United States Department of the Interior
U.S. GEOLOGICAL SURVEY
Biological Resources Discipline
Forest and Rangeland Ecosystem Science Center
3200 SW Jefferson Way
Corvallis, OR 97331
May 3, 2010
Memo:
From: Jason Dunham and Robert Hoffman, U.S. Geological Survey, Forest and Rangeland
Ecosystem Science Center, Corvallis, Oregon 97330; jdunham@usgs.gov;
robert_hoffman@usgs.gov
To: Kim Clarkin, USDA-Forest Service San Dimas Technology and Development Center
(360) 766-4171 (office phone and fax); (951) 533-2067 (cell); kclarkin@fs.fed.us
Re: Forest Service Agreement Number 09-IA 11138150-041
This memo provides a summary of preliminary findings from an ongoing agreement (Forest
Service Agreement Number 09-IA 11138150-041). Information provided here is not finalized
and is subject to change pending further analysis or data collection. Reporting herein is
intended to satisfy reporting requirements and provide the cooperator with an opportunity to
engage in project development. A final product will be available for distribution upon project
completion and adherence to the USGS Fundamental Science Practices.
Herein we describe progress toward attaining the following objectives outlined in the original
Agreement. The intent of this Agreement is to work with the Forest Service to develop
guidelines for monitoring the effectiveness of aquatic organism passage that can be used by
managers, particularly on Forest Service lands. To serve this end, USGS agreed to 1) host a
workshop on the topic of aquatic organism passage and effectiveness monitoring, and 2) produce
a series of guidelines in the form of an internal peer-reviewed publication (e.g., a USFS General
Technical Report or USGS Open-File Report). This product could be published in more concise
form in a scientific journal or book chapter.
Workshop
We organized and hosted a workshop held in Portland Oregon over 16-18 March 2010 to gather
information from a team of national experts on the topic of aquatic organism passage and
effectiveness monitoring. The objectives of the workshop are outlined in the Appendix 1, and
included scientific presentation and discussion of four major methods for monitoring aquatic
organism passage, including: Occupancy, Molecular Markers, Individual Movement, and
Demography. Attendees represented the following:
Name
James Peterson
Expertise
Occupancy modeling
Michael Adams
Occupancy modeling
Douglas Peterson
Demography
Benjamin Letcher
Demography
Theodore CastroSantos
Keith Nislow
Individual movement
Deborah Finn
Molecular markers
Winsor Lowe
Demography
Helen Neville
Brett Albanese
Molecular Markers
Individual movement
Mark Hudy
Individual movement
Jason Dunham
Workshop organizer
Robert Hoffman
Workshop organizer
Bruce Hansen
Workshop organizer
Guillermo Giannico
Workshop organizer
Kim Clarkin
Workshop organizer
Individual movement
Affiliation
University of Georgia, USGS Cooperative
Fisheries Research Unit
U.S. Geological Survey, Forest and Rangeland
Ecosystem Science Center
U.S. Fish and Wildlife Service, Ecosystem
Services
U.S. Geological Survey, Leetown Science
Center
U.S. Geological Survey, Leetown Science
Center
U.S. Forest Service, Northeast Research
Station
Oregon State University, Department of
Zoology
University of Montana, Division of Biological
Sciences
Trout Unlimited
State of Georgia Department of Natural
Resources
U.S. Forest Service, Fisheries, Washington
Office
U.S. Geological Survey, Forest and Rangeland
Ecosystem Science Center
U.S. Geological Survey, Forest and Rangeland
Ecosystem Science Center
U.S. Forest Service, Pacific Northwest
Research Station
Oregon State University, Department of
Fisheries and Wildlife and OSU Extension
U.S. Forest Service, San Dimas Technology
and Development Center
2010 May Memo: AOP, Not for citation or circulation, Page 2
Live presentations were recorded during the workshop (work by Ben Nieves), with DRAFT
internet links provided by the Forest Service Pacific Northwest Research Station (Jeffrey
Guntle):
Helen Neville (Molecular Markers): http://www.fsl.orst.edu/geowater/PEP/aopw/neville/
Ben Letcher (Demography): http://www.fsl.orst.edu/geowater/PEP/aopw/letcher-demography/
Ben Letcher (Molecular Markers, Sibship): http://www.fsl.orst.edu/geowater/PEP/aopw/letchersibship/
Ted Castro-Santos (Individual Movement): http://www.fsl.orst.edu/geowater/PEP/aopw/castrosantos/
James Peterson (Occupancy): http://www.fsl.orst.edu/geowater/PEP/aopw/peterson
Notes from the workshop were taken by all workshop organizers and graduate students from
Oregon State University, Department of Fisheries and Wildlife (Art Bass, Sierra Lewis, Becky
Miller) and Heidi Andersen, U.S. Forest Service Aquatic-Riparian Ecosystem Monitoring
Program.
Additional workshop attendees included local management agency representatives from the U.S.
Forest Service, Region 6, U.S. Fish and Wildlife Service, Region 1, and National Fish and
Wildlife Foundation. These attendees were present to listen and ask questions, but we did not
solicit input for scientific guidelines.
2010 May Memo: AOP, Not for citation or circulation, Page 3
Guidelines
A major objective of this effort is to produce concise guidelines in a document for managers
seeking to monitor the effectiveness of aquatic organism passage, particularly as it relates to
national design standards (http://www.stream.fs.fed.us/fishxing/aop_pdfs.html).
AOP document outline
1. Introduction – Background on the evolution of management guidance for aquatic
organism passage, including a brief review of the Forest Service approach involving
methods for assessing fish passage impairment (FishXing:
http://www.stream.fs.fed.us/fishxing/ ) and guidelines for restoring passage
(http://www.stream.fs.fed.us/fishxing/aop_pdfs.html). General issues regarding passage
restoration will be introduced, including the issue of “isolation versus invasion” in
addressing tradeoffs between benefiting native species versus facilitating invasion of
undesirable nonnative species
(http://www.fs.fed.us/rm/boise/publications/fisheries/rmrs_2009_fauschk001.pdf).
The major objectives will be to A) review species movements in stream networks and
their vulnerabilities to loss of connectivity (e.g., as related to stream crossings); B) review
methods for measuring impacts of connectivity (e.g., passage restoration); c) produce a
concise set of guidelines for use by managers in designing effectiveness monitoring.
2. Understanding movement and species vulnerability – this section of the report will entail
a broad overview of the types of species that depend on stream networks for movement
and how they can be affected by loss of connectivity. Summary tables (see below) will
provide a complement to this text narrative.
3. Evaluation/assessment of major responses – this section will focus on the four major
classes of methods we considered in the workshop: Occupancy, Molecular Markers,
Individual Movement, and Demography. Summary tables (see below) will provide a
complement to this text narrative.
4. Study design – A separate section will be devoted to discussing general parameters to
consider in study designs and provide examples of specific applications to highlight the
challenges that managers will face in the field in terms of structuring their monitoring to
focus on the impacts of aquatic organism passage and to avoid common pitfalls. This
will include a discussion of topics such as “before-after” versus “retrospective” study
designs, and the importance of understanding context (e.g., histories of culverts, species
introductions, etc.) in developing a study design or monitoring program.
5. Review and recommendations – This section will provide conclusions and a summary of
the major findings. It will provide a concise series of recommendations about monitoring
and a decision tree that can be easily adopted by managers for application to their
monitoring efforts.
2010 May Memo: AOP, Not for citation or circulation, Page 4
List of Tables and Figures – The AOP document will build from summary tables and figures
providing an overview of key issues. Draft examples of tables and figures to be included in the
final report are included here:
TABLE 1. General movement patterns of stream fish as expressed by 21 species
10
TABLE 2. General movement patterns of frogs and toads
15
