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78 records · Page 5Linked to original sources
USGS2009

Pre-Restoration Habitat Use by Chinook Salmon in the Nisqually Estuary Using Otolith Analysis: An Additional Year

The Nisqually Fall Chinook population is one of 27 stocks in the Puget Sound evolutionarily significant unit listed as threatened under the Federal Endangered Species Act (ESA). Preservation and extensive restoration of the Nisqually delta ecosystem is currently taking place to assist in recovery of the stock as juvenile Fall Chinook salmon are dependent upon the estuary. A pre-restoration baseline that includes characterization of life history types, estuary residence times, growth rates, and habitat use is needed to evaluate the potential response of hatchery and natural origin Chinook salmon to restoration efforts and determine restoration success. Otolith analysis was selected to examine Chinook salmon life history, growth, and residence in the Nisqually Estuary. Previously funded work on wild samples collected in 2004 established the growth rate and length of residence associated with various habitats. The purpose of the current study is to build on the previous work by incorporating otolith microstructure analysis from 2005 (second sampling year), to verify findings from 2004, and to evaluate between-year variation in otolith microstructure. Our results from this second year of analysis indicated no inter-annual variation in the appearance of the tidal delta check (TDCK) and delta-flats check (DFCK). However, a new life history type (fry migrant) was observed on samples collected in 2005. Fish caught in the tidal delta regardless of capture date spent an average of 17 days in the tidal delta. There was a corresponding increase in growth rate as the fish migrated from freshwater (FW) to tidal delta to nearshore (NS) habitats. Fish grew 33 percent faster in the tidal delta than in FW habitat and slightly faster (14 percent) in the delta flats (DF) habitat compared to the tidal delta.

Open-File Report↗
USGS2022

Comparison of methods for estimating density and population trends for low-density Asian bears

Populations of bears in Asia are vulnerable to extinction and effective monitoring is critical to measure and direct conservation efforts. Population abundance (local density) or growth (λ ) are the most sensitive metrics to change. We discuss the value in implementing spatially explicit capture-recapture (SCR), the current gold standard for density estimation, and open population SCR (OPSCR) to monitor changes in density over time. We provide guidance for designing studies to provide estimates with sufficient power to detect changes. Because of the wide availability of camera traps and interest in their use, we consider six density estimation methods and their extensions developed for use with camera traps, with specific consideration of assumptions and applications for monitoring Asian bears. We conducted a power analysis to calculate the precision in estimates needed to detect changes in populations with reference to IUCN Red List criteria. We performed a systematic review of empirical studies implementing camera trap abundance estimation methods and considered sample sizes, effort, and model assumptions required to achieve adequate precision for population monitoring. We found SCR and OPSCR, reliant on “marked” individuals, are currently the only methods with enough power to reliably detect even moderate to major (20–80%) declines. Camera trap methods with unmarked individuals rarely achieved precision sufficient to detect even large declines (80–90%), although with some exceptions (e.g., situations with moderate population densities, large number of sampling sites, or inclusion of ancillary local telemetry data. We describe additional estimation options including line transects, direct observations, monitoring age-specific survival and reproductive rates, and hybrid/integrated methodologies that may have potential to work for some Asian bear populations. We conclude monitoring changes in abundance or density is possible for most Asian bear populations but will require collaboration among researchers over broad spatial extents and extensive financial investment to overcome biological and logistical constraints. We strongly encourage practitioners to consider study design and sampling effort required to meet objectives by conducting simulations, power analyses, and assumption checks prior to implementing monitoring efforts, and reporting standardized dispersion measures such as coefficients of variation to allow for assessment of precision. Our guidance is relevant to other low-density and wide-ranging species.

