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USGS2020

Multi‐species occupancy models: Review, roadmap, and recommendations

Recent technological and methodological advances have revolutionized wildlife monitoring. Although most biodiversity monitoring initiatives are geared towards focal species of conservation concern, researchers are increasingly studying entire communities, specifically the spatiotemporal drivers of community size and structure and interactions among species. This has resulted in the emergence of multi‐species occupancy models (MSOMs) as a promising and efficient approach for the study of community ecology. Given the potential of MSOMs for conservation and management action, it is critical to know whether study design and model assumptions are consistent with inference objectives. This is especially true for studies that are designed for a focal species but can give insights about a community. Here, we review the recent literature on MSOMs, identify areas of improvement in the multi‐species study workflow, and provide a reference model for best practices for focal species and community monitoring study design. We reviewed 92 studies published between 2009 and early 2018, spanning 27 countries and a variety of taxa. There is a consistent under‐reporting of details that are central to determining the adequacy of designs for generating data that can be used to make inferences about community‐level patterns of occupancy, including the spatial and temporal extent, types of detectors used, covariates considered, and choice of field methods and statistical tools. This reporting bias could consequently result in skewed estimates, affecting conservation actions and management plans. On the other hand, comprehensive reporting is likely to help researchers working on MSOMs assess the robustness of inferences, in addition to making strides in terms of reproducibility and reusability of data. We use our literature review to inform a roadmap with best practices for MSOM studies, from simulations to design considerations and reporting, for the collection of new data as well as those involving existing datasets.

Ecography↗
USGS2017

Deep-sea coral research and technology program: Alaska deep-sea coral and sponge initiative final report

Deep-sea coral and sponge ecosystems are widespread throughout most of Alaska’s marine waters. In some places, such as the central and western Aleutian Islands, deep-sea coral and sponge resources can be extremely diverse and may rank among the most abundant deep-sea coral and sponge communities in the world. Many different species of fishes and invertebrates are associated with deep-sea coral and sponge communities in Alaska. Because of their biology, these benthic invertebrates are potentially impacted by climate change and ocean acidification. Deepsea coral and sponge ecosystems are also vulnerable to the effects of commercial fishing activities. Because of the size and scope of Alaska’s continental shelf and slope, the vast majority of the area has not been visually surveyed for deep-sea corals and sponges. NOAA’s Deep Sea Coral Research and Technology Program (DSCRTP) sponsored a field research program in the Alaska region between 2012–2015, referred to hereafter as the Alaska Initiative. The priorities for Alaska were derived from ongoing data needs and objectives identified by the DSCRTP, the North Pacific Fishery Management Council (NPFMC), and Essential Fish Habitat-Environmental Impact Statement (EFH-EIS) process. This report presents the results of 15 projects conducted using DSCRTP funds from 2012-2015. Three of the projects conducted as part of the Alaska deep-sea coral and sponge initiative included dedicated at-sea cruises and fieldwork spread across multiple years. These projects were the eastern Gulf of Alaska Primnoa pacifica study, the Aleutian Islands mapping study, and the Gulf of Alaska fish productivity study. In all, there were nine separate research cruises carried out with a total of 109 at-sea days conducting research. The remaining projects either used data and samples collected by the three major fieldwork projects or were piggy-backed onto existing research programs at the Alaska Fisheries Science Center (AFSC).

NOAA Technical Memorandum↗
USGS2019

Scientific integrity issues in environmental toxicology and chemistry: Improving research transparency, reproducibility, and credibility

High‐profile reports of detrimental scientific practices leading to retractions in the scientific literature contribute to lack of trust in scientific experts. Although the bulk of these have been in the literature of other disciplines, environmental toxicology and chemistry are not free from problems. While we believe that egregious misconduct such as fraud, fabrication of data, or plagiarism is rare, scientific integrity is much broader than the absence of misconduct. We are more concerned with more commonly encountered and nuanced issues such as poor reliability and bias. We review a range of topics including conflicts of interests, competing interests, some particularly challenging situations, reproducibility, bias, and other attributes of ecotoxicological studies that enhance or detract from scientific credibility. Our vision of scientific integrity encourages a self‐correcting culture that promotes scientific rigor, relevant reproducible research, transparency in competing interests, methods and results, and education.

