphologies that facilitate species separations (i.e., allow for a wide range of water depth and velocities) may be beneficial (e.g., fencing cattle from streams, promoting natural bankful flows during spring)

Oklahoma↗

USGS2006

Drainage effects on the transient, near-surface hydrologic response of a steep hillslope to rainfall: Implications for slope stability, Edmonds, Washington, USA

Shallow landslides on steep (>25??) hillsides along Puget Sound have resulted in occasional loss of life and costly damage to property during intense or prolonged rainfall. As part of a larger project to assess landslide hazards in the Seattle area, the U.S. Geological Survey instrumented two coastal bluff sites in 2001 to observe the subsurface hydrologic response to rainfall. The instrumentation at one of these sites, near Edmonds, Washington, consists of two rain gauges, two water-content probes that measure volumetric water content at eight depths between 0.2 and 2.0 m, and two tensiometer nests that measure soil-water suction at six depths ranging from 0.2 to 1.5m. Measurements from these instruments are used to test one- and two-dimensional numerical models of infiltration and groundwater flow. Capillary-rise tests, performed in the laboratory on soil sample from the Edmonds site, are used to define the soil hydraulic properties for the wetting process. The field observations of water content and suction show an apparent effect of porosity variation with depth on the hydraulic response to rainfall. Using a range of physical properties consistent with our laboratory and field measurements, we perform sensitivity analyses to investigate the effects of variation in physical and hydraulic properties of the soil on rainfall infiltration, pore-pressure response, and, hence, slope stability. For a two-layer-system in which the hydraulic conductivity of the upper layer is at least 10 times greater than the conductivity of the lower layer, and the infiltration rate is greater than the conductivity of the lower layer, a perched water table forms above the layer boundary potentially destabilizing the upper layer of soil. Two-dimensional modeling results indicate that the addition of a simple trench drain to the same two-layer slope has differing effects on the hydraulic response depending on the initial pressure head conditions. For slope-parallel flow conditions, pressure head is significantly reduced near the drain; however, for transient, vertical infiltration in a partially saturated soil, conditions consistent with those observed during monitoring at the Edmonds site, the drain decreases the thickness of a perched water table by a small amount.

Natural Hazards and Earth System Sciences↗

USGS2019

Patterns of primary production and ecological drought in Yellowstone

Introduction: Photosynthesis converts sunlight into stored energy in millions of leaves, flowers and seeds that maintain the web of life in Yellowstone. This transformation of energy fixes carbon, supplies organic matter to soils, and can become fuel for wildfire. As the first link of the food chain, new plant biomass is called primary production and provides energy to consumers, including wildlife. While Yellowstone is a mountain environment with deep winter snowpack, the park can get very dry in some years as evidenced by massive wildfires in 1988 and 2016. Droughts like these not only contribute to fire potential, but they affect primary production, the food chain and likely will play an increasingly important role in transforming vegetation structure and composition in the future. Meteorological, agricultural, and hydrological drought have been assessed quantitatively for many years, but key indicators of drought in wildland ecosystems have not been formally defined until recently (Crausbay et al., 2017). One promising new method to do this is by measuring how vegetation responds to negative effects of drought, and positive effects of favorable conditions that offset negative effects of drought. The balance of drought stress and growth has important implications for future vegetation condition as the climate of Yellowstone changes. Monitoring primary production, and predicting future vegetation changes are needed to provide a comprehensive view of park health and anticipate future ecosystem changes (Crabtree et al. 2009, Nemani et al. 2009). Although an important indicator of ecosystem condition, primary production can be time and resource-intensive to monitor in wildland settings using traditional ground-based methods such as clipping and weighing. Fortunately, ground-based methods can be complemented and enhanced by monitoring primary production with satellite imagery. Measurements of solar radiation reflectance in visible and near infra-red wavelengths can indicate primary production at frequent weekly intervals from the Moderate Resolution Imaging Spectrometer (MODIS) on satellites operated by NASA. The Greater Yellowstone Inventory and Monitoring Network (GRYN) uses this information to track changes in primary production across Yellowstone over time. They link these measurements to vegetation types, soils, and climate to understand where and when changes in production have occurred and may occur in the future.