Global Ecology and Conservation↗
USGS2010

Otolith analysis of pre-restoration habitat use by Chinook salmon in the delta-flats and nearshore regions of the Nisqually River Estuary

The Nisqually Fall Chinook population is one of 27 salmon stocks in the Puget Sound (Washington) evolutionarily significant unit listed as threatened under the federal Endangered Species Act (ESA). Extensive restoration of the Nisqually River delta ecosystem is currently taking place to assist in recovery of the stock as juvenile Fall Chinook salmon are dependent on the estuary. A pre-restoration baseline that includes the characterization of life history strategies, estuary residence times, growth rates, and habitat use is needed to evaluate the potential response of hatchery and natural origin Chinook salmon to restoration efforts and to determine restoration success. Otolith analysis was selected as a tool to examine Chinook salmon life history, growth, and residence in the Nisqually River estuary. Previously funded work on samples collected in 2004 (marked and unmarked) and 2005 (unmarked only) partially established a juvenile baseline on growth rates and length of residence associated with various habitats (freshwater, forested riverine tidal, emergent forested transition, estuarine emergent marsh, delta-flats and nearshore). However, residence times and growth rates for the delta-flats (DF) and nearshore (NS) habitats have been minimally documented due to small sample sizes. The purpose of the current study is to incorporate otolith microstructural analysis using otoliths from fish collected within the DF and NS habitats during sampling years 2004-08 to increase sample size and further evaluate between-year variation in otolith microstructure. Our results from this analysis indicated the delta-flats check (DFCK) on unmarked and marked Chinook samples in 2005-08 varied slightly in appearance from that seen on samples previously analyzed only from 2004. A fry migrant life history was observed on otoliths of unmarked Chinook collected in 2005, 2007, and 2008. Generally, freshwater mean increment width of unmarked fish, on average, was smaller compared to marked Chinook followed by tidal delta and DF/NS portions respectively. On average, the complete tidal delta growth rate was higher for marked Chinook compared to unmarked Chinook. The DF/NS growth rate was highest for unmarked and marked Chinook during 2008 compared to all other sampling years. The average DF/NS growth rate on unmarked Chinook was consistently lower than marked Chinook during all years; however, sample sizes were small during some years. Unmarked Chinook, on average, spent longer in the tidal delta compared to marked Chinook. Our results from this report suggest that otolith microstructural analysis can be a valuable tool in establishing baseline information on the utilization of Nisqually River estuary habitats by juvenile Chinook salmon prior to the newly funded restoration efforts.

Open-File Report↗
USGS1987

Improving atlas methodology

We are studying a sample of Maryland (2 %) and New Hampshire (4 %) Atlas blocks and a small sample in Maine. These three States used different sampling methods and block sizes. We compare sampling techniques, roadside with off-road coverage, our coverage with that of the volunteers, and different methods of quantifying Atlas results. The 7 1/2' (12-km) blocks used in the Maine Atlas are satisfactory for coarse mapping, but are too large to enable changes to be detected in the future. Most states are subdividing the standard 7 1/2' maps into six 5-km blocks. The random 1/6 sample of 5-km blocks used in New Hampshire, Vermont (published 1985), and many other states has the advantage of permitting detection of some changes in the future, but the disadvantage of leaving important habitats unsampled. The Maryland system of atlasing all 1,200 5-km blocks and covering one out of each six by quarterblocks (2 1/2-km) is far superior if enough observers can be found. A good compromise, not yet attempted, would be to Atlas a 1/6 random sample of 5-km blocks and also one other carefully selected (non-random) block on the same 7 1/2' map--the block that would include the best sample of habitats or elevations not in the random block. In our sample the second block raised the percentage of birds found from 86% of the birds recorded in the 7 1/2' quadrangle to 93%. It was helpful to list the expected species in each block and to revise this list annually. We estimate that 90-100 species could be found with intensive effort in most Maryland blocks; perhaps 95-105 in New Hampshire. It was also helpful to know which species were under-sampled so we could make a special effort to search for these. A total of 75 species per block (or 75% of the expected species in blocks with very restricted habitat diversity) is considered a practical and adequate goal in these States. When fewer than 60 species are found per block, a high proportion of the rarer species are missed, as well as some of the common ones. Similarity indices based on fewer than 60 species per block reflect coverage rather than habitat affinities. Atlas blocks that are ecologically similar should have similarity indices (S) of at least 0.80 to be considered adequately covered. S = 2C/(A + B), where C is the number of species in common and A and B are species totals for each of the two blocks being compared. A series of 15 13-minutes roadside stops yielded more species than 15 off-road stops, but off-road stops always had some species not detected at the roadside stops. A series of timed stops is an excellent way to map relative abundance if the stops are standardized with respect to time of day and weather, and the counts are made by observers of comparable ability. Efforts to estimate Atlas block populations in powers of 10 (as in the French Atlas) have not gained acceptance in U.S.A. Most observers feel unqualified to make estimates. An efficient way to Atlas a block is to make at least 3 early morning visits to 15 or more specific stops. Arrive in the block early enough to check for nocturnal species on at least two days; and after completing the specific stops, search the block for other species and for confirmations.

