genetic relationships among populations of alaskan chinook salmon ( oncorhynchus...
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Genetic Relationships among Popu ations of A askan Chinook Salmon (Oncorhynchus tsha wytscha
A. I . Gharrett, S. M. Shirley, and 6 . R. Tromble School sf Fisheries and Science, University of Alaska, luneaer, 1 1 120 Glacier Wwy., juneau, A# 99887, USA
Gharrett, A. j., 5. M. Shirley, and G. R. Tromble. 1987. Genetic relationships among populations of Alaskan chinook salmon (Oncoshynchus tshawytscha). Can. J. Fish. Aquat. Sci. 44: 765-774.
Chinook salmon (Oncorhynchus tshawytscha) coileeted from 13 Alaskan drainages were genetically charac- terized at 28 protein coding loci using starch-gel electrophoresis. Chinook salmon in western Alaska are generally quite similar to each other but are distinct from the more diverse southeastern Alaskan populations. Genetic compositions of southeastern Alaskan populations are generally intermediate between those of western Alaska and previously studied nsn-Alaskan populations to the south. Given that chinook salmon survived the Wisconsin glaciation in both the Bering and Pacific refuges, we propose that chinook salmon from 910th refuges participated in the post-Wisconsin colonization sf southeastern Alaskan rivers.
A l'aide de I'electrophorGse sur gel d'arnidon, les auteurs ont determine les caracteristiques g6netiques de 28 locus codeurs de proteines chez des saurnons quinnats (Oncorhynchus tshawytscha) captures dans 7 3 bassins versants de I'Alaska. En ghbral, les saurnons quinnats de I'ouest de I'AIaska se ressernblent mais ils ssnt distincts des populations du sud-est de I'Alaska, plus diversifikes. Les compositions genetiques de ces derni&res popula- tions sont gkneralement intermediaires entre celles des populations de I'ouest de I'Alaska et celles des popula- tions d'autres regions du sud deja etudikes. Etant donne que le saurncsn quinnat a survecu 2 la glaciation du Wisconsin dans les refuges de Bering et du Pacifique, les auteurs formulent B'hypothese que le saumon quinnat de ces deuw refuges a participk la colonisation post-glaciaire des cours d'eau du sud-est de ItAlaska.
Received May 27,1986 Accepted December 85, 1984 (.!a81 7)
C hinook salmon (Oncorbzp?nchus W ~ ~ W J ~ ~ S C ! ~ ) are dis- tributed in western North America from the Ventura River in southern California to Point Hope in north- eastern Alaska and in eastern Asia from northern
Hokkaido to the Anadyr River (McPhail and Lindsey 1970). A variety of anadromous Bife cycles are found within the natural range of this species. Different populations return to their natal streams to spawn in the spring, summer, or fall. Juveniles may rear in freshwater for I or 2 mo (ocean-type) or a year or more (stream-type) before migrating to the sea (HeaIey 1983). Some populations spawn very close to salt water, while others migrate over 1000 mi up Iong rivers such as the Yukon to their spawning grounds. The variety of Bife histories, restricted potential for gene Wow because of homing behavior, and the broad geographical distribution suggest that considerable genetic diversity may exist among populations of chinook salmon.
All Alaskan chinook populations that have been studied return in late spring or early summer to spawn and are stream- type fish (Healy 1983). However, because of the turbidity of many of the river systems and the remoteness of chinook spawning grounds, infomation about the biology and distribu- tion of Alaskan chinook salmon is incomplete. At least one river system, the Kenai River draining into Cook Inlet, is characterized by two runs that spawn at different times (July and August) and in different areas within that drainage (Burger et al. 198%).
Information pertaining to diversity and number of popula- tions of fish in a region can often be obtained from genetic
compositions of collections of fish taken throughout the region. The genetic structures of fish populations may be used for stock identification by managers ( e . g . Grant et al. 1980), for $ r o d stock selection and management in hatcheries (e.g. Ryman and S t a l I980), and for inferring relationships among populations (e.g. Utter et al. 1980). Starch-ge! elec- trophoresis has proven fruitful for examining the genetic compositions sf chinook salmon in the Columbia River and western Washington (e.g. Milner et al. 1981, 1983). Charac- terization of the genetic compositions of these chinook ppula- tions has revealed differences among populations related to their watershed and to the timing of spawning runs. Studies in British Columbia indicate allozyme differences related to juve- nile life history (Carl and Healey 1984). To obtain more information on the distribution and diversity of Alaskan chinook salmon populations and data that may be useful to managers and cu!turists, we have genetically characterized populations covering a broad geographical range of Alaska. In this paper, we examine genetic relationships among Alaskan chinook populations and compare them with some more south- erly non-Alaskan, wild populations previously described by Miher et al. (1983).
Materials and Methods
Samples
Thirty-seven collections of young chinook salmon or tissue samples from adults, representing more than 2580 individuals,
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Hes. B . Sites s f collection of Alaskan chinook salmon from western (left) and southeastern Alaskan (right) drainages. Numben comespond to collections Iisted in Table 2. Collections from the same drainage which were p o l e d for analysis are designated by letters A - 0 and comespnd those in Tables 2, 3, and 4.
were taken from or near 13 major Alaskan river systems (Fig. I ; Table 2). Juveniles md smolts were captured with baited minnow traps and seines. Tissue samples of eye, liver, hem, and skeletal muscle were taken fmm adult fish netted in test fisheries, fish sacrificed in remote gamete collections for hatchery brood stock, and from commercial plants processing chinook caught by gill net. Samples were kept on ice until they were frozen and stored at -20 or - 80°C. Hn most river systems, collections were made at more than one location and/or in more than one year.