Yellowstone National Park↗

USGS2025

Quality assessment of past spawning mark estimations from a long-term survey in the Connecticut River watershed

The calcified structures of fishes provide insight into their periodic growth rates and can be combined with other biological variables to identify metrics such as size or age at maturity and mortality rates. Collecting this information on growth and life history can help evaluate the success of conservation efforts and inform future management decisions for a species in need. However, before these life history data can be applied to larger stock assessments that direct management decisions, confidence in the validity of the data needs to be reported through metrics of accuracy and precision. For this report, we assessed the bias and precision of paired reader estimations of spawning marks on scales of Blueback herring (Alosa aestivalis) collected in the U.S. Fish & Wildlife (USFWS) Annual Adult River Herring Stock Assessment for the lower Connecticut River basin. The paired reads on scales from a total of 8,698 fish over the ten years of the long term monitoring program were evaluated for the annual presence of systematic bias and precision using a combination of qualitative (i.e., frequency tables) and quantitative (i.e., Evan’s and Hoenig’s Test of Symmetry, and Coefficient of Variation (CV) calculations) analyses. While seven out of the ten survey years had systematic bias detected by the tests of symmetry, only three years (2013, 2016, 2018) had imprecision values >10% CV threshold. Data were further categorized into specific age classes within survey years to increase our resolution on where bias and imprecision was most prevalent. While the ability for accurate bias detection was limited by sufficient sample sizes (>25 fish), average imprecision values increased with age, and median age classes (4 through 6) commonly had bias detected. However, the removal of insufficient age classes prior to calculating average annual CV did not significantly change the initial average. Lastly, 2023, which was the first year to implement a standardized training procedure prior to production estimating, had the highest precision for both the annual average and specific age classes compared to all prior survey years. This standardized training procedure will continue to be used by USFWS for the lower Connecticut River tributaries, and can be modified for other river systems. Overall, this report’s results highlight the importance of assessing precision and encourage the standardization of spawning mark identification quality control and assurance for future studies. With more quality assessments and baseline information on precision and bias, there can be more beneficial discussion on defining thresholds and how to implement spawning history variability into catch curve analyses.

Connecticut, Massachusetts↗

USGS2009

Sand resources, regional geology, and coastal processes of the Chandeleur Islands Coastal System: An evaluation of the Breton National Wildlife Refuge

