Evolutionary and Ecological Connectivity in Washington, Idaho, and British Columbia

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2022–1084

Prepared in cooperation with the University of British Columbia, Biodiversity Research Centre

and Beaty Biodiversity Museum and Idaho State University, Department of Biological Sciences,

Fish Ecology Laboratory

Evolutionary and Ecological Connectivity in Westslope

Cutthroat Trout (Oncorhynchus clarkii lewisi) and Mountain

Whitefish (Prosopium williamsoni) in Relation to the

Potential Influences of Boundary Dam, Washington, Idaho,

and Parts of British Columbia

Evolutionary and Ecological Connectivity in

Westslope Cutthroat Trout (Oncorhynchus

clarkii lewisi) and Mountain Whitefish

(Prosopium williamsoni) in Relation to

the Potential Influences of Boundary

Dam, Washington, Idaho, and Parts of

British Columbia

By Jason B. Dunham, Eric B. Taylor, and Ernest R. Keeley

Prepared in cooperation with the University of British Columbia, Biodiversity

Research Centre and Beaty Biodiversity Museum and Idaho State University,

Department of Biological Sciences, Fish Ecology Laboratory

Open-File Report 2022–1084

U.S. Department of the Interior

U.S. Geological Survey

U.S. Geological Survey, Reston, Virginia: 2022

For more information on the USGS—the Federal source for science about the Earth, its natural and living resources,

natural hazards, and the environment—visit https://www.usgs.gov or call 1–888–ASK–USGS.

For an overview of USGS information products, including maps, imagery, and publications, visit

https://store.usgs.gov/.

Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the

U.S. Government.

Although this information product, for the most part, is in the public domain, it also may contain copyrighted materials

as noted in the text. Permission to reproduce copyrighted items must be secured from the copyright owner.

Suggested citation:

Dunham, J.B., Taylor, E.B., and Keeley, E.R., 2022, Evolutionary and ecological connectivity in westslope cutthroat

trout (Oncorhynchus clarkii lewisi) and mountain whitefish (Prosopium williamsoni) in relation to the potential

influences of Boundary Dam, Washington, Idaho, and parts of British Columbia: U.S. Geological Survey Open-File

Report 2022–1084, 22 p., https://doi.org/ 10.3133/ ofr20221084.

ISSN 2331-1258 (online)

iii

Acknowledgments

This work benefitted greatly from discussions with Ryan Simmons, Harry Rich, Al Solonsky,

and Troy Jaecks with Seattle City Light. Emily Heaston (U.S. Geological Survey, Forest and

Rangeland Ecosystem Science Center) prepared maps for this report. Reviews by Tom Quinn

(University of Washington, School of Aquatic & Fishery Sciences) and Carl Ostberg

(U.S. Geological Survey, Western Fisheries Research Center) improved an earlier draft of the

manuscript. Funding for this effort was provided by Seattle City Light.

Contents

Acknowledgments ........................................................................................................................................iii

Abstract ...........................................................................................................................................................1

Introduction.....................................................................................................................................................1

Part 1. Lake Pend Oreille and Pend Oreille River—Past to 2022 ...........................................................3

Overview.................................................................................................................................................3

Basin History: 15,000 Years to 2022 ....................................................................................................3

Contemporary Conditions ....................................................................................................................4

Boundary Dam and Reservoir .............................................................................................................4

Part 2. Evolutionary and Ecological Connectivity for Westslope Cutthroat Trout and

Mountain Whitefish .........................................................................................................................4

Westslope Cutthroat Trout ..................................................................................................................5

Biogeography ...............................................................................................................................5

Genetic Evidence of Connectivity .............................................................................................5

Ecological Evidence of Connectivity ........................................................................................8

Environmental Conditions ...........................................................................................................9

Mountain Whitefish ............................................................................................................................12

Biogeography .............................................................................................................................12

Genetic Evidence of Connectivity ...........................................................................................12

Ecological Evidence of Connectivity ......................................................................................14

Part 3. Conclusions and Recommendations for Upstream Passage over Boundary Dam ..............15

Westslope Cutthroat Trout ................................................................................................................15

Mountain Whitefish ............................................................................................................................16

Overall Conclusions .....................................................................................................................................16

References Cited..........................................................................................................................................17

Appendix 1. Summary and Update on Connectivity for Bull Trout (Salvelinus

confluentus) in the Pend Oreille River since Dunham and Others (2014) .............................22

Figures

1. Photograph showing Boundary Dam photographed after dark, December 8, 1998 ..........2

2. Map showing the lower Clark Fork River, Lake Pend Oreille, and Pend Oreille

River with major dams indicated ................................................................................................3

3. Map showing the Pend Oreille River and associated major rivers of British

Columbia, Washington, Idaho, and Montana ...........................................................................6

4. Bar graphs showing proportional composition of samples of westslope

cutthroat trout with respect to two major genetic groups based on the single

nucleotide polymorphism analysis of Small and others .........................................................7

5. Historical, mid-century, and end-of-century predicted presence of native

westslope cutthroat trout, assuming the absence of nonnative brook trout

within the Lake Pend Oreille– Pend Oreille River system in the United States ................10

6. Pie diagrams showing genetic assignment of westslope cutthroat trout

sampled from Boundary Reservoir and Box Canyon Reservoir into major spatial

groupings .....................................................................................................................................11

7. Dimensionless graph showing major genetic groups of mountain whitefish in

the Boundary Area resolved using microsatellite DNA analysis .......................................12

8. Dimensionless graph showing major genetic groups of mountain whitefish in

the Boundary Area resolved using allelic variation at microsatellite DNA loci

projected using factorial correspondence analysis .............................................................13

Conversion Factors

U.S. customary units to International System of Units

Multiply By To obtain

Length

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Flow rate

cubic foot per second (ft

/s) 0.02832 cubic meter per second (m

/s)

International System of Units to U.S. customary units

Multiply By To obtain

Length

meter (m) 3.281 foot (ft)

kilometer (km) 0.6214 mile (mi)

Area

hectare (ha) 2.471 acre

Volume

cubic meter (m

) 35.31 cubic foot (ft

)

Flow rate

cubic meter per second (m

/s) 35.31 cubic foot per second (ft

/s)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F = (1.8 × °C) + 32.

Datums

Vertical coordinate information is referenced to the North American Vertical Datum of 1988

(NAVD 88).

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).

vii

Abbreviations

WDFW Washington Department of Fish and Wildlife

SNP single nucleotide polymorphism

PIT passive integrated transponder

PoR-C Pend Oreille and Columbia Rivers

Evolutionary and Ecological Connectivity in Westslope

Cutthroat Trout (Oncorhynchus clarkii lewisi) and

Mountain Whitefish (Prosopium williamsoni) in Relation

to the Potential Influences of Boundary Dam, Washington,

Idaho, and Parts of British Columbia

By Jason B. Dunham, Eric B. Taylor, and Ernest R. Keeley

Abstract

In this report, we consider evolutionary and ecological

connectivity for westslope cutthroat trout (Oncorhynchus

clarkii lewisi) and mountain whitesh (Prosopium

williamsoni) within the Pend Oreille River in northeastern

Washington State, northern Idaho, and adjacent portions of

southeastern British Columbia, Canada. Specically, we

focused on the rationale for active translocation of individuals

of these species upstream from Boundary Dam both in

the context of natural patterns of pre-dam evolutionary

connectivity as well as preserving contemporary ecological

and evolutionary characteristics of local extant populations.

Boundary Dam impounds the Pend Oreille River (called the

Pend d’Oreille River in Canada) with the resulting reservoir

inundating two historical barriers to upstream movement

of sh (Metaline Falls and Z Canyon). Historically, it was

thought these barriers impeded the upstream movement of

westslope cutthroat trout and mountain whitesh, as well

as Pacic salmon (Oncorhynchus spp.), steelhead trout

(O. mykiss), and other resident species such as bull trout

(Salvelinus conuentus). To address connectivity, we consider

historical and contemporary processes and features. This

review includes an assessment of postglacial processes

within the Pend Oreille River and systems upstream that

include Priest Lake, Lake Pend Oreille, the Clark Fork River,

features of Boundary Reservoir and its tributaries, and areas

downstream in the Pend Oreille River such as the Salmo

River. Based on this information, we then give a more detailed

review of existing genetic and ecological data to summarize

what is known about connectivity for westslope cutthroat

trout and mountain whitesh. Our assessment of the collective

evidence leads us to conclude that moving sh upstream over

Boundary Dam is not warranted if the management objective

is to maintain natural patterns of evolutionary and ecological

connectivity or to conserve unique ecological and evolutionary

characteristics of extant local populations of these species

in the system. These ndings parallel that of a previous

analysis of bull trout. Although we were able to arrive at

well-supported conclusions in relation to Boundary Dam, we

suggest that more work on connectivity further upstream in the

Pend Oreille River would help to better understand the role of

historical processes and dams further up in the system.

Introduction

Across the United States, there are over 91,000 large

dams

on rivers (U.S. Army Corps of Engineers, 2018

Assessing their eects on riverine ecosystems is complicated

because dams have inuences downstream and upstream

from their location and create novel reservoir habitats

within the waters they hold back (Bellmore and others,

2019). Furthermore, the unique setting of where dams are

constructed, how they are operated, their relationships to

other barriers, and a host of other potential inuences defy

simple generalizations. Accordingly, it is important to consider

the unique context within which any given dam is located.

Although dams inuence riverine ecosystems in many ways,

one of the most fundamental involves how they inuence

evolutionary and ecological connectivity of physical and

biological systems.

Here, we consider how dams impact connectivity

for two species: westslope cutthroat trout (Oncorhynchus

clarkii lewisi) and mountain whitesh (Prosopium

williamsoni) within the Pend Oreille River in northeastern

The Army Corps of Engineers National Inventory of Dams includes dams

that either (1) pose a threat to human life if the dam fails, (2) pose economic

loss, environmental damage, disruption of lifeline facilities or other important

concerns, (3) equal or exceed 7.6 meters in height or 82,000 square meters of

storage, or (4) equal or exceed 1.8 meters in height and exceed 164,000 square

meters of storage.

Army Corps of Engineers National Inventory of Dams database can be

accessed at https:/ /nid.usace .army.mil/ #/

2 Evolutionary and Ecological Connectivity in Washington, Idaho, and British Columbia

Washington State and adjacent portions of southeastern

British Columbia, Canada (where the river is known as the

Pend d'Oreille River). The geographic focus of this report

is Boundary Dam (g. 1), which is located on the Pend

Oreille River near the U.S. - Canada border, and is one of

several dams in this watershed (g. 2). Like most salmonid

shes, westslope cutthroat trout and mountain whitesh are

inuenced by and rely on connectivity within river networks

or riverscapes (Northcote and Ennis, 1994; Neville and others,

2006a). Our specic objective in this report is to evaluate

historical and contemporary evolutionary and ecological

connectivity for westslope cutthroat trout and mountain

whitesh to address the rationale of potentially providing

upstream passage over Boundary Dam for these species.

A previous analysis (Dunham and others, 2014) examined

similar questions concerning connectivity in bull trout

(Salvelinus conuentus) in relation to Boundary Dam (app. 1).

To address our objective, Part 1 of this report begins

with a review of historical and contemporary processes

and features of the riverscape that inuence connectivity

relative to Boundary Dam within the lower Pend Oreille

system. Historically, it was thought that the upstream extent

of anadromous Pacic salmon (Oncorhynchus spp.) and

migratory rainbow trout (O. mykiss, commonly referred

to as steelhead trout) in the Pend Oreille River was just

downstream from Metaline Falls, the current approximate

location of Boundary Dam (Scholz and others, 1985). From

this foundation, in Part 2, we review existing genetic and

ecological information to evaluate what is known about

connectivity for westslope cutthroat trout and mountain

whitesh within the system. In Part 3, we assess this

evidence with respect to the evolutionary or ecological

rationale for passing these species upstream over Boundary

Dam. Throughout, we identify important uncertainties

and information gaps that could be addressed to inform

management decisions and actions to benet westslope

cutthroat trout and mountain whitesh within the area.