Western Alaskan drainages sampled were the klna8akleet, Yukon, and Kuskokwlm rivers md Bristol Bay. Chinook caught in Bristol Bay gillnet fisheries (see C, Fig. I; Table 2) off the Igushik and Togiak rivers were sampled at processing plants in Billingham and Togiak, respectively. Fish from gillnet fisheries in the lower Kuskokwirn River (D) were sampled at plants in Bethel. Chinook caught in the lower Yukon (F and G ) were sampled at processors and from a test fishery near Emmonak. These collections were ma& at dif- ferent times during the mn and in different years. Other collec- tions from the Yukon drainage were taken from tributaries to the Tanana River system (H) in interior Alaska. From the paorthem-most river system, the UnalskHeet River (E), collec- tions of tissues were obtained from test fisheries.
In south-central Alaska, juveniles were collected from the Indian River, a Susitna River tributary (B). Adult chinook
T&u, Stikine, Chilkat, Fanagut, Uwuk, a d King Salmon (Admiralty Islmd) rivers. Samples of tissues from adults were taken during remote gamete coIlections from King Salmon (K) and Farragut (N) rivers, Andrew Creek (M), a Stikine River tributary, and from the Chilkat drainage (I). Juveniles were also sampled from the Chilkat system (I), the Stikine River and upper tributaries (L), the Unuk River (O), and both the Bower Taku River system and upper Taku River tributaries (J). The Taku and Stikine rivers we transmountain systems, crossing the coastal range into Cmada near the headwaters of the Yu~QII.
Sample preparation and electrophoresis followed Utter et al. (1974). Small juveniles were macerated in water; larger juve- niles were dissected to obtain individual tissues. Buffers used for electrophoresis were 1 (Ridgway et aE. 1970), I1 (Mukert and Faaalhaber 1965), 611 (Clayton and T ~ t i & B972), and 1'4, a pH 7.0 ~is(hydroxyme~gr1)aminomethane buffer described by Shaw and R a a d (1 970). The enzymatic activities were stained using methods described by Harris and Hopkinson (1996) and Shaw and Prasad (1978) modified for use in our Eaboratory (McGregor 1982; Lane IL 984). Genetic loci and related data are given in Table I . PepbLgg) is peptidase B activity. Peg('Pp-2) is peptidase D activity (Frick 1983).
intercepted by the gillnet fishery as they returned to Copper Analysis River (A) were sampled at processing plants in Cordova,
In southeastern Alaska, six river systems were sampled, the Departure of the genotypic frequencies of collections from
766 Can. J . Fish. Aquas. Sci., Vof. 44, 1987
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TABLE 1. Rotein coding itxi, their Enzyme Commission (EC) numbers (international Union of Biochemistry 1984) and designations (May 19801, and the tissues and buffers in which they were resolved. m e peptidaae 1wi ape designated according to their substrate specificity. Buffers used are numbered as in the text.
EC Enzyme No. Designation Tissue Buffer
Liver Eye Muscle Muscle Muscle
II, 11% H 1 I I Glucose-&phosphate isomerase
GIyceroE-3-phosphate dehydrogewase Heart
Heart Heart Liver, eye Muscle Heart Liver Eye Heart, eye Liver, muscle Muscle
I11 III III IV I I I I II I11 III
laoci tmte dehydrogenase Lactate dehydrogewase
Manmose-6-phosphate isomerase Malate dehydrogenase
Peptidases Leucyl-glycyl-glycine activity PhenylalanyI-proline activity
Muscle Heart, muscle Heart, muscle Muscle Eye Muscle
GBycyl-leucine activity
Liver Liver Liver
Hardy-Weinberg equilibrium expectations was examined easing chi-square godness-of-fit tests with a continuity conec- tion of 0.25 (Emigh 1988). Pooling of genotypic frequencies eliminated classes with expected values less than four.
Variability obsewd at co-migrating duplicated loci (issloci; Allendorf and Thorgad 1984) was treated as if all variation appeared at one of the loci and the other locus was mono- morphic. This treatment tends to give conservative estimates of genetic distances and heterozygosities.
Homogeneity of allelic frequencies among collections within a drainage, among drainages within a region, and among regions was examined using Isg-iikelihmd ratio (G-test) (Sokal and Wohlf 1981). When no heterogeneity was detected, the frequencies of the collections were pooled for subsequent analyses, since there was no reason to believe that the collections reflected genetically distinct populations. To examine the basis 0% the heterogeneity within a drainage, a stepwise test procedure (Sokal and WohIF 1981) was used to partition the collections into groups within which no significant heterogeneity existed. Pooling of allelic frequencies eliminated classes with expected values less than two. Where multiple tests were performed, a csmction for the level of significance was made (Cooper 1968). Levels of heterogeneity were csm- pared using F-distributions: F(wl ,w2) = (GI /'w~>/' (G2/'w2).
Gene diversity analysis (Nei 1973; Chakroborty 1980) was perfoppaad to decompose the genetic variability (hetero- zygosity) into hierarchical levels: HT = & + DnR 4- DRT, where HT is the t o I heterozygosity sbsewed, HD the average
heterozygosity within drainages (or major saabdivisisns of drainages) within regions, DDR = HE - HD the variability attributable to diversity among drainages within regions, and DRT = HT - HR that among regions. Coefficients of gene differentiation (Nei 1943) were computed to estimate the pro- portion of total gene diversity due to each level of hierarchy.
