NOAA Technical Memorandum NMFS-AFSC-165


Stock Composition, Run Timing, and 

Movement Patterns of Chinook Salmon 

Returning to the Yukon River Basin in 

2004 

by 

J. H. Eiler, T. R. Spencer, J. J. Pella, and M. M. Masuda 

U.S. DEPARTMENT OF COMMERCE 

National Oceanic and Atmospheric Administration


National Marine Fisheries Service


Alaska Fisheries Science Center


September 2006 
NOAA Technical Memorandum NMFS 

The National Marine Fisheries Service's Alaska Fisheries Science Center 

uses the NOAA Technical Memorandum series to issue informal scientific and 

technical publications when complete formal review and editorial processing 

are not appropriate or feasible. Documents within this series reflect sound 

professional work and may be referenced in the formal scientific and technical 

literature. 

The NMFS-AFSC Technical Memorandum series of the Alaska Fisheries 

Science Center continues the NMFS-F/NWC series established in 1970 by the 

Northwest Fisheries Center. The NMFS-NWFSC series is currently used by 

the Northwest Fisheries Science Center. 

This document should be cited as follows: 

Eiler, J. H., T. R. Spencer, J. J. Pella, and M. M. Masuda. 2006. Stock 

composition, run timing, and movement patterns of Chinook salmon 

returning to the Yukon River Basin in 2004 U.S. Dep. Commer., NOAA 

Tech. Memo. NMFS-AFSC-165, 107 p. 

Reference in this document to trade names does not imply endorsement by 

the National Marine Fisheries Service, NOAA. 
NOAA Technical Memorandum NMFS-AFSC-165


Stock Composition, Run Timing, and 

Movement Patterns of Chinook Salmon 

Returning to the Yukon River Basin in 

2004 

by

 J. H. Eiler1, T. R. Spencer2, J. J. Pella1, and M. M. Masuda1 

1

Auke Bay Laboratory


Alaska Fisheries Science Center


National Marine Fisheries Service


National Oceanic and Atmospheric Administration


11305 Glacier Highway


Juneau, AK 99801


www.afsc.noaa.gov


2Alaska Department of Fish and Game


333 Raspberry Road,


Anchorage, AK 99518


U.S. DEPARTMENT OF COMMERCE 

Carlos M. Gutierrez, Secretary 

National Oceanic and Atmospheric Administration 

Vice Admiral Conrad C. Lautenbacher, Jr., U.S. Navy (ret.), Under Secretary and Administrator 

National Marine Fisheries Service 

William T. Hogarth, Assistant Administrator for Fisheries 

September 2006 
This document is available to the public through: 

National Technical Information Service 

U.S. Department of Commerce 

5285 Port Royal Road 

Springfield, VA 22161 

www.ntis.gov 
Notice to Users of this Document 

This document is being made available in .PDF format for the convenience of users; however, the 

accuracy and correctness of the document can only be certified as was presented in the original hard 

copy format. 

iii 

ABSTRACT 

A radio telemetry study was conducted on Yukon River Chinook salmon (Oncorhynchus 

tshawytscha) during 2004 to provide information on stock composition and run timing, migration 

patterns, and locations of important spawning areas. A total of 995 fish were radio tagged in the 

lower Yukon River near the village of Russian Mission. After tagging, most (958, 96.3%) fish 

resumed upriver movements, with 329 fish harvested in fisheries and 629 fish tracked to upriver 

areas using remote tracking stations and aerial surveys. Stock composition estimates were 

developed for the 2004 return based on the distribution of daily releases of radio-tagged fish 

weighted by daily measures of abundance and adjusted for fish harvested in fisheries. The 

Chinook salmon run was composed primarily of Tanana River (24.4%) and upper basin (55.2%) 

stocks. Canadian-origin fish comprised a substantial proportion of the return (47.5%), with most 

traveling to reaches of the Yukon River (46.2%) and only small numbers to the Porcupine River 

(1.3%). Yukon River fish in Canada returned to large headwater tributaries including the 

Stewart, Pelly, Big Salmon, and Teslin rivers (27.3%), small tributaries associated with the main 

river (8.2%), and reaches of the Yukon River main stem (10.7%). Chandalar and Sheenjek River 

fish (2.9%) were the principle U.S. stocks in the upper basin. Tanana River fish were 

predominantly Chena, Salcha, and Goodpaster River stocks (17.9%), with small populations 

located in other tributaries. Middle basin fish traveling to the Koyukuk, Melozitna, Nowitna, and 

Tozitna rivers were a minor component of the run (5.5%). Stocks returning to lower basin 

tributaries (7.6%) were primarily Bonasila, Anvik, and Nulato River fish (7.1%). The two major 

stock groups, Canadian Yukon River and Tanana River fish, exhibited similar run timing with 
iv 

most fish passing through the lower river in mid-June, although several distinct pulses were also 

observed in early June and late June-early July. In Canada, upper headwater stocks displayed a 

later and more protracted run timing. Lower basin stocks consisted primarily of late run fish, 

although other stocks, particularly Canadian Yukon River fish, were also present during this 

period. Movement rates for radio-tagged fish averaged 51.8 km/day. Middle and upper basin 

stocks averaged 46.4 km/day and 55.1 km/day, respectively. However, these stocks exhibited 

comparable movement rates in reaches of the Yukon River main stem, while slower swimming 

speeds were recorded as the fish approached their natal streams. Movement rates for lower basin 

stocks were substantially less, averaging from 34.6 km/day, possibly due to the shorter distances 

traveled to reach their spawning areas. 
v 

CONTENTS

 Page

Abstract.......................................................................................................................................iii

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

Materials and Methods..................................................................................................................3

Fish Capture and Handling................................................................................................3

Tracking Procedures..........................................................................................................6

Stock Composition Estimates............................................................................................8

Migration Rates................................................................................................................16

Results..........................................................................................................................................16

Fish Capture and Tagging................................................................................................16

Fish Response to Tagging................................................................................................18

Fishery Recoveries..........................................................................................................19

Distribution of Radio-tagged Fish...................................................................................20

Stock Composition and Timing.......................................................................................22

Movement Patterns..........................................................................................................27

Discussion....................................................................................................................................29

Acknowledgments.......................................................................................................................41

Citations.......................................................................................................................................43

Tables...........................................................................................................................................47

Figures..........................................................................................................................................69

Appendices...................................................................................................................................89

INTRODUCTION 

Large numbers of Chinook salmon (Oncorhynchus tshawytscha) return to the Yukon 

River basin to spawn. These returns support important fisheries in both the United States and 

Canada and have been the focus of numerous discussions between the two countries over 

management and harvest allocations. Ultimately these discussions contributed to the passage of 

the Yukon River Salmon Agreement, which provides for cooperative management of salmon 

returns in the basin (Yukon River Salmon Act 2000). However, Yukon River Chinook salmon 

declined dramatically in recent years (Joint Technical Committee of the Yukon River 

U.S./Canada Panel 2002), a phenomenon observed in other major river systems in western 

Alaska, and information is needed to better understand and manage these returns, and to facilitate 

conservation efforts. 

The Yukon River basin drains a watershed of more than 855,000 km2. The main river 

alone flows for more than 3,000 km from its headwaters in Canada to the Bering Sea (Fig. 1). 

Several major tributaries flow into the Yukon River main stem, including the Koyukuk and 

Tanana rivers in the United States; the Stewart, White, Pelly, and Teslin rivers in Canada; and 

the Porcupine River, which transects both countries. Most reaches of the drainage consist of a 

primary river channel with occasional side channels and sloughs, although the Yukon River main 

stem is extensively braided between the villages of Rampart and Circle--an area commonly 

referred to as the Yukon Flats. Sections of the Canadian main stem and the White River are also 

extensively braided. Water visibility in many areas is extremely poor, particularly in the Yukon 

River main stem, due to turbidity from the upper reaches of the drainage. The basin is remote 

with limited access to many areas. 
2 

Salmon are a major source of food in many remote communities within the basin, and 

often it provides the primary source of income for local residents. Subsistence, commercial, and 

personal use fisheries occur throughout the drainage with most fishing effort concentrated near 

villages along the Yukon River main stem. Fish are also harvested in reaches of the Koyukuk, 

Tanana, Chandalar, Porcupine, Stewart, Pelly, and Teslin rivers. Limited sport fishing takes 

place in a number of clearwater tributaries within the basin. The fisheries are managed to 

maintain essential spawning escapements, support adequate subsistence harvests for local 

residents, and provide commercial and sport fishing opportunities when appropriate. Chinook 

salmon harvests from 1961 to 2003 averaged 134,100 fish in the United States and 12,100 fish in 

Canada, with catches ranging from 45,300 fish (2000) to 198,400 fish (1983) in the United 

States, and 2,600 fish (1969) to 22,800 fish (1980) in Canada (Joint Technical Committee of the 

Yukon River U.S./Canada Panel 2004). From 1961 to 1999, commercial fishing accounted for 

more than 76% of the U.S. harvest and 42% of the Canadian harvest. These fisheries have been 

severely restricted in recent years due to declining returns, resulting in harvests composed 

primarily of fish caught for subsistence. 

A basin-wide radio telemetry study was initiated in 2000 by the Alaska Department of 

Fish and Game (ADFG) and the National Marine Fisheries Service (NMFS). The primary 

objective of this study was to provide information on the run characteristics of Yukon River 

Chinook salmon returns, including stock composition and run timing, country of origin, 

migration patterns, and the location of important spawning areas. Information was also collected 

to evaluate other projects in the basin that assess run abundance. The study faced severe 

logistical challenges due to the large size and physical characteristics of the drainage. In 
3

addition, the sizeable runs of Chinook salmon returning to the basin to spawn required the 

tagging of large numbers of fish to obtain meaningful results. Chinook salmon reputedly travel 

in deep water during their spawning migration, further complicating efforts to monitor their 

movements. Work in 2000-2001 focused on the development of capture methods, improved 

telemetry equipment for tracking the fish, and the infrastructure necessary for a study of this size 

and scope. Distribution and movement data collected during this exploratory phase were used 

primarily to evaluate the response by Chinook salmon to the capture and handling procedures, 

and to provide preliminary information on migration patterns. Large-scale tagging and basinwide monitoring programs were conducted in 2002 and 2003, which provided new information 

on the stock composition, run timing, and movement patterns of Yukon River Chinook salmon. 

A third year of the basin-wide study was conducted in 2004 to address questions related to study 

findings and annual variation, particularly in relation to run characteristics during years with 

greater run abundance. 

MATERIALS AND METHODS

Fish Capture and Handling

Adult Chinook salmon returning to spawning areas in the Yukon River basin were 

captured with drift gill nets near the village of Russian Mission (Fig. 1). This site was selected 

because it 1) consisted of relatively narrow, unbraided sections of river, increasing the probability 

of capturing a representative sample, 2) was downriver of most known Chinook salmon 

spawning areas (i.e., only the Andreafsky River, located approximately 190 km downriver, was 
4

not included), and 3) was upriver of significant commercial and subsistence fisheries lower in the 

basin. Results from feasibility work in 2000-2001 (Spencer et al. 2003) and basin-wide 

programs in 2002 and 2003 (Eiler et al. 2004, 2006) indicated that sufficient numbers of Chinook 

salmon could be captured at this site. Local fishers were contracted to fish the site from early 

June to mid-July (Table 1), with project personnel handling the fish and collecting data. Two day 

shifts (0900-1700) and two night shifts (1800-0200) were fished throughout the tagging period. 

Fishing effort was divided between the lower and upper sections of the tagging area to minimize 

the recapture of tagged individuals by the other crew. 

The site was fished with drift gill nets that were constructed with No. 21 seine twine, had 

21.5 cm mesh size, and were 46 m long, 7.6 m deep, and hung at a 2:1 ratio. This configuration 

was effective in capturing Chinook salmon while minimizing chum salmon (O. keta) bycatch. 

Nets were monitored continually and fish were removed immediately after capture. The netting 

was cut to facilitate removal and minimize injuries. A dip net, constructed with soft, fine-mesh 

netting, was used to lift fish into the boat. A maximum of two fish were tagged per drift to 

minimize both handling time and potential sampling bias if stocks of fish were poorly mixed. 

Fish selected for tagging were placed in a neoprene-lined tagging cradle submerged in a trough of 

fresh water. A pump was used to circulate river water into the trough while fish were being 

processed. Anesthesia was not used during the tagging procedure. 

Fish were tagged with pulse-coded radio transmitters (Fig. 2) manufactured by Advanced 

Telemetry Systems (Isanti, Minnesota)

1

. The transmitters (which were 5.4 cm long, 2.0 cm in 

1

 Reference to trade names does not imply endorsement by the National Marine Fisheries 

Service, NOAA. 
5

diameter, had a 30-cm transmitting antenna, and weighed 20 g) were gently inserted through the 

mouth and into the stomach using a plastic tube 0.7 cm in diameter. Each transmitter emitted a 

unique signal (i.e., transmitters were placed on 11 discrete frequencies in the 150-151 MHz 

frequency range spaced a minimum of 20 kHz apart, with up to 100 distinct pulse codes per 

frequency), making it possible to identify each individual fish. Transmitters were also equipped 

with a motion sensor and activity monitor. The motion sensor, an integrated tilt switch sensitive 

to movement, inserted additional signal pulses distinct from the basic signal pattern each time the 

transmitter moved. The activity monitor altered the signal pattern to an inactive mode (Eiler 

1995) if the motion sensor was not triggered for 24 hours; the signal reverted to the original 

pattern if the motion sensor was activated. Transmitters had a minimum battery life of 90 days. 

Fish were marked externally with yellow spaghetti tags attached below the dorsal fin (Wydoski 

and Emery 1983). A subsample of fish was tagged with radio-archival tags, which recorded 

water depth and temperature every 3 minutes as well as transmit a signal. Fish with radioarchival tags were marked externally with pink spaghetti tags. 

Information on length (mid-eye to fork of tail), skin color (bright iridescent silver, dull 

silver, and blush--silver with reddish tinges), and condition of the fish was also recorded. Data 

on gender were not collected because of difficulties in distinguishing the sexes in the lower river 

due to the lack of distinct external characteristics (Eiler et al. 2004). A tissue sample was taken 

from the axillary process for genetic stock identification studies being conducted by ADFG, and 

scales were collected to provide age data. Fish were released back into the main river 

immediately after the tagging procedure was completed. Handling, from removal of the net from 

the water to release, took from 6 to 8 minutes depending on the number of fish tagged per drift. 
6 

Tracking Procedures 

Radio-tagged fish that moved upriver were tracked with remote tracking stations (Fig. 3) 

located at 40 sites throughout the basin (Table 2; Fig. 4). Sites selected were on important 

migration corridors and major tributaries of the drainage. When possible, the stations were 

placed on bluffs overlooking straight, narrow, single-channel sections of the river to maximize 

reception range and increase the probability of detecting fish moving past the site. Stations 

consisted of several integrated components, including a computer-controlled receiver developed 

by Advanced Telemetry Systems, and satellite uplink (Campbell Scientific, Logan, Utah). A 

self-contained power system--consisting of a bank of six 6-volt, sealed lead-acid batteries 

connected in series and parallel (12 V, 610 Ah) and charged by two 80-W solar panels--supplied 

power to the stations. Radio-tagged fish within reception range were identified and recorded by 

the stations. Information collected included the date and time tagged fish were present at the site, 

signal strength of the transmitter, and the orientation of the fish in relation to the station 

(i.e., upriver or downriver from the site). The information was summarized and recorded at 

10-minute intervals. Because of the isolated nature of the sites, the telemetry data collected, 

including information on station operations (e.g., voltage levels for the station components, and 

whether the reference transmitter at the site was properly recorded) were transmitted every hour 

to a geostationary operational environmental satellite (GOES) and relayed to a receiving station 

near Washington D.C. (Fig. 3). Information was accessed daily via the Internet and uploaded 

into a computer database for analysis (Eiler and Masters 2000). 
7 

Radio-tagged Chinook salmon that passed the first set of tracking stations (hereafter 

referred to as Paimiut, Fig. 4), located approximately 62 km upriver from Russian Mission, were 

considered to have resumed upriver movements. Stations were operated at sites on the Yukon 

River main stem, including Paimiut, Yukon-Anvik River confluence, Yukon-Yuki River 

confluence, Rampart Rapids, Circle, U.S.-Canada Border (hereafter referred to as Yukon 

Border), downriver from the Yukon-White River confluence, upriver from the Yukon-White 

River confluence, Selkirk, Yukon-Tatchun Creek confluence, Yukon-Teslin River confluence, 

and Hootalinqua. United States tributaries monitored by tracking stations included the Bonasila, 

Anvik, Innoko, Nulato, Koyukuk (including sites near the mouth, Gisasa River, Hogatza River 

and upper section of the main stem), Melozitna, Nowitna, Tozitna, Tanana (including sites near 

Manley, Nenana, Chena River, Salcha River, and upper section of the main stem), Chandalar, 

and Porcupine (including sites on the Sheenjek River, Black River, Porcupine-Coleen River 

confluence, and U.S.-Canada Border, hereafter referred to as the Porcupine Border) rivers. 

Tracking stations were also operated on Canadian tributaries including the Stewart (including 

sites near the mouth and above Fraser Falls), Pelly, Big Salmon, and Kluane rivers (Yukon River 

drainage), and Fishing Branch River (Porcupine River drainage). Pairs of stations were operated 

at locations with special significance, including Paimiut, lower Koyukuk River, lower Tanana 

River, Rampart Rapids, Yukon Border, and Porcupine Border, to avoid potential loss of data 

from unforseen events (e.g., technical problems with equipment, damage from bears and other 

causes). Fish tracked to terminal reaches of the drainage were classified as distinct spawning 

stocks. The status of fish that remained in non-terminal areas, such as sections of the Yukon 

River main stem, was less certain because these fish could represent local spawners or fish 
8

destined for spawning areas farther upriver. Many non-terminal areas were turbid and hard to 

access, making verification of spawning activity difficult. 

