639.21

F2MRDW

2009

Madison River Drainage Fisheries

and

Madison River Drainage

Westslope Cutthroat Trout

Conservationand Restoration Program

2009 Annual Report

to

PPL Montana

Environmental Division

Butte
www.pplmontana.com

and

Turner Enterprises, Inc. "^Mtlji''^ ^'

Bozeman ilrr^l

by

Pat Clancey & Travis Lohrenz

Montana Fish, Wildlife, & Parks

Eimis

June 2010

www.fwp.mt.gov

Montana State Library

3 0864 1006 2564 2

INTERNET WEB PAGES CITED IN THIS REPORT, OR OF LOCAL INTEREST

(in alphabetical order)

Aquatic Nuisance Species Task Force www.anstaskforce.gov

Blue Ribbon Flies www.blueribboiiflies.com

Madison River Foundation www.madisonnverfoundation.org

Lower Madison River Monitoring page. . ..

www.madisondss.com/ppl-river.cfg/ppl-madison.php

Montana Fish, Wildlife, & Parks www.fwp.mt.gov

New Zealand Mudsnail in the Western USA

www.esg.montana.edu/aim/moIlusca/nzms

PPL Montana www.pplmontana.com

Protect Your Waters www.protectyourwaters.net

Whirling Disease Foundation www.whirling-disease.org

MFWP personnel took all photos in this report unless otherwise credited.

An electronic version of this and other FWP reports are available at
http://fwp.mt.gov/wildthings/wildlifelib/default.aspx

FERC Articles addressed in iMs report

FERC Article

item

report topic

gagi

Metiiods

£ number
Results

403

NA

River Discharge

6

32

408

(1)

Hebgen gillnetting, disease
monitoring - Effect of project
operations on fish populations

21

39

(3)

Reservoir drawdown effects on fish
populations

21

39

(5)

Population Estimates - project
operations effects

4

28

(7)

Enhance upper river tributary
spawning

21

39

(9)

Flushing Flow

6

32

409

(1)

Aquatic Nuisance Species - Whirling
Disease

9,21

33,39

(3)

Fish habitat enhancement

19

38

412

(1)

Population Estimates - pulse flow
effects

4

28

(5)

Species Spec. Concern - Madison
Grayling

4

26

Species Spec. Concern -Westslope
Cutthroat Trout

12

37

(9)

Flushing Flow

6

32

(11)

Population Estimates - thermal
effects

4

28

413

(1)

Temperature Monitoring

9

33

419

NA

Flushing Flow

6

32

EXECUTIVE SUMMARY

Beach seining for yoimg-of-the-year Arctic grayling and mountain whitefish was conducted
in October. One young-of-the-year Arctic grayling and 5 young-of-the-year whitefish were
captured in Meadow Creek Bay. Other species captured at index sites were juveniles of
rainbow trout, brown trout, Utah chub, long-nose dace and white sucker. Rainbow trout
over six inches were estimated at 1 500 - 2500/mile in the Pine Butte and Norris sections, hi
Vamey, the rainbow trout estimate decreased significantly to less than 500/mile from the
most recent estimate of over 1 500/mile in 2007. Brown trout were estimated at 1 000 -
2000/mile in all three sections. Water temperature was monitored at 14 sites and air
temperature at 7 sites within the Madison Drainage. Eighteen locations in the Madison
Drainage were sampled for New Zealand mudsnails and selected other aquatic nuisance
species. Sentinel fish from captive rainbow trout stock are still severely infected by whirling
disease in the river, but the wild rainbow trout population has rebounded to approximately
60 percent of its pre-whirling disease level . The Sun Ranch hatchery was used to incubate
eggs for the southwest Montana westslope cutthroat trout conservation and restoration
program. The Cherry Creek Native Fish Introduction Project continued in 2009 with a
treatment of a portion of Phase 3 where fish were located. Westslope cutthroat trout eyed
egg introductions were continued in Phase 2 and initiated in Phase 3 . The number of
rainbow trout captured during annual Hebgen Reservoir gillnetting decreased from 2008 but
remained near the high end of annual catch over the past 1 5 years. The proportion of
rainbow trout over 14 inches in the Hebgen gillnet catch has increased noticeably since
2005. Trapping of rainbow trout immigrating into Hebgen tributaries to spawn continued.
Zooplankton density in Hebgen Reservoir was monitored.

TABLE OF CONTENTS

Introduction .....,.,. 1

Methods

Madison Grayling --..-_. 4

Population Estimates ....... 4

River Discharge -__.... 5

Temperature Monitoring , ...... 9

Aquatic Nuisance Species ...... 9

Westslope Cutthroat Trout Conservation

and Restoration . . . . . . 12

Fish Habitat Enhancement- - - - - - - 19

Hebgen Basin ........ 21

Results and Discussion

Madison Grayling --,--_. 26

Population Estimates ,...,,. 28

River Discharge - - - - - - - 32

Temperature Monitoring . . . . . . . 33

Aquatic Nuisance Species --.-._ 33

Westslope Cutthroat Trout Conservation

and Restoration ...... 37

Fish Habitat Enhancement ------ 38

Hebgen Basin . . . , . . 39

Conclusions and Future Plans- - - - - - - 57

Literature Cited »...,,. 59

Appendix A: MacConnell-Baldwin whirling disease ratings

Appendix B: Ennis Reservoir beach seining

Appendix C: Madison River population monitoring

Appendix D: Madison River temperature recordings

Appendix E: Montana Aquatic Nuisance Species Plan summary

Appendix F: Beaverhead-Deerlodge National Forest and Yellowstone National Park

Native Fish Habitat Restoration Monitoring
Appendix G: Sun Ranch Hatchery Production
Appendix H: Madison westslope cutthroat trout genetics results

INTRODUCTION

Montana Fish, WildHfe, & Parks (MFWP) has conducted fisheries studies in the Madison
River Drainage since 1990 to address effects of hydropower operations at Hebgen and Ennis dams
on fisheries and to assess the status of the Arctic grayling Thymdlm arcticm population of Ennis
Reservoir (Byorth and Shepard 1990, MFWP 1995, MFWP 1996, MFWP 1997, MFWP 1998a,
MFWP 1999a, MFWP 2000, MFWP 2001, MFWP 2002, MFWP 2003, MFWP 2004a, MFWP
2005 MFWP 2006, MFWP 2007a, MFWP 2008, MFWP 2009). This work has been funded
through an agreement with the owner and operator of the dams, initially Montana Power Company
(MFC) now PPL Montana. The original agreement between MFWP and MFC was designed to
anticipate relicensing requirements for MFC's hydropower system on the Madison and Missoun
rivers which includes Hebgen and Ennis dams, as well as seven dams on the Missoun River
(Figure 1) PPL Montana has maintained the direction set by MFC, and convened several
committees to address fisheries, wildlife, water quality, and recreation issues related to the operation
of the hydropower facilities on the Madison and Missouri rivers. These committees are composed
of representatives of PPL Montana and several agencies. Each committee has an annual budget and
authority to spend money that is provided to them by PPL Montana to address the requirements of
PPL Montana's FERC Ucense for operating the Madison & Missouri dams. The Madison Fisheries
Technical Advisory Committee (MadTAC) is composed of personnel of PPL Montana, MFWP, the
U.S. Fish & Wildlife Service (USFWS), the U.S. Forest Service (USPS), and the U.S. Bureau of
Land Management (BLM). Each entity has equal authority in decision making within the TAG.
Collectively the nine dams on the Madison and Missouri rivers are called the 21 88 Project, which
refers to the Federal Energy Regulatory Commission (FERC) license number that authori2es their
operation. The Federal Energy Regulatory Commission issued PPL Montana a license to operate
the 2188 Project for 40 years (Federal Energy Regulatory Comnussion 2000). The license details
the terms and conditions PPL Montana must meet during the license term, including fish, wildhfe,
and recreation protection, mitigation, and enhancement measures.

During the late 1990' s, numerous entities developed the Memorandum of Understanding
and Conservation Agreement for Westslope Cutthroat Trout in Montana (MUCAWCTM). The
MUCAWCTM, which was formaUzed in 1999 (MFWP 1999b), identifies Conservation &
Restoration Goals and Objectives for westslope cutthroat tirout (WCT) Oncorhynchus clarki lewisi
in Montana. The Plan states "The management goal for westslope cutthroat tiout m Montana is to
ensure the long-term, self-sustaining persistence of the subspecies within each of the five major
river drainages they historically inhabited in Montana (Clark Fork, Kootenai, Flathead, upper
Missouri, aad Saskatchewan), and to maintain tiie genetic diversity and Ufe history stiategies
represented by the remaining populations." Objectives are:

1 . Protect all genetically pure WCT populations

2. Protect intiogressed (less than 1 0% introgressed) populations

3. Ensure the long-term persistence ofWCT within their native range

4. Providing technical information, administrative assistance, and fiiiancial resources to
assure compliance with listed objectives and encourage conservation of WCT

<^N

/

Morony
Ryan
Cochrane
Rainbow

Black hagle

> Hotter Dam

>Hauser Dam

Hebgen Dam

Figure 1. Locations of PPL Montana dams on the Madison and Missouri rivers (FERC Project
2188).

5.

Design and implement an effective monitoring program by the year 2002 to
document persistence and demonstrate progress towards goal

Objective 3 further states "The long-term persistence of westslope cutthroat trout within
their native range will be ensured by maintaining at least ten population aggregates throughout the
five major river drainages in which they occiff, each occupying at least 50 miles of connected
habitat. . .". Within the Missouri River Drainage, four geographic areas are identified, including the
upper Missouri, which consists of the Big Hole, Gallatin, and Madison subdrainages.

Entities participating in the development of the MUCAWCTM were American Wildlands,
Montana Chapter of the American Fisheries Society, Montana Department of Natural Resources
and Conservation (MDNRC), Montana Farm Bureau, MFWP, Montana Stockgrowers Association,
Montana Trout Unlimited, Montana Wildlife Federation, Natural Resource Conservation Service,
BLM, USPS, USFWS, and private landowners.

In 2006, the MUCAWCTM was updated and combined with a similar document for
Yellowstone Cutthroat Trout Oncorhynchus darki bouvieri (MFWP 2007b).

Late in 1996, MFWP initiated a program entitled "The Madison River Drainage Westslope
Cutthroat Trout Conservation and Restoration Program". The goal of this effort is to conserve and
restore the native westslope cutthroat trout in the Madison River drainage. Fieldwoik for this effort
began in 1997 in tributaries of the Madison River. The agreement between MFWP and PPL
Montana includes provisions to address issues regarding species of special concern.

In recognition of the severity of the situation faced by the westslope cutthroat trout, and in
keeping with the philosophy of promoting native species on their properties. Turner Enterprises,
Incorporated (TEI) offered access to the Cherry Creek drainage on the Flying D Ranch to assess its
suitability for introducing westslope cutthroat. Cherry Creek, a tributary to the Madison River, was
identified as an opportune location to introduce genetically pure WCT, and it will provide an
opportunity to meet or fiilfill MUCAWCTM objectives 3, 4, & 5. MFWP detemiined in 1997 that
introducing westslope cutthroat to Cherry Creek is feasible, but would require the removal of all
non-native trout presently in that portion of the drainage (Bramblett 1998, MFWP 1998b). MFWP,
TEI, and the Gallatin National Forest (GNF) subsequently entered into an agreenient to pursue this
effort. The agreement outlines the roles and responsibilities of each party, including the GNF,
which manages the pubUc land at the upper end of the Cherry Creek dramage. Administrative and
legal challenges to the Cherry Creek Project delayed its implementation firom 1999 - 2002. The
project was successfully implemented in 2003 .

In 2001 , the Sun Ranch entered mto an agreement to assist MFWP with westslope
cutthroat trout conservation and recovery. The ranch built a small hatchery facility and a rearing
pond to facilitate development of a westslope cutthroat trout broodstock for the Madison and
Missouri river drainages, and provided personnel to assist with fieldwork and conduct hatchery
operations.

METHODS

Madison Grayling

A beach seine (Figures 2 & 3) is used to monitor index sites in Ennis Reservoir (Figure 4)
for young-of-the-year grayling and otiier fish species. Seining is conducted by pulling a 125 x 5
foot fine-mesh net along shallow areas in the reservoir.

Figure 2. Beach seining in Ennis Reservoir.

125'

5'x5'x5'

collection

bag

Figure 3. Depiction of seine used during beach seining

Population Estimates

Electrofishing firom a driftboat mounted mobile anode system (Figure 5) is the principle
method used to capture Madison River trout for population estimates in several sections of the
Madison River (Figure 6), Fish captured for population estimates are weighed and measured,

«

J

.^•^

x\ n

\ '>]>

Figure 4. Locations of Ermis Reservoir 2009 seining sites.

Figure 5. Electrofishing (shocking) in the Norris section of the Madison River.

marked with a fin clip, and released. A log-likelihood statistical analysis (MFWP 2004b) is used to
estimate trout populations.

fa. recent years estimates for all sections and all years have been converted fi*om age-based
estimates to lengdi-based estimates due partially to the major time requirement necessary to age
fish, and to maximize the statistical probability that the estimates are accurate.

River Discharge

Pulse Flaws

Article 413 of the FERC license mandates PPL Montana to monitor and mitigate thermal
effects in the lower river (downstream of Ennis Reservoir). In coordmation with ^encies, the
company has developed and implemented a remote temperature monitoring system and a 'pulsed'
flow system to accomplish this. Real-time or near real-time meteorological and temperature
monitoring is conducted to predict water temperature the following day, which determines the
volume of discharge that will occur. Pulsed flows are triggered when water temperature at the
Madison (Ennis) Powerhouse is 68° F or higher and forecast air temperature at Three Forks for the
following day is 80° F or higher. The volume of water released in the pulse is determined by how
much the water and/or air temperature exceeds the minimum thresholds (Table 1). The increase in
water volume in the lower river reduces the peak water temperature that would occur at the 1 100 cfs
base flow. Discharge fi^om Ennis Dam is increased in the early morning so that the greatest volume
of water is in the area of Black's Ford and downstream during the late afternoon when daily solar
radiation is greatest. The increased volume of water reduces the peak water temperature in the
lower river reducing or eliminating the potential for thermally induced fish kills. Discharge fix)m
Hebgen Dam typically does not fluctuate on a daily basis during pulse flow^, but is occasionally

JEFFERSON
RIVER

GALLATIN RIVER

Warm Springs
Creek

ENNIS
RESERVOIR

Standard
Creek

HEBGEN
RESERVOIR

WesTFork
Madison River

Figure 6. Locations of Montana Fish, Wildlife, & Parks 2009 Madison River population estimate
sections.

Table 1 . Pulse flow trigger criteria

Water

temperature at
Madison
(Ennis)
Powerhouse

Tomorrow's Maximum Forecast Air Temperature at
Three Forks

Pulse Flow Rate (McAllister Discharge)

No Pulsing
Required

Less than 68°F

No action

Pulsing
Contingent on
Weather
Forecast

> 68°, < 70°

<80°

>80°

No action

1400 cfs

Pulsing
Required,
Volume
Contingent of
Weather
Forecast > 90°F

> 70°, < 72°

<90°

>90°,<95°

>95°

1400 cfs

1600 cfs

2100 cfs

Pulsing
Required,
Volume
Contingent of
Weather
Forecast > 85°F

> 72°, < 73°

<85°

> 85°, < 90°

>90°

1400 cfs

1600 cfs

2100 cfs

Pulsing
Required,
Volume
Contingent of
Weather
Forecast > 85°F

>73°

<85°

>85°

1800 cfs

2400 cfs

adjusted to increase or decrease the volume of water going into Ennis Reservoir, where daily
fluctuations in the lower river are controlled.

The meteorological and temperature data monitored in the lower river may be viewed in
real-time or near-real time at http://www.madisondss.com/ppl-river.cfg/ppl-madison.php.

Flushing Flows

Article 419 of the FERC license requires the company to develop and implement a plan to
coordinate and monitor flushing flows in the Madison River downstream of Hebgen Dam. A
flushing flow is a flood stage of runoff that mobilizes streambed materials, resulting in scour in
some locations and deposition in other locations. This is a natural occurrence in unregulated
streams and rivers, and renews spawning, rearing, and food producing areas for fish, as well as
providing fresh mineral soil for terrestrial vegetation and other wildlife needs.