Unbiased average heherozygosities and their sampling vari- ances (Nei and Roychoudhaary 1944; Nei 1948) were estimated using a FORTRAN program obtained from Nei and modified.
Relationships among the coHIectisns were examined from a maximum-Hikelihood evs%bationary tree obtained using Felsens- tein9s (1973, 1984) CONTML program. This unrmted tree (network) is constructed from a chord measure of genetic distances (Cavalli-Sforza and Edwards 1967) by computing the topology with the maximum likelihood for the genetic dis- tances between all pairs inchded in the data set. The program was run as recommended by the author.
Of the 28 bimhemical genetic Iwi examined (Table 2), 12 were mmonaomop~~hie and identical in all collections; these were Adh, Pgd, Pgm-2, Pep(Pp-I), Ck-B and -2, Ldh-1, -3, and -5, and G3p-I, -2, and -3. Six loci that had low levels of poly- morphism (frequency s f the common allele p 8.95 in all collections) weE Gpi-3, Ldh-4, Bep(GP -21, Bep(Pp-2), and isoloci Mdh-12. Loci dispjaying more p%ymorphisrn (the frequency of the most common allele < 0.9 in at least one
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TABLE 2.
Bio
chem
ical
gen
etic
var
iatio
n in
lca
lllec
aion
s of
chi
nook
sal
mon
fro
m d
rain
ages
in A
lask
a. A
llelic
fre
quen
cies
and
colle
ctio
n si
zes (N) fo
r bi
oche
mic
al g
enet
ic lo
ci. C
olle
ctio
ns
are
num
bere
d as
in F
ig.
I an
d gr
oupe
d un
der
desi
gnat
ions
for d
rain
ages
and
sub
divi
sion
s of
drai
nage
s. A
llele
s m
e de
sign
ated
by
thei
r m
obili
ty r
elat
ive
to t
he m
ost
com
mon
alle
le (
100)
.
Loci
Sour
ce o
f sa
mpl
e M
pi
Sod-
I M
dh-3
,4
Pep(
G1-
I)
P~
P~
LR
R)
Gpi
-3
Mdh
-I,?
Ldh-
4 an
d ye
ar o
f G
mup
cd
lest
ioo
N
100
110
95
N
100
260
N
100
80
121
N 10
0 (P
O N
10
0 13
0 95
N
10
0 10
5 93
N
I(
X)
120
82
N
100
117
A
Cop
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46
1.00
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00
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46
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0.00
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45
1.00
0.
00
2. 1
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82
0.92
0.
08
0.00
82
0.
96
0.04
0.
00
82
1.00
0.
00
0.00
82
1.
00
0.00
J
asks
r R
iver
juve
nile
s 24
. N
ahlio
R.
1982
42
0.
81
0.19
0.
00
42
0.83
0.
17
42
0.99
0.
01
0.00
34
0.
93
0.07
42
0.
96
0.04
0.
00
42
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0.
04
0.00
42
1.
00
0.00
0.
00
42
1.00
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00
25. L. N
akin
a 19
82
85
0.76
0.
24
0.00
73
0.
80
0.20
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0.
94
0.00
0.
06
84
0.91
0
90
1.00
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W
0.0
50
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99
0.01
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W
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1.00
0.
00
0.00
90
8.CX
) 0.
00
26.
Main
stem
198
1 10
0 0.
82
0.18
0.
00
98
0.92
0.
08
100
0.98
0.
02
0.00
0.
88
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10
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98
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11
100
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0.
04
0.00
-
--
--
-
27.
Main
fitem
198
2 92
0.
78
0.19
0.
03
95
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10
95
0.97
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03
0.00
85
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95
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59
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00
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00
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2 47
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00
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00
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00
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47
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00
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00
K A
dmira
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sland
egg
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gSal
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83
64
0.94
0.
06
0.00
21
0.
95
0.05
64
1.00
0.
00
0.00
64
0.
78
0.22
68
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00
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00
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64
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0.00
64
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00
3Q.K
ingS
alm
nR.
1984
64
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0.
05
0.00
66
0.%
0.
04
64
1.00
0.
00
0.00
(6
4 0.
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0.12
64
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02
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64
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00
0.00
0.
00
64
1.00
0.
00
0.00
64
1.00
0.
00
Stik
ine
Riv
er
L U
pper
Stik
ine
juve
nile
s 38
. Litt
le T
ahlta
n 19
81
170
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0.
15
0.00
11
0 0.
89
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1 14
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96
0.04
0.
00
88
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0.
03 - -
-
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140
1.00
0.
00
0.00
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-
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92
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00
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33. M
ains
tem
198
4 15
2 0.
84
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0.
00
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05
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02
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15
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10
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995
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03
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20
4 1.
00
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M
152
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80
M Lo
wer
Stik
ine
egg
take
34
. A
ndre
w C
r. 89
82
125
0.73
0.
27
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11
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94
0.06
12
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98
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00
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14
116
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03
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93
0.
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W
126
1.00
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0.0
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9 N
Fa
mgu
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take
35
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83
26
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12
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26
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75
0.25
26
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00
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00
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00
26
1.00
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00
0.00
26
1.
00
0.0
0.
00
26
1.00
0.
00
36.
1984
24
0.
92
0.08
0.
00
24
0.81
0.
19
24
1.00
0.