Figure 1. Boundary Dam (downstream view) photographed after dark, December 8, 1998 (from City of Seattle Archives, Item 126710,

Record Series 0207–01).

Part 1. Lake Pend Oreille and Pend Oreille River—Past to 2022 3

Figure 2. Lower Clark Fork River, Lake Pend Oreille, and Pend Oreille River with major dams indicated.

Part 1. Lake Pend Oreille and Pend

Oreille River—Past to 2022

Overview

The system of interest includes Lake Pend Oreille in

northern Idaho and its outlet: the Pend Oreille River (g. 2).

Lake Pend Oreille is the terminus of the Clark Fork River,

which ows westward and drains much of western Montana,

with some drainages extending north of the U.S. - Canada

border. The Pend Oreille River produces an annual average

discharge of 26,267 cubic feet per second (ft

/s) according

to a U.S. Geological Survey streamgage (USGS streamgage

12396500, 68 water years of record) located near Box

Canyon Dam, which is 55.2 kilometers (km) upstream from

the conuence of the river with the mainstem of the upper

Columbia River in southeastern British Columbia. From Lake

Pend Oreille to the Columbia River, the Pend Oreille River

ows for 210 km. A major Pend Oreille River tributary near

the outlet of Lake Pend Oreille and just upstream from Albeni

Falls (

g. 2) is the Priest River, which drains Priest Lake and

discharges an annual average of 1,705 ft

/s (USGS streamgage

12395000, 71 water years of record) into the system.

Basin History: 15,000 Years to 2022

Between approximately 13,000–15,000 years ago, most

of the Pend Oreille River was beneath the Purcell Lobe of the

Cordilleran Ice Sheet. The Purcell Lobe covered the bottom

of present-day Lake Pend Oreille and dammed the Clark Fork

River, forming glacial Lake Missoula. This massive water

body (over 320 km long and 610 meters [m] deep) was the

largest ice-dammed lake known to have existed (O'Connor

and others, 2020). The waters behind the ice dam were

released with catastrophic ooding downstream extending

across eastern Washington and occurring several times as the

dam re-formed and failed in relation to uctuations in the Ice

Sheet. Following glacial retreat about 11,000 years ago, Lake

Pend Oreille and the Pend Oreille River began to assume their

present forms (McPhail and Lindsey, 1986; Pielou, 1991; Link

and Keeley, 2018; O'Connor and others, 2020).

4 Evolutionary and Ecological Connectivity in Washington, Idaho, and British Columbia

With the river and lake system formed, native shes

gained access to the area from glacial refugia located upstream

and downstream from the inuence of the Cordilleran

Ice Sheet (McPhail and Lindsey, 1986). Although native

salmonids such as bull trout, mountain whitesh, and

westslope cutthroat trout were able to colonize throughout

the system, anadromous Pacic salmon and rainbow trout in

the Pend Oreille River are thought to have been limited to

areas below the hydraulic barriers posed by Z Canyon and

Metaline Falls (near the present site of Boundary Dam, see

below; Scholz and others, 1985). Historical accounts indicate

that anadromous shes were limited by the falls and cascades

in the lower Pend Oreille River. There is some uncertainty,

however, if any single waterfall completely blocked the

passage of salmon and steelhead trout in all years, at least

up to Albeni Falls (Scholz and others, 1985). Within most

tributaries to Boundary Reservoir (the impoundment above

Boundary Dam), natural waterfalls and steep cascades also

likely acted to restrict the movement of native shes and this

continued with the construction of Boundary Dam. Beyond

migratory shes, accounts of resident sh consumption by the

Kalispel tribe indicate signicant whitesh, char (Salvelinus,

sp.), trout, and sucker (Catostomidae) populations in the Pend

Oreille River (Scholz and others, 1985).

Contemporary Conditions

Today the Pend Oreille River is inuenced by a series

of large dams, beginning with Cabinet Gorge Dam, which

is located just upstream from Lake Pend Oreille on the

Clark Fork River and controls ows into the lake (g. 2).

Downstream from Lake Pend Oreille, major dams include

the Priest Lake Outlet Dam on the Priest River, and on the

Pend Oreille River, three dams in the United States (Albeni

Falls, Box Canyon, and Boundary dams) as well as two in

British Columbia (Seven Mile and Waneta dams). There are

a few dams on key tributaries, including Mill Pond Dam

(removed in 2017) and Sullivan Lake Dam in the Sullivan

Creek basin. Numerous stream-road crossings (for example,

culverts) and other human-built structures are present and

sometimes hinder or prevent sh passage. A host of nonnative

aquatic animals, ranging from mysid shrimp (Mysis spp.)

to northern pike (Esox lucius) and dozens of other species

have become established in the Pend Oreille system from

intentional human introductions and subsequent dispersal.

Active suppression eorts are occurring to control nonnative

lake trout (S. namaycush; Hansen and others, 2010), brook

trout (S. fontinalis; Dunham and others, 2002), and northern

pike (Carim and others, 2019) to minimize their inuences

on native species and ecosystem processes. In short, ow

regulation, introductions and invasions of nonnative species,

and other changes wrought by humans to Lake Pend Oreille

and the Pend Oreille River have fundamentally transformed

the ecosystem. Despite such transformations, native species

persist throughout much of the system.

Boundary Dam and Reservoir

This report focuses on the specic question of how

Boundary Dam inuences connectivity for westslope cutthroat

trout and mountain whitesh. Accordingly, it is important

to describe a few essential details of the dam, the associated

reservoir, and tributaries. The salient characteristics of

Boundary Dam were summarized from the City of Seattle's

description of the project (Frantilla, 2022, http s://www.se

attle.gov/ cityarchives/ exhibits- and- education/ online- exhibits/

boundary- dam). Construction of Boundary Dam was

completed in 1967, stands at just over 100 m tall, and can

produce 127 million kilowatts of electricity on an annual

basis. The impoundment upstream from Boundary Dam, the

Boundary Reservoir, has a maximum depth of about 82 m, a

maximum surface area of about 726 hectares (ha), and extends

for 28 km upstream to the base of Box Canyon Dam. Water

ow through the reservoir is relatively fast, with a residence

time that ranges between 2 and 4 days (Pickett, 2004).

Correspondingly, temperatures are fairly consistent up and

downstream, and the reservoir is not thermally stratied at any

time of the year (Seattle City Light [SCL], 2006).

Seattle City Light’s (2006) assessment listed 28

tributaries to Boundary Reservoir that oer a total of nearly 25

km of stream distance that is accessible to upstream-migrating

salmonids (Washington Department of Fish and Wildlife

[WDFW], 2020). For individual tributaries, accessible stream

distance ranges from 0 km (barrier falls at the conuence) to

potentially 32 km in Sullivan Creek after the 2017 removal

of Mill Pond Dam (Federal Energy Regulatory Commission

[FERC], 2011). Despite the removal of this dam, however, a

seasonal velocity barrier approximately 1 km from the mouth

of Sullivan Creek remains (Powers, 2008).

Part 2. Evolutionary and Ecological

Connectivity for Westslope Cutthroat

Trout and Mountain Whitefish

In this section, we review evidence describing historical

and contemporary patterns of connectivity for westslope

cutthroat trout and mountain whitesh. Although the focus

of our review is on upstream passage over Boundary Dam,

we review salient local and regional factors inuencing

connectivity. In Part 3 below, we rely on the body of evidence

reviewed here to draw conclusions regarding the value of

providing passage for these species upstream over Boundary

Dam. In addition to considering these species, we briey

revisit the case for bull trout (Dunham and others, 2014; app.

1) to provide a more complete and updated review of upstream

passage over Boundary Dam.

Part 2. Evolutionary and Ecological Connectivity for Westslope Cutthroat Trout and Mountain Whitefish 5

Westslope Cutthroat Trout

Biogeography

The Pend Oreille River represents a transitional region

in the distribution between two native trout species in western

North America: rainbow trout and westslope cutthroat trout.

The natural biogeographic history of the boundary area is

thought to have been strongly inuenced by the various

Pleistocene glaciations (roughly 2.8 million to 18,000 before

present [B.P.]) that covered vast swaths of land and had

dramatic inuences on streamow and watershed connectivity

over time (McPhail and Lindsey, 1986; Pielou, 1991).

Although the exact biogeographic history of the area cannot be

fully reconstructed today, recolonization of ice-covered areas

by sh species must have occurred following glacial retreat.

Areas outside of the extent of glaciation may have also been

greatly aected by historical oods, elevated stream ows,

and interconnection of watersheds, allowing dispersal of sh

species over areas now presently isolated from each other.

Based on historical records and observations from the late

1800s, Z Canyon (immediately upstream from the present-day

location of Boundary Dam and Metaline Falls on the Pend

Oreille River 15 km farther upstream) appears to have limited

or at least impaired upstream movement of anadromous shes,

which would likely have included steelhead trout (Scholz and

others, 1985; Nellestijn and Ells, 2008).

Contemporary evidence for connectivity of westslope

cutthroat trout relative to Boundary Dam is available from

genetic and distribution data as well as from studies of sh

movements and demographic characteristics of populations

within tributary systems. Arguably, the most comprehensive

description of trout distribution patterns in North America

was written by R.J. Behnke (1992, 2002). He described the

native distribution of westslope cutthroat trout to follow the

west side of Kootenay Lake in British Columbia and south

into Idaho but outside most of the Priest Lake watershed

and the downstream sections of the Pend Oreille River

(g. 3). Although McPhail (2007) recorded observations of

westslope cutthroat trout in the watersheds noted by Behnke

(1992, 2002) around the Kootenay River of southeast British

Columbia, McPhail (2007) also reported that westslope

cutthroat trout populations occur in the Salmo River

downstream from Boundary Dam and in other tributaries

of the upper Columbia River outside of the continuous

distribution estimated by Behnke (1992, 2002). More recent

sampling in the boundary area established that westslope

cutthroat trout populations exist in tributaries of the Pend

Oreille River and in the Priest Lake watershed (g. 3; Small

and others, 2020).

Genetic Evidence of Connectivity

As with bull trout (Dunham and others, 2014), the

relationship of westslope cutthroat trout in the Salmo

River to populations upstream from Boundary Dam and

historical barriers to upstream passage (in other words,

Metaline Falls and Z Canyon) in the Pend Oreille system can

provide important clues about historical and contemporary

connectivity. Overall, there is little evidence that suggests

any appreciable connectivity between native westslope

cutthroat trout below Boundary Dam and upstream areas. For

instance, genetic analysis of westslope cutthroat trout began

with an analysis of 10 microsatellite DNA loci in 2007 by the

Washington Department of Fish and Wildlife (Washington

Department of Fish and Wildlife [WDFW], 2020; Small and

others, 2007). This study included 77 localities within the

Pend Oreille and Priest Lake watersheds as well as several

groups of hatchery sh used in various stocking programs

(westslope cutthroat trout, Yellowstone cutthroat trout,

and rainbow trout). The Salmo River collection included

samples from near the conuence with the Pend Oreille River

(Swift Creek, about 12 km upstream) and a small lake in the

headwaters (Waldie Lake). Unfortunately, owing to variable

and uncertain scoring of microsatellite loci for the Salmo

River samples, little insight was gained on the status of these

sh (M. Small, oral comm., May 2020). The few analyses

that were completed indicated that the Waldie Lake and Swift

Creek samples were quite distinct from one another (both were

more similar to samples outside the Salmo River drainage than

they were to each other) as well as from other sh from the

Pend Oreille study area.

