Results for “Endangered Species Research” — Page 13

USGS2019

Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River fall Chinook Salmon ESU

The portion of the Snake River fall Chinook Salmon Oncorhynchus tshawytscha ESU that spawns upstream of Lower Granite Dam transitioned from low to high abundance during 1992–2018 in association with U.S. Endangered Species Act recovery efforts and other federally mandated actions. This annual report focuses on (1) numeric and habitat use responses by natural- and hatchery-origin spawners, (2) phenotypic and numeric responses by natural-origin juveniles, and (3) use of a small unmanned aerial system (sUAS) to search for fall Chinook salmon redds and carcasses. Spawners have located and used most of the available spawning habitat and that habitat is gradually approaching redd capacity. Timing of spawning and fry emergence has been relatively stable, but effects of density dependence are evident in juvenile life stages. Apparent abundance of juvenile fall Chinook salmon has increased and we noted the following responses: parr dispersal from riverine rearing habitat into Lower Granite Reservoir has become earlier; growth rate (g/d) and dispersal size of parr declined; and passage timing of smolts from the two Snake River reaches has become earlier and downstream movement rate faster. These findings coupled with stock-recruitment analyses presented in this report provide evidence for density-dependence in the Snake River reaches and in Lower Granite Reservoir that was influenced by the expansion of the recovery program. The long-term goal is to use this information in a comprehensive modeling effort to conduct action-effectiveness and uncertainty research and to inform Fish Population, Hydrosystem, Harvest, Hatchery, and Predation and Invasive Species Management Research, Monitoring, and Evaluation (RM&E). In 2018, the U.S. Geological Survey (USGS) searched 10 shallow-water spawning sites and 25 deepwater spawning sites in conjunction with the Idaho Power Company (IPC). A total of 103 redds were counted at shallow-water sites and 61 redds were counted at deepwater sites. We recovered 17 carcasses and 13 live fish, which were spawned out, and collected biological information and tissue samples that are currently being analyzed for parentage to determine the percentage of hatchery-origin spawners on the spawning grounds.

Idaho, Oregon, Washington↗

USGS2023

Historical fire regimes and contemporary fire effects within sagebrush habitats of Gunnison Sage-grouse

The historical role of fire in sagebrush ( Artemisia tridentata ) landscapes remains poorly understood, yet is important to inform management and conservation of obligate species such as the threatened Gunnison Sage-grouse (GUSG; Centrocercus minimus ). We reconstructed fire histories from tree-ring fire scars at sagebrush–forest ecotones (10 sites, 111 trees) to better understand the role of fire in sagebrush landscapes of the Upper Gunnison Basin (UGB), Colorado, and how fire may have changed following Euro-American settlement. We assessed likely influences of historical fire by surveying plant composition and structure at 100 sagebrush sites with and without recent (2001–2020) fires. Tree-ring fire scars revealed a history of repeated low-severity fire at sagebrush–forest ecotones until 1892, followed by over a century without fire. Between 1684 and 1892, the mean fire interval (MFI) among sites averaged 49.6 years (ranging from 18.2 to 119 years). Fire over this period occurred synchronously at two or more sites on average every 23.6 years, potentially indicative of spread between sites. Most (70%) of the historical fires burned in the early growing season, consistent with times of strong wind. Recent burns exhibited reductions in sagebrush cover (5% vs. 25% in unburned sites) and concomitant increases in herbaceous cover (55% vs. 40%). These differences declined over time but persisted for at least two decades. Burned sites were dominated by native perennial grasses, forbs, and resprouting shrub species. Historically, such openings may have served as seasonal GUSG habitat. Our results indicate that parts of the UGB sagebrush landscapes were characterized historically by frequent fire and dynamic vegetation mosaics that included open, grassy patches. These findings support the use of prescribed fire to restore and maintain this ecological process and vegetation heterogeneity. However, the contemporary context for fire has changed and now includes substantially reduced, Endangered Species Act (ESA)-listed GUSG populations, increased risk of non-native plant invasion, and climate warming. These circumstances highlight new risks, information needs, and opportunities for key knowledge co-production via management–research partnerships.