Breton National Wildlife Refuge, the Chandeleur Islands chain in Louisiana, provides habitat and nesting areas for wildlife and is an initial barrier protecting New Orleans from storms. The U.S. Geological Survey (USGS) in partnership with the University of New Orleans Pontchartrain Institute for Environmental Sciences undertook an intensive study that included (1) an analysis of island change based on historical maps and remotely sensed shoreline and topographic data; (2) a series of lidar surveys at 3- to 4-month intervals after Hurricane Katrina to determine barrier island recovery potential; (3) a discussion of sea level rise and effects on the islands; (4) an analysis of sea floor evolution and sediment dynamics in the refuge over the past 150 years; (5) an assessment of the local sediment transport and sediment resource availability based on the bathymetric and subbottom data; (6) a carefully selected core collection effort to groundtruth the geophysical data and more fully characterize the sediments composing the islands and surrounds; (7) an additional survey of the St. Bernard Shoals to assess their potential as a sand resource; and (8) a modeling study to numerically simulate the potential response of the islands to the low-intensity, intermediate, and extreme events likely to affect the refuge over the next 50 years. Results indicate that the islands have become fragmented and greatly diminished in subaerial extent over time: the southern islands retreating landward as they reorganize into subaerial features, the northern islands remaining in place. Breton Island, because maintenance of the Mississippi River-Gulf Outlet (MRGO) outer bar channel requires dredging, is deprived of sand sufficient to sustain itself. Regional sediment transport trends indicate that large storms are extremely effective in transporting sand and controlling the shoreline development and barrier island geometry. Sand is transported north and south from a divergent zone near Monkey Bayou at the southern end of the Chandeleur Islands. Numerical simulation of waves and sediment transport supports the geophysical results and indicates that vast areas of the lower shoreface are affected and are undergoing erosion during storm events, that there is little or no fair weather mechanism to rework material into the littoral system, and that as a result, there is a net loss of sediment from the system. Lidar surveys revealed that the island chain immediately after Hurricane Katrina lost about 84 percent of its area and about 92 percent of its prestorm volume. Marsh platforms that supported the islands’ sand prior to the storm were reduced in width by more than one-half. Repeated lidar surveys document that in places the shoreline has retreated about 100 m under the relatively low-energy waves since Hurricanes Katrina and Rita; however, this retreat is nonuniform. Recent high-resolution geophysical surveys of the sea floor and subsurface within 5–6 km of the Chandeleur Islands during 2006 and 2007 show that, in addition to the sand that is rebuilding portions of the island chain, a large volume of sand is contained in Hewes Point, in an extensive subtidal spit platform that has formed at the northern end of the Chandeleur Islands. Hewes Point appears to be the depositional terminus of the alongshore transport system. In the southern Chandeleurs, sand is being deposited in a broad tabular deposit near Breton Island called the southern offshore sand sheet. These two depocenters account for approximately 70 percent of the estimated sediment volume located in potential borrow sites. An additional large potential source of sand for restoration lies in the St. Bernard Shoals, which are estimated to contain approximately 200 × 10 6 m 3 of sand. Successful restoration planning for the Breton National Wildlife Refuge should mimic the natural processes of early stages of barrier island evolution including lateral transport to the flanks of the island chain from a centralized sand source that will ultimately enhance the ability of the islands to naturally build backbarrier marsh, dunes, and a continuous sandy shoreline. Barrier island sediment nourishment should be executed with the understanding that gulf shoreline erosion is inevitable but that island area can be maintained and enhanced during retreat (thus significantly prolonging the life of the island chain) with strategic sand placement.

Louisiana↗

USGS2014

Behavior of feral horses in response to culling and GnRH immunocontraception

Wildlife management actions can alter fundamental behaviors of individuals and groups,which may directly impact their life history parameters in unforeseen ways. This is especially true for highly social animals because changes in one individual’s behavior can cascade throughout its social network. When resources to support populations of social animals are limited and populations become locally overabundant, managers are faced with the daunting challenge of decreasing population size without disrupting core behavioral processes. Increasingly, managers are turning to fertility control technologies to supplement culling in efforts to suppress population growth, but little is quantitatively known about how either of these management tools affects behavior. Gonadotropin releasing hormone (GnRH) is a small neuropeptide that performs an obligatory role in mammalian reproduction and has been formulated into the immunocontraceptive GonaCon-BTM. We investigated the influences of this vaccine on behavior of feral horses ( Equus caballus ) at Theodore Roosevelt National Park, North Dakota, USA, for a year preceding and a year following nonlethal culling and GnRH-vaccine treatment. We observed horses during the breeding season and found only minimal differences in time budget behaviors of free-ranging female feral horses treated with GnRH and those treated with saline. The differences observed were consistent with the metabolic demands of pregnancy and lactation. We observed similar social behaviors between treatment groups, reflecting limited reproductive behavior among control females due to high rates of pregnancy and suppressed reproductive behavior among treated females due to GnRH-inhibited ovarian activity. In the treatment year, band stallion age was the only supported factor influencing herding behavior (P < 0.001), harem-tending behavior (P < 0.001), and agonistic behavior (P = 0.02). There was no difference between the mean body condition of control females (4.9 (95% CI = 4.7–5.1)) and treated females(4.8 (95% CI = 4.7–4.9)). Band fidelity among all females increased 25.7% in the year fol-lowing vaccination and culling, despite the social perturbation associated with removal of conspecifics. Herding behavior by stallions decreased 50.7% following treatment and culling (P < 0.001), while harem-tending behavior increased 195.0% (P < 0.001). The amount of available forage influenced harem-tending, reproductive, and agonistic behavior in the year following culling and treatment (P < 0.04). These changes reflected the expected nexus between a species with polygynous social structure and strong group fidelity and the large instantaneous change in population density and demography coincident with culling.Behavioral responses to such perturbation may be synergistic in reducing grazing pressure by decreasing energetically expensive competitive behaviors, but further investigation is needed to explicitly test this hypothesis.

