Electronic Supplementary Material
Study population
The Hood River, Oregon, is located in a sub-basin of the Columbia River in the Northwest
United States. The supplementation program for winter-run steelhead in this river has been operated
since1991. Only wild broodstock have been used in this program (i.e., wild-born parents are used to
created first-generation hatchery fish), except for five years (1995-1999) during which returning firstgeneration hatchery fish were used in some of the hatchery crosses (Araki et al. 2007a). Hatchery-born
steelhead offspring are released into the Hood River each year as one year olds that then go to sea and
return to spawn after 2-4 years at sea (Olsen 2003). Wild fish usually spend two years in fresh water,
and so return, on average, one year older than hatchery fish.
A dam and trap are located near the mouth of the river, below all suitable spawning habitat
(Araki 2008). The dam is a complete barrier for up-migrating salmonid fish. Tissue sampling from
returning adult fish has been operated daily by the Oregon Department of Fish and Wildlife (ODFW)
at the trap. Hatchery-born adults are distinguished from wild-born adults by the presence of a fin clip.
Captured fish are released above the dam immediately after sampling. Therefore, tissue samples have
been collected from almost every up-migrating (spawning) adult fish for the last 17 years. About 17000
winter-run steelhead (either wild or hatchery-reared) returned to the river during 1991-2007. The age of
each returning adult is determined by counting the rings on a sample of scales by ODFW staff and their
brood years were used as the baseline information for parentage assignments.
Fitness comparisons
Because both hatchery and wild fish reach the spawning grounds at the same time of year,
three types of wild-born, F2 offspring are produced in the wild: W[CxC] from matings between two
captive-bred (hatchery) parents, W[CxW] from one hatchery and one wild-born parent, and W[WxW] from
two wild-born parents (Fig. 1). Note that these F2 are all wild-born (hence the W) and spend their entire
lives in the natural environment, and that all comparisons in this study are made among wild-born F2s
that returned to the river and spawned in the same year. Because our sample consists only of returning
adults, we use ‘reproductive fitness’ to mean the number of returning adult offspring produced by each
adult fish that was passed above the dam.
Like many wild populations of O. mykiss, the Hood River population consists of two life
history forms, the anadromous form known as steelhead and the resident (non-anadromous) form
known as rainbow trout. Both forms can interbreed and produce the other form of O. mykiss in the
wild (Zimmerman & Reeves 2000). This interbreeding between life history forms results in missing
parents in our parentage assignment even though we sampled almost all the anadromous fish that
returned to the river (Araki et al. 2007b, c). Fish for which we identified only one parent are labeled
W[Cx-] or W[Wx-], where C = captive-bred anadromous parent, W = wild-born anadromous parent, and = missing, presumably resident parent. Resident and anadromous fish in the Hood River appear to be
part of one gene pool (Araki et al. 2007b, c), so W[Cx-] and W[Wx-] should be genetically equivalent to
W[CxW] and W[WxW] fish, respectively. Nevertheless, it is possible that some of the missing parents are
residualized (non-anadromous) hatchery fish that never went to sea. Therefore, we conducted a
separate analysis of the reproductive fitness of W[Cx-] relative to W[Wx-].
For this specific study, we added genetic data for 455 wild-born fish that returned in 20062007 in the genotype database used in Araki et al. (2007a). We extracted DNA from fin-clip or scale
tissues using a Chelex method (Nelson et al. 1998), and obtained genotype information for 8
microsatellite loci, Omy1001, Omy1011, Omy1191, Omy77, One108, One2, Ssa407, and Str2 (Araki
et al. 2007b). Of ~17000 fish samples in the Hood River steelhead database, we obtained genotype
information for 6-8 loci (on average 7.82 loci/sample) from 11323 samples. They include 98.1% of
wild-born fish that passed above the dam in 1991-2007 and 94.0% of hatchery-born fish that passed
above the dam in 1995-1998. Exclusion method was used for the parentage assignments, and putative
parent-offspring pairs sharing at least 6 loci and having no or one mismatching loci were assigned as
parent-offspring pairs with the CERVUS program (Marshall et al. 1998). To obtain an unbiased
estimate of relative reproductive success, a potential bias due to errors in the parentage assignments was
corrected using Araki and Blouin’s (2005) method.
892 wild-born fish and 774 hatchery-born fish were passed above the dam to spawn in 19951998. 2520 of their wild-born, F2 offspring returned to the river and passed above the dam in 19992001. 779 of these 2520 F2 adults were successfully assigned to two parents and categorized as W[WxW],
W[CxW] or W[CxC]. We identified only one parent for each of 1240 of the wild-born F2 (705 W[Cx-] and
535 W[Wx-]). In the next generation, 1348 wild-born F3 returned as adults in 2001-2007. We assigned
those F3s to their F2 parents (ESM Supporting tables 1, 2) and calculated an unbiased RRS for each of
the different F2 groups.