Acta Oecologica Oecologia Generalis↗
USGS2017

Building a state-space life cycle model for naturally produced Snake River fall Chinook salmon

In 1992, Snake River basin fall Chinook salmon (Oncorhynchus tshawytscha) were listed for protection under the U.S. Endangered Species Act (NMFS 1992) and the population remained below 1000 individuals until 2000. Since then, returns from natural production has rebounded to over 20,000 spawners owing to a host of factors including reduced harvest (Peters et al. 2001), stable minimum spawning flows (Groves and Chandler 1999), summer flow augmentation (Connor et al. 2003), predator control (Beamesderfer et al. 1996), hatchery supplementation (Rosenberger et al. 2017), improved juvenile passage structures (Adams et al. 2014), summer spill operations (Perry et al. 2006; Adams et al. 2008), and periods of favorable ocean conditions and food availability (Logerwell et al. 2003; Peterson et al. 2014). Given this change in abundance coincident with numerous management actions and fluctuation in environmental drivers, quantifying which factors contributed to the observed rebound in natural production can provide critical insights into future management actions for this at-risk population. Multistage life cycle models provide a powerful analytical framework for understating how each life stage of a population contributes to population growth rate (Moussalli and Hilborn 1986; Greene and Beechie 2004). Multistage models may also be used as an analytical framework to explicitly estimate demographic parameters of a population model. This approach has an advantage over single-stage stock-recruitment models by allowing population growth rates to be partitioned among life stages rather than aggregated over an entire life cycle. Such partitioning allows for estimating 1) stage-specific density dependence, and 2) stage-specific effects of environmental factors or management actions. For example, Zabel et al. (2006) estimated parameters of a multistage model used in the context of a population viability analysis for spring/summer Chinook salmon in the Snake River, but such an approach has yet to be applied to fall Chinook salmon in the Snake River basin. Typically, data informing estimates of abundance at particular “check points” in the life cycle determines the complexity of the multistage model that can be fit to the data. For fall Chinook salmon, we are developing a two-stage model that encompasses: 1) upstream passage of spawners at Lower Granite Dam (LGR) to the subsequent downstream passage of their progeny at the dam, and 2) downstream passage of juveniles at LGR to their subsequent return from the ocean and passage at the Dam 2‒6 years later. This approach partitions the life cycle of fall Chinook salmon both spatially and temporally, which allows us to fit and compare alternative models with covariates specific to each stage. Our previous report to the ISAB (Zabel et al. 2013) detailed methods for estimating abundance of naturally produced adults and juveniles passing Lower Granite Dam, which provides the requisite data for fitting a two-stage model. The intent of this report is to describe the structure of the two-stage life cycle model, present preliminary results from fitting the model to data, and outline future directions and developments. As is clear from the diversity of models presented in this report, “life cycle models” range from very simple theoretically based population models (e.g., the Beverton-Holt stock- recruitment model) to very complex spatially explicit simulation models linked to hydrosystem hydrodynamic models (e.g., the COMPASS model for a single transition in a life cycle model, Zabel et al. 2008). We chose to develop a model of intermediate complexity that casts the two- stage life cycle model in a state-space framework (Newman et al. 2014). We chose to use a state-space framework implemented in a Bayesian framework because: • It provides both a statistical estimation framework for retrospective statistical analysis and a stochastic simulation framework for prospective analysis to evaluate alternative management actions. • Abundance estimates are uncertain. A state-space framework accounts for observation uncertainty in the abundance estimates and other data (e.g., age structure) while simultaneously estimating process uncertainty. • It allows for missing data. By drawing missing data from an appropriate probability model, uncertainty owing to missing data can be propagated without having to omit data or assume fixed values for missing data. Thus, a two-stage state-space life cycle model for fall Chinook salmon strikes an appropriate balance between model complexity, tractability, and applicability given the goals of performing both retrospective and prospective analysis to guide future management of this population.

