Natural salmon production estimation.

DRAFTNOT FOR CITATION, May 9, 2003 1

Estimating natural chinook salmon production using tagged and marked
hatchery releases as surrogates
K.B. Newman
a
, A.C. Hicks
a
, and D.G. Hankin
b
a
Division of Statistics, University of Idaho, Moscow, Idaho 83844, USA
b
Department of Fisheries, Humboldt State University, Arcata, California, USA
May 9, 2003
The authors thank California Department of Fish and Game for nancial support. We also
thank Lyman McDonald and Randy Bailey for helpful suggestions and Bailey Environmental and
CH2M-Hill for nancial support during earlier stages of this work.
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 2
Abstract
Information about the abundance of naturally produced salmon is necessary for harvest man-
agement and for monitoring the status of endangered and threatened species. Tagging, marking,
and recovering naturally produced stocks would be the most direct means of estimating abundance
of natural stocks. It is generally quite dicult, however, to capture large enough numbers of natu-
rally produced sh, in particular of juveniles, to provide suciently precise information. Hatchery
produced juvenile salmon, in contrast, are easily and relatively inexpensively marked and tagged
in very large numbers. Assuming that some hatchery releases can serve as surrogates for natu-
rally produced salmon, we develop tagging and marking schemes for hatchery releases along with
statistical procedures such that release and recovery data in combination with adult escapement
data can be used to estimate natural salmon abundances. Estimation procedures are developed
for the case of selective sheries where adipose-clipped sh are harvested and unmarked sh are
returned to the water. Estimates of the delayed mortality of caught sh returned to the water are
also proposed. An interactive computer program, CFM Sim, was developed to simulate the life
history and sampling processes and to estimate life history parameters and measures of incidental
mortality. The program can be used to compare the eects on estimate quality for alternative
marking, tagging, and sampling rates.
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 3
1 Introduction
Throughout California and the Pacic Northwest, stocks of naturally produced salmon are believed
to be in serious decline (Nehlsen et al. 1991). A wide variety of state and federal regulations
and recovery planning eorts are hoped to rebuild abundances of these natural stocks. For ex-
ample, the Central Valley Project Improvement Act (CVPIA) mandates that natural production
of chinook salmon (Oncorhychus tshawytscha) doubles from each of the Sacramento-San Joaquin
river system watersheds relative to a 1967-1991 baseline abundance period (Public Law 102-575,
Section 3406(b)(1)). Measures to increase natural production include those designed to improve
habitat conditions (restoration projects and changes in water management) and those intended
to improve harvest management for natural stocks. To reduce harvest impacts on natural stocks
to levels more consistent with their underlying productivities, but still allow substantial harvest
of abundant hatchery stocks, shery managers have recently introduced mark-selective sheries.
In these sheries, only marked hatchery sh may be retained whereas captured unmarked sh,
consisting of both hatchery and natural stocks, must be released. As Lawson and Sampson (1996)
showed, a large number of factors determine whether or not the non-catch (hook and release) mor-
tality suered by unmarked sh in such selective sheries will be substantially less than the shing
mortality rates on targeted marked hatchery sh. Non-catch mortality in intense selective sheries
may in some cases be large and will be very dicult to estimate.
The external mark relied upon in these mark selective sheries has been an adipose n clip.
Since the mid-70s, it has been permissible to release hatchery sh with adipose n clips only if
such sh also received coded-wire tags (CWT). Heightened interest in mark-selective sheries has
resulted in the mass marking of large number of hatchery sh that have been released with adipose
n clips but without coded-wire tags, in conict with the earlier rule that adipose n clips should
be used only for hatchery sh receiving coded wire tags. Such desequestering of the adipose
n clip results in substantial analytical complications with respect to how one might estimate
important life history and shery parameters based on returns of marked sh. Groups of coded
wire-tagged hatchery salmon have been used routinely as surrogates, also known as indicator stocks
(e.g., Shaul, et al. (2003)), for natural stocks by shery management agencies. The suitability of
using a hatchery stock as a surrogate for a natural stock has always been problematic in that it
may or may not be true that a hatchery surrogate group and the intended natural stock share
ocean survival rates, migration paths, and maturation rates. With the advent of mass marking and
selective sheries, however, the shing mortality rates on marked sh from surrogate groups that
are subject to selective sheries are no longer equivalent those of natural stocks. Also, although
the adipose n clip unambiguously identied a sh as of hatchery origin, the watershed of origin
remains unknown if the sh do not receive CWT.
In most river systems with signicant production of hatchery chinook salmon, absence of or
variability in hatchery marking practices has made it extremely dicult or impossible to estimate
the separate contribution to production by natural and hatchery stocks (Hankin 1982). In this
paper, we propose several alternative general tagging and marking procedures for hatchery releases
and associated statistical procedures for estimating natural stock abundances, and we present ex-
ample applications of these procedures to the Sacramento-San Joaquin river system where hatchery
sh and natural production originate from a large number of sources. For all alternatives, we as-
sume that suitable releases of hatchery stocks have been identied as good surrogates for associated
natural stocks. We formulate marking (ad-clip), tagging (CWT), and estimation procedures for
three general situations: (a) no selective sheries; (b) selective harvest in all marine and freshwa-
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 4
ter sheries; and (c) selective harvest in freshwater sheries only. For selective sheries cases, we
examine the use of recoveries of stealth hatchery sh - sh receiving CWT but not ad-clipped
- as a device for estimating non-catch mortalities of natural stocks that may result from selective
sheries; elsewhere, stealth sh have been called double-index tagged (SFEC 2002; Zhou 2002).
The structure of the remainder of our paper is as follows. In the next section, we introduce
notation and a simplied sketch of chinook salmon life history. In section 3, we introduce some
additional denitions and notation along with four dierent marking and tagging schemes. In
section 4, we present statistical procedures for estimating natural stock abundances for the three
general harvest scenarios. In section 5, we discuss a computer program, CFM Sim, that allows users
to examine the eects of dierent marking, tagging, and recovery levels on the quality of abundance
estimates. We conclude with a discussion of how our procedures compare with other procedures,
we consider the costs of implementing tagging and marking programs suitable for selective sheries,
and mention a more general state-space modeling framework for the interaction between salmon
population dynamics, harvest, and observations made on the stocks.
2 Chinook salmon life history sequence and notation
The following oversimplication of chinook salmon life history was assumed. Juvenile chinook
salmon leave freshwater and enter the ocean sometime during their rst year (age 1). Next follows
a sequence of binary events experienced by sh still alive at each point in time: overwinter survival
or not, harvest or not by the ocean shery, maturation or not. If a sh matures, the next sequence
is harvest or not by a freshwater mainstem shery, movement to a particular watershed, then
terminal harvest or not, then escapement to a hatchery (if one is present) or in-river escapement.
For maturing sh, between the end of the ocean shing period and the time the sh escape inland,
100% survival is assumed. If maturation is less than 100%, those sh not maturing repeat the
above cycle of overwinter survival, ocean harvest, and maturation. One oversimplication of this
sequence is the omission of sex distinctions; for example, maturation probabilities are age-specic
but not sex-specic.
Our notation follows somewhat from Hankin and Healey (1986) and is summarized in Table
1. The term stock is used to designate a particular hatchery release group or sh that are the
progeny of naturally spawning returns to a particular watershed. In this section the sux i denotes
a particular stock, but in later sections n and h will be used to distinguish natural and hatchery
stocks.
Production of a stock is dened as the total catch and escapement of the stock in a given year,
which may or may not match with a single calendar year. Escapement includes all sh that return
to spawn, whether they stray from their natal stream or in the case of hatchery sh spawn in the
wild. For estimation purposes we will later distinguish between in-river escapement (spawning in
the wild) and in-hatchery escapement (returning to a hatchery).
We use the term natural production to dene the catch plus escapement of sh that derives
from wild sh and/or stray hatchery sh spawning naturally in streams and successfully generating
surviving progeny. We use the term wild sh to refer to these surviving progeny, regardless of
parental origin, and we distinguish them from hatchery sh which are sh that were spawned
and reared at sh hatcheries rather than on natural spawning grounds.
Given the assumed sequence of events, the expected abundance at age a (N
a
) is a function of
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 5
survival (S), harvest (), and maturation () rates; for example, assuming harvest begins at age 2,
E[N
i4
] = R
i
S
i0
(1
O2
)(1
2
)S
3
(1
O3
)(1
3
)S
4
.
Conditional on the abundance at age a, N
ia
, the expected catches and escapements for age a sh
are
E[C
Oia
] = N
ia

