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USGS1990

Reference manual for generation and analysis of Habitat Time Series: version II

The selection of an instream flow requirement for water resource management often requires the review of how the physical habitat changes through time. This review is referred to as 'Time Series Analysis." The Tune Series Library (fSLIB) is a group of programs to enter, transform, analyze, and display time series data for use in stream habitat assessment. A time series may be defined as a sequence of data recorded or calculated over time. Examples might be historical monthly flow, predicted monthly weighted usable area, daily electrical power generation, annual irrigation diversion, and so forth. The time series can be analyzed, both descriptively and analytically, to understand the importance of the variation in the events over time. This is especially useful in the development of instream flow needs based on habitat availability. The TSLIB group of programs assumes that you have an adequate study plan to guide you in your analysis. You need to already have knowledge about such things as time period and time step, species and life stages to consider, and appropriate comparisons or statistics to be produced and displayed or tabulated. Knowing your destination, you must first evaluate whether TSLIB can get you there. Remember, data are not answers . This publication is a reference manual to TSLIB and is intended to be a guide to the process of using the various programs in TSLIB. This manual is essentially limited to the hands-on use of the various programs. a TSLIB use interface program (called RTSM) has been developed to provide an integrated working environment where the use has a brief on-line description of each TSLIB program with the capability to run the TSLIB program while in the user interface. For information on the RTSM program, refer to Appendix F. Before applying the computer models described herein, it is recommended that the user enroll in the short course "Problem Solving with the Instream Flow Incremental Methodology (IFIM)." This course is offered by the Aquatic Systems Branch of the National Ecology Research Center. For more information about the TSLIB software, refer to the Memorandum of Understanding. Chapter 1 provides a brief introduction to the Instream Flow Incremental Methodology and TSLIB. Other chapters in this manual provide information on the different aspects of using the models. The information contained in the other chapters includes (2) acquisition, entry, manipulation, and listing of streamflow data; (3) entry, manipulation, and listing of the habitat-versus-streamflow function; (4) transferring streamflow data; (5) water resources systems analysis; (6) generation and analysis of daily streamflow and habitat values; (7) generation of the time series of monthly habitats; (8) manipulation, analysis, and display of month time series data; and (9) generation, analysis, and display of annual time series data. Each section includes documentation for the programs therein with at least one page of information for each program, including a program description, instructions for running the program, and sample output. The Appendixes contain the following: (A) sample file formats; (B) descriptions of default filenames; (C) alphabetical summary of batch-procedure files; (D) installing and running TSLIB on a microcomputer; (E) running TSLIB on a CDC Cyber computer; (F) using the TSLIB user interface program (RTSM); and (G) running WATSTORE on the USGS Amdahl mainframe computer. The number for this version of TSLIB--Version II-- is somewhat arbitrary, as the TSLIB programs were collected into a library some time ago; but operators tended to use and manage them as individual programs. Therefore, we will consider the group of programs from the past that were only on the CDC Cyber computer as Version 0; the programs from the past that were on both the Cyber and the IBM-compatible microcomputer as Version I; and the programs contained in this reference manual as Version II.

Report↗
USGS1994

Relations between habitat variability and population dynamics of bass in the Huron River, Michigan