00
0.00
23
1.
00
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98
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00
24
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02
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24
1.
00
0.00
0.
00
24
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00
O
Un&
Riv
er ju
veni
les
37.
1982
$2
0.
82
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00
82
0.87
0.
13
82
0.98
0.
02
0.00
82
0.
98
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54
1.
00
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0.
00
40
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01
0.00
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00
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IX)
Can
. J. F
ish.
Aqu
at. S
ci. D
ownl
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d fr
om w
ww
.nrc
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arch
pres
s.co
m b
y C
ON
CO
RD
IA U
NIV
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11/1
2/14
For
pers
onal
use
onl
y.
TA
BL
E 2.
(Con
c!ud
ecd)
Sam
ple
size
s of
mon
omor
phic
loci
So
urce
of
sam
ple
Fsp
(G1-
2)
Sod-
2 A
at-3
Id
h-3,
Q
and
year
of
PepV
'p-2
) PC
P G
roup
co
llect
ion
M
100
70
105
N
100
142
N
100
85
N
100
136
74
127
50
N
100
110
105
Uh
-3
Ck-
1 C
k-2
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G
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p-1)
U
h-l
Ad
h
A
Cop
per R
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gill
net
fishe
ry
1. 1
983
42
1.00
0
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, 43
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W
0.00
45
0.
68
0.32
- - - - - -
46
8.0
00
.00
0.0
0
45
34
34
45
43
43
43
41
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00
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00
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00
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80
97
101
80
80
102
74
B
Susi
tna
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er ju
veni
les
3. I
ndim
R.
1983
86
1.
00
0.00
0.
00
-- - -
75
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0.
14
81
1.00
0.
00
0.00
0.
00
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86
O.W
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0
86
77
77
86
86
86
86
86
86
86
86
76
4. I
ndia
n R.
198
4 10
0 1.
00
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0.
08,
92
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0.
08 - - -
82
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W
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00
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10
0 8.
00
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00
100
100
100
100
100
lrOO
100
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100
1CX)
10
0 @
C
B
risto
l Ba
y gi
llnet
fish
ery
5. T
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k 19
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109
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00
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83
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92
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10
9 0.
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10
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995
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00
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00
109
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00
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19
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25
10
9 $4
8.1
109
72
84
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109
108
6. D
illin
ghar
n 19
83
%
1.0
0.
00
0.00
73
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95
0.05
93
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92
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0
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005
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00
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46
0.
99
0.01
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W
40
87
87
102
72
72
%
97
72
46
95
105
D
Kus
kokw
im g
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t fis
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7.
198
2 37
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W
0.00
0.
00
16
0.91
0.
59 - - - - -
- - - -
58
0.99
0.
00
0.01
65
57
57
68
63
63
65
-
63
58
65
43
8. 1
983
103
1.08
0.
00
0.00
11
2 0.
95
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10
5 0.
86
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65
1.
00
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00
0.00
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00
101
1.00
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00
0.W
10
5 98
98
10
5 11
2 11
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11
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1 10
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198
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00
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00
156
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07
105
0.83
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17
108
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02
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00
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11
5 1.
00
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0.
00
119
119
I19
119
119
119
119
87
119
115
119
76
E U
nala
klee
t gill
net
fishe
ry
10.
1982
38
1.
00
0.00
0.
00
37
O.%
0.
04 - - - - - - - - -
38
0.97
0.
03
0.00
38
37
37
38
38
38
38
38
38
38
38
78
ll.
1983
27
1.
00
0.00
0.
00
26
0.94
0.
068
25
0.86
0.
14
27
0.98
0.
02
0.00
0.
00
0.00
27
1.
00
0.00
0.
00
27 - -
27
25
25
27
25
25
27
27
27
Low
er Y
ukon
gill
net
fishe
ry
F Su
bdiv
isio
n I
12. E
mm
onak
198
2 45
1.
00
0.00
0.
00
35
0.93
0.
07 - - - - - - - - -
45
1.00
0.
00
0.00
45
- -
45
45
45
45
45
45
45
45
45
13. B
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dy 1
982
133
1.00
0.
00
0.00
10
9 0.
95
0.05
- - -
-- - - - - -
112
0.9%
0.00
0
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131
102
102
127
80
80
107
35
80
112
133
81
14. B
ig E
ddy
1983
41
1.
00
0.00
0.
00
41
0.90
0.
10
48
0.92
0.
08
38
0.96
1 0.
039
0.00
0.
00
0.00
41
1.
00
0.00
0.
00
45
27
27
48
41
41
41
42
41
41
48
41
G
Subd
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ion
I1 15
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mon
ak 1
983
45
1.00
0.
00
0.00
45
0.
96
0.04
45
0.
81
0.19
45
1.
00
0.00
0.
00
0.00
0.
00
45
1.00
0.
00
0.00
45
27
27
45
-
-
45
23 -
45
45
38
16. S
t. M
ary'
s 19
83
98
0.99
5 0.
005
0.00
89
0.
90
0.10
95
0.
76
0.24
86
0.
994
0.00
6 0.
00
0.00
0.
00
83
1.00
0.
00
0.00
98
45
45
98
75
75
86
87
75
94
85
10
1 H
Tana
na R
iver
juve
nile
s 17
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116
1.00
0.
00
0.00
36
0.
92
0.08
- - - - -
- - - -
78
1.00
0.
00
0.00
$1
6 76
76
40
11
6 11
6 76
-
116
78
116
-
18.U
.Che
naR
.198
2 13
4 1.