Oa
E[C
Fia
] = N
ia
(1
Oa
)
a

Fa
E[C
Tia
] = N
ia
(1
Oa
)
a
(1
Fa
)
k

j=1

ij

Tiaj
E[E
ia
] = N
ia
(1
Oa
)
a
(1
Fa
)
k

j=1

ij
(1
Tiaj
)
where
ij
is the probability a stock i sh returns to watershed j.
Figure 1 contains schematic diagrams of the life history sequence for a single cohort, distin-
guishing the marine phase and freshwater phase. The freshwater phase is oversimplied in that
once a sh enters a terminal area or watershed, it is rst vulnerable to a shery (if one takes
place) and then escapes either to a hatchery or to the river.
3 Marking and tagging schemes and data collection needs
Each of the marking and tagging schemes is developed with current hatchery practices in mind
along with the need to generate particular kinds of data for estimating catch and escapement in
the presence or absence of selective sheries. Hatchery practices will need to be modied to some
extent, however, in that uniquely identiable tag codes are needed for releases that are specied
surrogates for a particular natural stock. In general, releases from a hatchery will fall into one of
ve categories which are denoted by the subscripts a, b, c, d, and e. The ve release categories are:
Ad hoc releases, a: these sh are not assumed to represent natural sh, e.g., experimental
releases, and are internally tagged with CWT and adipose-clipped. There are no restrictions
on the numbers in this group and multiple CWT codes can be used.
Surrogate releases, b: these sh are assumed to have the same natural survival rates, migration
paths, sheries vulnerability (in non-selective sheries), and maturation probabilities as a
designated natural stock. These sh are marked and tagged and the CWT code must be
unique for later identication.
CFM releases, c: sh that are CWTd and adipose-clipped and are a constant fraction, f,
of a larger group of releases (Hankin 1982). This larger group (CFM and Remainder) may
be a mixture of types of releases, ngerlings or yearlings, for example, and include so-called
production releases. The CWT codes need to be unique, however, for each of the subgroups
in the mixture if inferences about the subgroups are desired.
Remainder releases, d: sh that are not CWTd and may or may not receive an adipose-clip.
They are the complement of the CFM releases, i.e., the remainder is a constant fraction, 1-f,
of a larger group of releases.
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 6
Stealth releases, e: sh that are CWTd but not marked and assumed to be biologically
equivalent to the Surrogate release (thus represent the same natural stock as the Surrogates).
These sh are assumed to have the same straying rates (if any) as the natural stock. The
CWT code needs to be unique.
The combination of Surrogate and Stealth releases have been called Double Index Tag (DIT) releases
elsewhere (SFEC 2002; Zhou 2002), and we discuss this related work in Section 6 .
In the next section we discuss procedures for estimating production under dierent marking and
tagging schemes and sheries combinations. The dierent sheries situations, referred to previously,
are no selective sheries (NS), all sheries are selective (AS), and only freshwater mainstem and
terminal area sheries are selective (FS). With each sheries situation, two dierent marking and
tagging schemes are considered. For the no selective sheries case, the two schemes, labelled NS1
and NS2, dier in that in the former case all Remainder sh receive an adipose-clip and in the
latter case none of the Remainder sh are marked (and none are tagged). Also, under NS1 and
NS2 there are no Stealth releases. For both selective sheries cases, the schemes are labelled AS1,
AS2, FS1, and FS2, where, like the NS case, all Remainder sh are adipose-clipped under AS1 and
FS1, while all Remainder sh are unmarked under AS2 and FS2.
For estimation purposes, some sh recovered in catch and escapement samples will have to
be scanned or wanded to detect CWTs. Under all tagging and marking schemes and all sheries
scenarios, the estimation procedures assume that adipose-clipped sh will be scanned for tags. We
assume that when a CWT is detected, the sh head will be removed and the CWT will be extracted
and read, recognizing the possibility of false positives and false negatives (see Vander Haegen, et al.
(2002) for scanning diculties, especially with large chinook salmon). Whether or not sh without
adipose-clips are scanned varies with the marking and tagging scheme, the sheries situation, and
whether the sample is from a catch or from escapement.
For reference purposes the dierent marking and tagging schemes are summarized in Table 2.
Table 3 summarizes the CWT scanning protocol and whether or not aging is of unmarked sh in
samples is necessary.
4 Production estimates
Dierent estimation procedures are described for the six dierent marking, tagging, and harvest
combinations (Table 2). The underlying basis for the estimation procedures is a combination
of simple random sample mean expansions (Cochran 1977) and a method of moments approach
(Mood, Graybill, and Boes 1974).
The estimation procedures are oversimplied in that we ignore the details of how total ocean,
freshwater mainstem, and terminal area catches and watershed-specic escapement are estimated.
To some degree the particulars of estimating these values are not important in that the point
estimates of stock specic production will be calculated the same way given such estimates of totals.
Simple random samples (SRS) are assumed for the sampling of both harvest and escapement. Thus
all temporal (and spatial) stratication is ignored. In the case of harvest, SRSs of sizes n
O
, n
F
,
and n
Tj
are taken from the total ocean, freshwater, and terminal area j catches, C
O
, C
F
, and C
Tj
.
Likewise for escapement, a SRS of size n
Ej
is taken from the total escapement to watershed j,
denoted E
j
. Or in the case of a hatchery being present in a watershed, SRSs of size n
Ej,
and
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 7
n
Ej,
are taken from the in-river and in-hatchery escapements.
This oversimplication is disadvantageous in that the precision of catch data may be underes-
timated compared to the stratied samples typically taken from ocean sheries. For escapement
estimation, it is dicult to say what the actual precision is, or will be, but some degree of strati-
cation would likely be done. Conversely, the oversimplication is advantageous in that the essential
dierences in estimation procedures for dierent marking and tagging alternatives are more appar-
ent.
While hatchery sh may stray to other watersheds, for estimation purposes we assume that
natural sh do not. Thus the natural sh sampled from the terminal catch and escapement are
assumed native to that watershed. This assumption can be relaxed but the estimation becomes
more complicated.
Finally, while we assume that the Surrogate and Stealth releases are biologically identical, natural
sh can dier from both groups in one important regard. The initial survival rates from time of
release to age 2 can dier between the natural sh and the Surrogate and Stealth sh. Our
estimation procedures lead to a convenient cancellation of the Surrogate or Stealth initial survival
rates.
Table 4 contains some of the notation used in the estimation equations.
4.1 NS1
For this situation there is no selective shery, there are no Stealth releases, and all Remainder sh
are adipose-clipped. Thus all hatchery releases are receiving at least an adipose clip.
NS1: Hatchery specic production
For hatchery i releases, the estimates of total catches in the ocean, freshwater, and terminal area
sheries are simple mean expansion estimates assuming simple random samples are taken from each
shery. Letting

C
O
,

C
F
, and

C
Tj
be estimates of the total non-stock specic catches, and letting x,
y, and t refer to sample recoveries in ocean, freshwater mainstem, and terminal area catches with
additional subscripting for the hatchery release group categories (a, b, and c),

C
Ohi
=

C
O
n
O

xa
i
+ xb
i
+
xc
i
f

(1)

C
Fhi
=

C
F
n
F

ya
i
+ yb
i
+
yc
i
f

(2)

C
Thi
=
k

j=1

C
T
j
n
T
j

ta
ij
+ tb
ij
+
tc
ij
f

. (3)
Recall that f is the constant fraction marking fraction; this fraction could in practice vary between
hatcheries and would then be denoted f
i
.
For escapement estimation it is assumed that hatchery sh can return to any watershed (in
addition to the one the natal hatchery is located in). The escapement to any watershed is estimated
in a similar manner as harvest. The escapement of hatchery stock i is the sum of k watershed specic
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 8
escapement estimates. The subscripts and refer to sh that escaped either in-river or in-
hatchery, respectively. Letting z denote escapement sample recoveries with additional subscripting
and and hatchery release group categories,

E
hi,
=
k

j=1

E
j,
n
E
j,

za
ij,
+ zb
ij,
+
zc
ij,
f

(4)

E
hi,
=
k

j=1

E
j,
n
E
j,

za
ij,
+ zb
ij,
+
zc
ij,
f

. (5)
The total escapement is simply the sum of the in-river and in-hatchery escapements.

E
hi
=

E
hi,
+

E
hi,
(6)
NS1: Watershed specic natural production
The natural escapement and terminal area catch are estimated rst, and then the catches of natural
stocks in the ocean and freshwater are estimated with a method of moments style estimator based
on the escapement estimates. Recall the assumption that natural sh from watershed j do not
stray to other watersheds, and the same holds for other natural stocks. Because all hatchery sh
have at least an ad-clip, any sh in the in-river escapement without an ad-clip is a natural sh. Let
tn
j
, zn
j,
, and zn
j,
be the number of unclipped sh, thus natural sh, observed in the samples
taken from the terminal area j catch, watershed j in-river escapement sample, and watershed j
in-hatchery escapement sample (equalling zero in the absence of a hatchery), respectively. Then
the estimates of terminal catch and natural escapement to watershed j are

C
Tnj
=

C
Tj
n
Tj
tn
j
(7)

E
nj
=

E
j,
n
E
j,
zn
j,
+

E
j,
n
E
j,
zn
j,
(8)
The ocean and freshwater mainstem catches of natural stock j are estimated using the recoveries
of the Surrogate group and the estimated escapement for both the natural and the Surrogate group.
The ages of recoveries of natural and hatchery Surrogate sh need to be known because of variation
between cohorts in the number of Surrogate sh released, in natural stock outmigration numbers,
and in survival, maturation, and harvest rates. Let the Surrogate group come from hatchery i
and denote the age specic recoveries with an additional subscript a for age a. The ocean and
freshwater catches of natural stock j are estimated as follows.