Integrated Environmental Assessment and Management↗
USGS2007

Seagrass status and trends in the northern Gulf of Mexico: 1940-2002

Over the past century, seagrass habitats from the bays of Texas to the gulf shores of Florida have decreased. Seagrass beds, which are highly dependent on water quality and clarity for survival, are home to a multitude of aquatic plants and animals and a source of economic activity through commercial and recreational fishing and ecotourism. The U.S. Environmental Protection Agency’s Gulf of Mexico Program (GMP) and its partners have made a commitment to restore, enhance, and protect this important ecosystem. As seagrass habitats decrease, the need for information on the causes and effects of seagrass loss, current mapping information, and education on the importance of seagrassess becomes greater. This report is the initial effort of the GMP’s research and restoration plan for seagrasses. The purpose of this report is to provide scientists, managers, and citizens with valuable baseline information on the status and trends of seagrasses in coastal waters of the Gulf of Mexico. Within the northern Gulf of Mexico region, 14 individual estuarine systems where seagrasses occur, as well as statewide summaries for Texas, Louisiana, Mississippi, Alabama, and Florida, are examined in this study. Each estuarine system is detailed in vignettes that address current and historical extent and quality of seagrasses, seagrass mapping and monitoring, causes of status change, restoration and enhancement activities, background information for the entire study area as well as the subareas for study, and the methodology employed to analyze and document the historical trends and current status of seagrasses. The systems, moving from west to east, include the Laguna Madre, Texas Coastal Bend region, and Galveston Bay in Texas; the Chandeleur Islands in Louisiana; the Mississippi Sound; and Perdido Bay, Pensacola/Escambia Bay, Choctawhatchee Bay, St. Andrew Bay, Florida’s Big Bend region, Tampa Bay/St. Joseph Sound, Sarasota Bay, Greater Charlotte Harbor, and Florida Bay in Florida. (Mobile Bay is dealt with only in the statewide summary for Alabama.)

Gulf Of Mexico↗
USGS2014

Progress report on an international decade for hydrology

As reported in the Transactions of March 1961 (p. 96), the ad hoc Panel on Hydrology convened to report on ways of stimulating research in scientific hydrology , recommended a program of international cooperation in hydrology —more specifically a plan for an ‘ International Decade for Hydrology ,’ as drawn for the Panel by R. L. Nace. The proposal for an international program in scientific hydrology was submitted to the Council of the International Association of Scientific Hydrology (IASH), meeting at Athens during October 1961, and was explained to them by Nace. The proposal was endorsed in principle by the country representatives who were present, and further endorsement is being requested of national committees not represented at Athens. The report of the ad hoc Panel on International Cooperation in Hydrology will be published in a forthcoming Bulletin of the International Association of Scientific Hydrology .

Article↗
USGS2020

Black abalone surveys at Naval Base Ventura County, San Nicolas Island, California: 2019, annual report

The U.S. Geological Survey Western Ecological Research Center’s Santa Cruz Field Station, Santa Cruz, California, has been funded by the U.S. Navy to continue monitoring a suite of intertidal black abalone sites at San Nicolas Island, California. The nine rocky intertidal sites were established in 1980 by Glenn VanBlaricom (then of the U.S. Fish and Wildlife Service) to study the potential impact of translocated sea otters on the intertidal black abalone population at the island. The sites were monitored from 1981 to 1997, usually annually or semi-annually. Monitoring resumed in 2001, and regular annual monitoring cycles have been conducted at the sites since then. The study sites became particularly important, from a management perspective, after a virulent disease decimated black abalone populations throughout southern California beginning in the mid-1980s. The disease, withering syndrome, was first observed on San Nicolas Island in 1992 and during the next few years reduced the population there by approximately 99 percent. The species was subsequently listed as endangered under the Endangered Species Act in 2009. The subject of this report is the 2019 monitoring cycle of the sites and how the current status fits into the long-term data at San Nicolas Island. Since 2001, the monitored population has increased nearly tenfold to approximately 8.7 percent of the pre-disease level. This increase has resulted from generally higher levels of recruitment than seen in the first two decades of monitoring, punctuated by a few high recruitment events. Most of the population growth has been at two of the nine sites (sites 7 and 8). This pattern continued in 2019 with increasing numbers at sites 7 and 8 and the highest number of abalone counted and measured island-wide since 1996. However, counts declined at six of the sites during the last year and the increases in counts at sites 7 and 8 barely offset these losses. Recruitment rates have fallen since a peak in 2017 but 2019 continued to show some additional recruitment. The distance between adjacent black abalone, a metric relevant to potential reproduction, has decreased substantially since it was first consistently measured in 2005. Although sand burial can have devastating localized consequences to black abalone, the sand cover data we collected was not sufficient to suggest an obvious temporal or site-based pattern to sedimentation, and there is no indication that this was a factor in any of the declines recorded in 2019. Continued monitoring of these sites can provide island biologists with species trends to aid in adaptive management of the resource.