00
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0.
00 - - - - - - - -
- - - -
135
1.00
0.
00
0.00
13
5 13
5 13
5 13
5 45
45
13
5 -
45
135
135
-
19. L.
Ckn
a R
. 19
83
78
1.00
0.
00
0.00
11
1.
00
0.00
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41
8.00
0.
00
0.00
0.
00
0.00
79
1.
00
0.W
0.
00
79
79
79
79
77
77
28
41
77
79
79
73
20.
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tinik
a R
. 19
84
119
1.00
0.
00
0.00
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117
0.70
0.
30
97
1.00
0.
00
0.00
0.
00
0.00
18
9 1.
00
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00
119
818
118
lj9
11
9 11
9 11
9 11
9 11
9 11
9 11
9 11
9 I
Chi
lkat
Riv
er
21. T
ahin
i R.
1983
egg
take
18
1.
00
0.00
0.
00
34
1.00
0.
00
32
0.93
0.
07
34
1.0
0.
00
0.00
0.
00
0.00
34
1.
00
0.00
0.
00
34
16
16
34
34
34
16
34
34
34
34
26
22.
Tah
ini R
. 19
% e
g ta
ke
34
8.00
0.
00
0.00
34
1.
00
0.00
34
0.
94
0.06
34
0.
93
0.00
0.
07
0.00
0.
00
34
1.00
0.
00
0.00
34
331
31
34
34
34
34
34
34
34
34
34
23.
Tah
ini R
. 19
8.1 ju
veni
les
82
1,00
0.
00
0.00
- - -
81
0.96
0.
M
65
0.92
0.
00
0.08
0.
00
0.00
$1
1.
00
0.00
0.
00
82
82
82
82
82
82
82
81
82
82
62
82
J Ta
ku R
iver
juve
nile
s 24
. N
ahlin
R.
1982
39
0.
97
0.00
0.
03
42
1.00
0.
00 - - - - -
- - - -
39
1.00
0.
00
0.00
42
42
42
42
42
42
-
42
42
42
42
42
25.
E. N
akin
a 19
82
89
1.00
0.
00
0.00
- - - - - -
90
1.00
0.
00
0.00
0.
00
0.00
50
0.
99
0.01
0.
00
90
YD
90 -
90
90
-
WW
45
9Q
W
26.
Mai
nste
rn 1
981
100
0.89
0.
01
0.04
0.
06
0.00
- - - -
- - - -
-
-
800
- -
.-
- 7
27.
Mai
nste
m 1
982
85
1.00
0.
00
0.00
95
1.
00
0.00
46
0.
95
0.05
14
1.
00
0.00
0.
00
0.W
0.
00
91
1.00
0.
00
0.00
95
85
85
95
95
95
45
94
95
93
95
90
28
. K
ing
Salm
on C
r. 19
82
47
1.00
0.
00
0.m
- - - - - -
47
11.00
0.
00
0.00
0.
00
0.00
47
O
.%
0.04
0.
00
47
47
47
42
47
47
47
45
47
47
47
47
K A
dmid
ty I
sland
egg
tak
e 2!2
. K
ing
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on R
. 19
83
63
1.00
0.
00
0.00
21
1.
00
0.00
51
1.
00
0.00
40
1.
00
0.00
0.
00
0.00
0.
00
64
1.00
0.
00
0.00
- -
64
64
64
64
64
64
64
6
46
46
4
30.
Kin
g Sd
rnca
n R
. 19
84
64
1.00
0.
00
0.M
64
1.00
0.
00
44
0.98
0.
02
53
1.00
0.
00
0.00
0.
m
0.00
64
1.00
0.
00
0.00
64
59
59
64
@
64
64
59
64
64
64
64
Stik
im R
iver
L
U
pper
Stik
ine
juve
nile
s 31
.Lin
kT;a
hl#a
n198
1 - -
-
- - - - - - - - - - - - - - - - -
- - - -
-
-
17
0-
-
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--
32
. M
ains
tem
198
1 -
- - -
--
--
--
108
0.96
0.
W
0.04
0.
00
0.00
-
--
- -
- - - -
-
10
8-
--
--
--
33
. M
ains
tern
898
2 50
1.
00
0.00
0.
00
204
1.00
0.
00
147
0.90
0.
10
144
1.00
0.
00
0.00
0.
00
0.00
15
1 1.
00
0.00
0.
00
102
130
130
152
142
142
152
90
142
152
I02
142
M b
w S
tikin
e e
g ta
ke
34.
Mr
ew
Cr.
198
2 82
6 1.
00
0.00
0.
00
69
1.00
0.
W
33
0.83
0.
17
68
0.89
0.
1 1
0.00
0.
00
0.00
67
8.
00
0.00
0.
00
826
126
126
126
126
126
109
81
126
125
126
92
N F
arra
pt R
iver
egg
tak
e 34
. 19
83
23
1.00
0.
00
0.00
26
1.
00
0.00
- - -
26
1.00
0.
00
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TABLE 3. Heterogeneity of Alaskan chinook salmon. Log-likelihood ratio analysis (Sokarl and Rohlf 198 1 ) of allelic frequencies. Group designations refers to drainages or subdivisisms within drainages (see Table 2). N o test indicates presence of a single collectiesn. *P<0.04)1; $40.05 for all others.