Colorado↗

USGS2011

Climate change links fate of glaciers and an endemic alpine invertebrate

Climate warming in the mid- to high-latitudes and high-elevation mountainous regions is occurring more rapidly than anywhere else on Earth, causing extensive loss of glaciers and snowpack. However, little is known about the effects of climate change on alpine stream biota, especially invertebrates. Here, we show a strong linkage between regional climate change and the fundamental niche of a rare aquatic invertebrate—themeltwater stonefly Lednia tumana—endemic toWaterton- Glacier International Peace Park, Canada and USA. L. tumana has been petitioned for listing under the U.S. Endangered Species Act due to climate-change-induced glacier loss, yet little is known on specifically how climate impacts may threaten this rare species and many other enigmatic alpine aquatic species worldwide. During 14 years of research, we documented that L. tumana inhabits a narrow distribution, restricted to short sections (&sim;500 m) of cold, alpine streams directly below glaciers, permanent snowfields, and springs. Our simulation models suggest that climate change threatens the potential future distribution of these sensitive habitats and persistence of L. tumana through the loss of glaciers and snowfields. Mountaintop aquatic invertebrates are ideal early warning indicators of climate warming in mountain ecosystems. Research on alpine invertebrates is urgently needed to avoid extinctions and ecosystem change.

Waterton-Glacier International Peace Park↗

USGS2018

Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River fall Chinook salmon ESU

The portion of the Snake River fall Chinook Salmon Oncorhynchus tshawytscha ESU that spawns upstream of Lower Granite Dam transitioned from low to high abundance during 1992–2017 in association with U.S. Endangered Species Act recovery efforts and other federally mandated actions. This annual report focuses on (1) numeric and habitat use responses by natural- and hatchery-origin spawners, (2) phenotypic and numeric responses by natural-origin juveniles, (3) USGS use of a small unmanned aerial system (sUAS) to search for fall Chinook salmon redds and carcasses, and (4) the detection of 8-mm PIT tags at Lower Granite Dam. Spawners have located and used most of the available spawning habitat and that habitat is gradually approaching redd capacity. Timing of spawning and fry emergence has been relatively stable; whereas the timing of parr dispersal from riverine rearing habitat into Lower Granite Reservoir has become earlier as apparent abundance of juveniles has increased. Growth rate (g/d) and dispersal size of parr also declined as apparent abundance of juveniles increased. Passage timing of smolts from the two Snake River reaches has become earlier and downstream movement rate faster as estimated abundance of fall Chinook Salmon smolts in Lower Granite Reservoir has increased. These findings coupled with stock-recruitment analyses presented in this report provide evidence for density-dependence in the Snake River reaches and in Lower Granite Reservoir that was influenced by the expansion of the recovery program. The long-term goal is to use the information covered here in a comprehensive modeling effort to conduct action effectiveness and uncertainty research and to inform Fish Population, Hydrosystem, Harvest, Hatchery, and Predation and Invasive Species Management RM&E. In 2017, the USGS searched 15 shallow water spawning sites in conjunction with the Idaho Power Company (IPC). Redd counts agreed with those of IPC for a little more than half the sites suggesting that we need more training in redd counting. We recovered 67 carcasses, and tissue samples are currently being analyzed for parentage to ultimately determine the percentage of hatchery-origin spawners on the spawning grounds. Redd fading was examined to determine the frequency at which aerial surveys should be conducted. Most redds surveyed through time were visible for at least 4 weeks after the redd was initially constructed. Redd fading was variable amongst sites and depended on location. In 2017, we conducted a second year of evaluating detection efficiency of 8-mm PIT tags in the Lower Granite Dam juvenile fish collection system. Groups of 75–78 fish were tagged with 8-mm Biomark, 8-mm Oregon RFID, 9-mm Biomark, and 12-mm Biomark PIT tags and released into the bypass upstream of the upwell. From 97.4 to 100% (depending on tag type) of tagged fish were detected on at least one antenna in the Lower Granite Dam bypass system. Mean detection efficiency within the predominant passage route (i.e., diversion river exit) exceeded 0.98 for all tag types in both years. These results suggest that fish tagged in the field with 8-mm PIT tags should be detected at rates similar to larger tags at main-stem hydroelectric dams.

Snake River Basin↗

USGS2008

Conservation genetics and species recovery

Recent advances in molecular genetics have proven to be extremely useful in efforts to conserve imperiled species. Genetics data are used to identify appropriate units of management (e.g., populations, metapopulations), effective sizes of breeding populations, population mixing rates, and other variables. These data help managers make decisions about which populations to preserve, whether to move individuals from one site to another, how to breed species most effectively in captivity, and even, in some cases, what taxonomic classification is most appropriate. Many U.S. Geological Survey (USGS) Science Centers and Cooperative Fish and Wildlife Research Units have developed capabilities in genetics research. The two case studies that follow illustrate how USGS geneticists are assisting managers in recovering species on the brink.

