Geology topics

James T. Peterson

Publications and source records attributed to James T. Peterson.

86 records · Page 5Linked to original sources

USGS2012

Dealing with uncertainty when assessing fish passage through culvert road crossings

Assessing the passage of aquatic organisms through culvert road crossings has become increasingly common in efforts to restore stream habitat. Several federal and state agencies and local stakeholders have adopted assessment approaches based on literature-derived criteria for culvert impassability. However, criteria differ and are typically specific to larger-bodied fishes. In an analysis to prioritize culverts for remediation to benefit imperiled, small-bodied fishes in the Upper Coosa River system in the southeastern United States, we assessed the sensitivity of prioritization to the use of differing but plausible criteria for culvert impassability. Using measurements at 256 road crossings, we assessed culvert impassability using four alternative criteria sets represented in Bayesian belief networks. Two criteria sets scored culverts as either passable or impassable based on alternative thresholds of culvert characteristics (outlet elevation, baseflow water velocity). Two additional criteria sets incorporated uncertainty concerning ability of small-bodied fishes to pass through culverts and estimated a probability of culvert impassability. To prioritize culverts for remediation, we combined estimated culvert impassability with culvert position in the stream network relative to other barriers to compute prospective gain in connected stream habitat for the target fish species. Although four culverts ranked highly for remediation regardless of which criteria were used to assess impassability, other culverts differed widely in priority depending on criteria. Our results emphasize the value of explicitly incorporating uncertainty into criteria underlying remediation decisions. Comparing outcomes among alternative, plausible criteria may also help to identify research most needed to narrow management uncertainty.

Environmental Management↗

USGS2012

Linking river management to species conservation using dynamic landscape scale models

Efforts to conserve stream and river biota could benefit from tools that allow managers to evaluate landscape-scale changes in species distributions in response to water management decisions. We present a framework and methods for integrating hydrology, geographic context and metapopulation processes to simulate effects of changes in streamflow on fish occupancy dynamics across a landscape of interconnected stream segments. We illustrate this approach using a 482 km 2 catchment in the southeastern US supporting 50 or more stream fish species. A spatially distributed, deterministic and physically based hydrologic model is used to simulate daily streamflow for sub-basins composing the catchment. We use geographic data to characterize stream segments with respect to channel size, confinement, position and connectedness within the stream network. Simulated streamflow dynamics are then applied to model fish metapopulation dynamics in stream segments, using hypothesized effects of streamflow magnitude and variability on population processes, conditioned by channel characteristics. The resulting time series simulate spatially explicit, annual changes in species occurrences or assemblage metrics (e.g. species richness) across the catchment as outcomes of management scenarios. Sensitivity analyses using alternative, plausible links between streamflow components and metapopulation processes, or allowing for alternative modes of fish dispersal, demonstrate large effects of ecological uncertainty on model outcomes and highlight needed research and monitoring. Nonetheless, with uncertainties explicitly acknowledged, dynamic, landscape-scale simulations may prove useful for quantitatively comparing river management alternatives with respect to species conservation.

Georgia↗

USGS2011

Estimation of mussel population response to hydrologic alteration in a southeastern U.S. stream

The southeastern United States has experienced severe, recurrent drought, rapid human population growth, and increasing agricultural irrigation during recent decades, resulting in greater demand for the water resources. During the same time period, freshwater mussels ( Unioniformes ) in the region have experienced substantial population declines. Consequently, there is growing interest in determining how mussel population declines are related to activities associated with water resource development. Determining the causes of mussel population declines requires, in part, an understanding of the factors influencing mussel population dynamics. We developed Pradel reverse-time, tag-recapture models to estimate survival, recruitment, and population growth rates for three federally endangered mussel species in the Apalachicola–Chattahoochee–Flint River Basin, Georgia. The models were parameterized using mussel tag-recapture data collected over five consecutive years from Sawhatchee Creek, located in southwestern Georgia. Model estimates indicated that mussel survival was strongly and negatively related to high flows during the summer, whereas recruitment was strongly and positively related to flows during the spring and summer. Using these models, we simulated mussel population dynamics under historic (1940–1969) and current (1980–2008) flow regimes and under increasing levels of water use to evaluate the relative effectiveness of alternative minimum flow regulations. The simulations indicated that the probability of simulated mussel population extinction was at least 8 times greater under current hydrologic regimes. In addition, simulations of mussel extinction under varying levels of water use indicated that the relative risk of extinction increased with increased water use across a range of minimum flow regulations. The simulation results also indicated that our estimates of the effects of water use on mussel extinction were influenced by the assumptions about the dynamics of the system, highlighting the need for further study of mussel population dynamics.