FIGURE 1. Movement patterns of frogs and toads (created by Dr. Ivan Arismendi)
16
FIGURE 2. Relevant characteristics of frogs/toads to study their movement
(created by Dr. Ivan Arismendi)
17
TABLE 3. General movement patterns of salamanders
18
FIGURE 3. Movement patterns of salamanders (created by Dr. Ivan Arismendi)
19
FIGURE 4. Relevant characteristics of salamanders to study their movement
(created by Dr. Ivan Arismendi)
20
TABLE 4. General movement patterns of aquatic insects
21
TABLE 5. General movement patterns of 3 crayfish species and mussels
22
TABLE 6. Things to consider when interested in the DEMOGRAPHY of
aquatic organisms as an indicator of stream passage impairment
and passage restoration
23
TABLE 7. Things to consider when interested in the MOVEMENT of aquatic
organisms as an indicator of stream passage impairment and
passage restoration
25
TABLE 8. Things to consider when interested in the OCCUPANCY of aquatic
organisms as an indicator of stream passage impairment and
passage restoration
28
TABLE 9. Things to consider when interested in the GENETICS of aquatic
organisms as an indicator of stream passage impairment and
passage restoration
30
2010 May Memo: AOP, Not for citation or circulation, Page 5
STREAM AQUATIC ORGANISM MOVEMENT TABLE SUMMARIES 1
FISH (TABLE 1).—Stream fish species express many different types and patterns of movement
that vary within as well as between species. These movements and patterns range from limited
and localized movement within a small home range or territory, roundtrip exploratory ranging
movements into areas outside of their home range, one-way dispersal to a new location, regular
and predictable long-distance roundtrip migrations, as well as accidental displacement due to
stochastic events that impact stream dynamics. Many stream fish species can be quite mobile and
their patterns of movement can extend over long temporal and large spatial scales. Such
movements are fundamental to the persistence of populations across generations, and are an
expression of their diverse life histories and capacity to respond to dynamic environments.
Stream fishes are differentially susceptible to barriers to upstream movement, and potential
impacts include: 1) reduction or elimination of the ability of fish to disperse to or reach upstream
habitats; 2) eventual extirpation of mobile life history types from upstream populations; 3)
fragmentation and isolation of upstream populations; 4) increased vulnerability to the negative
impacts of stochastic environmental and habitat disturbances; 5) restriction of upstream
populations to potentially marginal and degraded habitats; 6) prevention of the recolonization of
disturbed upstream habitats; and 7) population genetic impacts such as the disruption of gene
flow from downstream populations , increased genetic drift in upstream populations,
development of genetic bottlenecks, loss of genetic diversity, and reduced effective population
size.
AMPHIBIANS (TABLE 2, TABLE 3).—Mode and pattern of amphibian movement and level of
activity in streams and stream corridors varies with life-stage. The pattern of movement of larvae
of species that breed in streams tends to be relatively limited and localized. Larvae (as well as
juveniles and adults) are susceptible to accidental displacement downstream during high-flow
events. Individuals that transform to the terrestrial life-stage (juveniles and adults) can occupy
home ranges of varying sizes (e.g., 12-350 m along a stream bank) within a stream riparian area.
Adults that breed in ponds (primarily frogs and toads) undertake overland breeding migrations
from streams to breeding sites; these migrations tend to be relatively rapid and of varying
distance. Migrating adults and transformed juveniles undertake [return] migrations to streams.
1
The final draft of this document will include supporting citations for all statements made herein.
2010 May Memo: AOP, Not for citation or circulation, Page 6
Riparian areas and stream channels are used by juveniles and adults as migration corridors, with
some species capable of moving as much as 670 m/day and up to 1.5 km over a period of 6 days.
Salamanders, in general, move upstream in spring-summer and downstream in winter; juveniles
and adults can move overland, typically within stream riparian areas; have been shown to be
susceptible to barriers to upstream movement (although results are mixed); and responsive to
stream crossing structures that are as wide as the stream channel, at the same grade as the
streambed, and contain rubble substrate. Frogs and toads, in general, move upstream and
overland (adults and juveniles) in spring-summer and downstream movements have been
associated with heavy rain events; have been shown to be somewhat susceptible to barriers to
upstream movement, with artificial structures affecting direction of movement; and able to move
through slotted-drain culverts designed to facilitate amphibian passage. Amphibian species in
isolated streams are predominantly restricted to a single stream; whereas in drainages with high
complexity and connectivity, adults (and to a lesser extent juveniles) are capable of inter-stream
and inter-catchment dispersal.
AQUATIC INSECTS (TABLE 4).—Mode and pattern of movement and level of activity varies with
species and life-stage. In general, aquatic larval activity and range of movement is limited and
localized, with downstream drift recognized as being the primary mechanism for longer
downstream movement. Drift is active when individuals select to enter the stream current for
transport to new locations with increased availability of resources for growth and survival. Drift
also can be passive or accidental when caused by stochastic events. Research indicates that drift
is a response correlated with upstream density-related factors and predators which initially
causes a decrease in density. Population densities upstream, however, are most probably
maintained because recruitment from upstream oviposition by non-drifting individuals as well as
adults flying upstream from downstream locations is sufficient to over-ride depletion due to
downstream drift. Aquatic insects also have differing abilities and opportunities for dispersal,
related in part to the complexity and connectivity of streams and drainage networks. Species in
isolated streams are predominantly restricted to a single stream, while the adults of species with a
flying life-stage are capable of inter-stream and inter-catchment dispersal in drainages with high
complexity and connectivity. Aquatic insects, in general, do not appear to be overly susceptible
to barriers to upstream passage.
2010 May Memo: AOP, Not for citation or circulation, Page 7
CRAYFISH (TABLE 5).—General pattern of movement of crayfish is characterized by a relatively
long period of limited, localized activity in a relatively small home range, followed by an
episode of longer distance dispersal to a new location or home range. Crayfish are capable of
movements over land for short periods of time. The direction of dispersal can be down- or
upstream. Some species appear to be susceptible to accidental displacement downstream during
high-flow events. These events are usually followed by a period of dispersal upstream as flow
decreases. This group has been documented to be susceptible to barriers to upstream passage.
MUSSELS (TABLE 5).—We consider mussels in the family Unionoidae, which represents the most
imperiled group of freshwater species in North America. Unionids are highly sedentary and their
movement and level of activity is life-stage specific. They are also primarily obligate parasites of
fishes, with movement dependent on attachment of larvae (glochidia) to host fish; therefore,
movement of glochidia is determined by the movement characteristics of the host species to
which they attach. Juveniles, after releasing from attachment to their hosts, burrow into sediment
where they remain relatively immobile. Adults are primarily sedentary, although they do
undertake limited short-range movements, and may be subject to accidental displacement during
high flows. The susceptibility of this group to barriers to upstream passage is most likely directly
related to the glochidia host organisms susceptibility to barriers.
DEFINITIONS OF TERMS USED IN TABLES:

