Geology topics

J. B. Dunham

Publications and source records attributed to J. B. Dunham.

12 recordsLinked to original sources

USGS2011

Flow regime, temperature, and biotic interactions drive differential declines of trout species under climate change

Broad-scale studies of climate change effects on freshwater species have focused mainly on temperature, ignoring critical drivers such as flow regime and biotic interactions. We use downscaled outputs from general circulation models coupled with a hydrologic model to forecast the effects of altered flows and increased temperatures on four interacting species of trout across the interior western United States (1.01 million km 2 ), based on empirical statistical models built from fish surveys at 9,890 sites. Projections under the 2080s A1B emissions scenario forecast a mean 47% decline in total suitable habitat for all trout, a group of fishes of major socioeconomic and ecological significance. We project that native cutthroat trout Oncorhynchus clarkii , already excluded from much of its potential range by nonnative species, will lose a further 58% of habitat due to an increase in temperatures beyond the species' physiological optima and continued negative biotic interactions. Habitat for nonnative brook trout Salvelinus fontinalis and brown trout Salmo trutta is predicted to decline by 77% and 48%, respectively, driven by increases in temperature and winter flood frequency caused by warmer, rainier winters. Habitat for rainbow trout, Oncorhynchus mykiss , is projected to decline the least (35%) because negative temperature effects are partly offset by flow regime shifts that benefit the species. These results illustrate how drivers other than temperature influence species response to climate change. Despite some uncertainty, large declines in trout habitat are likely, but our findings point to opportunities for strategic targeting of mitigation efforts to appropriate stressors and locations.

Proceedings of the National Academy of Sciences of↗

USGS2010

A trial of two trouts: Comparing the impacts of rainbow and brown trout on a native galaxiid

Rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta are the world's two most widespread exotic fishes, dominate the fish communities of most cold-temperate waters in the southern hemisphere and are implicated in the decline and extirpation of native fish species. Here, we provide the first direct comparison of the impacts of rainbow and brown trout on populations of a native fish by quantifying three components of exotic species impact: range, abundance and effect. We surveyed 54 small streams on the island of Chilo?? in Chilean Patagonia and found that the rainbow trout has colonized significantly more streams and has a wider geographic range than brown trout. The two species had similar post-yearling abundances in allopatry and sympatry, and their abundances depended similarly on reach-level variation in the physical habitat. The species appeared to have dramatically different effects on native drift-feeding Aplochiton spp., which were virtually absent from streams invaded by brown trout but shared a broad sympatric range with rainbow trout. Within this range, the species' post-yearling abundances varied independently before and after controlling for variation in the physical habitat. In the north of the island, Aplochiton spp. inhabited streams uninvaded by exotic trouts. Our results provide a context for investigating the mechanisms responsible for apparent differences in rainbow and brown trout invasion biology and can help inform conservation strategies for native fishes in Chilo?? and elsewhere. ?? 2010 The Authors. Journal compilation ?? 2010 The Zoological Society of London.

Animal Conservation↗

USGS2010

Relationships between water temperatures and upstream migration, cold water refuge use, and spawning of adult bull trout from the Lostine River, Oregon, USA

Understanding thermal habitat use by migratory fish has been limited by difficulties in matching fish locations with water temperatures. To describe spatial and temporal patterns of thermal habitat use by migratory adult bull trout, Salvelinus confluentus, that spawn in the Lostine River, Oregon, we employed a combination of archival temperature tags, radio tags, and thermographs. We also compared temperatures of the tagged fish to ambient water temperatures to determine if the fish were using thermal refuges. The timing and temperatures at which fish moved upstream from overwintering areas to spawning locations varied considerably among individuals. The annual maximum 7-day average daily maximum (7DADM) temperatures of tagged fish were 16-18 ??C and potentially as high as 21 ??C. Maximum 7DADM ambient water temperatures within the range of tagged fish during summer were 18-25 ??C. However, there was no evidence of the tagged fish using localized cold water refuges. Tagged fish appeared to spawn at 7DADM temperatures of 7-14 ??C. Maximum 7DADM temperatures of tagged fish and ambient temperatures at the onset of the spawning period in late August were 11-18 ??C. Water temperatures in most of the upper Lostine River used for spawning and rearing appear to be largely natural since there has been little development, whereas downstream reaches used by migratory bull trout are heavily diverted for irrigation. Although the population effects of these temperatures are unknown, summer temperatures and the higher temperatures observed for spawning fish appear to be at or above the upper range of suitability reported for the species. Published 2009. This article is a US Governmentwork and is in the public domain in the USA.

