Research Teams
Fisheries Projects
Updated information on the Air, Water, and Aquatic Enviroments Science Program page
The Effects of Wildfire and Ecological Context on Aquatic
Biological Diversity
Description of Project: In 2002, the Boise Aquatic Sciences
Laboratory initiated a multi-year study of the effects of wildfire
and ecological context on aquatic biological diversity. Products
from this work will assist management by providing new tools for
monitoring stream-living aquatic vertebrate (fish and amphibian)
responses to fire, predicting the effects of wildfire on nonnative
species invasions, and predicting the effects of wildfire on native
species and species assemblages. The linked work plan provides
background and details on completed and planned research for
2002-2003. This research is part of a larger collection of projects
representing collaborations within the Forest Service and with
external cooperators, including the University of Idaho and U.S.
Geological Survey. Through these collaborations, our research will
provide an integrated view of both biological and physical responses
of headwater streams to wildfire.
Draft Study Plan
Contacts: Jason Dunham,
Amanda Rosenberger, Bruce Rieman
Collaborators: University of Idaho, John Buffington, Mark
Wipfli (Pacific Northwest Research Station)
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Synthesis of knowledge on fire and fire related management in
aquatic ecosystems
Description of Project: Wildfire, forest health, and the
status of many aquatic species frame an important debate about land
management. Fire and management related to fire have direct effects
on aquatic organisms. As a result there has been significant
controversy regarding new fire management initiatives. Planning and
implementation are often mired in regulatory debate that struggles
to interpret available information. Emerging theory and a growing
body of empirical research on fire and disturbance to aquatic
ecosystems can provide an important context for a more informed
dialogue. Unfortunately, no comprehensive synthesis has been
available to guide managers struggling to embrace diverse
fire-related issues. A recent workshop began that synthesis by
involving leading scientists working with fire, disturbance, and the
related processes structuring aquatic ecosystems. A special issue of
the
Journal of Forest Ecology and Management was a primary result.
Continuing work will summarize existing data across the west on the
response of native fishes and their habitat to recent fires.
Contacts: Bruce Rieman,
Charlie Luce, Sherry
Wollrab
Collaborators: Pacific Northwest Research Station, United
States Geological Survey, Pacific Southwest Research Station
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Defining effects of wildfire on stream ecosystems: Development of
indicators and monitoring approaches
Description of Project: The long term goals of our work are
to understand the role of fire in structuring aquatic ecosystems of
the intermountain region. Does fire play a dominant role in creating
and maintaining habitats for aquatic organisms? Is the nature of
that influence predictable across landscapes of the intermountain
west? Ideally we could address these questions most directly by
monitoring many individual stream following fires, but that would
require decades, if not centuries, to describe the important
dynamics. Long term monitoring should be maintained to provide
perspective, but it may also be possible to gain an important
understanding by substituting space for time in the experimental
design. In a space-for-time approach it will be important to
stratify sampling to minimize unwanted, potentially confounding
effects as much as possible. If we hope to build a generalizable
understanding of fire in aquatic ecosystems, however, it is also
important to determine whether the signal from past disturbances is
even recognizable against the background noise imposed by the
inherent variability in landscapes across the region. The primary
objectives of this project are two fold: 1) to develop sampling
protocols and metrics useful for describing the trends in channel
and habitat conditions follow fire; and 2) to determine whether
important successional trends in stream channels can be recognized
with stratification of sampling sites across environmental gradients
related to landscape characteristics and the time and nature of
disturbance related to fire.
Contacts: Charlie Luce,
John Buffington
Collaborators: Payette National Forest, Nez Perce National
Forest, University of Idaho
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Intraspecific diversity in cutthroat trout and bull trout at
subbasin scales
Description of project: To effectively secure as much of the
biological diversity and evolutionary potential represented in
native fish populations, it will be necessary to understand
variation at two levels of organization: genetic and phenotypic.