California↗
USGS2011

An evaluation of traditional and emerging remote sensing technologies for the detection of fugitive contamination at selected Superfund hazardous waste sites

This report represents a remote sensing research effort conducted by the U.S. Geological Survey in cooperation with the U.S. Environmental Protection Agency (EPA) for the EPA Office of Inspector General. The objective of this investigation was to explore the efficacy of remote sensing as a technology for postclosure monitoring of hazardous waste sites as defined under the Comprehensive Environmental Response Compensation and Liability Act of 1980 (Public Law 96-510, 42 U.S.C. §9601 et seq.), also known as \"Superfund.\" Five delisted Superfund sites in Maryland and Virginia were imaged with a hyperspectral sensor and visited for collection of soil, water, and spectral samples and inspection of general site conditions. This report evaluates traditional and hyperspectral imagery and field spectroscopic measurement techniques in the characterization and analysis of fugitive (anthropogenic, uncontrolled) contamination at previously remediated hazardous waste disposal sites.

Open-File Report↗
USGS2017

The Snowmastodon Project

Studies of terrestrial biotic and environmental dynamics of the last interglacial period, Marine Oxygen Isotope Stage (MIS) 5, provide insight into the effects of long-term climate change on Pleistocene ecosystems. In North America, however, there are relatively few fossil sites that definitively date to MIS 5. Even fewer contain multiple ecosystem components (vertebrates, invertebrates, plants) that have been studied in detail, and none are located at high elevation. Thus, our view of North American ecosystems during MIS 5 is, at best, an incomplete composite view, and alpine ecosystems are entirely undocumented. The Ziegler Reservoir fossil site allows us to begin filling these gaps. Discovered on October 14, 2010 by a construction crew while enlarging a small reservoir near Snowmass Village, Colorado (USA), the site is situated high in the Rocky Mountains at an elevation of ~ 2705 m. Initial excavations exposed a series of stacked fossil ecosystems, including abundant faunal and floral components. Subsequent work revealed an exceptionally diverse biota composed of nearly 6000 large bones of late Pleistocene megafauna, including mastodons, mammoths, ground sloths, horses, camels, deer, bison, black bear, coyotes, and big horn sheep. This collection is complemented by more than 200 bones from at least 40 species of small animals including otters, muskrats, minks, rabbits, beavers, frogs, lizards, snakes, fish, and birds, and more than 20,000 salamander bones. Geomorphic evidence and multiple dating techniques show that the small, ridge-top basin containing the site was formed by a lateral lobe of a valley glacier that filled, and ultimately overtopped, the Snowmass Creek drainage during the Bull Lake glaciation (MIS 6). When the glacier receded, a lake that occupied the basin began to fill slowly with what is hypothesized to be eolian sediment and occasional input from slope failures of the impounding moraine. As sedimentation continued, the lake transformed first into a shallow pond, then a marsh, and later an alpine meadow. In all, the Ziegler Reservoir sedimentary record spans the time encompassed by the end of MIS 6, all of MIS 5 and MIS 4, and the earliest part of MIS 3. MIS 5e, which is considered to be the peak warmth of the last interglacial period, is especially well represented. Preservation of organic material at the Ziegler Reservoir fossil site is exceptional. Even after more than 100,000 years of burial, sedge and willow leaves were still green, mollusks and gastropods showed color, beetle parts remained iridescent, fossil conifer cones were intact, and an entire beach of 20-meter-long driftwood logs was found intact. The exquisite preservation allowed for detailed analysis of pollen, plant macrofossils, conifer cones, and fossil wood, as well as insects, chironomids, mollusks, ostracodes, and other invertebrates — all in addition to the spectacular faunal remains. This special volume of Quaternary Research represents a comprehensive scientific report of “The Snowmastodon Project,” as the investigations at the Ziegler Reservoir fossil site came to be known. Summarizing the work of scientists from more than 20 institutions, the volume details the environments in which the animals lived, provides insight into how they died, and forms the foundation of our understanding of alpine ecosystem dynamics during the last interglacial period in the Rocky Mountains.