Ecology of Freshwater Fish↗

USGS2008

Effects of food limitation and emigration on self-thinning in experimental minnow cohorts

1. &ensp;The theory of food-regulated self-thinning (FST) for mobile animals predicts population density ( N ) to be an inverse function of mean body mass ( W ) scaled to an exponent ( b ), such that N = k W −b , where k is a constant. FST also predicts energy requirements (or energy flow) to remain constant over time (termed energetic equivalence) as losses to cohorts (e.g. emigration and mortality) are balanced by increased growth of surviving individuals. 2. &ensp;To test these predictions, we analysed the dynamics of six experimental minnow cohorts. Replicate populations of fish were held under identical conditions with a constant and limited supply of food over a 126-day period. Half of the cohorts were open to emigration, and half were closed so that fish could only be lost through starvation mortality. 3. &ensp;Patterns of self-thinning indicated non-linear changes in population density and energy flow in relation to changes in mean body mass and time, respectively. Non-linear patterns of self-thinning were probably due to a delayed growth response to changes in population density effected through mortality and/or emigration. Contrary to results of similar experiments on other fish, emigration did not have a significant influence on the pattern of self-thinning. 4. &ensp;These results may be attributed to trophic interactions within cohorts and the importance of social behaviour to cohort dynamics. Both population density and energy flow in our experimental populations appeared to cycle, with episodes of starvation and mortality alternating with food recovery and weight gain, as predicted by recent models of stepwise die-off and stunted growth in animal cohorts. 5. &ensp;Most of the support for FST in mobile animals comes from observational data on mean body mass and population density. Potentially important mechanisms, including the manner in which individuals are lost or retained in populations, are usually not investigated directly. Such tests of FST can only provide equivocal support. Detailed observational study and controlled experiments are needed to understand casual mechanisms.

Journal of Animal Ecology↗

USGS2008

Analysis of trade-offs between threats of invasion by nonnative brook trout (Salvelinus fontinalis) and intentional isolation for native westslope cutthroat trout (Oncorhynchus clarkii lewisi)

Native salmonid fishes often face simultaneous threats from habitat fragmentation and invasion by nonnative trout species. Unfortunately, management actions to address one may create or exacerbate the other. A consistent decision process would include a systematic analysis of when and where intentional use or removal of barriers is the most appropriate action. We developed a Bayesian belief network as a tool for such analyses. We focused on native westslope cutthroat trout (Oncorhynchus clarkii lewisi) and nonnative brook trout (Salvelinus fontinalis) and considered the environmental factors influencing both species, their potential interactions, and the effects of isolation on the persistence of local cutthroat trout populations. The trade-offs between isolation and invasion were strongly influenced by size and habitat quality of the stream network to be isolated and existing demographic linkages within and among populations. An application of the model in several sites in western Montana (USA) showed the process could help clarify management objectives and options and prioritize conservation actions among streams. The approach can also facilitate communication among parties concerned with native salmonids, nonnative fish invasions, barriers and intentional isolation, and management of the associated habitats and populations. ?? 2008 NRC.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2007

Chinook salmon use of spawning patches: Relative roles of habitat quality, size, and connectivity