Phenotypic diversity includes variation in morphology, life history
pattern, and behavior. Phenotypic variation is the product of both
genetic and environmental influences. From an ecological and
practical perspective it does not matter so much whether the
proximate cause of intraspecific diversity and variation is genetic
or environmental. Conserving genetic variation and plasticity alone
will do little to insure the persistence, productivity, and
resilience of populations or rare species, if the environmental
template that allows the full expression of phenotypic and spatial
diversity among populations does not exist. Effective management
must conserve both. Ultimately, conservation of a diverse physical
template may prove to be the most effective and efficient
conservation strategy we can devise. We are using otolith
microchemistry, population demographic analyses, molecular genetics,
and morphological analysis to explore the variation in salmonids at
the scale of individual subbasins. We hope to characterize patterns
in intraspecific diversity and ultimately link them to patterns in
landscapes that may be used to identify potential important
watersheds for conservation management.
Contacts: Bruce Rieman,
Dona Horan
Collaborators: University of Idaho, University of Montana
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Population genetics of bull trout in the Boise River Basin
Description of project: We are using DNA microsatellite
analysis to characterize the patterns of genetic variation within
and among watersheds of the Boise River basin. Results will be used
to characterize the appropriate scale of conservation units for bull
trout in this part of the range and to consider the underlying
processes (e.g. metapopulation dynamics, habitat loss, patterns of
glaciation and colonization, and human constructed barriers) that
may explain the existing patterns of occurrence.
Contact: Bruce Rieman
Collaborators: University of Montana, U.S. Bureau of
Reclamation
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Occurrence and displacement of bull trout in streams invaded by
brook trout
Description of project: We are attempting to test the assumption
that brook trout displace bull trout in headwater streams. We are
contrasting the general distribution of bull trout in streams in
allopatry and sympatry with brook trout to determine whether
longitudinal distributions are truncated in the latter. We are using
hierarchical modeling techniques to address the typical problems of
non-independence with replicate samples in individual streams.
Preliminary results suggest that the influence of brook trout is
highly variable and more likely to be important in small than large
streams.
Contact: Bruce Rieman
Collaborators: Boise National Forest, University of Georgia
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Factors Influencing the
Distribution and Persistence of Wild Chinook salmon
Description of project: A multitude of
regional program documents emphasize the need for long-term
monitoring and analysis of the spatial structure of Snake River
Chinook salmon. Effective salmon conservation and restoration
strategies will ultimately depend on information collected at
relevant spatial and temporal scales. Since 1995, we have
georeferenced salmon redds in more than 700 km of the Middle Fork
Salmon River drainage. The resulting continuous, spatially explicit,
and temporally extensive dataset is unique within the Columbia River
Basin. We are applying this dataset to: perform a detailed analysis
of population spatial structure, assess distributional shifts at
various escapement levels, identify core areas, validate redd
sampling designs, develop population monitoring programs, and
validate physical models to predict suitable spawning habitats. This
research is advancing our understanding of the relationship between
landscape characteristics and the distribution, pattern, and
persistence of Chinook salmon. Our results illustrate that salmon
spawning distributions are dynamic in both space and time,
particularly as population abundance changes. Cumulative redd
distribution curves suggest spawning aggregates contract into core
areas during periods of very low escapement and key core areas
persist across years. Gradients exist in the strength of spatial and
temporal structuring of redd distributions. Although we have focused
on larger scale spatial questions addressing population
persistence, this research has simultaneously provided data for
intensively monitoring an ESA listed Chinook salmon stock as well as
assessing population responses to various mitigation and restoration
efforts. Twelve years of data have been gathered since project
inception in 1995. By censusing redds in additional years, we
continue to build upon this unique and valuable dataset and advance
key analyses of wild Chinook salmon temporal and spatial dynamics.
Contact Persons:
Dan Isaak and
Russ Thurow
Collaborators: Idaho Department of Fish and Game; Boise, Payette,
Salmon-Challis, and Sawtooth National Forests; University of Idaho; Nez Perce
and Shoshone-Bannock Tribes; NOAA Fisheries.