One of the assumption of the Instream Flow Incremental Methodology (IFIM) is that the dynamics of fish populations are directly or indirectly related to habitat availability. Because this assumption has not been successfully tested in coolwater streams, questions arise regarding the validity of the methodology in such streams. The purpose of our study was to determine whether relations existed between habitat availability and population dynamics of smallmouth bass ( Micropterus dolomieu ) and rock bass ( Ambloplites rupestris ) in a 16-km reach of the Huron River in southeastern Michigan. Both species exhibited strong to moderate carryover of year classes from age 0 through age 2, indicating that adult populations were related to factors affecting recruitment. Year-class strength and subsequent numbers of yearling bass were related to the availability of young-of-year habitat during the first growing season for a cohort. Number of age-0, age-1, and adult smallmouth bass were related to the average length at age 0 for the cohort. Length at age 0 was associated with young-of-year habitat and thermal regime during the first growing season. Rock bass populations exhibited similar associations among age classes and habitat variables. Compared to smallmouth bass, the number of age-2 rock bass was associated more closely with their length at age 0 than with year-class strength. Length at age 0 and year-class strength of rock bass were associated with the same habitat variables as those related to age-0 smallmouth bass. We hypothesize that an energetic mechanism linked thermal regime to length at age 0 and that increased growth resulted in higher survival rates from age 0 to age 1. We also postulate that young-of-year habitat provided protection from predators, higher production of food resources, and increased foraging efficiency. We conclude that the IFIM is a valid methodology for instream flow investigations of coolwater streams. The results for our study support the contention that the dynamics of bass populations are directly or indirectly related to habitat availability in coolwater streams. Our study also revealed several implications related to the operational application of the IFIM in coolwater streams: 1. Greater emphasis should be placed on the alleviation of habitat impacts to early life history phases of bass. 2. Effects of the thermal regime are important in some coolwater streams even if temperatures remain within nonlethal limits. Degree-day analyses should be routinely included in study plans for applications of the IFIM in coolwater streams. 3. The smallest amount of habitat occurring within or across years is not necessarily the most significant event affecting population dynamics. The timing of extreme events can be as important as their magnitude. 4. Population-related habitat limitations were associated with high flows more often than with low flows (although both occurred). Negotiations that focus only on minimum flows may preclude viable water management options and ignore significant biological events. This finding is particularly relevant to negotiations involving hydrospeaking operations. 5. IFIM users are advised to consider the use of binary criteria in place of conventional suitability index curves in microhabitat simulations. Criteria defining the optimal ranges of variables are preferable to broader rangers, and criteria that simply define suitable conditions should be avoided entirely.

Michigan↗
USGS1998

Results from the hydrodynamic element of the 1994 entrapment zone study in Suisun Bay

The entrapment zo as long been considered an important region of the San Francisco estuary. It has been the subject of several previous studies, and its location has been suggested as an index of condition of the estuarine ecosystem.A close correlate of this location, X2 1, is now used as a management objective on the basis that X2 is correlated with the abundance or survival of several estuarine-dependent species. X2 is a crude tool to use for this purpose, but it can be refined only through improved understanding of the various mechanisms underlying these correlations. These mechanisms probably differ among species, but for species resident in and near the entrapment zone, the correlation with X2 may be due to variations in intenSity oftrapping mechanisms with pOSition of the entrapment zone. Therefore, it is worthwhile to investigate these trapping mechanisms, the nature of the entrapment zone as habitat, and the responses of the entrapment zone to changes in X2 or outflow from the Sacramento-San Joaquin Delta. Studies ofthe entrapment zone ofthe San Francisco estuary have been conducted in springs of 1994, 1995, and 1996. These studies have been funded by the Interagency Ecological Program and conducted by scientists from IEP member agencies, the Romberg Tiburon Center for Environmental Studies, Bodega Marine Laboratory, and the University of California at Santa Cruz. This report presents results from 1994, a low-flow year. Subsequent reports will describe results from 1995 and 1996 and highlight differences among years. This report is organized in chapters that comprise more-or-Iess independent papers, with an introductory chapter for the entire study. This Executive Summary presents highlights of the overall study plan and summarizes the major findings.

California↗
USGS2012

Ecosystem restoration: Chapter 4

The Department of the Interior extensively supports―through its mission, policy, programs, and funding― the study, planning, implementation, and monitoring of ecosystem restoration. This commitment is reflected in the Department's FY2011-2016 Strategic Plan.

Report↗
USGS2003

Guidelines for long-term monitoring protocols

Monitoring protocols are detailed study plans that explain how data are to be collected, managed, analyzed, and reported, and are a key component of quality assurance for natural resource monitoring programs. Protocols are necessary to ensure that changes detected by monitoring actually are occurring in nature and not simply a result of measurements taken by different people or in slightly different ways. We developed and present here guidelines for the recommended content and format of monitoring protocols. The National Park Service and United States Geological Survey have adopted these guidelines to assist scientists developing protocols for more than 270 national park units.