Aerial surveys were conducted in selected reaches of the drainage to locate radio-tagged 

fish that traveled to areas between station sites and upriver of stations on terminal tributaries. 

Fish were tracked from fixed-wing aircraft and helicopters equipped with 4-element Yagi 

receiving antennas mounted on both sides of the aircraft and oriented forward. Tracking 

receivers contained an integrated global positioning system (GPS) receiver to assist in identifying 

and recording locations. Areas surveyed in the United States included the Yukon River main 

stem from Russian Mission to the Yukon Border, and reaches of the Anvik, Innoko, Nulato, 

Koyukuk, Nowitna, Tanana, Chandalar, Sheenjek, Black, Charley, Kandik, Nation, and Tatonduk 

rivers. In Canada, surveys were flown along reaches of the Yukon River main stem, and in 

numerous mainstem tributaries including Chandindu River, Klondike River, White River, 

Stewart River, Pelly River, Tatchun Creek, Nordenskiold River, Little Salmon River, Big Salmon 

River, and Teslin River. Surveys were also flown in Canadian reaches of the Porcupine River, 

including Old Crow, Whitestone, Miner, and Fishing Branch rivers. 

Stock Composition Estimation 

Returning Chinook salmon passing through the lower Yukon River are composed of a 

number of distinct stocks. These stocks travel to spawning areas throughout the basin and differ 

in entry timing and magnitude. A portion of these fish are intercepted in Yukon River fisheries 

before reaching their spawning areas. Stock composition at the tagging site is assessed by 
9 

capturing, radio tagging, and tracking individuals to their final destination. The upriver 

distribution of the fish tagged per day is weighted by daily measures of abundance at the tagging 

site and adjusted to account for tagged fish removed in upriver fisheries. This approach provides 

an estimate of the relative abundance of stocks passing through the lower river on both a daily 

and seasonal basis. 

The number of radio-tagged fish released on day t at the capture sites in the lower Yukon 

′ River are denoted as R = (R K RT . 1, , ) Radio-tagged fish are assumed to represent a random 

sample from the mixture of Chinook salmon stocks passing the tagging site each day. A total of 

46 separate stocks (Fig. 5) are considered in the analysis, and the unknown stock proportions of 

′ this mixture on day t are denoted by θt ( ,1, ,θt, = θ . t K 46 ) Final destinations include 42 terminal 

spawning areas and 4 non-terminal areas (i.e., U.S. reaches of the Yukon River main stem 

potentially used for spawning or as a corridor for fish traveling farther upriver; these areas 

potentially include mainstem tributaries not surveyed during the study). The numbers of radio-

′ tagged fish escaping to spawning areas from releases on day t are denoted as rt (rt 1,, r = , K t , 46 ) . A

total of 15 fisheries that harvest fish upriver from the tagging site were defined during the study 

(Table 3; Fig. 5); 14 of these fisheries (Fisheries B through O, numerically indexed in the 

estimation formulas as Fisheries 1 through 14, respectively) presumably alter the initial stock 

composition because together they disproportionally intercept stocks traveling to upriver 

spawning areas; that is, stocks traveling farther upriver are exposed to more fisheries than lower 

river stocks. The first of the 15 fisheries, Fishery A, is lowest in the study area, below all 
10

spawning areas, and therefore is assumed to exploit the stocks equally. Hereafter, radio-tagged 

fish caught in Fishery A are subtracted from the initial releases to provide a corrected set of daily 

′ releases, namely, R = (R K R ) ; fish caught in Fishery A are not considered further in this 1, , T 

analysis. Tagged fish destined for any spawning stock, such as stock s, are exposed to a 

downriver subset of the 14 fisheries, and the collection of these fishery indices is denoted by Fs . 

′ Catches in the 14 fisheries from releases of day t are denoted by C = (c , , K c ) and the t t ,1 t ,14 

corresponding exploitation rates, or fractions of tagged fish entering and removed by each 

′ fishery, are denoted by φt = (φt,1, , K φt,14 ) . The set of stock indices of upriver stocks passing 

through fishery f will be denoted by S f , = 1,K,14 . f

Observed counts of radio-tagged fish among spawning areas and catches were modeled so 

the effects of unequal harvests among the stocks would not bias estimates of the stock 

composition at the tagging site. The naive estimate of stock composition, equal to the observed 

distribution of radio-tagged fish escaping to spawning areas, was rejected out-of-hand because of 

its inherent bias. A probability model was developed using the schematic for the migration 

routes, fisheries, and spawning areas in the Yukon River basin (Fig. 5). Counts of fish in the 

escapements and catches from a daily release are assumed to have the multinomial distribution, 
11

( ,K, r c ,K, c ) = ⎜

⎛ Rt ! ⎟⎞ 46 ( ⋅ )

rt s, 14 (μ )

ct f , 

pr t ,1 t , 46 , t ,1 t ,14 ∏ θ ψ ∏ ⎜ 46 14 ⎟ s=1 t s, t . s f =1 t f ,

∏r !∏ct f ! ⎝ s=1 t s, f =1 , ⎠ (1) 

46 14

∑θ ψ + μ = 1, t = 1,K,T, t s, t , s ∑ t , f s=1 f =1 

where ψ t s, = ∏(1 − φt, j ) is the probability that a fish destined for stock s escapes downriver 

j F∈ s

fisheries, μt f , = ∏ (1 − φt, j ) ⋅ φt f , ⋅

∈

∑ θt, s is the probability that a tagged fish released on day t is 

j H∈ f s S f 

caught in fishery f, and H f is the set of indices for fisheries downstream from fishery f. The 

Lagrange function for the unknowns given the recoveries and catches from day t, which is the 

likelihood function with an added term to constrain the daily probabilities to equal 1, is 

, ) κ 46 rt s log ( ⋅ t s, ) 14 log L r( , c ; θ φt t = + ∑ , θts , ψ + ∑ c t, f log (μt, f ) + s=1 f =1 

46 14 

γ

⎛

∑θ ψ t s + ∑ μ , −1

⎞ , 

(2) 

⎝

⎜ t s, , t f ⎠

⎟ s=1 f =1 

where 6 is a constant and ( is a constant called the Lagrange multiplier. The Lagrange function 

is maximized by values of θt s, given in Table 4 with known values of φt f , given by 

⎛ ⎞ = ⎜ Rt − ∑ rt, s − ∑ c φ t j , ⎟ , f = 1,K,14 , (3) t f , ct f , ⎝ s G∈ f j H∈ f ⎠

where Gf is the set of indices for stocks downstream from fishery f . 
12 

The numbers of radio-tagged fish released on any particular day, however, are quite 

limited for the estimation of the unknown daily fractions destined for the various stocks. 

Therefore, releases over longer periods than a single day are considered. The daily fractions 

destined for the various stocks are expected to be more similar on days nearby than they are on 

days distant. Therefore, this estimation for the days of release, t = 1, 2, ..., T, is accomplished by 

use of a moving window of width equal to 2d + 1 days (d = 0, 1, ..., dmax) centered on the day t, 

d namely, [t - d, t + d]. The moving-window estimate on day t, θ

$() , is computed from the t s, 

( ) d ( ) d d d t d () () +

equations of Table 4, substitutingRt for Rt, rt s, for rt,s and ct f , for ct,f . Here Rt = ∑ Rj is the 

j t = − d 

total number of radio-tagged fish released during days included in the window about t, 

t d + ( ) rt s, 

d = ∑ ri s, is the total number of radio-tagged fish migrating to stock s from releases of days i t = − d 

t d + ( ) included in the window about t, and ct f , 

d = ∑ c j f , . j t = − d 

The estimated fractions at day t destined for the stocks are the fractions of total releases 

during the window centered on day t that would have ultimately tracked to the various stocks had 

the fisheries not intercepted them. At the beginning and the end of the tagging interval, [1, T], 

the window includes days for which no releases were made. These days represent periods of few 

migrants and have little effect on estimates. The recoveries from these days are set to zero in the 

moving-window estimator. For example, if window width is 2d + 1 = 3, the moving-window 

estimator of migration composition at day 1 includes no recoveries of day 0, and r0,s is set to zero 

for s = 1, 2, ..., S. At day T, the window includes no recoveries of day T + 1, so rT+1,s is set to 
13

zero for s = 1, 2, ..., S. In effect, the window width is reduced at the beginning and end of the 

tagging interval during which minimal numbers of migrants passed the tagging site. We chose 

d = 3, or a window width of 1 week, as reasonable. 

Although the estimates of daily stock composition are of interest, they do not reflect the 

changes in magnitude of daily returns to the Yukon River. The unknown daily numbers of 

T

fish passing the capture site are denoted as E1, E2,ÿ, ET, and their season total is E⋅ = ∑ Ei . i=1 

The daily fractions of the total return passing the capture site are denoted as 

π i = i / ,. EE i = 1 ,K, T . (4)

Daily fractions of the total season return of Chinook salmon to the Yukon River that pass the 

capture site are estimated from the catch rates of gill nets used to capture fish for tagging. Gill 

nets are expected to capture fish in proportion to daily effort. Daily catches, K XT X , are 1, ,

assumed to be Poisson random variables with expected values, 

λt = λh Et = (λ ) E

E = λ ht

π , t = 1,K, T t , (5) E h . t

t 

0 t 

. 

where λ0 = λE . is a constant proportional to the total return, and ht is the number of units of effort 

fished on day t. Maximum likelihood estimates of the daily migration fractions, π = ( , π1 K,π T )′ , 
14

can be shown to be the time series of normalized catch per effort,

T 

π$t = Yt ∑Yj = ( Xt ht′

⎞

⎠ h ⎟ , t = 1,K,T . (6) t ) ⎛⎝

⎜ ∑

T 

Xt′ j=1 t′ =1 

The maximum likelihood estimate of is λ

$

0 = ∑

T

X ht λ . 0 t t=1 

Daily fractions of the total season return to the Yukon River basin that are destined for 

any particular stock equal the products of the stock’s daily proportions, θt s, , and the 

corresponding daily fractions of the total season return passing the tagging site, namely, 

ω = π θ . These stock-specific daily fractions of the total return are estimated by the daily t s, t t, s 

products of the estimates of stock composition (Table 4) and the daily migration fractions, π$t , t 

= 1, ÿ,T, from Equation 6,

ω$ π t θ , s = ,K, ; t = 1 K, T . (7) t s, = $ $

t, s 1 46 , 

Finally, the estimated fraction of the total season return to the Yukon River basin that belonged 

to any stock s equals the sum, 
15

T 

. α$ ω$ , s = 1,K,46 (8) s t,s t=1 

=

* * * 

1 , 2 T 

and equal to X = λ π h t , , . These random catches were used to compute $ $ t 0 t $t , = 12 K, T

* * * * corresponding bootstrap catch rates YY , ,K, , Y and daily migration fractions, π , t = 1,K,T. 1 2 T t 

Next, independent daily multinomial samples of radio-tagged fish, either migrating to the 

* * K * * * possible stocks, r r, , , r , or caught in the various fisheries, c K , from the daily known 1,, c t, 1 t,2 t, S t, t,14 

∑

To evaluate the sampling variation in estimates, a parametric bootstrap was performed. 

First, random bootstrap samples of daily gillnet catches, X X ,K, X , were drawn from Poisson 

* distributions with expected values of the X determined from the maximum likelihood estimates t

numbers released, R , were drawn with probabilities equal to the original maximum likelihood t

estimates, 

⎞

⎟

⎟

⎟

⎠

⎛

⎜

⎜

⎜ ! 

Rt ! S $( ) d ( ) d rt s, 14 

$() c d

(θ ψ )

* 

(μ )

* 

t s, t s. t f , 1 f 1

* * * * t f ,

p rt, K, rt S , ct,1 ( , ,K, c 1 , t ,14 ) = S 14 ∏ ⋅ ∏ * * . (9) ∏ ! ∏ s= = r c t s, t, f ⎝ s=1 f =1

Bootstrap samples of tagged fish in catches and escapements were used to compute the 

$( )* corresponding bootstrap estimates for stock proportions, such as θt

d , just as with the original 

counts of tagged fish. Finally, bootstrap estimates for stock proportions were weighted by the 

bootstrap daily migration fractions. The next bootstrap sampling began with another draw of the 
16

daily gillnet catches and tagged numbers migrating to the possible stocks or caught in the 

fisheries, followed by computation of the bootstrap estimates of daily catch rates, daily migration 

fractions, daily stock compositions, and weighted stock compositions. 

Migration Rates 

Migration rates for radio-tagged Chinook salmon were calculated by comparing the date 

and time that the fish moved upriver past the Paimiut tracking stations with information 

(i.e., date and time of passage, and the distance traveled upriver from Paimiut) from the station 

farthest upriver that last recorded the fish. Movements by the fish between the tagging site and 

Paimiut were not included in these calculations to avoid incorporating tagging-induced behavior 

that would bias the results, although these data were used as a relative measure to evaluate how 

the fish responded to the capture and tagging procedures. Migration rates between tracking 

stations were also calculated to determine movement patterns within different reaches of the 

basin. 

RESULTS

Fish Capture and Tagging

Drift gill nets were an effective method for capturing large numbers of adult Chinook 

salmon in suitable condition for tagging. Fishing commenced early in the run and continued 

until the end of the run when catch rates were low. A total of 583 hours were fished at Russian 
17

Mission from 3 June to 19 July, and 2,107 Chinook salmon were captured (Table 1). Catch per 

unit effort (CPUE) data from the upper section of the tagging area was used as a daily measure of 

abundance during the study, and indicated that several distinct pulses of fish moved through the 

lower river, with the peak of the run passing Russian Mission during 13-20 June (Fig. 6). 

Of the 2,107 Chinook salmon captured, 995 fish were radio tagged, ranging from 319 fish 

in Week 25 (13-19 June) to 5 fish in Week 30 (18-19 July) (Table 1). Six-year-old fish were the 

dominant age group in the tagged sample (68.4%). The remaining fish were primarily 5-yearolds (18.1%), with smaller percentages of 4-year-olds (8.3%), 7-year-olds (5.0%), 8-year-olds 

(0.1%), and 3-year-olds (0.1%). Radio-tagged fish averaged 825 mm in length, ranging from 

395 mm to 1,060 mm. Fish were primarily bright, iridescent silver in color during the first 

4 weeks of tagging, ranging from the entire sample in Week 23 to 59.7% of the sample in Week 

26 (Table 5). This color phase was less prominent near the end of the run, ranging from 38.2% 

of the sample in Week 27 to 16.2% of the sample in Weeks 29-30. Increasing numbers of fish 

exhibited a dull silver coloration later in the run, with 70.3% of the sample displaying this color 

phase in Weeks 29-30. Fish with pre-spawning colors, ranging from blush (silver with reddish 

tinges) to a pronounced reddish coloration, were first observed in Week 26 (1.0% of the sample) 

and became more prevalent later in the run (13.5% of the sample in Weeks 29-30) (Table 5). 

Fish color in the lower river was also influenced by the final destination of the fish. Most 

Chinook salmon traveling to Canadian reaches of the basin were iridescent silver when passing 

the Russian Mission tagging site (85.6% of the Yukon River fish and 90.9% of the Porcupine 

River fish). Only a small percentage were dull silver, and no Canadian fish displayed prespawning coloration (Fig. 7). Iridescent silver color was also prominent for U.S. stocks traveling 
18

to upper reaches of the basin, ranging from 49.2% of the Tanana River fish to 72.7% of the 

Porcupine River fish. These stocks also exhibited the dull silver color (ranging from 27.3% of 

the Porcupine River fish to 50.8% of the Tanana River fish). Most fish traveling to lower and 

middle reaches of the basin were dull silver in color, including 53.6% of the Koyukuk River fish, 

78.6% of the middle basin tributary fish, and 83.1% of the lower basin tributary fish. Fish 

destined for lower basin tributaries (8.5%) and the Koyukuk River (10.7%) also displayed prespawning coloration (Fig. 7). 

Fish Response to Tagging 

Chinook salmon responded well to the capture and tagging procedure, with most fish 

resuming upriver movements after release (Table 6; Fig. 8). A total of 958 (96.3%) radio-tagged 

fish passed Paimiut, and traveled to upriver reaches (626, 62.9%) or were caught in upriver 

fisheries (332, 33.4%). Thirty-seven (3.7%) fish did not resume upriver movements, and either 

regurgitated their tags or died due to handling, predation, or undocumented encounters with 

fisheries. Radio-tagged fish averaged 1.7 days after release to pass Paimiut, traveling an average 

of 31.0 km/day (Table 7). Comparable rates were observed throughout the tagging period (i.e., 

weekly averages), ranging from 27.8 km/day (Week 28) to 37.0 km/day (Week 24). Movement 

rates between the tagging area and Paimiut did not vary substantially by fish age or length, 

although average rates were faster for fish released in the lower section of the tagging area and 

that had farther to travel prior to reaching Paimiut (Table 8). 
19 

Fishery Recoveries 

A total of 332 radio-tagged fish were harvested in fisheries throughout the Yukon River 

basin (Table 6). Most (276, 83.1%) of these fish were caught in U.S. fisheries (Table 9; Fig. 8). 

Harvest rates differed between regions, with 44 (13.4%) fish caught from Russian Mission to 

Holy Cross, 88 (26.5%) fish caught from Anvik to Ruby, and 108 (32.5%) fish caught in the 

upper Yukon River from the Yukon-Tanana River confluence to Eagle (Table 9; Appendix A). 