Minimum Flows

Fish, Wildlife & Parks and PPL Montana (and PPL Montana's predecessor Montana
Power Company) have an agreement established in 1968 to maintain minimum instantaneous
river flows at the USGS Kirby and McAllister gauges in the upper and lower river of 600 and
1 100 cfs, respectively. These instream flow levels were determined by FWP to provide
favorable overwinter habitat for yearling trout, and also protect against summer and fall drought
in low water years. These minimum flows were incorporated into Article 403 of the FERC
license for the 2188 Project and are required elements of operating Hebgen and Ennls dams.

Temperature Momitoring

Water temperature was recorded at 14 sites and air temperature at seven sites throughout the
course of the Madison River from above Hebgen Reservoir to the mouth of the Madison River at
Headwaters State Park (Figure 7). Optic StowAway temperature loggers recorded temperature in
Fahrenheit every 30 minutes. Air temperature recorders were placed in areas that were shaded 24
hours per day.

Aqaatte NwisaBce Species

Highway signs announce FWP's West Yellowstone Traveler Information System (TIS)
(Figure 8). The five signs are located near major highway intersections in the West Yellowstone
area, notifying drivers entering and leaving the area of the TIS system. The TIS notifies anglers and
water recreationists of the presence of New Zealand mudsnails in the Madison River and Hebgen
Reservoir, and mstructs them on methods of reducing the likelihood of transporting New Zealand
mudsnails and other ANS to other waters. Additional messages broadcast by the system include
messages on whirling disease, zebra mussels, weed control, and TIPMont, the FWP hotline to report
hunting & fishing violations. The system broadcasts at the AM fi:equency of 1600 KHz. Funding
for the purchase, installation and signage of the system was provided by a $9,800 grant from the
Pacific States Marine Fisheries Commission as part of an effort to prevent the westward spread of
zebra mussels.

The State of Montana hired an Aquatic Nuisance Species Coordinator in 2004. The position
is responsible for developing and coordinating ANS control & management activities among state
agencies as well as between state and non-state entities. The ANS Coordinator is responsible for
developing and coordinating Hazard Analysis and Critical Control Point (HACCP) Training to State
employees and other groups. The HACCP Program is a method to proactively plan and implement
measures to prevent the inadvertent spread of ANS during work activities. The ANS Coordinator is
an employee of FWP.

In 2009 FWP initiated monitoring of dissolved calcium concentration in state waters to
evaluate risk of zebra and quagga mussel estabUshment. The calcium level of a vrater body is a
critical characteristic for zebra and qu^ga mussel establishment. These mussel species do not
survive when there is a low calcium concentration in the water, since calcium is an essential element
in the composition of the bivalve shell. Calcium concentrations of 15 mg/hter or less are thought to

JEFFERSON
RIVER

COBBLESTONE

GALLATIN RIVER

-COBBLESTONE

reI^K^oir

ENNIS

McATEE

WALL—X
CREEK
HQ

West Fork
Madison River

1 J ~iC»'L3iZ:l\

Figure 7. Locations of Montana Fish, Wildlife, Sc Parks annual temp^ature monitoring sites. Air
temperature sites are blue, water temperature sites are in red.

10

ANGLERS - BOATERS

TUNE RADIO TO

1600 AM

STOP AQUATIC
HITCHHIKER"-

Figure 8, Roadside sign announcing the Traveler Information System at West Yellowstone.

limit the distribution of zebra and quagga mussels. Survival of the larvae and size of aduh
established populations are both thought to uicrease with increasing levels of calcium.

New Zealand Mudsnails

New Zealand Mudsnails have spread throughout the Madison River since first detected in
1994. PPL Montana and FWP each maintain monitoring sites at various
locations within the Madison Drainage.

Whirling Disease

Whirling disease monitoring has been conducted in the Madison River since 1996 by using
sentinel cage techniques. Each cage holds 50 young-of-the-year rainbow trout for 10 days. At the
end of the 10 day period, fish are transferred to whirling disease free water in a laboratory where
they are held until they are 90 days old, at which time they are euthanized and sent to the
Washington Animal Disease Diagnostic Lab (WADDL) for analyses. Juvenile rainbow trout used
in the studies are not offspring of Madison River fish, but are fi-om the same captive stock used
since studies began in 1996. Tliis stock has been used continuously over the years to allow
comparison over time and between various rivers by using a consistent measuring base.

In 2009, eight sites in the Madison below Hebgen were monitored for whirling disease
infection risk. Two cages were simultaneously deployed at each site to measure risk at the upper
and lower ends of each site. The sites monitored were side channels at South SUde, Shde Inn, Pine
Butte, Kirby, Lyons, Palisades and Vamey, and the main channel of the West Fork near the West
Folk Camp bridge.

Dave Kumlien, Executive Director of the Whirling Disease Foundation, presents two
articles regarding whirhng disease on the Blue Ribbon Flies webpage. These articles summarize
some of the advances that have been made by whirling disease researchers and additional
information that is needed. To view these and other articles, go to vvww.blueribbonflies.com, click
on Journal, then on Articles and Essays.

11

Efforts to conserve and restore genetically pure westslope cutthroat trout in the Madison
Drainage center on maintaining genetically pure population, high quality stream habitat, adequate
instream flow, and, where necessary, removal of competing or hybridizing non-native trout. Stream
habitat surveys were conducted throughout much of the Madison Drainage Scorn. 1997 - 1999
(MFWP 1998a, Sloat et al. 2000). Backpack electrofisMng was used to survey fish species.
Removal of non-native species will require use of the EPA registered piscicides (fish-pesticides)
rotenone or antimycin.

The Madison District of the U.S. Forest Service and Yellowstone National Park are
conducting projects to benefit westslope cutthroat trout and/or to restore stream habitat in tributaries
to the Madison River. Grant money firom the PPL Montana relicensktg agreement was granted to
each of those federal agencies to assist their efforts.

Sun Ranch Westslope Cutthroat Trout Brood

Gametes (eggs & sperm) for the Sun Ranch Westslope Cutthroat Trout program were
collected fi-om three streams in 2009. No eggs were collected fix)m the Sun Ranch Broodstock io
2009 due to poor production of the brood fish. All fertihzed eggs were transported to the Sun
Ranch Hatcheiy for incubation and hatching (Figure 9). A portion of the resulting fiy from two of
the streams and the Sun brood were introduced to the Sxsn Ranch Brood Pond (Figure 10) to
contribute to the Sun Ranch brood development. One of the two contributing streams was a new
population not previously represented in the brood. Two of the wild populations did not contribute
to the Sun brood in 2008 because they contributed in previous years. Fry fi-om the Sun Ranch Pond
broodstock were used for introductions in Cherry Creek and stocked into the pond to facilitate
development of the Sun Ranch brood.

Occasionally, when project personnel are unavailable to do so, USFWS personnel fi*om the
Ennis National Fish Hatchery caretake the eggs or fiy at the Sun Ranch Hatchery. Generally, this
requires few days each year, but is an important contribution to the program.

Cherry Creek Native Fish Introduction Project

The Cherry Creek Native Fish Introduction Project was initiated in 2003, The project
area is comprised of over 60 miles of stream habitat and the 7-acre, 105 acre-foot Cherry Lake,
and mcludes all of the Cherry Creek Drainage upstream of a 25-foot vraterfall (Figure 1 1)
approximately 8 miles upstream of the Madison River confluence. The only fish species present
in the project area in 2003 were brook trout, rainbow trout, and Yellowstone cutthroat trout
(YCT) (Figure 12). The large size of the project area requires that the project be completed in
phases. Each phase will be treated for at least two consecutive years. In 2009 a portion of the
Phase 3 mainstem was treated to remove fish that leapt the barrier during Spring runoff.

Preparatory fieldwork consisted of determining stream flow time, placing application
station markers, posting sentinel fish, setting up the detoxification station, and some
electrofisMng to assess thoroughness of previous years treatments.

12

Figure 9. Sun Ranch Hatchery rearing troughs.

Figure 10. Sun Ranch Brood Pond.

13

Figure 1 1 . Cherry Creek waterfall at stream mile 8.0. This falls is the downstream extent of the
project area.

Fintrol became unavailable for use at Cherry Creek in 2007 due to a production problem,
so a rotenone product called CFT Legumine was used beginning that year. Bioassays were
conducted in the East Fork Cherry Creek in July 2007 to determine the effective exposure time
of the CFT (Table 2). Based on bioassay results, CFT label instructions, and results of the 2007
treatment, CFT was applied to the stream during the 2008 treatment at no more than 1 .0 part-per-
million (ppm) for four hours. Treatments were initiated on August 4.

Stream discharge was measured following standard USGS protocols, and a staff gauge
was temporarily placed to determine if discharge changed appreciably during or prior to treating
a given section of stream. Discharge was measured in a stream section the evening prior to
treatment of that section, which allowed calculation and preparation of the piscicide that night or
the next morning.

14

Cherry Creek

Tributary to Madison River, IViontana

Fish Distribution

Gallatin Nfailooai Forest

Map produced by:

Jeffirey Hutten

Montana Fish, Wildlife & Paris

Information Services Unit

490 N. Meridian Rd.

KalispeU, MT 59901

4G6-7S1-4371

Fish distrlbatlon and barrieis data obtained by Global Fosltlaning
System (GPS) and differentially corrected. HydrORraplly fiom StreamNet
and digitized at 1:100,000. Public landowneiship data from the Natural
Resource Information System (NRIS) at tile Montana State Ubiary.

/fwp/spot/jeCE^emhyditj/cheny.cmp
February 20, 1998

^»V1C*

Figure 12. Cherry Creek Drainage. Landownership patterns have changed since this map was
produced.

15

Table 2. Results of CFT Legumine rotenone bioassays in the East Fork of Cherry Creek to

determine effective exposure time, July 2007. Rim time of the application station was 7
hours 52 minutes. CFT application was initiated at 09:33.

Sentinel fish
station'^

Time of initial
exposure

Time of 100%
mortality

Hours of exposure
til 100% mortality

30

10:03

10:50

0:47

60

10:33

12:55

2:22

90

11:03

12:55

1:52

120

11:33

14:00

2:27

150

12:03

14:55

2:52

180

12:33

16:15

3:42^'

210

13:03

16:15

2:48

240

13:33

NA^'

"^Minutes of stream flow time downstream of CFT application station

'^' 2 fish dead, 1 gravely ill at 1455 hrs (2:22 hours of exposure)

^' 100% mortality of sentinel fish was confirmed the following morning at 1 1 :45

Stream treatments were made using trickle application systems (Figure 13). The system
consists of a 3'/2 gallon plastic bucket & Hd, garden hose, a gate valve, and a commercially available
automatic dog watering bowl. A plastic elbow is fixed to a hole drilled in the bottom of the bucket,
a short section of garden hose and the gate valve are clamped to the elbow (Figure 14), and a longer
section of garden hose attach the assembly to the dog waterer. The bucket is partially filled with
filtered stream water, the CFT is added, then the bucket is topped off with filtered stream water and
stirred with a wooden dowel. At a predetermined time, the gate valve is opened, allowing the
mixture to flow into the bowl, where it then trickles into the stream through a small hole drilled
in the bottom of the bowl (Figure 15). Typically, one bucket empties in 3^2 - 4 hours.
Applications of CFT are designed using a 4-hour application period. In previous years,
Antimycin applications were designed using a 7-hour application period, but rotenone acts on the
fish more quickly than Antimycin, so the treatment period is shortened.

Stations were placed at selected pomts along the stream and started at predetermined
times to coordinate application of the mixture with other stations along the stream. Backpack
sprayers were used each day to treat off-channel water and larger pools.

Westslope cutthroat eggs fi-om three wild donor streams, the Sun Ranch brood, and the
Washoe Park Hatchery were reared to the eyed stage then placed in remote streamside incubators
(RSI) (Figure 16) in the Cherry Lake fork of Phase 1 and in Phase 2. Eggs completed incubation
hi the RSI, hatched, and fiy departed the RSI into the stream under their own power. The RSI is
plumbed to allow stream water to flow into the bottom of the bucket, percolate up through an
artificial substrate where the eggs are placed, and out the RSI near the top of the bucket. When
ready to enter the stream, fiy follow the water out the hole near the top of the bucket.

A capture bucket was placed on the outflow of the RSI to captnure and enumerate
departing fiy to allow estimation of survival in the RSI.

16

Figure 13. Trickle system and sentinel fish bag on Cherry Lake Creek. The sentinel fish bag is
upstream of the CFT application pouit to monitor the effectiveness of the station
above the one shown here.

Pat Clancey photo

Figure 14. Elbow & gate valve assembly.

17

Figure 15. Close-up view of the dog waterer trickling CFT/streamwater mixture into the stream
during the Cherry Creek Project

Figure 16. Remote streamside incubator (round bucket) and capture bucket (square bucket) in
Cherry Creek

18

Fish Habitat Enhancement

Smith Lake

Smith Lake Dam on Lake Creek, a tributary to the West Fork of the Madison River, is a
four foot Mgh cobble and earthen dam believed to have been constructed in the 1920s to funnel
water for operation of a sluice box and water wheel pump (Figure 17) to deliver water 500 vertical
feet to an offsite water trough for livestock. Brovwi trout migrate up Lake Creek for spawning, but
in some years fish passage around the dam is blocked by tarps used to reduce leakage tlu-ough the
dam and the bypass channel. Several alternative methods were explored to provide stockwater and
reduce or eliminate the need for the water wheel pump.

Q'Dell Creek

O'lDell Creek is a spring creek that originates south of Ennis and flows north
approximately 12 miles to its confluence with the mainstem Madison River, hn 1955 a ditch was
excavated to intercept groundwater flow and portions of O'Dell Creek were channelized to
dewater a wetland complex, maximize available rangeland for cattle, and simplify irrigation. In
2005, DJP Consulting and the Granger Ranches received funding from PPL Montana Madison
Fisheries and PPL Montana Wildlife technical advisory committees and other sources to restore
form and fiinction to portions of O'Dell Creek and associated wetlands on Granger Ranch
property (Table 3, Figure 18). Backfilling of the East Ditch resulted in groundwater resuming its
original flow pattern into the wetland and also resulted in increased streamflow in other stream
dmmels. Fisheries monitoring is conducted at six sites ui the project area (Figure 19). Future
plans include channel narrowuig and vegetation development in the Above Falls and Below Falls
sections.

Figure 17. Water wheel at Smith Lake Dam on Lake Creek. MFWP photo by Travis Lohrenz.

19

Table 3. Summary of stream restoration actions on fisii momtoring sites at O'Deil Creek, 2005
2009.

Fish Momtoring Site

Result of Stream Channel Modification

r O'Deil Ditch

Backfilled

O'Deil Spring North

Increase in stream discharge, no physical modifications

Old Middle

Historic channel reconnected and reconstructed

O'Deil West

Charmel naiTowed & deepened, increase in stream discharge

Above Falls

Increase in stream discharge, stream channel restoration

Below Falls

Increase in stream discharge, no physical modifications

M:idisoT)
jyvcr

20l(5&200fi

Cnnicron
Bcndi

Main Cliaime]
Tjoriglioni lianch
Completed 2007 •

1 lY.iKt Jjfiierai
LonuJiom Jianch
Completed 2007

West Lateral
Longliorn Handi
Completed 2007

Vamey Bridge Road

"Google

Figure 18. Schedule of stream improvement activities on O'Deil Creek, Granger and Longhom
ranches, fi^om Peters 2009.

20

O'Dell below Falls

O'Dell above Falls

O'Dell West

Ola ivxiaaie itiiannei

O'Dell Ditch

"Google

Figure 19. Map depicting approximate locations offish sampling sites on O'Dell Creek, from
Peters 2009.

Hebgen Basin

Hebgen Reservoir and its tributaries are shown in Figure 20.

Hebgen Reservoir Gillnetting

Gillnetting has been conducted annually on Hebgen Reservoir by MFWP for over thirty
years to monitor trends in reservoir fish populations, including species assemblage, age structure,
and the contribution of hatchery reared rainbow trout to the Hebgen fishery.

Variable mesh experimental gilhiets, 125 foot long, were deployed overnight at index
sites on Hebgen Reservoir (Figure 21) over a three-day period during New Moon in early June.
A total of 25 gill nets (14 surface and 1 1 bottom nets) were fished during this period, with a
maximimi of nine nets fished per night.