C
Onj
=
5

a=2

C
O
n
O
xb
ia

C
Tnja
+

E
nja

k
j=1

C
Tj
n
Tj
tb
ija
+

E
j,
n
Ej,
zb
ija,
+

E
j,
n
Ej,
zb
ija,
(9)

C
Fnj
=
5

a=2

C
F
n
F
yb
ia

C
Tnja
+

E
nja

k
j=1

C
Tj
n
Tj
tb
ija
+

E
j,
n
Ej,
zb
ija,
+

E
j,
n
Ej,
zb
ija,
(10)
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 9
where

C
Tnja
=

C
Tnj
p
Tnja
(11)

E
nja
=

E
nj,
p
nja,
+

E
nj,
p
nja,
. (12)
The estimated percentage of age a natural sh in the terminal catch, the in-river escapement, and
the in-hatchery escapement is denoted p
Tnja
, p
nja,
and p
nja,
. These estimates are assumed based
upon scale samples taken from subsamples of recoveries of unclipped sh, namely subsamples of
tn
j
, zn
j,
, and zn
j,
. Letting n
T(age)j
, n
E(age)j,
, and n
E(age)j,
be the size of samples taken from
tn
j
, zn
j,
, and zn
j,
, and vn
ja
, wn
ja,
, and wn
ja,
are the respective number of natural sh in the
aging subsamples identied as age a,
p
Tnja
=
vn
ja
n
T(age)j
p
nja,
=
wn
ja,
n
E(age)j,
p
nja,
=
wn
ja,
n
E(age)j,
(13)
n
T(age)j
=
5

a=2
vn
ja
n
E(age)j,
=

5
a=2
wn
ja,
n
E(age)j,
=
5

a=2
wn
ja,
(14)
The intuition behind the estimates of C
Onj
and C
Fnj
can be seen by substituting expected
values for the estimated values on the right hand sides of equations (9) and (10). For example,
with ocean catch,

C
Onj
=
5

a=2

C
O
n
O
xb
ia

C
Tnja
+

E
nja

k
j=1

C
Tj
n
Tj
tb
ija
+

E
j,
n
Ej,
zb
ija,
+

E
j,
n
Ej,
zb
ija,

a=2
N
bia

Oa
N
nja
(1
Oa
)
a
(1
Fa
)(
Tja
+ (1
Tja
))

k
j=1
N
bia
(1
Oa
)
a
(1
Fa
)
ij
(
Tja
+ (1
Tja
))
=
5

a=2
N
bia

Oa
N
nja
(1
Oa
)
a
(1
Fa
)
N
bia
(1
Oa
)
a
(1
Fa
)

k
j=1

ij
=
5

a=2
N
bia

Oa
N
nja
N
bia
=
5

a=2
N
nja

Oa
where N
bia
and N
nja
is the abundance of age a sh from the hatchery i Surrogate group and the
natural stock j prior to ocean harvest.
The estimated production for the natural stock from watershed j is the sum of equations (7)-
(10).

P
nj
=

C
Onj
+

C
Fnj
+

C
Tnj
+

E
nj
(15)
4.2 NS2
With NS2 there is no selective shery, no Stealth releases, and, in contrast to NS1, the entire
Remainder group is unmarked. Subsequently, some of the estimation procedures dier from NS1
due to the need to separate natural production and the Remainder sh in the terminal area catch
and escapement.
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 10
NS2: Hatchery specic production
Estimation of hatchery production, with its catch and escapement components, is identical with
NS1, using equations (1)-(6).
NS2: Watershed specic natural production
To estimate natural terminal catch and escapement to a given watershed, estimates of hatchery
terminal catch or escapement to the watershed are subtracted from the estimate of total terminal
catch or escapement. Assuming that there are r hatchery stocks that contribute to the escapement
in watershed j,

C
Tnj
=

C
T
j

r

i=1

C
T
hij
(16)

E
nj
=

E
j,

i=1

E
hij,
+

E
j,

i=1

E
hij,
, (17)
where

C
Thij
=

C
T
j
n
C
T
j

ta
ij
+ tb
ij
+
tc
ij
f

E
hij,
=

E
j,
n
E
j,

za
ij,
+ zb
ij,
+
zc
ij,
f

, and

E
hij,
=

E
j,
n
E
j,

za
ij,
+ zb
ij,
+
zc
ij,
f

.
The catches of the natural stock in the ocean and freshwater mainstem sheries, C
Onj
and C
Fnj
are estimated as for NS1, using equations (9) and (10). However, estimation of the age-specic
natural stock numbers in the terminal catch and the escapement is more dicult because unmarked
sh are not solely natural sh, i.e., unmarked Remainder sh are present. For both the terminal
catch and the in-river and in-hatchery escapements, unmarked sh in the samples (n
Tj
, n
Ej,
,
and n
Ej,
) need to be aged, or at least subsamples of the unmarked sh need to be aged. We
assume that random subsamples of the unmarked sh in the samples of the terminal catch and
escapement are taken to age the unmarked sh. Let tu
j
, zu
j,
, and zu
j,
be the unmarked sh in
the terminal catch, in-river escapement, and in-hatchery escapement samples, respectively. Then
n
T(age)j
, n
E(age)j,
, and n
E(age)j,
are the corresponding subsample sizes, where n
T(age)j
tu
j
,
n
E(age)j,
zu
j,
, and n
E(age)j,
zu
j,
. Let vu
ja
, wu
ja,
, and wu
ja,
be the age a sh in the
terminal catch, in-river escapement, and in-hatchery escapement subsamples. The catch, in-river
escapement, and in-hatchery escapement of age a unmarked sh is estimated by multiplying the
estimated proportion of unmarked sh (denoted p
Tu
j
, p
Eu
j,
, and p
Eu
j,
) and the (conditional)
proportion of age a unmarked sh (denoted p
a|Tu
j
, p
a|Eu
j,
, and p
a|Eu
j,
) against the estimated
catch and escapements.

C
Tuja
=

C
Tj
p
Tu
j
p
a|Tu
j

E
uja,
=

E
j,
p
Eu
j,
p
a|Eu
j,

E
uja,
=

E
j,
p
Eu
j,
p
a|Eu
j,
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 11
where,
p
Tu
j
=
tu
j
n
Tj
, p
a|Tu
j
=
vu
ja
n
T(age)j
p
Eu
j,
=
zu
j,
n
Ej,
, p
a|Eu
j,
=
wu
ja,
n
E(age)j,
p
Eu
j,
=
zu
j,
n
Ej,
, p
a|Eu
j,
=
wu
ja,
n
E(age)j,
The unmarked hatchery components of the terminal catch and the escapement, namely the Re-
mainder groups, are estimated using the sample recoveries of CFM sh and the constant marking
fraction f. For hatchery i,

C
Tdija
=

C
Tj
n
Tj

tc
ija
1 f
f

E
dija,
=

E
j,
n
Ej,

zc
ija,
1 f
f

E
dija,
=

E
j,
n
Ej,

zc
ija,
1 f
f

Estimates of the age-specic natural components of the terminal catch and escapement are then
calculated by subtraction.

C
Tnja
=

C
Tuja

i=1

C
Tdija
(18)

E
nja,
=

E
uja,

i=1

E
dija,
(19)

E
nja,
=

E
uja,

i=1

E
dija,
(20)
Finally, the total natural terminal catch and escapement are estimated by summing over ages.

C
Tnj
=
5

a=2

C
Tnja
(21)

E
nj
=
5

a=2
(

E
nja,
+

E
nja,
) (22)
4.3 AS1
With AS1, selective sheries occur in all locations, ocean, freshwater mainstem, and terminal areas,
Remainder sh are marked, and Stealth releases are made. All unmarked sh in escapement samples
are scanned for CWTs, thus recoveries from the Stealth group are identied. It is further assumed
that the selective sheries do not retain any unmarked sh, but some unmarked sh will die after
being caught and released.
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 12
AS1: Hatchery specic production
The estimates of hatchery specic ocean (

C
Ohi
), freshwater mainstem (

C
Fhi
), and terminal (

C
Thi
)
catches are the same as the NS1 catch equations (1)-(3). Fish from the Stealth group are not kept in
the shery, thus do not appear in the catch sample. The expansion of the CFM recoveries remains
appropriate because the harvest rate on the ad-clipped Remainder should be the same as for the
CFM group.
The estimate of hatchery specic escapement,

E
hi
, is nearly the same as for NS1 with the
addition of Stealth recoveries in the escapement sample.

E
hi,
=
k

j=1

E
j,
n
E
j,

za
ij,
+ zb
ij,
+
zc
ij,
f
+ ze
ij,

(23)

E
hi,
=
k

j=1

E
j,
n
E
j,

za
ij,
+ zb
ij,
+
zc
ij,
f
+ ze
ij,

(24)
The total escapement is the sum of the in-river and in-hatchery escapements (equation (6)).
AS1: Watershed specic natural production
No natural sh are kept in any sheries, thus natural production is escapement alone. Because of
Stealth groups, escapement sample recoveries will include hatchery sh without ad-clips. Because
unclipped sh in escapement samples are scanned for CWTs, however, any unclipped sh without
CWTs are natural sh and equation (8) can be used.
AS1: Incidental shing mortality
In a selective shery natural sh will not be retained, but there will be incidental shing mortality,
which includes hook drop-o mortality and shaker mortality (Lawson and Sampson 1996). This
mortality is of interest to sheries managers for several reasons, including knowing the impact on
natural stocks. Unfortunately this mortality cannot be separately estimated for dierent sheries
and ages because of identiability problems.
However, a dierence of the expected escapement if there was no incidental mortality (or no
shery intervention with the stock) and the actual escapement can be calculated. This is denoted
by
snt
, where s stands for selective, n for natural and t is the year of return, and is dened as

snt
=
5

a=2
[E(E
nat
|
at
= 0) E(E
nat
|
at
= 0)] (25)
where E is expected value and E
nat
is the escapement of an age a natural sh in year t (without
the watershed identier). The parameter
a,t
is the probability an unmarked age a sh is killed by
any of the selective sheries by year t, the year it would have reached age a, conditional on not
dying from natural causes before age a and maturing at age a. More concisely,

at
= 1

g=2
(1

Og,t+ga
)

(1

Fat
)(1

Tajt
), (26)
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 13
where

Oat
,

Fat
, and

Tajt
are the incidental shing mortality probabilities for age a sh during
year t in the ocean, freshwater mainstem, and watershed j terminal sheries (the presumed natal
watershed of the natural sh).