Quaternary Research↗
USGS1992

Resistance of young wolf pups to inclement weather

Based on information about young dog ( Canis familiaris ) pups, it was thought that wolf ( Canis lupus ) pups 0-2 weeks of age do not thermoregulate well. This problem, plus the relative immobility of young pups, was thought to explain why pups generally remain inside dens until about 3 weeks of age, and pups younger than 3-weeks-old were thought to be highly vulnerable to loss from exposure. this report details more information about the tolerance of young wolf pups to exposure.

Research Information Bulletin↗
USGS2013

Wind River watershed restoration. Annual report. November 2011 through October 2012

Introduction This report summarizes work by U.S. Geological Survey’s Columbia River Research Laboratory (USGS-CRRL) in the Wind River subbasin, from November 2011 through October 2012. Funding was provided by Bonneville Power Administration (BPA) under contract 55275. The primary focus of USGS activities during this time was tagging of parr steelhead Oncorhynchus mykiss with Passive Integrated Transponder (PIT) tags, and establishing a network of instream PIT tag interrogation systems (PTIS). The PIT-tagged parr steelhead will provide movement and life history data through recapture events and detections at instream PTIS systems, will contribute to estimates of adult steelhead returning to the Wind River, and aid in the evaluation of the removal of Hemlock Dam on Trout Creek steelhead populations. The Wind River Watershed project (BPA Project Number 1998-019-00) is a collaborative effort to restore wild steelhead in the Wind River, WA. The four partner agencies are the U.S. Forest Service (USFS), Washington Department of Fish and Wildlife (WDFW), USGS-CRRL, and Underwood Conservation District (UCD). This partnership was established in the early 1990s with support from BPA, and has continued to conduct extensive habitat, research, monitoring, and coordination activities across the subbasin. The project works at multiple levels to identify and characterize key limiting habitat factors in the Wind River; restore degraded habitats and watershed processes; document fish populations, life histories, and interactions; investigate efficacy of restoration actions; and to share information across agency and non-agency boundaries. Long-term research in the Wind River has focused on assessments of steelhead/rainbow trout populations, relationships with introduced populations of spring Chinook salmon O. tshawytscha and brook trout Salvelinus fontinalis , and effects of habitat variables and habitat restoration on fish productivity. During the period covered by this report, we PIT tagged steelhead parr in headwater sections of the subbasin (Figure 1), maintained a PTIS in Trout Creek, installed a PTIS in the Wind River, and installed smaller scale PTISs in Trapper Creek, Paradise Creek, and the Wind River upstream of Paradise Creek (Figure 2). Additionally we maintained thermologgers to collect water temperature data near the PIT tagging sites. A statement of work (SOW) was submitted to BPA in October 2011 that outlined work to be performed by USGS-CRRL. The SOW was organized by Work Element (WE), with each describing a research task. This report summarizes the progress completed under each WE.