With the exception of the fishery near Eagle, these fish were likely from both U.S. and Canadian 

stocks. Fish caught near Eagle were assumed to be destined for spawning areas in Canada. 

Thirty-three (9.9%) fish were harvested in the Tanana River, with most (23, 6.9%) caught near 

Nenana and Fairbanks, including 8 fish caught in sport fisheries in the Chena and Salcha rivers 

(Appendix A). Three (0.9%) fish were caught near villages on the Koyukuk River. Aerial 

surveys, flown over villages along the Tanana River and Yukon River main stem, documented 

that 84 of the 332 (25.3%) fish harvested were not reported by fishers. 

Fifty-six (16.9%) fish were harvested in Canadian reaches of the basin (Table 9). Fiftythree (16.0%) of these fish were destined for Yukon River spawning areas, with most of the 

recoveries from Dawson, Stewart River, Carmacks, Pelly River, and Teslin River (Appendix A). 

Three (0.9%) fish were caught in the Porcupine River fishery near the village of Old Crow. 
20 

Distribution of Radio-Tagged Fish 

Radio-tagged Chinook salmon traveled to areas throughout the Yukon River basin 

(Fig. 9). A total of 719 fish were tracked to upriver reaches or recovered in terminal fisheries. 

Fish traveling to sections of the Yukon River upstream of the Yukon-Tanana River confluence 

(hereafter referred to as the upper basin) comprised the largest component of the sample, with 

346 (48.1%) fish returning to the upper Yukon and Porcupine rivers (Table 10; Fig. 10). A 

substantial number of these fish traveled to Canadian reaches, including 284 (39.5%) Yukon 

River fish and 8 (1.1%) Porcupine River fish (Fig. 10). Most (195, 27.1%) Canadian fish were 

tracked to tributaries of the Yukon River main stem (Table 10), including the Stewart (26, 3.6%), 

Pelly (48, 6.7%), Big Salmon (25, 3.5%), and Teslin (49, 6.8%) rivers (Appendices B, C). Small 

numbers of fish were also located in the Chandindu (1, 0.1%), Klondike (12, 1.7%), Sixtymile 

(1, 0.1), White (12, 1.7%), Nordenskiold (2, 0.3%), and Little Salmon rivers (3, 0.4%), and in 

headwater areas upriver of the Yukon-Teslin River confluence (13, 1.8%) including 5 (0.7%) fish 

in the Takhini River (Appendix B). Fifty-seven (7.9%) fish remained in reaches of the Yukon 

River main stem or traveled to associated tributaries not monitored by tracking stations or 

surveyed by aircraft (Table 10); most (42, 5.8%) of these fish were located upriver of Selkirk 

(Appendix B). Canadian fish in the Porcupine River were tracked to headwater tributaries 

including the Old Crow (1, 0.1%) and Miner (3, 0.4%) rivers (Appendices B, D). One (0.1%) 

fish that passed the Porcupine Border, and was not harvested in the Old Crow fishery, was not 

located during aerial surveys flights, suggesting that Chinook salmon may utilize other spawning 

areas in the Porcupine River drainage. 
21 

Fifty-four (7.5%) fish were tracked to the U.S. portion of the upper basin, including 

43 (6.0%) Yukon River fish and 11 (1.5%) Porcupine River fish (Table 10). Twenty (2.8%) fish 

in the upper Yukon River were tracked to tributaries (Fig. 10; Appendix E). Most of these fish 

returned to the Chandalar River (14, 2.0%), although small numbers were located in Beaver 

Creek (2, 0.3%), and the Hodzana (1, 0.1%), Charley (1, 0.1%), and Nation (2, 0.3%) rivers 

(Appendices B, E). Twenty-three (3.2%) fish remained in reaches of the Yukon River main stem 

or traveled to associated tributaries not monitored by tracking stations or surveyed by aircraft 

(Fig. 10), including 20 (2.8%) fish downriver from Circle and 3 (0.4%) fish upriver from Circle. 

Porcupine River fish returned to the Sheenjek River (6, 0.8%), Coleen River (4, 0.6%), and upper 

reaches of the Black River (1, 0.1%)(Appendices B, E). 

Tanana River fish comprised a major component of the sample, with 195 (27.1%) fish 

returning to areas within the Tanana River drainage (Table 9; Fig. 8). Most (144, 20.0%) Tanana 

River fish traveled to tributaries in the upper reaches of the drainage, including the Chena 

(30, 4.2%), Salcha (68, 9.4%), and Goodpaster (28, 3.9%) rivers (Appendices B, F). Fish were 

also located in reaches of the Kantishna River (9, 1.3%), Tolovana River (5, 0.7%), Nenana 

River (1, 0.1%), and Clear Creek (3, 0.4%). Twenty-eight (3.9%) fish remained in reaches of the 

Tanana River main stem or traveled to associated tributaries not surveyed, including 8 (1.1%) 

fish upriver from Manley, 9 (1.3%) fish upriver from Nenana, and 11 (1.5%) fish upriver from 

the Tanana-Salcha River confluence (Appendix B). 

Seventy-one (9.9%) fish traveled to tributaries in the lower basin (Table 10; Fig. 10). 

Anvik (40, 5.6%), Bonasila (14, 2.0%), and Nulato River (11, 1.5%) fish were most prevalent, 

with smaller numbers of fish traveling to the Innoko River (5, 0.7%) and Kako Creek (1, 0.1%) 
22

(Appendices B, G). Fourteen (2.0%) fish returned to tributaries associated with the middle 

Yukon River (Table 10; Fig. 10), including the Melozitna (3, 0.4%), Nowitna (3, 0.4%), and 

Tozitna (8, 1.1%) rivers (Appendices B, H). Twenty-eight (3.9%) fish returned to the Koyukuk 

River (Table 10; Fig. 10), including 8 (1.1%) Gisasa River fish and 5 (0.7%) fish that traveled to 

middle drainage tributaries. Twelve (1.7%) Koyukuk River fish were tracked to upper reaches of 

the drainage, including the South Fork River (5, 0.7%) and Henshaw Creek (2, 0.3%). The 

5 (0.7%) remaining fish were not located during aerial surveys of the upper headwaters, 

suggesting that Chinook salmon may utilize other spawning areas within the Koyukuk River 

drainage. Sixty-five (9.0%) fish were last recorded in non-terminal reaches of the Yukon River 

main stem, including 49 (6.8%) fish in the lower basin and 16 (2.2%) fish in the middle Yukon 

River (Table 10; Fig. 10). Some of these non-terminal fish may have traveled to mainstem 

tributaries not surveyed during the study. 

Stock Composition and Timing 

Stock composition estimates were derived for the Chinook salmon return based on the 

distribution of radio-tagged fish, adjusted to account for both the harvest of tagged individuals in 

upriver fisheries and changes in run abundance at the Russian Mission tagging site. The Chinook 

run was composed primarily of Tanana River (24.4%) and upper basin (55.2%) stocks (Fig. 11). 

Canadian fish comprised a substantial proportion of the return (47.5%), with the majority 

(46.2%) traveling to reaches of the Yukon River and only a small percentage (1.3%) traveling to 

the Porcupine River (Table 11; Fig. 11). Most Canadian fish (35.4%) returned to tributaries of 
23

the Yukon River main stem, primarily the Stewart (4.7%), Pelly (8.4%), Big Salmon (4.9%), and 

Teslin (9.2%) rivers (Fig. 12). Smaller stocks included the Klondike River (2.2%), White River 

(2.1%), Tatchun Creek (0.5%), Nordenskiold River (0.4%), Little Salmon River (0.5%), and 

reaches upriver of the Yukon-Teslin River confluence (2.5%)(Appendix I). Canadian fish also 

remained in reaches of the Yukon River main stem and small associated tributaries (10.8%), 

including 0.9% downriver from Dawson (i.e., the lower Canadian Yukon River, including fish in 

the Chandindu River), 4.9% between Dawson and the Yukon-Tatchun Creek confluence (i.e., the 

mid-Canadian Yukon River), and 5.0% upriver of the Yukon-Tatchun Creek confluence (i.e., the 

upper Canadian Yukon River). Most (0.7%) Porcupine River fish traveled to the Miner River, 

although small numbers also returned to the Old Crow River and other small tributaries within 

the drainage. 

Chinook salmon stocks returning to U.S. reaches comprised a substantial proportion 

(52.5%) of the run, including 24.4% Tanana River fish and 7.7% upper basin fish (Table 11; 

Fig. 11). Fish returning to the Chena (4.1%), Salcha (10.1%), and Goodpaster (3.7%) rivers were 

the dominant Tanana River stocks (Table 11; Fig. 13). Tanana River fish also returned to the 

Kantishna River (1.3%), Tolovana River (0.6%), and other small tributaries (Appendix I). A 

proportion of the return (4.6%) also remained in reaches of the Tanana River main stem or 

traveled to small associated tributaries not surveyed during the study, including fish in the lower 

(1.1%), middle (1.3%), and upper (2.2) drainage. Upper basin fish traveled to U.S. reaches in 

both the Yukon (5.9%) and Porcupine (1.8%) rivers (Fig. 11). Spawning populations were 

documented in Yukon River tributaries including the Chandalar River (1.9%), Charley River 

(0.2%), Nation River (0.4%), and reaches of Beaver Creek and the Hodzana River (0.4%) 
24

(Fig. 13; Appendix I). Fish also remained in reaches of the Yukon River main stem or traveled 

to small associated tributaries not surveyed during the study (3.0%), including 2.7% downriver 

from Circle and 0.3% between Circle and Eagle. Most Porcupine River fish returned to the 

Sheenjek (1.0%) and Coleen (0.7) rivers (Fig. 13; Appendix I), although small numbers also 

spawned in upper reaches of the Black River (0.1%). 

Chinook salmon also spawned in reaches of the lower basin and middle Yukon River. A 

total of 7.6% of the run returned to tributaries in the lower basin (Table 11; Fig. 11), including 

the Innoko (0.5%), Bonasila (1.5%), Anvik (4.3%), and Nulato (1.3%) rivers (Fig. 13; 

Appendix I). Middle Yukon River tributaries comprised 1.9% of the return, with most fish 

traveling to the Tozitna River (1.1%), and smaller numbers spawning in the Melozitna (0.4%) 

and Nowitna (0.4%) rivers. Chinook salmon returned to the Koyukuk River (3.6%), with fish 

traveling to the Gisasa River (0.9%), and tributaries in the middle (0.8%) and upper (1.9%) 

reaches of the drainage (Table 11; Appendix I). Fish also remained in reaches of the Yukon 

River main stem downstream of the Yukon-Tanana River confluence or traveled to small 

associated tributaries not surveyed during the study (7.3%), with most (5.6%) of these in the 

lower basin (Table 11; Fig. 11).

 Most Chinook salmon stocks passing through the lower Yukon River exhibited similar 

run timing patterns. Tanana River and Canadian Yukon River stocks were present throughout 

the return, but were most abundant from middle to late June (Fig. 14). Several distinct pulses 

were also observed during early June and late June-early July. A similar pattern was observed 

for Porcupine River fish and stocks returning to tributaries in U.S. reaches of the upper Yukon 

River. Koyukuk and middle Yukon River tributary fish were present in small numbers 
25

throughout the return; however, they too were most abundant in mid-June. Fish allocated to nonterminal areas in the Yukon River exhibited a similar pattern. Although present throughout the 

run, fish traveling to lower basin tributaries were more abundant during late June and July 

(Fig. 14). 

Run timing differences were also observed within regions of the basin. Canadian stocks 

returning to tributaries in the upper Yukon River, including the Klondike, Stewart, White, and 

Big Salmon rivers, were primarily early and middle run fish, while the timing for Teslin River 

fish was more protracted (Fig. 15). Fish remaining in middle and upper reaches of the Canadian 

main stem also exhibited a protracted and somewhat later run timing, while headwater fish 

traveling to areas upriver of Hootalinqua were middle run fish. Porcupine River stocks were 

present during the early and middle run, although the timing of fish returning to U.S. reaches was 

more protracted than that observed for Canadian stocks (Figs. 15, 16). Black River fish were 

present in early June, while Sheenjek River and Coleen River fish were observed from mid-June 

to early July. Stocks returning to U.S. reaches of the upper Yukon River were primarily early run 

fish, with Hodzana River, Beaver Creek, Charley River, and Kandik River fish passing through 

the lower river during the first and second week of June. However, the Chandalar River return 

was more protracted, extending into mid-July (Fig. 16). In the Tanana River drainage, 

Kantishna, Chena, Salcha, and Goodpaster River fish were primarily early and middle run fish, 

although Chena River and Salcha River stocks were still present in mid-July. Koyukuk River 

fish were present throughout the return; however, upper headwater stocks were observed during 

the early and late run, compared to Gisasa River fish, which were present primarily during the 
26

middle run. The timing for Bonasila, Anvik, and Nulato River fish, the dominant stocks in the 

lower basin, was later than that exhibited by middle and upper basin fish (Fig. 16). 

Differences were also observed in the daily composition of stocks moving through the 

lower river (Fig. 17; Appendix J). Canadian stocks were predominant throughout the run, 

comprising an average of 40.4% of the fish passing the Russian Mission tagging site per day. 

These stocks were somewhat more prevalent during early and mid-June, with daily composition 

averaging 51.7% and 29.0% during the first and last half of the run, respectively. Although less 

abundant than Canadian stocks, Tanana River fish (19.5% daily average) exhibited a similar 

pattern with daily averages of 27.9% and 11.2% during the first and last half of the run, 

respectively. Fish returning to tributaries in U.S. reaches of the upper basin also tended to enter 

the river during the early and middle run (Fig. 17). In contrast, fish returning to tributaries in the 

lower and middle basin were more prevalent later in the run. Although relatively minor in terms 

of overall abundance (Table 11; Fig. 14), these stocks comprised a substantial portion of the late 

run with daily composition averaging 35.2%, compared to 6.2% during the first half of the return. 

A similar pattern was observed for fish remaining in non-terminal areas, with low daily averages 

throughout most of the run, and higher levels in July. 

Stock composition estimates were based on the assumption that fish allocated to 

designated stock groups, including those in non-terminal areas, represented spawning 

populations. Non-terminal stock groups that included fish in-transit to areas farther upriver 

(i.e., fish that were harvested in fisheries but not reported, or died due to disease, injuries, or 

predation prior to reaching their final destination) would bias composition estimates, and 

underestimate the contribution of upriver stocks. To address this concern, stock composition 
27

estimates were recalculated with fish remaining in non-terminal areas categorized as in-transit 

and treated as fishery recoveries. Composition estimates for most stocks were similar using the 

two approaches (Fig. 18). The greatest difference was observed for Yukon River fish in Canada, 

with estimates ranging from 46.2% of the return when non-terminal fish were categorized as 

spawning populations to 53.4% of the return when these fish were considered in-transit to 

spawning areas farther upriver. Similarly, stock composition estimates for Tanana River fish 

increased from 24.4% when non-terminal fish were categorized as spawning populations to 

26.3% of the return when these fish were considered in-transit to spawning areas farther upriver. 

Movement Patterns 

Radio-tagged fish traveled an average of 51.8 km/day; however, regional and stock 

differences were observed. Upper basin fish traveled an average of 55.1 km/day. Fish returning 

to the Yukon River in Canada averaged 54.8 km/day, ranging from 50.5 km/day for fish traveling 

to reaches of the Yukon River main stem to 61.9 km/day for Klondike River fish (Table 12). 

Similar rates were observed for stocks traveling to U.S. reaches in the upper Yukon River, with 

averages of 54.6 km/day for tributary fish and 55.0 km/day for fish remaining in non-terminal 

areas (i.e., reaches of the main stem or associated tributaries not monitored during the study). 

Porcupine River fish generally traveled faster than upper Yukon River fish, averaging 

58.5 km/day for U.S. stocks and 60.0 km/day for Canadian stocks (Table 12); fish traveling to the 

Coleen and Old Crow rivers displayed movement rates of more than 63 km/day (Appendix E). 

Tanana River fish exhibited slower migration rates (44.8 km/day), with rates for Chena, Salcha, 
28

and Goodpaster River fish ranging from 43.0 km/day to 45.6 km/day. Fish remaining in the 

Tanana River main stem and associated tributaries not surveyed averaged 43.8 km/day, while fish 

returning to middle drainage tributaries averaged 53.2 km/day (Table 12). Tributary fish 

returning to the middle Yukon River, including the Melozitna, Nowitna, and Tozitna rivers, 

averaged 49.3 km/day; a similar rate (46.3 km/day) was observed for non-terminal fish within 

this section of the basin. In the Koyukuk River drainage, Gisasa River fish averaged 

34.0 km/day, compared to 68.6 km/day for fish traveling to the upper headwaters of the drainage 

(Table 12). Chinook salmon returning to reaches in the lower basin moved substantially slower 

than middle and upper basin stocks. Fish located in lower river tributaries averaged 34.6 km/day, 

ranging from 31.2 km/day for Anvik River fish to 43.1 km/day for Nulato River fish (Table 12; 

Appendix K). 