at
= 0 means that no shery intercepted the chosen stock of age a that would return in year
t, or that no sh died upon release from any shery. Therefore,
snt
is an indication of how many
more sh would have escaped if there was no shery or all unmarked sh survived all sheries.
Each age-specic component of
snt
can be rewritten in terms of
at
. Let R
n,ta
denote the
number of outmigrating natural sh a years prior to the year t return and S
0,ta
be the initial
survival rate for that cohort.
E(E
n2t
|
2t
= 0) E(E
n2t
|
2t
= 0) = R
n,t2
S
0,t2

2t
R
n,t2
S
0,t2
(1

O2t
)
2t
(1

F2t
)(1

T2jt
)
= R
n,t2
S
0,t2

2t

1 (1

O2t
)(1

F2t
)(1

T2jt
)

= R
n,t2
S
0,t2

2t

2t
E(E
n3t
|
3t
= 0) E(E
n3t
|
3t
= 0) = R
n,t3
S
0,t3
(1
2,t1
)S
3t

3t

3t
E(E
n4t
|
4t
= 0) E(E
n4t
|
4t
= 0) = R
n,t4
S
0,t4
(1
2,t2
)S
3,t1
(1
3,t1
)S
4t

4t

4t
E(E
n5t
|
5t
= 0) E(E
n5t
|
5t
= 0) = R
n,t5
S
0,t5
(1
2,t3
)S
3,t2
(1
3,t2
)S
4,t1
(1
4,t1
)S
5t

5t
To estimate
snt
, the E(E
nat
|
at
= 0) are calculated using the Surrogate and Stealth groups. We
assume either that the maturation rates for all ages are known and constant or that natural survival
rates for ages 3, 4, and 5 are known and constant. There may be ways to avoid assuming known
maturation or survival rates, but some other parameters will likely have to be assumed known. We
show how to calculate

snt
assuming known and constant natural survival rates, but due to the
length of the calculations and cumbersome notation the details of the estimating equation are given
in Appendix A. We also note that aging of escapement samples is an additional data requirement.
It is worth highlighting some critical aspects of the estimation procedure. First, the procedure
can yield negative estimates of
set
for the Stealth sh (see equation (51)), in particular when
estimated escapements exceed the expected escapements in the absence of shing mortality. The
probability of negative estimates increases as errors in catch and escapement estimates increase.
Second, the data requirements in terms of which years of catch and escapement data are needed is
a limiting factor of this approach. When assuming known survival rates for ages 3, 4, and 5, data
for the preceding three years, the current year, and the next three years are required. Assuming
known maturation may be less restrictive on the data requirements, but this assumption may be
considered less believable than xed age 3 and higher survival rates. Dierences in the time of
release for hatchery sh are known to have an eect on maturation probabilities (Hankin 1990).
Third, neither assuming known maturation rates nor assuming known survival rates (age 3, 4, or
5) is a desirable assumption. Both maturation rates and survival rates are likely to vary naturally
within cohorts of the same stock and between dierent stocks. One possibility is to specify a
probability distribution for the known set of survival rates and then randomly sample from that
distribution and compute dierent estimates of the above parameters, which will then partially
reect the uncertainty in the estimates. Finally, the assumption that Stealth sh behave exactly as
the natural stock, particularly with regard to not straying from the natal watershed, is crucial to
the estimate of
snt
. In Appendix E we show how straying of the Stealth group aects the estimate
and give a procedure for adjusting the estimate when the Stealth group does stray.
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 14
4.4 AS2
As with AS1, selective sheries occur in the ocean, mainstem, and terminal areas, but catches of
the unmarked Remainder sh would be released along with Stealth sh.
AS2: Hatchery specic production
The estimates are similar to those for NS1, except that expansions for the Remainder sh based
on the CFM sh are not made in the catch estimates.

C
Ohi
=

C
O
n
O
(xa
i
+ xb
i
+ xc
i
) (27)

C
Fhi
=

C
F
n
F
(ya
i
+ yb
i
+ yc
i
) (28)

C
Thi
=
k

j=1

C
T
j
n
T
j
(ta
ij
+ tb
ij
+ tc
ij
) . (29)
However, as for NS2, estimates of the Remainder sh in the escapement sample are needed.

E
hi
=
k

j=1

E
j,
n
E
j,
(za
ij,
+ zb
ij,
+ zc
ij,
+ ze
ij,
) +
5

a=2

E
dija,

+
k

j=1

E
j,
n
E
j,
(za
ij,
+ zb
ij,
+ zc
ij,
+ ze
ij,
) +
5

a=2

E
dija,

(30)

E
dija,
and

E
dija,
are estimates of unmarked Remainder sh from hatchery i age a sh in the
in-river and in-hatchery escapement to watershed j. How these are estimated in shown in the next
section.
AS2: Watershed specic natural production
Let E
uj,
and E
uj,
denote the in-river and in-hatchery escapement of unmarked sh to watershed
j and zu
j,
and zu
j,
be the number of unmarked sh observed in the escapement samples. Note
that zu
j,
and zu
j,
include Remainder sh and natural sh, but not the unmarked Stealth sh.

E
uj,
=

E
j,
n
E
j,
zu
j,
(31)

E
uj,
=

E
j,
n
E
j,
zu
j,
(32)
The escapements of age a Stealth sh from hatchery i sh, denoted E
eija,
and E
eija,
, are estimated
as follows.

E
eija,
=

E
j,
n
E
j,
ze
ija,
(33)

E
eija,
=

E
j,
n
E
j,
ze
ija,
(34)
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 15
The escapements of age a Remainder sh from hatchery i, E
dija,
and E
dija,
, are estimated using
the ratio of release numbers for this group and a stealth group assumed to have the same life
history parameters. Note that this stealth group may or may not be the same as that used for
the natural sh. If not, yet another subcategory of hatchery releases is required. In particular a
subset of the Remainder group may require that a CWT is implanted. To reduce the notation, and
complexity, we suppose that a single Stealth group suces. Then

E
dija,
=
R
di,ta
R
ei,ta

E
eija,
(35)

E
dija,
=
R
di,ta
R
ei,ta

E
eija,
(36)
where R
di,ta
and R
ei,ta
are the number of type d and e sh released from hatchery i that are now
age a. The escapement of natural sh to watershed j is estimated by subtracting these estimates
of Remainder sh from the estimated escapement of unmarked sh.

E
nj
=

E
uj,

i=1
5

a=2

E
dija,
+

E
uj,

i=1
5

a=2

E
dija,
(37)
AS2: Incidental shing mortality
The procedure for estimating
snt
is similar to that for AS1. Details are given in Appendix B.
4.5 FS1
Selective sheries occur in freshwater sheries (mainstem and terminal areas) but not in the ocean
sheries. The estimation procedures are a mixture of the non-selective and all-selective alternatives,
with some minor dierences.
FS1: Hatchery specic production
Estimation of ocean catch is similar to that in alternative NS1, except that the catch of the Stealth
sh must be accounted for. It is highly unlikely that some or all of the unclipped sh caught in
the ocean sheries will be scanned for a CWT tag in the head, thus the Surrogate group will be
used to represent the Stealth group. Release numbers for Surrogate groups will likely vary between
years and that needs to be accounted for in the estimation. Further, aging of some sh from the
ocean catch sample will have to be done. Ocean catch can then be estimated as follows.

C
Ohi
=

C
O
n
O

xa
i
+ xb
i
+
xc
i
f
+
5

a=2
xe
ia

(38)
where
xe
ia
= xb
ia
R
ei,ta
R
bi,ta
. (39)
The freshwater and terminal catches are estimated the same as in alternatives NS1 and AS1
(equations (2) and (3)). Hatchery escapement is estimated as in alternative AS1, using equations
(23) and (24).
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 16
FS1: Watershed specic natural production
The natural production is ocean catches and escapement. The escapement of natural stock j, E
nj
,
would be estimated as in NS1, using equation (8). The ocean catches for the natural stock from
watershed j can be estimated using the Stealth recoveries.

C
Onj
=
5

a=2

C
O
n
O
xe
i
a

E
nja

k
j=1

E
j,
n
E
j,
ze
ija,
+

E
j,
n
E
j,
ze
ija,
(40)
where

E
nja
=

E
nj,
p
nja,
+

E
nj,
p
nja,
(41)
The proportions at age in the escapement sample, p
nja
, would be estimated as for NS1 (see equation
(13)).
FS1: Incidental shing mortality
As for AS1, the expected incidental mortality suered in the selective sheries,
sn
, can again be
estimated, but with FS1 the mortality arises only from the mainstem and terminal area sheries.
Details of the estimation procedure are given in Appendix C.
The incidental mortality rates,
at
, suered in all freshwater sheries (mainstem and terminal
sheries combined) can be estimated for each age. The ocean shery is not a selective shery
and the ocean exploitation rate can be estimated, assuming known survival parameters (equations
(58)-(61) in Appendix C). Similar to AS1, age a freshwater incidental mortality for a stock that
returns to watershed j with certainty is dened by

at
= 1 (1

Fat
)(1

Tjat
). (42)
Estimates of
at
for natural stocks use estimates of expected escapement for Stealth sh in the
absence of selective sheries (equations (63)-(66) in Appendix C).

at
= 1

E
eat

E(E
eat
|
at
= 0)
(43)
The intuition behind this can be shown with the method of moments. For example, the incidental
mortality on age 3 sh would be (substituting parameters for estimates),

e3t
1
R
e,t3
S
0,t3
(1
O2,t1
)(1
2,t1
)S
3
(1
O3t
)
3t
(1

F3jt
)(1

Tj3t
)
R
e,t3
S
0,t3
(1
O2,t1
)(1
2,t1
)S
3
(1
O3t
)
3t
= 1 (1

F3t
)(1

Tj3t
)
Note that under AS1 and AS2,
at
can also be estimated, but its interpretation is more compli-
cated than for the FS cases, in that
at
can include incidental mortality rates from more than one
year.
The expected incidental mortality for natural sh,
snt
, can, as for AS1 and AS2, be dened in
terms of
at
using equation (25).
snt
can be estimated using estimates of E(E
nat
|
at
= 0) (shown
in equation (56)) and using the estimated escapement in place of E(E
nat
|
at
= 0).
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 17
4.6 FS2
Selective sheries occur in the freshwater sheries, as in FS1, but the Remainder group is completely
unmarked and indistinguishable from natural sh.
FS2: Hatchery production
Estimation of hatchery specic ocean catches is identical to the procedure for FS1 (equation (38)).
Estimating hatchery specic freshwater catch is similar to FS1, except that the Remainder group
is not kept in these sheries, thus is not accounted for in the equations.