Georgia↗

USGS2011

Misidentification of freshwater mussel species (Bivalvia:Unionidae): Contributing factors, management implications, and potential solutions

Surveys of freshwater mussel populations are used frequently to inform conservation decisions by providing information about the status and distribution of species. It is generally accepted that not all mussels or species are collected during surveys, and incomplete detection of individuals and species can bias data and can affect inferences. However, considerably less attention has been given to the potential effects of species misidentification. To evaluate the prevalence of and potential reasons for species misidentification, we conducted a laboratory-based identification exercise and quantified the relationships between mussel species characteristics, observer experience, and misidentification rate. We estimated that misidentification was fairly common, with rates averaging 27% across all species and ranging from 0 to 56%, and was related to mussel shell characteristics and observer experience. Most notably, species with shell texturing were 6.09× less likely than smooth-shelled species to be misidentified. Misidentification rates declined with observer experience, but for many species the risk of misidentification averaged >10% even for observers with moderate levels of experience (5–6 y). In addition, misidentification rates among observers showed substantial variability after controlling for experience. Our results suggest that species misidentification may be common in field surveys of freshwater mussels and could potentially bias estimates of population status and trends. Misidentification rates possibly could be reduced through use of regional workshops, testing and certification programs, and the availability of archived specimens and tissue samples in museum collections.

Journal of the North American Benthological Societ↗

USGS2011

Adaptive management of bull trout populations in the Lemhi Basin

The bull trout Salvelinus confluentus , a stream-living salmonid distributed in drainages of the northwestern United States, is listed as threatened under the Endangered Species Act because of rangewide declines. One proposed recovery action is the reconnection of tributaries in the Lemhi Basin. Past water use policies in this core area disconnected headwater spawning sites from downstream habitat and have led to the loss of migratory life history forms. We developed an adaptive management framework to analyze which types of streams should be prioritized for reconnection under a proposed Habitat Conservation Plan. We developed a Stochastic Dynamic Program that identified optimal policies over time under four different assumptions about the nature of the migratory behavior and the effects of brook trout Salvelinus fontinalis on subpopulations of bull trout. In general, given the current state of the system and the uncertainties about the dynamics, the optimal policy would be to connect streams that are currently occupied by bull trout. We also estimated the value of information as the difference between absolute certainty about which of our four assumptions were correct, and a model averaged optimization assuming no knowledge. Overall there is little to be gained by learning about the dynamics of the system in its current state, although in other parts of the state space reducing uncertainties about the system would be very valuable. We also conducted a sensitivity analysis; the optimal decision at the current state does not change even when parameter values are changed up to 75% of the baseline values. Overall, the exercise demonstrates that it is possible to apply adaptive management principles to threatened and endangered species, but logistical and data availability constraints make detailed analyses difficult.

Lemhi River Basin↗

USGS2011

Turning students into problem solvers: integrating adaptive management into wildlife curricula

No abstract available.