Applied Animal Behaviour Science↗

USGS2020

Population and habitat analyses for greater sage-grouse (Centrocercus urophasianus) in the bi-state distinct population segment—2018 update

Executive Summary The Bi-State Distinct Population Segment (Bi-State DPS) of greater sage-grouse ( Centrocercus urophasianus , hereinafter “sage-grouse”) represents a genetically distinct and geographically isolated population that straddles the border between Nevada and California. The primary threat to these sage-grouse populations is the expansion of single-leaf pinyon ( Pinus monophylla ) and Utah juniper ( Juniperus osteosperma ) into sagebrush ecosystems, which fragments and reduces population connectivity and survival. Other important threats include low water availability during brood-rearing, particularly during drought, and increased predation by common ravens ( Corvus corax ), a generalist predator often associated with anthropogenic resource subsidies. Although the Bi-State DPS occurs at high elevations relative to sage-grouse range-wide, changes in historical wildfire cycles and the conversion of native shrubs to invasive annual grasslands still threaten these populations. The Bi-State DPS has undergone multiple federal status assessments and associated litigation. For example, in October of 2013, the Bi-State DPS was proposed for listing as threatened under the Endangered Species Act of 1973 by the U.S. Fish and Wildlife Service (USFWS), then withdrawn in April 2015. The withdrawal decision was challenged, and in May 2018, a Federal district court ordered the withdrawal decision to be vacated, and USFWS was required to re-open the October 2013 listing evaluation. In response, the U.S. Geological Survey (USGS), with State and Federal collaborators, embarked on a multipronged analysis to provide current and best available science regarding population status of sage-grouse within the Bi-State DPS. Using data from a long-term monitoring program, we carried out four analytical study objectives, and here, we provide preliminary results of these analyses. First, we used integrated population modeling (IPM) to predict annual population abundance and annual finite rate of population change for the Bi-State DPS, as a whole, and for each subpopulation between 1995 and 2018. Because sage-grouse exhibit population cycles (periodic increases and decreases in abundance across approximately 6- to 10-year wavelengths), we estimated trends across three nested temporal scales that represent one (11 years), two (18 years), and three (24 years) complete population cycles. These estimates of relatively long-term averaged population change account for temporal (that is, interannual) variation. Our model predicted population abundance for the Bi-State DPS during 2018 at 3,305 individuals (2,247–4,683), with the majority occupying Bodie Hills and Long Valley. The model also predicted cyclic dynamics in abundance through time with evidence of 24-year population growth and slight trends of decline over the past 18 years. Specifically, across the Bi-State DPS as a whole, we estimated annual average at 0.99, 0.99, and 1.02 over the one, two, and three population cycles, which equated to a 10.5 percent, 16.6 percent decrease, and 60.0 percent increase in abundance over the 11-, 18-, and 24-year cycles. Estimated abundance in 2018 had not reached numbers lower than those predicted during 1995. However, we found spatial variation in population trends across the three cycles. Bodie Hills subpopulation comprised the greatest (1,521) and exhibited average annual greater than 1.0 across all periods resulting in average annual increases of 7 percent. This relatively large subpopulation has grown 5 times larger than what was predicted in 1995 while experiencing cyclical dynamics within that period. Conversely, other smaller subpopulations within the Bi-State DPS exhibited average annual equal to or less than 1.0 resulting in estimated 10-year risks of extirpation ranging from 2.0 to 76.1 percent. In general, evidence of decline among smaller subpopulations was greatest for the most recent period (2008–18) compared to a period that encompassed three full population cycles (24-year). This difference coincides with an intense period of drought that began in 2012. For comparative purposes as part of this first objective, we conducted a similar analysis for populations of sage-grouse within Nevada and California but outside the Bi-State DPS. We developed a region-wide and distance-weighted IPM using lek count from Nevada Department of Wildlife (NDOW) and California Department of Fish and Wildlife (CDFW) databases and with telemetry data collected by USGS across 12 sage-grouse subpopulations. Our models predicted similar patterns in population cycling outside the Bi-State DPS but with much stronger evidence of long-term declines across 24 years. Specifically, median averaged across each year of the 11-, 18-, and 24-year periods resulted in average annual values of 0.94, 0.97, and 0.99, respectively. These values equate to 41.0 percent, 38.5 percent, and 21.3 percent declines over the corresponding periods. Second, we used lek