C
Fhi
=

C
F
n
F
(ya
i
+ yb
i
+ yc
i
) (44)

C
Thi
=
k

j=1

C
T
j
n
T
j
(ta
ij
+ tb
ij
+ tc
ij
) . (45)
Escapement of hatchery sh is estimated the same as for AS2 (equation (30)).
One piece of the hatchery production left out of the calculations is the incidental mortality of
the Remainder sh. In general this will be estimable only if surrogates for the Remainder group
are identied (see related remarks for AS2 and estimation of hatchery and natural escapement).
FS2: Watershed specic natural production
The natural production is ocean catch and escapement. The escapement for natural stock j is
estimated as in NS2, using equation (17). The ocean catch is estimated as for FS1, using equation
(40), except that

E
nja
is estimated dierently, using equations (19) and (20).
FS2: Incidental shing mortality
Details of the estimation of
snt
for FS2 are given in Appendix D. As for alternative FS1, the
incidental mortality of natural sh in the freshwater sheries (mainstem and terminal) can be
estimated using the Stealth and Surrogate groups (see equation (57)).
5 Simulation and estimation program, CFM Sim
CFM Sim, short for Constant Fractional Marking Simulation, is an IBM PC compatible computer
program that simulates the following processes for multiple stocks of chinook salmon over multiple
years:
1. the initial marking and tagging of sh, followed by natural mortality, shing mortality, and
maturation processes, each repeated for ages 2, 3, 4, and 5;
2. the sampling of marine and freshwater catches and escapements, where the catches and es-
capements generally include a mixture of stocks;
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 18
3. the statistical estimation of catches and escapements for each stock separately, based on the
catch and escapement sample data.
The program was designed to simulate these processes for hatchery-raised and naturally-spawned
chinook salmon from Californias Central Valley using any of the six alternatives described above.
The user can model hatchery and natural stocks in 14 dierent watersheds in the Central Valley
simultaneously, with a limit of one hatchery and one natural stock per watershed. Multiple years
can be simulated to determine trends over time, and any number of simulations can be performed
to determine the natural and sampling variability.
5.1 User input
The primary reason for developing CFM Sim was to provide a tool for sheries biologists and
biometricians that could be used to study the eects of dierent constant fractional marking (cfm)
rates on the quality of estimates of production. CFM Sim can be used to compare the accuracy
of production estimates when a cfm rate of f=20% or a cfm rate of f=40% is applied to releases
from a Central Valley articial production facility.
Many other factors besides the CFM rate aect the quality of production estimates. Some of
the factors that the user of CFM Sim can manipulate include the following:
marine survival rates (S
0
, S
3
, S
4
, and S
5
);
age-specic ocean, freshwater, and terminal shing harvest rates (
Oa
,
Fa
,
Taj
);
sampling rate of catches in the marine sheries (n
O
/C
O
);
sampling rate of catches in the freshwater sheries (n
F
/C
F
and n
T
j
/C
T
j
);
sampling rate of spawning escapement (n
E
j,
/E
j,
);
sampling rate of the hatchery return (n
E
j,
/E
j,
);
maturation rates (
2
,
3
, and
4
).
For example, the user can evaluate changes in the accuracy of production estimates for the water-
sheds in the Central Valley due to changes in age 4 marine harvest rates while holding the cfm rate
f and other rates constant.
CFM Sim can also be used to analyze the eect of selective sheries on the spawning escapement
of natural and hatchery bound Central Valley chinook salmon stocks. A user can vary any shaker
mortality rate (Lawson and Sampson 1996), which is dened as a fraction of the harvest rate, to
study the eects on both escapement and total shaker mortality.
A simple spreadsheet format is used to input stock specic parameters, which include age specic
survival, harvest and maturation rates, hatchery release numbers, stock-recruitment parameters for
the natural stocks, straying rates, sampling rates, sub-sampling rates for aging as well as aging error
probabilities, and latent hooking mortality parameters in the case of selective sheries. Parameters
are also watershed specic where applicable (i.e., escapement sampling rates).
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 19
5.2 Program output
The primary interest of CFM Sim is to determine the error and variability of estimated production.
Therefore, estimated production is compared to true production in order to provide a measure
of the quality of the estimates. CFM Sim uses the mean relative absolute error, labeled MAE, as
this measure. To calculate the MAE for a given stock, the relative absolute error is calculated for
each simulated year and then averaged across all the years of a single simulation.
MAE
i
=
1
recY rs
recY rs

j=1
|

P
i,j
P
i,j
|
P
i,j
, (46)
where recY rs is the total number of recovery years, P
i,j
is the true production, and

P
i,j
is the
estimated production, for simulation i and recovery year j. For example, suppose just two years
were simulated. The true production was 10,000 and 11,000 for both years and the corresponding
estimates were 9,500 and 11,200. Then
MAE =
1
2

|9, 500 10, 000|

10, 000
+
|11, 200 11, 000|
11, 000

=
1
2
(0.05 + 0.018) = 0.034
or a 3.4% relative absolute error for that single simulation. The two years would then be simulated
again and another MAE would be calculated.
The average, median, standard deviation, minimum, and maximum of the MAEs are calculated
over all simulations and output by stock into new spreadsheets. These statistics give an idea as to
the quality of the estimates of production and can be used to compare dierent marking, tagging,
and sampling scenarios, for example. A relatively large average or median MAE indicates that
production is not being estimated accurately, while a relatively large standard deviation shows that
the estimates of production are not precise.
Also output to a spreadsheet are the summary statistics for the ratio of the last years simulated
production to the rst years simulated production for each natural stock. Ratios of true production
and estimated production are reported and can be used to gauge the increase in natural production
over the time period entered and if it will be detected using the estimation procedures described
here.
Some estimates may be negative in alternatives NS2, AS2, and FS2. When any of these al-
ternatives are run, numbers of negative estimates that occurred are reported. This will help to
determine how frequently absurd estimates may occur given the parameters entered.
When selective shery alternatives are run, an additional worksheet outputs summary statistics
for the mean relative absolute prediction error between the true
s
, and the estimated

s
for each
natural and hatchery stock.
A number of dierent external les are also created. The true and estimated production is
reported for all stocks from the last simulation to give an insight into a simulation. The MAEs for
each stock and simulation are reported in case the summary statistics do not dene the accuracy
and precision well enough, and the total natural production for all recovery years and simulations
is also reported. When requested, more detailed les for each stock are created that contain values
such as true catches and escapement for each simulation.
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 20
6 Discussion
6.1 Related work
The Pacic Salmon Commission established an Ad-hoc Selective Fishery Evaluation Committee
(ASFEC) in 1993 which later developed into a standing Selective Fishery Evaluation Committee
(SFEC). Several reports by this committee (ASFEC 1995; SFEC 1998, 1999) have focused on
marking, tagging, and estimation techniques for coho salmon sheries in particular. The SFEC
refers to the combination of Surrogate and Stealth groups as Double Index Tagging (DIT) where
Surrogate sh are referred to as marked sh and Stealth sh are labelled unmarked.
Zhou (2002) summarized the SFEC procedures for estimating the incidental shing mortality
of unmarked hatchery sh and we restate his summary here using our notation. Zhou considers
the situation where selective shing occurs in a terminal shery and sheries prior to the terminal
shery are implicitly non-selective. In our framework this would mean non-selective ocean and
freshwater mainstem sheries followed by a selective terminal shery. Zhou shows how the number
of unmarked sh that die as a result of the selective shery is estimated (which he labels C
m
s
) and,
more directly, how the harvest rate on the unmarked sh (labelled H
u
s
) is estimated. The expected
value of C
m
s
is what we would label
se
(dropping the time subscript), while the expectation of
H
u
s
would be

T
. The SFEC describes two procedures for estimating
se
.
The SFECs rst method assumes that initial marine survival, S
0
, is the same for both the
Surrogate and Stealth groups, exactly as we assume, and label the procedure the equal marine
survival method. Implicitly the SFEC methods assume that harvest rates experienced by Surrogate
and Stealth groups are the same prior to the terminal area shery. Using our notation, we re-
formulate this procedure for coho salmon (thus S
0
corresponds to survival to year 2, not maturing,
and then surviving to the start of shing in year 3, and
3
=1). We assume just one shery prior
to the terminal area, say an ocean shery; also time subscripts are dropped.

se,1
=
R
e
R
b
(

C
Tb
+

E
b
)

E
e

R
e
R
b
(R
b
S
0
(1
O
)
T
+ R
b
S
0
(1
O
)(1
T
)) R
e
S
0
(1
O
)(1

T
)
= R
e
S
0
(1
O
)

T
Then incidental terminal area shing mortality or harvest rate is estimated by

T
=

se,1
Re
R
b
(

C
Tb
+

E
b
)

R
e
S
0
(1
O
)