The Wildlife Professional↗

USGS2010

Estimation and modeling of electrofishing capture efficiency for fishes in wadeable warmwater streams

Stream fish managers often use fish sample data to inform management decisions affecting fish populations. Fish sample data, however, can be biased by the same factors affecting fish populations. To minimize the effect of sample biases on decision making, biologists need information on the effectiveness of fish sampling methods. We evaluated single-pass backpack electrofishing and seining combined with electrofishing by following a dual-gear, mark–recapture approach in 61 blocknetted sample units within first- to third-order streams. We also estimated fish movement out of unblocked units during sampling. Capture efficiency and fish abundances were modeled for 50 fish species by use of conditional multinomial capture–recapture models. The best-approximating models indicated that capture efficiencies were generally low and differed among species groups based on family or genus. Efficiencies of single-pass electrofishing and seining combined with electrofishing were greatest for Catostomidae and lowest for Ictaluridae. Fish body length and stream habitat characteristics (mean cross-sectional area, wood density, mean current velocity, and turbidity) also were related to capture efficiency of both methods, but the effects differed among species groups. We estimated that, on average, 23% of fish left the unblocked sample units, but net movement varied among species. Our results suggest that (1) common warmwater stream fish sampling methods have low capture efficiency and (2) failure to adjust for incomplete capture may bias estimates of fish abundance. We suggest that managers minimize bias from incomplete capture by adjusting data for site- and species-specific capture efficiency and by choosing sampling gear that provide estimates with minimal bias and variance. Furthermore, if block nets are not used, we recommend that managers adjust the data based on unconditional capture efficiency.

North American Journal of Fisheries Management↗

USGS2010

Conservation planning for imperiled aquatic species in an urbanizing environment

As the global area devoted to urban uses grows, an increasing number of freshwater species will face imperilment due to urbanization effects. Management of these impacts on both private and public lands is necessary to ensure species persistence. Such management entails several hallenges: (1) development of a management policy appropriate to the stressors; (2) linking stressor levels to species population attributes; (3) forecasting the effects of alternative management policy decisions on the species, and (4) using adaptive management to adjust the policy in the future. We illustrate how these challenges were addressed under the Etowah Habitat Conservation Plan (Etowah HCP), a management plan for three federally protected fish species in Georgia, USA. The plan involved the creation of a management policy to address the impacts of the greatest stressor, stormwater runoff, as well as other stressors. Models were constructed to link population indices of the three species with a key indicator of stormwater runoff, effective impervious area (EIA). Then, models were applied to projected levels of EIA under full watershed buildout to fine-tune the parameters of the management policy. Forecasting indicated that the most sensitive species, the Etowah darter, was likely to decline by 84% in the absence of the Etowah HCP, but only 23% if the Etowah HCP were implemented. Although there was substantial uncertainty in model predictions, an adaptive management plan was established to incorporate new data and to adjust management policies as necessary.

Landscape and Urban Planning↗

USGS2009

Does mobility explain variation in colonisation and population recovery among stream fishes?

1. Colonisation and population recovery are crucial to species persistence in environmentally variable ecosystems, but are poorly understood processes. After documenting movement rates for several species of stream fish, we predicted that this variable would influence colonisation rates more strongly than local abundance, per cent occupancy, body size and taxonomic family. We also predicted that populations of species with higher movement rates would recover more rapidly than species with lower movement rates and that assemblage structure would change accordingly. 2. To test these predictions, we removed fishes from a headwater and a mainstem creek in southwest Virginia and monitored colonisation over a 2-year period. Using an information–theoretic approach, we evaluated the relative plausibility of 15 alternative models containing different combinations of our predictor variables. Our best-supported model contained movement rate and abundance and was 41 times more likely to account for observed patterns in colonisation rates than the next-best model. Movement rate and abundance were both positively related to colonisation rates and explained 88% of the variation in colonisation rates among species. 3. Population recovery, measured as the per cent of initial abundance restored, was also positively associated with movement rate. One species recovered within 3 months, most recovered within 2 years, but two species still had not recovered after 2 years. Despite high variation in recovery, the removal had only a slight impact on assemblage structure because species that were abundant in pre-removal samples were also abundant in post-removal samples. 4. The significance of interspecific variation in colonisation and recovery rates has been underappreciated because of the widely documented recovery of stream fish assemblages following fish kills and small-scale experimental defaunations. Our results indicate that recovery of the overall assemblage does not imply recovery of each component species. Populations of species that are rare and less mobile will recover more slowly and will be more vulnerable to extinction in systems where chemical spills, hydrological alteration, extreme droughts and other impacts are frequent.