Washington↗
USGS2020

Appendix C: Interim report on subtask focused on resampling historic Kennedy/ITD plots for RP-284

In October 2019, an Idaho Transportation Department (ITD) Cooperative Transportation Research Program award was made to Boise State University in partnership with the U.S. Geological Survey to investigate the use of weed-suppressive bacteria (Pseudomonas fluorescens strain ACK55) with preemergent herbicides (imazapic and indaziflam) to reduce exotic annual grasses (cheatgrass, medusahead) on ITD right-of-ways. The work includes a subtask in which ITD right-of-ways treated with ACK55 by Dr. Ann Kennedy 4-5 years previously (2017 report; ITD-RP-258) were resampled in summer 2020, focusing only on ACK55 and not the herbicides (which are tested separately and will be reported on in the future). The 2020 sampling protocol was similar but more intensive than the ITD-RP-258. There were no differences in annual grasses on areas sprayed with ACK55 and nearby untreated areas.

Idaho↗
USGS2025

Responding to ecological transformation in Capitol Reef National Park, Utah—Employee perspectives from pilot interviews from the Cross-Park Resist-Assist-Direct Project

Executive Summary Climate change is causing a range of changes that can affect the natural, cultural, and built resources of the Nation’s protected areas and affect opportunities to visit and recreate in these spaces. Changes in temperature and precipitation patterns also affect species and habitats, leading to ecological transformation. This report describes findings from pilot research conducted in Capitol Reef National Park, Utah (hereinafter referred to as “Capitol Reef” or “the Park”) as part of a larger interagency study of how National Park Service (NPS) staff are considering management of transforming ecosystems. Semi-structured interviews were used to assess how Capitol Reef employees (n=9) understand the challenge of ecological transformation, including their perceptions of how climate change is affecting the Park’s natural and cultural resources, the multiple timeframes over which employees respond to climate change impacts, and their awareness and understanding of ecological transformation and the Resist-Accept-Direct (RAD) framework, which was developed to address ecological transformation, that is, ecosystems changing in response to changes in climate conditions (Schuurman and others, 2020, 2022). The interviews also solicited employee perceptions about constraints and enabling factors that allow Capitol Reef to effectively respond to ecological transformation. The report uses a conceptual framework that has been used by the National Park Service Climate Change Response Program (Clifford and others, 2022) to structure the reporting of the data about constraints and enabling factors, with sections describing the role of factors internal to an individual employee (culture, worldviews, and understanding of an ecological system) and contextual factors external to an individual (institutional context, social feasibility and scientific uncertainty as influenced by available scientific information). Participating Capitol Reef staff perceived the most pressing climate impacts in the Park as increasing air temperatures, aridity, and flash floods, which are impacting natural and cultural resources, public safety, and infrastructure. Staff mostly agreed on what the future landscape (approximately 50 years into the future) may look like at Capitol Reef in terms of changes in vegetation and future temperature and precipitation conditions. However, staff had more divergent views or were uncertain about how specific species will adapt to future conditions (for example, how endemic plants might shift their ranges) and are grappling with which management strategies to take at which times. Staff also had differing opinions about how much data is needed to prompt action. Interviewees agreed that leadership in the Park had made climate change a priority and created a climate-attuned culture among staff. Participating employees described the park culture at Capitol Reef as collaborative, with frequent communication and work across divisions, which, as an example, shapes responses to flash floods and other events (for example, working across divisions on search and rescue, or repairing fencing that is washed out by storms). This collaborative, climate-attuned culture may help Capitol Reef in future problem-solving as it grapples with how to respond to climate change and ecological transformation in the Park.

Utah↗
USGS2010

Factors influencing reporting and harvest probabilities in North American geese

We assessed variation in reporting probabilities of standard bands among species, populations, harvest locations, and size classes of North American geese to enable estimation of unbiased harvest probabilities. We included reward (US10,20,30,50, or100) and control (0) banded geese from 16 recognized goose populations of 4 species: Canada (Branta canadensis), cackling (B. hutchinsii), Ross's (Chen rossii), and snow geese (C. caerulescens). We incorporated spatially explicit direct recoveries and live recaptures into a multinomial model to estimate reporting, harvest, and band-retention probabilities. We compared various models for estimating harvest probabilities at country (United States vs. Canada), flyway (5 administrative regions), and harvest area (i.e., flyways divided into northern and southern sections) scales. Mean reporting probability of standard bands was 0.73 (95 CI 0.690.77). Point estimates of reporting probabilities for goose populations or spatial units varied from 0.52 to 0.93, but confidence intervals for individual estimates overlapped and model selection indicated that models with species, population, or spatial effects were less parsimonious than those without these effects. Our estimates were similar to recently reported estimates for mallards (Anas platyrhynchos). We provide current harvest probability estimates for these populations using our direct measures of reporting probability, improving the accuracy of previous estimates obtained from recovery probabilities alone. Goose managers and researchers throughout North America can use our reporting probabilities to correct recovery probabilities estimated from standard banding operations for deriving spatially explicit harvest probabilities.