count data in a state-space modeling framework to compare trends in population abundance across different spatial scales (that is, leks versus Bi-State DPS). This hierarchical framework allowed us to disentangle declines associated with climate conditions as opposed to other local level factors that might signal the need for management intervention. Specifically, we identified 7 leks that were both declining and recently decoupled from larger spatial scale trends, typically governed by climatic conditions (referred to as soft or hard signals). The goal of this analysis was to provide an early warning system that might have implications for conservation actions at local scales. Third, we developed phenological (spring, summer–fall, and winter) and reproductive life stage (nesting, early brood-rearing, and late-brood rearing) based resource selection functions using various environmental covariates. We report rankings of variable importance for each season and life stage, developed maps of habitat selection indices (HSI), binned categories representing low, moderate, and high classes of quality (where any category greater than or equal to low indicated selected habitat) for each phenological season and life stage, and produced composite maps by selected phenological and reproductive stage to estimate annual habitat. Fourth, we used for each lek within the Bi-State DPS to carry out a spatial analysis that quantified substantial changes in the distribution of occupied habitat across long- (24-year) and short- (11-year) term periods. Owing to differences among available datasets, the long-term analysis primarily reflected spatial shifts among subpopulations comprising the majority of the Bi-State DPS (that is, Bodie Hills and Long Valley) while the short-term analysis also quantified changes among subpopulations along the periphery. Over long and short-term periods, the overall distribution of occupied habitat (as measured by 99 percent utilization distributions intersecting any quantified habitat) was reduced by 20,573 ha and 55,492 ha, respectively. Occupied core areas (as measured by 50 percent utilization distributions intersecting any quantified habitat) over long-term periods were solely located in Bodie Hills and Long Valley. Although nearly all subpopulations experienced contractions in occupied overall and core distribution, Bodie Hills experienced spatial expansion that occurred with concomitant spatial contraction at Long Valley over both periods. Subpopulations at the northern (Pine Nuts), central (Sagehen) and southern (White-Mountains) extents of the Bi-State DPS also experienced spatial contraction over the short-term period. These findings, coupled with those of population trends, indicate long-term patterns in redistribution of sage-grouse from Long Valley and peripheral subpopulations to Bodie Hills. That is, sage-grouse subpopulations at the periphery are declining while the largest population at the core is increasing, which could have meaningful impacts on overall metapopulation persistence. We provide evidence for loss of occupied habitat (reduced distribution) given local extirpation of subpopulations. Fifth, we calculated percentages of selected phenological, life stage, and annual habitat that each subpopulation contributed to the Bi-State DPS. We then intersected these maps with a composite estimate of occupied habitat from the fourth objective and calculated percentages of selected habitat likely occupied by sage-grouse that each subpopulation contributed to the Bi-State DPS. These values provide evidence for loss of occupied habitat and subsequent reductions in spatial distribution given reductions in abundance and, in some cases, extirpation of leks within subpopulations. Lastly, we carried out an initial in-depth analysis of selection for irrigated pastures and wet meadows during the brood-rearing stage for the Long Valley subpopulation. We chose this subpopulation because it represents a population core, representing 26.5 percent of total sage-grouse within the Bi-State DPS, and has exhibited long-term declines in abundance and distribution. This subpopulation is highly sensitive to precipitation and other factors that influence water availability. Models predicted higher use of the interior portions of irrigated pastures and wet meadows during late brood-rearing period, which represented a potentially risky use of habitat that was exacerbated during periods of low moisture (for example, drought, reduced water delivery, or both). Sage-grouse typically used edges of riparian areas and pastures, largely because the interior of these mesic areas consisted of considerably less overhead concealment cover (for example, shrubs) that likely resulted in a higher risk of mortality. We found that a lack of water delivery to pastures in the form of overwinter precipitation or diversion ditches increased the movements of sage-grouse to the interior of pastures. Although further investigation of water delivery impacts on chick survival are warrented, our initial findings regarding resource selection may explain recent declines in population growth at Long Valley.