STATION KEEPING movements and activities include foraging, commuting, and territorial
behavior , and typically occur within an animal’s home range.
o
Foraging is a regular, reiterative set of movements and activities (e.g., searching, hunting,
gathering, collecting, etc.) that facilitate the acquisition of resources.
o
Commuting is also a regular, reiterative movement or activity that facilitates resource
acquisition and the avoidance of predators.
o
Territorial behavior includes any number of agonistic movements or behaviors used by an
animal to establish or defend territory within its home range; and are usually of short
duration and tend to occur irregularly.

RANGING can be differentiated into movements and activities that facilitate the exploration of
or dispersal to new habitat.
2010 May Memo: AOP, Not for citation or circulation, Page 8
o
Exploring individuals are ones that leave their home range and travel to a contiguous or
disjunct location, and in a short period of time return to the original home range; this type of
movement tends to be irregular and relatively erratic.
o
Dispersing individuals do so by making one-way excursions from their present home range
to a new location where they establish a new home range; the new home range can be
contiguous or disjunct with the original home range.

MIGRATION is generally a regular and predictable long-distance movement undertaken by
animals to seasonally move between contiguous or disjunct locations. The general expression
of migratory movement is for an animal to move relatively quickly through multiple
contiguous or disjunct habitats from a location that provides resources for growth and
maturation to a location that provides resources for reproduction, birth, and the nurturance of
offspring.
2010 May Memo: AOP, Not for citation or circulation, Page 9
TABLE 1. GENERAL MOVEMENT PATTERNS OF STREAM FISH AS EXPRESSED BY 21 SPECIES (1 OF 5).
SPECIES
 Bonneville Cutthroat Trout
(Oncorhynchus clarkii utah)
DOMINANT TYPES OF MOVEMENT
 Station Keeping: summer-winter
 Migration: spawning; spring
GENERAL MOVEMENT PATTERNS
 Relatively mobile, although seasonal
 Greatest movement activity and
distance: spring (spawning, postspawning)
 Variable-sporadic movement and
limited distance: summer-winter (≤0.5
km)
STUDY LOCATIONS
 southeast Idaho
 western Wyoming
 northern Utah
 Coastal Cutthroat Trout (Oncorhynchus
clarkii clarkii)
 Station Keeping
o No movement (0 channel units)
o Local movement (1-5 channel units)
o Longer distance movements (>5
channel units)
o Pulsed movement (variable 1-3
above)
 Relatively short within-basin distances,
primarily at the channel unit-scale with
smaller proportion of population
making reach- and segment-scale
movements
 Seasonal component
o Greatest movement in April
o Least movement in October
 Unit-scale movements common
throughout year
 Reach- and segment-scale movements
typically occur in winter and spring
 western British Columbia
 southwest Oregon
 Westslope Cutthroat Trout
(Oncorhynchus clarkii lewisi)
 Station Keeping: summer and winter
 Migration: fall downstream; spring
upstream
 Seasonal, long distances, wide-spread
distribution
o Fall: downstream migration up to
194 km
o Winter: sedentary downstream
o Spring: upstream migration up to 475
km
o Summer: sedentary upstream
 Many individuals demonstrate homing
behavior, returning to the same
upstream channel habitat previously
occupied
 central Idaho
 central Oregon
 Rainbow Trout (Oncorhynchus mykiss;
non-anadromous)
 Station Keeping: summer-winter
 Migration: spring
 Unique seasonal movements suggest
potential for discrete within-basin
population structure
o Summer-winter: sedentary
o Spring: increased upstream
movement (up to >372-607 km)
 north-central British Columbia
 southwest Alaska
 southeast Idaho
TABLE 1. GENERAL MOVEMENT PATTERNS OF STREAM FISH AS EXPRESSED BY 21 SPECIES (2 OF 5).
2010 May Memo: AOP, Not for citation or circulation, Page 10
SPECIES
 Bull Trout (Salvelinus confluentus)
DOMINANT TYPES OF MOVEMENT
 Station Keeping
 Migration: variable distances for
spawning and return to non-spawning
habitat
GENERAL MOVEMENT PATTERNS
 Seasonal upstream and downstream
migrations vary by:
o Population
o Time of year (spring, fall)
o Distance (reported mean distances of
33 and 63 km; range 9-129 km)
 Migrations usually occur at night and
are relatively rapid
 Individuals typically return to or near
sites from which they migrated
 Juvenile emigration from natal habitat
can occur in two pulses (spring and fall)
– juveniles can stay in natal tributaries
for up to 3 years
 Some populations can be non-migratory
residents in headwater tributaries
STUDY LOCATIONS
 northwest Washington
 northwest Idaho
 northwest Montana
 Brook Trout (Salvelinus fontinalis)
 Station Keeping with upstream
dispersal
 Upstream dispersal typically occurs in
summer
 Movement of up to 3.4 km relatively
common
 central Idaho
 northern Colorado
 Mountain Whitefish (Prosopium
williamsoni)
 Station Keeping
 Migration: roundtrip to over-wintering
habitat
 Variable types of seasonal movement
o Single summer reach-no fall
migration
o Single summer reach-fall migration
to over-wintering habitat-return to
summer habitat (3-95 km)
o Multiple summer reaches-fall
migration to over-wintering habitatreturn to summer habitat
o Summer reach-fall migration to overwintering habitat-no return to
summer habitat
 northeast Oregon
 southeast Washington
2010 May Memo: AOP, Not for citation or circulation, Page 11
TABLE 1. GENERAL MOVEMENT PATTERNS OF STREAM FISH AS EXPRESSED BY 21 SPECIES (3 OF 5).
SPECIES
DOMINANT TYPES OF MOVEMENT
GENERAL MOVEMENT PATTERNS
STUDY LOCATIONS
 Largescale Sucker (Catostomus
macrocheilus)
 Station Keeping
 Migration: roundtrip to over-wintering
habitat
 Seasonal movement from upstream
habitats (spring-early summer) to
downstream over-wintering habitats
(beginning mid-summer through early
fall)
 Can be long distance movements: 17300 km; mean = 111 km
 Minimal movement during winter
 Return to upstream habitats in spring
 northeast Oregon
 southeast Washington
 Coastrange Sculpin (Cottus aleuticus)
 Station Keeping
 Ranging: short-distances downstream
 Distributed throughout mainstem and
tributaries
 In longer systems: downstream
migration (transport) of larvae toward
estuaries with subsequent upstream
migration of young and some older
individuals
 In shorter systems: downstream
spawning migration of adults with
subsequent upstream migration of
young and older individuals
 coastal northern California
 Prickly Sculpin (Cottus asper)
 Station Keeping
 Ranging – Migration: inter-tributary
 Distributed throughout mainstem and
tributaries
 Movement between mainstem and
tributaries (and vice versa)
 No apparent downstream transport of
larvae or migration of adults with
subsequent upstream migration of
young and older individuals
 coastal northern California
 Torrent Sculpin (Cottus rhotheus)
 Station Keeping
 Limited Migration
 Restricted to clear, cold streams with
swift current
 Limited migration to upstream
spawning sites by adults
 Larvae emerge around early August,
and drift and disperse downstream
(suggests upstream migration of young
individuals)
 northwest Montana
 Columbia River basin of the Pacific
Northwest
2010 May Memo: AOP, Not for citation or circulation, Page 12
TABLE 1. GENERAL MOVEMENT PATTERNS OF STREAM FISH AS EXPRESSED BY 21 SPECIES (4 OF 5).
SPECIES
DOMINANT TYPES OF MOVEMENT
GENERAL MOVEMENT PATTERNS
STUDY LOCATIONS
 Mottled Sculpin (Cottus bairdi)
 Station Keeping
 Restricted movement (1.3 – 4.4 m over
45 days) with sedentary and “mobile”
individuals
 Small home range = 12.9 m linear
stream distance
 Maximum distance traveled = 55 m
 Juvenile movement influenced by
interactions with adults and stream flow
 Adult movement influenced by
competitive interactions for suitable
space (habitat)
 western North Carolina
 Longnose Dace (Rhinichthys
cataractae)
 Station Keeping
 Restricted movement
 Small home range = 13.7 m linear
stream distance
 Maximum distance traveled = 40 m
 Territorial during spawning and
incubation
 Limited movement or transport out of
home range
 western North Carolina
 Blacknose Dace (Rhinichthys atratulus)
 Station Keeping
 Restricted movement
 Seasonal habitat shift:
o Late November = crevices under
rubble
o Late March = open water
 Can be territorial during spawning
 Short relocation movements in response
to predators
 southern Ontario
 Rosyside Dace (Clinostomus
funduloides)
 Station Keeping
 Restricted movement
 Small home range = 19.3 m linear
stream distance
 Maximum distance traveled = 98 m
 western North Carolina
2010 May Memo: AOP, Not for citation or circulation, Page 13
TABLE 1. GENERAL MOVEMENT PATTERNS OF STREAM FISH AS EXPRESSED BY 21 SPECIES (5 OF 5).
SPECIES
DOMINANT TYPES OF MOVEMENT
GENERAL MOVEMENT PATTERNS
STUDY LOCATIONS
 Central Stoneroller (Campostoma
anomalum)
 Station Keeping
 Restricted movement
 Small home range = 35.2 m linear
stream distance
 Maximum distance traveled = 135 m
 Most marked individuals recaptured in
initial capture pool or riffle
 Ohio
 Smallmouth Bass (Micropterus
dolomieui)
 Station Keeping
 Ranging
 Migration
 Varies seasonally
o Fall: sedentary or migrate >45 miles
to winter habitat
o Winter: typically inactive in deep
water; however some individuals are
active with regular short-term
movement
o Spring: spawn in mainstem or move
from mainstem to spawn in
tributaries; can move long distances
in mainstem (38 miles) and
tributaries (3 miles)
o Summer: migrate to summer habitat
with restricted area (e.g., single pool)
and movement; although home range
size varies (i.e., 70 yards to 1 mile)
and movement distance can be up to
3 miles