Endangered Species Bulletin↗

USGS2013

The silent threat of low genetic diversity

Across the Caribbean, protected coastal waters have served as primary feeding and breeding grounds for the endangered Antillean manatee. Unfortunately, these same coastal waters are also a popular “habitat” for humans. In the past, the overlap between human and manatee habitat allowed for manatee hunting and threatened the survival of these gentle marine mammals. Today, however, threats are much more inadvertent and are often related to coastal development, degraded habitats and boat strikes. In the state of Florida, decades of research on the species’ biological needs have helped conservationists address threats to its survival. For example, low wake zones and boater education have protected manatees from boat strikes, and many of their critical winter refuges are now protected. The Florida population has grown steadily, thus increasing from approximately 1,200 in 1991 to more than 5,000 in 2010. It is conceivable that in Florida manatees may one day be reclassified as “threatened” rather than “endangered.” Yet, in other parts of the Caribbean, threats still loom. This includes small, isolated manatee populations found on islands that can be more susceptible to extinction and lack of genetic diversity. To ensure the species’ long-term viability, scientists have turned their sights to the overall population dynamics of manatees throughout the Caribbean. Molecular genetics has provided new insights into long-term threats the species faces. Fortunately, the emerging field of conservation genetics provides managers with tools and strategies for protecting the species’ long-term viability.

livebetter Magazine↗

USGS2007

Sturgeon research update: Confirmed pallid sturgeon spawning in the Missouri River in 2007

The U.S. Geological Survey (USGS) in partnership with the Nebraska Game and Parks Commission (NGPC) and the U.S. Army Corps of Engineers have confirmed spawning of two female pallid sturgeon in the upstream reaches of the lower Missouri River in May 2007. Combined with supporting research in reproductive physiology, identification of spawning habitat, and early life history this result provides new understanding of environmental factors (for example, photoperiod, temperature, water quality, and flow regime) that might affect reproduction of this endangered species. The purpose of this fact sheet is to provide stakeholders, scientists, and managers with some of the preliminary results from the 2007 field assessment of sturgeon reproduction in the lower Missouri River.

Fact Sheet↗

USGS2002

Loss of sagebrush ecosystems and declining bird populations in the Intermountain West: Priority research issues and information needs

Sagebrush lands in the Intermountain West are declining rapidly in quality and extent. Consequently, populations of many bird species dependent on these ecosystems also are declining. The greater sage-grouse has been petitioned for listing as a threatened and endangered species, and other species of sagebrush-obligate birds have special conservation status in most states. We identified the primary issues and information needs during a multi-agency workshop, conducted in response to concerns by management agencies related to declining bird population trends in sagebrush habitats. Priority needs were to (1) obtain a better understanding of bird response to habitat and landscape features, (2) develop monitoring designs to sample habitats and bird populations, (3) determine the effects of land use on sagebrush habitats and dependent bird species, and (4) identify linkages between breeding and wintering ranges. This agenda will identify causes and mechanisms of population declines in birds dependent on sagebrush ecosystems and will lead to better management of the ecosystems upon which they depend.

Fact Sheet↗

USGS2021

Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River Fall Chinook salmon ESU