T
R
e
S
0
(1
O
)
=

T
.
We also note that in the case of coho salmon, 1-

T
, is equivalent to (with no age subscript
needed).
The SFECs second method implicitly allows for dierent initial survival rates for the Surrogate
and Stealth groups but assumes equal harvest rates in the preceding non-selective shery. This
procedure is labelled the equal exploitation rate method. The ratio of (estimated) catches for
the two groups is substituted for the ratio of release numbers in this case. Here we denote dierent
initial survival rates by S
b0
and S
e0
for the Surrogate and Stealth groups.

se,2
=

C
e

C
b
(

C
Tb
+

E
b
)

E
e
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 21

R
e
S
e0

O
R
b
S
b0

O
(R
b
S
b0
(1
O
)
T
+ R
b
S
b0
(1
O
)(1
T
)) R
e
S
e0
(1
O
)(1

T
)
= R
e
S
e0
(1
O
)

T
And incidental terminal area shing mortality or harvest rate is estimated by

T
=

se,2

Ce

C
b
(

C
Tb
+

E
b
)

R
e
S
e0
(1
O
)

T
R
e
S
e0
(1
O
)
=

T
.
Zhou (2002) studied the performance of both procedures for estimating

T
by introducing
randomness in actual survival and harvest rates (making number initially surviving and number
caught Binomial random variables), and randomness in catch and escapement estimates. He found
that the relative errors in estimates of

T
can be quite large over a range of reasonable expected
survival and harvest rates and catch and escapement estimation errors. For example, if the true
incidental harvest rate,

T
, was 6% (40% encounter rate times 15% hook-and-release mortality
rate), the average absolute relative deviation, |

T
6|/6 ranged from 56.9% to 16.0% given S
0
ranging from 1% to 12%. Thus in the case of S
0
=1%, on average

T
was 3% above or below 6%.
6.2 Remarks on estimation
As the number of equations indicate, estimation of life history parameters, catches, and natural
escapement for chinook salmon can be quite complex, and the complexity greatly increases with
the introduction of selective sheries (as can be seen from the Appendices). More subtle is the fact
that, in the case of selective sheries, estimates of natural escapements and incidental mortality
can occasionally be negative. This was also demonstrated by Zhou (2002) with the simpler coho
salmon situation. This may be seen from equations that estimate maturation rates and involve
subtracting estimates of catches and escapements from estimates of abundance prior to catch and
escapement. When estimates of catches and escapements exceed estimated initial abundance,
estimated maturation is negative, subsequently estimates of
set
can be negative. Simulation
studies we have done indicate that the chance of negative estimates increases as the imprecision
of escapement estimates, in particular, worsens. Relatively precise estimates of escapement are
then crucial for yielding sensible estimates of incidental mortality under the proposed method of
moments style procedures we have described.
We are currently working on an alternative approach to the problem of simultaneously modeling
life history processes, harvest, and data collection uncertainty by using a state-space model (Schnute
1994; Newman 1998 and 2000). The parameter estimates would be either maximum likelihood or
Bayesian and are theoretically more ecient than method of moments approaches (and will not
yield nonsensical negative estimates of escapement, for example). The estimation procedures, in
contrast to the estimators given here, would not be closed form, however, and the procedures
will be even more numerically and computationally intensive. The state-space model framework is
extremely exible, however, and allows one to readily incorporate dierent estimates of abundances,
e.g., two estimates of a given stocks escapement.
6.3 Management implications and issues
For managing and monitoring natural stock abundances, the use of marked and tagged hatchery
stocks is an economic alternative to marking and tagging natural stocks directly. Besides complex
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 22
estimation problems, there are other basic management issues and implications worth raising.
First, a key condition for the applicability of all the estimators we have developed is that the
life history and shery experiences of Surrogate and/or Stealth hatchery releases are representative
of those experienced by wild sh. To increase the likelihood that this is so, hatchery managers need
to know the time and duration of outmigration of wild stocks, and perhaps sh size, condition,
and other relevant variables. The rearing and release of the Surrogate stock should therefore mimic
the wild stock outmigration strategy as closely as possible. Also, releases of Surrogate and Stealth
groups need to be made directly from hatcheries so as to minimize straying rates and make it more
likely that the assumption of equal straying rates of wild, Surrogate, and Stealth releases are met.
Ultimately, the best way to determine representativeness of a surrogate release is to mark and tag
(or just tag) some outmigrating wild stock juveniles. This would be expensive and collecting large
numbers might be dicult, but the eort would yield invaluable information.
Second, the introduction of selective sheries greatly complicates both data requirements and
data analysis methods. The complexity is considerably greater for chinook salmon, because of
the multiple maturation ages, than for coho salmon. In particular, it is worth emphasizing that
estimates of incidental mortality losses to a wild chinook salmon stock (due to catch and release in
mark-selective sheries) for a particular year t would not be possible until a few years later because
escapement estimates in several years past year t are needed. Tag detection is also more dicult for
chinook salmon than coho salmon because of the formers larger size (Vander Haegen, et al. 2002);
thus the time required to thoroughly scan an unmarked chinook salmon, a possible Stealth sh, for
a CWT, increases data collection costs. A related data issue, and estimation complication, that we
have not dealt with is tag loss. Many hatcheries currently hold samples tagged juveniles for at least
two weeks prior to release so that such sh can be scanned to determine CWT tag retention rates.
The introduction of selective sheries and mass marking practices will certainly increase the scope
and importance of such tag retention studies. We have not yet explored how one might attempt to
statistically account for possible tag loss following release, especially if large numbers of hatchery
sh are deliberately released with adipose n clips but without CWTs.
Third, additional complications to estimation, and data record keeping, can be lessened by
maintaining constant fractional marking across years, and ideally across hatcheries. To increase
the probability that a given CFM is biologically similar to particular Remainder sh, the fractional
marking rate f needs to be applied within each unique breeding and rearing combination. There
may be several release types (dierent months or sizes of release) among the Remainder production-
type releases and each type will need to be marked at rate f. Ideally, the same marking and tagging
rate f should be applied within each raceway from which both CFM and Remainder sh will be
released.
Fourth, the levels of marking, tagging, sampling, aging sh, and reading tags that are required
to eectively implement the estimation procedures presented in this paper, in non-selective or
selective sheries, greatly exceed current data generation and collection eorts. A key concern is
whether resource management agencies will have sucient funds for generating and gathering the
necessary data, and for doing so at levels that yield suciently precise estimates. for example,
samples of untagged and unmarked sh in spawning escapements and at hatcheries will need to
be aged. Unmarked sh in escapements will need to be scanned for tags in the case of selective
sheries. For many systems current escapement estimation procedures are likely inadequate for
yielding the desired level of precision in production estimates, and for lessening the chance of
nonsensical estimates, thus more time and money needs to be invested in improving escapement
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 23
estimates.
Fifth, while our primary objective was to develop procedures for estimating wild chinook salmon
production, with particular attention to Sacramento river system stocks, a recent U.S. statute,
signed into law in February 2003, requires that all federal and federally funded salmon and steel-
head hatcheries mark all the sh they release. This new requirement for mass marking places an
increased and critical importance on rapid development and renement of the kinds of statistical
procedures that we have described in this paper. Mass marking has apparently now become a re-
quirement, but analytical procedures necessary for handling the mass marked sh have not yet been
fully developed. The intent behind the legislation is to maintain, or increase, harvest of hatchery
sh while protecting wild sh, and the legislation eectively increases the scope of selective sheries.
But mass marking and selective sheries may seriously compromise the integrity of the coded wire
tag data base and the nature of how CWT recovery data have been used in salmon management for
the past 25 years. For chinook salmon, the complexity of the analysis with selective sheries and
Stealth sh is such that we question that the complex estimation procedures will be used correctly
in practice. Also, at best our procedures can only estimate the overall incidental shing mortality
rates. We have been unable to develop estimation procedures that might estimate such incidental
mortality rates for individual, time, area, and gear-specic sheries, but current management reg-
ulations are often made at that ne level of resolution (see, for example, the 2003 ocean salmon
sheries plan of the Pacic Fisheries Management Council, http:www.pcouncil.org).
References
ASFEC (Ad-hoc Selective Fishery Evaluation Committee). 1995. Selective shery evaluation.
Pacic Salmon Commission, Ad-hoc Selective Fishery Evaluation Committee, Vancouver.
Cochran, W.G. 1977. Sampling Techniques, 3rd Ed. John Wiley and Sons, New York.
Hankin, D.G. 1982. Estimating escapement of Pacic salmon: marking practices to discriminate
wild and hatchery sh. Transactions of the American Fisheries Society 111: 286298.
Hankin, D.G. 1990. Eects of month of release of hatchery-reared chinook salmonon size at age,
maturation schedule, and shery contribution. ODFW Information Report 904.
Hankin, D.G., and Healey, M.C. 1986. Dependence of exploitation rates for maximum yield and
stock collapse on age and sex structure of chinook salmon (Oncorhynchus tshawytscha) stocks.
Canadian Journal of Fisheries and Aquatic Sciences 43:17461759.
Lawson, P.W., and Sampson, D.B. 1996. Gear-related mortality in selective sheries for ocean
salmon. North American Journal of Fisheries Management 15:512520.
Mood, A.M., Graybill, F.A., and Boes, D.C. 1974. Introduction to the Theory of Statistics, 3rd
Ed.. McGraw-Hill, New York.
Nehlsen, W., Williams, J.E., and Lichatowich, J.A. 1991. Pacic salmon at the crossroads: stocks
at risk from California, Oregon, Idaho, and Washington. Fisheries 16(2): 421.
Newman, K.B. 1998. State-space modeling of animal movement and mortality with application to
salmon. Biometrics 54: 274297.
Newman, K.B. 2000. Hierarchic modeling of salmon harvest and migration. Journal of Agricultural,
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 24
Biological, and Environmental Statistics 5:98123.
Schnute, J. 1994. A general framework for developing sequential sheries models. Canadian Journal
of Fisheries and Aquatic Sciences 51:16761688.
Shaul, L., McPherson, Jones, E., and Crabtree, K. 2003. Stock status and escapement goals for
coho salmon stocks in Southeast Alaska. Alaska Department of Fish and Game, Special Publication
No. 03-02, Anchorage.
SFEC (Selective Fishery Evaluation Committee). 1998. Pacic Salmon Commission, Selective
Fishery Evaluation Committee progress report, December 1998. SFEC, Vancouver.
SFEC (Selective Fishery Evaluation Committee). 1999. 1998 annual report. Pacic Salmon Com-
mission, Selective Fishery Evaluation Committee, SFEC(99)-1, Vancouver.
SFEC (Selective Fishery Evaluation Committee). 2002. Investigation of methods to estimate
mortalities of unmarked salmon in mark-selective sheries through the use of double index tag
groups. Pacic Salmon Commission, Selective Fishery Evaluation Committee, Analytical Work
Group, TCSFEC(02)-1. (Available at www.psc.org/Pubs/SFEC02-1.pdf.)
Vander Haegen, G.E., Swanson, A.M., and Blankenship, H.L. 2002. Detecting coded wire tags with
handheld wands: eectiveness of two wanding techniques.
Zhou, S. 2002. Uncertainties in estimating shing mortality in unmarked salmon in mark-selective
sheries using double-index-tagging methods. North American Journal of Fisheries Management
22: 480493.
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 25
A AS1: Estimation of Incidental Mortality
The estimation procedure assumes that the age three through ve survival rates, S
3
, S
4
, and S
5
, are
known and constant. The approach can be partitioned into three parts: (a) estimating life history
parameters using the Surrogate group; (b) estimating
se
for the Stealth group using the estimated
parameters; (c) estimating
sn
for the natural stock using the Stealth
se
and escapement estimates
for Stealth and natural stocks.
A.1 Estimating life history parameters using the Surrogate group
The notation is complicated. The year of interest is denoted by a subscript t. Catch, C, and
escapement, E, have three subscripts. The rst is either b for the Surrogate group or e for the
Stealth group. The second is age of the sh, a= 2, 3, 4, or 5. The third subscript is the year of
catch or escapement. For example, C
b4,t3
is the catch of Surrogate age 4 sh three years prior to
year t. Release number, R, has two subscripts, the rst is either b or e and the second is the brood
year. Harvest rates
O
,
F
, and
T
are rst subscripted b or e, then by age at harvest, and then
the year of interest. Survival rate, S, is subscripted rst by I, 3, 4, or 5 and then the brood year.
Similarly, maturation rates, , are subscripted by age of maturation, a, and the cohort year, t a.
The symbol P
F
, with the same subscripts, denotes the sum of all of the freshwater observations
for a given stock, including freshwater mainstem catch, terminal area catch, and escapement. For
example, in year t, the age a freshwater return,
P
Fbat
= C
Fbat
+ C
Tbat
+ E
Fbat
.