 Black-spotted Topminnow (Lepomis
olivaceus)
 Green Sunfish (Lepomis cyanellus)
 Longear Sunfish (Lepomis megalotis)
 Creek Chub (Semotilus maculates)
 Station Keeping
 Limited Ranging
 Movement generally not complex
 Restricted (“non-mobile”) movement:
67 – 88% of recaptured individuals did
not move out of pool of initial capture
 “Mobile” individuals: fish captured
outside of pool of initial capture (12 –
33%)
o Typically captured in adjacent pools
o 70% moved <100 m
o Longest distances moved = 453 and
506 m
 Arkansas (Ouachita River drainage)
southwest Wisconsin
Alabama
Tennessee
Massachusetts
Oregon
Ontario
Michigan
2010 May Memo: AOP, Not for citation or circulation, Page 14
TABLE 2. GENERAL MOVEMENT PATTERNS OF FROGS AND TOADS (1 OF 1).
LIFE STAGE

Larval

Juvenile and Adult
GENERAL MOVEMENT PATTERNS
 In-stream movement
 Reported maximum distance moved during 3
summer field seasons = 64 m in old-growth
streams and 3 m in clearcut streams
 Movement tends to be downstream from egg
deposition sites located near source of
streams







Movement typically semi-aquatic and
terrestrial in stream riparian areas
Adults of species that breed at wetland and
lentic locations can undertake overland
migratory movements to these sites
Juveniles that transform at wetland and lentic
sites migrate overland back to stream sites
Streams and stream riparian areas are also
used as migration corridors by juveniles and
adults
Home ranges have been estimated to be 12350 m along stream banks
Species such as B. b. boreas have been
documented to move 1.5 km upstream over a
period of 6 days
Some species can move 10-670 m/day
SPECIES

Ascaphus truei









Ascaphus truei
Bufo boreas boreas
Hyla cadaverina
Rana clamitans
Rana muscosa
Rana palustris
Rana pipiens
Rana pretiosa pretiosa
Rana sylvatica
2010 May Memo: AOP, Not for citation or circulation, Page 15
Movement patterns of frogs and toads
larval
non-breeding season
juvenile
adult
downstream
• movements close to the stream (25 m)
• up to 670 m x day-1
• home range = up to 350 m along the shore
• philopatry level = medium high
• upstream movements in summer
dispersal
• up to 75 m during summer
• philopatry level = low
• mostly during summer
breeding season
• upstream up to 100 m after
breeding (late summer - low flows)
• highly variable distances moved
after breeding
• fast and extensive movements
after breeding
ing
d
e
bre
growth
bre
ed
ing
• short distances between habitats (25 m)
• up to 10 m x day-1
• home range = up to 12 m along the shore
• philopatry level = high
• movements may also occur in winter
post-bre
eding
multiyear life stages
• spring breeding
Species included: Ascaphus truei, Bufo boreas boreas, Hyla cadaverina, Rana clamitans,
R. muscosa, R. palustris, R. pipiens, R. p. pretiosa, R. sylvatica,
Figure 1.
2010 May Memo: AOP, Not for citation or circulation, Page 16
Relevant characteristics of frogs/toads to study their movements
larval
juvenile
adult
non-breeding season
methods
methods
• sampling season = summer
• traps; direct sampling;
mark and recapture
• leaf litter traps biased to
larger individuals (> 15 mm);
dip net biased in smaller
individuals (<15 mm)
• sampling season = summer-fall
• in-stream traps; direct sampling;
mark and recapture; pit-tags;
telemetry
predictors (association)
• POSITIVE: location in the
basin; basalt stream; > 300
m altitude; fast flow;
cobble substrate; cold
water
• NEGATIVE: Low thermal
tolerance; road presence
(erosion); logs presence
(do not allow larval
dispersal)
management
• very specific in habitat use
• densities old-growth >
clear-cut
predictors (association)
• POSITIVE: water temperature;
water depth; air temperature;
food presence
• NEGATIVE: trout presence
management
• density clear-cut > old-growth
• movements clear-cut upstream
• movements in old-growth toward
the stream
• clear-cut reduces habitat patch size
• beaver dams may act as barriers
• movements in females > males
• movements are age-specific
• downstream movements detected
after heavy rains
breeding season
methods
• sampling season = year-round
• direct sampling; mark and
recapture; traps
predictors (association)
• POSITIVE: large boulder;
precipitation; min air
temperature; humidity
• NEGATIVE: fine sediment; peat
mining activities
management
• densities old-growth > clear-cut
• road hindering movements
• artificial structure change
directionality of movements
• bridges used as spots
predictors (association)
• POSITIVE: sites without
trout
management
• densities old-growth >
clear-cut
• slotted-drain culverts facilitate amphibian
crossings by allowing sunlight and air exchange
Figure 2.
2010 May Memo: AOP, Not for citation or circulation, Page 17
TABLE 3. GENERAL MOVEMENT PATTERNS OF SALAMANDERS (1 OF 1).
LIFE STAGE
 Larval and Gilled-Adult (neotene)






Juvenile and Adult (transformed)