Wildlife Society Bulletin↗
USGS2022

Real-time telemetry and multi-state modeling

This project will result in real-time data and other invasive carp movement information to inform realtime management decisions and refine the SEICarP model. FY 2022 funding will produce final transition probability estimates from the newly-developed Bayesian multi-state model, continue the maintenance of real-time telemetry to inform contingency actions, and produce a study plan to refine fishing mortality estimates using telemetry data.

Illinois↗
USGS2002

Managing for biodiversity in young Douglas-fir forests of western Oregon

This project addressed potential contributions of forest thinning to enhancing biodiversity and accelerating development of old-growth characteristics in relatively young Douglas-fir forests typical of those managed according to the Northwest Forest Plan. Studies focused primarily on 32 paired unthinned and thinned stands and 20 associated old-growth stands in the Coast Range and Cascade mountains of western Oregon. Data were collected on vascular plants in most stands surveyed, and on epiphytic lichens and bryophytes, moths, and birds in subsets of these stands. Studies assessed whether or not (1) communities of organisms differed among stand types, (2) communities in thinned stands were more similar to those in old-growth stands than were those in unthinned stands, (3) species diversity or abundance was related to specific stand features, and (4) these specific stand features were shared across taxa. Results indicated that communities differed among stand types, and that communities in thinned stands were not necessarily more similar to old-growth communities than were those in unthinned stands. Variation in stand conditions appeared to enhance biodiversity, and hardwood trees and shrubs were important for many species. These and other results form the basis for general thinning guidelines, which are presented here, and will guide future research.

Biological Science Report↗
USGS1982

Plan for hydrologic study of an area to be surface mined for coal in northwestern Colorado

A data-collection network was established in 1980 in northwestern Colorado in a drainage basin which may be surface mined for coal. This report describes the work plan set up to study the premining hydrology of this area near Steamboat Springs, Routt County, Colorado. The bedrock, alluvial, and surface-water systems as well as the climatic inputs to these systems, are monitored for this study.

Open-File Report↗
USGS2022

Species distributions and the recognition of risk in restoration planning: A case study of salmonid fishes

One of the risks faced by habitat restoration practitioners is whether habitats included in restoration planning will be used by the target species or, conversely, whether habitats excluded from restoration planning would have benefited the target species. With the goal of providing a quantitative decision-making approach that represented varying levels of risk tolerance, we used multiple probability decision thresholds (PDT) to predict the range of occurrence for three anadromous fishes ( Oncorhynchus spp.) in a watershed in southwestern Washington, USA. For each species, we compared the predicted range of occurrence to the distribution used for restoration planning and quantified the amount of habitat blocked by anthropogenic barriers. Coho salmon ( O. kisutch ) had the broadest predicted range of occurrence (3061.6–6357.9 km; 0.75–0.25 PDT), followed by steelhead trout ( O. mykiss ; 1828.8–2836.8 km) and chum salmon ( O. keta ; 1373.9–1629.1 km). For each species, the predicted range of occurrence was similar or greater than the distribution used for restoration planning, suggesting that the current plan may exclude habitats that would benefit each species. Coho salmon had the greatest percentage of habitat blocked by anthropogenic barriers, followed by steelhead trout and chum salmon, respectively. Modeling species distributions at multiple risk-tolerance scenarios acknowledges uncertainty in restoration planning and allows practitioners to weigh the ecological benefits and budgetary constraints when considering locations for restoration. To effectively communicate restoration science to support practitioners in decision-making, we developed an R Shiny application online user interface available at: https://shiny.wdfw-fish.us/ChehalisRiverBasinSalmonidRangeOfOccurence/ .