California, Nevada↗

USGS2017

Variation and plasticity and their interaction with urbanization in Guadalupe Bass populations on and off the Edwards Plateau

The Colorado River Basin in Texas has experienced major alterations to its hydrologic regime due to changing land and water use patterns. These anthropogenic influences on hydrologic variability have had major implications for riparian and aquatic ecosystems and the species dependent upon them. However, impacts are often assessed at a limited temporal and spatial scale, tending to focus on relatively short and discrete periods or portions of a river basin. It is not clear how basin-wide alterations occurring over decades affect species. Guadalupe Bass Micropterus treculii are endemic to central Texas and are typically associated with shallow runs and riffles in small streams. However, Guadalupe Bass are found throughout the Colorado River Basin, including the mainstem portion of the lower river downstream of the city of Austin where they support a popular fishery. Because Guadalupe Bass exist across a wide range of stream orders within the basin, it is unclear whether populations respond similarly to anthropogenic disturbances or to conservation and restoration activities. Therefore, our objectives were to: Assess the effects of urbanization and hydrology on the population structure and dynamics of Guadalupe Bass. Evaluate the effects of environmental gradients on ecomorphological variation in Guadalupe Bass populations across multiple spatial scales. Describe the life history, habitat use, and behavior of the Guadalupe Bass population in the lower Colorado River and compare it to populations in more “typical” habitats. Results contribute to an understanding of the response of Guadalupe Bass to anthropogenic disturbances, including increased urbanization in central Texas and further assist in the conservation of the species. The ability of the population to not only persist, but flourish downstream of a heavily populated urban area presented a unique opportunity to investigate a native species response to anthropogenic disturbance. This research revealed differences in Guadalupe Bass habitat associations and movements, contrasts in age and growth, and morphological variation across a gradient of disturbance throughout the Colorado River Basin. Results of this work provide information on the potential effects of human population growth and increased water withdrawals on Guadalupe Bass populations. Additionally, this work adds to an understanding of the unique Guadalupe Bass population found in the lower Colorado River and how it differs from upstream tributary populations. Gathering additional population-level information facilitates conservation actions critical to preserving preferred habitat and promoting growth rates for Guadalupe Bass in streams of different sizes and flow conditions while highlighting interpopulation differences that may warrant consideration for stocking programs and other management strategies. Key findings of this study were: The similarity in response of growth rates to streamflow throughout the Colorado Basin suggests phenotypic plasticity in this trait rather than population-specific adaptations. Reductions in streamflows in the Colorado River Basin, whether due to increased frequency of drought or increased anthropogenic water withdrawal, will likely result in lower Guadalupe Bass growth rates with the potential to impact the structure of populations. Growth and recruitment showed a positive correlation with increased baseflows and mean monthly flows; however, continued assessment is necessary to determine a true relationship. We documented morphological divergence among Guadalupe Bass populations in response to spatial and temporal environmental variation. These ecomorphological differences among populations provide insight into the ability of Guadalupe Bass to respond to the differing in-stream habitat and flow conditions between small ‘typical’ tributary systems and the mainstem Colorado River. Morphological variation may be a population-level adaptation that potentially needs to be taken into consideration when choosing broodstock to maximize stocking success within a system. Understanding the morphological differences between Guadalupe Bass populations in response to local conditions could improve the success of restoration and supplemental stocking programs, especially in the ever-changing landscape of central Texas. We established a baseline for understanding the morphological response of Guadalupe Bass to increased population growth and the threats posed by increased water withdrawals and impervious surface. The mainstem population of Guadalupe Bass was generally more mobile, and more responsive to changes in streamflow, than tributary populations. The observed differences could influence the response of Guadalupe Bass populations to conservation and management actions, such as habitat restoration efforts. Continued monitoring of recruitment and angler exploitation may be beneficial to identify any changes that could negatively impact the population. Conservation initiatives solely focused on physical instream or riparian habitat are unlikely to be as beneficial to Guadalupe Bass as those focused on restoring or maintaining adequate streamflow