Samples were sorted by net and processed systematically by species. Total length and
weight were recorded and scales removed from rainbow trout, brown trout and mountain whitefish
for age determination. Rainbow trout were also visually examined for physical anomalies seen in
hatchery-reared stocks, and for external and internal tags applied to wild juvenile and adult rainbow
trout at tributary traps in previous years.

21

\ Sift; ■^ «~^ -V -<: - 77- i

!^ ^.K

Figure 20. Hebgen Reservoir and surrounding area.

22

Additionally, vertebrae were extracted from rainbow trout specimens and examined for the
presence of oxy-tetracycline marics, a biological stain that appears in ossified structures.
Tetracycline can be added to hatchery pellets to put a mark in the vertebrae, creating a positive
identification feature for hatchery raised fish. Oxy-tetracycline is typically administered to
hatchery-reared fish through feeding prior to stocking.

^ » zot^laisktoii site
G = gillitetling site
B => beach seining site

Figure 21. Locations of Hebgen Reservoir zooplankton, gillnetting, and beach seinmg sites.

23

Hebgen Basin Disease Monitoring

Whirling Disease

Sentinel fish cages containing young-of-the-year Eagle Lake rainix>w trout were
deployed in two 1 0-day exposures, June 18-28 and June 28 - My 8, in three Hebgen tributaries
(Duck Creek, Black Sands Springs, and South Fork Madison) to test for the presence of whirling
disease. Sentinel fish were reared in isolation tanks for another 80 days at the MFWP Whirling
Disease Laboratory in Pony, Montana. At the conclusion of the 90-day period fish were
sacrificed and sent to the Washington Animal Disease Diagnostic Lab (WADDL) at Washington
State University where they underwent histological examination for whirling disease infection
and were rated on MacConnell-Baldwin scale (Appendix A), which grades infection from 0-5
with 0 bemg no infection and 5 being severe infection.

Hebgen Basin Tributary Trapping

Rigid panel weirs (Figure 22) were constructed and operated on Duck Creek and the
South Fork Madison River and a floating panel weir (Figure 23) was constructed and operated on
the mainstem Madison River above Hebgen Reservoir to monitor rainbow trout spawning
escapement and recruitment to the adult population in 2008. Weirs were placed in a shallow
glide with uniform streambed elevation and water depth between two and three feet at base flow.
The trap box was positioned to capture rainbow trout ascending tributaries to spawn. When
numbers offish captured fell below five fish/day for a one- week duration, the trap was removed.

Figure 22. Rigid weir assembly used to trap immigrating rainbow trout on Duck Creek and the
South Fork Madison. MFWP photo by Travis Lohrenz.

24

Figure 23. Rigid panel weir used on the Madison River, 2007 - 2009. MFWP photo by Travis
Lohrenz.

All fish captured were anesthetized prior to being worked to reduce handling time and
stress. Data collection for individual fish included total length and weight, scale collection for
age determination, and external examination. Additionally, individuals were inspected for
coded-wire-tags, administered to young-of-the-year and yearling rainbow trout at the Duck
Creek and South Fork Madison rotary screw traps from 2004-2006, and a uniquely numbered
floy-tag which were attached to adult rainbow trout during weir operations from 2005-2007
(Figure 24). If no floy-tag was observed, one was administered to the fish for future
identification.

Hebgen Reservoir Shoreline Juvenile Fish Sampling

Beach seining was not conducted at Hebgen index sites in 2009.

Hebgen Reservoir Zooplankton Monitoring

Monthly zooplankton tows were conducted at seven established sites on Hebgen
Reservoir to evaluate plankton community densities and composition (Figure 21). Plankton were
collected with a Wisconsin plankton net towed vertically through the entire water column at one
meter per second. Tows were taken at locations with a minimum depth of 10 meters. Samples
were rinsed and preserved in a 95% ethyl alcohol solution for enumeration.

25

Figure 24. Floy tagged Hebgen Reservoir rainbow trout

Zooplankton were identified to order Cladocera (daphnia) or Eucopepoda (copepods),
and densities from each sample were calculated. Carapace length was measured on six
individuals of each Cladocera and Eucopopoda from each aliquot. Length adjustments were
made to convert from micrometers to millimeters, and individual lengths were recorded in
millimeters. Mean length was calculated for each sample and each site to determine if spatial
and temporal variation existed.

RESULTS AND DISCUSSION

Madison Grayling

One young-of-the-year Arctic grayling was captured during beach seining in Ennis
Reservoir in 2009 (Appendix B).

Arctic grayling require loose, recently scoured gravels and cobbles to broadcast their eggs
over during spawning each spring (Byordi and Shepard 1990). Generally, normal spring runoff
creates these conditions, but it is possible that winter and spring ice scour also make such conditions
available. The duration and severity of the Madison River ice gorge (Figure 25) may affect the
spawning success of the Ennis Reservoir grayling.

The USFWS re-evaluated the petition to list fluvial (river-dwelling) Arctic grayling as a
Threatened species in light of a lawsuit filed in 2003 by the Center for Biological Diversity (CDB),
concluding in 2007 that listing Arctic grayling under the Threatened and Endangered Species Act
was not warranted. A listing would have likely included all grayling populations regardless of
behavioral traits or genetic similarity to Big Hole River fluvial grayling.

26

Figure 25. The Madison River at the U.S. Highway 287 Bridge at Ennis, illustrating ice-gorged and
ice-free conditions.

27

Madison grayling exhibit adfluvial behavior. They reside in Ennis Reservoir aU year except
when they enter the Channels area of the Madison River in April to spawn, though penodically
FWP receives reports of grayling in the Madison River as far as 30 miles upstream of Enms
Reservoir into the Fall.

MFWP has developed a Candidate Conservation Agreement with Assurance (CCAA) for
fluvial Arctic grayUng in the Big Hole Drainage. Landowners who sign onto the CCAA must
develop and implement pro-active site-specific land management conservation measures m
cooperation with agencies that will reduce or eliminate detrimental habitat conditions for the
grayling Despite the USFWS ruling that listing grayling is not warranted, landowners and
irrigators continue to enroll in the program. Currently 36 landowners have enroUed 157,291 acres,
with an additional 5,390 acres of State land enrolled.

Pojssslation Estimates

Population estimates were conducted in the Norris section in March and in the Pine Butte
and Vamey sections in September (Figure 6).

Figures 26-28 illustrate population levels of six inch and larger rainbow trout per mUe. The
rainbow population in Pine Butte exhibited a slight increase from 2008, but in the Vamey section
decreased significantly to levels not seen since the mid-late 1990's. In the Norris section rambows
increased shghtly over the 2008 level.

Figures 29 - 3 1 illustrate numbers of sk inch and larger brown trout. Brown trout in the
Pine Butte and Norris sections exhibited sHght increases from the previous year, but decreased in
Vamey.

In 2005, FWP Regional Management personnel began reporting population numbers greater
than six inches rather than using fish length to assign fish as yearling or two year old & older.
Appendix CI contains charts iUustrating fish numbers as yearling and two year old & older fish per
mile as reported in previous years of this report (MFWP 1995 - 2008). Appendix C2 contains
historic total population levels of two year old & older rainbow and brown trout (+ 80% C.I.) for
each section.

28

1995 1997 1999 2001 2003 2005 2007 2009

Figure 26. Rainbow trout (> 6") estimates in the Pine Butte section of the Madison River, 1995-
2009, faU estimates.

1500

e 1000 ■ - -

1

1995 1997 1999 2001 2003 2005 2007 2009

Figure 27. Rainbow trout (> 6") estimates in the Vamey section of the Madison River, 1995-2009,
fall estimates.

29

2500

1995 1997 1999 2001 2003 2005 2007 2009

Figure 28. Rainbow trout (> 6") estimates in the Norris section of the Madison River, 1995-2009,
spring estimates.

1995 1997 1

2001 2003 2005 2007 2009

Figure 29. Brown trout (> 6") estimates in the Pine Butte section of the Madison River, 1 995-2009,
fall estimates.

30

2500 -

2000

1500

1995 19

1999 2001 2003 2005 2007 2009

Figure 30. Brown trout (> 6") estimates in the Vamey section of the Madison River, 1995-2009,
fall estimates.

1995 1997 1999 2001 2003 2005 2007 2009

Figure 3 1 . Brown trout (> 6") estimates in the Norris section of the Madison River, 1 995-2009,
spring estimates.

31

River Discharge

Pulse Flows

In 1994 PPL Montana implemented a pulse flow system on the Madison River
downstream of Ennis Reservoir in years of high water temperature to prevent thermally induced
fish kills. Despite being developed as a stop-gap measure for extremely warm and dry years,
pulse flows were necessary every year from 2000 - 2007. Pulse flows were not necessary in
2008 or 2009. Table 4, adapted from PPL Montana data, summarizes statistics regarding pulse
flows in the Madison in years pulsing was conducted.

Table 4. Summary statistics for years in which pulse flows were conducted on the Madison
River.

Year

Hebgen October 1 pool

elevation^'

Feet

below

full pool

Feet of Hebgen draft

due to

pulsing

Number of
days
pulsing
occurred

2000

6531.21

3.66

0.61

29

2001

6530.53

4.34

0.05

13

2002

6530.46

4.41

0.70

18

2003

6528.59

6.28

2.68

39

2004

6532.07

2.8

0.28

12

2005

6531.52

3.35

0.30

17

2006

6530.86

4.01

1.74

15

2007

6526.05

8.82

2.12

43

^^Hebgen full pool is 6534.o7 msl. The FERC license requires FPL Montana to maintain Hebgen
pool elevation between 6530.26 and 6534.87 from June 20 through October 1.

Flushing Flows

Flushing flows were not conducted in the Madison River in 2009.

Minimum Flows

Minimum and maximum instream flows in various sections of the Madison River are
mandated in Article 403 and in Condition No. 6 of the FERC license to PPL Montana.
Specifically, Condition 6 in its entirety states:

''During the operation of the facilities authorized by this license, the Licensee shall maintain
each year a continuous minimum flow of at least 150 cfs in the Madison River below Hebgen
Dam (gage no. 6-385), 600 cfs on the Madison River at Kirby Ranch (USGS gage no. 6-388),
and 1,110 cfs on the Madison River at gage no. 6-410 below the Madison development. Flows at
USGS gage no. 6-388 (Kirby Ranch) are limited to a maximum of 3,500 cfs under normal
conditions excepting catastrophic conditions to minimize erosion of the Quake Lake spillway.

32

Establish a permanent flow gauge on the Madison River at Kirby Ranch (USGS Gauge No. 6-
388). Include a telephone signal at the gauge for link to Hebgen Dam operators and the Butte-
based System Operation Control Center.''

TeMperatnre Mofflltoring

Optic StowAway temperature recorders were deployed throughout the Madison River to
document air and water temperatures (Figure 7). Table 5 summarizes the data
collected at each location in 2009, Appendix D contains thermographs for each location.

Aquatic Nwisance Species

The annual economic cost of invasive species management and control in the United
States is estimated to be nearly $120 billion (Pimentel et al 2005). It is estmiated that about 42%
of the species on the Threatened or Endangered species lists are at risk primarily because of
alien-invasive species.

In 1994, two invasive species were detected in the Madison Dramage - New Zealand
mudsnails (Potamopyrgus antipodarum) and wMrling disease {Myxobolus cerebralis). Montana
has an active multi-agency ANS program coordinated through FWP (Appendix E).

Within FWP Region 3 dissolved calcium levels varied from 1 lmg/1 at the Big Hole River
Fish Trap FAS to 62 mg/1 at Clark Canyon Reservoir. The sole site sampled m the Madison
Drainage was Ennis Reservoir, which showed a calcium concentration between 20 - 24 mg/1.
Calcium concentrations of 15 mg/Iiter or less are thought to limit the distribution of zebra/ and
quagga mussels. During the 2010 the FWP ANS crew will continue efforts toward early
detection and monitoring of existing ANS throughout Region 3, including collection of
additional samples to evaluate calcium levels throughout the region.

New Zealand Mudsnails

Sampling for NZMS vras conducted at 18 sites withm the Madison Drainage m 2009
(Ryce 2009). Notable NZMS densities occurred at Darlinton Ditch and in the Madison River
upstream of Hebgen Reservoir.

The Montana Aquatic Species Coordmator has developed a plan to address New Zealand
mudsnails. Specifically, these actions include:

1) Listing New Zealand mudsnails as a Prohibited species in Montana.

2) Assisting in development of a regional management plan for New Zealand mudsnails, an
important portion of which vwll describe actions to be undertaken when New Zealand
mudsnails are found in or near a hatchery.

3) Establishing statewide monitoring efforts.

33

Table 5. Maximum and minimum temperatures (°F) at selected locations in the Madison River

Drainage, 2009. Air and water temperature data were recorded from April 24 -October 6
(43,456 data points). Thermographs for each location are in Appendix D.

-

Site

Max

Min

Water Hebgen inlet

77.8

41.9

Hebgen discharge

66.6

37.2

Quake Lake inlet

67.2

35.9

Quake Lake outlet

65.1

37.7

Kirby Bridge^'

70.4

35.6

McAtee Bridge

70.2

34.0

Ennis Bridge

71.8

35.7

Ennis Reservoir^' Inlet

NA

NA

Ennis Dam

73.0

40.0

Bear Trap Mouth

78.4

39.6

.

Norris

78.2

34.7

Blacks Ford

79.6

37.9

~

Cobblestone

80.8

38.0

Headwaters S.P.'^

NA

NA

(Madison mouth)

Air Kirkwood

93.4

18.0

SHde

NA^

21.1

Wall Creek HQ

91.7

20.9

Ennis

99.1

25.5

Ennis Dam

91.5

24.7

Norris

84.8

30.2

Cobblestone

89.6

22.8

■

" Recorders at Ennis Reservoir Inlet and Headwaters State Park were not recovered
^ Maximum temperature at Slide was 1 37.9, but the recorder had been moved by an unknown party
from its shaded position to a point in the fiill sun.

34

4) Conducting boat inspections at popular FAS, many of which are on the Madison River.
This effort assists with public education/outreach and also ensures boats are not spreading
New Zealand mudsnails or other ANS.

5) Purchasing portable power washing systems for cleaning boats and trailers at fishing
access sites.

The MFWP Fisheries office in Ennis uses a power washer to clean project equipment to

reduce the chance of spreading ANS through work activities.

NZMS have not been found in any state or federal hatcheries. Strategies have been
implemented to prevent the spread of NZMS from the sole private hatchery in which they were
discovered. The spread of New Zealand mudsnails has slowed and appears to be confined to east of
the Continental Divide.

Additional information on Aquatic Nuisance Species is on the web at
www.anstaskforce.gov and www.protectvourwaters.net. and for New Zealand mudsnails
specifically, is available at www.esg.montana.edu/aim/mollusca/nzms.

Whirling Disease

Caged young-of-the-year rainbow trout in the Madison River continue to exhibit high
infection rates & severity (Table 6) and still exceed the level that results m population effects
according to the MacConnell- Baldwin Scale (Appendix A).

The juvenile rambow trout used in the sentinel cage studies are not offspring of Madison
River rainbow trout, but are from the c^tive stock that has been used in sentinel cages since smdies
began in 1996. The high infection rate exhibited by this captive stock shows that whirling disease is
still at high levels in the Madison River, but offspring of Madison River rainbow trout appear to be
developing a resistance to whirling disease as evidenced by rainbow trout population estimates in
the upper river (Figures 26-27). In 1998, and again in 2004, eggs were collected from spawning
rainbow trout near the SHde Inn below Quake Lake and the resulting fry exposed to a controlled
number of TAMs in the Wild Trout Laboratory in Bozeman. Fry from the 2004 spawners exhibited
a lower proportion of fish m the highly infective categories compared to those froni 1998 (Figure
32). For rainbow trout, average histology scores above 2.5 are associated with high mortality of
young-of-the-year and significant decreases in population. In Figure 32, the average histology
score of the 1998 test fish is 4.13, while that of the 2004 test fish is 2.42.

35

Table 6. Sentinel rainbow trout whirling disease infection rates, Madison River, June 9-19,
2009.