The portion of the Snake River fall Chinook salmon Oncorhynchus tshawytscha evolutionary significant unit (ESU) that spawns upstream of Lower Granite Dam transitioned from low to high abundance during 1992–2020 in response to U.S. Endangered Species Act recovery efforts and other federally mandated actions. This annual report focuses on changes in population abundance and habitat use by natural- and hatchery-origin spawners. Typically, we also report on population attributes of natural-origin juveniles, but data on juveniles were not collected in 2020 due to Covid-19. Spawners have located and used most of the available spawning habitat and that habitat is gradually approaching the point that no more redds can be supported. Timing of spawning and fry emergence have been relatively stable, but effects of density dependence are evident in juvenile life stages. Apparent abundance of juvenile fall Chinook salmon has increased and we noted the following changes: parr dispersal from riverine rearing habitat into Lower Granite Reservoir has become earlier; growth rate (g/d) and dispersal size of parr has declined; and passage timing of smolts from the two Snake River reaches has become earlier and downstream movement rate has increased. These findings coupled with stock-recruitment analyses presented in this report provide evidence for density-dependence in the Snake River reaches and in Lower Granite Reservoir resulting from the expansion of the recovery program. The long-term goal is to use this information in a comprehensive modeling effort to conduct action-effectiveness and uncertainty research and to inform Fish Population, Hydrosystem, Harvest, Hatchery, and Predation and Invasive Species Management Research, Monitoring, and Evaluation (RM&E) programs. In 2020, the U.S. Geological Survey (USGS) focused survey efforts in the Snake River on deepwater redd searches and fish collection for parentage-based tagging (PBT) analyses. We use a boat-mounted underwater video camera to count 170 deepwater redds at 19 of the 28 sites surveyed. Redd depths averaged 4.2 m. We collected genetic samples from 297 live fall Chinook salmon and 16 carcasses at 44 unique geographic locations that spanned 89 river kilometers. Seventy-two fish were recovered at Eureka Bar (rkm 307.1) and Corral Creek (rkm 349.7), which accounted for 23% of all collected fish in 2020. Most (238 fish) post-spawned salmon were collected from early to mid-November just after peak spawning. A summary of 2019 PBT results can be found in Appendix A.1. In 2020, we PIT tagged subyearling fall Chinook salmon in the Clearwater River to obtain population and growth data. In the Clearwater River, we tagged 2,192 subyearlings and recaptured 79 (3.6%) fish in the river and 187 fish (78 tagged by the U.S. Geological Survey, 109 tagged by the Nez Perce Tribe) at Lower Granite Dam during October which provided information for growth estimation. Within riverine habitats, growth in both length and mass were higher for fish tagged with 8-mm tags than with 9- and 12-mm tags. Estimated growth in length and mass of subyearlings was generally lower in Lower Granite Reservoir than in riverine habitats. Information on prey resources and juvenile fall Chinook salmon prey consumption was collected to better understand the growth opportunity of late-migrating fish in Lower Granite Reservoir. Zooplankton and surface drifting prey were collected from three reservoir locations from July through October during 2019 and 2020. Fall Chinook salmon diet data were collected from angled fish using gastric lavage. Cladocera and Copepoda were the most abundant zooplankton taxa collected while Diptera was the most common invertebrate taxon collected in surface drift samples. Totals of 49 and 94 juvenile fall Chinook salmon were captured in 2019 and 2020, respectively, and most fish were caught in the lower reach of the reservoir in October of each year. Juvenile fall Chinook salmon consumed mainly dipterans in July and October 2019 and mainly Daphnia during August–October in 2020. Fish showed selection mainly for dipterans in 2019 but strong selection for Daphnia during October 2020. Stomach fullness values were relatively low (<1.1%) during both years. Results show that prey resources are adequate in Lower Granite Reservoir to support positive fish growth during late summer and early autumn.

Idaho, Oregon, Washington↗

USGS1980

Whooping crane recovery plan

This plan has been prepared under the authority of the Endangered Species Act of 1973 and subsequent amendments. The Plan is designed to provide decision makers with an orderly set of events which, if carried out to a successful completion, will result in changing the status of the species from the endangered to the threatened level. It must be recognized that this Plan has been prepared 40 years after attempts to preserve the species began. As such, it covers events that have taken place, that are taking place, and that need to take place. The Plan, therefore, not only compiles in one place all whooping crane management and research efforts which are underway, but also proposes additional efforts needed for the recovery of the whooping crane. The Plan also establishes funding evels, time schedules, and priorities for each management and research effort. The Plan is organized into three parts. the first part includes an account of the whooping crane's history, biology, present status, and the factors believed to have resulted in its endangered status. Also included in this part is a synopsis of research and management activities that have taken place through 1978. The second part is a step-down pan wherein all existing and needed research and management efforts are organized into an orderly set of events. The prime objective is to move the whooping crane to non-endangered status. Minimum requirements for the attainment of this objective are the increase of the historical Wood Buffalo-Aransas population to at least 40 nesting pairs and the establishment of at least two additional, separate, and self-sustaining populations consisting of at least 20 nesting pairs each. the third part identifies the responsibility, time schedule, and cost for each element of the step-down plan.