Cooperator Science Series↗

USGS2025

Calibration of the Stream Salmonid Simulator (S3) model to estimate annual survival, movement, and food consumption by juvenile Chinook salmon (Oncorhynchus tshawytscha) in the restoration reach of the Trinity River, California, 2006–18

Executive Summary The Trinity River is managed in two sections: (1) from the upper 64-kilometer “restoration reach” downstream from Lewiston Dam to the confluence with the North Fork Trinity River, and (2) the 120-kilometer lower Trinity River downstream from the restoration reach. The Stream Salmonid Simulator (S3) has been previously applied to these reaches and the Klamath River. To estimate fish growth, past S3 calibration efforts in the Trinity and Klamath Rivers used maximum likelihood methods that considered only the abundance of juvenile Chinook salmon ( Oncorhynchus tshawytscha ) passing a fish trap to estimate survival and movement parameters, but not fish consumption. Previous calibrations did not estimate the average proportion of maximum consumption ( C y ) when estimating survival ( S y ) and movement ( M 0 y ) parameters across years ( y ) of data, but because no other information was available in the literature a fixed value of C y =0.66 was assumed. Therefore, the goal of this report is to present an alternative approach that calibrates the S3 model to multivariate data (that is, abundance and size), enabling the estimation of the average proportion of maximum consumption, in conjunction with survival and movement parameters for a particular migration year. We fit the S3 model to individual years of weekly trap abundance estimates and mean fish sizes (fork length) at the Pear Tree Gulch (hereafter referred to as Pear Tree) fish trap representing the restoration reach. We used the Earth Mover’s Distance (EMD) as the objective value to be minimized in parameter optimization. This approach estimated survival, movement, and consumption parameters for each migration year. Because we had information on the abundance of natural and hatchery produced juvenile salmon at the fish traps, we estimated survival and movement for natural and hatchery fish. S3 is a deterministic life-stage-structured population model that tracks daily growth, movement, and survival of juvenile Chinook Salmon. A key theme of the model is that river discharge affects habitat availability and capacity, which in turn drives density-dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily timeseries of discharge, water temperature, and useable habitat area or carrying capacity. In turn, the physical characteristics of each habitat unit and the number of fish occupying each unit drive survival and growth within each habitat unit and movement of fish among habitat units. The physical template of the restoration reach of the Trinity River was classified into 356 meso-habitat units comprised of runs, riffles, and pools. For each habitat unit, we developed a timeseries of daily discharge, water temperature, amount of available spawning habitat, and fry and parr carrying capacity. Capacity time series were constructed using state-of-the-art models of spatially explicit hydrodynamics and quantitative fish habitat relationships developed for the Trinity River. These variables were then used to drive population dynamics such as egg maturation and survival, and in turn, juvenile movement, growth, and survival. We estimated movement, survival, and consumption parameters by calibrating the model to 12 years of weekly juvenile abundance estimates and fish sizes at the Pear Tree fish trap near the downstream end of the restoration reach. We estimated parameters for 12 years that included a wide range of female spawner abundances (1,414–11,494) and water year types (critically dry–extremely wet). We contrast the estimated parameters to the corresponding number of female spawners and the total annual volume of water discharged for the Trinity River (Trinity River Restoration Program; https://www.trrp.net/restoration/flows/summary/ ). The calibration consisted of replicating historical conditions as closely as possible (for example, discharge; temperature; spawner abundance, spawning