Heterogeneity Heterogeneity Heterogeneity within in drainage within
Group drainages subdivisions regions
designation Regism/ drainage G d f G d f G d f
South-central Alaska Copper River Susitna River
Western Alaska BristoI Bay Kbaskokwirn River klnalakleet River Yukon River
Lower river I Lower river 11 Tanana River
Southeastern Alaska ChiIkat River Taku River Admiralty lsland Stikine River
Upper river Lower river
Fanagut River Unuk River
13.28 8 25.56 I2 5.09 2
93.21 15" 18.42 8
N o test 0.86 2 N o test
Heterogeneity among regions 956.66 14"
collection) were Mpk, Sod-] and -2, Pep(CI-I), Pep(&gg), Aab-3, and isoloci Mdh-3,4 and I&-3,4. No deviations from Hardy - Weinberg equilibrium expectations were observed ( P > 0.05); however, only large deviations would be detect- able given the collection sizes.
For most drainages, collections were made at more than one site and/or in more than one year to examine spatial and temporal heterogeneity existing within each drainage. After correction for multiple testing (Cooper 1968), heterogeneity was observed only in the Stikine and Yukon ( P < 0.001) (Table 3). No spatial or temporal variability was obsewed in the other systems.
To examine the nature of the heterogeneity within the Yukon and Stikine drainages, a stepwise test procedure (Sokal and Rohlf B 98 1) was used to partition the collections within each drainage into groups within which no significant hetero- geneity existed. The Yukon collections produced three groups, two groups of lower Yukon gillnet and test fishery ccsliections (Subdivisions I and %I) and the collections fmm the Tanana River tributaries (Table 2 ) . The Tanana csllections were juve- niles taken near their natal grounds and probably reflect one or a very few populations. In contrast, the Bower Yukon collec- tions were taken from the particular mixture of populations passing through the fishery at the time of capture.
Heterogeneity within the Stikine River was attributable to the collection taken from Andrew Creek, near the mouth of the Stikine River, suggesting that divergence has meurred between upstream and downstream chinook populations. All subsequent analyses were pE-Fowaaed using data pooled from a drainage or from groups of collections minimizing ketero- geneity within a drainage (Table 3).
The drainages or significant subdivisions of the three major geographic regions, western, south-central, and southeastern Alaska, were further examined using log-likelihood ratio anal- ysis to determine the extent of divergence within and among regions (Table 3). Significant heterogeneity ( B < 0.001) was obsewed at both levels of hierarchy; however, relatively more (P < 0.01) was observed among regions than within regions;
Gene diversity analysis was used to partition the variation observed at 28 genetic loci into component% attributable to regional differences, to differences among significant subdivi- sions within regions, and to the average amount observed within drainages (or their subdivisions). The Unuk River col- lection was not included in this analysis because data were not available for two of the loci, Most of the variability observed was expressed within drainages (94.09%). Divergence within regions accounted for 3.32% of the variability and differences among regions for 2.59% {Table 4).
To examine the genetic relationships sf Alaskan chinook and chinook fmm other more southerly drainages, an unrooted maximum-likelihod tree (Felsenstein 1973, 1984) was con- structed from allelic frequencies of 23 loci common to our data and to four groups of southern populations previously reported by Milner et aE. (1983). The loci not used had little or no po8yrnogphism; they were PepdPp-I), Pep(@-28, Ldh-H , Adh, and G3p-3. Southern collections used included spring-run and fall-run wild populations chosen as representative of two life history types. Unweighted means of the allelic frequencies of chinook from Nosksack and Solduc rivers in Washington are referred to as Washin@on (spring). Similarly, allelic frequen- cies of chinook from Hoh and Queets rivers in Washington were combined as Washington (fall). Data from three Fraser
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TABLE 4. Gene diversity analysis of Alaskan chinook salmon using 28 loci.
Coefficient sf Source Gene diversity gene differentiation
Average within drainages HD = 0.03267 PdDIHT = 0.949 and subdivisions
Average among drainages dB,, = 0.00115 GDR = 0.0332 within regions
Among regions DRT = 0.00090 GRT = 0.0259
Total gene diversity HT = 0.034'72
Tanana River (HI Lower Yukon I! ( 0 ) /
Lower Yukon i (F) Susitne River QB) Kuskokwim River QD) Unalokleet Rivgr (El
\ Columbia 0.1 (Deachutesl 0;o
Qenetic Distance Frc. 2. Phenetic relationships among Alaskan chinook and other more southerly groups of chinook. The maximum-likelihood method of Felsenstein (1973, 1984) was employed to estimate this unrooted tree using data from 23 loci. The tree is oriented to approximate the geographical relationships among the col8ectioras. 'The distances between mdes and csllections are chord measure genetic distances (Cavalli-Sforza and Edwards 196'9). Angles are arbitrary. Data for nsn-Alaskan collections are from MiIner et a]. (1983).
River collections were pooled in the same way and included because of their proximity to southeastern Alaska. Spring-run
springs on the Deschutes River, a Colum- bia River tributary, were chosen because of their geographical distance from all other collections.
Western Alaskan and southeastern Alaskan chinook are clearly separated from each other (Fig. 2). Chinook from one south-central drainage, Susitna River (B), were more closely related to chinook from western Alaska, while the Copper River (A) fish were intemediate between western and south- eastern collections but more similar to western Alaskan chinook. Other trees generated from the CONTME program were similar to the maximum-likelihood tree presented. Only details of the relationships within the southeastern Alaskan region or within the western Alaskan region varied among the less likely trees produced.