Migration rates recorded for Chena, Salcha, and Goodpaster River fish were substantially 

slower than most middle and upper basin stocks. However, the tracking stations used to monitor 

these tributaries were located relatively close to spawning areas, and the lower rates likely reflect 

slower swimming speeds as the fish approached their natal streams. When comparing swimming 

rates based on movements from Paimiut to the lower Tanana River, these stocks averaged 

between 55.7 km/day and 56.8 km/day (Table 13), movement rates comparable to upper basin 

fish. A similar phenomenon was observed for other stocks, including fish traveling to the Gisasa 

and Nulato rivers. In contrast, tracking stations on tributaries associated directly with the Yukon 

River main stem, such as the Chandalar, Sheenjek, Stewart, Pelly, Big Salmon, and Teslin rivers, 

were typically placed near the confluence, and often located a substantial distance from spawning 

areas. The average movement rates for fish passing these stations were comparable to rates 
29

observed lower in the basin (Table 13; Fig. 19). For example, Stewart River fish averaged 

57.7 km/day between Paimiut and the Stewart River station (located approximately 20 km from 

the Yukon-Stewart River confluence), compared to 58.7 km/day between Paimiut and the Yukon 

Border stations. Similarly, Chandalar River fish averaged 53.7 km/day between the Paimiut and 

Chandalar tracking station (located approximately 10 km from the Yukon-Chandalar River 

confluence), compared to 57.8 km/day between Paimiut and Rampart Rapids stations. 

DISCUSSION 

Management of Yukon River Chinook salmon is complicated by recent declines in run 

abundance and the international nature of their spawning distribution, which makes it necessary 

to address harvest allocation issues in both the United States and Canada. Radio telemetry has 

been used effectively to provide information on Pacific salmon (Burger et al. 1985, Eiler et al. 

1992, Bendock and Alexandersdottir 1993); however, the logistical problems associated with 

capturing, tagging, and tracking large numbers of highly mobile fish in the Yukon River basin are 

unique and severe. Feasibility work in 2000-2001 and large-scale studies in 2002 (Eiler et al. 

2004) and 2003 (Eiler et al. 2006), demonstrated that basin-wide radio telemetry programs on 

Yukon River Chinook salmon are feasible, and provide useful information on run characteristics 

and fish movements. The 2004 basin-wide study was conducted to collect additional data on 

Chinook salmon returns and address questions related to annual variation. Drift gill nets were 

effective in capturing adequate numbers of fish in the lower Yukon River in suitable condition 

for tagging, with approximately 1,000 fish tagged and released. The system of satellite-linked 
30

tracking stations, combined with aerial surveys in selected reaches of the basin, was able to 

collect and summarize telemetry data in-season, making it possible to monitor fish movements 

effectively and prioritize field activities.

 A primary assumption in tagging studies is that the capture and tagging procedures do 

not adversely affect the fish (i.e., tagged fish behave the same as untagged fish), or that any effect 

is limited in severity and duration, and ultimately has negligible impact. Chinook salmon tagged 

during this study appeared to recover promptly from the procedures used, with most (96.3%) 

resuming upriver movements after release. Similar results were observed during basin-wide 

studies on Yukon River Chinook salmon in 2002 and 2003 when more than 97% of the tagged 

fish traveled to upriver areas or were recovered in upriver fisheries (Eiler et al. 2004, 2006). The 

percentage of Chinook salmon not moving upriver after release during the 2002-2004 studies 

(<4%) is lower than reported for many radio-tagging studies (Burger et al. 1985, Milligan et al. 

1985, Johnson et al. 1992). 

Fish adversely affected by tagging would likely show reduced vitality as they moved 

upriver, particularly those individuals traveling long distances. However, the movement rates 

observed during this study did not exhibit this pattern, with upper basin fish traveling an average 

of 55 km/day throughout their upriver migration. A similar pattern was observed during 2002 and 

2003, with upper basin fish averaging 54 km/day (Eiler et al. 2004, 2006). Untagged Chinook 

salmon in the Yukon River are thought to travel between 48 km/day and 56 km/day based on 

estimated arrival times of distinct pulses of fish at village fisheries along the drainage (T. Vania, 

Fishery Management Biologist, ADFG, 333 Raspberry Road, Anchorage, AK 99518. Pers. 

commun). These estimates are comparable to migration rates observed for radio-tagged fish 
31

during this study. Information from previous tagging studies also suggests that handling had a 

negligible effect. Chinook salmon radio tagged at Rampart Rapids in 1998 traveled an average 

of 53 km/day (Joint Technical Committee of the Yukon River U.S./Canada Panel 1998), rates 

comparable to those for upper basin fish tagged during the 2004 study, even though these 

individuals traveled substantially greater distances after being tagged. By comparison, radiotagged Chinook salmon in the Columbia River traveled between 43 km/day and 65 km/day 

through dam reservoirs in the lower basin (i.e., slow-moving water with minimal current), and 

about half that rate in free-flowing rivers in the upper basin (Bjornn et al. 2000). 

A common response observed in tagging studies is for fish to hold in localized areas or 

drift with the current immediately after release prior to resuming normal patterns of movement. 

The initial response exhibited by fish tagged at Russian Mission (i.e., movement rates between 

the tagging site and the Paimiut tracking stations) indicates that the fish experienced a delay in 

upriver movements or slower swimming speeds initially after release. However, movement rates 

increased substantially after passing Paimiut (Table 12), suggesting that any adverse effect was 

limited. Differences in response rates observed for fish released in the lower and upper sections 

of the tagging area also support this interpretation, with faster movement rates recorded for fish 

released in the lower section. These fish traveled greater distances prior to passing Paimiut 

(Table 8), and the faster rates suggest that they had recovered from the initial handling affects 

and were swimming in a more typical manner as they moved farther upriver. Migration rates 

calculated for Chinook salmon (Table 12; Appendix K) were based on the movements of radiotagged fish upriver from Paimiut to avoid including tagging-induced behavior that would bias the 

results and not reflect typical movements of untagged fish. 
32

Regional differences were observed in migration rates of Chinook salmon stocks in 2004. 

Upper basin fish generally exhibited faster upriver movements, traveling an average of 

55 km/day. These movements are noteworthy considering the distances traveled by the fish, with 

the uppermost Canadian headwater stocks traveling more than 2,300 km prior to reaching their 

spawning areas. Lower basin fish exhibited substantially slower rates (34.6 km/day) than middle 

and upper basin fish. The slower movements may be associated with the shorter distances these 

fish are traveling, and may reflect reduced swimming speeds as the fish approach their natal 

streams. This phenomenon was documented for fish leaving the Yukon River main stem and 

traveling up the Tanana River, with movement rates dropping substantially as the fish 

approached their spawning tributaries. Migration rates exhibited by stocks were remarkably 

similar while moving through reaches of the Yukon River main stem even for fish returning to 

reaches of the lower basin. Although Nulato River fish traveled an average of 43.1 km/day 

between Paimiut and the Nulato River, migration rates between Paimiut and the Yukon-Anvik 

River confluence averaged 57.6 km/day (Table 13), a rate comparable to the rate for upper basin 

fish. Milligan et al. (1985) reported migration rates of 36 km/day for Chinook salmon radio 

tagged above the Yukon Border in 1982-1983 compared to 54.8 km/day observed for Canadian 

stocks during this study. The slower speed reported in the 1985 report may relate to a variety of 

factors including differences in water levels, handling and tagging procedures, or tracking 

methods. 

Chinook salmon returning to the Yukon River in 2004 were primarily Tanana River 

(24.4%) and upper basin stock (55.2%), comprising approximately 80% of the return. Similar 

patterns were observed during the 2002 and 2003 studies (Eiler et al. 2004, 2006). Canadian 
33

stocks were the dominant component in the upper basin during 2004, with most (29.3% of the 

return) traveling to large headwater tributaries, including the Stewart, White, Pelly, Big Salmon, 

and Teslin rivers. Smaller tributaries also supported spawning population (6.1% of the return). 

Substantial numbers of fish remained in Canadian reaches of the Yukon River main stem (10.7% 

of the return), although turbid conditions made it impossible to verify spawning activity. 

Chinook salmon spawning has been previously reported in these areas (Milligan et al. 1985), 

suggesting that these fish may represent spawning populations. However, local fishers in the 

Carmacks area have been reluctant to report harvests of radio-tagged fish, which could bias this 

estimate. Small numbers of fish also returned to Canadian reaches in the Porcupine River (1.3% 

of the return). 

United States Chinook salmon stocks were also an important component of the 2004 

return. Similar to the Canadian component, these fish included a combination of major and 

minor stocks. Chinook salmon returning to the Tanana River were predominantly Chena, Salcha, 

and Goodpaster River fish (17.9% of the return), although minor spawning populations were also 

documented in the Kantishna, Tolovana, and Nenana rivers, as well as in small tributaries 

associated with the Tanana River main stem. Salcha River fish were the most abundant 

individual stock within the basin (10.1% of the return). Although spawning has been reported 

for Chinook salmon in U.S. reaches of the upper basin, it was generally thought to be 

insignificant. However, these fish comprised 4.7% of the 2004 return, with Chandalar River and 

Sheenjek River fish as the primary stocks. Radio-tagged fish were also located in small 

mainstem tributaries, and remained in non-terminal areas or traveled to associated tributaries not 

surveyed during the study. 
34 

Relatively few radio-tagged fish returned to the middle Yukon River compared to other 

regions of the basin. The small middle river tributaries (i.e., Melozitna, Nowitna, and Tozitna 

rivers) comprised only 1.9% of the return combined. Although the Koyukuk River drains a large 

watershed, the percentage of fish returning to this tributary was also relatively low (3.6%). 

Chinook salmon traveled to lower basin tributaries, comprising 7.6% of the return. These stocks 

were composed primarily of Anvik, Bonasila, and Nulato River fish (7.1%), with small numbers 

of fish traveling to other areas. 

Chinook salmon returns passing through the lower Yukon River are composed of a 

number of distinct stocks. These stocks travel to spawning areas throughout the basin, and differ 

in timing and magnitude. The two major stock groups, Canadian Yukon River and Tanana River 

fish, exhibited similar run timing patterns, with most fish passing through the lower river during 

the peak of the run in mid-June with several distinct pulses during the early and late run, while 

lower basin stocks were composed primarily of late-run fish (Fig. 14). Differences in run timing 

were also observed within regions. For example, fish returning to the Teslin River and middleupper Yukon River main stem displayed a more protracted run timing that extended later into the 

run than other Canadian stocks (Fig. 15). Porcupine River fish traveling to U.S. reaches 

exhibited a more protracted run timing than Canadian stocks within this drainage (Figs. 15, 16). 

However, in general, most stocks were not temporally distinct, making it difficult to separate 

stocks based on run timing.

 Daily stock composition estimates for Chinook salmon further illustrated the 

predominance of Canadian Yukon River and Tanana River stocks. Canadian fish were the most 

abundant stock group per day moving through the lower river during the early and middle run 
35

(Fig. 17). Although less abundant, Tanana River fish displayed a similar pattern during this 

period. Fish destined for the Porcupine River and U.S. tributaries in the upper basin were present 

from early June to mid-July, although these stocks were a minor component throughout the run. 

Lower basin fish were prevalent later in the run, although the Canadian contribution 

was comparable during this period until mid-July when almost all fish were from lower basin 

tributaries. 

Country of origin estimates for 2004 indicate that Canadian stocks comprised 

approximately 48% of the Yukon River Chinook salmon return, with most of these fish traveling 

to the Canadian portion of the Yukon River (46.2%) and a relatively minor component to the 

Porcupine River (1.3%). Comparable estimates were obtained from previous basin-wide 

telemetry studies on Yukon River Chinook salmon with Canadian contributions ranging from 

53% in 2002 (Eiler et al. 2004) to 55% in 2003 (Eiler et al. 2006). The increased contribution of 

U.S. stocks in 2004 was due primarily to stronger returns of Tanana River fish. 

Country of origin estimates based on telemetry information during 2002-2004 are also 

consistent with other estimates reported for the drainage. Scale pattern analysis from the early 

1980s suggested that Canadian-origin fish comprised between 42% and 54% of the return 

(Anon 1985). Milligan et al. (1985) estimated that approximately 50% of the Chinook salmon 

return was made up of Canadian stocks, based on catch and escapement information, ranging 

from 44% to 51% in years with low returns and 48% to 57% during years of greater abundance. 

Genetic stock identification estimates of the Canadian contribution from 1987 to 1990 averaged 

53% of the return, ranging from 42% to 61% (Wilmot et al. 1992). However, not all stocks were 

included in the genetic baseline used for this analysis, including U.S. stocks in the upper basin, 
36

notably fish returning to the Chandalar and Sheenjek rivers, which could bias the results. 

Similarities were also observed between the run timing of the significant stock groups reported 

by Wilmot et al. (1992) and those observed during the 2004 study. Although differences existed, 

particularly when comparing results from the different years of genetic sampling, the general 

agreement between the two methods suggests that the estimates derived from the 2004 telemetry 

study are credible. 

Questions exist about the status of fish remaining in non-terminal areas (i.e., U.S. reaches 

of the Yukon River main stem). Non-terminal areas not only serve as migration corridors for fish 

traveling farther upriver, but potentially support spawning populations. However, many nonterminal areas are turbid and hard to access, making verification of spawning activity difficult. 

Ancillary observations in the lower and upper basin indicate that Chinook salmon spawners 

travel to tributary streams not surveyed during this study (Johnson and Weiss 2006), although 

these populations are thought to be minor. Radio-tagged fish were located during a partial survey 

of the upper Hodzana River, a small tributary of the Yukon River main stem located near the 

village of Beaver. It is not known if other fish last located in non-terminal reaches of the Yukon 

River main stem ultimately traveled to this river or other nearby tributaries. Mainstem spawning 

has been reported for Chinook salmon in the Canadian portion of the Yukon River (Milligan et 

al. 1985), although the extent has not been determined due to turbid conditions. It is not know if 

suitable salmon spawning habitat exists in U.S. reaches, although evidence of non-salmonid 

spawning has been reported (Brown 2000). 

An alternative explanation is that non-terminal fish represent tagged individuals that have 

died while in-transit to upriver spawning areas due to handling, predation, disease, or injuries 
37

from encounters with fishing gear. These fish may also have been harvested in fisheries but not 

reported. Reluctance by fishers to provide information on tag recoveries is often a problem as 

demonstrated by the substantial number (25.3%) of unreported recoveries in 2004. Similar 

problems were encountered during the 2002 and 2003 telemetry studies. There is also ancillary 

information that tags were periodically thrown back into the river or left on the shore, further 

limiting our ability to determine fish status. Incidents of radio-tagged fish regurgitating their tags 

when captured and removed from fishing gear have also been reported by fishers within the 

basin. Although it is difficult to substantiate or to rule out these factors, tracking data collected 

during the study does provide some insights. The distribution pattern of non-terminal fish was 

clumped in the lower basin between Holy Cross and Nulato, and in the upper Yukon River 

between Tanana and Fort Yukon--both areas with intensive fishing--while relatively few nonterminal fish were observed in the middle Yukon River between Galena and Tanana, or in the 

upper Yukon River between Circle and the Yukon Border. Many non-terminal fish were last 

located in outlying areas near villages or in the general vicinity of fish camps (i.e., areas where 

their status could not be readily verified), suggesting some interaction with local fisheries (e.g., 

unreported harvests or mortalities associated with injuries from encounters with fishing gear) 

may have occurred. 

Adverse impacts from handling are always a concern in tagging studies. Numerous 

studies have been conducted to assess tagging effects on fish, and anomalous behavior has 

periodically been reported (McCleave and Stred 1975, Mellas and Haynes 1985, Brown and 

Eiler 2000). However, the large percentage of fish that moved upriver (Table 6), the relatively 
38

rapid, sustained movement rates observed (Table 12), and the presence of non-terminal fish in 

the upper basin, suggests that adverse impacts from tagging were minimal.

 Since the late 1990s, the fish parasite Ichthyophonus has been reported in Yukon River 

Chinook salmon (Kocan and Hershberger 1999). Recent sampling studies in the basin have 

suggested that infected fish destined for the Tanana River and the upper basin may succumb to 

the parasite while in-transit to upriver spawning areas. Although some of the non-terminal fish 

may be infected individuals that died prior to reaching spawning areas farther upriver, the 

distribution pattern observed during the study does not fully fit this explanation. Although 

Ichthyophonus-related mortality would potentially explain the presence of non-terminal fish 

between Rampart and Fort Yukon, it does not address the concentration of non-terminal fish in 

the lower basin or the general absence of non-terminal fish in the middle basin; however, it has 

been shown that the severity of the infection increases as the fish move farther upriver 

(Kocan and Hershberger 1999). Another explanation is that non-terminal fish represent a 

combination of factors, including fish that spawned in associated areas not monitored during the 

study, or that died while in-transit to spawning areas farther upriver because of undocumented 

encounters with fisheries, disease, or handling mortality. 

Stock composition estimates for the 2004 Chinook salmon return were based on the 

assumption that fish in designated stock groups, including those in non-terminal areas, represent 

spawning populations. Stock groups that include fish that died while in-transit to spawning areas 

would bias these estimates and under-represent the contribution of fish traveling farther upriver, 

particularly for upper basin stocks, and to a lesser extent, Tanana River fish. However, estimates 

that assume all non-terminal fish were in-transit would potentially overestimate upper river 
39

stocks. Composition estimates derived for 2004 based on both assumptions were similar, 

suggesting minimal bias related to the treatment of non-terminal fish. In regard to country of 

origin, the estimates suggest that Canadian Yukon River stocks comprised from 46.2% to 53.4% 

of the Yukon River return; these proportions are consistent with other estimates reported for the 

basin.

 The basin-wide telemetry study in 2004 was successful in obtaining additional 

information on the stock composition, run timing, spawning distribution, and movement patterns 

of Yukon River Chinook salmon. Adequate numbers of fish were captured, tagged, and tracked 

upriver, making it possible to identify and compare the principal components of the return. The 

system of satellite-linked tracking stations, in combination with the automated database and 

mapping program, was able to collect and summarize telemetry data in-season, making it 

possible to prioritize field activities and address management issues within the basin. Stock 

composition and run timing estimates derived from these data provide a detailed look at the 

temporal and spatial dynamics of the 2004 return, information needed to better address 

conservation and harvest allocation issues within the basin. The data collected will also be useful 

in addressing other research needs, such as expanding the genetic stock identification baseline by 

identifying spawning populations not currently included, evaluating abundance estimates from 

other assessment projects, and providing movement and behavioral data to address other 

concerns, such as the impacts of Ichthyophonus on Chinook salmon returns. Results from this 

study, combined with telemetry data from 2002 and 2003, will also be useful in addressing 

questions related to annual variation, particularly in relation to run characteristics during years 

with different levels of abundance. 