Furthermore, Small and others (2017) reported the results

of analyses of about 1,850 samples, including sh from ve

sites within the Salmo River watershed, using a panel of 215

single nucleotide polymorphism (SNP) loci. In this analysis,

sh were rst screened for hybridization with rainbow trout

using four loci that were diagnostic for dierences between

the species. Results indicated that 29 percent of sh sampled

from the Salmo River sites (range 3–68 percent) were

interspecic hybrids between rainbow trout and cutthroat trout

(table 3 in Small and others, 2017). Even the most upstream

sample sites (Crutch and Watch Creeks) showed some

evidence of introgression with rainbow trout although at much

lower levels (3–6 percent) than in downstream reaches of the

Salmo River system. Of the remaining Salmo River sh that

were deemed to be westslope cutthroat trout from four sites

(two were pooled as they were so similar to one another), all

showed very high genetic anity to the King's Lake (Priest

Lake drainage origin) hatchery samples of westslope cutthroat

trout (g. 4). These sh showed a similar “hatchery genetic

signal” to sh from other localities within the Pend Oreille

drainage that have been subject to hatchery supplementation

(for example, Sweet, Slate, Lunch, Lost, and Harvey Creeks).

The U.S. part of the Salmo River has also received at least

some supplementation of westslope cutthroat trout using the

King's Lake hatchery source (Small and others, 2017).

6 Evolutionary and Ecological Connectivity in Washington, Idaho, and British Columbia

Figure 3. Pend Oreille River and associated major rivers (blue lines) of British Columbia, Washington, Idaho, and Montana. Brown

polygon represents the estimated western extent of the native distribution of westslope cutthroat trout (Oncorhynchus clarkii lewisi) in

southeastern British Columbia (McPhail, 2007). The light brown polygon is the estimated extent of westslope cutthroat trout by Behnke

(1992, 2002). Hatched area indicates the estimated overlap in range between McPhail (2007) and Behnke (1992, 2002). Red circles

represent sampling locations for westslope cutthroat trout populations reported in Small and others (2020). Black crosses indicate the

location of major dams in the region. Blue crosses indicate the location of known waterfalls (World Waterfall Database, 2022, https://w

ww.worldwa terfalldat abase.com/ ).

Part 2. Evolutionary and Ecological Connectivity for Westslope Cutthroat Trout and Mountain Whitefish 7

KLH

16Slumber

99KingLk

12KingBY11

12KingBY12

02Sweet

12Sweet1

12Sweet2

14Watch

04Lost

14Crutch

14SSalR5UpST

12Uncas

99Slate

12Slate1

12Slate2

13Slate2.6

12Slate3

12SFSlate

12Styx

02Lunch

12Lunch1

12Lunch2

12Pewee

12MFFlume

11Deem0.6

12Deem3.6

12DeemUp

11_13Gypsy1

11GypsyNE

11_13GypsyWB

11_12John

11Kinyon0.8

11Kinyon0.6

11Leola0.7

11_13LeolaNE

11Leola1.6

13Leola0

13Leola1.6

13LeolaNW

99NFSull

03NFSull

12NFSull1

13NFSull1

12NFSull2

11Pass0.5

12PassUp

11_12RainyUp

11Rainy0.2

12RainLo

13Rain

13Smart

11Stony2.2

03SullLk

12Harvey1

02Harvey

12Noisy

99UpSull

14SullCr

12Sull11

12Sull14.5

13Sull16.5

11Sull16.4

13Sull18.5

11Sull19

11Sull20.7

13Sull21

KingsLk

Sullivan

Figure 4. Bar graphs showing proportional composition of samples of westslope cutthroat trout (Oncorhynchus clarkii lewisi) with

respect to two major genetic groups (blue and red shading) based on the single nucleotide polymorphism analysis of Small and others

(2017). Each bar represents the mean proportional contribution (0.0 to 1.0) of fish from each locality across multiple admixture analyses.

Fish from the King's Lake hatchery (KLH, three samples) are predominantly composed of the blue genetic group. Fish from localities

within the Salmo River (SR, three samples) are also predominantly composed of the blue group, as are some tributaries of the Sullivan

Creek (“Sull”) drainage and the Pend Oreille River upstream from Boundary Dam that have been subject to hatchery supplementation

with King's Lake hatchery westslope cutthroat trout (indicated by blue stars; for example, Harvey, Lunch, Lost, Slate, North Fork Sullivan

(NFSull) Creeks, see Small and others 2017, table 1 and fig. 2). The red genetic group is thought to be characteristic of native fish from

the Sullivan Creek watershed.

8 Evolutionary and Ecological Connectivity in Washington, Idaho, and British Columbia

Next, Small and others (2019a) reported the results

of genetic tests that used a baseline of SNP information on

potential source populations to genetically assign sh (N = 16)

sampled from various non-tributary localities to these potential

source populations. One sh was sampled from the Boundary

Dam tailrace, and it was estimated to have originated from

either Watch Creek (a tributary of the uppermost reaches of

the Salmo River in Washington) or Slate Creek, a tributary of

the Pend Oreille about 10 km upstream from the Boundary

Dam. Consequently, identication of this tailrace westslope

cutthoat trout was ambiguous relative to whether it may have

originated from upstream or downstream from the dam site.

The remaining 15 sh were all sampled from areas upstream

from the dam and were identied as either rainbow trout

(N = 1), westslope cutthroat trout x rainbow trout hybrids

(N = 3 sh of varying levels of admixture between the two

species), King’s Lake hatchery westslope cutthroat trout (N =

1), either native or hatchery sh (N = 2), or native sh from

localities upstream from the dam, including the Sullivan Creek

drainage (N = 8).

Finally, A similar analysis was conducted by Small and

others (2020) for a sample of 47 sh, all but seven of which

were sampled in river sections between Boundary and Box

Canyon dams. The largest percentage of sh were either

introgressed (up to 75 percent introgression) with rainbow

trout (19 of 47 sh, 40.4 percent), or were assigned to the

King’s Lake westslope cutthroat trout hatchery stock (13 of 47

sh, 27.7 percent). Two more sh were identied as rainbow

trout. Of the remaining 13 sh, a single individual was

considered to have originated from the Salmo River or King's

Lake hatchery, and another was assigned to the Salmo River or

Granite Creek (one of the original brood sources for the King's

Lake hatchery strain; Small and others, 2007, 2020), three sh

were assigned as Salmo River watershed westslope cutthroat

trout, and eight sh were assigned to various localities

between Boundary and Box Canyon dams. In summary, of

40 sh sampled above the Boundary Dam, only one was

unequivocally assigned to the Salmo River drainage (and

thus suggests some historical connectivity between the Salmo

River and the Pend Oreille River upstream of Metaline Falls).

Additionally, of the seven sh sampled below Boundary Dam,

only one could be unequivocally assigned to a site upstream

from the dam (to Lunch Creek), suggesting either entrainment

through the dam or some historical connectivity through

Metaline Falls.

In sum, the extensive genetic sampling and analysis

by WDFW strongly suggest that westslope cutthroat trout

sampled from the Salmo River (and the few sh sampled in

the tailrace sections and genetically assigned to the Salmo

River baseline) are either: (1) hybrids between rainbow

trout and westslope cutthroat trout or, (2) are genetically

indistinguishable from the King's Lake hatchery strain. Small

and others (2017) concluded that Salmo River westslope

cutthroat trout included in their study were either a population

founded from hatchery plantings or a native population

that has been substantially inuenced by introgression with

hatchery sh. The likelihood of a hatchery origin of westslope

cutthroat trout in at least the mainstem reaches of lower

Salmo River is considered to be high by sheries workers in

the Nelson, BC, area (J. Baxter, FortisBC, written commun.

with Eric Taylor, May 2020). Furthermore, consultation with

local authorities could not conrm any native populations

of westslope cutthroat trout between the conuence of the

Salmo and Pend Oreille Rivers and the conuence of the latter

with the Columbia River (C. Lee, WDFW, Spokane, and T.

Anderson, Kalispel Tribe Fish and Wildlife Dept., written

commun. with Eric Taylor, May 2020).

The lack of signicant historical connectivity between

populations of westslope cutthroat trout downstream and

upstream from Boundary Dam is consistent with conclusions

for bull trout (Dunham and others, 2014). Finally, Chinook

salmon (O. tshawytscha) and steelhead trout have migrated

to the conuence of the Salmo River (formerly referred to

as the “Salmon” River) and the Pend Oreille River as well

as upstream in the Salmo River, but Metaline Falls and Z

Canyon probably represented barriers to further upstream

migration for anadromous sh in the Pend Oreille River, and

thus almost surely served as barrier to upstream migration for

westslope cutthroat trout and mountain whitesh (Nellestijn

and Ells, 2008).

Ecological Evidence of Connectivity

Inferences from molecular markers can provide important

insights into potential patterns of historical and contemporary

connectivity (Neville and others, 2006a, b). Many forms

of connectivity cannot be easily evaluated using molecular

markers alone, however. Complex patterns of sh movement

and consequences for growth, survival, and reproduction

require tracking of tagged sh or indirect methods (for

example, observational or modeling studies) to evaluate the

importance of connectivity in riverscapes (Young, 1996; Falke

and Fausch, 2010).

Direct evidence of movement of westslope cutthroat

trout in Boundary Reservoir and its tributaries comes from

tagging and tracking studies. In the reservoir and tailrace,

56 westslope cutthroat trout were tagged and tracked using

acoustic telemetry between 2016 and 2019 (Hydroacoustics

Technology, Inc., 2018, 2020). Tagged sh were tracked

between the tailrace of Boundary Dam and downstream

areas, as well as in Boundary Reservoir up to the base of

Box Canyon Dam. Available reports mention that the length

and mass of tagged individuals were recorded, but were not

reported, so eects of size on movement cannot be evaluated

(for example Monnot and others, 2008). These sh were

captured over the course of 24 electroshing events, each of

which involved at least 1 day of eort and yielded a catch

rate of less than two sh per event. Interestingly, over the

course of the 3-year study and sampling eorts,10 of the 56

(18 percent) tagged sh were recaptured. Of all sh tagged

and tracked over 3 years, eight individuals (14 percent) were

entrained downstream through Boundary Dam. The average

Part 2. Evolutionary and Ecological Connectivity for Westslope Cutthroat Trout and Mountain Whitefish 9

size of westslope cutthroat trout entrained (x

= 286 millimeter

fork length; standard deviation [SD]= 61) were statistically

indistinguishable to those that were not entrained (x

= 310

mm fork length; SD = 66; Hydroacoustics Technology

Incorporated, 2018, 2020, 2021).

Overall, studies of westslope cutthroat trout indicate

that very few individuals currently occupy Boundary

Reservoir, though precise density estimates are not available.

Furthermore, only a few of these individuals were entrained

downstream through Boundary Dam (14 percent). Low

numbers of tagged and tracked individuals, uncertainties

about size-related movement patterns, and lack of tracking of

individuals from the reservoir into tributaries limit what can be

concluded from this work in terms of patterns of connectivity

beyond the simple question of entrainment.

Tagging of westslope cutthroat trout in tributaries to

Boundary Reservoir has involved considerably more locations

and individuals relative to work in the main-stem river

(West Fork Environmental, 2020). Tributary studies have

used Passive Integrated Transponders (PIT tags), and results

from work conducted from 2012 to 2019 were available for

this report. Of the 28 tributaries identied by Seattle City

Light (2006), tagging of individual westslope cutthroat

trout has been conducted in Peewee, Slate, Sullivan, Flume,

Pocahontas, and Sweet-Lunch Creeks. It is important to note

these tributaries have complete or partial natural barriers to

upstream movement of sh that occur near their conuences

with Boundary Reservoir, and that PIT tagging has occurred

upstream from these barriers. Over 8 years (2012–19), a

total of 13,975 westslope cutthroat trout were PIT-tagged.

Individuals were recaptured by electroshing at locations

distributed across tributaries. Between 2014 and 2019,

numerous 200 m locations have been annually sampled 1–6

times by single-pass electroshing. The total number of sites

sampled across all years was not reported, but in 2018, for

example, eorts included 46 sites sampled in previous years

and 32 new sites located next to previously sampled sites.