Washington↗
USGS1985

Proposed work plan for the study of hydrologic effects of ground-water development in the Wet Mountain Valley, Colorado

Large-scale development of groundwater resources in the Wet Mountain Valley, Colorado, could adversely affect other water rights in the valley or in the Arkansas River Basin. Such infringement on senior water rights could severely limit development of additional water supplies in the valley. A work plan is presented for a study that is intended to define the hydrologic system in the valley better, and to determine the extent that the quantity and chemical quality of both surface and groundwater in the valley might be affected by proposed development. (USGS)

Open-File Report↗
USGS2013

Knowledge and understanding of dissolved solids in the Rio Grande–San Acacia, New Mexico, to Fort Quitman, Texas, and plan for future studies and monitoring

Availability of water in the Rio Grande Basin has long been a primary concern for water-resource managers. The transport and delivery of water in the basin have been engineered by using reservoirs, irrigation canals and drains, and transmountain-water diversions to meet the agricultural, residential, and industrial demand. In contrast, despite the widespread recognition of critical water-quality problems, there have been minimal management efforts to improve water quality in the Rio Grande. Of greatest concern is salinization (concentration of dissolved solids approaching 1,000 mg/L), a water-quality problem that has been recognized and researched for more than 100 years because of the potential to limit both agricultural and municipal use. To address the issue of salinization, water-resource managers need to have a clear conceptual understanding of the sources of salinity and the factors that control storage and transport, identify critical knowledge gaps in this conceptual understanding, and develop a research plan to address these gaps and develop a salinity management program. In 2009, the U.S. Geological Survey (USGS) in cooperation with the U.S. Army Corps of Engineers (USACE), New Mexico Interstate Stream Commission (NMISC), and New Mexico Environment Department (NMED) initiated a project to summarize the current state of knowledge regarding the transport of dissolved solids in the Rio Grande between San Acacia, New Mexico, and Fort Quitman, Texas. The primary objective is to provide hydrologic information pertaining to the spatial and temporal variability present in the concentrations and loads of dissolved solids in the Rio Grande, the source-specific budget for the mass of dissolved solids transported along the Rio Grande, and the locations at which dissolved solids enter the Rio Grande. Dissolved-solids concentration data provide a good indicator of the general quality of surface water and provide information on the factors governing salinization within the Rio Grande study area. The pattern in dissolved-solids concentrations along the Rio Grande is one of increasing concentration with increasing distance downstream from Elephant Butte and Caballo Reservoirs. The concentration of dissolved solids in the Rio Grande doubles (approximately 500 to 1,000 mg/L) from below Elephant Butte Reservoir to El Paso and increases by more than a factor of 5 (approximately 500 to 3,200 mg/L) from below Elephant Butte Reservoir to Fort Quitman. Marked increases in the concentration of dissolved solids commonly coincide with contributions from agricultural drains, wastewater-treatment plants, regional groundwater, and upward-flowing saline groundwater. The greatest factor, from the surface-water system, in controlling dissolved solids in the Rio Grande is the amount of water that is being transported or stored. Annual variation in streamflow is influenced primarily by climate (precipitation and evaporation) and management of Elephant Butte and Caballo Reservoirs (water storage and release cycles). Seasonal variation in streamflow within the Rio Grande study area is generally categorized generally as irrigation (March–September) and nonirrigation (October–February) seasons; with streamflow in the Rio Grande is highest during the irrigation season and lowest during the nonirrigation season. Dissolved-solids loads during the irrigation season decrease between Leasburg and Fort Quitman primarily because of irrigation diversions and losses to the underlying alluvial aquifer. Conversely, dissolved-solids loads during the nonirrigation season increase between Caballo Dam and Fort Quitman primarily because of the inflow of dissolved solids from agricultural drains, wastewater-treatment plants, and groundwater with elevated concentrations of dissolved solids. Many studies have mass-balance budgets that account for the mass of dissolved solids transported along the Rio Grande. Results from mass-balance budgets developed for dissolved solids indicated that (1) the inflow of saline groundwater, inflow of regional groundwater, and chemical reactions between mineral phases are the primary sources controlling dissolved solids in the Rio Grande, and (2) groundwater pumping and mineral precipitation are causing a net storage of dissolved solids in the Leasburg to El Paso and El Paso to Fort Quitman reaches of the Rio Grande. Looking forward, multiple water-resource managers from State and local agencies in New Mexico and Texas and Federal agencies formed the Rio Grande Salinity Management Coalition with the goal to reduce the amount of dissolved solids that are transported and stored in the Rio Grande study area. The recommendations for additional monitoring to assist the coalition are as follows: -Monitoring: Couple water-quality and streamflow monitoring in the Rio Grande and agricultural drains; perform groundwater-seepage investigations in the Rio Grande and major agricultural drains; nonitor groundwater water-quality conditions in the Mesilla and Hueco Basins. -Focused Hydrogeology Studies at Inflow Sources: Map dissolved-solids concentrations in the Rio Grande and underlying alluvial aquifer; perform hydrogeologic characterization of subsurface areas containing unusually high concentrations of dissolved solids. -Modeling of Dissolved Solids: Develop models to simulate the transport and storage of dissolved solids in both surface-water and groundwater systems.