Declines in many native fish populations have led to reassessments of management goals and shifted priorities from consumptive uses to species preservation. As management has shifted, relevant environmental characteristics have evolved from traditional metrics that described local habitat quality to characterizations of habitat size and connectivity. Despite the implications this shift has for how habitats may be prioritized for conservation, it has been rare to assess the relative importance of these habitat components. We used an information-theoretic approach to select the best models from sets of logistic regressions that linked habitat quality, size, and connectivity to the occurrence of chinook salmon (Oncorhynchus tshawytscha) nests. Spawning distributions were censused annually from 1995 to 2004, and data were complemented with field measurements that described habitat quality in 43 suitable spawning patches across a stream network that drained 1150 km 2 in central Idaho. Results indicated that the most plausible models were dominated by measures of habitat size and connectivity, whereas habitat quality was of minor importance. Connectivity was the strongest predictor of nest occurrence, but connectivity interacted with habitat size, which became relatively more important when populations were reduced. Comparison of observed nest distributions to null model predictions confirmed that the habitat size association was driven by a biological mechanism when populations were small, but this association may have been an area-related sampling artifact at higher abundances. The implications for habitat management are that the size and connectivity of existing habitat networks should be maintained whenever possible. In situations where habitat restoration is occurring, expansion of existing areas or creation of new habitats in key areas that increase connectivity may be beneficial. Information about habitat size and connectivity also could be used to strategically prioritize areas for improvement of local habitat quality, with areas not meeting minimum thresholds being deemed inappropriate for pursuit of restoration activities. ?? 2007 by the Ecological Society of America.

Ecological Applications↗

USGS2006

Microsatellite variation reveals weak genetic structure and retention of genetic variability in threatened Chinook salmon (Oncorhynchus tshawytscha) within a Snake River watershed

Pacific salmon ( Oncorhynchus spp.) have been central to the development of management concepts associated with evolutionarily significant units (ESUs), yet there are still relatively few studies of genetic diversity within threatened and endangered ESUs for salmon or other species. We analyzed genetic variation at 10 microsatellite loci to evaluate spatial population structure and genetic variability in indigenous Chinook salmon ( Oncorhynchus tshawytscha ) across a large wilderness basin within a Snake River ESU. Despite dramatic 20th century declines in abundance, these populations retained robust levels of genetic variability. No significant genetic bottlenecks were found, although the bottleneck metric (M ratio) was significantly correlated with average population size and variability. Weak but significant genetic structure existed among tributaries despite evidence of high levels of gene flow, with the strongest genetic differentiation mirroring the physical segregation of fish from two sub-basins. Despite the more recent colonization of one sub-basin and differences between sub-basins in the natural level of fragmentation, gene diversity and genetic differentiation were similar between sub-basins. Various factors, such as the (unknown) genetic contribution of precocial males, genetic compensation, lack of hatchery influence, and high levels of current gene flow may have contributed to the persistence of genetic variability in this system in spite of historical declines. This unique study of indigenous Chinook salmon underscores the importance of maintaining natural populations in interconnected and complex habitats to minimize losses of genetic diversity within ESUs.

Idaho↗

USGS2006

Landscape attributes and life history variability shape genetic structure of trout populations in a stream network

Spatial and temporal landscape patterns have long been recognized to influence biological processes, but these processes often operate at scales that are difficult to study by conventional means. Inferences from genetic markers can overcome some of these limitations. We used a landscape genetics approach to test hypotheses concerning landscape processes influencing the demography of Lahontan cutthroat trout in a complex stream network in the Great Basin desert of the western US. Predictions were tested with population- and individual-based analyses of microsatellite DNA variation, reflecting patterns of dispersal, population stability, and local effective population sizes. Complementary genetic inferences suggested samples from migratory corridors housed a mixture of fish from tributaries, as predicted based on assumed migratory life histories in those habitats. Also as predicted, populations presumed to have greater proportions of migratory fish or from physically connected, large, or high quality habitats had higher genetic variability and reduced genetic differentiation from other populations. Populations thought to contain largely non-migratory individuals generally showed the opposite pattern, suggesting behavioral isolation. Estimated effective sizes were small, and we identified significant and severe genetic bottlenecks in several populations that were isolated, recently founded, or that inhabit streams that desiccate frequently. Overall, this work suggested that Lahontan cutthroat trout populations in stream networks are affected by a combination of landscape and metapopulation processes. Results also demonstrated that genetic patterns can reveal unexpected processes, even within a system that is well studied from a conventional ecological perspective. ?? Springer 2006.