Based on existing tagging and electroshing eorts

and the distribution of sites sampled in space and time, few

westslope cutthroat trout were recaptured within or beyond

the site of initial capture. Recaptured individuals in 2019

represented sh that were tagged in previous years, including

71, 19, 6, 3, and 1 percent for sh initially PIT-tagged in

2018, 2017, 2016, 2015, and 2014, respectively. A total of

six PIT-tag arrays are being used for the detection of tagged

individuals as they swim past the antennas, including ve

in Sullivan Creek and one in Slate Creek. All but one of the

PIT array locations include three channel-spanning arrays to

ascertain the directional movement of detected individuals.

Since the antennas were installed in 2014 and 2015, the PIT

tag arrays have recorded a total of 516,602 detections from

486 unique sh. This low number of unique sh suggests that

movement across PIT arrays is generally infrequent and that

tagged sh reside primarily within tributaries (Lukacs and

Landguth, 2020). While data from the PIT arrays suggests

very few individuals leave Sullivan Creek for Boundary

Reservoir, there have been considerable challenges with

maintaining the most downstream antenna near the outlet of

Sullivan Creek, adding an unknown degree of uncertainty to

these ndings (Lukacs and Landguth, 2020). Overall, captured

sh (tagged and untagged) were relatively small (43–228 mm,

fork length) but is consistent with sizes that may be expected

for small streams. Growth rates based on recaptured sh did

not exhibit any obvious outlying values or bi-modality as may

be expected of a population composed of a mixture of resident

and migratory individuals (Kendall and others, 2015).

Environmental Conditions

Current conditions within Boundary Reservoir are

marginal for supporting westslope cutthroat trout due in part

to warm seasonal water temperatures. Consistently colder

water temperatures are available in tributary systems feeding

Boundary Reservoir and at tributary mouths. A recent report

(Environmental Science Associates [ESA], 2019) documenting

seasonal temperatures within Boundary Reservoir indicated

extended seasonal (July–Sept) occurrences of temperatures

above 20 °Celsius (C) at all locations sampled. Temperatures

in the Boundary Reservoir forebay recorded at 10 m depth

exceeded 20 ° C from July 10th through September 14th,

2019, with a maximum of 23 °C. Temperatures recorded

at 60 m were similar, reecting isothermal conditions that

should be expected in a system with water discharge that has

a short residence time. Small, coldwater refuges at Boundary

tributary mouths (H. Rich and R. Simmons, Seattle City

Light, oral communication, April 2021) are not apparent in

that dataset. Similarly, some locations of the Pend Oreille

River upstream from Box Canyon Dam, have colder patches

or thermal refuges near tributary conuences. It is not clear,

however, if the use of these cold refuges can be expected to

improve conditions for coldwater sh (for example, mountain

whitesh, westslope cutthroat trout, bull trout) as the benets

of thermal refuge use depend on many contingencies such

as other measures of habitat quality, including vulnerability

to predators, lack of feeding opportunities (Snyder and

others, 2020), poor water quality (for example, low dissolved

oxygen), or possibly the presence of other nonnative species,

such as brook trout.

Although temperatures within the Boundary Reservoir

exceed levels considered suitable for coldwater taxa such as

salmonids (Richter and Kolmes, 2005), tributaries within the

system are a potential source of cold-water habitat. Modeled

presence of cold-water species such as westslope cutthroat

trout is predicted to be high in many locations, particularly

within Sullivan Creek (Isaak and others, 2016; g. 5).

10 Evolutionary and Ecological Connectivity in Washington, Idaho, and British Columbia

Figure 5. Historical, mid-century, and end-of-century (based on climate change scenarios in

1980, 2040, and 2080) predicted presence of native westslope cutthroat trout (Oncorhynchus clarkii

lewisi), assuming the absence of nonnative brook trout (S. fontinalis) within the Lake Pend Oreille–

Pend Oreille River system (fig. 2) in the United States (from Isaak and others, 2016).

Part 2. Evolutionary and Ecological Connectivity for Westslope Cutthroat Trout and Mountain Whitefish 11

Colder tributaries to Boundary Reservoir could act as

thermal refuges if they are accessible. In the largest system,

Sullivan Creek, a series of chutes and cascades begin about 1

km upstream from the conuence with Boundary Reservoir.

Such conditions are considered to pose a barrier to upstream

passage of bull trout less than 457 mm when ows exceed

about 3 m

/s Existing stream discharge records (USGS gage

12398000) indicate that ows often exceed those levels during

much of the year, but larger sh may be able to move upstream

into Sullivan Creek as ows decline in late summer through

fall. It is worth noting that none of the 16,980 westslope

cutthroat trout captured in tributary surveys from 2012 to

2018 were larger than 350 mm (West Fork Environmental,

2020). Sizes of individuals tracked using acoustic telemetry

in Boundary Reservoir averaged 276 mm (SD 47.3) with a

maximum length of 395 mm. Access to other tributaries of

Boundary Reservoir with available cold water is not possible

due to the presence of natural barriers near the conuences of

Peewee, Slate, Sweet, Flume, and Sand Creeks.

Before large dams were constructed in the Pend Oreille

system, it is possible that westslope cutthroat trout exhibited

migratory patterns that were similar to those exhibited by

bull trout in the system (DuPont and others, 2007, Dunham

and others, 2014). Historical patterns of movement by bull

trout included a strong inuence of seasonal emigration of

individuals from systems upstream from the Pend Oreille

River, with some of these individuals passing downstream

over the barriers of Z Canyon and Metaline Falls. There is

little doubt that the numbers of westslope cutthroat trout from

the Priest Lake, Lake Pend Oreille, and Clark Fork River

systems could also have produced individuals that migrated

downstream seasonally into the Pend Oreille River. Such

individuals would, however, have been unable to historically

access downstream tributaries between present-day Boundary

and Box Canyon dams due to natural barriers near their

conuences with the Pend Oreille River. Furthermore, the

presence of such migratory individuals would be limited to the

section of the river (which is now part of Boundary Reservoir)

that is located upstream from Metaline Falls (just downstream

from the conuence of Sullivan Creek). Individuals moving

downstream from Metaline Falls would not have been able to

return upstream.

Today, westslope cutthroat trout in Boundary Reservoir

represent a mixture of origins, including individuals from

populations upstream from Box Canyon Dam (see “Genetic

Evidence of Connectivity” above, and g. 6). Of 40 westslope

cutthroat trout sampled for n tissues in Boundary Reservoir

during 2018–19, the proportion of individuals genetically

assigned to populations upstream in Box Canyon Reservoir or

Priest River tributaries (35 percent; n = 14) was double that

assigned to Boundary Reservoir tributaries (15 percent, n = 6;

g. 6; Small and others, 2020). The proportion of individuals

assigned to the King's Lake Hatchery was even higher (40

percent; n = 16) in Boundary Reservoir. A similar genetic

analysis of westslope cutthroat trout in Box Canyon Reservoir

(n = 202) showed only 2 percent (n = 3) assigning to King's

Lake Hatchery (g. 6; Small and others, 2020).

Figure 6. Genetic assignment of westslope cutthroat trout (Oncorhynchus clarkii lewisi) sampled from Boundary Reservoir (n = 40;

left panel) and Box Canyon Reservoir (n = 202; right panel) into major spatial groupings (Boundary Reservoir tributaries, Box Canyon

Reservoir tributaries, Priest River tributaries, King's Lake Hatchery, and phenotypic westslope cutthroat trout that were assigned as

rainbow trout (Oncorhynchus mykiss); Small and others 2020).

12 Evolutionary and Ecological Connectivity in Washington, Idaho, and British Columbia

Mountain Whitefish

Biogeography

Mountain whitesh is one of the most widely distributed

yet least studied inland salmonid shes in western North

America. The species occurs south from the Lahontan and

Bonneville basins within the hydrographic Great Basin

desert into the Columbia River basin, upper Missouri River

and in other inland and coastal tributary streams north to

the Mackenzie River in the Northwest Territories, Canada

(Warren and Burr, 2014). Its widespread distribution suggests

a complex historical biogeography, but this has not been

well studied (Miller, 2006). Unlike westslope cutthroat trout

and other salmonids, mountain whitesh have not been

widely introduced by humans. Thus, indirect inferences

from molecular markers are not as subject to biases from this

potential inuence.

Genetic Evidence of Connectivity

Limited work has been conducted on mountain whitesh

in the Pend Oreille River. The most salient data are those

of Small and others (2019b), who examined variation at 15

microsatellite DNA loci in 163 individuals. The samples

ranged from one sh collected in the Boundary Dam tailrace

to sh from the former Mill Pond Dam area of the Sullivan

Creek watershed, sh from Sullivan Creek itself, and sh

from a range of localities between Boundary Dam forebay and

Albeni Falls.

This analysis showed a major dierence between samples

in the Mill Pond/Sullivan Creek area and those collected

between Boundary Dam and Albeni Falls (g. 7). The one

sample collected in the Boundary Dam tailrace was very

similar to the sh collected from the Boundary Reservoir to

Albeni Falls area, suggesting that it originated in this area and

was entrained downstream through the dam. Furthermore,

one sh collected in the Pend Oreille River upstream from

Boundary Dam appeared to originate above the former site of

Mill Pond Dam (g. 7, grey symbol indicted by grey arrow).

By contrast, there were no dierences found among samples

collected between Boundary Dam to Albeni Falls, nor between

sh from the Mill Pond area and upper Sullivan Creek

(although sample sizes were very small in the latter group).

This analysis was augmented by further work on 41

Mountain whitesh collected from Sullivan Lake and ve

sh collected from the Pend Oreille River between Boundary

Dam and Box Canyon Dam (Small and others, 2020).

The Sullivan Lake sh were strikingly distinct from those

Mill Pond/upper Sullivan Creek

Pend Oreille River

mainstem (Albeni Falls

downstream to

Metaline Falls),

reservoir tributaries,

tailrace of Boundary

Dam

14Mill

14Boundary Tailrace

17Sullivan

12PendOreille_12AK

12PendOreille_12DF

12SweetCr_12HH

Individual site code

Figure 7. Major genetic groups of mountain whitefish (Prosopium williamsoni) in the Boundary Area resolved using microsatellite DNA

analysis. Samples are projected in factorial correspondence analysis space and the ellipses denote two genetic groups of mountain

whitefish: Mill Pond/upper Sullivan Creek and Pend Oreille main stem and tributaries, and membership of individual fish within those

two groups. Modified from Small and others (2019b). The grey closed symbol within the left-most ellipse represents a fish sampled from

the Boundary Reservoir and the black solid diamond within the right-most ellipse represents a fish sampled from the Boundary Dam

tailrace.

Part 2. Evolutionary and Ecological Connectivity for Westslope Cutthroat Trout and Mountain Whitefish 13

collected from the Pend Oreille River (F

ranged from 0.10

to 0.11) but were only modestly (but signicantly) distinct

from Mill Pond Mountain whitesh (F

= 0.025, g. 8).

Despite these average dierences among the dierent groups

of mountain whitesh, three sh collected in the mainstem

Pend Oreille River (between upstream from Boundary Dam

and downstream from Box Canyon Dam) were genetically

similar to sh from the Sullivan Lake/Mill Pond group and

remarkably similar to the Mill Pond sh (g. 8). These data

suggest the occasional downstream movement of Sullivan

Lake/Mill Pond sh into the area between Boundary Dam and

Box Canyon Dam. Notwithstanding occasional downstream

movements, the dierence between the Mill Pond/Sullivan

Creek/Sullivan Lake samples and the Boundary Dam/Albeni

Falls samples suggests that there has been restricted movement

of sh between these areas, even though the Sullivan Creek

watershed enters the Pend Oreille River above Metaline Falls.