Virginia↗

USGS2009

Converting nonstandard fish sampling data to standardized data

Fishery biologists spend considerable effort over multiple years collecting data on fish population and community status using a particular sampling method or set of methods. However, new (and often more effective) sampling methods and technologies are continuously being developed. To incorporate these new sampling techniques, fishery biologists need a means for converting sample data collected using old methods so they can be compared with data collected using new methods. Similarly, fishery biologists often need a means to compare fish sample data collected using the same method over time (e.g., from year to year) and space (e.g., between sample sites). If fish abundance, species presence, or richness are estimated using an unbiased statistical estimator, the estimates can be validly compared, even if the fish sample data were collected with different methods. However, if unbiased statistical estimators were not used, biologists need methods for adjusting fish sampling data collected using different methods or using the same method collected under different sampling conditions. In this chapter, we describe and provide examples of statistical techniques for converting nonstandard fish sampling data to standardized data and for making comparisons of fish sampling data collected at different times or at different locations. We define standard fish sampling data as data collected using the standardized fish sampling methods described throughout this book. Any other sampling methods and associated data are thus defined as nonstandard. Before delving into the details of the statistical modeling techniques, we describe the nature of fish sample data, their uses, and their limitations. Catch-effort measures, such as relative abundance and catch per unit effort (CPUE), are more formally described as indices. Here, we define an index as any measure or count of a species or community (e.g., species richness) based on direct observation without an estimate of the ability to count individuals or species. Indices have some very desirable characteristics for use in fisheries research and management. In general (but not always), indices require less effort to collect and are usually more precise than unbiased population estimators (e.g., CPUE versus capture–recapture estimates of abundance). The proper use of indices for assessment of fish populations or communities, however, requires that the relationship between an index and the true value (e.g., fish density, species richness) is relatively constant (1) across the observable range of true values, (2) through time when evaluating trends at a single location, and (3) across space when making comparisons among locations.

Book chapter↗

USGS2009

Warmwater fish in wadeable streams

Both “warmwater” and “wadeable” are terms of convenience without precise definition and are used by biologists to describe streams that are generally too warm to have sustainable salmonid populations and can be safely traversed by walking (i.e., a section of stream should have the majority of its length less than 1 m deep, and it should be possible to cross in chest waders in nearly all areas). Warmwater streams in North America are estimated to provide more than a half-million kilometers of fishable waters and many times that amount of waters containing fish (Rabeni and Jacobson 1999). Warmwater streams have experienced a surge of attention in the past three decades because of increased sportfishing opportunities due to point-source pollution abatement and because of the popularity of using fish assemblages as indicators of biological integrity for regulatory and management purposes. At least 38 states have fish bioassessment programs in place (USEPA 2002). Sampling fish in warmwater streams is usually done for one of two reasons: (1) to evaluate a targeted species (e.g., sport fish or endangered species), or (2) to evaluate the entire fish assemblage. Thirty-two species of sport fishes, as defined by state and provincial agencies, occur in warmwater streams. The most popular are largemouth bass, smallmouth bass, spotted bass, striped bass, muskellunge, northern pike, walleye, several catfishes, and common carp. Important species regionally are rock bass, pumpkinseed, bluegill, white crappie, black crappie, other sunfishes, white perch, yellow perch, chain pickerel, buffalo, other suckers, and freshwater drum.