GENERAL MOVEMENT PATTERNS
In-stream movement
Movement tends to be relatively localized
with ability to move documented to be up to
19 m/day, an average of <30 m during 2
summer field seasons, and 51 m/2 month
period
Spring-summer in-stream movement is
primarily upstream
Tend to move downstream in winter
Presence of pipe culverts and culverts with
perched outlets have been shown to impair
larval upstream passage
Movement typically semi-aquatic and
terrestrial in stream riparian areas and
relatively localized (e.g., up to 4 m/day)
Home range can be up to 85 m along stream
bank
Juveniles have been documented to move as
much as 600 m along stream bank
Summer movement primarily upstream
Winter movement primarily downstream
Presence of culverts have been shown to
affect upstream passage




SPECIES
Dicamptodon tenebrosus
Gyrinophilus porphyriticus
Pseudotriton ruber
Rhyacotriton variegatus











Cryptobranchus alleganiensis
Desmognathus fuscus
Dicamptodon copei
Dicamptodon ensatus
Dicamptodon tenebrosus
Gyrinophilus porphyriticus
Psudotriton ruber
Rhyacotriton cascadae
Rhyacotriton kezeri
Rhyacotriton olympicus
Rhyacotriton variegatus
2010 May Memo: AOP, Not for citation or circulation, Page 18
Movement patterns of salamanders
multiyear life stages
juvenile
downstream
larval
• upstream movements in
summer; downstream in winter
• those w/better body condition
moved upstream and those w/poor
body condition moved downstream
• up to 19 m x day
during spring-summer
-1
• downstream during
winter
breeding season
adult
• up to 600 m during
summer
• philopatry level = medium
dispersal
non-breeding season
growth
• up to 4 m x day-1
• home range = up to 85 m
along the shore
• philopatry level = high
• lateral movements during night
• upstream movements when
moisture is low
• microhabitat temperature less
than air but warmer than
stream = they are more active
ing
d
e
bre
• crossed forest edges
to breeding pools
bre
ed
ing
• active and feed during winter
• found under the soil
Species included: Cryptobranchus alleganiensis, Desmognathus fuscus, Dicamptodon copei, D. ensatus, D. tenebrosus, Gyrinophilus
porphyriticus, Pseudotriton ruber, Rhyacotriton cascadae, R. kezeri, R. olympicus, R. variegatus
Figure 3.
2010 May Memo: AOP, Not for citation or circulation, Page 19
Relevant characteristics of salamanders to study their movements
larval
adult
juvenile
non-breeding season
methods
• sampling season = springsummer
• direct sampling; mark and
recapture
• leaf litter traps biased for
larger individuals (> 15 mm);
dip net biased for smaller
individuals (<15 mm)
predictors (association)
• POSITIVE: large substrate;
periphyton; food
• NEGATIVE: road presence
(erosion); fine sediment
management
• culvert: outlet drops initial
barrier (lack of jump
capacity); absence of bottom
substrate in culvert may
affect negatively; negative
effect in survival and
growth; higher density
found in arch culvert than in
pipe culvert (3.1-18 times);
cannot pass upstream in
pipe culvert
methods
• sampling season = spring-summer
• direct sampling; mark and recapture; traps
predictors (association)
• POSITIVE: small stream; splash zones;
waterfalls; confluence of first order
streams; body condition with movement
direction; large streambed substrate with
diversity and richness; cold and faster
waters
• NEGATIVE: fish presence; logging
management
• roads cause erosion affecting their presence
• intermittent stream beds facilitate
movements
• culverts need to be as wide as the stream
channel, at the same grade as the streambed,
and dominated by rubble substrate
breeding season
methods
• sampling season = springsummer-fall
• direct sampling; mark and
recapture; traps
predictors (association)
• POSITIVE: pool density; LWD in
riparian zones; proportion of
active channel; gradient of
logging and rocky substrate;
cobble-sized rocks
• NEGATIVE: fine sediment; low
management
gradient + logging; road presence • movements in
females = males
management
• roads cause erosion which
• densities oldaffects their presence
growth > clear-cut
• movements depend on
landscape characteristics
• roads limit movement, open land can be crossed without
roads, streambeds facilitate movements
• culverts need to be as wide as the stream channel, at
the same grade as the streambed, and dominated by
rubble substrate
• slotted-drain culverts facilitate crossings by allowing
sunlight and air exchange
Figure 4.
2010 May Memo: AOP, Not for citation or circulation, Page 20
TABLE 4. GENERAL MOVEMENT PATTERNS OF AQUATIC INSECTS (1 OF 1).

TYPE OF MOVEMENT
Crawling and Swimming
LIFE-STAGE
Larval - Adult
PATH
Localized - Multidirectional
ACTIVE- PASSIVE
Active

Flying
Adult
Multidirectional
Active

Drift
Larval - Adult
Downstream
Active - Passive

Rafting – Egg Broadcast
Egg - Larval
Localized and Downstream
Passive
CAVEATS:







Typical periods of no movement: pupation, diapause, eggs – early instars
Upstream flight of adults probably more random than directional
Population densities upstream most probably maintained because recruitment from upstream oviposition by non-drifting individuals is sufficient to
over-ride depletion due to downstream drift
Habitat heterogeneity in streams is high and the range of local environmental conditions can be wide
In general, taxonomic richness is highly variable, and species richness increases with stream size and is highest in mid-order streams
Aquatic insects have differing abilities and opportunities for dispersal, with some species restricted to a single stream while others are capable of
inter-catchment dispersal
Complexity and connectivity of stream and drainage network are important factors to consider relative to taxonomic and species richness, and the
presence-absence of aquatic invertebrates
2010 May Memo: AOP, Not for citation or circulation, Page 21
TABLE 5. General movement patterns of 3 crayfish species and mussels (1 OF 1).
GROUP - SPECIES
 Red Swamp Crayfish (Procambarus clarkii)
DOMINANT TYPES OF MOVEMENT
 Station Keeping
 Ranging (episodic dispersal)
GENERAL MOVEMENT PATTERNS
 Typically stationary with periods of episodic
movement to new location up- or downstream

Rusty Crayfish (Orconectes procericambarus
rusticus)


Station Keeping
Ranging (episodic dispersal)

Typically stationary with periods of episodic
movement to new location, although
apparently not inclined to migrate upstream
nor to be flushed downstream
 Home range: 9.7 – 60 m2 area; 9.4 – 47 m
length
 Susceptible to barriers to upstream movement

Signal Crayfish (Pacifasticus lenisculus)

Stationary to relatively mobile






Mussels (Unionoidae)