Alternatively, it is possible that the distinction between areas

could be an artifact of the isolation created by the Mill Pond

Dam that was removed in 2017. This, however, seems unlikely

given that there was a natural water velocity barrier in Sullivan

Creek where the Mill Pond Dam was located and another

at the outlet of Sullivan Lake (Small and others, 2020).

Furthermore, despite smaller sample sizes, the Mill Pond/

Sullivan Creek/Sullivan Lake samples contained ten alleles

(at low to moderate frequencies of 1–12 percent) not observed

in the Boundary Dam/Albeni Falls samples. This observation

suggests the Mill Pond/Sullivan Creek/Sullivan Lake sh

have been isolated long enough from the Pend Oreille sh

for these novel mutations to accumulate. Furthermore, strong

genetic drift induced by isolation from Mill Pond Dam

construction would be expected to eliminate rare, unique

16_17_18SullLk

14Mill

12PendOrR

12BoxCany

12HH_Sweet

Individual site codes

1.5

1.0

0.5

0 1.51.00.5−1.5 −1.0 −0.5

0.5

1.0

1.5

2.0

2.5

Figure 8. Major genetic groups of mountain whitefish (Prosopium williamsoni) in the Boundary Area resolved using allelic variation at

microsatellite DNA loci projected using factorial correspondence analysis. The genetic group to the right of the thin vertical grey line

consists of mountain whitefish from Mill Pond and Sullivan Lake as well as three fish sampled from the Pend Oreille River (large orange

symbols with arrows) and one fish sampled from a tributary above Metaline Falls (Sweet Creek, green symbol with arrow right of grey

vertical line). From Small and others (2020) and also includes fish assayed in Small and others (2019a, b).

14 Evolutionary and Ecological Connectivity in Washington, Idaho, and British Columbia

alleles. Consequently, the substantial divergence between the

Mill Pond/Sullivan Creek/Sullivan Lake and Boundary Dam/

Albeni Falls mountain whitesh is probably not an artifact of

Mill Pond Dam or Sullivan Lake Dam construction.

The distinction between Mill Pond/Sullivan Creek/

Sullivan Lake mountain whitesh and those from below the

Mill Pond site is also consistent with similar dierences found

in westslope cutthroat trout (for example, Small and others

2017, 2020).

Five sh that were collected below falls, as well as

current or former dam sites were more similar to sh above

these sites suggesting that mountain whitesh can survive

entrainment through natural geographic barriers and dams.

In the case of the single sh inferred to be of upper Sullivan

Creek origin that was collected in the Boundary Dam to

Box Canyon Dam area, the “baseline” sample of sh from

the Sullivan Creek area was likely sucient to support the

inference of downstream movement from Sullivan Creek.

By contrast, the single sh collected in the Boundary Dam

tailrace that was inferred to have originated above the dam

(Small and others, 2019a, b) could not be compared to

mountain whitesh from the mainstem Pend Oreille River

downstream from Boundary Dam or the Salmo River because

there were no baseline samples available for these areas.

Given the limitations of these small sample sizes and their

spatial distributions, a dierent result could arise once baseline

samples from below Boundary Dam are analyzed.

Whiteley and others (2006) used six microsatellite DNA

loci to assay variation among samples of mountain whitesh,

including those collected at the conuence of the Pend Oreille

and Columbia Rivers (PoR-C) and upstream from this area

in the Clark Fork River. The PoR-C sample was more similar

to samples upstream in Canadian portions of the Columbia

River (Beaver Creek, BC, and Kootenay Lake each about

100–110 km upstream from PoR-C) and localities from the

upper (Eagle River, BC) and lower Fraser River (Chilliwack

River, BC, both several hundreds of km away and in a distinct

drainage from PoR-C) than it was to samples from the Clark

Fork drainage (at least 170 km upstream from Boundary

Dam, Z Canyon, and Metaline Falls; Whiteley and others,

2006). High similarity of lower Pend Oreille River mountain

whitesh to sh from the Fraser River compared to sh from

the Clark Fork is inconsistent with high levels of historical

gene ow between the lower Pend Oreille River and areas

upstream.

Ecological Evidence of Connectivity

As for westslope cutthroat trout, water temperature is

a major control on the distribution of mountain whitesh in

stream networks (Isaak and others, 2017a). In a comprehensive

analysis of thermal requirements of 73 sh species in

Wyoming, Mandeville and others (2019) classied species

into ve thermal guilds: cold, cool-cold, cool, cool-warm,

and warm. Cutthroat trout (O. clarkii) was identied as one

of two species (including nonnative brook trout, S. fontinalis)

belonging to the cold-water species guild. Mountain whitesh

was classied as a member of the cool water guild of shes.

Isaak and others (2017a) modeled the presence of mountain

whitesh based on estimated August mean temperatures (Isaak

and others 2017b) in streams located in the upper Columbia

River (including the Pend Oreille River), Snake River, and

Missouri River headwaters. August mean temperatures

associated with estimated probabilities of occurrence of 0.5

for mountain whitesh were 15.3 °C and 9.7 °C for univariate

and multivariate models. It is worth noting that condence

bounds associated with these estimates were relatively wide,

which should be expected with eld-based studies of thermal

associations, as numerous factors interact with temperature

to determine species presence (Mandeville and others, 2019).

Furthermore, associations can vary, depending on descriptors

used to associate sh with thermal regimes (for example,

magnitude, timing, duration, frequency of thermal exposures;

Benjamin and others, 2016). While many uncertainties remain,

available evidence suggests that mountain whitesh are more

likely to be observed using water that is a few degrees warmer

than what can be generally expected of cutthroat trout (Isaak

and others, 2017b). As discussed for westslope cutthroat

trout, summer maximum temperatures within Boundary

Reservoir approach and potentially exceed levels that could

lead to physiological stress in mountain whitesh (Quinn and

others, 2010).

While limited data are available, inferences from

molecular markers (preceding section) indicate little gene

ow and connectivity in the Pend Oreille River downstream

from Boundary Dam for mountain whitesh. Similarly, within

Boundary Reservoir, only six mountain whitesh have been

tagged and tracked, but no individuals were detected being

entrained through Boundary Dam (Hydroacoustics Technology

Incorporated, 2018, 2020, 2021). More individuals would need

to be tracked to draw more denitive conclusions. Movement

studies of mountain whitesh in other systems, along with

knowledge of constraints on connectivity in the Boundary

Reservoir system and Pend Oreille River, can be applied to

draw a few qualied inferences. Direct tracking of individual

movements as well as inferences from otolith microchemistry

of mountain whitesh in other systems indicate seasonal

movements are extensive (for example, up to and potentially

extending over 100 km), complex, and generally limited to

larger streams within riverscapes (for example, Davies and

Thompson, 1976; Northcote and Ennis, 1994; Baxter, 2002;

Benjamin and others, 2014; Boyer and others, 2017). An

improved understanding of spatial and temporally dynamic

habitat features that mountain whitesh may depend on

within Boundary Reservoir could provide useful insights for

maintaining or improving connectivity within the system.

For instance, Davies and Thompson (1976) proposed a host

of proximate (for example, environmental conditions) and

ultimate (for example, growth, survival, reproduction) drivers

of diverse seasonal movements they observed for mountain

whitesh throughout the life cycle.

Part 3. Conclusions and Recommendations for Upstream Passage over Boundary Dam 15

Aside from the isolated distribution of mountain

whitesh in the Sullivan Lake/Creek watershed and the lowest

reach of Sweet Creek, tributary connectivity within Boundary

Reservoir may have little ecological signicance. Given the

lack of access (upstream movement barriers) and limited

suitability (that is, small size) of many tributaries to Boundary

Reservoir, opportunities for mountain whitesh to exploit

seasonally variable conditions within the system are limited.

Evidence from molecular genetic markers indicating lack of

genetic drift in isolated populations of mountain whitesh in

the Sullivan Creek watershed indicates that current and recent

historical population sizes are large enough to overcome the

eects of genetic drift, in spite of their isolation or lack of

connectivity to the Pend Oreille River. Such patterns have

been observed for other salmonid shes upstream from

human-constructed barriers (culverts), where only the smallest

systems show evidence of loss of genetic diversity (Neville

and others 2009). Although some studies have identied

loss of genetic diversity in some instances upstream from

human-constructed and natural passage barriers (for example,

Woord and others, 2005; Neville and others, 2006a, b; Carim

and others, 2016), populations of westslope cutthroat trout

often persist upstream from barriers (Loxterman and others,

2014; Peterson and others, 2014), and at least in the case of

culverts, population persistence times may exceed the lifespan

of culverts (Reagan, 2015). Other structures (for example,

concrete and metal erosion control dams; Morita and others,

2009) may last longer and pose threats to the long-term

persistence of isolated populations.

The importance of upstream connectivity to the Pend

Oreille River above Box Canyon Dam is less clear for

mountain whitesh. As with westslope cutthroat trout, the

ecological importance of connectivity of mountain whitesh

to the Pend Oreille River and associated lakes upstream from

Albeni Falls Dam is unknown. Movements of mountain

whitesh observed in other systems have been extensive

however (for example, Davies and Thompson, 1976;

Northcote and Ennis, 1994; Baxter, 2002; Benjamin and

others, 2014; Boyer and others, 2017), so this is a potential

consideration. As with westslope cutthroat trout and bull trout

(Dunham and others, 2014), there is little possibility, however,

that mountain whitesh were able to move upstream over Z

Canyon and Metaline Falls.

Part 3. Conclusions and

Recommendations for Upstream

Passage over Boundary Dam

Westslope Cutthroat Trout

The historical biogeography of the Pend Oreille River

system, molecular genetic analyses, and contemporary

ecological observations were assembled to draw conclusions

regarding westslope cutthroat trout and the role that Boundary

Dam plays in aecting connectivity for this species. Notably,

the available molecular genetic evidence suggests westslope

cutthroat trout in the Salmo River may: (1) be introgressed

with rainbow trout, and (2) derived from a source outside of

the Salmo basin (King's Lake hatchery strain). We discuss

each of these in turn below.

Introgression between cutthroat trout and rainbow trout

can lead to reduced tness (Strait and others, 2021) and

thus pose a threat to westslope cutthroat trout if one or both

species are introduced outside their natural ranges. There

are likely remnants of native and nonnative rainbow trout

in the Salmo River, owing to historical stocking of rainbow

trout and isolation by downstream dams that have prevented

anadromous (steelhead trout) life history expression (Hagen

and Baxter, 2004). Consequently, westslope cutthroat trout

likely coexist with a mix of native and introduced rainbow

trout in the Salmo River. The potential spread of hybridization

between westslope cutthroat trout and rainbow trout

throughout connected river networks has been documented in

tributaries upstream from the Pend Oreille River (Muhlfeld

and others, 2014), which may be exacerbated by rapid climate

warming observed across the western United States (Isaak and

others, 2016). Similar outcomes are possible if Salmo River

westslope cutthroat trout are connected to native westslope

cutthroat trout in the Pend Oreille River. Given the evidence

from upstream systems, threats posed from hybridization with

nonnative rainbow trout or backcrossing with hybrids merit

serious consideration when evaluating the potential risks

and benets of connecting to isolated native populations of

westslope cutthroat trout in the Pend Oreille River. One option

to facilitate sh passage but protect upstream populations from

introgression would be to remove hybrid individuals passing

over sh passage structures during spawning migrations

between mainstem habitats and tributaries, but this can be a

costly endeavor.

With respect to the hatchery origin (King's Lake

hatchery stock) of westlope cutthroat trout in the Salmo

River,the absence of readily detectable and genetically

unique westslope cutthroat trout in the Salmo River contrasts

strongly with Sullivan Creek immediately upstream, where

westslope cutthroat trout likely represent a native population.