Book↗

USGS2012

Ecological effects of climate change on salt marsh wildlife: a case study from a highly urbanized estuary

Coastal areas are high-risk zones subject to the impacts of global climate change, with significant increases in the frequencies of extreme weather and storm events, and sea-level rise forecast by 2100. These physical processes are expected to alter estuaries, resulting in loss of intertidal wetlands and their component wildlife species. In particular, impacts to salt marshes and their wildlife will vary both temporally and spatially and may be irreversible and severe. Synergistic effects caused by combining stressors with anthropogenic land-use patterns could create areas of significant biodiversity loss and extinction, especially in urbanized estuaries that are already heavily degraded. In this paper, we discuss current ideas, challenges, and concerns regarding the maintenance of salt marshes and their resident wildlife in light of future climate conditions. We suggest that many salt marsh habitats are already impaired and are located where upslope transgression is restricted, resulting in reduction and loss of these habitats in the future. In addition, we conclude that increased inundation frequency and water depth will have negative impacts on the demography of small or isolated wildlife meta-populations as well as their community interactions. We illustrate our points with a case study on the Pacific Coast of North America at San Pablo Bay National Wildlife Refuge in California, an area that supports endangered wildlife species reliant on salt marshes for all aspects of their life histories.

Journal of Coastal Research↗

USGS2025

Summary of selenium in the lower Gunnison River Basin, Colorado—Information and data gaps

The Cretaceous Mancos Shale is a geologic source of selenium in the lower Gunnison River Basin. Natural weathering processes and human activity mobilize selenium from the Mancos Shale and derived materials, and surface water, groundwater, and sediment all affect the transport of selenium from source areas to receiving streams and biota. Selenium accumulates through the aquatic food chain, and its toxic effects can result in invertebrate mortality and mortality, decreased reproduction, and deformities to fish and birds. The Bureau of Reclamation, in cooperation with the State of Colorado and Gunnison River Basin water users, is implementing a Selenium Management Program to reduce selenium concentrations in the lower Gunnison River Basin of Colorado. Goals of the Selenium Management Program are to (1) achieve compliance with the State of Colorado chronic aquatic-life standard for dissolved selenium (4.6 micrograms per liter) in the Gunnison River near Grand Junction, Colorado; (2) sufficiently improve water-quality conditions to assist in the recovery of endangered species in the Gunnison and Colorado Rivers by reducing selenium concentrations; and (3) support continued water uses in the basin. Many previous studies have contributed to the understanding of selenium in the environment; however, monitoring and research data gaps exist in the lower Gunnison River Basin. The purpose of this report is to summarize information regarding selenium in the lower Gunnison River Basin and describe strategies for scientific research and monitoring to potentially improve understanding of selenium sources; processes affecting the mobilization, transport, and fate of selenium; and the effects of selenium-mitigation projects in the lower Gunnison River Basin. Monitoring and research data gaps discussed in this report include geologic mapping and geochemical source characterization, long-term and ongoing monitoring of the surface-water and groundwater networks, developing and refining statistical models, characterizing selenium on suspended sediment, modeling selenium in the food web, evaluating best management practices, and more.

Colorado↗

USGS2019

Using UAS capabilities to help identify hummock-hollow formation and fragmentation in critical marsh habitat ( Spartina patens ) for mottled ducks in southeast Texas

For many years, marshes in the coastal areas from Texas to Louisiana have served as critical habitat for Anas fulvigula , the mottled duck. Mottled ducks are a priority species in the Texas/Louisiana Gulf Coast area and have been affected by critical habitat reduction. In recent years, mottled duck habitats have been threatened by natural and anthropogenic changes including urbanization, flooding, saltwater intrusion, and hydrologic alterations. These impacts are affecting the quality of habitat that is essential for the mottled duck nesting, feeding, and livelihood. Cumulative and synergistic effects of contamination and invasive species encroachment have also caused mottled duck habitat to be considered as some of the most critically endangered habitats in the United States. To help understand the environmental conditions that characterize the coastal landscape, U.S. Geological Survey researchers used an unmanned aerial system (UAS) to acquire high-resolution imagery to document current land and water spatial configuration and wetland health at McFaddin National Wildlife Refuge, Texas.

Texas↗

USGS2015

Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River fall Chinook salmon ESU, 1/1/2014 - 12/31/2014