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Bias and Precision of
Chinook Salmon Redd Counts
Description of project: Despite the widespread use of redd
counts to monitor trends in salmonid population performance, little
is known regarding the accuracy of redd counts or the factors that
decrease precision and introduce bias. Observers often assume that
uncorrected redd counts represent a constant proportion of true
numbers of redds across time, which is unlikely given the myriad of
environmental and other factors affecting redd sightability or redd
distribution. We are evaluating factors influencing bias and
precision of Chinook salmon redd counts. We will determine the true
number of redds within a series of study reaches; apply the true
counts to determine the accuracy of both aerial and ground-based
redd counts; measure environmental and habitat factors and model
which variables most influence redd sightability; assess inter- and
intra- year sources of variation in redd counts; quantify inter-
observer variation in ground-based surveys; compare accuracy of
single versus multiple pass counts; evaluate and compare the
effectiveness of a modified two-sample, Lincoln-Petersen mark-resight
estimator for obtaining unbiased and precise abundance estimates of
redds, and evaluate the potential for crew training to reduce the
bias in redd counts. Results from this research will have important
implications for improving Chinook salmon redd surveys conducted
across the Snake River basin.
Contact Person:
Claire McGrath,
Russ Thurow,
Dan Isaak
Collaborators: Peter Hahn (Washington Department of Fisheries and
Wildlife), Chris Brun (Warm Springs Tribe), Bill Thompson (National Park
Service)
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Landscape-Level
Assessment of Chinook Salmon Genetic Population Structure
Description of project: Salmon are famous for long distance migrations
and their ability to return to the streams where they were born. Because of this
“homing” fish populations are genetically adapted to the unique environmental
characteristics of each stream. Adaptation allows a population to maximize its
growth and abundance within a particular stream, but finely-tuned genetic
adaptations can be lost when salmon numbers are severely reduced, large numbers
of hatchery salmon interbreed with wild fish, or when stream environments change
rapidly. Although patterns of genetic variation have been studied in many salmon
species, most studies have been conducted across broad areas. Less is known
about the fine-scale genetic variation across individual river basins, although
this knowledge is needed to effectively implement management activities. This
project has three objectives: 1) describe local patterns in microsatellite
variation at population and individual levels using standard genetic analyses
and recently developed spatial autocorrelation techniques; 2) determine the
effects of environmental factors on genetic structure; and 3) assess possible
differences between sexes in genetic structure.
Contact Person:
Dan Isaak and
Russ Thurow
Collaborators: Helen Neville (Trout Unlimited), Jason Dunham (USGS),
Bruce Rieman (RMRS), Tim Copeland (Idaho Department of Fish and Game).
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Analysis of Otolith Microchemisty to Describe Life History
Types and Dispersal of Chinook Salmon
Description of project:
Understanding spatial and temporal patterns of habitat use by anadromous salmon
is critical for quantifying gene flow among subpopulations and assessing overall
metapopulation structure. Salmon throughout the Columbia River basin are
currently the subject of intense quantitative assessment efforts as well as
contentious conservation measures. However, due to the complex life history,
which includes a migrational shift from freshwater to marine and back to
freshwater, some key questions about population structure and site fidelity
remain to be answered. In this pilot study, we are employing a geochemical
tracer technique, which has been developed for distinguishing Atlantic salmon
populations, to identify distinct life histories, source habitats, and to
quantify straying rates of returning adult Chinook salmon. Our ultimate goal is
to develop a methodology that can relate recruitment processes in Chinook salmon
to habitat-specific information across the lifetime of individual fish. If
successful, we believe that this method could be generally applied throughout
the Columbia River basin in order to separate hatchery and wild populations, to
identify the natal tributaries of returning fish, and to quantify the degree of
straying in mixed populations.
