Interim Report---Scientific/Educational Permit \# 344

Submitted by Warren Colyer, Research Fisheries Biologist, Trout
Unlimited

December 17, 2004

This is an interim report to document 2004 field activities carried out
under scientific/education collection permit number 344 and is submitted
in compliance with the 12/31/04 deadline as per notification from the
Wyoming Game and Fish Department. A complete annual report will be
published in March 2005 and will be sent to the Wyoming Game and Fish
Department as the official documentation of research activities.

**SUMMARY OF 2004 RESEARCH ACTIVITIES**

***Introduction.*** Bonneville cutthroat trout (BCT) currently occupy
\<5% of their historic range and the subspecies is designated as
'Sensitive' by the USDA Forest Service and 'a Species of Concern' by the
states of Utah, Idaho, and Wyoming. The Thomas Fork, the neighboring
Smith's Fork, and sections of the Bear River between these two fourth
order tributaries support one of the most genetically pure populations
of Bonneville cutthroat trout (BCT) throughout its native range and
comprise what is likely the last connected large river habitat available
to fluvial BCT. Independent research projects were initiated in 1998 and
1999 by the University of Wyoming and Utah State University,
respectively, with the goal of gaining a better understanding of the
life history characteristics, habitat requirements, and movement
patterns of BCT within the Thomas Fork and Bear River drainages (Colyer
2002, Shrank 2002). These studies showed that large fish in this system
exhibited a fluvial life history strategy, using habitats in the lower
elevation, mainstem rivers for growth and maintenance and migrating
large distances (up to 90 km) to headwater habitats to spawn. This
research also indicated that three full-spanning diversion structures on
the Thomas Fork were blocking access to upstream spawning habitats and
entraining downstream migrants in irrigation canals (Colyer 2002,
Schrank 2002).

In 2002 Trout Unlimited partnered with the US Forest Service, the US
Fish and Wildlife Service, Idaho Department of Fish and Game, Faucet
Irrigation Co., and several private landowners in the Thomas Fork Valley
in southeastern Idaho to begin retrofitting these full-spanning
irrigation diversion structures and their associated irrigation canals
with fish screens and fish bypass facilities. Whereas most of the
funding for these projects has come from federal agency sources, Trout
Unlimited is conducting all monitoring and evaluation activates
associated with the project. As part of our BACI
(before-after-control-impact) study design we began in June 2003 to
monitor downstream BCT movements in Hobble Creek in western Wyoming.
This tributary is known to provide spawning habitat for fluvial migrants
from the lower Smith's Fork and the Bear River. We used two way picket
weirs and trap boxes to capture all fish greater than 100 mm moving
upstream and downstream in Hobble Creek. We also conducted three pass
electrofishing sampling in 100 m reaches throughout the upper drainage.

In 2004 we also began weir trapping in the upper Thomas Fork (Salt
Creek) in Wyoming. We located this trap on the mainstem of the Thomas
Fork just downstream from the confluence with Giraffe Creek, intending
to intercept adults en route to upstream spawning habitats and juveniles
moving downstream towards mainstem rearing habitats. We hypothesized
that we would catch few, if any, fluvial adults in 2004 in the Thomas
Fork, given the diversion barriers downstream. Those diversion barriers
are currently being retrofitted with fish ladder bypass channels and
fish screens, and we expect to see future increases in the numbers of
migratory adults upstream in the drainage once the mainstem migration
corridor is restored.

We plan to use our trapping data to both gain a better understanding of
juvenile and sub-adult BCT movements in the system (primarily
outmigration numbers and timing) and to evaluate population recovery in
the Thomas Fork following our restoration activities.