41 

ACKNOWLEDGMENTS 

Primary funding for this study was provided by the U.S.-Canada Yukon River Treaty 

Implementation Fund, Arctic-Yukon-Kuskokwim Sustainable Salmon Initiative Fund, ADFG, 

and NMFS. Support was also provided by the U.S. Fish and Wildlife Service (USFWS), U.S. 

Bureau of Land Management, Department of Fisheries and Oceans Canada (DFO), Bering Sea 

Fisherman’s Association (BSFA), Yukon River Drainage Fisheries Association (YRDFA), 

National Park Service, U.S./Canada Yukon River Grant No. 03NMF4380185, and the 

Restoration and Enhancement Fund of the Yukon River Panel. We thank J. Baumer, 

J. Browning, K. DeYong, R. Driscoll, P. Duffy, M. Eisenman, Y. Kakizaki, K. Maledy, 

C. Mason, and B. Stephanoff (ADFG), P. Stephanoff (YRDFA), and T. Ferguson and B. Fost 

(University of Tennessee) for their assistance with field work. Local assistance provided by 

A. Alexie, P. Alexie, S. Askoak, J. Changsak, J. Duffy, L. Evan, R. Housler, R. James, 

P. Kozevnikoff, P. Larson, G. Nicholi, M. Nickoli, W. Pitka, V. Sergie, A. Stephanoff, and 

B. Stephanoff was invaluable to the success of the tagging effort in Russian Mission. Pilots 

S. Pfeifer and R. Swisher (Quicksilver Air), D. Lorring (Wrights Air Service), D. Miller 

(Caribou Air), K. Scholz (Fireweed Helicopters), D. Washington (Capitol Helicopters), and 

J. Webster (Webster Flying Service) provided aerial support for tracking surveys and logistical 

operations. We thank B. Mercer (B. Mercer and Associates), E. Kahler, T. Lingnau, and 

P. Salomone (ADFG), C. Osborne (Haldane Environmental Services), J. Duncan and G. Couture 

(Yukon Salmon Committee), I. Anderton (North Yukon Renewable Resources Council), and 

R. Brown (USFWS) for their assistance with aerial surveys. C. Osborne also assisted with the 
42

installation and maintenance of tracking stations in Canada. B. Busher, K. Boeck, P. Costello, A. 

Estes, E. Kahler, and K. Nyberg (ADFG), B. Berkbigler and G. Beyersdorf (USFWS), 

P. Milligan and M. Jarvis (DFO), and K. Gillis and C. Stark (BSFA) helped facilitate tag 

recoveries. Essential technical support for the telemetry equipment used during the study was 

provided by N. Christensen, L. Kuechle, A. Mayer, and R. Reichle (Advanced Telemetry 

Systems). We are particularly grateful to M. Masters (NMFS) for developing and maintaining 

the database and GIS mapping program used during the study, and providing critical support in 

processing the data. The report was critically reviewed by J. Hilsinger (ADFG), and J. Helle and 

R. Wilmot (NMFS). We thank G. Sandone (ADFG) and J. Helle (NMFS) for administrative 

support during the study. 
43 

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47 

Table 1. -- Weekly and total numbers of Chinook salmon captured with drift gill nets and radio 

 tagged in the lower Yukon River near the village of Russian Mission during 2004. 

Capture Week Dates Fish Captured Fish Tagged 

23 3-5 June 19 8 

24 6-12 June 290 160 

25 13-19 June 784 319 

26 20-26 June 414 196 

27 27 June - 3 July 391 199 

28 4-10 July 150 76 

29 11-17 July 54 32 

30 18-19 July 5 5 

Total 3 June - 19 July 2,107 995 
48 

Table 2. -- Location of remote tracking stations used to monitor the movements of radio-tagged

 Chinook salmon in the Yukon River during 2004. Distances from Paimiut, located 

 62 km upriver from the village of Russian Mission, and the previous downriver 

station are indicated. 

Distance Traveled (km)

Region Tracking Station From Paimiut From Previous Station1

Lower Yukon River Basin2 Paimiut3 -- --

Bonasila 112 112 

Anvik 142 142 

Innoko 261 261 

Yukon-Anvik4 134 134 

Nulato 396 262 

Koyukuk River Lower Koyukuk3,4 448 314 

Gisasa 522 74 

Hogatza 895 447 

Upper Koyukuk 934 486 

Mid-Yukon River Basin5 Yukon-Yuki4 519 385 

Melozitna 566 47 

Nowitna 709 190 

Tozitna 732 213 

Tanana River Lower Tanana3,4 835 316 

Nenana4 1,012 177 

Lower Chena 1,086 76 

Chena 1,150 62 

Salcha 1,158 146 
49 

Table 2. -- Continued. 

Distance Traveled (km) 

Region Tracking Station From Paimiut From Previous Station1 

Salcha 1,158 146 

Upper Tanana 1,204 192 

Upper Yukon River (U.S.)6 Rampart Rapids3,4 811 292 

Chandalar 1,231 420 

Circle4 1,401 590 

Upper Yukon River (Can) Yukon Border3,4 1,704 303 

Stewart 1,901 197 

Fraser Falls 2,207 306 

Below Yukon-White4 1,898 197 

Above Yukon-White4 1,904 6 

Kluane 2,216 312 

Selkirk4 2,028 124 

Pelly 2,065 37 

Tatchun4 2,136 108 

Big Salmon 2,320 184 

Yukon-Teslin4 2,335 199 

Hootalinqua 2,354 19 

Porcupine River (U.S.) Black 1,405 594 

Sheenjek 1,313 502 

Lower Porcupine4 1,450 137 
50 

Table 2. -- Continued. 

Region 

Porcupine River (Can) 

Porcupine River (Can) 

Tracking Station 

Porcupine Border3,4 

Fishing Branch 

Distance Traveled (km) 

From Paimiut From Previous Station1 

1,573 123 

2,062 489 

1

 Station located immediately downriver on migration route traveled by fish.

2

 Section of the Yukon River from Russian Mission to the Yukon-Koyukuk River confluence.

3

 Two tracking stations located at site. 4

 Located on primary migration route, and used to calculate rates of fish traveling farther upriver. 5

 Section of the Yukon River from Galena to the Yukon-Tanana River confluence.

6

 Section of the Yukon River from Yukon-Tanana River confluence to Eagle.
51 

Table 3. -- Fishery designations used to model stock composition estimates of Yukon River

 Chinook salmon. The corresponding fishing districts managed by the Alaska

 Department of Fish and Game (ADFG) and Department of Fisheries and Oceans

 Canada are noted. 

Fishery Area Covered by Fishery Fishing District 

A Yukon River from Marshall to Holy Cross ADFG District 3 

B Yukon River from Anvik to Nulato ADFG District 4a 

C Yukon River from Nulato to Ruby ADFG District 4b, 4c 

D Yukon River from Ruby to below Tanana ADFG District 4b, 4c 

E Lower Tanana River ADFG District 6a 

F Tanana River near Nenana ADFG District 6b 

G Tanana River near Fairbanks ADFG District 6c 

H Yukon River from Tanana to Beaver ADFG District 5a, 5b, 5c, 5d 

I Yukon River near Fort Yukon ADFG District 5d 

J Lower Porcupine River ADFG District 5d 

K Porcupine River near Old Crow Porcupine River Fishery, Canada 

L Yukon River near Circle ADFG District 5d 

M Yukon River near Eagle ADFG District 5d 

M Yukon River from the Border to Dawson Yukon River Fishery, Canada 

N Yukon River from Dawson to Carmacks Yukon River Fishery, Canada 

O Yukon River from Carmacks to Whitehorse Yukon River Fishery, Canada 
52 

Table 4. -- Yukon River Chinook salmon stocks and the maximum likelihood estimates of their

 proportions among fish passing the Russian Mission tagging site. 

Stock Name Stock Index Estimates of Stock Proportions 

Innoko 1 θ

$

t ,1 = r R t ,1 t = rt ,1 Dt ,1 

Bonasila 2 θ

$

t ,2 = r R t ,2 t = rt ,2 Dt ,1 

Anvik 3 θ

$

t ,3 = r R t ,3 t = r D t ,3 t ,1 

⎡ ⎤ ⎢ Ct

⎢

⎢⎣

⎥

⎥

⎥⎦

θ

$

t ,4 = rt Rt − , 1, 4 3

θ

$ 1− ∑ t s, Lower Yukon 4 s=1 

= r D t ,4 t ,2 

Nulato 5 θ

$

t ,5 = r D t ,5 t ,2 

θ

$ Lower Koyukuk 6 t ,6 = r D t ,6 t ,2 

θ

$ Gisasa 7 t ,7 = r D t ,7 t ,2 

θ

$ Middle Koyukuk 8 t ,8 = r D t ,8 t ,2 

θ

$ Hogatza 9 t ,9 = r D t ,9 t ,2 
53 

Table 4. -- Continued. 

Stock Name Stock Index Estimates of Stock Proportions 

Upper Koyukuk 10 θ

$

t ,10 = rt ,10 Dt ,2 

θ

$ = rt ,11 

t ,11 C C

Rt − 3 

t ,1 − 10 t ,2 

Melozitna 11 1− ∑ θ

$

t s, 1− ∑ θ

$

t s, s=1 s=1 

= rt ,11 Dt ,3 

Nowitna 12 θ

$

t ,12 = rt ,12 Dt ,3 

t ,13 θ$ = r t ,13 C C C

R − t ,1 

− t , 2 

− t ,3 

3 10 12 t

1− ∑θ$ 1− ∑θ$ 1− ∑θ$ t s, t s, t s, s=1 s=1 s=1 

Tozitna 13 ⎡ C ⎤

= r ⎢D − t ,3 

t ,13 t , 3 12 ⎥ = r D t ,13 t , 4

⎢ 1− ∑θ$ ⎥ t s, ⎣ s=1 ⎦

Mid-Yukon 14 θ$

t ,14 = r D t ,14 t , 4 

22 6 22 

∑ θ

$

t s, = ⎡

∑ C, + ∑ rt s

⎤

Entire Tanana 15-22 Dt ,4 s=15 ⎢⎣f =4 t f s=15 , ⎥⎦
54 

Table 4. -- Continued. 

Stock Name Stock Index Estimates of Stock Proportions 

=

⎡ ⎤ ⎢ Ct

⎢

⎢⎣

⎥

⎥

⎥⎦

θ

$

t ,15 Dt − ,4 rt , 15 , 4 22

θ

$ Lower Tanana 15 ∑ t s, s=15 

= rt ,15 Dt ,5 

Kantishna 16 θ

$

t ,16 = rt ,16 Dt ,5 

Tolovana 17 θ

$

t ,17 = rt ,17 Dt ,5 

=

⎡

⎢ Ct

⎢

⎢⎣

θ

$

t ,18 Dt − ,5 rt , 18 , 5 22 17

θ

$ θ$

t s, Mid-Tanana 18 ∑ t s, − ∑ s=15 s=15 

= rt ,18 Dt ,6 

⎢

⎢

⎢

⎢

⎣

Ct 6

θ

$ ,

t,19 = rt,19 Dt,6 − 22 18 Chena 19 ∑ θ

$

t s, − ∑ θ

$

t s, 

s=15 s=15 

= rt,19 Dt,7 

Salcha 20 θ

$

t ,20 = rt ,20 Dt ,7 

Goodpaster 21 θ

$

t ,21 = rt ,21 Dt ,7 

Upper Tanana 22 θ

$

t ,22 = rt ,22 Dt ,7 

[ ]

⎤

⎥

⎥

⎥⎦

⎡ ⎤

⎥

⎥

⎥

⎥

⎦

46 14 46

Entire Yukon above Tanana 23-46 ∑θ$

t s, = ∑Ct f , + ∑rt s, Dt , 4 s= 23 f = 7 s= 23 
55 

Table 4. -- Continued. 

Stock Name Stock Index Estimates of Stock Proportions 

t , 23 θ$ = r

C t , 23 

D − t , 7 

22 

Upper Yukon (Rapids) 23 t , 4 1− ∑θ$

t s, s=1 

= r D t , 23 t ,8 

Beaver/Hodzana 24 θ

$

t ,24 = rt ,24 Dt ,8 

Chandalar 25 θ

$

t ,25 = rt ,25 Dt ,8 

30 10 

30 ∑rt s, + ∑Ct f , s= 26 f = 9

∑θ$

t s, = s= 26 C

D − t ,8 

t ,8 25 

Entire Porcupine 26-30 1− ∑θ$

t s, s=1 

30 10 

= [∑rt s, + ∑Ct f , ] Dt ,9 s= 26 f = 9 

t , 26 θ$ = r t , 26 C

D − t ,9 

t ,9 30 Black 26 ∑θ$

t s, s= 26 

= r D t , 26 t ,10 

Sheenjek 27 θ

$

t ,27 = rt ,27 Dt ,10 

Coleen/U.S. Porcupine 28 θ

$

t ,28 = rt ,28 Dt ,10 
56 

Table 4. -- Continued. 

Stock Name Stock Index Estimates of Stock Proportions 

t , 29 θ$ = r t , 29 Ct ,10 Dt ,10 − 30 28 

∑ t s, t s, 

Canadian Porcupine 29 θ$ − ∑θ$ s= 26 s= 26 

= rt , 29 Dt ,11 

Miner 30 θ$

t ,30 = r D t , 30 t ,11 

46 14 46

Upper Yukon above ∑θ$ = [∑C + ∑r ] Dt , 9 31-46 s= 31 t s, f =11 t f , s= 31 t s, 

Porcupine 

t , 31 θ$ = r

C t , 31 

D − t ,11 

t , 9 46 Upper Yukon (Circle) 31 ∑θ$

t s, s= 31 

= r D t , 31 t ,12 

Charley 32 θ$

t , 32 = r D t , 32 t ,12 

Kandik/Nation 33 θ$

t , 33 = r D t ,33 t ,12 

t , 34 θ$ = r t ,34 Ct ,12 D − Lower Canadian Yukon 34 t ,12 46 33 

∑θ$ − ∑θ$ t s, t s, s= 31 s= 31 

= r D t ,34 t ,13 

Klondike 35 θ$

t , 35 = r D t , 35 t ,13 

Stewart 36 θ$

t , 36 = r D t , 36 t ,13 
57 

Table 4. -- Continued. 

Stock Name 

White 

Stock Index 

37 

Estimates of Stock Proportions 

$θt , t , t , 37 = r D 37 13 

Pelly 38 θ$

t , 38 = r D t , 38 t ,13 

Mid-Canadian Yukon 39 θ$

t , 39 = r D t , 39 t ,13 

t , 40 θ$ = r

C t , 40 

D − t ,13 

Tatchun 40 46 39 t ,13 ∑θ$ − ∑θ$ t s, t s, s= 31 s= 31 

= r D t , 40 t ,14 

t , 41 θ$ = r t , 41 = r D t , 41 t ,15 

Upper Canadian Yukon 41 D − Ct ,14 

t ,14 46 40 

∑θ$ − ∑θ$ t s, t s, s= 31 s= 31 

Nordenskiold 42 θ$

t , 42 = r D t , 42 t ,15 

Little Salmon 43 θ$

t , 43 = r D t , 43 t ,15 

Big Salmon 44 θ$

t , 44 = r D t , 44 t ,15 

Teslin 45 θ$

t , 45 = r D t , 45 t ,15 

Hootalinqua 46 θ$

t , 46 = r D t , 46 t ,15 
58 

Table 5. -- Coloration of Chinook salmon captured with drift gill nets and radio tagged in the

 lower Yukon River near the village of Russian Mission during 2004. Percentages of 

 the weekly totals are in parentheses. 

Capture week Fish tagged Iridescent silver Dull silver Pre-spawning* 

23 8 8 (100) 0 (0.0) 0 (0.0) 

24 160 143 (89.4) 17 (10.6) 0 (0.0) 

25 319 229 (71.8) 90 (28.2) 0 (0.0) 

26 196 117 (59.7) 77 (39.3) 2 (1.0) 

27 199 76 (38.2) 108 (54.3) 15 (7.5) 

28 76 28 (36.8) 44 (57.9) 4 (5.3) 

29-30 37 6 (16.2) 26 (70.3) 5 (13.5) 

Total 995 607 (61.0) 362 (36.4) 26 (2.6) 

*

 Ranging from blush (silver with reddish tinges) to pronounced reddish coloration. 

Table 6. -- Tracking results for Chinook salmon radio tagged in the lower Yukon River near the

 village of Russian Mission during 2004. Percentages of the total are in parentheses. 

Final Status 2004 

Moved Upriver 958 (96.3)

 Upriver Location1 626 (62.9)

 Harvested in Fishery2 332 (33.4) 

Not Located Upriver 37 (3.7) 

Total 995 

1

 Fish recorded upriver from the tagging site and not caught in fisheries. 

2

 Including fish caught in terminal tributaries. 
59 

Table 7. -- Elapsed time and movement rates (km/day) by capture week for radio-tagged

 Chinook salmon traveling between the Russian Mission tagging area and the Paimiut

 tracking stations in 2004. 