Site

Average infection
score

Percent of fish
infected

Upper
cage

Lower
cage

Upper
Cage

Lower
cage

South Slide

0.08"

4.94

2.0

1 00.0

Slide Inn

0.42

0.11

16.7

7.1

Pine Butte

4.69

4.74

100.0

97.4

Kirby

4.53

4.24

100.0

93.1

Lyons

4.42

4.98

88.5

100.0

Palisades

4.93

2.96

100.0

52.0

Vamey

4.79

5.00

95.8

100.0

West Fork

2.64
• _ . • ^1 „ „ _ .

4.73
1 _. ^ _ 1

60.7

97.8

•a

0)

to

c

12 3 4

MacConnell-Baldwin Histology score

Figure 32. Percent of young-of-the-year Madison River rainbow trout within MacCoimell-
Baldwln histology ratings in 1998 and 2004. See Appendix A for MacConnell-
Baldwin definitions.

36

Vincent (2007) speculated that high levels of whirling disease spores persist in the
Madison River hecause some rainbow trout produced in the late 90's through early 2000's still
survive in the river, and their offspring are not resistant. He fiirther speculated that as those older
fish fall out of the spawning population, only fish that have developed resistance to whirling
disease will remain, and the number of whirling disease spores m the river will diminish.

Information on whirlmg disease, including numerous links, is available online at
•www.whirling-disease.org.

Habitat projects conducted by the Madison Ranger District of the Beaverhead-Deerlodge
National Forest and project feasibility surveys by Yellowstone National Park are summarized in
Appendix F.

Sun Ranch Westslope Cutthroat Trout Program

The Sun ranch Brood produced no viable eggs or fiy ui 2009 but three donor streams
produced 6,55 1 eyed eggs for introduction into Cherry Creek and 609 fiy for introduction into the
Sun Pond.

Over 9,872 eggs fix)m donor stream wild populations were incubated at the Sun Hatchery in
2009. Eyed eggs were introduced into Cherry Creek, into Cottonwood Creek in FWP Region 4,
into the Specimen Creek Drainage m YNP, and each donor stream contributed to the Sun Ranch
Brood Pond. Additionally, over 400 fry produced from eggs reared in the Sun Hatchery were
introduced mto Cherry Lake. No Sun Ranch brood fish produced viable eggs 2009.

Appendix G Hsts tiie contributions to and production of the Sun Hatchery since 2001, and

Appendix H provides a list of streams for which PPL Montana funding has been used to test genetic
purity.

Cherry Creek Native Fish Introduction Program

In 2009, 9,140 eyed eggs firom three wild donor streams and 1,714 eyed eggs firom the
Washoe Park Hatchery were placed in RSIs in Phases 2 and 3 (Figure 33), resulting in 4,024 and
4,241fiy, respectively, released into each Phase. Wild eggs were reared to the eyed stage at the Sun
Ranch Hatchery then placed in RSI's (Figure 1 6). Genetic samples will be collected fi-om the
developing population as the WCT population establishes and stabilizes to ascertain the proportion
fix)m each donor source relative to the proportion of eggs introduced.

37

Cherry Creek

Tributary to Madison River, Montana

Fish Distribution

vvcr

intiTidtctions
06-08

VVCT
irstroduetions
09

Legend

-.^ Brook Trout
RaintoK Trout

. . . Brown Trout

Yellowstone Cutthroat Trout
Rslitess (Pole Creek not part of study)

♦ Barrier: w>waierfall,B»Beaver Dam

Figure 33. Phases 1 - 3 of the Cherry Creek Native Fish kitroduction Project where westslope
cutthroat trout were introduced in 2006 - '09 following eradication of non-native
Yellowstone cutthroat, rainbow, and brook trout in 2003 - '08.

Personnel from MFWP, Montana State University, Gallatin National Forest, and Turner
Enterprises spent approximately 16 worker-days completing the project in 2009, including all
preparatory and support activities and chemical treatments. A total of 5.7 gallons of CFT and '/a
pound of powdered rotenone were required to complete treatments in 2009, all m Cherry Creek
and tributaries (Table 7).

Fish Habitat Enhancement

Smith Lake

The aged stock water delivery system on Lake Creek is being deactivated in favor of a
more efficient system that will eliminate the need to manipulate streamflow at Smith Lake Dam.
Plans were developed and grants applied for to drill a well and develop a delivery system that
will deliver water to the stock tanks, eliminating the need to seal the dam and bypass with tarps,
allowing brown trout and other fish to freely pass the dam for spawning and other needs. The
well was completed in 2009, and the pipeline to the stock tanks is expected to be completed in
2010.

38

Table 7. Schedule of Cherry Creek piscicide treatments, the nmnber of stream miles treated,
mmxber of worker days, and quantity of piscicide used, 2003 - 09.

Year

Phase

miles treated

# worker-days

piscicide quantity

2003

1

11

284

4.9 gallons Antimycin

2004

1

11

240

6.4 gallons Antimycin;
1.0 gallon rotenone

2005

2

8

220

7.0 gallons antimycin

1.0 gallons rotenone Iqd

1 lb rotenone pwdr

2006

2

8

256

5.9 gallons Antimycin

2007

2,3

4,23

264

9.0 gallons rotenone

2008

3

23

158

14.6 gallons rotenone
2 lbs rotenone pwdr

2009

3

5

16

5.7 gallons rotenone
0.5 lbs. Rotenone pwdr

O'Dell Creek

No fish monitoring activities were conducted on the O'Dell Creek restoration in 2009,
but will resume in 2010 and are expected to be conducted biannually thereafter.

Hebgen Basin

Hebeen Reservoir Gilhiettirig

Table 8 summarizes characteristics offish captured during 2009 Hebgen gilbetting.

The number of rainbow trout captured by gilbetting in 2009 decreased from 2008, but
the trend over the past seven years is increasing, and in 2008 and 2009 the number captured
re^ed to the level seen m the mid - late 1990's (Figure 34). The number of rainbows captured
per year has varied from 47 in 2001 to 194 in 2008.

Table 8. Summary of 2009 Hebgen Reservoir gilhiet catch

Species

Rainbow trout

Brown trout

Whitefish

Utah Chub

Nimiber caught

110

212

127

701

Average Length
(range)

15.8

17.1

15.8

10.5

Average weight
(range)

1.49

1.72

1.58

0.59

39

•a
9>

a.

(0

o
«

E

3

I

B

CO
0)

a

3
(Q

1995 1997 1999 2001 2003 2005 2007 2009

Figure 34. Rainbow trout average length (inches) vs. number captured during annual Hebgen
gillnetting, 1995-2009. 2004 data set not shown because of sampling error.

Average length of rainbow captured has been higher in the 2000's than in the mid-late
1990's. Additionally, the proportion of the rainbow trout giUnet catch under 14 inches has
decreased noticeably since 2003 (Figure 35).

Four of 91 (4.4%) rainbow trout vertebrae examined were positive for tetracycline marks,
indicating fish of hatchery origin. Tetracycline can be added to hatchery pellets to put a mark in
the vertebrae, creating a positive identification feature for hatchery raised fish. Three of the four
marked fish also exhibited dorsal fin erosion. Dorsal fish erosion is often associated with
hatchery produced trout. Applying the 4.4% tetracycline ratio to the fiill 1 1 0 rainbow captured,
five rainbow trout can be assigned to hatchery origin.

Two (1 .0%) coded-wire-tagged rainbow trout firom tributary traps were recovered during
giUnetting. One fish was snout tagged, which indicates its tributary of origin was the South
Fork Madison. The location of the tag on the other fish failed to be recorded during processing.

40

2001

60 50 40 30 20 10 0 20 40 60 80 100
Percent under 14 inches Percent 14 inches and larger

Figure 35. Percent of Hebgen Reservoir rainbow trout gillnet catch under and over 14 inches,
1999-2009. 2004 data set not shown because of sampling error.

Brown trout numbers have fluctuated widely with no consistent trend evident for more
than a few consecutive years (Figure 36). The number offish captured annually has ranged firom
61 in 2002 to 326 in 1999. Average length is trending upward over the past ten years.

1995 1997 1999 2001 2003 2005 2007 2009

Figure 36. Brown trout average length (inches) vs. number captured during amiual Hebgen
gillnetting, 1995-2009. 2004 data set not shown because of samplmg error.

41

The number of whitefish captured decreased significantly in 2002, but has remained
relatively stable smce (Figures 37). The number captured per year has varied from 83 in 2005 to
272 in 1999. Average length has shown a generally upward trend, though it has decreased each
of the past two years.

•a
<l>

k-

3
.1^
Q.

to

O

m
£

1995 1997 1999 2001 2003 2005 2007 2009

Figure 37. Mountain whitefish average length (inches) vs. number captured during annual

Hebgen gilhietting, 1995-2009. 2004 data set not shown because of sampling error.

The number of Utah chub captured decreased significantly in 2005, but average length
has shown no consistent trend since 1995 (Figure 38). The number of Utah chub captured
annually has ranged from 305 in 2007 to 2308 in 1999.

Utah chub comprised 90.9 percent of the total Hebgen gilbiet catch in 2002, but have
averaged 60 percent over the past five years (Figure 39). Utah chub were illegally introduced
into Hebgen Reservoir in the 1930's.

42

1995 1997 1999 2001 2003 2005 2007 2009

Figure 38. Utah chub average length (inches) vs. number captured during annual Hebgen
gilhietting, 1995-2009. 2004 data set not shown because of sampling error.

3500
3000

.a

en

2500
2000

s

{3

2

1500

1000

500

0

■Utah chub4«UC % □Whitefish
EHBrown DRainbow

1995 1997 1999 2001 2003 2005 2007 2009

Figure 39. Species composition of Hebgen gillnet catch, 1995 - 2009.

Hebgen Basin Disease Monitoring

Whirling Disease

The 2009 whirling disease samples for Hebgen tributaries were inadvertently destroyed
prior to processing for analyses. Monitoring in previous years indicates a moderate - high

43

infection on the MacConnell-Baldwin scale (Appendix A) in the South Fork Madison but no
Section L other Hebgen tributaries (Table 9). Some rainbow trout spawners ascendmg Duck
Creek in previous years exhibit external characteristics of whirling disease.

T^H;9"WhMki^^i^^^^ rainbow trout

2007-2008. The 2009 samples were inadvertently destroyed prior to completing the

proper incubation period.

Dates of exposure Average infection score

2007

May 10-20

4.29

May 20 - 30

4.66

May30-Jun9

3.96

Jun9-19

3.67

Jun 19-29

2.52

2008

Jun 18-28

3.30

Jun 28 -Jul 8

2.46

"nTo^ Hebgen Mbutaries have exhibited whirling disease scores higher than 0.20.

Uphpe,n Rasin Tributary Trapping

Table 10 summarizes characteristics of Spring spawnmg rainbow trout in Duck Creek
and the Soul Fork Madison River, and Fall spawning rainbow .trout brown trout and whitefish
in the mainstem Madison River upstream of Hebgen Reservon: m 2009.

Table 10. S^aty ^^^^ ^^^ ^^^^ ^^^^ ^^^^^ ^^^^^ ^^ Fall spawmng rambowhmim
the mainstem Madison River, 2009. Rb = rambow trout, LL = brown trout, MWF -

wmieiisn.

Duck Creek

SF Madison

Mi
Rb
90

18.2
16.2-21.3

2.29
1.71-3.46

idison River
LL

MWF

Number captured

Average Length
Length range

Average Weight
Weight range

279

17.5
8.5-20.5

1.82
0.18-2.53

145

17.8
15.0-20.8

2.03
1.24-2.84

28

17.8
16.7-20.2

2.12
1.88-2.65

19

17.4
14.6-18.6

2.33
1.33-3.00

44

Duck Creek

In 2009, adult trapping efforts on Duck Creek captured 279 rainbow trout (147 $, 132 (5^)
and one brown trout. Peak 2009 spawning immigration occurred May 26 - May 29 with 158
rainbow trout passing through the trap.

Three of the 279 rainbow trout sampled (1.1%) were positive for the presence of a coded-
wire-tag that they received while emigrating as juvenile fish. To date, ten of 2,628 (0.4%) fish
injected with coded-wire tags have been recaptured, all at the Duck Creek spawner trap.
Juvenile Duck Creek fish injected with a coded-wire tag were all yearlings or older when
captured in the screw trap, at least 3-4 inches in length at emigration.

Another three individuals (1.1%) had floy-tags that they received in previous years after
being captured in the upstream spawner trap. One of those fish was tagged m 2006, the other
two in 2008.

None of the rainbow trout captured in 2009 exhibited hatchery dorsal fin characteristics
and none were missing adipose fins. Adipose fins were removed fi:om a portion of hatchery
reared fish planted in the reservoir in an effort to determine hatchery contnbution to the fishery.

South Fork of the Madison

The South Fork Madison adult trap was operated fi-om April 16 - May 19, capturing 145
(71 ?, 74 6*) rainbow trout. Peak immigration of spawning adults occurred m mid - late April
when mean daily water temperatures were approximately 45°F.

Three of the 145 rainbow trout sampled (2.1%) in 2009 were positive for the presence of
a coded-wire-tag that they received while emigrating as young-of-the-year fish, hi the South
Fork 4 fish of 29 951 (0 01%) have been recovered, three in the South Fork spawner trap m
2009, and one during giUnettmg in 2008. All South Fork fish injected with coded-wke tags were
young-of-the-year captured in the screw trap, all less than one inch at emigration. Additionally,
three rainbows (2.1%) had floy-tags they received in previous years after bemg captured m the
upstream spawner trap. One of those fish was tagged m 2007, the other two m 2008.

There was no external evidence of hatchery reared fish among those captured in the
South Fork spawner trap.

Holton and Johnson (2003) concluded that, m general, rainbow trout in lentic
environments in Montana live to be no more than 7 or 8 years old. Analysis of rambow trout
scale samples from fish captured in the Duck Creek and South Fork Madison traps shows that
66% and 40%, respectively, of the 2009 spawmng runs were composed of six years old or older
fish (Figure 40).

45

Figure 40. Age composition of rainbow trout captured in the Duck Creek (left) and South Fork
Madison (right) adult spawning traps in 2009.

Madison River mainstem

The Madison River resistance panel weir was operated periodically from September 24 to
October 23, 2009. A total of 137 fish were captured (Table 11). One rainbow trout was
originally captured and tagged October 24, 2007. The greatest movement offish occurred
October 21, when the mean daily water temperature was 52° F and daily discharge was 416 cubic
feet per second (cfs). One rainbow trout exhibited hatchery dorsal fin characteristics. Gender
composition offish captured at the weir in 2009 is shown in Figure 41.

Table 1 1 . Number of fish handled by month at the Madison weir in 2009.

Month

Rainbow

Brown

Whitefish

Total

September

35

6

0

41

October

55

22

19

96

Total

90

28

19

137

Percent of
Total

65.7

20.4

13.9

One rainbow trout mortality was attributed to handling at the Madison weir in 2009,
while weir mortality accounted for one rainbow and eight whitefish mortalities. A fishing
closure was implemented from 100 yards upstream of the frap to 100 yards downstream of it to
prevent angling offish concentrated just below the trap and on fish that had been released after
capture in the trap. The incidence of hooking scars on fish captured in the tr^ decreased 90
percent from a rate of 7 percent in 2008 to 0.7 percent in 2009.

46

T3
9)

Q.
CO

o

a
o

H

c
2
a.

Rainbow trout

Brown trout

Whitefish

Figure 41. Percent gender composition offish handled at the Madison weir in 2009.

Table 12 compares catch at the Madison weir in 2007 - 2009.

The contribution of the Madison River rainbow trout spawning run to the Hebgen
Reservoir fishery is unquantified. High Spring flows make operation of the screw trap difficult
and decrease capture efficiency of the trap. Large floating debris often plugs the trap or jams the
rotating drum, which prevents capture of emigrating fish. Sampling efforts m 2006 & 2007
indicate that young-of-the-year and juvenile rainbow trout are emigrating as early as March,
prior to the time of rainbow spawning in other Hebgen tributaries.