Contact Person:
Dan Isaak and
Russ Thurow
Collaborators: Brian Kennedy (University of Idaho),
Claire McGrath, and Bruce Rieman (RMRS)
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Geomorphic Controls on Basin-Scale Distribution of Salmon
Spawning Areas
Description of project: Our goal
is to understand geomorphic controls on the spatial distribution of spawning
gravels within a large basin supporting wild salmon, and to predict how spawning
habitat changes over space and time in response to basin disturbances (e.g.,
floods, debris flows, and anthropogenic activity). We will use three approaches
for modeling geomorphic controls on spawning habitat: 1) correlation of the
observed location and quality of spawning gravels with landscape features
(geology, channel gradient and confinement, land use, etc.); 2) prediction of
the abundance and spatial distribution of spawning gravels as a function of
channel type and associated hydraulics; and 3) development of a dynamic model
for routing sediment through the river network as a function of basin hydrology
and stochastic sediment inputs (floods, debris flows), allowing investigation of
the spatial and temporal changes in spawning habitat availability.
Contact Person:
John Buffington, Mik Lewicki,
Russ Thurow,
Dan Isaak
Collaborators: Yantao Cui (Stillwater Sciences), University of Idaho
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Development
of Protocols for Sampling Stream Dwelling Salmonids
Description of project: Biologists and managers need reliable methods to
assess the status and distribution of stream dwelling salmonids. The behavior
and specific habitat requirements of various species and life stages, however,
may make them difficult to sample. Although snorkeling and electrofishing are
widely used to assess salmonid abundance and distribution, the bias and
precision of the methods has rarely been assessed. Consequently, a critical
feature to consider when designing a monitoring protocol is the influence of
sampling efficiency. Fish sampling efficiency is influenced by the size and
species of fish as well as physical habitat features. Failure to account for
differences in sampling efficiency introduces an error or bias into the data,
which can significantly affect abundance and trend estimates. Presence and
absence estimates are similarly affected by sampling efficiency because the
probability of detecting a species is a function of its probability of capture
and its density, both of which are influenced by habitat features that vary. One
method to deal with bias in snorkel estimates is to correct the estimates
through the application of a statistical model. This approach relies on a
statistical modeling procedure that derives empirical estimates of
method-specific sampling efficiency as a function of stream habitat features and
fish size and species. The model produces a statistically valid method to
correct raw survey data for sampling bias. Our goal is to continue to refine
procedures for estimating the sampling effort and techniques required to achieve
a desired level of accuracy in detecting the status and distribution of
salmonids in streams. Our objectives are 1) empirically estimate detection
efficiency and 2) apply statistical models to examine the influence fish species
and size and habitat features on detection efficiency. The results of this
research will enable correction of extant and future data over a broad
geographic area.
Contact Person:
Russ Thurow and
John Guzevich
Collaborators: James Peterson (U. of Georgia), Tim Copeland (Idaho
Department of Fish and Game), State and Federal Fisheries Agencies in Idaho,
Montana, and Washington, Turner Endangered Species Fund
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Fluvial Bull Trout Movements and Habitat Use
Description of project: Most existing knowledge of migratory bull trout
is focused on adfluvial populations. We are using radio telemetry and weirs to
describe seasonal movements and habitat use by fluvial bull trout in 2nd to 6th
order streams. In concert with the telemetry data, we are developing detailed
descriptions of the habitats adult fish are using during three stages:
pre-spawning, spawning, and post spawning. More than 70 bull trout have been
successfully tracked. Results to date illustrate that movements and the onset of
spawning were strongly influenced by water temperatures. Habitats with overhead
cover were important staging areas during both upstream and downstream
movements. Overwintering adults displayed high site fidelity, typically
remaining in the same habitats from November to March. Adult bull trout
displayed home ranges exceeding 100 km and used habitats in 2nd to 6th order
streams. The wide range of seasonal habitat requirements emphasizes the need for
improved understanding of spatial and temporal dynamics for effective
conservation and restoration efforts. Field studies have been completed and a
series of manuscripts are in preparation.