New Mexico;Texas↗
USGS2012

Developing a quality assurance plan for telemetry studies: A necessary management tool for an effective study

Telemetry has been used to answer various questions associated with research, management, and monitoring programs and to monitor animal behavior and population dynamics throughout the world. Many telemetry projects have been developed to study the passage, behavior, and survival of migrating adult and juvenile salmonids at hydroelectric projects on the mainstem Columbia and Snake rivers (Skalski et al. 2001a, 2001b; Skalski et al. 2002; Keefer et al. 2004; Goniea et al. 2006; Plumb et al. 2006). Telemetry based field evaluations of the survival of salmon through hydroelectric projects are costly because of the technology (tags, telemetry systems, infrastructure, etc.) and personnel required to conduct the evaluations. Given the cost of implementing these projects, and the financial and conservation implications of the decisions made from the research results (e.g., forgone electricity production and conservation of threatened and endangered animals), ensuring quality data are collected by documenting all procedures, training, data checks, and that sound protocols and quality assurance and control procedures are in place is paramount. Telemetry studies can pose unique data collection, processing, and analysis challenges. For instance, inferences about entire populations of animals are made from study animals that are captured, held, and tagged at disparate locations. Consequently great care must be taken to ensure that any potential biases that could arise from field procedures must be minimized (Peven et al. 2005). Interrogations of released study animals are remotely conducted by telemetry systems throughout the study area. The continuous recording of telemetry systems can result in large numbers of detections over a short time frame and the potential for false positive detections from records that are weak or erroneous. Thus, there is the potential to generate large data sets (many thousands of lines) that require significant postprocessing. Data reduction can be done using software or programming code within a software package or manually to discern noise from valid data and pull out the pertinent information for analysis. In either case, consistent well-documented procedures need to be in place to ensure quality results and allow for repeatability of study methods.

Book chapter↗
USGS2001

A national pilot study of mercury contamination of aquatic ecosystems along multiple gradients" Bioaccumulation in fish

Water, sediment, and fish were sampled in the summer and fall of 1998 at 106 sites from 20 U.S. watershed basins to examine relations of mercury (Hg) and methylmercury (MeHg) in aquatic ecosystems. Bioaccumulation of Hg in fish from these basins was evaluated in relation to species, Hg and MeHg in surficial sediment and water, and watershed characteristics. Bioaccumulation was strongly (positively) correlated with MeHg in water (r = 0.63, p < 0.001) but only moderately with the MeHg in sediment (r = 0.33, p < 0.001) or total Hg in water (r = 0.28, p < 0.01). Of the other significantly measured parameters, pH, DOC, sulfate, sediment LOI, and the percent wetlands of each basin were also significantly correlated with Hg bioaccumulation in fish. The best model for predicting Hg bioaccumulation included Me Hg in water, PH of the water, % wetlands in the basin, and the AVS content of the sediment. These four variables accounted for 45% of the variability of the fish fillet Hg concentration normalized (divided) by total length; however, the majority was described by MeHg in water. A MeHg water concentration 0.12 ng/L was on average, associated with a fish fillet Hg concentration of 0.3 mg/kg wet weight for an age-3 fish when all species were considered. For age-3 largemouth bass, a MeHg water concentration of 0.058 ng/L was associated with the 0.3 mg/kg fillet concentration. Based on rankings for Hg in sediment, water, and fish, sampling sites from the following five study basins had the greatest Hg contamination: Nevada Basin and Range, South Florida Basin, Sacramento River Basin (California), Santee River Basin and Caostal Drainages (South Carolina), and the Long Island and New Jersey Coastal Drainags. A sampling and analysis strategy based on this pilot study is planned for all USGS/NAWQA study units over the next decade.