The portion of the Snake River fall Chinook Salmon Oncorhynchus tshawytscha ESU that spawns upstream of Lower Granite Dam transitioned from low to high abundance during 1992–2014 in association with U.S. Endangered Species Act recovery efforts and other Federally mandated actions. This annual report focuses on (1) numeric and habitat use responses by natural- and hatchery-origin spawners, (2) phenotypic and numeric responses by natural-origin juveniles, and (3) predator responses in the Snake River upper and lower reaches as abundance of adult and juvenile fall Chinook Salmon increased. Spawners have located and used most of the available spawning habitat and that habitat is gradually approaching redd capacity. Timing of spawning and fry emergence has been relatively stable; whereas the timing of parr dispersal from riverine rearing habitat into Lower Granite Reservoir has become earlier as apparent abundance of juveniles has increased. Growth rate (g/d) and dispersal size of parr also declined as apparent abundance of juveniles increased. Passage timing of smolts from the two Snake River reaches has become earlier and downstream movement rate faster as estimated abundance of fall Chinook Salmon smolts in Lower Granite Reservoir has increased. In 2014, consumption of subyearlings by Smallmouth Bass was highest in the upper reach which had the highest abundance of Bass. With a few exceptions, predation tended to decrease seasonally from April through early July. A release of hatchery fish in mid-May significantly increased subyearling consumption by the following day. We estimated that over 600,000 subyearling fall Chinook Salmon were lost to Smallmouth Bass predation along the free-flowing Snake River in 2014. More information on predation is presented in Appendix A.3 (page 51). These findings coupled with stock-recruitment analyses presented in this report provide evidence for density-dependence in the Snake River reaches and in Lower Granite Reservoir that was influenced by the expansion of the recovery program. The long-term goal is to use the information covered here in a comprehensive modeling effort to conduct action effectiveness and uncertainty research and to inform fish population, hydrosystem, harvest, hatchery, and predation and invasive species management RM&E.

Oregon, Washington↗

USGS2020

Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River Fall Chinook Salmon ESU: January 2019 - December 2019

The portion of the Snake River fall Chinook salmon Oncorhynchus tshawytscha evolutionary significant unit (ESU) that spawns upstream of Lower Granite Dam transitioned from low to high abundance during 19922019 in association with U.S. Endangered Species Act recovery efforts and other federally mandated actions. This annual report focuses on (1) numeric and habitat use responses by natural- and hatchery-origin spawners, (2) phenotypic and numeric responses by natural-origin juveniles, and (3) use of a small unmanned aerial system (sUAS) to search for fall Chinook salmon redds and carcasses. Spawners have located and used most of the available spawning habitat and that habitat is gradually approaching redd capacity. Timing of spawning and fry emergence have been relatively stable, but effects of density dependence are evident in juvenile life stages. Apparent abundance of juvenile fall Chinook salmon has increased and we noted the following responses: parr dispersal from riverine rearing habitat into Lower Granite Reservoir has become earlier; growth rate (g/d) and dispersal size of parr declined; and passage timing of smolts from the two Snake River reaches has become earlier and downstream movement rate faster. These findings coupled with stock-recruitment analyses presented in this report provide evidence for density-dependence in the Snake River reaches and in Lower Granite Reservoir that was influenced by the expansion of the recovery program. The long-term goal is to use this information in a comprehensive modeling effort to conduct action-effectiveness and uncertainty research and to inform Fish Population, Hydrosystem, Harvest, Hatchery, and Predation and Invasive Species Management Research, Monitoring, and Evaluation (RM&E) progams. In 2019, the U.S. Geological Survey (USGS) shifted survey efforts in the Snake River toward deepwater redd searches and fish collection for parentage-based tagging (PBT) analyses because all unmanned aerial system (UAS) activities were suspended by the Department of the Interior two weeks into the spawning season. We counted 81 deepwater redds at 17 of the 29 sites surveyed. Redd depths averaged 3.6 m. We collected a total of 123 live fall Chinook salmon from 16 unique geographic locations that spanned 55 river kilometers. Forty-six fish were recovered at Eureka Bar (rkm 307.1) and Kirby Creek (rkm 352.0), which accounted for 37% of all collected fish in 2019. Most (73 fish) post-spawned salmon were collected from early to mid-November just after peak spawning. A summary of 2019 PBT results can be found in Appendix A.1. In 2019, we PIT tagged subyearling fall Chinook salmon in both the Snake and Clearwater rivers. In the Snake River, we tagged 410 fish with 8-mm tags, 666 fish with 9-mm tags, and 1,082 fish 12-mm tags. During seining, our recapture rate of previously tagged fish was slightly higher in the lower reach at 11.4% than in the upper reach at 10.6%. In an effort to represent more of the population through tagging, we tagged fish as small as 45 mm with 8-mm tags at one site in the upper reach. This allowed us to increase the number of fish tagged in that reach by 17.7%. An additional 10.6% of collected fish could have been tagged in the lower reach had we used 8-mm tags in that reach. In the Clearwater River, we tagged 2,451 subyearlings and recaptured 260 (10.6%) fish in the river and 66 fish (48 tagged by USGS, 18 tagged by the Nez Perce Tribe) at Lower Granite Dam during October to provide information for growth estimation. Within riverine habitats, growth in both length and mass were higher for fish tagged with 8-mm tags than with 9- and 12-mm tags. Estimated growth in length and mass of subyearlings was higher in Lower Granite Reservoir than in riverine habitats. We adapted existing statistical models used to estimate abundance of steelhead and spring/summer Chinook salmon for fall Chinook salmon passing Lower Granite Dam. Run reconstruction efforts to date at Lower Granite Dam for Snake River fall Chinook salmon have provided estimates of the number of returning adults but with no measure of uncertainty about the estimates. The objective of this study was to estimate the abundance, with uncertainty, of marked (coded-wire tagged CWT or adipose clipped) and unmarked fall Chinook salmon past Lower Granite Dam for return years 20032018. Estimating uncertainty is important for informing the state-space life cycle model (Chapter 5), which incorporates both observation and process uncertainty into parameter estimates. The coefficient of variation (CV) for log- abundance was 1.0% or less in all years, whereas the CV for abundance averaged 4.2% and ranged from 1.4% to 10.4% among years. Over the past five years, we have been developing a two-stage state-space life-cycle model for naturally produced fall Chinook salmon in the Snake River basin. Initial efforts focused on generating juvenile and adult abundance estimates, with estimates of uncertainty, for informing the life-cycle model. In this report we 1) describe the statistical life-cycle model and improvements made since our last report to the Independent Scientific Advisory Board (ISAB), 2) estimate the effects of covariates on key demographic parameters, and 3) use the fitted life- cycle model to simulate population trajectories under hydrosystem actions proposed for the NOAA 2020 Biological Opinion (hereafter, the Proposed Action). Major recent advancements to the model include revised juvenile abundance estimates, the ability to estimate smolt-to-adult return rates (SAR) separately for subyearling and yearling juvenile fall Chinook salmon, and improvements in the observation model for estimating age, sex, and outmigration structure in adult returns. We examined the effect of numerous environmental, hydrosystem, and ocean covariates on key demographic parameters but only a few covariates were significant. For the adult-to-juvenile transition, we found the maximum weekly river flows during the winter egg- incubation period had a significant negative effect on the juvenile outmigrant abundance from that brood year. For subyearling outmigrants, percent spill during the summer had a significant positive effect on SAR and the mean winter PDO (Pacific Decadal Oscillation) had a significant negative effect on SAR. For yearling outmigrants, NPGO (North Pacific Gyre Oscillation) had a significant positive effect on SAR. We used the fitted model to simulate population trajectories under the Proposed Action, and the median 10-year geometric mean abundance was 8,222 female spawners (interquartile range: 2,592 26,714). Overall, the probability of quasi- extinction (probability of falling below 50 female spawners for 4 consecutive years) was low, with only 1.6% of all simulations having a quasi-extinction probability >0.95. Although quasi-extinction probability was low, we did not assess the additional effect of climate change, which would be expected to increase quasi-extinction probability.