Contact Person:
Russ Thurow and
John Guzevich
Collaborators: D. Schill and S. Elle (Idaho Department of Fish and Game)
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Dispersal and Homing of Migratory and Non-migratory Bull Trout
Description of project: Dispersal and straying rates of bull trout are
poorly understood although they may have important implications for species
persistence and development of recovery efforts. We are attempting to describe
dispersal and homing of migratory and resident bull trout. Our approach has
been to capture and insert Passive Integrated Tags (PIT) in juvenile bull
trout within each of two geographically separated study reaches. Reach 1
supports what appears to be a resident bull trout population while Reach 2
supports extensive spawning by migratory bull trout. We are measuring
movements and dispersal rates of tagged fish by two methods: a) we capture
tagged juveniles from previous years during subsequent marking efforts and b)
we capture adult bull trout at a permanent salmon weir and scan them for PIT
tags. When a PIT tagged bull trout is captured at the weir, we surgically
implant a radio tag and track the fish to its spawning location. This data
will enable us to assess homing and straying of fish from both reaches. In
addition to describing dispersal rates, this work could provide information to
assess whether resident forms can refound migratory populations.
Contact Person:
Russ Thurow and
John Guzevich
Collaborators: Idaho Department of Fish and Game, Payette and Nez Perce
National Forests
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Characteristics of
Spawning Sites Used by Fluvial Bull Trout
Description of project: Although attributes of bull trout spawning areas
have been described, there is limited understanding of why specific areas are
selected for redd construction and how redd distributions may change temporally
and spatially. To address these questions, we are annually georeference fluvial
bull trout redd distributions. At each redd, we are collecting macro and
microhabitat information (habitat type, water depth, water velocity, substrate,
temperature, proximity to cover, etc.) that will be applied to predict
characteristics of occupied spawning sites.
Contact Person:
John Guzevich and
Russ Thurow
Collaborators: Idaho Department of Fish and Game
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Evaluation of Stream Sediment Monitoring Techniques
Description of project: Improved
approaches for monitoring conditions in salmonid spawning gravels are needed.
Through a suite of field studies, we have characterized spawning sites and
redds, evaluated the effects of fine sediment on salmonid life stages ranging
from newly fertilized eggs deposition to emergent fry, and tested monitoring
approaches. We have focused on six native salmonids (steelhead, rainbow trout,
Chinook salmon, Yellowstone cutthroat trout, westslope cutthroat trout, and
kokanee) across three lithologies (granitic, metasedimentary, and volcanic). The
following field studies have been completed: evaluation of the utility of
artificial redds for monitoring incubation conditions, determination of the most
sensitive substrate indices and required sample sizes for characterizing
spawning substrate, development of gravel intrusion models, use of surrogates
locations to predict conditions in redds, comparison of surface and subsurface
techniques for characterizing substrate, and considerations for sampling
dissolved oxygen in streams. Field studies have been completed and a series of
manuscripts are in preparation.
Contact Person:
Russ Thurow
Collaborators:
Jack King (Retired RMRS), Idaho Division of Environmental Quality, Montana State
U, University of Idaho, Idaho Department of Fish and Game, National Park
Service, and National Forests in Idaho and Montana.
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Use of archival temperature tags to record thermal habitat use by
migratory bull trout
Description of Project: Our studies of bull trout
distributions in relation to temperature are limited primarily to
juvenile bull trout and spawning use. To provide better resolution
on thermal habitat use by bull trout, and to provide data on
migratory fish, we have initiated a collaborative study using
archival temperature tags. Archival tags are miniaturized (e.g., 5g)
temperature dataloggers that can be attached externally or
internally to fish to monitor their thermal “histories.” Instead of
matching the fish distributions with observed temperatures, we are
tracking thermal habitat use by individually tagged fish. Archival
tags have been deployed on migratory bull trout from northeast
Oregon (Imnaha and Lostine Rivers) and eastern Washington (Wenatchee
River). We hope to retrieve data from these tags over the next year
or two to obtain detailed information on thermal habitat use by
individual fish.
Contact Person: Jason Dunham
Collaborators: Phil Howell (PNW Research Station), Judy
Delavergue, Barb Kelley(USFWS), Tammy Salow (USBR).