Information regarding the Fall rainbow spawning run initially came from limited yoiing-
of-year emigration and temperature data collected in 1990 (Fredenberg 1991), which indicated
that rainbows may be spawning as early as January. Water temperature dkectly affects the rate
of egg development and hatching. For example, rainbow trout eggs incubated at a constant water
temperature of 40° F require 640 temperature units to hatch (Piper et al. 1982), where a
temperature unit is defined as 1° above 32° F for a 24-hour period. A constant water temperature
of 40° F would provide 8 temperature-units per day, requiring 80 days for eggs to hatch.
Another 1,080 temperature-units are required by sac fry for yoUc absorption before swim up
(Fredenburg 1991). Back calculation to time of emergence, based upon first observance of
young-of-the-year rainbow trout m the Madison screw trap and water temperature, suggests that
rainbow trout are spawning as early as mid September in the Madison River. This is four months
earlier than Fredenburg (1991) suggested, but coincides with local angler reports of catching
sexually mature or "ripe" rainbow trout during the months of September and October. The
Madison weir was installed to investigate the Fall rainbow trout spawning run.

47

Table 12,

Summary of Madison weir operation, 2007 - 2009. Handling mortality is defined as
mortality caused directly by handling, or mortality of handled fish found wi&in 24
hours after handling. Weir mortality is defined as mortality caused by fish becoming
impinged in the weir panels or mortality caused by stress/crowding in the trap box.
H^dled fish exhibited unique marks or tags that did not occur on unhandled fish,
allowing their differentiation.

2007

2008

2009

Begin operation

Sept 15

Sept 3

Sept 24

Fnd operation

Nov 7

Oct 31

Oct 23

Begin & end

6526.12

6532.87

6533.13

reservoir
pipvfltions

6526.70

6525.63

6532.89

Total # days
operated

36

35

15

Trap not
operated some
weekends or if
adequate number
of crew
unavailable

Total rainbows

733 (4 handling;

197 (0)

90

(1 handling;

1 weir)

captured (#
morts^

4 weir)

Total brown

772 (2 handlmg;

233 (0 handling;

28(0)

captured (#

5 weir)

1 weir)

Total whitefish
captured (#
morts)

491
(4 handling; 158

weir )

154

(1 handling; 22

weir)

19
(0 handling;

8 weir)

49 whitefish
weir morts on
10/24/07 when
143 whitefish
caught in
trapbox.
47 whitefish
morts on
ll/6&7/07when
panels were
raised to
maximize
capture for
whitefish egg-
take for whirling
disease research

Total Captured
— all species

1996
[10 handling

584
[1 handling

137
[1 handling

Weir morts may
not be handled

(# morts)

(0.5%), 167
weir (8.4%)]

(0.2%),
22 weir (3.8%)]

(0.7%); 9
weir (6.6%)]

fish

48

It is uncertain why rainbow trout are spawning in the Madison River in the Fall. The Fall
spawning run may be linked to the warm thermal regime of the Gibbon and Firehole rivers in
Yellowstone National Park. In a study of the reproductive biology of rainbow trout and brown
trout in the Firehole River above the Firehole Falls, rainbow trout were observed spawning in the
Fall of the year. It was hypothesized that the Fall spawning was likely an adaptation to the
thermal regime of the river (Kaya 1 977). Another possible explanation is that the run developed
out of past stocking practices. Since 1954, several strains of rainbow trout have been used to
augment the Hebgen Reservoir fishery. MFWP began stocking wild strains of Eagle Lake and
DeSmet rainbow trout in 1987. Prior to that domesticated Arlee and Shasta strains were used. In
some instances, domesticated hatchery strains have been observed to spawn at times
uncharacteristic of rainbow trout as a result of selective breeding in hatchery systems. In order
to maximize productivity and increase the size offish being stocked, hatcheries developed Fall
spawning individuals to maximize the size offish to be planted (Leitritz 1959). Strain analysis
of rainbow trout collected in Duck and Grayling creeks Spring spawning run and the mainstem
Madison River Fall spawning run indicates genetic differences between the three sources are
insignificant. All three sources contain relatively similar ratios of primarily Eagle Lake, but also
Kamloops and one unknown source of rainbow genes. These results indicate that the Madison
Fall spawning run is from the same population as the normal Spring spawning Hebgen rainbows.

Hebgen Basin Juvetiile Fish Sampling

Rotary screw traps (Figure 42) were operated in Duck Creek and the SF Madison in 2009
to evaluate juvenile rainbow trout escapement and to investigate production of juvenile rainbow
trout in the presence of whirling disease in the South Fork Madison.

The majority of yearling rainbow trout emigration fi-om Duck Creek June 1 1 - 27 when
mean daily water temperatures ranged fi-om 53.1° to 56.5° F (Figure 43).

Figure 42. Rotary screw trap used to sample young-of-the-year and juvenile fish on Hebgen
tributaries.

49

■ Number of RB Yearlings

Mean Temperature

I

70.00
60.00
50.00 ^

40.00 S

re

30.00 I

aa

20.00 °

10.00

0.00

Figure 43. Duck Creek rainbow trout emigration vs mean daily temp. The water temperature
recorder was not placed in the stream until May 7.

In 2005, upstream fish passage through the Duck Creek culvert on US Highway 191 was
improved by constructing a boulder cascade at the outlet. Prior to construction of this cascade,
adult fish were delayed and possibly prevented from passing at this culvert due to the vertical
height of the culvert outlet above the streambed. Juvenile fish trapping results show a
subsequent increase m outmigrant juvenile brown trout in 2006 and 2007, and an uicrease in
outmigrant juvenile whitefish in 2006. In 2009, screw trap capture of juveniles of both species
declined to pre-construction levels (Figure 44).

m Yearling Brown Trout " Whitefish

Figure 44. Number of juvenile brown trout and whitefish captured in the Duck Creek screw trap.
2005-2009.

50

The largest number of yearling rainbow trout captured in the South Fork Madison rotary
screw trap was 112 on May 8 when mean daily water temperature peaked at 55.1 °F (Figure 45).
Peak emigration duration of yearling rainbow trout lasted until May 1 9. Four yearling rainbow
trout had physical abnormalities characteristic of whirling disease.

E

I Yearling Rainbow trout

Mean Daily Temperature
—■- -r 60.00

v-a'*

^

<f

.<b\^

.O**

A*^

/

c
<u

<u
a

Figure 45. South Fork Madison rainbow trout emigration vs mean daily temperature.

The number of young-of-the-year rainbow trout captured in the South Fork Madison
rotary screw trap was down markedly from previous years with only 256 sampled, compared to
18,306 in 2005 and 1 1,027 in 2004. Additionally, the number of whitefish decreased from 54 in
2004 and 37 in 2005 to 4 in 2009.

Table 13 lists whirling disease scores for Hebgen Reservoir tributaries. The observed
reduction in young-of-tiie-year rainbow trout and whitefish in the South Fork may be attributable
to whirlmg disease. Significant reduction in young-of-tiie-year rainbow trout survival can occur
when infection grades are 3.0 or greater; with 99% mortality observed witiiin 30 days in
laboratory tiials and 97% mortality observed witiiin one year in tiie field (Vincent 2004; Sipher
and Bergersen 2001).

A list of all fish captiired at tiie Duck Creek and Soutii Fork Madison rotary screw ti^ps
in 2009 are listed in Table 14.

51

Table 13, Whirling disease scores for the South Fork Madison River, 2007 & 2008. Sentinel
fish from 2009 were inadvertently destroyed prior to completion of the required 90
incubation period, so test results are unavailable for 2009.

Year

Site

Test Penod

WU score

2007

South Fork

May 10-20
May 20 -30
May 30 -Jun 9
Jun 9 -19
Jun 19 - 29

4.29
4.66
3.96
3.67

2.52

Black Sands
Spring

May 10 -20
May 20 -30
May 30 - Jun 9
Jun 9 -19
Jun 19 - 29

0.02
0
0
0
0

DuckCk

May 10-20
May 20 -30
May 30 - Jun 9
Jun 9 -19
Jun 19 -29

0.12

0
0.08
0.06

0

2008

South Fork

Jun 18-28
Jun 28 - Jul 8

3.30
2.46

Duck Ck

Jun 18-28
Jun 28 - Jul 8

0
0

Cougar Ck

Jun 18 -28
Jun 28 - Jul 8

0
0

Grayling Ck

Jun 18-28
Jun 28 - Jul 8

0
0

Table 14. Numbers of young-of-the-year and juvenile trout, and numbers of other fish species
captured in the Duck Creek and South Fork Madison screw traps, 2009.

SF. Madison

Duck Creek

Species

Yearling

Y-O-Y

Rainbow trout
Brown trout
Brook trout
Whitefish
Longnose dace
Mottled sculpin
Utah chub

683

98

59

6

850
213

5

20
15
0
0
0
0
0

Yearling

Y-O-Y

402
2251

0

0

1

18

0

256
1127

0

0

0

0

0

52

studies of lake versus tributary rearing Bonneville Cutthroat trout in Strawberry
Reservoir, Utah (Knight et al 1999) and rainbow trout in Lake Alexandria, New Zealand (Hayes
1995) show the recruitment of early migrants to lake or reservoir populations is significantly less
than that offish that rear in natal streams until at least age 1 before emigratmg. Factors that may
be limiting the recruitment of early migrant rainbow trout are susceptibility to predation, habitat
and forage availability due to reservoir storage conditions, and competition with other fishes.
Availability of littoral cover can greatly increase juvenile fish survival by reducing the
probability of an encounter with a predator. Additionally, both intra and interspecific
competition for forage and other resources is amplified when habitat availability is condensed
(Walls et al. 1990). A study of brown trout on Lake Eucumbene, New South Wales, New
Zealand showed higher lake levels to be positively linlced to year class survival (Tilzey 1999).
By rearing m the natal stream for 2-3 years. Duck Creek juveniles likely experience less forage
and habitat competition and posses greater predator avoidance and forage capabilities when they
enter the reservoir than do the South Fork Madison young-of-the-year emigrants. Table 15 lists
tlie actual and estimated number of yearling and older rambows and young-of-the-year for each
stream since 2004.

Table 15.

Actual and estimated number of captured yearluig & older and actual captured young-
of-the-year rainbow trout for Duck Creek and the South Fork Madison, 2004 - 2009.

Duck

actual

SF Madison

estimated

Year

actual
1,070

estimated

v-o-v

2004

4,313

455

1,481

11,027

2005

1,338

3,552

1,162

2,942

18,306

2006

656

3,561

—

—

—

2007

317

4,467

—

—

—

2009

683

2,421

402

608

256

53

Hebgen Reservoir Shoreline Juvenile Fish Sampling

Shoreline juvenile fish monitoring was not conducted in 2009. Results of previous years
monitoring are shown in Figure 47.

2000

1500

1000

500

1758

671

"■377fe:,

177

187

54

75

16o48 19 1

100

ffl2006
E32007
□2008

Rainbows

Browns

Whitefish Utah chubs

Figure 47. Number of young-of-the-year captured during Hebgen Reservoir beach seining, 2006
-2008.

Utah chub spawning has been observed in May through late August in Hebgen Reservoir.
Typically, spawning takes place in shallow near-shore zones often with submergent or emergent
vegetation and inundated terrestrial vegetation. Vegetation has been suggested to be key to the
success of spawning for Utah chub (Teuscher and Lueke 1996). Similarly, studies have shown
that shoreline vegetation is important for the rearing of young-of-the-year adfluvial salmonids
that emigrate to lakes and reservoirs. However, given the fecund nature of the Utah chub, with
mature females from Hebgen averaging 40,750 eggs (Graham, 1955), a quick hatch rate,
typically 6 to 9 days at 65.0°F to 67.0°F, and territorial behavior of young chubs, emigrating
young-of-the-year rainbow trout may be precluded from rearing habitat within the vegetated
near-shore portion of the reservoir.

Hebgen Reservoir Zooplankton Monitoring

Densities (individuals/liter) of cladoceran and copepod zooplankton in Hebgen Reservoir
have been monitored since 2006. Annual temporal trends in abundance show peak densities
occurring in late spring and early summer (Figures 48 & 49). Hebgen Reservoir ice-off
generally occurs in May.

54

Figure 48. Cladoceran densities (individuals/liter) by month, 2006-2009.

Number/liter

7
6
5
4
3
2
1
0

--2006—2007 2008
4-2009

4

"^^T&^^— -Q

\j// /

f

/

1

"

^^^^^ ^-.,_^

;;»

J

""^^^^^^S\

>

^^^

Jun

Jul

Aug Sep Oct

Figure 49. Copepod densities (individuals/liter) by month, 2006-2009.

55

Body size of both cladoceran and copepods increased as densities declined. This has
been observed in zooplankton populations in several temperate lakes. The warming of the
reservoir in early spring typically triggers a phytoplanfcton bloom promoting quick growth of the
zooplankton community'. However, size selective predation on larger cladocerans by fish
reduces their abundance and predation sliifts to copepods. Reduced predation on the remaining
cladoceran community could account for the increase in body size seen in the cladoceran
community through summer until densities are such that another predation shift occurs (Hall and
Threlkeld 1976).

Utah chub comprise the majority of the fish biomass in Hebgen Reservoir (Figure 39) and
may be influencing zooplankton densities through grazing. Cladoceran densities in Hebgen also
seem inversely related to the ratio of adult Utah chub/brown trout (Figure .50).

■S

o

CO

3
P

c

I

I

SL
O

sz

CD

XUtah chub/brown trout - -Number cladocerans/liter

2005

2006

2007

2008

2009

Figure 50. Number of Utah chub per brown trout (calculated fi-om"annual spring gilhietting) and
annual mean cladoceran density, 2005 - 2009.

Studies of Utah chub diet in several western reservoirs have shown zooplankton to be the
principle food item for Utah chubs. In Strawberry Reservoir, Utah,-Johnson (1988) reported that
shoreline grazing by Utah chub on zooplankton to be detrimental to the survival of young-of-the-
year cutthroat and rainbow trout. Similarly, enclosure experiments with Utah chub and kokanee
showed that increased densities of Utah chub reduced zooplankton densities and negatively
affected kokanee growth (Teuscher and Lueke 1996).

Short duration grovraig season is often associated with an increase in elevation, reduchig
the total number of days of primary production. Hebgen Reservoir, with a full pool elevation of
6,534.87 feet, may be more characteristic of an alpine lake than of lakes at lower elevations.
Johnson and Martinez (2000) found lake elevation and a shortened growuig season (the number

56

of days water surface temperature is at or exceeds 50°F) to be inversely related to lake
productivity. Mean surface water temperatures for Hebgen over the last five years equaled or
exceeded 50° F an average of 130 days. In 2007, surface temperatures equaled or exceeded 50°
F for 152 days, extending the growing season by ahnost a month, which may have contributed to
the increase in cladoceran densities observed.

CONCLUSIONS AND FUTURE PLANS

The Madison (Ennis) Reservoir grayling population continues to persist at low levels.
While the Madison population is very similar genetically to the Big Hole population, it exhibits an
adfluvial life history pattern versus the fluvial behavior of the Big Hole River population.

Population estimates will continue to be conducted annually in the Madison River. These
data are necessary for setting angling regulations, and to monitor environmental and biological
impacts on the populations.

New Zealand Mudsnail populations will continue to be monitored through the 2188
Biological and Biocontaminant monitoring program and through the FWP Aquatic Nuisance
Species Program.

Rainbow trout captive stock used m sentinel cage studies in the Madison River have
continued to show high infection rates and severity, hi laboratory studies, progeny of Madison
River rainbow trout exhibited resistance to whirling disease.

FWP has implemented a program and provided equipment to clean sampling gear to reduce
the chance of moving ANS between waters.

In 2009, adult WCT from the Sun Pond were spawned but the eggs were non-viable.
Fertilized eggs from three wild donor populations were reared in the Sun hatchery and introduced
into recipient sfreams as eyed eggs. Additionally, each wild donor population contributed fry to the
Sun Brood Pond.

The Cherry Creek Native Fish hifroduction Project will continue with the goal for 2010 to
be the completion of chemical removals of non-native fish from the project area and continued
introductions of wild donor populations into Phases 3 and 4.

In 2009 a well was drilled to provide water to stock tanks on a Forest Service livestock
pasture near Lake Creek, eliminating the need to use tarps to pool water behind Smith Lake Dam
to run a water-wheel driven pump. In 201 0 priority will be given to completmg installation of
the deUvery system from the well to the stock tanks. Activation of the well and delivery system
will allow permanent removal of tarps on Smith lake Dam and provide year-round passage for
spawning brown trout and other aquatic species.