The King's Lake hatchery stock is derived from tributaries

in the Priest Lake watershed (Small and others, 2007) and

can be considered native to the Pend Oreille/Priest Lake

watershed. Consequently, the Salmo River sh could be a

native population and their current similarity to the King's

Lake hatchery strain could be a function of the historical

connectivity between these areas as part of the Pend Oreille

River drainage. Given, however, that the Salmo River

watershed is at the lower end of the Pend Oreille drainage,

it seems unlikely that the genetic similarity between Salmo

River and King's Lake results from historical connectivity

when many other systems closer to the King's Lake hatchery

source populations in the Priest Lake drainage show no

such anity (Small and others, 2007, 2017). Introgression

16 Evolutionary and Ecological Connectivity in Washington, Idaho, and British Columbia

following known plantings of King's Lake hatchery sh in and

around the Salmo River seems a more plausible scenario for

the observed genetic structure of Salmo River sh.

Acoustic telemetry in Boundary Reservoir indicates some

tagged westslope cutthroat trout were entrained through the

dam and moved downstream. It is not dicult to imagine this

being the case prior to construction of Boundary Dam when

sh could easily pass downstream over Metaline Falls and

down through Z Canyon to access the Salmo River or other

downstream destinations. Given historical records indicating

that anadromous shes were limited by the falls, any resident

sh moving downstream would likely have been unable to

return upstream and would have been forced to complete their

life cycle downstream. Previous work on bull trout identied

a genetic signal of such interactions, indicating that bull trout

from upstream in the Pend Oreille River or Lake Pend Oreille

may have contributed to populations in the Salmo River but

not vice versa, at least historically (Dunham and others, 2014).

Additionally, our analyses suggest that if sh were passed

upstream from Boundary Dam it is clear that environmental

conditions within Boundary Reservoir are not well-suited to

support westslope cutthroat trout in the warmer months and it

does not appear that sh in the reservoir have easy access to

abundant colder thermal refugia within the system, based on

the presence of natural movement barriers near the mouths of

larger tributaries. In conclusion, the available evidence points

to no strong evolutionary or ecological rationale for passing

westslope cutthroat trout upstream from Boundary Dam.

Mountain Whitefish

Although less is known about mountain whitesh,

relative to westslope cutthroat trout, existing evidence

available within Boundary Reservoir and its tributaries, as

well as information from within and outside of the Pend

Oreille River indicate little support for passing sh upstream

over Boundary Dam. In contrast to westslope cutthroat trout

and bull trout (Dunham and others, 2014), mountain whitesh

within the Pend Oreille River exhibit little population

structure, indicating widespread historical gene ow across the

upper Columbia River downstream from Lake Pend Oreille,

although populations do show structuring at a broader regional

extent (Whiteley and others, 2006). A notable exception

is the uniqueness of mountain whitesh in Sullivan Lake,

which is consistent with the potential existence of a barrier

to upstream movement in the lower reaches of this system

(g. 6). Additional spatial sampling and consideration of a

larger diversity of molecular markers could potentially resolve

additional genetic relationships for mountain whitesh within

the Pend Oreille River and upper Columbia River basin and

potentially shed more light on the importance of upstream

connectivity to the Pend Oreille River and associated lakes

(for example, Dupont and others, 2007). An ecological

study of mountain whitesh within the Pend Oreille River

and Sullivan Creek may reveal important spatial ecological

processes that inuence populations (possibly implied by

patterns of genetic structure, g. 8) within each of those

systems and opportunities for restoration.

Overall Conclusions

Our review of the available evidence for westslope

cutthroat trout and mountain whitesh aligns with the case

for bull trout (Dunham and others, 2014, app. 1), with respect

to the question of whether or not to provide passage of

sh upstream over Boundary Dam. Although each species

exhibits unique characteristics, current evidence indicates that

moving sh upstream over Boundary Dam is not warranted

if the management objective is to maintain natural patterns

of evolutionary and ecological connectivity or to conserve

unique ecological and evolutionary characteristics of extant

local populations of these species in the system. There is

little evidence of natural upstream connectivity due to the

natural, pre-dam inuences of barriers posed by Z Canyon and

Metaline Falls. In the case of bull trout, moving sh upstream

could have adverse consequences for population numbers in

the Salmo River and gene ow between populations upstream

and downstream from Metaline Falls. Such does not seem

to be the case for westslope cutthroat trout, as there is no

denitive evidence of native populations in the Salmo River.

Additional work could, however, be done to verify that native

populations are not present in headwater tributaries of the

Salmo River. Even if such populations were discovered, it is

not clear they were likely connected to populations upstream

from Boundary Dam, as populations of bull trout have been

historically.

Mountain whitesh exhibit much less spatial variability

with respect to their distribution, which is conned to higher

order (larger) streams, and local populations that are weakly

dierentiated relative to westslope cutthroat trout and bull

trout (Whiteley and others 2004; Taylor and others, 2014). An

exception is the presence of unique populations of westslope

cutthroat trout and mountain whitesh in Sullivan Lake–the

largest tributary to Boundary Reservoir. Again, however,

the evidence for Sullivan Creek suggests these populations

have not been inuenced by connectivity with downstream

populations.

Our focus in this report was on the role of Boundary

Dam and the historical connectivity of the two species

considering the upstream migration barriers of Z Canyon

and Metaline Falls in the Pend Oreille River. It is important

to recognize, however, that we did not consider connectivity

farther upstream in the Pend Oreille River such as Box

Canyon Reservoir reaches and the associated systems of

Priest Lake and Lake Pend Oreille. This could be an important

consideration, as the case for bull trout appears to indicate

(app. 1). If connectivity for native shes such as westslope

cutthroat trout, mountain whitesh, and bull trout is a major

References Cited 17

objective within the Pend Oreille River, more work directed at

better understanding connectivity in upstream reaches of the

Pend Oreille River may be warranted.

References Cited

Baxter, C.V., 2002, Fish movement and assemblage dynamics

in a Pacic Northwest riverscape: Corvallis, Oregon State

University, PhD dissertation.

Bellmore, J.R., Pess, G.R., Duda, J.J., O’Connor, J.E., East,

A.E., Foley, M.M., Wilcox, A.C., Major, J.J., Shafroth,

P.B., Morley, S.A. and Magirl, C.S., 2019, Conceptualizing

ecological responses to dam removal—If you remove it,

what's to come?: BioScience, v. 69, no. 1, p. 26–39.

Behnke, R.J., 1992, Native trout of western North America:

American Fisheries Society, Monograph 6, 275 p.

Behnke R.J., 2002. Trout and salmon of North America: New

York, The Free Press, 382 p.

Benjamin, J.R., Brignon, W.R., and Dunham, J.B., 2019,

Decision analysis for the reintroduction of bull trout

into the lower Pend Oreille River, Washington: North

American Journal of Fisheries Management, v. 39, no. 5,

p. 1026-1045.

Benjamin, J.R., Wetzel, L.A., Martens, K.D., Larsen, K.,

and Connolly, P.J., 2014, Spatio-temporal variability

in movement, age, and growth of mountain whitesh

(Prosopium williamsoni) in a river network based upon PIT

tagging and otolith chemistry: Canadian Journal of Fisheries

and Aquatic Sciences, v. 71, no. 1, p. 131–140.

Benjamin, J.R., Heltzel, J.M., Dunham, J.B., Heck, M., and

Banish, N., 2016, Thermal regimes, nonnative trout, and

their inuences on native bull trout in the upper Klamath

River basin, Oregon: Transactions of the American Fisheries

Society, v. 145, no. 6, p. 1318–1330.

Benjamin, J.R., Vidergar, D.T., and Dunham, J.B., 2020,

Thermal heterogeneity, migration, and consequences for

spawning potential of female bull trout in a river–reservoir

system: Ecology and Evolution, v. 10, no. 9, p. 4128–4142.

Boyer, J.K., Guy, C.S., Webb, M.A., Horton, T.B., and

McMahon, T.E., 2017, Reproductive ecology, spawning

behavior, and juvenile distribution of mountain whitesh in

the Madison River, Montana: Transactions of the American

Fisheries Society, v. 146, no. 5, p. 939–954.

Carim, K.J., Eby, L.A., Barfoot, C.A., and Boyer, M.C., 2016,

Consistent loss of genetic diversity in isolated cutthroat

trout populations independent of habitat size and quality:

Conservation Genetics, v. 17, no. 6, p. 1363–1376.

Carim, K.J., Dysthe, J.C., McLellan, H., Young, M.K.,

McKelvey, K.S., and Schwartz, M.K., 2019, Using

environmental DNA sampling to monitor the invasion of

nonnative Esox lucius (northern pike) in the Columbia River

basin, USA: Environmental DNA, v. 1, no. 3, p. 215–226.

Corsi, M.P., Hansen, M.J., Quist, M.C., Schill, D.J., and Dux,

A.M., 2019, Inuences of lake trout (Salvelinus namaycush)

and Mysis diluviana on kokanee (Oncorhynchus nerka)

in Lake Pend Oreille, Idaho: Hydrobiologia, v. 840, no. 1,

p. 351–362.

Davies, R.W., and Thompson, G.W., 1976, Movements of

mountain whitesh (Prosopium williamsoni) in the Sheep

River watershed, Alberta: Journal of the Fisheries Research

Board of Canada, v. 33, no. 11, p. 2395–2401.

DeHaan, P.W., and Bernall, S.R., 2013, Spawning success of

bull trout transported above main-stem Clark Fork River

dams in Idaho and Montana: North American Journal of

Fisheries Management, v. 33, no. 6, p. 1269–1282.

DeHaan, P.W., Bernall, S.R., DosSantos, J.M., Lockard, L.L.,

and Ardren, W.R., 2011, Use of genetic markers to aid in

re-establishing migratory connectivity in a fragmented

metapopulation of bull trout (Salvelinus conuentus):

Canadian Journal of Fisheries and Aquatic Sciences, v. 68,

no. 11, p. 1952–1969.

Dunham, J.B., Taylor, E.B., and Allendorf, F.W., 2014, Bull

trout in the Boundary System—Managing connectivity and

the feasibility of a reintroduction in the lower Pend Oreille

River, northeastern Washington: U.S. Geological Survey

Open-File Report 2014–1229, 28 p., https://doi.org/ 10.3133/

ofr20141229.

Dunham, J.B., Adams, S.B., Schroeter, R.E., and Novinger,

D.C., 2002, Alien invasions in aquatic ecosystems—Toward

an understanding of brook trout invasions and potential

impacts on inland cutthroat trout in western North America:

Reviews in Fish Biology and Fisheries, v. 12, no. 4,

p. 373–391.

DuPont, J.M., Brown, R.S., and Geist, D.R., 2007, Unique

allacustrine migration patterns of a bull trout population in

the Pend Oreille River drainage, Idaho: North American

Journal of Fisheries Management, v. 27, no. 4, p.

1268–1275.

Dux, A.M., Hansen, M.J., Corsi, M.P., Wahl, N.C., Fredericks,

J.P., Corsi, C.E., Schill, D.J., and Horner, N.J., 2019,

Eectiveness of lake trout (Salvelinus namaycush)

suppression in Lake Pend Oreille, Idaho—2006–2016:

Hydrobiologia, v. 840, no. 1, p. 319–333.

18 Evolutionary and Ecological Connectivity in Washington, Idaho, and British Columbia

Epifanio, J., Haas, G., Pratt, K., Rieman, B., Spruell, P.,

Stockwell, C., Utter, F., and Young, W., 2003, Integrating

conservation genetic considerations into conservation

planning—A case study of bull trout in the Lake Pend

Oreille–Lower Clark Fork River system: Fisheries, v. 28,

no. 8, p. 10–24.

Environmental Science Associates, 2019, Memorandum to

Seattle City Light—Data from temperature attainment

plan monitoring: Portland, Oregon, Environmental Science

Associations.

Falke, J.A., and Fausch, K.D., 2010, From metapopulations

to metacommunities—Linking theory with empirical

observations of the spatial population dynamics of stream

shes, in Community ecology of stream shes—Concepts,

approaches, and techniques: Bethesda, Maryland, American

Fisheries Society Symposium, v. 73, p. 207–233.