Stationary with indirect mobility via
parasitizing mobile host fishes

Active downstream movement: median
maximal distance = 15 m (range = 0 – 417 m)
Active upstream movement: median maximal
distance = 13.5 m (range = 0 – 283 m)
Capable of range expansion up to 2.4 km/y
Passive downstream movement due to drift or
flushing during high-flow events followed by
upstream dispersal with decreasing flow
Susceptible to barriers to upstream movement
Movement is life stage dependent
o Glochidia (larvae): parasitize host
(typically fish) and their mobility is
determined by movement characteristics of
host
o Juveniles: release from host and burrow
into sediment until mature
o Adults: highly sedentary with limited
mobility
2010 May Memo: AOP, Not for citation or circulation, Page 22
TABLE 6. CONSIDERATIONS FOR APPLYING DEMOGRAPHY OF AQUATIC ORGANISMS AS AN INDICATOR OF STREAM PASSAGE IMPAIRMENT AND PASSAGE
RESTORATION (1 OF 2).
VITAL SIGN
STRENGTHS
WEAKNESSES
CAVEATS
 Density of population
 Useful for documenting and characterizing
populations over time
 Primary assumption is that habitat and
population dynamics1 are similar above
and below stream crossing
 If interest is in populations immediately
above and below stream crossing then 1
time assessment is appropriate
 However, as scale of interest increases,
distance and network effects need to be
considered and spatial and temporal
assessments need to be increased to better
determine and characterize variability
 Must be spatially, temporally, and life
stage consistent (i.e., life-stage specific or
life-stage inclusive)
 Habitat data should be collected for
assessing how much of the variation in
population density is correlated with
differences in habitat characteristics
above and below stream crossing
 Composition of the
 Useful for documenting and characterizing
assemblages over time
 Simple to calculate
 Easy to understand
 Readily appreciated
 Easy to communicate to managers and
policy makes
 Very sensitive to sample unit area and
skill of observer-technician
 Measurement error is high for small,
cryptic, mobile, or taxonomically
difficult organisms
 Requires relatively long term data set to
determine and characterize variability
 Must be spatially, temporally, and lifestage consistent (i.e., life-stage specific or
life-stage inclusive)
 Habitat data should be collected for
assessing how much of the variation in
assemblage measures are correlated with
differences in habitat characteristics
above and below stream crossing
of species of interest
(SI) above and below
stream crossing
species assemblage
above and below stream
crossing
1
Such as recruitment, mortality, emigration, immigration, etc.
2010 May Memo: AOP, Not for citation or circulation, Page 23
TABLE 6. CONSIDERATIONS FOR APPLYING DEMOGRAPHY OF AQUATIC ORGANISMS AS AN INDICATOR OF STREAM PASSAGE IMPAIRMENT AND PASSAGE
RESTORATION (2 OF 2).
VITAL SIGN
 Density of population of
species of interest (SI)
above and below stream
crossing
 Composition of the
species assemblage
above and below stream
crossing
POTENTIAL IMPACT OF
STREAM CROSSING
PREDICTION AFTER
RESTORATION
 No upstream impasse: no significant
difference between density of SI
population above and below stream
crossing
 Partial upstream impasse: density of
SI population above stream crossing <
SI population density below stream
crossing
 Complete upstream impasse: density
of SI population above stream
crossing significantly diminished
relative to SI population density below
stream crossing; or SI population
above stream crossing extirpated
 No upstream impasse: no significant
difference in richness and diversity
measures above and below stream
crossing
 Partial upstream impasse: richness and
diversity of assemblage above stream
crossing < richness and diversity of
assemblage below stream crossing;
some mobile species extirpated
 Complete upstream impasse: richness
and diversity of assemblage above
stream crossing significantly <
richness and diversity of assemblage
below stream crossing; many mobile
species extirpated
MEASURE
SPATIAL / TEMPORAL SCALES
 Population size similar above
and below stream crossing
 Density as CPUE
2
 Spatial: sample, habitat, multiple
habitats
 Temporal: season, year, multiseason and year
 Assemblages similar above
 Species richness
 Alpha diversity3
 Gamma diversity4
 Spatial: sample, habitat, multiple
habitats
 Temporal: season, year, multiseason and year
and below stream crossing
2
Such as number of individuals of species of interest per sample, single habitat, multiple or all habitats, reach, total area sampled, unit of time, etc.
Number of species per individual sample unit
4
Richness of species over a range of habitats
3
2010 May Memo: AOP, Not for citation or circulation, Page 24
TABLE 7. CONSIDERATIONS FOR APPLYING MOVEMENT OF AQUATIC ORGANISMS AS AN INDICATOR OF STREAM PASSAGE IMPAIRMENT AND PASSAGE
RESTORATION (1 OF 3).
VITAL SIGN
 Movement of aquatic organisms through stream
crossing
POTENTIAL IMPACT OF STREAM CROSSING
 No upstream impairment: Organisms documented to
be present below stream crossing are at time n
documented to be above stream crossing (and vice
versa) at level of abundance that suggests no impasse
to movement through crossing; this can be measured in
terms of rate of movement, population density, species
richness, number of individuals of species of interest,
life-stage of interest, etc
 Partial upstream impairment: Organisms documented
to be present below stream crossing are at time n
documented to be above stream crossing (and vice
versa) at level of abundance that suggests that
movement through stream crossing is compromised;
although organisms are detected moving through
stream crossing
 Complete upstream impairment: Organisms
documented to be present below stream crossing are
not detected above stream crossing; downstream
organisms not detected moving upstream through
stream crossing
PREDICTION AFTER RESTORATION
 Movement of aquatic organisms up- and downstream
through stream crossing not restricted based on
parameter(s) or metric(s) of interest
2010 May Memo: AOP, Not for citation or circulation, Page 25
TABLE 7. CONSIDERATIONS FOR APPLYING MOVEMENT OF AQUATIC ORGANISMS AS AN INDICATOR OF STREAM PASSAGE IMPAIRMENT AND PASSAGE
RESTORATION (2 OF 3).
MEASURE
SPATIAL / TEMPORAL
SCALES
STRENGTHS
WEAKNESSES
CAVEATS
 Capture-Mark-Recapture –
minnow traps; electrofishing;
seining; fyke;, etc.
 Spatial: multiple units (e.g.,
habitat, reach, watershed)
 Temporal: multiple units
(e.g., diurnal, nocturnal, diel,
lunar, seasonal, annual)
 Can provide a relatively useful
estimate of population size
 Repeated sampling of marked
individuals can generate
additional demographic and
ecological data
 Can be useful for identifying
and documenting biases that
influence population
estimation
 Can be labor and gear
intensive and costly
 Assumes constant population
size
 May effect behavior of some
individuals or species
 Marked individuals not readily
recaptured (i.e., time
restricted)
 Designed more for population
size estimate
 Difficult to determine
directionality of movement
 No continuous monitoring
 Requires physical capture and
recapture
 Individuals can be similarly
marked or marked to be
individually recognizable
 Important to separate effect of
capture method from
volitional movement
 Technique can be constrained
by life stage, season, size and
sex of organism, direction of
movement, etc.
 Time interval required
between capture and recapture
 Telemetry - PIT
 Spatial: fixed position or
mobile
 Temporal: intermittent or
continuous
 Potential for continuous
monitoring
 Mobile tracking
 Scale from cm to meters
 Can be used for small
organisms
 Allows for direct
quantification of movement
 Unlimited number of codes
 relatively high start up cost
 Can be somewhat labor
intensive
 Requires electrical power
source
 Telemetry - Radio
 Spatial: continuous
 Temporal: continuous
 Potential for continuous