Journal of Wildlife Management↗
USGS1976

Geological Survey research 1976

This U.S. Geological Survey activities report includes a summary of recent (1976 fiscal year) scientific and economic results accompanied by a list of geologic and hydrologic investigations in progress and a report on the status of topographic mapping. The summary of results includes: (1) Mineral resources, Water resources, (2) Engineering geology and hydrology, (3) Regional geology, (4) Principles and processes, (5) Laboratory and field methods, (6) Topographic surveys and mapping, (7) Management of resources on public lands, (8) Land information and analysis, and (9) Investigations in other countries. Also included are lists of cooperating agencies and Geological Survey offices.

Professional Paper↗
USGS1978

Geological Survey research 1978

This U.S. Geological Survey activities report includes a summary of 1978 fiscal year scientific and economic results accompanied by a list of geologic and hydrologic investigations in progress and a report on the status of topographic mapping. The summary of results includes: (1) Mineral and water resources, (2) Engineering geology and hydrology, (3) Regional geology, (4) Principles and processes, (5) Laboratory and field methods, (6) Topographic surveys and mapping, (7) Management of resources on public lands, (8) Land information and analysis, and (9) Investigations in other countries. Also included are lists of cooperating agencies and Geological Survey offices. (Woodard-USGS)

Professional Paper↗
USGS1982

Geological Survey research 1981

This U.S. Geological Survey activities report includes a summary of 1981 fiscal year scientific and economic results accompanied by a list of geologic, hydrologic, and cartographic investigations in progress. The summary of results includes: (1) Mineral, (2) Water resources, (3) Engineering geology and hydrology, (4) Regional geology, (5) Principles and processes, (6) Laboratory and field methods, (7) Topographic surveys and mapping, (8) Management of resources on public lands, (9) Land information and analysis, and (10) Investigations in other countries. Also included are lists of investigations in progress.