Western Alaskan Chinook
Two observations may be made from the genetic rela- tionships among the chinook salmon from western Alaskan drainages. Although heterogeneity exists among most of the drainages, the overall genetic differentiation among the dif- ferent populations was small for the 28 loci considered in this
study. Secondly, the chinook in the Tanana drainage, tribu- taries s f the upper Yukon (H, Fig. I), are unique. While no fixed differences were observed in the Tanana collections, Mpi variability was Bower and Mdh-3,4 higher than observed among any of the other drainages. Similar results were obtained using other measures of genetic distances (Rogers 19'32; Nei 19'38) and other clustering algorithms (results not shown). Western Alaskan collections were generally more variable at PegsdLgg), Sod-2, and Aat-3. The average hetero- zygosity per locus of these collections is low, 0.032 t 0.006 (mean k SE).
Southeastern Alaskan Chinook
Analysis of southeastern Alaskan collections (Fig. 2) indi- cated more differentiation among drainages than was observed in western Alaska. The greater extent of differentiation is paralleled by a small increase (P < 0.05) in variation of the average hetemzygosity per Boeus (0.033 9 01.012) a m n g southeastern Alaskan collections. Southeastern Alaskan col- lections generally showed more polymorphism at Mpi , Sod-1, and Gpi-3. By excluding data from Sod-2 and Pgm-1, the Unuk River collection was included in the analysis (not shown). Unuk River chinmk were most similar to the Sikine and Taku collections. Similar results were obtained using other genetic distance measures (Rogers 1942; Nei 19'98) and other clustering algorithms (results not shown).
The genetic compositions of most of the southeastern Alas- kan chinook populations were intermediate between those of western Alaskan chinook and of Washington fall-mn (Queets and Msh) and Fraser River chinook (Fig. 2). An exception is Chilkat River chinook, which differ from other southeastern Alaskan collections and which branch between the branch for the Fraser River and Washington fall-run (Queets and Hok) and the branch for Washington spring-mn (Soledtic and Nook- sack) chinook. Some of the uniqueness of the Chilkat fish was due to more variability at the Mpi locus.
Discussion
Fisheries Management ErnpBications
With the exception of the Yukon and Stikine rivers, no significant heterogeneity was observed within Alaskan drain- ages; however, small but statistically significant differences did exist among most of the drainages, indicating that no substantial straying among drainages takes place; sthewise, the regi~)li$ would be homogeneous. The absence of hetero- gene@ among collections made within a drainage in different years suggests that the genetic comg%ositisns of chinook are temporally stable. Similarly, no spatial heterogeneity was
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observed within the Tanana, Bristo% Bay, Chilkat, or Taku drainages or in the upper Stikine River tributaries. Of course, the degree of differentiation among collections taken to exam- ine spatial and temporal variation may have been too small to measure.
Several collections were taken from gillnet and test fisheries which often exploit mixtures of populations. The conformity with Hardy- Weinberg expectations and the absence of hetero- geneity within the UnalakHeet, Kuskokwim, and Copper River drainages and within Bsistol Bay suggest that little difference exists in the genetic compositions of the populations com- prising these fisheries. Such small divergence among stocks would preclude the use of biochemical genetics as a rnanage- ment tool for these fisheries. Tests for Hardy-Weinberg fre- quencies are weak, however, and additional loci which reflect divergence may exist.
One of the exceptions to the overall genetic similarity of collections within a drainage was the Yukon system. This heterogeneity is not surprising. The Yukon River is compara- ble in size to the Columbia River in which considerable dif- ferentiation of chinook populations has taken place (Milner et al. 1981). The collections taken from gillnet and test fisheries at the Yukon Wiver mouth probably reflect mixtures of a number of such populations. The heterogeneity observed among these collections (Table 3) shows that the composition of stocks passing through the fishery varies during the spawn- ing run.
Collections from the Tanana system were composed of juve- niles; and while some mixing among local populations may have occurred, our results indicate that the contributing popu- lations are closely related. The Tanana Rives enters the Yukon in central Alaska near Fairbanks; the Yukon River, however, extends much further into Canada. Because of the size of the Yukon and remoteness of many tributaries, we were unable to obtain samples either from adults or from emerging juveniles near their natal grounds. The heterogeneity observed within the Yukon suggests that biochemical genetic methods may be applicable to management of Yukon fisheries if adequate base- line information can be obtained. The existence of one geneti- cally distinct group of chinook salmon in the Yukon suggests that others may exist. The heterogeneity among lower Yukon gillnet and test fishery collections also indicates that mixtures of distinct populations had been sampled.
Among southeastern Alaskan chinook, more genetic diver- gence was observed than among those from western Alaskan drainages. The differences in degree of differentiation were not reflected by avemge heterozygosities of the two regions. Dif- ferences also exist between southeastern Alaskan and more southerly populations. Biochemical genetic methods can be useful to fisheries management as a stock separation tool. Whether the variability we have observed is sufficient to resolve components of mixed Alaskan stocks or to separate Alaskan and rac~n-Alaskan stocks wi!l require simdation studies (e.g. Beacham et al. 1985).