S0,tg =

C
Ob2,tg
+

P
Fb2,tg
+
C
Ob3,tg
+ P
Fb3,tg
+
C
Ob4,tg
+ P
Fb4,tg
+
C
Ob5,tg
+ P
Fb5,tg
S
5
S
4
S
3
R
b,tg2
g = 0, 1, 2, 3 (47)
2,tg =

P
Fb2,tg
R
b,tg2

S0,tg2

C
Ob2,tg
g = 0, 1, 2, 3 (48)
3,tg =

P
Fb3,tg
[R
b,tg2

S0,tg2 (

C
Ob2,tg
+

P
Fb2,tg
)]S3

C
Ob3,tg
g = 1, 2, 3 (49)
4,tg =

P
Fb4,tg

[R
b,tg2

S0,tg2 (

C
Ob2,tg
+

P
Fb2,tg
)]S3 (

C
Ob3,tg
+

P
Fb3,tg
)

S4

C
Ob4,tg
g = 2, 3(50)
A.2 Estimating
se
for the Stealth group

set
=
5

a=2

E(E
eat
|
at
= 0)

E
eat

(51)

E(E
e2t
|
2t
= 0) = R
e,t2

S
0,t2

2t
(52)

E(E
e3t
|
3t
= 0) = R
e,t3

S
0,t3
(1
2,t1
)S
3

3t
(53)

E(E
e4t
|
4t
= 0) = R
e,t4

S
0,t4
(1
2,t2
)S
3
(1
3,t1
)S
4

4t
(54)

E(E
e5t
|
5t
= 0) = R
e,t5

S
0,t5
(1
2,t3
)S
3
(1
3,t2
)S
4
(1
4,t1
)S
5
(55)
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 26
We emphasize here that
at
is assumed to have the same meaning for the Stealth sh as for natural
sh. In particular, Stealth sh cannot stray to other terminal areas, else they would be subjected
potentially to a mixture of dierent terminal area harvest rates. Although see Appendix E for a
way of dealing with straying Stealth sh.
A.3 Estimating
sn
for the natural stock
To calculate

sn
for natural sh represented by the Stealth group, the expected escapement of
natural sh in the absence of shing mortality is rst calculated. Using equations (52)-(55) and
age-specic estimates of the natural stock and Stealth group escapements.

E(E
nat
|
at
= 0) =

E(E
eat
|
at
= 0)

E
nat

E
eat
(56)
Again making a method of moments style argument, the intuition behind equation (56) can be
seen. For example, at age 2,

E(E
e2t
|
2t
= 0)

E
n2t

E
e2t
R
e2,t2
S
0,t2

2t
R
n2,t2
S
n0,t2
(1

O2t
)
2t
(1

F2t
)(1

Tj2t
)
R
e2,t2
S
0,t2
(1

O2t
)
2t
(1

F2t
)(1

Tj2t
)
= R
n2,t2
S
n0,t2

2t
We include an additional subscript n for the natural stocks initial survival rate to emphasize the
point that the initial survival rate can dier between Stealth and natural sh. The age-specic
natural stock escapement estimates,

E
na,ta
, would be calculated as for NS1, using equation (12).
Then, using the age-specic escapement estimates and estimate of the expected escapement for
natural sh,

snt
=
5

a=2

E(E
nat
|
at
= 0)

E
nat

(57)
B AS2: Estimation of Incidental Mortality
Notation is the same as for AS1 in Appendix A.
B.1 Estimating life history parameters using the Surrogate group
The life history parameters are estimated exactly as for AS1, using equations (47)-(50).
B.2 Estimating
se
for the Stealth group
The estimate of
s
for Stealth sh can be found using equations (51)(55).
B.3 Estimating
sn
for the natural stock
To estimate the shing induced mortality on the natural stock, E(E
nat
|
at
= 0) is rst estimated,
using equation (56), where the age specic natural escapement estimate,

E
na
, is found with a
procedure similar to that used for NS2. Then
snt
is estimated with equation (57).
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 27
C FS1: Estimation of Incidental Mortality
Notation is the same as for AS1 in Appendix A. The estimation sequence is as for AS1, with life
history parameters estimated using the Surrogate sh, incidental mortality of Stealth sh estimated
next, and incidental mortality of the natural sh estimated last. As discussed previously the
denition of
at
is dierent for the FS than the AS cases.
C.1 Estimating life history parameters using the Surrogate group
The initial survival rates, S
0
, and the maturation probabilities,
a
, are estimated as for AS1, using
equations (47)-(50). The ocean harvest rates, however, need to be estimated with FS1.

O2t
=

C
Ob2t
R
b,t2

S
0,t2
(58)

O3t
=

C
Ob3t
R
b,t3

S
0,t3
(1
O2,t1
)(1
2,t1
)S
3
(59)

O4t
=

C
Ob4t
R
b,t4

S
0,t4
(1
O2,t2
)(1
2,t2
)S
3
(1
O3,t1
)(1
3,t1
)S
4
(60)

O5t
=

C
Ob5t
R
b,t5

S
0,t5

4
g=2
(1
Og,t+g5
)(1
g,t+g5
)S
g+1
(61)
C.2 Estimating
se
for the Stealth group

set
=
5

a=2

E(E
eat
|
at
= 0)

E
eat

(62)

E(E
e2t
|
2t
= 0) = R
e,t2

S
0,t2
(1
O2t
)
2t
(63)

E(E
e3t
|
3t
= 0) = R
e,t3

S
0,t3
(1
O2,t1
)(1
2,t1
)S
3
(1
O3t
)
3t
(64)

E(E
e4t
|
4t
= 0) = R
e,t4

S
0,t4
(1
O2,t2
)(1
2,t2
)S
3
(1
O3,t1
)(1
3,t1
)S
4
(1
O4t
)
4t
(65)

E(E
e5t
|
5t
= 0) = R
e,t5

S
0,t5
(1
O2,t3
)(1
2,t3
)S
3
(1
O3,t2
)(1
3,t2
)S
4
(1
O4,t1
)(1
4,t1
)S
5
(1
O5t
) (66)
C.3 Estimating
sn
for the natural stock
To calculate

sn
for natural sh represented by the Stealth group, the equations used for AS1 are
used, namely equations (56) and (57). The expected escapements of natural sh in the absence
of freshwater shing mortality are calculated using equations (63)-(66) and age-specic estimates
of the natural stock and Stealth group escapements. The age-specic natural stock escapement
estimates,

E
na,ta
, would be calculated as in equation (41).
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 28
D FS2: Estimation of Incidental Mortality
Assumptions and notation are as given in Appendix C.
D.1 Estimating life history parameters using the Surrogate group
As for FS1, the initial survival rates, S
0
, and the maturation probabilities,
a
, are estimated as
for AS1, using equations (47)-(50). Like FS1, the ocean harvest rates need to be estimated, using
equations (58)-(61).
D.2 Estimating
se
for the Stealth groups
Identical with FS1, the expected change in production in the absence of sheries can be estimated
for the Stealth groups, using equations (62) - (66).
D.3 Estimating
sn
for the natural stock
The procedure to estimate

s
for natural sh is identical to that for FS1 in terms of estimating the
expected escapement of Stealth sh in the absence of freshwater sheries. First equations (63)-(66)
are used to estimate the expected escapements by age class, then the ratio of estimated escapements
of natural to Stealth sh by age class is used to estimate expected escapement of the natural sh,
using equation (56), and nally
snt
is estimated with equation (57).
E Estimating
sn
when Stealth sh stray
To correctly estimate the expected escapement of natural sh (equation (56)), the Stealth group
must not stray, as is assumed for natural sh, or the straying rate () must be accounted for. The
eect of straying can be seen below, using age 2 in the AS case as an example.