Federal Energy Regulatory Commission, 2011, Final

environmental impact statement application for hydropower

license for the Boundary Hydroelectric Project FERC

Project No. 2144–038, Washington and application

for surrender of Hydropower License for the Sullivan

Creek Project FERC Project No. 2225–015, Washington:

Washington, DC, Federal Energy Regulatory Commission,

460 p., accessed November 27, 2021, at http:// www.millpo

nddam.com/ wp- content/ uploads/ 2016/ 04/ FEIS- Boundary-

Sullivan.pdf.

Frantilla, Anne, 2022, Boundary Dam: City of Seattle,

Seattle Municipal Archives, accessed July 3, 2022, at http

s://www.se attle.gov/ cityarchives/ exhibits- and- education/

online- exhibits/ boundary- dam.

Hagen, J., and Baxter, J.S., 2004, Conservation status of

Salmo River rainbow trout—Radio telemetry investigations

of habitat use and abundance: BC Hydro, prepared by John

Hagen and Associates, British Columbia, Canada, accessed

November 27, 2021, at http:// www.sgrc.s elkirk.ca/ bioatlas/

pdf/ Salmo_ Telemetry_ Fina l%20Report PUBLIC.pdf.

Hansen, M.J., Schill, D., Fredericks, J., and Dux, A., 2010,

Salmonid predator-prey dynamics in Lake Pend Oreille,

Idaho, USA: Hydrobiologia, v. 650, no. 1, p. 85–100.

Hydroacoustic Technology Incorporated, 2018, Boundary

Dam sheries biotelemetry study, 2017 Annual Report

HTI-VEMCO Project Ref: P3824: Seattle City Light,

Washington, Agreement Number CC2015-011, 30 p.

Hydroacoustic Technology Incorporated, 2020, Boundary

Dam sheries biotelemetry study, 2019 Annual Report

HTI-VEMCO Project Ref: P3824: Seattle City Light,

Washington, Agreement Number CC2015-011, 31 p.

Hydroacoustic Technology Incorporated, 2021, Boundary

Dam sheries biotelemetry study, 2020 Annual Report

HTI-VEMCO Project Ref: P3824: Seattle City Light,

Washington, Agreement Number CC2015-011, 33 p.

Isaak, D.J., Young, M.K., Nagel, D.E., Horan, D.L., and

Groce, M.C., 2015, The cold‐water climate shield—

Delineating refugia for preserving salmonid shes through

the 21st century: Global Change Biology, v. 21, no. 7,

p. 2540–2553.

Isaak, D.J., Young, M.K., Luce, C.H., Hostetler, S.W.,

Wenger, S.J., Peterson, E.E., Ver Hoef, J.M., Groce,

M.C., Horan, D.L., and Nagel, D.E., 2016, Slow climate

velocities of mountain streams portend their role as refugia

for cold-water biodiversity: Proceedings of the National

Academy of Sciences of the United States of America,

v. 113, no. 16, p. 4374–4379.

Isaak, D.J., Wenger, S.J., and Young, M.K., 2017a, Big

biology meets microclimatology—Dening thermal niches

of ectotherms at landscape scales for conservation planning:

Ecological Applications, v. 27, no. 3, p. 977–990.

Isaak, D.J., Wenger, S.J., Peterson, E.E., Ver Hoef, J.M.,

Nagel, D.E., Luce, C.H., Hostetler, S.W., Dunham, J.B.,

Roper, B.B., Wollrab, S.P., Chandler, G.L., Horan, D.L.,

and Parkes-Payne, S., 2017b, The NorWeST summer stream

temperature model and scenarios for the Western U.S.—A

crowd‐sourced database and new geospatial tools foster

a user community and predict broad climate warming of

rivers and streams: Water Resources Research, v. 53, no. 11,

p. 9181–9205.

Kendall, N.W., McMillan, J.R., Sloat, M.R., Buehrens,

T.W., Quinn, T.P., Pess, G.R., Kuzishchin, K.V., McClure,

M.M., and Zabel, R.W., 2015, Anadromy and residency in

steelhead and rainbow trout (Oncorhynchus mykiss)—A

review of the processes and patterns: Canadian Journal of

Fisheries and Aquatic Sciences, v. 72, no. 3, p. 319–342.

Link, P.K., and Keeley, E.R., 2018, Geologic constraints on

Snake-Columbia River drainage changes and the associated

evolutionary diversication of cutthroat trout over the last

17 million years, in Trotter, P.C., Bisson, P.S., Roper, B.,

and Schultz, L., eds., Cutthroat trout—Evolutionary biology

and taxonomy: Bethesda, Maryland, American Fisheries

Society, p. 53–75.

Loxterman, J.L., Keeley, E.R., and Njoroge, Z.M., 2014,

Evaluating the inuence of stocking history and barriers to

movement on the spatial extent of hybridization between

westslope cutthroat trout and rainbow trout: Canadian

Journal of Fisheries and Aquatic Sciences, v. 71, no. 7,

p. 1050–1058.

References Cited 19

Lukacs, P.M., and Landguth, E., 2020, Boundary hydroelectric

project area Westslope cutthroat trout capture update

2012–2018: Missoula, Montana, University of Montana,

Report prepared for Seattle City Light, 16 p.

Lusardi, R.A., and Moyle, P.B., 2017, Two-way trap and

haul as a conservation strategy for anadromous salmonids:

Fisheries, v. 42, no. 9, p. 478–487.

Mandeville, C.P., Rahel, F.J., Patterson, L.S., and Walters,

A.W., 2019, Integrating sh assemblage data, modeled

stream temperatures, and thermal tolerance metrics to

develop thermal guilds for water temperature regulation—

Wyoming case study: Transactions of the American

Fisheries Society, v. 148, no. 4, p. 739–754.

McPhail, J.D., 2007, The freshwater shes of British

Columbia: Edmonton, Alberta, University of Alberta, 620 p.

McPhail, J.D., and Lindsey, C.C., 1986, Zoogeography of

the freshwater shes of Cascadia (the Columbia system

and rivers north to the Stikine), in Hocutt, C.H., and

Wiley, E.O., eds., The zoogeography of North American

freshwater shes: New York, New York, Wiley Interscience,

p. 615–637.

Miller, B.A., 2006, The phylogeography of Prosopium in

western North America: Provo, Utah, Brigham Young

University, Master's thesis.

Mims, M.C., Day, C.C., Burkhart, J.J., Fuller, M.R., Hinkle, J.,

Bearlin, A., Dunham, J.B., DeHaan, P.W., Holden, Z.A., and

Landguth, E.E., 2019, Simulating demography, genetics,

and spatially explicit processes to inform reintroduction of a

threatened char: Ecosphere, v. 10, no. 2, p. e02589.

Monnot, L., Dunham, J.B., Hoem, T., and Koetsier, P.,

2008, Inuences of body size and environmental factors

on autumn downstream migration of bull trout in the

Boise River, Idaho: North American Journal of Fisheries

Management, v. 28, no. 1, p. 231–240.

Morita, K., Morita, S.H., and Yamamoto, S., 2009, Eects of

habitat fragmentation by damming on salmonid shes—

Lessons from white-spotted charr in Japan: Ecological

Research, v. 24, no. 4, p. 711–722.

Muhlfeld, C.C., Kovach, R.P., Jones, L.A., Al-Chokhachy,

R., Boyer, M.C., Leary, R.F., Lowe, W.H., Luikart, G.,

and Allendorf, F.W., 2014, Invasive hybridization in a

threatened species is accelerated by climate change: Nature

Climate Change, v. 4, no. 7, p. 620–624.

Nellestijn, G., and Ells, B., 2008, A history of the Salmo River

watershed—An overview of events that have had an impact

on our river ecology: Salmo Watershed Streamkeepers

Society, 16 p., accessed November 27, 2021, at h ttp://www.

streamkeep ers.bc.ca/ reports/ Salmo%20River- History

.Impacts.E cology.pdf.

Neraas, L.P., and Spruell, P., 2001, Fragmentation of riverine

systems—The genetic eects of dams on bull trout

(Salvelinus conuentus) in the Clark Fork River system:

Molecular Ecology, v. 10, no. 5, p. 1153–1164.

Neville, H., Dunham, J., and Peacock, M., 2006a, Assessing

connectivity in salmonid shes with DNA microsatellite

markers, in Crooks, K.R., and Sanjayan, M., eds.,

Connectivity conservation: New York, Cambridge

University Press, p. 318–342.

Neville, H.M., Dunham, J.B., and Peacock, M.M., 2006b,

Landscape attributes and life history variability shape

genetic structure of trout populations in a stream network:

Landscape Ecology, v. 21, no. 6, p. 901–916.

Neville, H., Dunham, J., Rosenberger, A., Umek, J., and

Nelson, B., 2009, Inuences of wildre, habitat size, and

connectivity on trout in headwater streams revealed by

patterns of genetic diversity: Transactions of the American

Fisheries Society, v. 138, no. 6, p. 1314–1327.

Northcote, T.G. and Ennis, G.L., 1994, Mountain whitesh

biology and habitat use in relation to compensation and

improvement possibilities: Reviews in Fisheries Science, v.

2, no. 4, p. 347–371.

O’Connor, J.E., Baker, V.R., Waitt, R.B., Smith, L.N.,

Cannon, C.M., George, D.L., and Denlinger, R.P., 2020,

The Missoula and Bonneville oods—A review of ice-age

megaoods in the Columbia River basin: Earth-Science

Reviews, v. 208, p. 1–51.

Peterson, D.P., Rieman, B.E., Horan, D.L., and Young, M.K.,

2014, Patch size but not short‐term isolation inuences

occurrence of westslope cutthroat trout above human‐

made barriers: Ecology of Freshwater Fish, v. 23, no. 4,

p. 556–571.

Pickett, P.J., 2004, Quality assurance project plan—Pend

Oreille River temperature total maximum daily load

technical study: Olympia, Washington, Washington State

Department of Ecology, Environmental Assessment

Program, No. 04-03-109, 49 p.

Pielou, E.C., 1991, After the ice age—The return of life to

glaciated North America: Chicago, Illinois, University of

Chicago Press, 376 p.

Powers, D., 2008, Sullivan Creek RM 0.65 sh barrier

assessment: Olympia, Washington, Waterfall Engineering,

LLC, Prepared for EES Consulting, 8 p., accessed

November 28, 2021, at http s://www.fs .usda.gov/ Internet/

FSE_ DOCUMENTS/ fsbdev3_ 034937.pdf.

20 Evolutionary and Ecological Connectivity in Washington, Idaho, and British Columbia

Quinn, A.L., Rasmussen, J.B., and Hontela, A., 2010,

Physiological stress response of mountain whitesh

(Prosopium williamsoni) and white sucker (Catostomus

commersoni) sampled along a gradient of temperature and

agrichemicals in the Oldman River, Alberta: Environmental

Biology of Fishes, v. 88, no. 2, p. 119–131.

Reagan, R.E., 2015, Where the stream meets the road—

Prioritizing culvert replacement for sh passage: Corvallis,

Oregon, MS Thesis, Oregon State University, 69 p.

Richter, A., and Kolmes, S.A., 2005, Maximum temperature

limits for Chinook, coho, and chum salmon, and steelhead

trout in the Pacic Northwest: Reviews in Fisheries

Science, v. 13, no. 1, p. 23–49.

Scholz, A., O’Laughlin, K., Geist, D., Uehara, J., Peone, D.,

Fields, L., Kleist, T., Zozaya, I., Peone, T., and Teesatuskie,

K., 1985, Compilation of information on salmon and

steelhead total run size, catch and hydropower related

losses in the upper Columbia River Basin, above Grand

Coulee Dam: Cheney, Washington, Upper Columbia United

Tribes Fisheries Center, Eastern Washington University,

Department of Biology, Fisheries Technical Report, no.