Professional Paper↗
USGS2024

Snake River Fall Chinook Salmon research and monitoring

In Chapter 1, we report on development and application of an integrated population model (IPM) for the natural-origin fall Chinook salmon population upstream of Lower Granite Dam. This year’s efforts represent the third update to the model. Initial efforts focused on generating juvenile and adult abundance estimates, with estimates of uncertainty, for informing the life-cycle model and estimating the effects of covariates on key demographic parameters. The goals of this year’s report are to 1) describe the modifications and advances made since the previous report, 2) to annually update and report the abundance estimates and other quantities used in the model, 3) to provide annual estimates of population parameters estimated by the IPM, and 4) to outline the next year’s tasks for advancing and/or applying the model. Since our last report on the life-cycle model, we have made a number of changes including: 1) incorporating jack abundance and age-structure data into the observation model, 2) changing smolt-to-adult survival (SAR) for subyearling and yearling to partial SARs that represent the joint probability surviving and entering the ocean at a given juvenile age, 3) combining age categories for rarely observed ages, 4) using scale data from unmarked fish to estimate age structure, and 5) generating composite life-cycle demographic parameters (cumulative capacity and productivity) from stage-specific parameters. We also generated juvenile abundance estimates, extended the model to include three additional brood years (1992– 2021), and ran the model to forecast returns to Lower Granite in 2022. For posterior medians of life stage-specific parameters, we estimated a mean productivity of 438 natural-origin juvenile recruits per female spawner, a capacity of 1.36 million juveniles, and a mean smolt-to-adult survival (SAR) of 1.2%. We detected strong density-dependent regulation, with juvenile recruits per spawner declining to about 50 juvenile recruits per female spawner at high spawner abundance. Across the entire life cycle, these stage-specific parameters resulted in a median cumulative intrinsic productivity of 1.93 adult female recruits per female spawner and a median equilibrium abundance of 2,851 female spawners (7,842 total spawners). Annual juvenile productivity varied from about 250–1,000 juveniles per spawner but displayed no temporal trends or patterns. For the three most recent brood years added to the model, recruits per spawner were higher than average but well within the range of uncertainty observed over the entire time series. In contrast to juvenile recruitment variability, SAR varied considerably among years and exhibited two periods of high survival (1996–2001 and 2007–2012) when SAR ranged from 2% to 6% and cumulative productivity ranged from 2 to 8 recruits per spawner. Partial SARs revealed that yearling outmigrants contributed substantially to the high SARs in the first high-survival period, but the second period was dominated by subyearlings. Yearlings contributed >30% to SAR in most years prior to 2007, and <30% since 2007. Our two-stage IPM provides a wealth of information about population dynamics affecting two key life-stage transitions (spawner to juvenile, and juvenile to spawner) centered on passage at Lower Granite Dam. By summarizing these stage-specific demographic parameters across the entire life cycle, this information will be useful for informing the recovery status of this threatened population. Whereas previous versions introduced hydrosystem and ocean covariates into the model, this phase of model development focused on solidifying the underlying model structure by introducing the concept of partial SARs and developing composite productivity and capacity as a function of underlying stage-specific parameters. Given this advancement, our next steps are to re-incorporate covariates into the model, specifically to understand how different factors affect partial SARs of subyearling and yearlings. Longer term model developments include:1) incorporating hatchery fish to explicitly estimate their survival as an alternative method for estimating natural-origin age composition, 2) expanding the model’s structure to include the three major spawning aggregates, 3) more explicitly modeling hydrosystem effects including transportation, and 4) using the model to assess retrospective and prospective management actions. In 2022, the U.S. Geological Survey (USGS) focused adult salmon survey efforts in the Snake River on deepwater redd searches and fish collection for parentage-based tagging (PBT) analyses. We use used a boat-mounted underwater video camera to count 99 deepwater redds at 16 of the 29 sites surveyed. Redd depths averaged 4.4 m. In conjunction with the Idaho Power Company, we collected genetic samples from 318 live fall Chinook salmon (Oncorhynchus tshawytscha) and 19 carcasses at 40 unique geographic locations that spanned 91 river kilometers. Eighty fish were collected at three sites (High Range [rkm 332.3], Dug Bar [rkm 315.4], and Three Creek [rkm 384.0]), which accounted for 23% of all collected fish in 2022. Most (333 fish) post-spawned salmon were collected from early to mid-November just after the peak of spawning. A summary of 2021 PBT results produced by the Idaho Power Company can be found in Appendix A.2. Beach seining and PIT tagging of subyearling fall Chinook salmon was conducted in Snake and Salmon rivers to obtain information on population metrics and growth as well as to provide data for ongoing life-cycle modeling. In the Snake River, we collected 7,496 subyearlings, tagged 4,139, and recaptured 502 (12.1%). Using 8-mm tags in 45–49-mm fish allowed us to represent an additional 25% of the juvenile population through PIT tagging beyond just using standard 9- and 12-mm tags. In the Salmon River, we captured 206 natural subyearlings with the majority (52%) of fish being captured at two sites: rkm 20 and 26. We tagged 145 subyearlings and recaptured 9 fish. Many of the subyearlings we tagged in the Snake River were detected passing Lower Granite Dam, but only 4 fish tagged in the Salmon River were detected. In total we detected 484 (11.3%) tagged fish at Lower Granite Dam, and detection rates varied by tag size and passage route. More subyearlings were detected passing via the removable spill weir (RSW) earlier in the season while more fish were detected passing through the juvenile fish bypass system (JBS) earlier in the season while more fish were detected passing via the removable spill weir (RSW) later in the season. In general, fish tagged with 12-mm PIT tags had higher detection rates than fish tagged with smaller tags. Survival to Lower Granite Dam was low and ranged from 0.22 to 0.36. Season-wide, growth of subyearlings was higher in the lower reach than in the upper reach of the Snake River.

Idaho, Oregon, Washington↗