Genetic variability is a valuable resource for brood stock development. In southeastern Alaska, many of the drainages are genetically distinct and may have unique characteristics advantageous to culturists. For example, the difference between the upstream and downstream populations of chinook in the Stikine and possibly Taku may be pertinent to selection of brood stock. Some of the genetic differences may have resulted from natural selection, and could be irnpo~tant for brood stock development. The current practice of using only
FIG. 3 . Proposed movements of chinook salmon colonizing south- eastern Alaska from the Bering and Pacific refuges following Wiscon- sin glaciation. Stipled areas represent land exposed at the peak of Wisconsin glaciation; diagonally striped areas represent oceans. The present coastline and locations of portions of drainages possibly involved are presented. (Figure after Karlstrorn 196 I ; McPhail and Lindsey 1970: Hamilton asld Thorson 1983.)
coastal populations of chinook salmon to develop brood stock for coastal hatcheries appears genetically justified. The exis- tence of genetic variability among southeastern Alaskan chinook provides an opportunity for future brood stock development and culture of chinook salmon. The few wild stocks of chinook that remain are relatively small in size and fragile. These valuable genetic resources must be responsibly managed and conserved.
Origin of Southeastern Alaskan Chinook
Chinook salmon emerged as a species and dispersed prior to the last major glaciation, the Wisconsin (McPhail and Lindsey 1970). At the peak of the Wisconsin, the north Pacific coast from southern British Columbia to the Alaskan Peninsula was ice covered F i g . 3). oliow wing the recession of the glaciers, river systems adequate to support chinook salmon were proba- bly colonized by fish surviving in either the Bering or Pacific refuges (McPhail and Lindsey 1970).
The unrooted tree derived from biochemical genetic charac- ters (Fig. 2) suggests that the Chilkat River populations are most closely related to the southern populations. The genetic compositions of the other southeastern Alaskan populations, however, appear to have been influenced by chinook from western Alaska as well as by southern chinook populations. It is interesting that the southern stocks which appear most closely related to the spring-run, stream-type southeastern Alaskan populations are Fraser Wiver (summer-run and both stream- and ocean-type) and Washington fall-mn chinook (ocean-type). These observations suggest that life history pat- terns may be selected for after colonization; but, because of the limited comparisons made with southern populations, the paucity of data available from wild British Columbia chinook populations, and limitations in choice of loci, further con- jecture on this relationship would not be productive.
The spread of chinook from river to river along the coast northward from the Pacific Refuge is plausible (Fig.3). A similar mode of dispersal from the Bering Refuge, along a much longer coastline which has fewer suitable rivers, seems less likely. A simpler means by which western Alaskan (spe- cifically Yukon Wiver) chinook could have colonized south-
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eastern Alaskan streams is headwater capture. The headwaters of the Taku and Stikine rivers are in close geographical pro%- imity to each other and to the headwaters of the Yukon. Geological evidence indicates that glaciers fmm the persistent ice cap periodically advance and block the Taku causing it to back up into the Yukon drainage (Kerr 1948) in a manner similar to the recent advance of Hubbard Glacier across RUS- sell Fjord. That such events have affected distribution of fishes is evidenced by the presence in the Taku headwaters of pri- mary freshwater fish including northern pike ( E s ~ w Bucius), lake trout (Sa kvelinus ~ a n r n y c ~ ~ h ) , and Arctic gray ling (Thy- ma8kras arcticus) as well as other freshwater species that most likely originated from the Yukon (Lindsey 19'75). Introduc- tions of Yukon River chinook into the T a h drainage may have fdlowed episodes during which the Taku drainage was blocked (Fig. 3). These populations could have subsequently interacted with populations derived from the Pacific Refuge. Other southeastern Alaskan transmountain rivers, Alsek and Chilkat, also possess primary freshwater fish and may have been involved in eslonization of salmonid populations via the Yukon River (Lindsey 1 9'75).
Our proposal for post-Wisconsin colonization of south- eastern Alaskan rivers by chinook salmon is based upon their genetic relationships but also requires the assumption that chinook salmon survived the Wisconsin glaciation in both Bering and Pacific refuges (McPhail and Lindsey 1970). If chinook survived in only one refuge, the larger variability in both biochemical genetic compositions and life histories found among southern populations suggests that the Pacific Refuge is the more likely of the two because more recently founded populations usually have less genetic variability (e.g. Gharrett and Thomason 1987). If chinook did not survive in the Bering Refuge, all Alaskan rivers may have been colonized from the Pacific Refuge and/or possibly from refuges in Asia. Unfor- tunately, little is known about the genetic composition of Asian chinook populations. The similarities shared by south- eastern and western Alaskan chinook and the logic presented above, however, make it seem likely that the transmountain givers in southeastern Alaska with headwaters wear those of the Yukon River would have been impoaant in colonizing the Yukon River and, subsequently, the rest of south-central and western Alaska.
We thank S. Bertoni, J . Brady, M. Geiger. H . Hamner, J. Holland, R . Josephson, P. Kissner, C. Lean, B. Lynch, D. McBride, D. Petersen, J . Reynolds, D. Schmidt, S. Sharr, M. Timompson, J. Wilcock, B. van Allen, W. Zorich, and the staff and students of the Alaska Cooperative Fishery Research Unit at UA Fairbanks for sam- ples. M. Thomason and C . Smoot provided technical assistance. C. Moritz, $3. Doneen, J . Ghamett, W. Heard, and two anonymous referees provided constructive comments and helpful conversation on drafts of the manuscript, We are grateful to Dr. F. M. Utter for his help and advice. This work is a result of research sponsored by the Alaska Sea Grant College Program, cooperatively sponsored by NOAA, Office of Sea Grant and Extramural Programs, Department of Commerce, under grant No. NABBAA-D-OW9, project No. R/ 06-17, and the University of Alaska with funds appropriated by the state.
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