Idaho, Oregon, Washington↗

USGS2011

Rare and endangered species of Hawai`i Volcanoes National Park; endangered, threatened, and rare animal, plant, and community handbook

Introduction Hawai`i Volcanoes National Park (HAVO) is the largest area in the State of Hawai`i protected for its geology and landscapes and its native flora and fauna. The park covers approximately 135,000 hectares or 333,000 acres in all. These lands stretch from the seacoast of Kīlauea Volcano to far above timberline on the summit of Mauna Loa (Figure 1). This vast area includes expanses of forests, woodlands, shrublands, and barren lava flows that represent an array of native ecosystems. Contained within these communities are a great many species of rare animals and plants, most of them unique to the island of Hawai`i, and some of them surviving only in the park. These are the biological treasures of Hawai`i Volcanoes National Park. Our book is a guide to all animal and plant species in HAVO that are specially recognized as endangered species in the general sense. (The official designations at four levels and the unofficial designation of species of concern are explained later.) There are 23 such animal species and 71 plant species covered in the handbook, including six species planted in HAVO but not naturally occurring. In addition, we describe seven rare communities. In some cases, HAVO offers the best opportunity to save these species and communities from extinction. Increasingly, the park has attempted to restore rare populations by conducting surveys to locate them, controlling threats such as feral livestock, and bolstering existing populations or creating new ones by planting nursery stock. To aid such efforts, our original intent was to publish an identification guide for researchers and field management personnel. Particularly, we wanted to familiarize the reader with the many rare plant species which otherwise are known mainly from the technical literature. Because we soon came to realize that this handbook would be useful to a much larger, general readership, our aim is to make this information available to anyone interested in endangered animals and plants at Hawai`i Volcanoes National Park.