95% Confidence Interval 

N1 Capture Week Distance (km)

2 Days (xb) Rate Lower Upper 

23 8 49.7 1.9 32.1 22.1 42.1 

24 158 55.2 1.7 37.0 35.1 38.9 

25 312 44.6 1.6 31.1 29.8 32.4 

26 186 40.3 1.6 28.6 27.0 30.2 

27 184 40.8 1.6 28.9 27.5 30.3 

28 62 40.3 1.8 27.8 25.1 30.6 

29-30 29 41.2 2.1 32.0 26.2 37.8 

Combined 939 44.4 1.7 31.0 30.3 31.7 

1

 Excluding radio-tagged fish not recorded passing the Paimiut tracking stations. 

2

 Average distance from the tagging area to Paimiut; distances for individual fish varied based on

 the specific location within the area where the fish were captured, tagged, and released. 
60 

Table 8. -- Elapsed time and movement rates (km/day) by capture location and distance for

 radio-tagged Chinook salmon traveling between the Russian Mission tagging area

 and the Paimiut tracking stations in 2004. 

Average 95% Confidence Interval 

Capture Location N1 Distance (km)

 2 Days Rate Lower Upper 

Lower Section3 5 70.0 - 79.7 1.7 44.4 35.7 53.0 

Lower Section3 247 61.2 - 69.6 1.8 39.8 38.4 41.1 

Combined3 252 61.2 - 79.7 1.8 39.9 38.5 41.2 

Upper Section4 201 40.1 - 44.4 1.7 30.6 29.1 32.1 

Upper Section4 486 28.5 - 39.9 1.5 26.6 25.7 27.4 

Combined4 687 28.5 - 44.4 1.6 27.8 27.0 28.5 

Entire Area 939 28.5 - 79.7 1.7 31.0 30.3 31.7 

1

 Not including radio-tagged fish not recorded passing the Paimiut tracking stations.

2

 Distance from the tagging area to Paimiut based on the specific location within the area where

 the fish were captured, tagged, and released.

3

 Section of the Russian Mission tagging area located in the general vicinity of the village. 4

 Section of the Russian Mission tagging area located about 20 km upriver from the village near

 an abandoned fish camp. 
61 

Table 9. -- Harvests of radio-tagged Chinook salmon in the Yukon River basin during 2004.

 Percentages of the total are in parentheses. 

Fishing Area Location Tagged Fish 

District 3 Russian Mission to Holy Cross 44 (13.3) 

District 4 Anvik to Ruby 88 (26.5) 

District 4 Koyukuk River 3 (0.9) 

District 5 Yukon-Tanana confluence to Eagle 108 (32.5) 

District 6 Tanana River1 33 (9.9) 

Combined U.S. Russian Mission to Eagle 276 (83.1) 

Canada Yukon River, Border to Dawson 25 (7.6) 

Canada Yukon River, upriver of Dawson 7 (2.1) 

Canada Yukon River tributaries2 21 (6.3) 

Canada Porcupine River, Old Crow 3 (0.9) 

Combined Canada Yukon and Porcupine rivers 56 (16.9) 

Total 332 

1

 Including sport fishery harvests in the Tolovana, Chena and Salcha rivers. 

2

 Including harvests in the Stewart, Pelly and Teslin rivers. 
62 

Table 10. -- Regional distribution of Chinook salmon radio tagged in the Yukon River basin

 during 2004. Fish harvested in terminal reaches of the basin are included.

 Percentages of the total are in parentheses. 

Region Final Location Number of Fish 

Lower Basin1 Yukon River main stem2 49 (6.8) 

Tributaries 71 (9.9) 

Combined Areas 120 (16.7) 

Koyukuk River Middle-Upper Koyukuk River2 10 (1.4) 

Koyukuk River fishery 3 (0.4) 

Tributaries3 15 (2.1) 

Combined Areas 28 (3.9) 

Middle Yukon River4 Yukon River main stem2 16 (2.2) 

Tributaries 14 (2.0) 

Combined Areas 30 (4.2) 

Tanana River Tanana River main stem2 28 (3.9) 

Tanana River fishery 23 (3.2) 

Tributaries3 144 (20.0) 

Combined Areas 195 (27.1) 

Upper Basin5 Yukon River main stem (U.S.)2 23 (3.2) 

Yukon River tributaries (U.S.) 20 (2.8) 

Yukon River main stem (Canada)2 57 (7.9) 

Yukon River main stem fishery (Canada) 32 (4.5) 

Yukon River tributaries (Canada)3 195 (27.1) 

Porcupine River tributaries (U.S.) 11 (1.5) 

Porcupine River (Canada)2 1 (0.1) 

Porcupine River fishery (Canada) 3 (0.4) 

Porcupine River tributaries (Canada) 4 (0.6) 
63 

Table 10. -- Continued. 

Region 

Upper Basin5 

Total 

Final Location 

Combined Areas 

Number of Fish 

346 (48.1) 

719 

1

 Section of the Yukon River from Russian Mission to the Yukon-Koyukuk River confluence.

2 Includes associated tributaries not monitored with tracking stations or aerial surveys.

3

 Includes fish harvested in terminal tributaries.

4

 Section of the Yukon River from Galena to the Yukon-Tanana River confluence.

5

 Section of the Yukon River upriver from the Yukon-Tanana River confluence. 
64 

Table 11. -- Stock composition estimates of the Yukon River Chinook salmon return in 2004

 based on the distribution of radio-tagged fish weighted by catch per unit effort

 information at the tagging site and adjusted for the harvest of tagged individuals in

 upriver fisheries. Bootstrap standard errors (SE) and 95% confidence intervals (CI)

 based on 10,000 bootstrappings are included. 

Region Stock Group Estimate (%) SE 95% CI 

Lower Basin1 Lower Yukon2 5.6 0.8 (4.2, 7.2) 

Lower Basin Tributaries 7.6 0.9 (5.9, 9.4) 

Koyukuk River Gisasa 0.9 0.3 (0.4, 1.6) 

Middle Koyukuk 0.8 0.4 (0.1, 1.7) 

Upper Koyukuk 1.9 0.5 (1.0, 2.8) 

Combined Areas 3.6 0.7 (2.3, 5.0) 

Middle Yukon River3 Mid-Yukon2 1.7 0.4 (0.9, 2.6) 

Mid-Yukon Tributaries4 1.9 0.5 (1.0, 3.0) 

Tanana River Tanana5 6.5 0.9 (4.8, 8.3) 

Chena 4.1 0.7 (2.8, 5.6) 

Salcha 10.1 1.1 (8.0, 12.4) 

Goodpaster 3.7 0.7 (2.4, 5.1) 

Combined Areas 24.4 1.5 (21.5, 27.5) 

Upper Yukon River (U.S.)6 Upper Yukon2 3.0 0.6 (1.9, 4.2) 

Upper Yukon Tributaries 2.9 0.6 (1.8, 4.3) 

Upper Yukon River (Canada) Lower Canadian Yukon7 3.1 0.7 (1.8, 4.4) 

Mid-Upper Can. Yukon8 15.9 1.4 (13.1, 18.7) 

Stewart 4.7 0.8 (3.1, 6.4) 

Pelly 8.4 1.1 (6.4, 10.5) 

Big Salmon 4.9 0.9 (3.2, 6.7) 
65 

Table 11. -- Continued. 

Region Stock Group Estimate (%) SE 95% CI 

Upper Yukon River (Canada) Teslin 9.2 1.1 (7.0, 11.4) 

Combined Areas 46.2 1.8 (42.6, 49.5) 

Porcupine River U.S. Porcupine 1.8 0.5 (0.9, 2.8) 

Canadian Porcupine 1.3 0.4 (0.5, 2.2) 

1

 Section of the Yukon River from Russian Mission to the Yukon-Koyukuk River confluence.

2

 Non-terminal areas and associated tributaries not surveyed during the study.

3

 Section of the Yukon River from Galena to the Yukon-Tanana River confluence.

4

 Including the Melozitna, Nowitna, and Tozitna rivers.

5

 Mainstem areas and associated tributaries including the Kantishna River, Tolovana River,

 Nenana River and Clear Creek. 

6

 Section of the Yukon River from Yukon-Tanana River confluence to Eagle, Alaska.

7

 Mainstem areas and associated tributaries including the Chandindu, Klondike and Sixtymile

 rivers.

8

 Mainstem areas and associated tributaries including the White River, Tatchun Creek,

 Nordenskiold River, Little Salmon River, Takhini River and reaches of the Yukon River

 upstream of Hootalinqua. 
66 

Table 12. -- Movement rates (km/day) of Chinook salmon radio tagged in the lower Yukon River

 during 2004 based on fish passage by tracking stations located at Paimiut and the

 farthest upriver station site. The 95% confidence intervals (CI) and sample sizes are

 included. 

Region Stock Group Average 95% CI N 

Lower Basin1 Lower Yukon2 45.3 38.4, 52.2 26 

Lower Basin Tributaries 34.6 31.9, 37.3 70 

Koyukuk River Gisasa 34.0 28.0, 40.0 8 

Middle Koyukuk 53.1 44.0, 62.2 5 

Upper Koyukuk 68.6 65.9, 71.3 12 

Middle Yukon River3 Mid-Yukon2 46.3 38.7, 53.9 16 

Mid-Basin Tributaries 49.3 43.3, 55.3 14 

Tanana River Tanana4 43.8 39.0, 48.6 22 

Middle Tanana Tributaries5 53.2 49.5, 56.9 16 

Chena 45.6 43.0, 48.2 27 

Salcha 43.2 41.9, 44.5 61 

Goodpaster 43.0 41.3, 44.7 23 

Upper Yukon River (U.S.)6 Upper Yukon2 55.0 49.9, 60.1 23 

Upper Yukon Tributaries 54.6 50.5, 58.7 19 

Upper Yukon River (Canada) Canadian Yukon4 50.5 48.7, 52.3 64 

Klondike 61.9 58.4, 65.4 12 

Stewart 57.7 53.9, 61.5 23 

White 59.5 56.6, 62.4 12 

Pelly 57.4 55.6, 59.2 40 

Little Salmon 56.3 41.8, 70.8 3 
67 

Table 12. -- Continued. 

Region 

Upper Yukon River (Canada) 

Porcupine River 

Stock Group 

Big Salmon 

Teslin 

Minor Canadian Stocks7 

U.S. Porcupine 

Canadian Porcupine 

Average 

54.9 

54.3 

53.1 

58.5 

60.0 

95% CI 

52.9, 56.9 

52.1, 56.5 

51.0, 55.2 

53.4, 63.6 

53.4, 66.6 

N 

25 

39 

22 

11 

8 

1

 Section of the Yukon River from Russian Mission to the Yukon-Koyukuk River confluence.

2

 Non-terminal areas and associated tributaries not surveyed during the study. 3

 Section of the Yukon River from Galena to the Yukon-Tanana River confluence.

4

 Including stocks in mainstem areas and associated tributaries not surveyed during the study. 5

 Including the Kantishna River, Tolovana River, Nenana River, and Clear Creek.

6

 Section of the Yukon River from Yukon-Tanana River confluence to Eagle, Alaska.

7

 Including the Chandindu River, Sixtymile River, Tatchun Creek, Nordenskiold River, Little

 Salmon River, Takhini River, and headwater areas upriver of Hootalinqua.
68

Table 13. -- Comparison of movement rates (km/day) of Chinook salmon traveling to tributaries

 in the Yukon River basin during 2004 based on the passage of radio-tagged fish by

 tracking stations. Average rates and 95% confidence intervals (CI) between Paimiut

 and the first station within the region the fish were destined for (i.e., travel primarily

 through reaches of the Yukon River main stem), and between Paimiut and the 

farthest upriver station are presented. 

Stock 

Paimiut to First Regional Station1 Paimiut to Terminal Station2 

Location &X CI Location &X CI 

Nulato 

Gisasa 

Upper Koyukuk 

Mid-Basin trib.4 

Chena 

Salcha 

Goodpaster 

Chandalar 

Stewart 

Pelly 

Big Salmon 

Teslin 

Yukon-Anvik 57.6 48.8, 66.4 

Lower Koyukuk 47.2 39.4, 55.0 

Lower Koyukuk 61.5 58.5, 64.5 

Yukon-Yuki 54.2 50.2, 58.2 

Lower Tanana 55.7 53.3, 58.1 

Lower Tanana 56.3 53.1, 59.5 

Lower Tanana 56.8 54.9, 58.7 

Rampart Rapids 57.8 54.5, 61.1 

Yukon Border 58.7 54.9, 62.5 

Yukon Border 58.2 56.4, 60.0 

Yukon Border 58.1 55.9, 60.3 

Yukon Border 57.4 55.2, 59.6 

Nulato3 43.1 37.4, 48.8 

Gisasa3 34.0 28.0, 40.0 

Mid-Koyukuk 68.5 65.8, 71.2 

Trib. mouth 49.3 43.3, 55.3 

Chena3 45.3 42.4, 48.2 

Salcha3 43.2 41.9, 44.5 

Upper Tanana 43.0 41.3, 44.7 

Chandalar3 53.7 49.1, 58.3 

Stewart3 57.7 53.9, 61.5 

Pelly3 57.4 55.6, 59.2 

Big Salmon3 54.9 52.9, 56.9 

Teslin3 54.3 52.1, 56.5 

1

 First station within the region containing the final destination of the fish (see Table 2).

2

 Last station passed by the fish prior to reaching its final destination.

3

 Station located near river mouth.

4

 Including the Melozitna, Nowitna and Tozitna rivers.
69

Porcupine River 

Koyukuk River 

Tanana River 

Russian Mission 

Holy Cross 

Anvik 

Galena 

Tanana Eagle 

Old Crow 

Nenana 

Fairbanks 

Circle 

Fort Yukon 

Dawson 

Whitehorse 

Carmacks 

Ruby 

Nulato 

Beaver 

0 100 200 

km

 Tagging site

 Town, village 

Yukon River 

Yukon

River 

Yukon River 

Rampart 

Chandalar River 

Stewart River 

Pelly River 

Teslin River 

White River 

Manley 

Figure 1. -- Map of the Yukon River basin showing the Yukon River main stem and major

 tributaries of the drainage, as well as the tagging site, and selected towns and

 villages. 
70

Figure 2. -- Radio transmitter used to tag Chinook salmon in the lower Yukon River near the

 village of Russian Mission during 2004. The transmitter is gently inserted through

 the mouth and placed in the stomach. 
71


Figure 3. -- Remote tracking station and satellite uplink used to collect and access movement

 information of Chinook salmon in the Yukon River basin. Radio-tagged fish

 passing the station sites are recorded; the information is transferred to a receiving

 station via satellite and downloaded for in-season analysis. 
72

 Tagging Site 

 Tracking Station

Porcupine Border 

Lower Porcupine 

Sheenjek Fishing Branch 

Chandalar Black 

Hogatza 

Upper Koyukuk Circle

Gisasa Tozitna Rampart Rapids Lower Koyukuk Melozitna Chena Yukon Border Nulato Lower Salcha

Yukon-Yuki Nowitna Tanana Nenana Upper Tanana 

Above Yukon-White 

Fraser Falls Stewart Below Yukon-White Pelly 

Selkirk Tatchun 

Yukon-Anvik Innoko Big Salmon 

Anvik Yukon-Teslin 

Bonasilla Kluane Hootalinqua 

Paimiut

Russian Mission

0 100 200 

km 

Figure 4. -- Map of the Yukon River basin showing the location of remote tracking stations used

 to track the upriver movements of radio-tagged Chinook salmon during 2004. 
73

B 

C D 

H 

E 

F 

G 

I L 

J 

K 

M 

N 

O 

Innoko Bonasila 

Anvik 

Nulato 

Gisasa 

Hogatza 

Upper Koyukuk 

Melozitna Tozitna 

Kantishna 

Tolovana 

Mid Tanana (Nenana) 

Chena 

Salcha 

Goodpaster 

Beaver/ 

Chandalar 

Sheenjek 

Coleen/U.S. Porcupine 

Charley Lower Canadian Yukon 

Klondike 

Stewart 

Pelly 

White Tatchun 

Upper Canadian Yukon 

Mid Canadian Yukon 

Black 

Nowitna 

Lower Koyukuk 

Lower Tanana 

Nordenskiold 

Big Salmon 

Little Salmon 

Teslin 

Hootalinqua 

Upper Tanana 

Lower 

Yukon 

Mid 

Yukon 

Upper Yukon U.S. (Circle) 

A 

(Fish Passing Paimiut Tracking Stations) 

Terminal Area Non-terminal Area X Fishery 

Upper Yukon U.S.

(Rapids) 

Kandik/Nation 

Canadian 

Porcupine 

Miner 

Koyukuk 

Middle 

Hodzana 

Figure 5. -- Migration model for calculating stock composition estimates of Chinook salmon

 returns in the Yukon River basin based on the distribution of radio-tagged fish.

 Spatial relationships of the fisheries and component stocks are indicated. Additional

 information on the fisheries, labeled as A through O, is contained in Table 3. 
74

Capture Date 

Number of Fish 

10 

30 

50 

70 

June 13 June 27 July 4 July 11 July 18 

Fish Tagged 

CPUE 

June 6 June 20 

Figure 6. -- Number of Chinook salmon radio tagged per day in the lower Yukon River and daily

 catch per unit effort (CPUE) information for Chinook salmon captured at the Russian

 Mission tagging site during 2004. 
75

100 

80 

60 

40 

20 

Iridescent Silver Dull Silver Pre-spawning 

N = 71 N = 28 N = 14 N = 195 N = 20 N = 284 N = 11 N = 11 

P

ercent of 

S

a

m

ple 

Lower Basin Koyukuk Mid-Yukon Tanana Up. Yukon Up. Yukon Porcupine Porcupine

Tribs. Tribs. Tribs. (U.S.) Canada (U.S.) (Canada) 

Figure 7. -- Lower River coloration of Chinook salmon captured with drift gill nets and radio

 tagged near the village of Russian Mission, and tracked to terminal reaches of the

 basin during 2004. Pre-spawning coloration ranged from blush (silver with reddish

 tinges) to a pronounced reddish coloration. 
76

Not Located Yukon Fishery (U.S.)