Idaho, Oregon, Washington, Wyoming↗
USGS1986

Shallow ground-water conditions, Tom Green County, Texas

Most of the water needs of Tom Green County, Texas, are supplied by ground water; however, the city of San Angelo is supplied by surface water. Groundwater withdrawals during 1980 (latest year for which data are available) in Tom Green County totaled about 15,300 acre-feet, all derived from shallow aquifers. Shallow aquifers in this report refer to the ground-water system generally less than 400 feet deep that contains water with less than a 10,000 milligrams per liter concentration of dissolved solids; aquifers comprising this system include: The Leona, Comanche Peak, Trinity, Blaine, San Angelo, Choza, Bullwagon, Vale, Standpipe, and Arroyo aquifers. The current (1983) water levels in shallow aquifers in Tom Green County are relatively unchanged from those levels listed in previous reports. In most wells, the change in water level is less than 10 feet, and only a few isolated wells or areas have changes of more than 20 feet. Based on long-term hydrographs of selected wells and precipitation, water levels are directly related to precipitation and associated pumpage for irrigation. Current (1983) water levels probably are higher than normal due to the above-normal precipitation during 1980-81. Ground water in Tom Green County commonly is very hard (greater than 180 milligrams per liter as calcium carbonate), and chemical types vary in the aquifers and in different parts of the county. The concentrations of dissolved solids range from 200 to 3,000 milligrams per liter, the dissolved-chloride concentrations range from about 40 to 1,000 milligrams per liter, and the dissolved-sulfate concentrations normally range from about 25 to 600 milligrams per liter. The dissolved-nitrate concentrations in samples from eight wells ranged from 2 to 37 milligrams per liter. Five of these samples exceeded the maximum contaminant level of 10 milligrams per liter set by the U.S. Environmental Protection Agency. Of the eight water samples analyzed for minor elements, two exceeded the maximum contaminant level for selenium, and one exceeded the maximum contaminant level for manganese. Samples from three wells were analyzed for selected pesticides; no pesticides were detected. Two groups of ground-water samples were tested for bacteria in April and August 1983. The first group consisted of samples from 25 wells; no samples contained fecal-coliform bacteria, but 15 samples contained fecal-streptococci bacteria. The second group consisted of samples from 29 wells and 1 spring; twelve of these samples contained fecal-coliform bacteria and all 30 contained fecal-streptococci bacteria. Water samples from seven wells were common to both groups, and the samples tested in August contained more bacteria. Counts of fecal-coliform bacteria ranged from 0 to 26 colonies per 100 milliliters with most less than 5 colonies per 100 milliliters. Counts of fecal-streptococci bacteria ranged from 0 to 400 colonies per 100 milliliters with most less than 20 colonies per 100 milliliters. The presence of fecal-coliform and fecalstreptococci bacteria in water is only an indicator that pollution from septic systems may be present and is not a positive check for fecal pollution. Generally, the aquifers are not contaminated by septic-system effluent, however, some individual wells or localized areas could be contaminated by nearby septic systems. Using dissolved-solids concentrations as an indicator, historical and current (1983) water-quality records were compared to determine if any changes in water quality had occurred. The quality of water from Cretaceous rocks underlying the Edwards Pleateau has not changed significantly; this water is the least mineralized ground water in the county. The quality of water from the Arroyo and Bullwagon aquifers in the eastern most part of the county also has not changed significantly; dissolved-solids concentrations range from 1,500 to 2,000 milligrams per liter. In the remainder of the county, dissolved-solids concentrations have increased from 10 to 500 milligrams per liter in ground water along the river valleys and in the Li pan Flat area and increases of 500 to 1,100 milligrams per liter have occurred in ground water southeast of San Angelo, west of Twin Buttes Reservoir, and about 10 miles east of San Angelo. Locally, dissolved-solids concentrations have increased by as much as 4,530 milligrams per liter in water from individual wells. Pollution from oil-field activities may affect the quality of water in some isolated wells and in some areas in the county. No historical records are available for determining any changes in pesticides, minor elements, or bacteria.

Texas↗