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Development of protocols for sampling stream temperatures using
digital dataloggers
Description of project: Digital temperature dataloggers are a
relatively new tool available to fishery managers. These dataloggers
provide an unprecedented opportunity to collect large volumes of
continuous temperature data with relatively minimal effort.
Effective use of dataloggers must consider two important issues: 1)
sampling and measurement error; and 2) effective processing and data
archiving. We are developing a protocol for use of dataloggers that
considers several components of error, including 1) instrument and
calibration error; 2) effect of logger housing; 3) sampling of
temperature within sites; 4) sampling within larger reaches or
streams; 5) sampling interval; 6) error screening. Our protocol is
being developed with an extensive database of stream temperatures
from over 1000 sites in streams in the Great Basin and Pacific
Northwest. We will also address the issue of data processing by
examining covariation among a number of temperature metrics,
including summaries of temperature based on mean temperatures,
maximum temperatures, cumulative exposure, and how different species
of salmonids have been shown to respond to these different measures.
Contact Person: Jason Dunham
Collaborators: Gwynne Chandler
(RMRS-Boise)
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Modeling landscape characteristics and predicting occurrence of
cutthroat trout in fragmented habitat
Description of project: Habitat fragmentation is believed to
be an important threat for many species. Most of the work on habitat
fragmentation has focused on terrestrial and aquatic systems where
boundaries of suitable habitat are relatively easy to identify (e.g.
forested versus non-forested habitat, lakes). We are defining
suitable habitat and habitat fragmentation for cutthroat trout in
streams of the Great Basin. Several different models of downstream
distribution limits were used in a GIS to define the size and
location of continuous areas of suitable habitat (habitat patches).
Patch structure defined by each of the models is being used to
predict the effects of patch size and isolation on occurrence of
cutthroat trout. A variety of other factors (occurrence of nonnative
salmonids, maximum basin elevation, and alternative measures of
patch connectivity) will be investigated as well. Models of habitat
fragmentation and broad-scale (GIS) models will be used with more
detailed information at specific sites to develop a
spatially-explicit classification of threats to guide recovery
activities.
Contact Person: Jason Dunham
Collaborators: With Bruce Rieman
and Debbie Myers (RMRS-Boise)
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Building population growth models with limited demographic data
for cutthroat and bull trout
Description of project: Time series of population data from several
streams supporting Lahontan cutthroat trout are being used to
develop demographic models of population persistence. Data analyses
indicate recruitment of age 1 fish can be predicted well by
variability in spring stream discharge in the first (age 0) and
second (age 1+) years of life. Dynamics of older (2+) age classes is
a function of density dependence within age classes. Persistence of
populations over various timeframes can be simulated in response to
existing conditions or hypothetical changes in discharge regimes and
amount of suitable habitat (e.g., as controlled by temperature or
stream desiccation).
Contact Person: Jason Dunham
Collaborators: With Chris Ray and Mary Peacock (University of
Nevada, Reno) (cutthroat trout), and Bruce Rieman (RMRS-Boise) and Danny Lee (PNW-Arcata) (bull
trout)
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Landscape controls on key habitat factors for salmonid fishes
Description of project: Many environmental factors combine to
provide habitat for a species, but some are of more obvious
importance. For salmonid fishes, stream thermal regimes and the
distribution and quality of spawning gravels are known to strongly
affect population health. If we are to fully understand the
consequences of land-management decisions for sensitive species, we
must understand how key habitat feature are linked to landscape
structure and driven by physical processes. The objective of this
project are to:
Develop models that link geomorphic attributes of watersheds to
stream temperature regimes.
·Characterize patterns of spatial autocorrelation in temperatures
across a large stream network.
Use fundamental hydrologic equations to link the distribution of
substrates suitable for salmonid spawning to landscape attributes
and validate model predictions.
Create a dynamic sediment routing model that accommodates spatial
and temporal variability in sediment movement across a network.
Contact Person: Dan Isaak
Collaborators: Charlie Luce
and John Buffington, principal
investigators; Russ Thurow,
Dan Isaak, and Mikolaj Lewicki
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