monitoring
 Capable of nested and discrete
scales
 Minimum resolution = 5 m
 Mobile tracking
 Possible 2D coverage
 100s of codes
 Relatively high start up cost
 Requires electrical power
source
 Telemetry - Acoustic
 Spatial: continuous
 Temporal: continuous
 Potential for 2D to 3D
continuous coverage
 Relatively high start up cost
 No mobile tracking
 Organisms need to be large
 Requires electrical power
source
2010 May Memo: AOP, Not for citation or circulation, Page 26
TABLE 7. CONSIDERATIONS FOR APPLYING MOVEMENT OF AQUATIC ORGANISMS AS AN INDICATOR OF STREAM PASSAGE IMPAIRMENT AND PASSAGE
RESTORATION (3 OF 3).
MEASURE
SPATIAL / TEMPORAL
SCALES
STRENGTHS
WEAKNESSES
CAVEATS
 Individual Marks – VI, Floy,
CWT, PIT
 Spatial: multiple units (e.g.,
habitat, reach, watershed)
 Temporal: multiple units
(e.g., diurnal, nocturnal, diel,
lunar, seasonal, annual)
 Relatively low startup costs
(less true for PIT)
 Unlimited codes
 Relatively high personnel
costs
 Low detection power
 High Type II error (less true
for PIT)
 Requires physical capture and
recapture
 Can be used with individuallevel metrics to assess factors
or conditions that effect partial
passage
 Can be used with relatively
small l sample size
 Batch Marking – Tetracycline;
fin-clip; freeze brand;
immersion dye; Elastomer
 Spatial: multiple units (e.g.,
habitat, reach, watershed)
 Temporal: multiple units
(e.g., diurnal, nocturnal, diel,
lunar, seasonal, annual)
 Can mark many individuals
quickly and cheaply
 Low start up costs
 High personnel costs
 No individual identification
 Limited resolution
 Requires physical capture and
recapture
 Can be used with populationlevel metrics
 Useful as a way of getting a
“snapshot” of whether
organisms are able to move
through stream crossing
 Requires relatively large
sample size
 Trapping – directional; whole
stream; with or without mark
 Spatial: multiple units (e.g.,
habitat, reach, watershed)
 Temporal: multiple units
(e.g., diurnal, nocturnal, diel,
lunar, seasonal, annual)
 Can be continuous in time
 Does not require marking
 Mobile species can be
captured
 Can be used to integrate
movement through time
 Can be vulnerable to flow
 Cost of implementation and
maintenance variable
 Measure assumes that traps
above and below stream
crossing have equal trapping
efficiency; and cannot assume
that efficiency is 100%
2010 May Memo: AOP, Not for citation or circulation, Page 27
TABLE 8. CONSIDERATIONS FOR APPLYING OCCUPANCY OF AQUATIC ORGANISMS AS AN INDICATOR OF STREAM PASSAGE IMPAIRMENT AND PASSAGE
RESTORATION (1 OF 2).
VITAL SIGN
STRENGTHS
WEAKNESSES
CAVEATS
 Simple occupancy (or presenceabsence) of single or multiple species
and single or multiple life stages above
and below stream crossing
 Relatively easy and cheap to assess
 Can be measured in a single season
 Flexible: Can be used to quantify
multiple species and life stages during
single site visit; many different ways to
accomplish the necessary multiple
surveys
 Can be used with redds and nest
surveys
 Results can be incorporated with other
methods (e.g., genetics and
demographics)
 Outcomes are context dependent
 This method is not necessarily effective
if there is nothing “missing” (i.e.,
species and life stages occur above and
below culvert)
 Coarse and simple measure (note: this
could also be a strength)
 Use this if simply want to know if a
species/life stage or multiple
species/life stages are present above a
stream crossing before and after
restoration; and if surveys sometimes
miss a species/life stage that is present
 Requires sample size of 20+ sites for
inference beyond single site
 Time dependent (for instance multiseason sampling provides more
information)
 Yields a probability that a species/life
stage is present for each site surveyed
 Change in occupancy of single or
multiple species and single or multiple
life stages above and below stream
crossing in the context of metademographic parameters such as
extinction or colonization
 Relatively easy and cheap to assess
 Allows for larger spatial sampling and
can be useful for network and
landscape-level assessment
 Flexible: Can be used to quantify
multiple species and life stages during
multiple surveys and/or seasons; many
different ways to accomplish the
necessary multiple surveys
 Can be used with redds and nest
surveys
 Results can be incorporated with other
methods (e.g., genetics and
demographics)
 Can be used to document colonization
and recruitment, and extinction over
time
 Outcomes are context dependent
 This method is not necessarily effective
if there are nothing missing (i.e.,
species and life stages occur above and
below stream crossing)
 Use if want to know more about
dynamics and persistence across a
broader landscape
 Requires sample size of 20+ sites for
inference beyond single site
 Requires multiple years of survey (e.g.,
3+ years)
2010 May Memo: AOP, Not for citation or circulation, Page 28
TABLE 8. CONSIDERATIONS FOR APPLYING OCCUPANCY OF AQUATIC ORGANISMS AS AN INDICATOR OF STREAM PASSAGE IMPAIRMENT AND PASSAGE
RESTORATION (2 OF 2).
VITAL SIGN
 Simple occupancy (or
presence-absence) of single or
multiple species and single or
multiple life stages above and
below stream crossing
 Change in occupancy of
single or multiple species and
single or multiple life stages
above and below stream
crossing in the context of
meta-demographic parameters
such as extinction,
colonization, reproduction,
etc.
POTENTIAL IMPACT OF STREAM
CROSSING
PREDICTION AFTER
RESTORATION
 No upstream impasse: no significant
difference in occupancy or presence
of single or multiple species and
single or multiple life stages above
and below stream crossing
 Partial upstream impasse: occupancy
or presence of some species and life
stages may be different between sites
above and below stream crossing
 Complete upstream impasse:
occupancy or presence of species
and life stages above stream crossing
significantly different than
occupancy or presence of species
and life stages below stream
crossing; many [if not all] species
and life stages above stream crossing
extirpated
 Occupancy of species
and species life stages
similar above and below
stream crossing
 No upstream impasse: no significant
difference in occupancy of single or
multiple species and single or
multiple life stages above and below
stream crossing
 Partial upstream impasse: occupancy
of some species and life stages may
be different between sites above and
below stream crossing [e.g.,
presence of life stages representing
recruitment and colonization above
stream crossing diminished]
 Complete upstream impasse:
occupancy of species and life stages
above stream crossing significantly
different than occupancy of species
and life stages below stream
crossing; many [if not all] species
and life stages above stream crossing
extirpated
 Passage restoration
results in colonization of
upstream site, with
increased presence of
life stages representing
successful recruitment,
and persistence is
equivalent to downstream reference site(s)
 Occupancy, extinction,
and colonization similar
above and below stream
crossing
MEASURE
 Survey presence of
species and life stages
above and below stream
crossing during single
site visit [“snap shot”]
using standard protocol
SPATIAL / TEMPORAL SCALES
 Spatial: multiple sites above and
below stream crossings; single or
multiple habitats
 Temporal: 1 season/year
 Survey presence of
species and life stages
above and below stream
crossing in multiple
seasons or years using
standard protocol
 Spatial: multiple sites above and
below stream crossings; single or
multiple habitats
 Temporal: multiple seasons or
[preferably] multiple years
2010 May Memo: AOP, Not for citation or circulation, Page 29
TABLE 9. CONSIDERATIONS FOR APPLYING GENETICS OF AQUATIC ORGANISMS AS AN INDICATOR OF STREAM PASSAGE IMPAIRMENT AND PASSAGE
RESTORATION (1 OF 3).
VITAL SIGN
STRENGTHS
WEAKNESSES
CAVEATS
 Genetic Variation