Upriver (3.7)

Yukon Fishery

Non-terminal (Canada) 

Reaches 

Koyukuk-Tanana 

Fisheries (3.3) 

Terminal Reaches 

N = 995 

24.1 

54.4 

5.6 

Non-terminal 

8.9 

Figure 8. -- Final status of Chinook salmon radio tagged in the lower Yukon River near the

 village of Russian Mission during 2004. Percentages of the total number of fish

 tagged are indicated. 
77

Final Aerial Location 

Tagging Site 

0 100 200

km 

Figure 9. -- Final locations of Chinook salmon radio tagged in the lower Yukon River near the

 village of Russian Mission and tracked upriver during their spawning migration

 based on aerial tracking surveys in 2004. 
9.0

78

Upper Yukon River (3.2) Lower Basin Tributaries 

N=719 

Upper Yukon River 

(Canada) 

Porcupine River

Canada (1.1) 

27.1 Tanana River 

U.S. Tributaries (2.8)

Upper Yukon River 

Porcupine River

U.S. Tributaries (1.5) 

9.9 

39.5 

6.8 

Non-terminal Reaches 

Koyukuk River (3.9) 

Middle Yukon River 

Tributaries (2.0) 

Middle Yukon River (2.2) 

Lower Yukon River 

Figure 10. -- Distribution of Chinook salmon radio tagged in the lower Yukon River near the

 village of Russian Mission during 2004. Percentage of the total number of fish that

 moved upriver and were not caught in non-terminal fisheries are indicated. 
9.0

79

Upper Yukon River (3.0) Lower Basin Tributaries 

Lower Yukon River 

Porcupine River

Canada (1.3)

U.S. Tributaries (2.9)

Upper Yukon River 

Porcupine River

U.S. Tributaries (1.8) 

5.6 

Koyukuk River (3.6) 

Middle Yukon River 

Tributaries (1.9) 

Middle Yukon River (1.7) 

24.4 

46.2 

7.6 

Tanana River 

Upper Yukon River 

(Canada) 

Non-terminal Reaches 

Figure 11. -- Stock composition estimates of the Yukon River Chinook salmon return in 2004

 based on the distribution of radio-tagged fish (Fig. 10) weighted by catch per unit

 effort information at the tagging site and adjusted for the harvest of tagged

 individuals in upriver fisheries. Percentages of the return are indicated. 
Klondike 

Lower Yu

kon 

Stewart 

Tatchun 

Porcupine 

Miner 

Hootalinqua 

Teslin 

Big 

Salmon 

Little

Salmon 

Nordenskiold 

Upper Yukon 

Middle

Yukon 

Pelly 

White 

80 

5. 0 

10 . 0 

15. 0 

Sto

ck C

omposition (%)

Porcupine River (Canada) 

Yukon River (Canada) 

Figure 12. -- Composition of Chinook salmon stocks returning to Canadian reaches of the Yukon

 River basin in 2004, based on the distribution of radio-tagged fish weighted by

 catch per unit effort information at the tagging site and adjusted for the harvest of

 tagged individuals in upriver fisheries. Composition estimates and 95%

 confidence intervals are provided. 
Innoko 

Bonasila 

Anvik 

Lower Yu

kon 

Nulato 

Gisasa 

Mid-Koyuku

k 

Upper Koyu

kuk 

Melozitna 

Nowitna 

Mid-Yukon 

Tozitna 

Lower Tanana 

Kantishna 

Tolovana 

Mid-Tanana 

Chena 

Salcha 

Goodpaster 

Upper Tanana 

Upper Yukon 

Chandalar 

Charley 

Kandik 

Black 

Sheenjek 

Coleen 

Beaver, Hodzana 

81 

Lower Basin 

Middle Yukon and Koyukuk Rivers 

Tanana River 

Upper Yukon and Porcupine Rivers 

5. 0 

10 .0 

15.0

Stock Compo

sition (

%) Figure 13. -- Composition of Chinook salmon stocks returning to U.S. reaches of the Yukon

 River basin in 2004, based on the distribution of radio-tagged fish weighted by

 catch per unit effort information at the tagging site and adjusted for the harvest of

 tagged individuals in upriver fisheries. Composition estimates and 95%

 confidence intervals are provided. 
82

Stock Composition (%

)

1.0 

2.0 

3.0 

4.0 Porcupine 

Upper Yukon (Canada) 

Upper Yukon (U.S.) 

Tanana 

2.0 Mid-Yukon Tributaries 

Koyukuk 

Lower Basin Tributaries 

1.0 

6 June 13 June 20 June 27 June 4 July 11 July 18 July 

Figure 14. -- Run timing of Yukon River Chinook salmon stock groups returning to terminal

 reaches of the basin in 2004, based on composition estimates for the entire return

 derived from the distribution of radio-tagged fish weighted by catch per unit effort

 information at the tagging site and adjusted for the harvest of tagged individuals in

 upriver fisheries. 
83

0.2 Porcupine (Can) 

0.2 Hootalinqua 

0.6 

0.2 

0.4 

Mid-Upper Yukon 

0.8 

0.6 

0.4 

0.2 

Teslin 

0.6 

0.2 

0.4 

Big Salmon 

1.0 

0.8 

0.6 

0.2 

0.4 

Pelly 

1.2 

Sto

0.4

ck Composition (%) 

White 0.2 

0.6 

0.4 

0.2 

0.4 

0.2 

Stewart 

Klondike 

6 June 13 June 20 June 27 June 4 July 11 July 18 July 

Figure 15. -- Run timing of major Chinook salmon stocks in Canadian reaches of the Yukon

 River basin in 2004, based on composition estimates for the entire return derived

 from the distribution of radio-tagged fish weighted by catch per unit effort

 information at the tagging site and adjusted for the harvest of tagged individuals in

 upriver fisheries. The mid-upper Yukon stock group represents fish remaining in

 mainstem areas and associated tributaries. 
v

Koyukuk

Salcha

Chandalar

84

0.2 Porcupine 

0.2 Nulato 

0.2 Bonasila 

0.2 

0.4 An ik 

0.2 

0.2 

0.4 Chena 

0.2 

0.4 Goodpaster 

1.0 

0.8 

0.6 

0.2 

0.4 

0.2 Tozitna 

0.2 Kantishna 

S

tock Compositi

on (%) 

0.2 

6 June 13 June 20 June 27 June 4 July 11 July 18 July 

Figure 16. -- Run timing of major Chinook salmon stocks in U.S. reaches of the Yukon River

 basin in 2004, based on composition estimates for the entire return derived from

 the distribution of radio-tagged fish weighted by catch per unit effort information

 at the tagging site and adjusted for the harvest of tagged individuals in upriver

 fisheries. 
85

Daily Stock Composition (%) 

Lower Basin - Middle Yukon River Tributaries 

20 

40 

60 

80 

100 

Tanana River 

20 

40 

60 

Upper Yukon River (U.S. Tributaries) 

20 

40 

Upper Yukon River (Canada) 

20 

40 

60 

80 

40 

20 

Porcupine River (U.S. and Canada) 

6 June 13 June 20 June 27 June 4 July 11 July 18 July 

Figure 17. -- Daily stock composition of Chinook salmon passing through the lower Yukon

 River near the village of Russian Mission in 2004, based on the observed

 distribution of radio-tagged fish. 
86

40 

Non-terminal 

Areas 

40 

20 

50 

30 

10 

Stock Composition (%) 

Non-terminal fish considered spawning populations 

Non-terminal fish considered in-transit 

Lower Koyukuk Mid-Yukon Tanana Upper Yukon Upper Porcupine Porcupine Lower-Mid Upper

Basin Tribs. Tribs. (U.S.) Yukon (U.S.) (Canada) Yukon Yukon Tribs. Canada (U.S.) (U.S.) 

Figure 18. -- Comparison of stock composition estimates of the Yukon River Chinook salmon

 return in 2004 based on the distribution of radio-tagged fish weighted by catch per

 unit effort information at the capture site and adjusted for the harvest of tagged

 individuals in upriver fisheries, and the presumed status of fish remaining in non-

 terminal reaches of the Yukon River main stem. Non-terminal areas include

 associated tributaries not monitored during the study. 
87

10 

30 

50 

70 

(133) (517) 

(810) 

(835) (1010) (1399) (1702) 

Movement Rate (km/day) 

Chena 

Salcha 

Goodpaster 

Chandalar 

Sheenjek 

Stewart, Pelly 

Big Salmon, Teslin 

(1148-1202) 

(1900-2333) 

(1230,1312) 

Yukon-Anvik Ruby Rapids Nenana Natal Circle U.S.-Canada Natal 

Confluence Lower Streams Border Streams 

Tanana 

Tracking Station Location (km from Paimiut Station) 

Figure 19. -- Movement rates (km/day) of radio-tagged Chinook salmon returning to tributaries in

 the upper Yukon River basin in 2004. Average rates by area and distances from the

 Paimiut tracking stations are provided. 

89

APPENDICES

91 

Appendix A. -- Fishery recoveries of Chinook salmon radio tagged in the lower Yukon River

 near the village of Russian Mission during 2004. Percentages of the total are in

 parentheses. 

Fishing Area Fishery Tagged Fish 

District 3 Russian Mission 12 (3.6) 

Holy Cross 32 (9.7) 

Combined Fisheries 44 (13.3) 

District 4 Anvik 5 (1.5) 

Grayling 15 (4.6) 

Kaltag 11 (3.3) 

Nulato 21 (6.3) 

Huslia, Hughes (Koyukuk River)1 3 (0.9) 

Galena 26 (7.8) 

Ruby 10 (3.0) 

Combined Fisheries 91 (27.4) 

District 5 Tanana 7 (2.1) 

Yukon River (upriver of Tanana) 6 (1.8) 

Rampart Rapids 16 (4.8) 

Yukon River (upriver of Rampart Rapids) 5 (1.5) 

Rampart 15 (4.6) 

Yukon Bridge 4 (1.2) 

Stevens Village 14 (4.2) 

Beaver 12 (3.6) 

Chandalar River1 1 (0.3) 

Ft. Yukon 15 (4.5) 

Circle 4 (1.2) 

Eagle 9 (2.7) 

Combined Fisheries 108 (32.5) 

District 6 Lower Tanana River1 8 (2.4) 

Tolovana River1,2 2 (0.6) 

Nenana1 5 (1.5) 
92 

Appendix A. -- Continued. 

Fishing Area Fishery Tagged Fish 

District 6 Fairbanks1 10 (3.0) 

Chena River1,2 2 (0.6) 

Salcha River1,2 6 (1.8) 

Combined Fisheries 33 (9.9) 

Canada Border-Dawson 25 (7.6) 

Stewart River1 3 (0.9) 

Pelly River1 8 (2.4) 

Minto Landing 1 (0.3) 

Carmacks 5 (1.5) 

Upper Yukon River 1 (0.3) 

Teslin River1 10 (3.0) 

Old Crow (Porcupine)1 3 (0.9) 

Combined Fisheries 56 (16.9) 

Total 332 

1

 Fish harvested in tributary of the Yukon River main stem. 

2

 Includes fish harvested in sport fishery. 
93 

Appendix B. -- Distribution of Chinook salmon radio tagged in the lower Yukon River near the

 village of Russian Mission during 2004, including fish caught in terminal

 fisheries in the U.S. and Canada. Percentages of total are in parentheses. 

Region Final Location Tagged Fish 

Lower Basin Yukon River main stem (upriver of Holy Cross)1 49 (6.8) 

Kako River 1 (0.1) 

Innoko River 5 (0.7) 

Bonasila River 14 (2.0) 

Anvik River 40 (5.6) 

Nulato River 11 (1.5) 

Combined Areas 120 (16.7) 

Koyukuk Middle Koyukuk River1 5 (0.7) 

Gisasa River 8 (1.1) 

Koyukuk Fishery 3 (0.4) 

Upper Koyukuk River1 5 (0.7) 

Henshaw Creek 2 (0.3) 

Koyukuk River South Fork 5 (0.7) 

Combined Areas 28 (3.9) 

Middle Yukon Yukon River main stem (upriver of Galena)1 16 (2.2) 

Melozitna River 3 (0.4) 

Nowitna River 3 (0.4) 

Tozitna River 8 (1.1) 

Combined Areas 30 (4.2) 

Tanana Tanana River fishery 23 (3.2) 

Lower Tanana River (upriver of Manley)

1 8 (1.1) 

Kantishna River 9 (1.3) 

Tolovana-Chatanika River2 5 (0.7) 

Nenana River 1 (0.1) 

Middle Tanana River (upriver of Nenana)1 9 (1.3) 

Clear Creek 3 (0.4) 
94 

Appendix B. -- Continued. 

Region Final Location Tagged Fish 

Tanana Chena River2 30 (4.2) 

Salcha River2 68 (9.4) 

Upper Tanana River (upriver of Salcha River)1 11 (1.5) 

Goodpaster River 28 (3.9) 

Combined Areas 195 (27.1) 

Upper Yukon (U.S.) Yukon River main stem (upriver of Tanana)1 20 (2.8) 

Hodzana River3 1 (0.1) 

Beaver Creek 2 (0.3) 

Chandalar River 14 (2.0) 

Yukon River main stem (upriver of Circle)1 3 (0.4) 

Charley River 1 (0.1) 

Nation River 2 (0.3) 

Combined Areas 43 (6.0) 

Upper Yukon (Canada) Yukon River main stem (upriver of Border)1 3 (0.4) 

Yukon River fishery 32 (4.5) 

Chandindu River 1 (0.1) 

Klondike River 12 (1.7) 

Sixtymile River 1 (0.1) 

Stewart River2 23 (3.2) 

Stewart River (upriver of Fraser Falls) 3 (0.4) 

White River 12 (1.7) 

Yukon River main stem (upriver of White River)1 12 (1.7) 

Pelly River2 48 (6.7) 

Yukon River main stem (upriver of Selkirk)1 16 (2.2) 

Tatchun Creek 3 (0.4) 

Yukon River main stem (upriver of Tatchun Cr)1 26 (3.6) 

Nordenskiold River 2 (0.3) 

Little Salmon River 3 (0.4) 

Big Salmon River 25 (3.5) 

Teslin River2 49 (6.8) 
95 

Appendix B. -- Continued. 

Region Final Location Tagged Fish 

Upper Yukon (Canada) Yukon River main stem (upriver of Hootalinqua)1 8 (1.1) 

Takhini River 5 (0.7) 

Combined Areas 284 (39.5) 

Porcupine (U.S.) Black River 1 (0.1) 

Sheenjek River 6 (0.8) 

Coleen River 4 (0.6) 

Combined Areas 11 (1.5) 

Porcupine (Canada) Porcupine River (upriver of Border)1 1 (0.1) 

Old Crow Fishery 3 (0.4) 

Old Crow River 1 (0.1) 

Miner River 3 (0.4) 

Combined Areas 8 (1.1) 

Total 719 

1

 Including associated tributaries not monitored with tracking stations or aerial surveys.

2

 Includes fish caught in terminal fisheries.

3

 Minimum count based on partial aerial survey.
96 

Klondike River 

Big Salmon 

Hootalinqua 

Little Salmon R. Nordenskiold R. 

Nisling River 

Tahkini R. 

Chandindu

R. 

U.S.A. 

Canada 

Tracking station 

Aerial location 

Yukon Border Stewart-Fraser 

Stewart 

Yukon-White Pelly 

Selkirk 

Yukon River Tatchun 

Teslin 

Kluane 

0 40 80 120 

Kilometers 

Appendix C. -- Final location of Chinook salmon radio tagged in the lower Yukon River near the village of Russian Mission and 

tracked to tributaries in Canadian reaches of the Yukon River during aerial tracking surveys in 2004. 
97 

Tracking station 

Aerial location 

Porcupine Border 

Fishing Branch 

Lower Porcupine 

Black 

Old Crow River 

Miner

River

Bell R. 

Eagle River 

Whitestone R. 

0 25 50 

Kilometers 

Porcupine River 

U.S.A. 

Canada 

Appendix D. -- Final location of Chinook salmon radio tagged in the lower Yukon River near the village of Russian Mission and 

tracked to tributaries in Canadian reaches of the Porcupine River during aerial tracking surveys in 2004. 
98 

Hodzana River 

Beaver Creek 

Charlie River 

Nation

River 

Coleen

River 

Yukon River 

Yukon River 

Porcupine River 

Tracking station 

Aerial location 

Lower 

Porcupine 

Sheenjek

Chandalar Black 

Circle 

0 25 50 75 

Rampart Rapids Kilometers 

Appendix E. -- Final location of Chinook salmon radio tagged in the lower Yukon River near the village of Russian Mission and

tracked to tributaries in U.S. reaches of the upper Yukon and Porcupine rivers during aerial tracking surveys in 2004. 
Ta

99 

K

nana River 

antishna

River 

Tolovana River 

Chatanika River 

Goodpaster River 

Chena

Tracking station


Aerial location


Manley Dam 

Chena 

Nenana 

Salcha 

Upper Tanana 

0 20 40 60 

Kilometers 

Appendix F. -- Final location of Chinook salmon radio tagged in the lower Yukon River near the village of Russian Mission and

tracked to Tanana River tributaries during aerial tracking surveys in 2004. 
100 

nokuY 

Ri

ev

r 

Anvik 

r e iv

R

anh is

D 

i

to

ls

oT 

keer C 

Tracking station


Aerial location


Nulato 

Innoko 

Yukon-Anvik


Bonasila


0 25 50 75 

Paimiut Kilometers 

Appendix G. -- Final location of Chinook salmon radio tagged in the lower Yukon River near the village of Russian Mission and 

tracked to lower basin tributaries during aerial tracking surveys in 2004. 
101 

Henshaw Cr. 