Landscape Ecology↗

USGS2004

Effects of constant and cyclical thermal regimes on growth and feeding of juvenile cutthroat trout of variable sizes

The effects of constant (12, 18, and 24 °C) and cyclical (daily variation of 15–21 and 12–24 °C) thermal regimes on the growth and feeding of Lahontan cutthroat trout ( Oncorhynchus clarki henshawi ) of variable sizes were examined. Higher constant temperatures (i.e., 24 °C) and more variable daily temperatures (i.e., 12–24 °C daily cycle) negatively affected growth rates. As fish mass increased (from 0.24 to 15.52 g) the effects of different thermal regimes on mass growth became more pronounced. Following 14 days exposure to the thermal regimes, feeding rates of individual fish were assessed during acute exposure (40 min) to test temperatures of 12, 18, and 24 °C. Feeding rate was depressed during acute exposure to 24 °C, but was not significantly affected by the preceding thermal regime. Our results indicate that even brief daily exposure to higher temperatures (e.g., 24 °C) can have considerable sublethal effects on cutthroat trout, and that fish size should be considered when examining the effects of temperature.

Ecology of Freshwater Fish↗

USGS2004

The case for regime-based water quality standards

Conventional water quality standards have been successful in reducing the concentration of toxic substances in US waters. However, conventional standards are based on simple thresholds and are therefore poorly structured to address human-caused imbalances in dynamic, natural water quality parameters, such as nutrients, sediment, and temperature. A more applicable type of water quality standarda??a a??regime standarda??a??would describe desirable distributions of conditions over space and time within a stream network. By mandating the protection and restoration of the aquatic ecosystem dynamics that are required to support beneficial uses in streams, well-designed regime standards would facilitate more effective strategies for management of natural water quality parameters.

BioScience↗

USGS2003

Combining inferences from models of capture efficiency, detectability, and suitable habitat to classify landscapes for conservation of threatened bull trout

Effective conservation efforts for at-risk species require knowledge of the locations of existing populations. Species presence can be estimated directly by conducting field-sampling surveys or alternatively by developing predictive models . Direct surveys can be expensive and inefficient, particularly for rare and difficult-to-sample species, and models of species presence may produce biased predictions. We present a Bayesian approach that combines sampling and model -based inferences for estimating species presence. The accuracy and cost-effectiveness of this approach were compared to those of sampling surveys and predictive models for estimating the presence of the threatened bull trout (Salvelinus confluentus) via simulation with existing models and empirical sampling data. Simulations indicated that a sampling-only approach would be the most effective and would result in the lowest presence and absence misclassification error rates for three thresholds of detection probability. When sampling effort was considered, however, the combined approach resulted in the lowest error rates per unit of sampling effort. Hence, lower probability-of-detection thresholds can be specified with the combined approach, resulting in lower misclassification error rates and improved cost-effectiveness.

Conservation Biology↗

USGS2002

Influences of spatial and temporal variation on fish-habitat relationships defined by regression quantiles

We used regression quantiles to model potentially limiting relationships between the standing crop of cutthroat trout Oncorhynchus clarki and measures of stream channel morphology. Regression quantile models indicated that variation in fish density was inversely related to the width:depth ratio of streams but not to stream width or depth alone. The spatial and temporal stability of model predictions were examined across years and streams, respectively. Variation in fish density with width:depth ratio (10th-90th regression quantiles) modeled for streams sampled in 1993-1997 predicted the variation observed in 1998-1999, indicating similar habitat relationships across years. Both linear and nonlinear models described the limiting relationships well, the latter performing slightly better. Although estimated relationships were transferable in time, results were strongly dependent on the influence of spatial variation in fish density among streams. Density changes with width:depth ratio in a single stream were responsible for the significant ( P < 0.10) negative slopes estimated for the higher quantiles (>80th). This suggests that stream-scale factors other than width:depth ratio play a more direct role in determining population density. Much of the variation in densities of cutthroat trout among streams was attributed to the occurrence of nonnative brook trout Salvelinus fontinalis (a possible competitor) or connectivity to migratory habitats. Regression quantiles can be useful for estimating the effects of limiting factors when ecological responses are highly variable, but our results indicate that spatiotemporal variability in the data should be explicitly considered. In this study, data from individual streams and stream-specific characteristics (e.g., the occurrence of nonnative species and habitat connectivity) strongly affected our interpretation of the relationship between width:depth ratio and fish density.

Transactions of the American Fisheries Society↗