***Trapping methods.*** We monitored upstream and downstream movements
in Hobble Creek from June 19, 2004 through September 27, 2004 and in
Salt Creek from June 8, 2004 through September 27, 2004, using picket
weirs with upstream and downstream trap boxes. The Hobble Creek weir was
located approximately 400 m downstream from the confluence of Hobble and
Coantag Creeks (4690144 N 517065 E, UTM NAD27, zone 12). The Salt Creek
weir was located approximately 2.5 km downstream from the confluence
with Giraffe Creek (4694023 N 498169 E). All BCT were weighed and
measured and those \>130 mm total length were implanted with Passive
Integrated Transponder (P.I.T.) tags. We implanted all BCT \>200 mm with
Visible Implant (V.I.) tags in addition to the P.I.T. tags. All captured
brown trout (BNT) were measured, and BCT and BNT were given adipose
clips. We counted and recorded the direction of movement for all other
fish species that we captured. Following handling, all fish were
released either upstream or downstream of the trap depending on their
direction of travel.

***Trapping results.***

*HOBBLE CREEK---*Between June 19 and September 27 we captured a total of
977 BCT, 181 BNT, 100 sculpins (S)^1^, 312 mountain whitefish (MWF), and
3 mountain suckers (MS).

*SALT CREEK---*Between June 8 and September 27 we captured a total of 11
BCT, 458 decapods, 332 S, 27 MWF, 215 longnose dace, 10 speckled dace,
16 redside shiners, 53 MS, 93 Utah suckers, 1 garter snake, and 1 frog.

^1^ We found field identification of sculpins to be difficult. Dr.
Ernest Keeley (Idaho State University) assisted with our identification
efforts on two occasions. We believe that we captured mostly Paiute
sculpins and a few mottled sculpins.

***Survey methods.*** We conducted depletion electrofishing surveys
upstream from the weir location site in both Hobble and Coantag Creeks.
We established 100 m survey sites at 1 km intervals as we moved upstream
from the trap, and used block nets and a standard three-pass depletion
methodology. We conducted a third pass only if the second pass yielded
\>20% of the total number of trout captured in the first *and* second
passes. All BCT were again weighed and measured and tagged according to
the above size criteria. All BNT were measured and numbers of MWF and
sculpins were recorded.

***Survey results.*** We surveyed 13 sites in Hobble Creek between 7/15
and 7/20 and captured a total of 99 BCT, 63 BNT, 2 MWF, and 990
sculpins. We implanted 5 BCT with P.I.T. tags and 14 BCT with V.I. tags.
We had a total of 4 BCT and 6 BNT mortalities, all apparently due to
electro-fishing injuries. We surveyed 8 sites in Coantag Creek between
8/09 and 8/11 and captured 85 BCT, 8 BNT, and 617 sculpins. We implanted
1 BCT with a P.I.T. tag and 10 with V.I. tags. We had 1 BCT mortality
due to injuries incurred during electro-fishing.

***Angling methods.*** Throughout the field season we angled for BCT and
implanted captured fish with P.I.T. and V.I. tags in order to document
trends in fluvial BCT densities in habitats upstream from our traps. All
angled fish were captured with flies tied on single barbless hooks and
kept in in-stream live wells for no longer than 15 minutes before
processing. All angled BCT were weighed and measured and tagged
according to the size criteria previously outlined. All angled BNT were
measured and recorded and given an adipose clip.

***Angling results.***

HOBBLE CREEK---We captured a total of 64 BCT and 8 BNT by angling. We
implanted 5 BCT with P.I.T. tags and 38 BCT with V.I. tags.

SALT CREEK---We captured a total of 128 BCT by angling. We implanted 40
BCT with P.I.T. tags and 84 BCT with V.I. tags.

***Future directions.*** We hope to continue with two more years of
trapping in the Smith's Fork (Hobble Creek) and Thomas Fork (Salt Creek
and tributaries) drainages. Two of the diversion barriers on the Thomas
Fork are currently under construction to install fish screens and bypass
channels, and will be completed in time to allow for upstream and
downstream fish passage during the spring of 2005. The third structure
is slated for removal in the fall of 2005 and will accommodate fish
passage by the spring of 2006. We expect to document increased numbers
of BCT outmigrants in the Thomas Fork as migration barriers are removed
and fluvial adults are afforded increased access to tributary spawning
habitats. By using outmigrant numbers in the Smith's Fork as a control
we will be able to isolate and quantify the treatment effect (barrier
removal) in the Thomas Fork.