location and timing, and hatchery releases), and then running the model to predict weekly abundance passing the trap location from each brood year of adults and subsequent migration year of their juvenile progeny. Because density-dependent movement was favored in past evaluations, we estimated S3 parameters based on density-independent survival and density-dependent movement. Likewise, each year’s estimated survival parameter for natural ( S N y ) and hatchery ( S H y ) fish may be interpreted as the mean daily survival probability from emergence or hatchery release to the Pear Tree fish trap. Under density dependence, the estimated movement parameter for natural ( M 0N y ) and hatchery ( M 0H y ) fish represents the intercept of the Beverton-Holt model; the probability of remaining in a habitat at near-zero abundance. We estimated C y by using EMD and incorporating abundance and fish size into model calibration. Average daily proportions of maximum consumption, , across the years were generally high (=0.640; standard deviation (SD) SD=0.176), suggesting that fish were feeding at about two-thirds of expected maximum consumption rates. This average proportion of maximum consumption,is very similar to what has been assumed (=0.66) in previous Trinity and Klamath River S3 calibration and simulation efforts. In 2017, we estimated the lowest C y , suggesting lower average consumption for juvenile salmon in high-discharge water years. When this high discharge year was excluded, there was no apparent trend in C y with annual water volume. Estimates of survival showed little trend over the range in spawner abundances, but a trend towards higher natural and hatchery fish survival with higher annual volumes of water was apparent. Over the 12 years, the average survival of hatchery fish was =0.888 (SD=0.079) and the average survival natural fish was=0.969 (SD=0.01). With respect to fish movement, we estimated higher M 0N y and M 0H y with higher annual volumes of water in the Trinity River. Higher M N0 y or M H0 y suggest greater probability of remaining in a habitat at low fish densities, with potential for density-dependent processes in movement to occur. The highest M 0N y = 0.676 was estimated during brood year 2012, and the overall average for natural fish was =0.276 (SD=0.188) and for hatchery fish was=0.467 (SD=0.235). Under the Beverton-Holt model, as M 0N y or M 0H y approach zero, there is less capacity for change in fish movement as fish density increases. The S3 model was initialized with only the spatiotemporal distribution of spawners, so it performed well at capturing the essential outmigration features that are ultimately governed by rates of growth, movement, and mortality. We used a new optimization method that could accommodate multivariate data on abundance and fish size collected at the Pear Tree fish trap, enabling the calibration of S3 to estimate five parameters for 12 separate years of data. Incorporating weekly fish size data for each year in our parameter optimization process made the estimation of C y possible and represents a step forward in the fitting of the S3 model to fish trap data for the purposes of parameter calibration and the estimation of growth parameters with respect to annual conditions. We identified lack of fit and adding important effects into the S3 model may improve the S3 estimation and simulation of water scenarios. The Trinity River Restoration Program (TRRP) Science Advisory Board recommended that the TRRP focus on developing core elements of a decision support system (DSS; Buffington and others, 2014). Toward that end, the habitat and S3 models described in this report are both core elements of the DSS. The structure of S3 makes it a particularly useful fish production model for the DSS because population dynamics are sensitive to (1) water temperature, (2) daily discharge management, and (3) habitat quality and quantity. Each of these variables are key management parameters under consideration in the TRRP. As such, the S3 model may provide valuable insights into the potentially variable effects of different management decisions on the Trinity River.

California↗