Though lower than 2008, the number of rainbow trout captured during Hebgen Resen^oir
giUnetting in 2009 remained at levels not seen in ten years. The proportion of the catch over 14
inches has increased noticeably since 2003.

57

The South Fork of the Madison, where juvenile rainbow trout emigrate to the reservoir as
young-of-the-year, is the only tributary of Hebgen Reservoir to show high whirling disease
infection of sentinel fish.

In 2009, rainbow trout six year old and older comprised 66 percent and 40 percent of the
fish ascending Duck Creek and the South Fork of the Madison, respectively, to spawn.

Only 137 fish were captured in the Madison weir in 2009, compared to 1996 in 2007 and
584 in 2008. Anecdotal reports fi-om anglers indicate that the Fall spawning run of rainbow trout
has been diminishing for over 10 years.

Cladoceran and copepod zooplankton densities in Hebgen Reservoir showed diverse
patterns in 2009. Cladoceran density was highest in early Spring and Fall, but copepod density was
highest in summer.

58

Bramblett, R.G. 1998. Environmental Assessment. Madison River Drainage Westsiope
Cutthroat Trout Conservation and Restoration Program: Cherry Creek Native Fish
Introduction. Prepared for Montana Fish, Wildlife, & Parks, April 15, 1998. 70 pages.

Byorth, P. and B. Shepard. 1990. Ennis Reservoir/Madison River Fisheries Investigations.

Montana Fish, Wildlife, & Parks Final Report to Montana Power Company. 90 pages.

Federal Energy Regulatory Commission. 2000. Order Issuing New License, Project No, 2188-
030. Issued September 27, 2000.

Fredenberg, W. 1991. Hebgen Lake fiy recruitment study, fmal report. Montana Fish, Wildlife
and Parks. BozemanMT.

Graham, R. J. 1955. Biology ofthe Utah chub in Hebgen Lake, Montana. Master's thesis.
Montana State University, Bozeman Montana.

Hall, D.J. and S.T. Threlkeld. 1976. The size -efficiency hypothesis and the size structure of
zooplankton communities. Annual Review of Ecological Systems. 7:177-208.

vvww.annualreviews.org/arQnline.

Hayes, J.W. 1995. Importance of stream versus early lake rearing for rainbow trout fiy in Lake
Alexandria, South Island, New Zealand, determined fi'om otolith daily growth patterns.
New Zealand Journal of Marine and Freshwater Research, 29:409-420.

Holton, G.D. and H.E. Johnson. 2003. A field guide to Montana fishes. Third edition. Montana

Fish Wildlife and Parks, Helena Montana.

Johnson, B. and P. Martinez. 2000. Trophic economics of lake trout management in reservoirs
of differing productivity. North American Journal of Fisheries Management. 20: 127.

Johnson, J. 1988. Environmental assessment of plans to restore Strawberry Reservoir fishery.
Utah Division of Wildlife Resources No 87-14. Salt Lake City, Utah.

Kaya, C. M. 1977. Reproductive biology of rainbow and brown trout in a geothermally heated
stream; The Firehole river of Yellowstone National Park. Transactions ofthe American
Fisheries Society. 106:354-361.

Knight, C.A., R.W. Oraie and D.A. Beauchamp. 1999. Growth, survival, and migration patterns
of juvenile adfluvial Bonneville cutthroat trout in tributaries of Strawberry Reservoir.
Transactions ofthe American Fisheries Society. 128:553-563.

Leitritz, E. 1959. Trout and Salmon Culture (hatchery methods). California Dept. of Fish and
Game.

59

Montana Fish, Wildlife, & Parks. 1995. Madison River/Ennis Reservoir Fisheries. 1994 Annual
Report to Montana Power Company, Environmental Division, Butte, from Montana Fish,
Wildlife, & Parks, Pat Clancey, Ennis. May 1995.

Montana Fish, Wildlife, & Parks. 1996. Madison River/Ennis Reservoir Fisheries. 1995 Annual
Report to Montana Power Company, Environmental Division, Butte, from Montana Fish,
Wildlife, & Parks, Pat Clancey, Ennis. February 1996.

Montana Fish, Wildlife, & Parks. 1997. Madison River/Emiis Reservoir Fisheries. 1996
Annual Report to Montana Power Company, Environmental Division, Butte, from
Montana Fish, Wildlife, & Parks, Pat Clancey, Ennis. March 1997.

Montana Fish, Wildlife, & Parks. 1998a. Madison River/Ennis Reservoir Fisheries. 1997 Annual
Report to Montana Power Company, Environmental Division, Butte, from Montana Fish,
Wildlife, & Parks, Pat Clancey, Ennis. June 1998.

Montana Fish, Wildlife, & Parks. 1998b. Decision Notice: Cherry Creek Native Fish
Introduction Project RegionS, July 6, 1998. Pat Clancey. 30 pages.

Montana Fish, Wildlife, & Parks. 1999a Madison River/Ennis Reservoir Fisheries and Madison
River Drainage Westslope Cutthroat Trout Conservation and Restoration Program. 1998
Annual Report to Montana Power Company, Environmental Division, Butte, and Turner
Enterprises, Inc., Gallatin Gateway, from Montana Fish, Wildlife, & Parks, Pat Clancey,
Ennis. April 1999.

Montana Fish, Wildlife, & Parks. 1999b. Memorandum of Understanding and Conservation

Agreement for Westslope Cutthroat Trout in Montana. May 1999.

Montana Fish, WildUfe, & Parks. 2000, Madison River/Ennis Reservoir Fisheries and Madison
River Drainage Westslope Cutthroat Trout Conservation and Restoration Program. 1999
Annual Report to PPL Montana (formerly Montana Power Company), Environmental
Division, Butte, and Turner Enterprises, Inc., Gallatin Gateway, from Montana Fish,
Wildlife, & Parks, Pat Clancey, Ennis. April 2000.

Montana Fish, Wildlife, & Parks. 2001. Madison River/Ennis Reservoir Fisheries and Madison
River Drainage Westslope Cutthroat Trout Conservation and Restoration Program. 2000
Annual Report to PPL Montana, Environmental Division, Butte, and Turner Enterprises,
Inc., Gallatin Gateway, from Montana Fish, Wildlife, & Parks, Pat Clancey and Dan
Downing, Ennis. April 2001.

Montana Fish, Wildlife, & Parks. 2002. Madison River/Ennis Reservoir Fisheries and Madison
River Drainage Westslope Cutthroat Trout Conservation and Restoration Program. 2001
Annual Report to PPL Montana, Environmental Division, Butte, and Turner Enterprises,
Inc., Gallatin Gateway, from Montana Fish, Wildlife, & Parks, Pat Clancey, Ennis. June
2002.

60

Montana Fish, Wildlife, & Parks. 2003. Madison River/Emiis Reservoir Fisheries and Madison
River Drain^e Westslope Cutthroat Trout Conservation and Restoration Program. 2002
Annual Report to PPL Montana, Environmental Division, Butte, and Turner Enterprises,
Inc., Gallatin Gateway, from Montana Fish, Wildlife, & Parks, Pat Clancey, Ennis.
March 2003.

Montana Fish, WildUfe, & Parks. 2004a. Madison River/Ennis Reservoir Fisheries and Madison
River Drainage Westslope Cutthroat Trout Conservation and Restoration Program. 2003
Annual Report to PPL Montana, Environmental Division, Butte, and Turner Enterprises,
Inc., Gallatin Gateway, from Montana Fish, Wildlife, & Parks, Pat Clancey, Ennis. May
2004.

Montana Fish, Wildlife, & Parks. 2004b. FA+. Montana Fish, Wildlife, & Parks, Information

Services Unit, Bozeman.

Montana Fish, Wildlife, & Parks. 2005. Madison River/Ennis Reservoir Fisheries and Madison
River Drainage Westslope Cutthroat Trout Conservation and Restoration Program. 2004
Annual Report to PPL Montana, Environmental Division, Butte, and Turner Enterprises,
Mc, Gallatin Gateway, from Montana Fish, Wildlife, & Parks, Pat Clancey & Travis
Lohrenz, Ennis. April 2005.

Montana Fish, Wildlife, & Parks. 2006, Madison River/Ennis Reservoir Fisheries and Madison
River Drainage Westslope Cutthroat Trout Conservation and Restoration Program. 2005
Annual Report to PPL Montana, Environmental Division, Butte, and Turner Enterprises,
Inc., Gallatin Gateway, from Montana Fish, Wildlife, & Parks, Pat Clancey, Ennis. June
2006.

Montana Fish, Wildlife, & Parks. 2007a. Madison River/Ennis Reservoir Fisheries and Madison
River Drainage Westslope Cutthroat Trout Conservation and Restoration Program. 2006
Annual Report to PPL Montana, Envhronmental Division, Butte, and Turner Enterprises,
Inc., Gallatin Gateway, from Montana Fish, Wildlife, & Parks, Pat Clancey, Ennis. June
2007.

Montana Fish, WildHfe, & Parks. 2007b. Memorandum of Understanding and Conservation

Agreement for Westslope Cutthroat Trout and Yellowstone Cutthroat Trout m Montana.
July 2007.

Montana Fish, Wildlife, & Parks. 2008. Madison River/Ennis Reservoir Fisheries and Madison
River Drainage Westslope Cutthroat Trout Conservation and Restoration Program. 2007
Annual Report to PPL Montana, Environmental Division, Butte, and Turner Enterprises,
Inc., Gallatin Gateway, from Montana Fish, Wildlife, & Parks, Pat Clancey, Ennis. July
2008.

Montana Fish, Wildlife, & Parks. 2009. Madison River/Ennis Reservoir Fisheries and Madison
River Drainage Westslope Cutthroat Trout Conservation and Restoration Program. 2008

61

Aimual Report to PPL Montana, Environmental Division, Butte, and Turner Enterprises,
Inc., Gallatin Gateway, from Montana Fish, Wildlife, & Parks, Pat Clancey and Travis
Lohrenz, Ennis. August 2009.

Pimentel, D., R. Zuniga, and D. Morrison. 2005. Update on the environmental and economic
costs associated with alien-species in the United States. Ecological Economics, 2005
(Vol. 52) (No. 3) 273-288.

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hatchery management. Second Printing, American Fisheries Society and United States

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Ryce, Eileen. 2009. Personal Communication

Sipher, C. R. and E. P. Bergersen. 2001. The effects of whirling disease on growth and survival
of snake river cutthroat and Colorado River rainbow trout fingerlings. 7 Annual
Whirling Diseases Symposium abstracts. Whirling Disease Foundation, Bozeman MT,
and Utah Division of Wildlife Resources, Logan, UT.

Sloat, M.R., B.B. Shepard, and P. Clancey. 2000. Survey of tributaries to the Madison River
from Hebgen Dam to Ennis, Montana with an emphasis on distribution and status of
westslope cutthroat trout. Report to Montana Fish, Wildlife, & Parks, Helena, Montana.
165 pages,

Tilzey, R.D.J. 1999. Environmental cues in the reproductive migrations of brown trout (Sabno
trutta) in Lake Eucumbene, New South Wales. Australian Society for Fish Biology.
Kingston ACT.

Teuscher D. and C. Luecke. 1996. Competition between kokanees and Utah chub in Flaming
Gorge Reservoir, Utah- Wyoming. Transactions of the American Fisheries Society.
125:505-511.

Vincent, Dick. 2004. Personal Communication.

Vincent, Dick. 2007. Personal Conraiunication.

Walls, M., I. Kortelainen and J. Sarvala. 1990. Prey responses to fish predation in freshwater
commxmities. Ann. Zool. 27:183-199.

62

Appendix A

The MacComiell-Baldwm whirling disease grade-of-severity scale and definitions.

Grade 0: No abnormalities noted. Myxobolus cerebralis is not seen.

Grade 1 : Small, discrete focus or foci of cartilage degeneration. No or few associated
leukocytes.

Grade 2: Single, locally extensive focus or several smaller foci of cartilage degeneration
and necrosis. Inflammation is localized, few to moderate numbers of leukocytes
infiltrate or border lytic cartilage.

Grade 3: Multiple foci (usually 3 ~A^') of cartilage degeneration and necrosis. Moderate
number of leukocytes are associated with lytic cartilage. Inflammatory cells
extend minimally into surrounding tissue. ^

Grade 4: Multifocal (usually 4 or more sites^') to coalescing areas of cartilage necrosis.
Moderate to large numbers of leukocytes border and/or infiltrate lytic cartilage.
Locally extensive leukocyte infiltrates extend into surrounding tissue.

Grade 5 : Multifocal (usually 6 or more^^) to coalescing areas of cartilage necrosis.

Moderate to large numbers of leukocytes border and/or infiltrate necrotic cartilage.
The inflammatory response is extensive and leukocytes infiltrate deeply into
suffoimding tissue. TTiis classification is characterized by loss of normal

architecture and is reserved for the most severely infected fish.

^' lesion numbers typical for hea4 not whole body sections.

Appendix Bl
Summary of Erniis Reservoir beach seining 1995 - 2009

Species abbreviations:
AG Arctic grayling

MWF mountain whitefish
LL brown trout
Rb rainbow trout

Date

AG

MWF

LL

Rb

7/27/95

12

177

4

0

9/1/95

23

89

4

0

6/18/96

0

6

1

2

7/22/96

0

0

0

0

8/22/96

0

0

1

0

8/20/97

1

0

3

0

10/27/97

0

5

0

0

9/4/98

0

0

0

0

9/22/99

2

34

0

0

11/2/00

0

14

3

0

8/29/01

0

0

0

0

10/2/02

1

2

4

0

10/6/03

0

2

3

1

9/28/04

1

9

96

0

9/27/05

0

11

19

5

11/5/07

0

0

0

0

9/29/08

0

0

3

1

10/1/09
10/22/09

0

1

0

5

139
0

30
0

Appendix B2

Description of yonng-of-the-year Arctic grayling beach seining locations in Ennis Reservoir,
and catch at each site. See Figure 3 for site locations.

Species abbreviations:

AG Arctic grayling

MWF

mountain whitefish

Rb

rainbow trout

LL

brovra trout

WSu

white sucker

UC

Utah chub

LND

long-nose dace

Sc

mottled sculpin

Site and time seined

AG

MWF

Note

Meadow Ck FAS
North shore & west
shore willows
10/22/09
Fig 3 site 1

1

5

No macrophytes
4 y-o-y UC
2 y-o-y WSU

South shore V* mile
eastofMooresCk

10/1/09
Fig 3 site 2

0

0

No macrophytes
75 y-o-y Rb

8 y-o-y LL
29 y-o-y UC

22 y-o-y LND

6 y-o-y WSu

Madison River mouth

10/1/09

Fig 3 site 3

0

0

No macrophytes
64 y-o-y Rb
22 y-o-y LL

4 y-o-y UC
3 y-o-y LND

6 y-o-y WSu

2Sc

Appendix CI

Historic population estimates of aged rainbow and brown trout per mile in the
Pine Butte, Vamey, and Norris sections of the Madison River

s

6,000

5,000

4,000

1 3,000
d

2,000

1,000

0

□Yearlings
sAge 2 & older

yppi

m

n

'^n M h

ir

77 79 81 83 85 87 89 91 93 95 97 99 01 03 05 07 09

Year

Figure CI - 1. Rainbow trout populations in the Pine Butte section of the Madison River,
1977-2009, faQ estimates. Estimates for 2004 - 2009 are not aged.

0

3,000

2,500

2,000

1 1,500
d

1,000

■ 500

0

-|

r-

1

zm

'k

1

□Yearlings per mile
HAge 2 & older per mile

67 69 71 73 75 77 79 81 83 85 87 89 91 93 95 97 99 01 03 05 07 09

Year

Figure CI - 2, Rainbow trout populations in the Vamey section of the Madison River, 1967-
2009, fall estimates. Estimates for 2000 - 2009 are not aged. Estimates were
not conducted in Vamey in 2008.