2, 165 p., accessed October 2021 at https: //www.nwco

uncil.org/ reports/ compilation- information- salmon- and-

steelhead- total- run- size- catch- and- hydropower- related.

Seattle City Light (SCL), 2006, Pre-application document

for the Boundary Hydroelectric Project (FERC no. 2144):

Seattle City Light, 692 p., accessed November 28, 2021, at

http s://www.se attle.gov/ light/ Boundary/ Relicense/ docs/ Pre_

Application_ Document_ 04_ 2006.pdf.

Small, M.P., Von Bargen, J., Bowman, C., and Frye, A., 2007,

Cutthroat trout population structure in the lower Pend

Oreille and Priest River subbasins using microsatellite

DNA: Olympia, Washington, Washington Department of

Fish and Wildlife, Conservation Biology Unit, Molecular

Genetics Lab, Report to Seattle City Light.

Small, M.P., Gee, G., and Bearlin, A., 2017, Boundary

hydroelectric project native salmonid genetics program

report—SNP genetic analyses of westslope cutthroat trout

in Sullivan Basin and nearby tributaries of the Pend Oreille

River: Olympia, Washington Department of Fish and

Wildlife, Conservation Biology Unit, Molecular Genetics

Lab, Report prepared for Seattle City Light.

Small, M.P., Kissler, M., and Simmons, R., 2019a, Boundary

hydroelectric project native salmonid genetics program

report—Assign unknown migratory westslope cutthroat

trout collected in Pend Oreille Basin: Olympia, Washington

Department of Fish and Wildlife, Conservation Biology

Unit, Molecular Genetics Lab, Report prepared for Seattle

City Light.

Small, M.P., Terepocki, A., and Simmons, R., 2019b,

Boundary region mountain whitesh genetic draft report:

Olympia, Washington Department of Fish and Wildlife,

Conservation Biology Unit, Molecular Genetics Lab, Report

prepared for Seattle City Light.

Small, M.P., Kissler, M., and Simmons, R., 2020, Boundary

hydroelectric project native salmonid genetics program

report—SNP genetic assignment of westslope cutthroat

trout collected in Boundary Reservoir and tailrace:

Olympia, Washington Department of Fish and Wildlife,

Conservation Biology Unit, Molecular Genetics Lab, Report

prepared for Seattle City Light.

Snyder, M.N., Schumaker, N.H., Dunham, J.B., Keefer, M.L.,

Leinenbach, P., Brookes, A., Palmer, J., Wu, J., Keenan,

D., and Ebersole, J.L., 2020, Assessing contributions of

cold-water refuges to reproductive migration corridor

conditions for adult salmon and steelhead trout in the

Columbia River, USA: Journal of Ecohydraulics, p. 1–13.

Spruell, P., Rieman, B.E., Knudsen, K.L., Utter, F.M., and

Allendorf, F.W., 1999, Genetic population structure within

streams—Microsatellite analysis of bull trout populations:

Ecology Freshwater Fish, v. 8, no. 3, p. 114–121.

Strait, J.T., Eby, L.A., Kovach, R.P., Muhlfeld, C.C., Boyer,

M.C., Amish, S.J., Smith, S., Lowe, W.H. and Luikart, G.,

2021, Hybridization alters growth and migratory life‐history

expression of native trout: Evolutionary applications, v. 14,

no. 3, p. 821–833.

Taylor, E.B., Yau, M.M., and Mattock, A.B., 2014, Population

structure in three species of co-distributed salmonid shes

in the Peace River and tributaries near a major proposed

hydro-electirc development in northeastern British

Columbia, Canada: River Research and Applications, v. 30,

no. 9, p. 1120–1133.

U.S. Fish and Wildlife Service, 2015, Recovery plan for

the conterminous United States population of bull trout

(Salvelinus conuentus): U.S. Fish and Wildlife Service,

Portland District, Oregon, accessed November 28, 2021,

at ht tps://www. federalreg ister.gov/ documents/ 2015/ 09/

30/ 2015- 24670/ endangered- and- threatened- wildlife- and-

plants- recovery- plan- for- the- coterminous- united- states.

Vidergar, D.T., 2000, Population estimates, food habits and

estimates of consumption of selected predatory shes in

Lake Pend Oreille, Idaho: Moscow, Idaho, Master's thesis,

University of Idaho, 109 p.

Warren, M.L., and Burr, B.M., eds., 2014, Freshwater shes

of North America—Petromyzontidae to Catostomidae:

Baltimore, Maryland, Johns Hopkins University Press,

v. 1, 664 p.

References Cited 21

Washington Department of Fish and Wildlife, 2020,

Salmonscape geographic information system: Washington

Department of Fish and Wildlife, accessed November 28,

2021, at htt ps://www.a rcgis.com/ home/ item.html? id= 1e

56a6487185 43ab952e75 9971f086.

Wenger, S.J., Isaak, D.J., Dunham, J.B., Fausch, K.D.,

Luce, C.H., Neville, H.M., Rieman, B.E., Young, M.K.,

Nagel, D.E., Horan, D.L., and Chandler, G.L., 2011,

Role of climate and invasive species in structuring trout

distributions in the interior Columbia River Basin, USA:

Canadian Journal of Fisheries and Aquatic Sciences, v. 68,

no. 6, p. 988–1008.

West Fork Environmental, 2020, Salmonid sampling—

Boundary hydroelectric project area, NE Washington—2019

boundary tributary surveys: Tumwater, Washington, West

Fork Environmental, 21 p.

Whiteley, A.R., Spruell, P., and Allendorf, F.W., 2004,

Ecological and life history characteristics predict population

genetic divergence of two salmonids in the same landscape:

Molecular Ecology, v. 13, no. 12, p. 3675–3688.

Whiteley, A.R., Spruell, P., and Allendorf, F.W., 2006,

Can common species provide valuable information

for conservation?: Molecular Ecology, v. 15, no. 10,

p. 2767–2786.

Woord, J.E., Gresswell, R.E., and Banks, M.A., 2005,

Inuence of barriers to movement on within‐watershed

genetic variation of coastal cutthroat trout: Ecological

Applications, v. 15, no. 2, p. 628–637.

World Waterfall Database, 2022, Homepage: World Waterfall

Database, web, accessed March 3, 2022, at

https://w ww.worldwa terfalldat abase.com/ .

Young, M.K., 1996, Summer movements and habitat use

by Colorado River cutthroat trout (Oncorhynchus clarki

pleuriticus) in small, montane streams: Canadian Journal of

Fisheries and Aquatic Sciences, v. 53, no. 6, p. 1403–1408.

22 Evolutionary and Ecological Connectivity in Washington, Idaho, and British Columbia

Appendix 1. Summary and Update on Connectivity for Bull Trout (Salvelinus

confluentus) in the Pend Oreille River since Dunham and Others (2014)

The dynamic historical and contemporary processes

and features within Lake Pend Oreille and the Pend Oreille

River have likely inuenced evolutionary and ecological

connectivity for native coldwater shes in the system. Of the

native shes present within Lake Pend Oreille and the Pend

Oreille River, bull trout (Salvelinus conuentus) is likely the

most sensitive to changes wrought by humans on the system,

including potential hydrologic changes associated with a

warming climate (Wenger and others, 2011; Isaak and oth-

ers, 2015). Prior to contemporary human inuences on the

system, bull trout likely moved widely throughout the Clark

Fork River, Lake Pend Oreille, and the Pend Oreille River.

Although upstream passage was almost certainly blocked at Z

Canyon and Metaline Falls on the lower Pend Oreille River,

downstream movement of bull trout likely contributed to

populations below these barriers (DuPont and others, 2007;

Dunham and others, 2014).

Genetic evidence indicates this is particularly important

for downstream populations of bull trout in the Salmo River

(Dunham and others, 2014). In fact, human-assisted movement

upstream of these barriers could pose threats to downstream

populations of bull trout, and would not be consistent with the

natural, historical pattern of movement and gene ow in the

system. Although no tributaries to the Pend Oreille River from

the Priest River downstream to the Salmo River are known

to support self-reproducing populations of bull trout, recent

modeling of a potential reintroduction suggest that certain

tributaries (for example Sullivan Creek and Sullivan Lake)

could potentially support local populations if a reintroduction

was implemented (Benjamin and others, 2019; Mims and oth-

ers, 2019). Both of these studies pointed to the importance of

maintaining downstream passage into the Pend Oreille River,

as well as maintaining connectivity within tributaries where

spawning and early rearing of bull trout can be supported.

The case of the Pend Oreille River contrasts with the

major inow to Lake Pend Oreille, the Clark Fork River.

In the Clark Fork River, upstream connectivity has been a

management priority. In that system, bull trout arriving at the

base of Cabinet Gorge Dam upstream of Lake Pend Oreille

are transported to upstream populations if they are genetically

identied as originating from upstream (Neraas and Spruell,

2001; Epifanio and others, 2003; DeHaan and others, 2011).

This program has been eective in connecting individuals

to their natal streams in the absence of their ability to natu-

rally migrate upstream (DeHaan and Bernall, 2013). Similar

success has been reported for other migratory salmonids (for

example, Lusardi and Moyle, 2017).

Existing evidence for the Clark Fork and Pend Oreille

Rivers, as well as smaller tributaries (Spruell and others,

1999) to Lake Pend Oreille, suggests that Lake Pend Oreille

acts as a major source of bull trout moving in and out of these

systems. Evidence also supports a similar dynamic for Priest

Lake and Priest River, the largest tributary to the Pend Oreille

River upstream of the historical upstream passage barriers

of Z Canyon and Metaline Falls. Notably, the movement of

bull trout throughout the system inuences patterns of genetic

connectivity and potentially allows migratory bull trout to

exploit spatial and seasonal variability in prey availability

and availability of refuge from environmental extremes. It is

noteworthy that the current angling record (19 kilograms [kg])

for bull trout was taken from Lake Pend Oreille in 1949. This

record was established as the system was beginning to experi-

ence signicant changes from introductions of a range of spe-

cies intended to support sport sheries, including kokanee (O.

nerka), rainbow trout (O. mykiss), lake trout (S. namaycush),

and Mysid shrimp (Mysis spp.) as forage (Vidergar, 2000).

These species introductions have dramatically altered food

webs within Lake Pend Oreille, and lake trout also prey on

bull trout (Corsi and others, 2019; Dux and others, 2019).

Despite these challenges to bull trout, Lake Pend Oreille still

supports some of the most robust populations of the species

within the Columbia Headwaters Recovery Unit recognized

by the U.S. Fish and Wildlife Service (U.S. Fish and Wildlife

Service, 2015).

In summary, it appears that Lake Pend Oreille, and to a

lesser extent Priest Lake, serve as core habitat for aduivial

bull trout that move in and out of these lakes to areas upstream

in the Clark Fork River and smaller tributaries, or down-

stream through the outlet of the Pend Oreille River, extend-

ing to the Salmo River, and possibly farther during historical

times (Dunham and others, 2014). Connectivity for bull trout

related to these systems, as well as patterns of connectivity

within them, have shaped patterns of genetic variability with

likely consequences for migratory bull trout to express diverse

behaviors and exploit the wide range of conditions available in

the system (for example, Benjamin and others, 2020).

For information about the research in this report, contact

Director, Forest and Rangeland Ecosystem Science Center

777 NW 9th Street, Suite 400

Corvallis, OR 97330

h ttps://www .usgs.gov/ centers/ forest- and- rangeland- ecosystem-

science- center

Manuscript approved on September 15, 2022

Publishing support provided by the U.S. Geological Survey

Science Publishing Network, Tacoma Publishing Service Center

Dunham and others—Evolutionary and Ecological Connectivity in Washington, Idaho, and British Columbia—OFR 2022–1084

ISSN 2331-1258 (online)

https://doi.org/ 10.3133/ ofr20221084