Hawaii↗

USGS2000

Population and habitat viability assessments for Golden-cheeked Warblers and Black-capped Vireos: Usefulness to Partners in Flight Conservation Planning

Golden-cheeked Warblers and Black-capped Vireos are Neotropical migratory birds that are federally listed as endangered. Recovery plans for both species advise the use of viability modeling as a tool for setting specific recovery and management targets. Population and Habitat Viability Assessment workshops were conducted to develop population targets and conservation recommendations for these species. Results of the workshops were based on modeling demographic and environmental factors, as well as discussions of management issues, management options, and public outreach strategies. The approach is intended to be iterative, and to be tracked by research and monitoring efforts. This paper discusses the consensus-building workshop process and how the approach could be useful to Partners in Flight. Population and Habitat Viability Assessments (PHVA) were used to develop population targets and conservation recommendations for Golden-cheeked Warblers (Dendroica chrysoparia) and Black-capped Vireos (Vireo atricapillus). This paper explains what PHVAs are, discusses how they are conducted, describes the general results that are produced, and suggests how Partners in Flight (PIF) might use a similar process for bird conservation planning. Detailed results of the assessments are not discussed here; however they can be found elsewhere (U. S. Fish and Wildlife Service 1996a, U. S. Fish and Wildlife Service 1996b). PHVAs were considered for Golden-cheeked Warblers and Black-capped Vireos because they are controversial, endangered species, and the species? recovery plans list PHVAs as tools to develop recovery recommendations. The U. S. Fish and Wildlife Service (USFWS) realized that the data needed to perform PHVAs for these species is limited, but that various conservation efforts, such as the Balcones Canyonlands Conservation Plan and other endeavors, were proceeding without benefit of the biological summarization and guidance that a PHVA could provide.

Book chapter↗

USGS2017

Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River Fall Chinook Salmon ESU, 1/1/2016 - 12/31/2016

The portion of the Snake River fall Chinook Salmon Oncorhynchus tshawytscha ESU that spawns upstream of Lower Granite Dam transitioned from low to high abundance during 1992–2016 in association with U.S. Endangered Species Act recovery efforts and other federally mandated actions. This annual report focuses on (1) numeric and habitat use responses by natural- and hatchery-origin spawners, (2) phenotypic and numeric responses by natural-origin juveniles, and (3) predator responses in the Snake River upper and lower reaches as abundance of adult and juvenile fall Chinook Salmon increased. Spawners have located and used most of the available spawning habitat and that habitat is gradually approaching redd capacity. Timing of spawning and fry emergence has been relatively stable; whereas the timing of parr dispersal from riverine rearing habitat into Lower Granite Reservoir has become earlier as apparent abundance of juveniles has increased. Growth rate (g/d) and dispersal size of parr also declined as apparent abundance of juveniles increased. Passage timing of smolts from the two Snake River reaches has become earlier and downstream movement rate faster as estimated abundance of fall Chinook Salmon smolts in Lower Granite Reservoir has increased. In 2016, we described estimated the consumption rate and loss of subyearlings by Smallmouth Bass before, during, and after four hatchery releases. Before releases, Smallmouth Bass consumption rates of subyearling was low (0–0.36 fish/bass/d), but the day after the releases consumption rates reached as high as 1.6 fish/bass/d. Bass consumption in the upper portion of Hells Canyon was high for about 1–2 d before returning to pre-release levels, but in the lower river consumption rates were reduced but took longer to return to pre-release levels. We estimated that most of the subyearlings consumed by bass were of hatchery origin. Smallmouth Bass predation on subyearlings is intense following a hatchery release, but the predation pressure is relatively short-lived as subyearlings quickly disperse downstream. This information will allow us to better estimate subyearling loss to predation from our past efforts at time intervals less than 2 weeks. These findings coupled with stock-recruitment analyses presented in this report provide evidence for density-dependence in the Snake River reaches and in Lower Granite Reservoir that was influenced by the expansion of the recovery program. The long-term goal is to use the information covered here in a comprehensive modeling effort to conduct action effectiveness and uncertainty research and to inform Fish Population, Hydrosystem, Harvest, Hatchery, and Predation and Invasive Species Management RM&E.

Snake River basin↗