1 time sample
Sensitive measurement
Demonstrated experimentally
Commonly understood
Can be bundled with other measures
 Time since barrier installed/ removed
 Barrier location
 Potential confounding factors such as
population size and habitat quality
 Colonization history
 Relevant for entire populations
 $3000 lab and analysis per stream
crossing
 Differentiation




1 time sample
Demonstrated performance
Commonly understood
Can be bundled with other measures
 Time since barrier installed/ removed
 Barrier location
 Potential confounding factors such as
population size and habitat quality
 Colonization history
 Relevant for entire populations
 Zero cost if combined with Genetic
Variation
 Estimation of effective population size
 Direct estimation of metric of concern
 Can be bundled with other measures
 Various data requirements
 Constraining assumptions
 Uncertain estimates (i.e., accuracy)
 Relevant for entire populations
 Zero cost if combined with Genetic
Variation
 Recent demographic history (stability
 Provides view of recent population
dynamics
 Multiple statistical tests available
 Can be bundled with other measures
 Constraining assumptions
 Uncertain estimates (i.e., accuracy)
 Relevant for entire populations
 Zero cost if combined with Genetic
Variation
 Isolation by distance
 1 time sample
 Demonstrated performance
 Commonly understood
 Time since barrier installed/ removed
 Barrier location
 Potential confounding factors such as
population size and habitat quality
 Colonization history
 Relevant for multiple populations
 6X more expensive than Genetic
Variation
 Individual movement
 current time frame
 Direct movement
 Can be detected in the absence of
differentiation
 Assignment methods and error depend
on differentiation (STRUCTURE)
 High probability of Type I error and
 Intensive sampling required to reduce
Type I error
 Relevant at the level of individuals
 Hatchery - hybrid markers
 high probability of detection
 Species dependent
 Can be bundled with other measures
 Number of markers determines power
 May miss n generation back crosses
 Relevance variable
 Individual based landscape genetics
 Minimal assumptions
 May uncover undetected barriers
 Requires intensive and well-designed
sampling
 Moderate feasibility
(EPS)
vs bottleneck)
2010 May Memo: AOP, Not for citation or circulation, Page 30
TABLE 9. CONSIDERATIONS FOR APPLYING GENETICS OF AQUATIC ORGANISMS AS AN INDICATOR OF STREAM PASSAGE IMPAIRMENT AND PASSAGE
RESTORATION (2 OF 3).
POTENTIAL IMPACT OF
STREAM CROSSING
PREDICTION AFTER
RESTORATION
 Genetic Variation
 Stream crossing increases drift
and inbreeding after n
generations
 Upstream population variation
and diversity is increased
relative to downstream
reference population
 HE
 Allelic richness
 Recent evolution within 2–5
(several) generations
 Differentiation
 Stream crossings cause drift &
reduced migration
 Differentiation between
upstream and downstream
populations is reduced relative
to natural conditions
 Fst, etc.
 Recent evolution within 2–5
(several) generations
 Estimation of effective
 Isolation above stream
crossings reduces effective
population sizes
 EPS approaches that of EPS
below stream crossing
 Ne
 Recent evolution within 2–5
(several) generations
 Recent demographic history
 Isolation increases
demographic stochasticity
 No evidence of bottleneck and
evidence of population growth
 M ratio
 Multiple methods
 Recent evolution within 2–5
(several) generations
 Isolation by distance
 Increased drift or decreased
gene flow results from loss of
connectivity
 Reduced residual variability
overall, but depends on
species biology
 Mantels test
 Network with longer temporal
span than 2–5 generations
 Individual movement
 Stream crossings reduce
individual movements,
asymmetrical movement
upstream to downstream
 Individual movement
comparable to reference area
 Assignment tests
 Sibship analysis
 Genetic mark/recapture
 Short spatial -temporal extent,
but could be increased
depending on methods
VITAL SIGN
population size (EPS)
(stability vs bottleneck)
MEASURE
SPATIAL / TEMPORAL
SCALES
2010 May Memo: AOP, Not for citation or circulation, Page 31
TABLE 9. CONSIDERATIONS FOR APPLYING GENETICS OF AQUATIC ORGANISMS AS AN INDICATOR OF STREAM PASSAGE IMPAIRMENT AND PASSAGE
RESTORATION (3 OF 3).
VITAL SIGN
POTENTIAL IMPACT OF
STREAM CROSSING
PREDICTION AFTER
RESTORATION
MEASURE
SPATIAL / TEMPORAL
SCALES
 Hatchery - hybrid markers
 Stream crossing reduces
probability of upstream
directed invasion if source is
downstream
 Stream crossing increases
impacts to upstream
population from downstream
directed invasion, but
downstream impacts below
barrier may be reduced
 Detection of invasive alleles
more likely
 Reduced proportion of
nonnative genes in upstream
population; increased
proportion in downstream
population
 Presence of nonnative alleles
 Variable
 Individual based landscape
genetics
 Disrupts patterns of spatial
relatedness or decreases
neighborhood size
Disruption of spatial relatedness
and decreased neighborhood size
reduced
 Individual genotypes and geocoordinates
 Auto-correlation
o Variable
2010 May Memo: AOP, Not for citation or circulation, Page 32
APPENDIX: AQUATIC ORGANISM PASSAGE WORKSHOP PROGRAM
AQUATIC ORGANISM PASSAGE WORKSHOP:
GUIDELINES FOR AN EFFECTIVENESS MONITORING PROTOCOL
Workshop Agenda –
Dates: 16-18 March 2010
Place: Portland, Oregon:
Tuesday 16 March 2010
9-945 AM Workshop introduction
 Why are we here, how did we get here?
o Kim Clarkin, San Dimas Technology Center, 10 min
 Quick review of workshop agenda, anticipated products
o Jason Dunham, USGS, 15 min
 Workshop logistics
o Guillermo Giannico, Oregon State University, 5 min
 Introductions
o Everybody, 15 min
945-10 AM
 Break –
PRESENTATIONS (MODERATED BY GIANNICO)
10-1045 AM
 PRESENTATION: OCCUPANCY
(Jim Peterson, University of Georgia/USGS)
1045-1130
 DISCUSSION: OCCUPANCY (Everybody)
1130-1230
 Lunch Break
1230-115 PM
 PRESENTATION: MOLECULAR MARKERS (Helen Neville, Trout Unlimited)
115-200 PM
 DISCUSSION: MOLECULAR MARKERS (Everybody)
200-215 PM
 Break – meeting continues in same room
215-300 PM
 PRESENTATION: INDIVIDUAL MOVEMENT (Ted Castro-Santos, USGS and Keith Nislow,
USFS)
300-345 PM
 DISCUSSION: INDIVIDUAL MOVEMENT (Everybody)
345-400 PM
 Break – meeting continues in same room
400-445 PM
 PRESENTATION: DEMOGRAPHY (Ben Letcher, USGS)
445-530 PM
2010 May Memo: AOP, Not for citation or circulation, Page 33

DISCUSSION: DEMOGRAPHY (Everybody)
Wednesday 17 March 2010
830-9:45 AM
 DISCUSSION: STUDY DESIGNS, NONNATIVES, DISCUSSION OF BREAK-OUT
SESSIONS (Jason Dunham)
1000-10:15 AM
 Break, assemble into groups for breakout sessions
10:15-130 PM
 Break-out groups: Occupancy, Molecular Markers, Individual Movement, Demography
 Lunch to be served while you work
130-200 PM
 Break
200-400 PM
 30 minutes for reporting and discussion of results from each break-out group
400 PM
 Concluding comments for Day 2 – Free time for remainder of the day
Thursday 18 March 2010
830-?
 Discussion of opportunities for implementation and effectiveness monitoring – consider this day
to be an opportunity to process information from the prior two days and to think about next steps
in terms of recommendations and perhaps doing some new work (monitoring and research) on the
ground if funding is available.
o Updates on funding opportunities
o Possible projects/issues (in no particular order)

Study designs, locations, extent, methods, species, etc.

What questions make the most sense to answer at different scales, for example
national policy (GAO/OMB/FHWA) vs. watershed (large/small) or district?


What methods are feasible/desirable for answering those questions?
What kind of effort is needed to get answers (extensive, distributed by
hydrographic/geographic region/other)

What base information (meta-data?) is needed?

How can field biologists contribute?
2010 May Memo: AOP, Not for citation or circulation, Page 34