Biological Science Report↗
USGS2016

Development of a study design and implementation plan to estimate juvenile salmon survival in Lookout Point Reservoir and other reservoirs of the Willamette Project, western Oregon

Survival estimates for juvenile salmon and steelhead fry in reservoirs impounded by high head dams are coveted data by resource managers. However, this information is difficult to obtain because these fish are too small for tagging using conventional methods such as passive-integrated transponders or radio or acoustic transmitters. We developed a study design and implementation plan to conduct a pilot evaluation that would assess the performance of two models for estimating fry survival in a field setting. The first model is a staggered-release recovery model that was described by Skalski and others (2009) and Skalski (2016). The second model is a parentage-based tagging N -mixture model that was developed and described in this document. Both models are conceptually and statistically sound, but neither has been evaluated in the field. In this document we provide an overview of a proposed study for 2017 in Lookout Point Reservoir, Oregon, that will evaluate survival of Chinook salmon fry using both models. This approach will allow us to test each model and compare survival estimates, to determine model performance and better understand these study designs using field-collected data.

Oregon↗
USGS2022

Genomics-informed delineation of conservation units in a desert amphibian

Delineating conservation units (CUs, e.g., evolutionarily significant units, ESUs, and management units, MUs) is critical to the recovery of declining species because CUs inform both listing status and management actions. Genomic data have strengths and limitations in informing CU delineation and related management questions in natural systems. We illustrate the value of using genomic data in combination with landscape, dispersal, and occupancy data, to inform CU delineation in Nevada populations of the Great Basin Distinct Population Segment of the Columbia spotted frog ( Rana luteiventris ). R. luteiventris occupies naturally fragmented aquatic habitats in this xeric region, but beaver removal, climate change, and other factors have put many of these populations at high risk of extirpation without management intervention. We addressed three objectives: (1) assessing support for ESUs within Nevada; (2) evaluating and revising, if warranted, the current delineation of MUs; and (3) evaluating genetic diversity, effective population size, adaptive differentiation, and functional connectivity to inform ongoing management actions. We found little support for ESUs within Nevada but did identify potential revisions to MUs based on unique landscape drivers of connectivity that distinguish these desert populations from those in the northern portion of the species range. Effective sizes were uniformly small, with low genetic diversity and weak signatures of adaptive differentiation. Our findings suggest that management actions, including translocations and genetic rescue, might be warranted. Our study illustrates how a carefully planned genetic study, designed to address priority management goals that include CU delineation, can provide multiple insights to inform conservation action.

Molecular Ecology↗
USGS1979

Hydrologic and related data for water-supply planning in an intensive-study area, northeastern Wichita County, Kansas

Data are presented that result from an intensive geohydrologic study for water-supply planning in a 12-square-mile area in northeastern Wichita County, Kansas. These data include records of wells, test drilling, chemical analyses, ground-water levels, rainfall, soilmoisture, well yield, solar radiation, crop yield, and crop acreage. Data indicate that water levels in the unconsolidated aquifer are declining at an average annual rate of about 1 to 2 feet per year (1950-78). This decline is the aquifer's response to pumping by irrigation wells for watering corn, wheat, grain sorghum, and other crops.

Kansas↗