South Fork R. 

Tracking station


Aerial location


Hogatza

Upper


Koyukuk


Rampart Rapids 

Gisasa 

Lower Koyukuk Tozitna Manley 

Melozitna 

Nulato Yukon-Yuki Nowitna Nenana 

0 25 50 75 

Kilometers 

Appendix H. -- Final location of Chinook salmon radio tagged in the lower Yukon River near the village of Russian Mission and

 tracked to middle basin tributaries during aerial tracking surveys in 2004. 
102 

Appendix I. -- Stock composition estimates of the Yukon River Chinook salmon return in 2004

 based on the distribution of radio-tagged fish weighted by catch per unit effort

 information at the Russian Mission tagging site and adjusted for the harvest of

 tagged individuals in upriver fisheries. Bootstrap standard errors (SE) and 95%

 confidence intervals (CI) based on 10,000 bootstrappings are included. 

Region Stock Group Estimate (%) SE 95% CI 

Lower Basin1 Lower Yukon2 5.6 0.8 (4.2, 7.2) 

Innoko 0.5 0.2 (0.1, 1.0) 

Bonasila 1.5 0.4 (0.7, 2.3) 

Anvik 4.3 0.7 (3.0, 5.8) 

Nulato 1.3 0.4 (0.6, 2.1) 

Koyukuk River Gisasa 0.9 0.3 (0.4, 1.6) 

Middle Koyukuk 0.8 0.4 (0.1, 1.6) 

Upper Koyukuk 1.9 0.5 (1.0, 2.9) 

Middle Yukon River3 Melozitna 0.4 0.2 (0.0, 0.9) 

Nowitna 0.4 0.3 (0.0, 1.0) 

Tozitna 1.1 0.4 (0.4, 1.9) 

Mid-Yukon2 1.7 0.4 (0.9, 2.6) 

Tanana River Lower Tanana4 1.1 0.4 (0.4, 1.9) 

Kantishna 1.3 0.4 (0.5, 2.2) 

Tolovana 0.6 0.3 (0.1, 1.3) 

Mid-Tanana4 1.3 0.4 (0.6, 2.2) 

Chena 4.1 0.7 (2.8, 5.6) 

Salcha 10.1 1.1 (8.0, 12.4) 

Goodpaster 3.7 0.7 (2.4, 5.1) 

Upper Tanana4 2.2 0.5 (1.2, 3.3) 

Upper Yukon River (U.S.)5 Upper Yukon (Rapids)2 2.7 0.6 (1.6, 3.8) 

Beaver Creek, Hodzana 0.4 0.2 (0.0, 1.0) 

Chandalar 1.9 0.5 (1.1, 3.1) 

Upper Yukon (Circle)2 0.3 0.2 (0.0, 0.8) 

Charley 0.2 0.2 (0.0, 0.6) 

Nation 0.4 0.2 (0.0, 0.9) 

Upper Yukon River (Canada) Lower Canadian Yukon 4 0.9 0.4 (0.3, 1.7) 

Klondike 2.2 0.6 (1.1, 3.3) 

Stewart 4.7 0.8 (3.1, 6.4) 

White 2.1 0.6 (1.1, 3.2) 
103

Appendix I. -- Continued. 

Region Stock Group Estimate (%) SE 95% CI 

Upper Yukon River (Canada) Pelly 8.4 1.1 (6.4, 10.6) 

Mid-Canadian Yukon4 4.9 0.8 (3.2, 6.4) 

Tatchun 0.5 0.3 (0.0, 1.2) 

Upper Canadian Yukon4 5.0 0.9 (3.4, 6.7) 

Nordenskiold 0.4 0.2 (0.0, 1.0) 

Little Salmon 0.5 0.3 (0.1, 1.2) 

Big Salmon 4.9 0.9 (3.2, 6.7) 

Teslin 9.2 1.1 (7.0, 11.4) 

Hootalinqua 2.5 0.6 (1.4, 3.9) 

Porcupine River, U.S. Black 0.1 0.1 (0.0, 0.4) 

Sheenjek 1.0 0.4 (0.3, 1.8) 

Coleen 0.7 0.3 (0.1, 1.4) 

Porcupine River, Canada Canadian Porcupine4 0.6 0.3 (0.0, 1.2) 

Miner 0.7 0.3 (0.1, 1.4) 

1

 Section of the Yukon River from Russian Mission to the Yukon-Koyukuk River confluence.

2

 Non-terminal areas.

3

 Section of the Yukon River from Galena to the Yukon-Tanana River confluence.

4

 Including stocks in mainstem areas and associated tributaries.

5

 Section of the Yukon River upriver from the Yukon-Tanana River confluence.
104 

Appendix J. -- Daily stock composition estimates of Chinook salmon passing through the lower

 Yukon River based on the distribution of radio-tagged fish in 2004. 

Non-Terminal Reaches1 Terminal Reaches 

Upper Lower Basin- Upper Basin 

Lower-Mid Yukon Middle Yukon Tanana Tributaries 

Date Yukon (U.S.)2 Tributaries River (U.S.) Canada2 

4 June 0.0000 0.1858 0.0294 0.2426 0.0000 0.5422 

5 June 0.0000 0.0917 0.0318 0.2641 0.0236 0.5889 

6 June 0.0000 0.0851 0.0232 0.2865 0.0341 0.5710 

7 June 0.0194 0.0645 0.0274 0.3010 0.0514 0.5362 

8 June 0.0171 0.0700 0.0242 0.2752 0.0582 0.5554 

9 June 0.0157 0.0853 0.0376 0.2530 0.0635 0.5450 

10 June 0.0309 0.0543 0.0309 0.2847 0.0623 0.5370 

11 June 0.0254 0.0288 0.0305 0.2720 0.0854 0.5578 

12 June 0.0279 0.0262 0.0418 0.2840 0.0839 0.5361 

13 June 0.0304 0.0181 0.0650 0.2682 0.0782 0.5402 

14 June 0.0297 0.0180 0.0771 0.2680 0.0718 0.5355 

15 June 0.0309 0.0105 0.0810 0.2934 0.0570 0.5273 

16 June 0.0283 0.0000 0.0706 0.3200 0.0609 0.5203 

17 June 0.0289 0.0044 0.0961 0.3055 0.0590 0.5061 

18 June 0.0332 0.0050 0.1142 0.3203 0.0465 0.4809 

19 June 0.0427 0.0112 0.1171 0.3132 0.0407 0.4751 

20 June 0.0475 0.0123 0.0985 0.3238 0.0392 0.4788 

21 June 0.0528 0.0118 0.0817 0.3162 0.0313 0.5061 

22 June 0.0533 0.0120 0.0778 0.2691 0.0317 0.5561 

23 June 0.0769 0.0134 0.0913 0.2359 0.0211 0.5614 

24 June 0.0717 0.0302 0.0495 0.2366 0.0161 0.5959 

25 June 0.0905 0.0395 0.0708 0.2330 0.0212 0.5450 

26 June 0.1072 0.0372 0.0881 0.2408 0.0262 0.5004 

27 June 0.1101 0.0418 0.1222 0.2186 0.0367 0.4705 

28 June 0.1208 0.0437 0.1775 0.1895 0.0386 0.4299 

29 June 0.1423 0.0509 0.2309 0.1831 0.0445 0.3483 

30 June 0.1367 0.0547 0.2743 0.1675 0.0480 0.3190 

1 July 0.1470 0.0463 0.2964 0.1480 0.0632 0.2992 

2 July 0.1522 0.0482 0.3357 0.1170 0.0584 0.2884 

3 July 0.1406 0.0446 0.3577 0.0669 0.0572 0.3330 

4 July 0.1653 0.0476 0.3614 0.0690 0.0374 0.3193 

5 July 0.1692 0.0720 0.3518 0.0614 0.0445 0.3011 

6 July 0.1862 0.0937 0.2906 0.1017 0.0642 0.2636 

7 July 0.1990 0.1050 0.2274 0.1012 0.0535 0.3140 
105 

Appendix J. -- Continued. 

Non-Terminal Reaches1 Terminal Reaches 

Upper Lower Basin- Upper Basin 

Lower-Mid Yukon Middle Yukon Tanana Tributaries 

Date Yukon (U.S.)2 Tributaries River (U.S.)2 Canada2 

8 July 0.2400 0.0884 0.2400 0.1000 0.0221 0.3095 

9 July 0.2292 0.0691 0.2083 0.1250 0.0230 0.3454 

10 July 0.2340 0.0709 0.2128 0.1277 0.0236 0.3310 

11 July 0.2326 0.0532 0.2558 0.1395 0.0266 0.2924 

12 July 0.2222 0.0321 0.1944 0.1667 0.0321 0.3526 

13 July 0.2222 0.0000 0.2593 0.1111 0.0000 0.4074 

14 July 0.2609 0.0000 0.2609 0.0870 0.0000 0.3913 

15 July 0.2105 0.0000 0.3684 0.1053 0.0000 0.3158 

16 July 0.2500 0.0000 0.4375 0.0625 0.0000 0.2500 

17 July 0.2500 0.0000 0.6250 0.1250 0.0000 0.0000 

18 July 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 

19 July 0.0000 0.0000 1.0000 0.0000 0.0000 0.0000 

1

 Reaches of the Yukon River main stem and associated tributaries not monitored by tracking

 stations. 

2

 Including reaches of the upper Yukon and Porcupine rivers. 
106 

Appendix K. -- Movement rates (km/day) of Chinook salmon radio tagged in the Yukon River 

 basin during 2004 based on fish passage by tracking stations located at Paimiut

 and the furthest upriver station site. 

Region 

Lower Basin 

Stock 

Lower Yukon1,2 

Average 

(km/d) 

45.3 

CI (95%) 

38.4, 52.2 

N 

26 

Innoko 35.6 14.5, 56.7 5 

Bonasila 37.6 30.6, 44.6 14 

Anvik 31.2 28.2, 34.2 40 

Nulato 43.1 37.4, 48.8 11 

Koyukuk River Gisasa 

Middle Koyukuk 

Upper Koyukuk 

Henshaw 

34.0 

53.1 

69.8 

67.0 

28.0, 40.0 

44.0, 62.2 

65.9, 73.7 

8 

5 

5 

2 

Middle Yukon 

South Fork 

Mid-Yukon1,3 

68.0 

46.3 

60.7, 75.3 

38.7, 53.9 

5 

16 

River Melozitna 40.2 21.4, 59.0 3 

Nowitna 55.2 31.0, 79.4 3 

Tanana River 

Tozitna 

Lower Tanana4,5 

50.5 

47.9 

41.8, 59.2 

36.9, 58.9 

8 

6 

Kantishna 55.2 51.1, 59.3 9 

Tolovana 49.3 3 

Middle Tanana4,6 44.4 31.7, 57.1 8 

Nenana 47.8 1 

Clear 52.9 3 

Chena 45.6 43.0, 48.2 27 

Salcha 43.2 41.9, 44.5 61 

Upper Yukon 

River (U.S.) 

Goodpaster 

Upper Tanana4,7 

Upper Yukon, Tanana-Circle1,8 

Upper Yukon, Circle-Eagle1,8 

Beaver 

43.0 

40.2 

54.6 

57.7 

62.6 

41.3, 44.7 

36.7, 43.7 

48.7, 60.5 

41.3, 74.1 

23 

8 

20 

3 

2 

Hodzana 52.3 1 

Chandalar 54.3 49.3, 59.3 13 

Charley 

Nation 

38.2 

57.5 

1 

2 

Upper Yukon 

River (Canada) 

Lower Canadian Yukon4 

Chandindu 

Klondike 

47.8 

59.2 

61.9 58.4, 65.4 

3 

1 

12 
107 

Appendix K. -- Continued. 

Average 

Region Stock (km/d) CI (95%) N 

Upper Yukon Sixtymile 49.9 1 

River (Canada) Stewart 57.7 53.9, 61.5 23 

White 59.5 56.6, 62.4 12 

Mid Canadian Yukon, White-Tatchun4 48.7 45.8, 51.6 28 

Pelly 57.4 55.6, 59.2 40 

Tatchun 50.1 3

 Upper Canadian Yukon, Tatchun-Teslin4 52.0 49.7, 54.3 26 

Nordenskiold 57.5 2 

Little Salmon 56.3 3 

Big Salmon 54.9 52.9, 56.9 25

 Teslin 54.3 52.1, 56.5 39 

Upper Canadian Yukon, upriver of Teslin4 52.8 48.1, 57.5 7 

Takhini 51.1 48.4, 53.8 5 

Porcupine River Black 43.5 1 

Sheenjek 

Coleen4 

57.2 

63.9 

51.7, 62.7 

55.9, 71.9 

6 

4 

Canadian reaches 56.8 1 

Old Crow River 64.0 1 

Miner 54.9 3 

1

 Non-terminal areas and associated tributaries not surveyed.

2

 Section of the Yukon River from Russian Mission to the Yukon-Koyukuk River confluence.

3

 Section of the Yukon River from Galena to the Yukon-Tanana River confluence.

4

 Including fish in mainstem areas and associated tributaries.

5

 Section of the Tanana River from the Yukon-Tanana River confluence to Nenana.

6

 Section of the Tanana River from Nenana to the Tanana-Salcha River confluence.

7

 Section of the Tanana River upriver from the Tanana-Salcha River confluence.

8

 Section of the Yukon River upriver from the Yukon-Tanana River confluence.
RECENT TECHNICAL MEMORANDUMS


Copies of this and other NOAA Technical Memorandums are available from the 

National Technical Information Service, 5285 Port Royal Road, Springfield, VA 22167 

(web site: www.ntis.gov). Paper and microfiche copies vary in price. 

AFSC164	 YANG, M-S., K. DODD, R. HIBPSHMAN, and A. WHITEHOUSE. 2006. Food habits of groundfishes in 

the Gulf of Alaska in 1999 and 2001. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-AFSC-164, 199 

p. NTIS number pending. 

163	 EILER, J. H., T. R. SPENCER, J. J. PELLA, and M. M. MASUDA. 2006. Stock composition, run timing, 

and movement patterns of chinook salmon returning to the Yukon River basin in 2003, 104 p.NTIS No. 

PB2006-108429. 

162	 IGNELL, S. E., B. L. WING, B. D. EBBERTS, and M. M. MASUDA. 2006. Abundance and spatial pattern 

of salps within the North Pacific Subarctic Frontal Zone, August 1991, 26 p. NTIS No. PB2006-108423. 

161	 ANGLISS, R. P., and R. OUTLAW. 2005. Alaska marine mammal stock assessments, 2005, 247 p. NTIS 

number pending. 

160	 SEPEZ, J. A., B. D. TILT, C. L. PACKAGE, H. M. LAZARUS, and I. VACCARO. 2005. Community 

profiles for North Pacific fisheries - Alaska, 552 p. NTIS No. PB2006-108282. 

159	 ETNIER, M. A., and C. W. FOWLER. 2005. Comparison of size selectivity between marine mammals 

and commercial fisheries with recommendations for restructuring management policies, 274 p. NTIS 

No. PB2006-102327. 

158 	 LANG, G. M., P. A. LIVINGSTON, and K. A. DODD, 2005. Groundfish food habits and predation on 

commercially important prey species in the eastern Bering Sea from 1997 through 2001, 222 p. NTIS 

number pending. 

157	 JOHNSON, S. W., A. DARCIE NEFF, and J. F. THEDINGA. 2005. An atlas on the distribution and 

habitat of common fishes in shallow nearshore waters of southeastern Alaska, 89 p. NTIS number 

pending. 

156	 HOFF, G. R., and L. L. BRITT. 2005. Results of the 2004 Eastern Bering Sea upper continental slope 

survey of groundfish and invertebrate resources, 276 p. NTIS No. PB2006-100504. 

155	 YANG, M-S., K. AYDIN, A. GRIEG, G. LANG, and P. LIVINGSTON. 2005. Historical review of capelin 

(Mallotus villosus) consumption in the Gulf of Alaska and Eastern Bering Sea, 89 p. NTIS No. 

PB2005-110464. 

154	 HOLLAND D. S. 2005. Economic analysis of protection of essential fish habitat in Alaskan fisheries: 

An analysis of research needs, 35 p. NTIS No. PB2005-110129. 

153	 FRITZ, L. W., and C. STINCHCOMB. 2005. Aerial, ship, and land-based surveys of Steller sea lions 

(Eumetopias jubatus) in the western stock in Alaska, June and July 2003 and 2004, 56 p. NTIS 

number PB2005-108287. 

152	 AMES, R. T., G. H. WILLIAMS, and S. M. FITZGERALD. 2005. Using digital video monitoring 

systems in fisheries: Application for monitoring compliance of seabird avoidance devices and seabird 

mortality in Pacific halibut longline fisheries, 93 p. NTIS No. PB2005-107312. 

151	 TESTA, J. W. (editor). 2005. Fur seal investigations, 2002-2003, 72 p. NTIS No. PB2005-104811. 

150 	 GULLAND, F. M. D., H. PÉREZ-CORTÉS M., J. URBÁN R., L. ROJAS-BRACHO, G. YLITALO, J. 

WEIR, S. A. NORMAN, M. M. MUTO, D. J. RUGH, C. KREUDER, and T. ROWLES. 2005. Eastern 

North Pacific gray whale (Eschrichtius robustus) unusual mortality event, 1999-2000: A compilation, 

33 p. NTIS No. PB2005-105795.