E(E
n2t
|
2t
= 0) =

E(E
e2t
|
2t
= 0)

E
n2t

E
e2t
R
e,t2
S
0,t2

2t
R
n,t2
S
n0,t2
(1

O2t
)
2t
(1

F2t
)(1

Tj2t
)
R
e,t2
S
0,t2
(1

O2t
)
2t
(1

F2t
)

k
j=1

2jt
(1

Tj2t
)
=
R
n,t2
S
n0,t2

2t
(1

Tj2t
)

k
j=1

2jt
(1

Tj2t
)
The straying rate, , is now subscripted with age and brood year, while the stock subscript is
assumed. This is because age and cohort variation may exist in the straying rates.
The bias may be reduced somewhat by using the Stealth escapement to the natal watershed j
only, assuming
2j
1.

E(E
n2t
|
2t
= 0) =

E(E
e2t
|
2t
= 0)

E
n2t

E
ej2t
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 29
R
e,t2
S
0,t2

2t
R
n,t2
S
n0,t2
(1

O2t
)
2t
(1

F2t
)(1

Tj2t
)
R
e,t2
S
0,t2
(1

O2t
)
2t
(1

F2t
)
2jt
(1

Tj2t
)
=
R
n,t2
S
n0,t2

2t

2jt
Rather than assume that the straying to non-natal watersheds is insignicant, the probability
of returning to the natal watershed can be estimated using the Surrogate group, which are also
used to calculate survival, maturity, and harvest parameters for stealth sh. However, as with the
other estimates, the implicit assumption that Surrogate and the Stealth sh have the same life
history parameters must hold, or bias will occur.

jat
=

C
bjat
+

E
bjat

k
j

=1

C
bj

at
+

E
bj

at

Using the above estimate

jat
, the estimate of the expected natural escapement without any
incidental mortality is

E(E
nat
|
2t
= 0) =

E(E
eat
|
2t
= 0)
jat

E
nat

E
ejat
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 30
Table 1: Notation for abundances and life history parameters. Summation over stocks and/or ages
is denoted by dropping the associated subscripts; e.g., C
O
is total ocean catch for a given year.
R
i
: number of juvenile sh released from hatchery stock i
or naturally produced juvenile sh leaving watershed i
N
ia
: abundance of age a sh from stock i prior to ocean harvest
C
Oia
: ocean sheries catch of age a sh from stock i
C
Fia
: freshwater catch of age a sh from stock i
C
Tiaj
: terminal area j catch of age a sh from stock i
E
iaj,
: in-river escapement in terminal area j of age a sh from stock i
E
iaj,
: in-hatchery escapement in terminal area j of age a sh from stock i
P
i
: total production of stock i,

5
a=2
[C
Oia
+ C
Fia
+ C
Tia
+ E
ia
]
S
ia
: probability an unharvested, immature age a 1 sh from stock i
is alive at age a prior to shing, a=3,4,5
S
i0
: probability of surviving from time of release
to beginning of ocean harvest, where I stands for initial
u
Oia
: ocean shery exploitation rate on age a stock i sh
u
Fia
: freshwater mainstem shery exploitation rate on age a stock i sh

ij
: probability a stock i sh goes to watershed j
conditional on surviving the freshwater mainstem shery
u
Taj
: terminal area j shery exploitation rate on age a sh from stock i

ia
: probability an age a sh from stock i matures
given survival to age a without maturing earlier
Table 2: Dierent hatchery sh adipose n clip and tagging schemes. NS, AS, and FS denote no
selective sheries, all selective sheries, and freshwater only selective sheries, respectively, and f
is the CFM fraction.
Release Groups NS1 NS2 AS1 AS2 FS1 FS2
Ad hoc Optional Optional Optional Optional Optional Optional
Surrogate Required Required Required Required Required Required
CFM Fixed f Fixed f Fixed f Fixed f Fixed f Fixed f
Remainder Marked Unmarked Marked Unmarked Marked Unmarked
Stealth None None Required Required Required Required
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 31
Table 3: Summary of scans for CWTs and aging requirements in catch and escapement samples
for each marking, tagging, and sheries combination. Y indicates that scanning is done, N
indicates that scanning is not necessary, and indicates that those type of sh are not present
in the sample.
Ocean Catch Mainstem Catch Terminal Catch Escapement
Adipose n Adipose n Adipose n Adipose n Adipose n Adipose n
Clipped Intact Clipped Intact Clipped Intact Clipped Intact
Scan Age Scan Age Scan Age Scan Age
NS1 Y N Y N Y N N Y Y N N Y
NS2 N N N N N N N Y N N N Y
AS1 Y Y Y N Y N Y Y
AS2 N N N N N N Y Y
FS1 Y N Y Y N Y N Y Y
FS2 N N N N N N N Y Y
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 32
Table 4: Notation for samples and sample recoveries.
n
O
: size of a simple random sample taken from C
O
n
F
: size of a simple random sample taken from C
F
n
Tj
: size of a simple random sample taken from C
Tj
n
Ej,
: size of a simple random sample taken from E
j,
, the watershed j in-river escapement
n
Ej,
: size of a simple random sample taken from E
j,
, the watershed j in-hatchery escapement
xa
i
: # of hatchery stock i Ad hoc recoveries in ocean catch sample
xb
i
: # of hatchery stock i Surrogate recoveries in ocean catch sample
xc
i
: # of hatchery stock i CFM recoveries in ocean catch sample
xd
i
: # of hatchery stock i Remainder recoveries in ocean catch sample
xe
i
: # of hatchery stock i Stealth recoveries in ocean catch sample
ya
i
: # of hatchery stock i Ad hoc recoveries in freshwater catch sample
yb
i
: # of hatchery stock i Surrogate recoveries in freshwater catch sample
yc
i
: # of hatchery stock i CFM recoveries in freshwater catch sample
yd
i
: # of hatchery stock i Remainder recoveries in freshwater catch sample
ye
i
: # of hatchery stock i Stealth recoveries in freshwater catch sample
ta
ij
: # of hatchery stock i Ad hoc recoveries in terminal area j catch sample
tb
ij
: # of hatchery stock i Surrogate recoveries in terminal area j catch sample
tc
ij
: # of hatchery stock i CFM recoveries in terminal area j catch sample
td
ij
: # of hatchery stock i Remainder recoveries in terminal area j catch sample
te
ij
: # of hatchery stock i Stealth recoveries in terminal area j catch sample
tn
j
: # of natural stock j recoveries in terminal area j catch sample
za
ij,
: # of hatchery stock i Ad hoc recoveries in watershed j in-river escapement sample
zb
ij,
: # of hatchery stock i Surrogate recoveries in watershed j in-river escapement sample
zc
ij,
: # of hatchery stock i CFM recoveries in watershed j in-river escapement sample
zd
ij,
: # of hatchery stock i Remainder recoveries in watershed j in-river escapement sample
ze
ij,
: # of hatchery stock i Stealth recoveries in watershed j in-river escapement sample
zn
j,
: # of natural stock j recoveries in watershed j in-river escapement sample
zu
j,
: # of unmarked sh in watershed j in-river escapement sample
za
ij,
: # of hatchery stock i Ad hoc recoveries in watershed j in-hatchery escapement sample
zb
ij,
: # of hatchery stock i Surrogate recoveries in watershed j in-hatchery escapement sample
zc
ij,
: # of hatchery stock i CFM recoveries in watershed j in-hatchery escapement sample
zd
ij,
: # of hatchery stock i Remainder recoveries in watershed j in-hatchery escapement sample
ze
ij,
: # of hatchery stock i Stealth recoveries in watershed j in-hatchery escapement sample
zn
j,
: # of natural stock j recoveries in watershed j in-hatchery escapement sample
zu
j,
: # of unmarked sh in watershed j in-hatchery escapement sample
Natural salmon production estimation. DRAFTNOT FOR CITATION, May 9, 2003 33
Figure 1: The top sketch is the sequence of life history processes and abundances of each category
or fate for a single cohort up to the point of maturation and entering freshwater. The bottom sketch
shows the sequence for age a sh entering freshwater that will go to watershed j with probability
j
.
Note that if the cohort is not vulnerable to a particular sh then the harvest rate, , is eectively
zero.
Marine Sequence.
Age
Initial 2 3 4 5
C
O2
C
O3
C
O4
C
O5

O2

O3

O4

O5

R
S0
N
2
(1
O2
)(12)S3
N
3
(1
O3
)(13)S4
N
4
(1
O4
)(14)S5
N
5

(1
O2
)
2

(1
O3
)
3

(1
O4
)
4

(1
O4
)
F
2
F
3
F
4
F
5
Freshwater Sequence.
CFa CTja E
ha

Fa

Tja

Fa
(1
Fa
)

(1
Tja
)

(1 j)
Era