Book chapter↗

USGS2008

Stream fish occurrence in response to impervious cover, historic land use, and hydrogeomorphic factors

We evaluated competing models explaining the occurrence of five stream fishes in an urbanizing watershed to determine the relative importance of ( a ) impervious surface and other indicators of current land use, ( b ) historic land use (e.g., agriculture, impoundments), and ( c ) hydrogeomorphic characteristics (e.g., stream size, elevation, geology). For four of five species, the best-supported models were those that included both current effective impervious cover and historic land use predictor variables, although models with only effective impervious cover were equally well supported for two of those species. For the best-supported models for three species, occurrence probability was predicted to approach zero at levels of development equivalent to about 2%–4% effective impervious cover in the surrounding region. Data were drawn from 357 fish collections made in the Etowah River basin, Georgia, USA, between 1998 and 2003 and analyzed using hierarchical logistic regression accounting for imperfect species detection. This is the first study we know of to examine the response of individual fish species to both increasing impervious cover and historic land use. Such individual species assessments will be increasingly necessary to guide policies for managing urban effects and preventing extirpations of sensitive species.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS1999

Modeling the effects of land use and climate change on riverine smallmouth bass

Anthropogenic changes in temperature and stream flow, associated with watershed land use and climate change, are critical influences on the distribution and abundance of riverine fishes. To project the effects of changing land use and climate, we modeled a smallmouth bass ( Micropterus dolomieu ) population in a midwestern USA, large river–floodplain ecosystem under historical (1915–1925), present (1977–1990), and future (2060, influenced by climate change) temperature and flow regimes. The age-structured model included parameters for temperature and river discharge during critical seasonal periods, fish population dynamics, and fishing harvest. Model relationships were developed from empirical field data collected over a 13-yr period. Sensitivity analyses indicated that discharge during the spawning/rearing period had a greater effect on adult density and fishing yield than did spawning/rearing temperature or winter discharge. Simulations for 100 years projected a 139% greater mean fish density under a historical flow regime (64.9 fish/ha) than that estimated for the present (27.1 fish/ha) with a sustainable fishing harvest under both flow regimes. Simulations under future climate-change-induced temperature and flow regimes with present land use projected a 69% decrease in mean fish density (8.5 fish/ha) from present and an unstable population that went extinct during 56% of the simulations. However, when simulated under a future climate-altered temperature and flow regime with historical land use, the population increased by 66% (45.0 fish/ha) from present and sustained a harvest. Our findings suggest that land-use changes may be a greater detriment to riverine fishes than projected climate change and that the combined effects of both factors may lead to local species extinction. However, the negative effects of increased temperature and precipitation associated with future global warming could be mitigated by river channel, floodplain, and watershed restoration.

Ecological Applications↗

USGS1996

Natural thermal refugia for temperate warmwater stream fishes

The seasonal use of an Ozark spring branch by fishes was evaluated from January 1993 to January 1995. Temperatures in the spring branch were fairly constant, at 13.5 ± 1°C, and usually exceeded the temperature of a receiving stream during the November–March coldwater period. Black redhorse Moxostoma duquesnei , smallmouth bass Micropterus dolomieu , shadow bass Ambloplites ariommus , and longear sunfish Lepomis megalotis showed a temporal pattern of use in the spring branch. The lowest use was during the April–October warmwater period, and the greatest use was during the coldwater period. During cold periods, biomass of these four species in the spring branch was significantly greater and fish size significantly larger than in similar habitats in the adjoining stream. The weight per unit length of fish using the spring branch during cold periods was also significantly greater. Shadow bass and longear sunfish had significantly greater relative stomach contents than conspecifics in equivalent habitats from the adjoining stream, but had similar relative numbers of eggs. Large concentrations of adult fish used spring branches during the coldwater period, and these fish may be more vulnerable to angling than conspecifics in similar habitats in adjoining streams dominated by surface water. Thus, we suggest that stream managers consider the usefulness of fish refuges in spring branches and adjacent thermally influenced areas.

Missouri↗