Figure CI - 3. Rainbow trout populations in the Norris section of the Madison River, 1986-
2009, spring estimates. Estimates for 2001 - 2009 are not aged.

s

□Yearlings
EiAge 2 & older

77 79 81 83 85 87 89 91 93 95 97 99 01 03 05 07 09

Year

Figure CI - 4. Brown trout populations in the Pine Butte section of the Madison River,
1977-2009, fall estimates. Estimates for 2004 - 2009 are not aged.

s

3,500

3,000

2,500

:i 2,000

o 1,500

1,000

500

0

□Yearlings per mile

mAge 2 & older per mile

-, n n El

' T

is i

Tr

PI

ri^illl

n nfl

nyiuin

r

III ii^

n

-, 1

iJ ■■

-\ JL

IP gi

iJ Jl§ ii

iiil

Byyil i

ip^i

, ! 19

^WM—HBIII

liii '' ,t '1 1

1 Sh

inuuiinLJ

67 69 71 73 75 77 79 81 83 85 87 89 91 93 95 97 99 01 03 05 07 09

Year

Figure CI - 5. Brown trout populations in the Vamey section of the Madison River,
1967-2009, fall estimates. Estimates for 2000 - 2009 are not aged.
Estimates were not conducted in Vamey in 2009.

s

5,000

4,000

^ 3,000

i 2,000

1,000

0

IMm

87 89 91 93 95 97 99 01 03 05 07 09
Year

Figure CI - 6. Brown trout populations in the Norris section of the Madison River, 1986-
2009, spring estimates. Estimates for 2001 - 2009 are not aged.

Appendix C2

Population estimates (total number in sectionj: 80 percent Confidence Intervals)
of age 2 & older rainbow and brown trout in the Madison River

See Figure 5 for section locations

section lengths

Pine Butte - 3 miles
Vamey - 4 miles
Norris - 4 miles

s

Pine Butte
Rainbow Trout
Age 2 & older

7,000

6,000

5,000

_2 4,000

CO §3,000

15 "2,000
o

^ 1,000
0

m5

^T

T

-f-

^rf

-*^-^

^— X

fef

"r

85 87 89 91 93 95 97 99 01 03 05 07 09

Year

s

Varney
Rainbow Trout
Age 2 & Older

3,500

3,000

^ 2,500
o

?. 2,000

c
o

0

1

_c
o

1,500

1,000

500

0

--T ■' -- _"t -^..-.^ _...-.. .

- X --T

* i i

- ****/ - - - *

85 87 89 91 93 95 97 99 01 03 05 07 09

Year

a

Norris
Rainbow Trout
Age 2 & Older

12,000

10,000

c

I 8,000
I 6,000
.£ 4,000
H 2,000
0

i

^^i.

i -1-

^***

* - * ***

86 88 90 92 94 96 98 00 02 04 06 08

Year

0

Pine Butte

Brown Trout

Age 2 & older

6,000 I ■-■■
5,000 i --

¥i-

c
o

I 4,000 1 y

I 3,000 j^txT^

CO

£ 2,000

CO

p

Ji

1

1

t

^i -t'

1,000
0

*** **

85 87 89 91 93 95 97 99 01 03 05 07 09

Year

a

Varney

Brown Trout

Age 2 & Older

6,000

5,000

1 4,000

to

I 3,000
^ 2,000

TO

|2 1,000
0

f

^f 1

v%

^1

:f

85 87 89 91 93 95 97 99 01 03 05 07 09

Year

s

Norris

Brown Trout

Age 2 & Older

20,000

I 15,000

o
<u
en

I 10,000

c

S 5,000
o

i

^^ rf^"^ *

86 88 90 92 94 96 98 00 02 04 06 08

Year

NOTES:

Appendix D

Temperature recordings from monitoring sites on the Madison River
See Figure 6 for locations

Recorders at Ennis Reservoir Inlet and Headwaters State Park were

not recovered

Maximum air temperature recorded at Slide was 137.9, but llie

recorder had been moved by an unknown party from its shaded

position to a point in the full sun. Only data prior to June 25 are

shown.

1001

«h

eon

70:

eo-

SO;

40-

30-.

2(H

Hebgen Inlet

10^

05/01/09

04/01/09 12:00:00 AM QMT-06:00

07/01/09

1

09/01/09

11/01/09
1 1/01/09 12:00:00 AM GMT-O6:00

lOCH

SCh

80-

7Ch

60-

50:

40^

3Ch

20:

Hebgen discharge

10-

04/01/09 12:00.00 AM GMT-06:00

T

asiovos

— ]

07/01/09

09/01/09

11/01/09
11/01/09 12:00:00 AM GMT-06:00

lOOq

80:

»:

TJh

80:

Sh

40;

30:

20:

10-

Quake Inlet

I

05/01/09

07/01/09

09/01/09

04/01/09 12:00:00 AM GMT-06:00

11/01/09
1 1/01/09 12:00:00 AM GMT-06:00

10Oa

9th

80:

70-.

ecn

50:

40-

ZOz

20:

10

Quake Lake outlet

1

OS/01/09

07/01/08

09/01/09

04/01/09 1 2;00;00 AM QMT-06:00

11/01/09
1 1/01/09 12:00:00 AM GMT-06:00

ioon

9Ch

80-

70:

6&:

51h

40:

30:

20:

Kirby

io

— I

05/01/09

07/01/09

09/01/09

04/01/09 12:00:00 AM GMT-06:00

11/01/09
11/01/09 12:00:00 AM GMT-06:00

100:1

Sth

80:

70::

60-

50:

40-:

30:

20:

McAtee

10-

— I —

05/01/09

— I

07/01/09

— I

09/01/09

04/01/09 12:00:00 AM QMT-06:00

11/01/09
11/01/09 12:00:00 AM GMT-0e:00

10thi

Sth

8Ch

7Ch

60-

SCh

40-

30:

20:

10

Ennis Bridge

1

05/01/09

1

07/01/09

1

09/01/09

04/01/09 12:00:00 AM OMT-06:00

11/01/09
11/01/09 12:00:00 AM GMT-06:00

10CH

90:

80:

70^

60:

50^

40:

30:

20r.

10-

Ennis Dam

0ia01/09

07/01/09

09/01/09

04/01/09 12:00:00 AM QMT-06:00

11/01/09
11/01/09 12:00:00 AM GMT-06:00

100a

Sth

80-

TCh:

60:

SO:

40:

30:

20:

Beartrap Mouth

10-

05/01/09

1

07/01/09

09/01/09

04/01/09 12:00:00 AM GMT-06:00

11/01/09
11/01/09 12:00:00 AM GMT-06:00

100:1

90:

80:

70:

60-

50:

40-

30:

20:

Norris

10

— I —

05/01/09

1

07/01/09

09/01/09

04/01/09 1 2:00.00 AM GMT-06:00

11/01/09
1 1/01 /09 1 2:00:00 AM GMT-06:00

100q

9(h

80:

70:

60;

SO:

40:

ah

iOr.

10-

Black's Ford

,

05/01/09

1
07/01/09

1

09/01/09

04/01/09 12;00;00 AM QMT-06;00

11/01/09
1 1/01/09 1 2:00:00 AM GMT-06:00

10t>a

9th

80:

70^

60-

Sth

40:

30:

20;

10

Cobblestone

— I

05/01/09

07/01/09

09/01/09

04/01/09 12:00:00 AM GMT-06:00

11/01/09
11/01/09 12:00:00 AM GMT-06:00

lOCH

90^

80-

7th

60:

SO:

40-

30:

20:

Kirkwood air

10

— I —

05«)1/09

[

07/01/09

1

09/01/09

04/01/09 1 2:00:00 AM GMT-06:00

_, 1

11/01/09
1 1/01/09 12:00:00 AM GMT-06.00

lOChi

8(h

SO-

TO:

60:

BO-.

40:

30:

20-

Slide air

10-

— I

05/01/09

1

07/01/09

1

09/01/OS

04/01/(» i; ;00:00 AM QMT-06:00

11/01/09
11/01/09 12:00:00 AM GMT-06:00

10Chi

90:

80-

7(h

60-

50:

40-

30:

20:

Wall Creek HQ air

10

— I

05/01/09

07/01/09

1

09/01/00

04/01/09 12;00;00 AM GMT-06:00

11/01/09
11/01/09 12:00:00 AM GMT-06:00

100-3

90^

60-

70:

60:

SO:

40-

30:

20:

Ennis air

10-

1

05/01/09

07/01/09

1

09/01/09

04/01/09 12:00.'00 AM GMT-06:00

11/01/09
1 1/01/09 12:00:00 AM GMT-06:00

« I

10Oq

8(h

80:

70:

eo:

SO:

40:

30:

^

Ennis Dam air

10

05/01/09

07/01/09

09/01/09

04/01/09 12:00:00 AM GMT-06:00

-1 1

11/01/09
1 1/01/09 12:00:00 AM GMT-06:00

lOtH

9(h

80-

70:

60:

50:

40:

30:

20:

Norris air

lO'

— f

05/01/09

1
07/01/08

1

09/01/09

04/01/09 12:00:00 AM QMT-06:00

11/01/09
11/01/09 12:00:00 AM GMT-06:00

lOthj

9CH

80-

7(h

60-

SQr.

40-

30^

20^

Cobblestone air

10-

OS/01/09

07/01/09

09/01/09

04/01/09 12:00.'00 AM GMT-06:00

-I 1

11/01/09
11/01/09 12:00:00 AM GMT-06:00

Appendix E

The Montana Aquatic Nuisance Species Management Plan was finalized in
October of 2002 and a foil time Aquatic Nuisance Species (ANS) Program Coordinator
was hired by Montana Fish, Wildlife and Parks in February of 2004. The emphasis of the
Montana ANS Program is on coordination, education, control and prevention of spread,
monitoring and detection, and rapid response. The species of emphasis are New Zealand
mudsnails, whirling disease, and Eurasian milfoil (all of which are established in
Montana), and zebra mussels (which is yet to be documented in the state). Strategies to
prevent the fiirther spread and introduction of these species are outlined below.

1 . Statewide distribution survey for New Zealand Mudsnails has been completed.
All state, federal and private hatcheries have been inspected for New Zealand
Mudsnails. One private hatchery contains New Zealand mudsnails, strategies
have been implemented to prevent the spread of this invasive through hatchery
operations. The spread of New Zealand mudsnails has slowed and appears to be
confined to east of the divide.

2. Zebra Mussel veliger sampling has been completed for all major reservoirs on the
Missouri River, and on other high priority lakes and reservoirs. To date no zebra
mussels have been found within the state.

3. Legislation and Rule making: In 2005 a rule making system was developed to
classify exotic wildlife (terrestrial and aquatic) as either non controlled, controlled
or prohibited. The following ANS have been since added to the prohibited list:
snakehead fish (29 species), grass carp, silver carp, black carp, bighead carp,
zebra mussels, rusty crayfish, nutria, African clawed fi-ogs, North American
bullfrogs, and New Zealand mudsnails. Legislation was also passed during the
2005 session to provide exceptions for the possession of prohibited species,
primarily for the purposes of research, in addition to providing for tougher
enforcement authority includmg the ability to confiscate illegally possessed exotic
wildlife.

4. Montana continues to actively participate m the 100* Meridian angler survey
program and during 2005 submitted more than 1,700 entries to the angler survey
database. The angler surveys are conducted as part of the Montana boat
inspection program, which was greatly expanded in 2005. Boat mspections have
occurred on all major lakes, reservoirs and popular cold-water trout rivers. The
fu-st boat with zebra mussels was found in Montana in March 2005.

5. Training: a one day workshop was provided dxiring the Annual Meeting of the
Montana Chapter of the American Fisheries Society on ANS identification, 2 day
HACCP workshops have been provided for Montana hatchery personnel and field
workers, a half day training was provided for Montana Firefighters on the
prevention of spread of ANS, and a half day training was provided on ANS

identification and prevention of spread as part of fish health training for fisheries
and hatchery personnel within FWS Region 6.

Public outreach: presentations on ANS have been made to several special interest
groups including Walleyes Unlknited, Fishing Outfitters Association of Montana
and Lake Associations. ANS informational booths were present at five Montana
outdoor shows: Billings, Bozeman, Great Falls, Missoula and Kalispell.
Informational packets have been developed and are being distributed for private
pond owners to encourage responsible pond ownership.

Illegal introductions: to date over 500 illegal fish introductions have been
recorded in Montana. Illegal introductions have been identified as a major source
of ANS introductions into Montana waters. An aggressive public outreach
campaign was launched during summer of 2005 with an increase in law
enforcement to discourage the activity of "bucket biology".

Appendix F
2009 Monitoring Reports

Madison Ranger District: Tepee Creek

Wigwam Creek

Yellowstone National Park: Grayling Creek

Stream Habitat Restoration Monitoring

Tepee Creek, Madison Ranger District

Beaverhead-Deerlodge National Forest

2009

Background

Tepee Creek originates on the east flank of tlie Gravelly Mountains as a tributary to Horse Creek, flowing into the Madison River
near Cameron, Montana. Historic trapping of beaver and over grazing have caused the stream channel to down cut and over-widen;
this system currently experiences a high fine sediment load. Although livestock grazing ceased 25 years ago, the channel had yet to
restore itself Tepee Creek still experiences light to moderate trampling and heavy browsing by ungulates associated with the
nearby Wall Creek Wildlife Management Area. Tepee Creek in the project area is Ashless due to a natural cascade barrier located
just downstream of the treatment area. Molecular analysis of westslope cutthroat trout (WCT) downstream in Horse Creek indicates
that this population is greater than 90% pure. Once habitat has been restored to acceptable levels in Tepee Creek, there is an
opportunity to introduce pure WCT into this headwater tributary.

The goal of restoration in Tepee Creek is to influence natural stream processes, particularly fine sediment deposition, to restore
channel morphology. A secondary objective is improved watershed fiinction by reducing fine sediment loads transported to the
Madison River, an impaired water body, on the MT Dept. of Environmental Quality's 303d list.

Installation of wil^w weirs - channel spanning dams constructed of wooden stakes, woven willow, and sedge clumps - has have
trapped fine sediments and built point bars and stream banks, particularly where sedges have expanded as they respond to increased
water storage and soil moisture. Weirs are particularly effective as they mimic beaver dams, trapping fine sediment and increasing
stream bed elevation (Fig. 1). Baffles, where wooden stakes are pounded into the stream bed in a triangle dot-grid and the
interstices are filled with cobble, willow, and sedge plugs to direct flow against the opposite bank and induce stream meandering
(Figure 2). Sediment also deposits on top of and in the back eddy created by these baffles, but not as effectively as the weirs. By
creating a series of baffles and weirs, the stream bed elevation is raised and a meander-pool-point bar morphology is created.

Figure 1 . View looking dovmstream at a series of baffles built in 2006 that induced meandering, July 2007.

9l"**IP^»i*W!iH*pi!9!9Vi*

Figure 2. Channel spanning log weir, inundating older structures in previous figure, August 2009.

Figure 3. Channel spanning log weir, viewed looking upstreairi, August 2009.

Results

Riffle and baffles were initially installed in September 2004, with monitoring and further construction continuing through 2008. In
2005 all structures survived winter ice jams and spring flows intact while trapping fine sediment. Channel cross sections were
established in order to monitor channel morphology (Figures 3-6), supplemented with photographs. The cross sections in 2005
showed an increase in stream bed elevation, indicating successiul sediment deposition. While the structures did survive the 2006
season, little increase in stream bed elevation occurred, indicating no further sediment deposition. It appeared that the structures had
reached their capacity to trap sediment in the first year. In 2006 weir structures were installed in an effort to increase the amount of
sediment deposition; monitoring results from subsequent years indicate that these structures have been quite effective in this regard.

In 2008, some weirs incurred small water breaches as a result of the long duration of spring runoff. This resulted in lowered water
surface elevations upstream of the structures. Breached weirs were sealed with bio-degradable sandbags and sedge chunks that
blocked upstream flow. The cross sections from 2008 indicate another year of sediment deposition, in addition to evidence of
channel narrowing (Figures 3-6). Photographs indicate that large quantities of sediment deposited upstream of weirs, creating bars,
recruiting sedges, and narrowing the channel (Figure 7).

While large amounts of sediment have been deposited, it is generally fine and highly mobile. In order to stabilize this sediment
sedge plugs were planted in 2007 and 2008. As these plugs mature, their root masses will stabilize the point bars. Also, baffle and
weir construction continued upsfream, expanding the restoration reach. Further monitoring, construction, and maintenance will
continue into the near liiture. However, someday, through sediment deposition and vegetation recruitment Tepee Creek should
return to historic conditions and support a native population of WCT.