To test the statistical significance in the difference between reproductive successes of two
groups, we performed a one-tailed permutation test. In this test, numbers of offspring assigned to each
parent are permutated 100,000 times without replacement, and the probability of obtaining a value
equal to or larger than the observed value is evaluated. We used a one-tailed test because we had a clear,
a priori, hypothesis that descendants from captive-bred parents might have fitness that is lower than
those from wild parents.
Estimating the effects of supplementation on population fitness
One can calculate the reduction rate of population fitness due purely to the effect of captive
breeding in the previous generation using relative reproductive success (RRS) and frequency of each
class of fish. Assuming the numbers of F2 shown in ESM Supporting tables 1 and 2 reflect the
population frequency of W[CxC], W[CxW], W[WxW], W[Cx-] and W[Wx-], the population average of RRS
weighted by the frequency of each class represents a fitness reduction rate at the population level owing
to having W[CxC] or W[CxW] (instead of W[WxW]) and W[Cx-] (instead of W[Wx-]) (similar to estimating the
average relative fitness of genotypes in a single locus model of viability selection). In 1999 males, for
example, RRS of the F2 classes are 0.065 for W[CxC], 0.859 for W[CxW], and 0.834 for W[Cx-] (Table 1).
Given that the RRS of W[WxW] and W[Wx-] are 1.0 (controls), and the absolute frequencies are 17 for
W[CxC], 57 for W[CxW], 44 for W[WxW] (ESM Supporting table 1), 44 for W[Cx-] and 86 for W[Wx-] (ESM
Supporting table 2), average population fitness in 1999 males, relative to the case that all W[CxC] and
W[CxW] were W[WxW] and that all W[Cx-] were W[Wx-], is obtained as 0.065*17 + 0.859*57 + 1.0*44 +
0.834*44 + 1.0*86 / (17 + 57 + 44 + 44 + 86) = 0.874. The population fitness ranged from 1.02 (males
in 2000) to 0.77 (females in 2001), and the weighted average among the three years and two sexes was
0.92. In other words, relative to a population of the same size in which all individuals were W[WxW] or
W[Wx-] , the average relative fitness of the Hood River population during 1999-2001 was reduced by 8%.
Electronic Supplementary Material References
Araki, H. & Blouin, M. S. 2005 Unbiased estimation of relative reproductive success of different groups:
evaluation and correction of bias caused by parentage assignment errors. Mol. Ecol. 14, 40974109.
Araki, H., Cooper, B. & Blouin, M. S. 2007a Genetic effects of captive breeding cause a rapid,
cumulative fitness decline in the wild. Science 318, 100-103.
Araki, H., Ardren, W. R., Olsen, E., Cooper, B. & Blouin, M. S. 2007b Reproductive success of
captive-bred steelhead trout in the wild: evaluation of three hatchery programs in the Hood River.
Conserv. Biol. 21, 181-190.
Araki, H., Waples, R. S., Ardren, W. R., Cooper, B. & Blouin, M. S. 2007c Effective population size of
steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic
compensation between life-history forms. Mol. Ecol. 16, 953-966.
Araki, H. 2008 Hatchery stocking for restoring wild populations: a genetic evaluation of the
reproductive success o hatchery fish vs. wild fish. In: Fisheries for global welfare and
environment, 5th world fisheries congress 2008 (eds. Tsukamoto, K., Kawamura, T., Takeuchi,
T., Beard, T. D. & Kaiser, M. J.), pp. 153-167. TERRAPUB, Tokyo, Japan.
Marshall, T. C., Slate, J., Kruuk, L. E. & Pemberton, J. M. 1998 Statistical confidence for likelihoodbased paternity inference in natural populations. Mol. Ecol. 7, 639-655.
Nelson, R. J., Beacham, T. D. & Small, M. P. 1998 Microsatellite analysis of the population structure of
a vancouver island sockeye salmon (Oncorhynchus nerka) stock complex using nondenaturing
gel electrophoresis. Mol. Mar. Biol. Biotechnol. 7, 312-319.
Olsen, E. A. 2003 Hood River and Pelton ladder evaluation studies. In: Annual report 2000-2001 of the
Oregon Department of Fish and Wildlife. Oregon Department of Fish and Wildlife, Portland.
Zimmerman, C. E. & Reeves, G. H. 2000 Population structure of sympatric anadromous and
nonanadromous Oncorhynchus mykiss: evidence from spawning surveys and otolith
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Supporting Table 1. Number of samples included in this study I: F2 with two assigned parents
F2 Male
1999
2000
2001
F3 assigned
W[CxC]
17
24
18
W[CxW]
57
47
45
W[WxW]
44
32
22
F2 Total
118
103
85
F2 Female
66
56
37
F3 assigned
1999
2000
2001
10
27
35
91
75
55
78
68
34
179
170
124
103
84
45
Total
131
370
278
779
391
Supporting Table 2. Number of samples included in this study II: F2 with only one assigned parent
F2 Male
1999
2000
2001
F3 assigned
W[Cx-]
W[Wx-]
44
68
78
86
70
95
F2 Total
130
138
173
F2 Female
109
79
69
F3 assigned
1999
2000
2001
74
129
142
143
152
159
217
281
301
146
100
107
Total
535
705
1240
610