Funding

This project has received considerable funding support from PPL-Montana in each year under the authority of Article 409 of the
PPL FERC license on the Madison River, specifically part (3) "fish habitat enhancement both in the main stem and tributary
streams, including enhancement for all life stages of fishes" and part (9) "riparian habitat restoration". The Madison-Beaverhead
Counties RAC also provided fijnds toward the purchase of supplies in 2005-6.

sS 92.5

a
o

68

I 91.5

.fi 91.0
S

2 90.5

■<-*
C/5

90.0
89.5

5 10 15 20 25

Horizontal distance from DR pin (feet)

j

30

Figure 3. Transect #1; note in 2009 the large sediment deposition at left and how sediment is now depositing in the floodplain.

93.5 i

o

s

-■- 2007
--•--2009

1

5 10 15

Horizontal distance from DR pin

20

Figure 4. Transect #2, relates annual increases in sediment deposition and strearabed elevation.

5 10 15

Horizontal distance from DR pin

Figure 5. Transect #3, located immediately over Riffle #6, depicts increases in sediment deposition from 2004 to 2009

30

4 8 12 16 20

Horizontal distance from DR pin

Figure 6. Transect #4, located just upstream of Riffle #6, depicts sediment deposition from 2004 through 2009.

28

Figure 7. A weir trapping large amounts of sediment and raising the surface water level, July 2008. Sedge recruitment
is already occurring on the point bars, and spawning gravel has been sorted in the thalweg below the weir.

Background

Wigwam Creek originates on the east flank of the Gravelly Mountains and flows into the Madison River near
Cameron, Montana. The removal of beaver from this drainage, combined with failed water diversions and
historic overgrazing by livestock, has resulted in considerable down cutting and over- widening of the stream
channel, along with an elevated fine sediment load. Wigwam Creek is currently grazed by livestock under
Amendment 7 riparian standards; light trampling and willow browse occurs from elk and moose. The
treatment segment of Wigwam Creek supports a population of WCT; molecular analysis indicates that the
genetic integrity of this population varies from 95-82%.

The goal of channel restoration in Wigwam Creek is to reverse its over-widened channel geometry. The
means to accomplishing this objective is to influence natural processes such as sinuosity, fine sediment
deposition, stream bank formation, and floodplain connectivity to accelerate the rate of chaimel recovery.
Secondary objectives include increased pool frequency and depth, along with improved watershed function
with reduced fine sediment load being exported downstream into the Madison River system.

The installation of low-head riffles and baffles using native rock and wooden stakes is designed to influence
deposition of fine sediments during springtime high flows. The elevated load of fine sediment in Wigwam
Creek, normally interpreted as a negative, actually provides the natural material to rebuild point bars and
stream banks. Riffles are constructed as channel-spanning features, generally installed to influence upstream
sediment deposition. Baffles are not intended to span the channel, instead acting to form point bars and
increase sinuosity in the channel. Riffles and baffles typically exhibit an elevation gradient across the
channel, influencing flow against one bank and deposition against the other bank, particularly in the
downstream backwater area.

Riffle and baffles were initially installed in September 2004, with work continuing during the summer of
2007. This project has received considerable ftinding support from PPL-Montana in each year under the
authority of Article 409 of the PPL FERC license on the Madison River, specifically part (3) "fish habitat
enhancement both in the main stem and tributary streams, including enhancement for all life stages of fishes"
and part (9) "riparian habitat restoration". In the past, the Madison-Beaverhead Counties RAC have provided
funds for supplies and funding and volunteer labor have been provided by the Madison River Foundation and
the Madison-Gallatin chapter of TU. Restoration efforts in this treatment reach are close to complete; in
2008 and 2009 only limited maintenance of structures was performed.

Results

In 2009, spring runoff was about average to above average for the second consecutive year. Duration of
runoff was also extended for a second year with a cool wet spring and early summer, resulting in greater
scouring of the channel. Considerable deposition of gravel and finer sediments was obvious from visual
inspection. Annual grazing impacts to the channel and riparian have varied in the restored channel reach,
however structure integrity appears relatively high, however continued trampling effects would, over time,
require considerable maintenance of structures for them to be effective. Wigwam Creek is scheduled to be
excluded from livestock grazing by the implementation of exclosures and improved water facilities in 2010,
which should allow these structures to fimction unhindered.

Quantitative monitoring of morphological parameters in 2009 indicates that the channel continues to adjust
and improve, with some interesting changes. Bankfull width actually increased slightly, likely due to grazing
impacts, but possibly also confounded by the extended spring runoff. Sinuosity and length of channel did not
change (Table 1), which may be a clue that the channel has reached its potential under its current alignment
and valley morphology.

Most interesting is how pool habitat has improved the last three years. Pool frequency and residual depth
both increased considerably after 2006, with a concurrent reduction in pool spacing, all likely a ftmction of
nfliTowinp of the channel fTable 1 Y alnnff with the extended snrinp nmofFin 9.008 and 9.00Q However 9.006

also experienced an above average and extended spring runoff, but without improvement in pool habitat
characteristics. This result suggests that this restoration technique is successful in initially influencing the
narrowing and sinuosity of a degraded channel, after which channel geometry and scouring flows allow pool
development.

These conclusions benefit from continued monitoring in foliowira the various changes in channri response,
and have been useful in making management decisions adaptivel}

Table 1. Channel characteristics, Wigwam Creek, 2004-2007

Channel characteristic

2004

2005

2006

2007

2008

2009

Channel length (m)

405

440

437

489

490

465

Stream bed gradient (%)

2.45

2.25

2.28

2.03

2.03

2.14

Sinuosity

1.02

1.11

1.10

1.23

1.23

1.17

Mean bankfiill width (m)

2.65

2.51

2.29

2.04

2.18

2.17

Pool frequency (pools /km)

24.7

34.1

34.3

49.1

57.1

62.4

Pool spacuig

15.3

11.7

12.7

10.0

8.0

7.8

Mean residual pool depth (m)

0.23

0.21

0.22

0.21

0.27

0.26

?»>*«■■■'>•■

-~-^?rT«iaP'.«SK'i ;*: .i . .

jS vW«^K!K5»B

Figure 1 . Wigwam Creek restored reach upstream of the bridge, early August 2009.

Graylimg Creek SMmmary;

Background

In 2009 multiple survey efforts were conducted in the Grayling Creek watershed within
Yellowstone National Park. The goal of these activities was to provide information on
fish distribution, composition, and genetic integrity that will be integral to proposed
future westslope cutthroat trout and Arctic grayling restoration projects. Initial surveys
of aquatic invertebrates and anq)hibians were also conducted in the drainage. While
Yellowstone National Park coordinated these efforts cooperation from other agencies and
partners was extensive (see below).

Methods

Over multiple sampling events the vast majority of the tributaries to Grayling Creek
upstream of the small waterfall (canyon reach adjacent to HWY 191) were sampled via
backpack electrofisher. Information collected included GPS locations of sampling
reaches; number, species, and length offish captured; and an estimate of tributary size.
Genetic samples (fin clips) were collected from all cutthroat/hybrids captured.

Genetic analyses will be completed using standard methods to detect hybridization by the
University of Montana Conservation Genetics Lab. Analysis of species composition and
distribution for aquatic invertebrates will be conducted by Aquatic Biology Associates
(Corvallis, OR).

Yellowstone National Park is incorporating the information collected into a GIS database
and wiU coordinate analysis of the genetic samples and aquatic invertebrates.

Results

Fish were found to be widely distributed throughout the drainage with cutthroat trout
(likely hybrids) occurring to the headwaters of the South Fork Grayling Creek and its
tributaries, and nearly to the headwaters of East Fork Grayling Creek. At least 4 other
tributary systems appear to support adult fish, and likely spawning enclaves. Many small
tributaries contained juvenile fish, suggesting they support spawning from Grayling
Creek.

While some fish populations that appear to be at least partially isolated were identified,
none appeared to be genetically pure WCT. Final determination of genetic status is
pending xmtil genetic analyses are completed.

Future Work

Several tributaries not found on existing maps were identified during the 2009 survey.
When encountered these waters were surveyed if time and logistics allowed, however,
some of these tributaries were not surveyed. Give this, at least one more survey trip into
the drainage will be required and is likely to occur in 2010. In addition to the fish
distribution surveys more coioplete aquatic invertebrate and amphibian surveys are being
planned for the coming years. In order to provide a detailed picture of all areas that

would require treatment in the event of a full-scale restoration project, a complete
hydrologic survey of the drainage is being considered.

Grayling Creek Partnership

The work being conducted on Grayling Creek is a cooperative effort being undertaken by

a network of partner agencies and work groups. Project partners are hsted below.

Ageacy

OSice/Work Grossp

Cfflffltact PersoM

Yellowstone National Park

Fisheries and Aquatic Sciences Section

ToddKoel

Montana State University

Big Sky Institute

MikeRuM

Montana Fish Wildlife and Parks

Ennis Fisheries Office

Pat Clancey

Montana Fish Wildlife and Parks

Arctic Grayling Recovery Program

Jim Magee

Gallatin National Forest

Bozeman Ranger District

Brace Roberts

PPL Montana Corp.

Hydro Licensing and Compliance

Brent Mabbott

Appendix G

Sun Hatchery Contributions and Production
2001-2009

Year

Donor Stream

M;Fsoawned_

FteclBLent Water

# eaa@/frv out

2001

Papoose Ck - Madison

NA

Sun Pond

356 fry total

MF Cabin Ck - Madison

23; 12

Sun Pond

2002

WF Wilson Ck - Gallatin

?;6

Sun Pond

483 fry

MF Cabin Ck - Madison

?:3

Sun Pond

104 fry 1

2003

Ray Ck - Elkhorns

25;9

Sun Pond
Bar None Pond

566 fry
560 fry

Prickly Pear Ck - Missouri

4;1

Prickly Pear
Eureka Ck
Little Tizer

28

120
S2

Hall Ck ■ Elkhorns

4;1

Hall
Little Tizer

20
91

2004

Cottonwood Ck - Blacktail

12;6

Sun Pond

820 fry

MuskratCk- Elkhorns

Ray F x McClure M (Madison)

Ray F X Hall M

15;7

4;8

2;1

Bar None Pond

814 fry

2005

Cottonwood Ck - Blacktail

13;6

Sun Pond
disease testing

528 fry
11 fry

Browns Ck - Beaverhead

10;6

Sun Pond

646 fry

Sun Pond

37;16

Sun Pond

Sun Pond disease sentinels

disease testing

euthanized to reduce hatchery load

Moret Pond

calibration of CWT injector

800 fry
120 fry
100 fry
750 fry
700 fry
5 fry

MuskratCk- Elkhorns

18;e

SF Crow Ck

2262 eyed eggs

2006

Browns Ck

MuskratCk- Elkhorns

Whites Gulch - Elkhorns

2007

MuskratCk- Elkhorns

Ray Ck - Elkhorns

Whites Gulch - Elkhorns

Sun Pond

Last Chance Ck - Madison (YNP)

2008

MuskratCk- Elkhorns

Ray Ck - Elkhorns

Whites Gulch - Elkhorns

Sun Pond

Last Chance Ck - Madison (YNP)

2009

MuskratCk- Elkhorns

Whites Gulch - Elkhorns

Ray Ck - Elkhorns

Geode Ck (YNP)

WF Wilson Ck - Gallatin

1;1

16;8

3:3

11;22

13:25

4;8

37; 17

12;8

28; 14

23; 12

11;6

28;

13;8

24; 12

8;5

20; 10

17;16

NA

Sun Pond

Sun Pond
Cherry Ck

Cherry Ck

Cherry Ck
Sun Pond

Cherry Ck
Sun Pond

Cherry Ck
Sun Pond

Cherry Ck

Sun Pond

High Lake (YNP)

High Lake YNP

Cherry Ck

Cherry Ck

Cherry Ck
Sun Pond

Cherry Ck

Sun Pond

High Lake (YNP)

High Lake (YNP)
Sun Pond

Cherry Ck
Sun Pond

Cherry Ck

Sun Pond

Cottonwood Ck (R4)

Cherry Ck
Sun Pond

High Lake YNP

eggs destroyed - hybridized

284 fry

184 fry
1750 eyed eggs

726 eyed eggs

5445 eyed eggs
291 fry

3467 eyed eggs
194 fry

1015 eyed eggs
59 fry

2994 eyed eggs

326 fry
1611 eyed eggs

1700 eyed egc

1015 eyed eggs
117 fry

286 eyed eggs
70 fr

838 eyed eggs

3199 eyed eggs

3218 eyed eggs

571 fry
2844 eyed eggs

4134 eyed egg§
311 fry

630 eyed eggs

283 fry
1350 eyed eggs

1911 eyed eggs
15 fry

Appendix H

PPL Montana funded Westslope Cutthroat Trout genetic testing results

Westslope cutthroat populations tested for genetic status under PPL Montana 2188 Program

W = westslope cutthroat trout; Y = Yellowstone cutthroat trout; R = rainbow trout

Stream

Collection date

Number
offish

lab analysis

Arasta

7/14/2005

25

87%Wx8%Rx5%Y

Bean Ck

10/29/2001

54

98% W X 2% R; only 1 fish
displayed R alleles

Bean Ck

9/18/2006

25

100% W

Bear Ck

10/29/2001

53

100% W

BearCk

9/19/2006

25

100% W

Brays Canyon

10/1/2009

50

100% W

Browns

6/28/2005

15

100% W

Browns

6/22/2006

25

100% W

Buford

???

11

85.7%Wxl2.6%Rxl.7%Y

Cabin Ck -malnstem

10/17/2005

15

97% Wx 3% R swarm

Cabin Ck- Middle Fork

10/11/2005

8

mixture of pure W & hybrid WxR

Cabin Ck - Middle Fork

10/11/2005

17

mixture of pure W & hybrid WxR

Cherry Lake

numerous dates 2009

50

100% W

Cottonwood Ck - Blacktail

6/1/2004

33

100% W

Cottonwood Ck - Blacktail

6/1/2005

19

swarm - 1 fish had 3 Rb
alleles; 18 fish no R alleles
detected

English George

8/4/2009

25

9B.4%W X 4.3%Y X 2.3%R

Halfway

9/26/2007

50

99.9% Wx 0.1% R

Hall

7/9/2004

2

100% W

Hall

9/20/2007

50

100% W

Hetlroaring Ck

7/26/2005

10

27%Wxl7%Yx56%R swarm

Hyde

8/5/2009

25

88.5%Wx7.3%Yx4.2%R

Jones Ck

10/30/2001

25

WxYxR; some Individuals exhibited Y
alleles, one exhibited R alleles

Last Chance

6/5/2006

30

100% w

Last Chance

6/18/2007

20

100% w

Last Chance

7/2/2008

21

100% w

Little Elk River

7/19/2005

10

100% Y

1

McClure

7/1/2004

8

100% w

McClure

10/7/2009

49

100% w

Muskrat

6/30/2004

22

100% w

Muskrat

6/21/2006

24

100% w

Muskrat

6/20/2007

38

100% w

Muskrat

6/18/2008

52

100% w

NF English George

10/18/2001

9

WxRxY, too few fish to discern
percentages

Prickly Pear

10/1/2009

50

100% W

Ray

7/1/2004

5

100% W

Ray

6/20/2006

35

100% W

Ray

6/21/2007

45

100% W

Ray

6/19/2008

60

100% w

SF English George Ck

10/18/2001

23

80,4%Wxl9.6%Y swarm

Soap Ck

6/8/2005

10

94% Wx3% R swarm

Soap Ck

?

51

98% W X 2% R

Stone

2004

50

100% WCT

Stone

2005

30

100% WCT

Tepee Ck of Grayling Ck

8/25/2008

8

S1.5%W X 26.6%Y X
21.9%R.

Little Tepee of Tepee of Grayling

10/1/2009

10

92.3%Wxl.9%Yx5.8%R

Upper Fox

9/18/2008

18

97% W x 3% R

Wall Ck

10/19/2001

25

99%Wxl%R

WF Wilson

10/1/2001

48

100% W

Whites Gulch

9/8/2005

50

100% W

Whites Gulch

6/12/2006

31

100% W

Whites Gulch

6/12/2007

24

100% W

Whites Gulch

6/11/2008

54

100% W

Wild Horse

7/17/2008

30

100% W