Fishery Stock Assessment
Fishery Stock Assessment
Fishery Stock Assessment
Ramón Bonfil
Wildlife Conservation Society
2300 Southern Blvd, Bronx
NY, 10460, USA
<[email protected]>
10.1 INTRODUCTION
Perhaps the most influential, but not necessarily the best, works on shark stock
assessment were those of Holden in the 1960s and 1970s. Holden (1977) was one of
the first scientists to consider the problem of shark fisheries stock assessment from a
general point of view. He correctly pointed out that sharks were different from bony
fishes in terms of their biology but unfortunately he wrongly concluded that classic
fisheries models such as stock production models could not be applied to sharks and
rays. Holden dismissed these models and called for new models to be developed.
He stated that the assumptions of surplus production models regarding immediate
response in the rate of population growth to changes in population abundance and
independence of the rate of natural increase from the age composition of the stock do
not hold for sharks. These conclusions were based mainly on the time delays caused
by the longer reproductive cycles of sharks and their reproductive mode, which in his
view would cause a linear and direct stock-recruitment relationship.
Because of his influential paper, surplus-production models have been mostly
ignored for shark stock assessment and scientists and non-scientists reading Holden’s
papers have sought new methods and models for dealing with shark fisheries stock
assessment. For a while, Holden’s thoughts influenced the works of other scientists
who opted for the more detailed approach offered by age structured models (e.g. Wood
et al., 1979; Walker, 1992).
The main problem of surplus production models is not that they are inadequate
when applied to sharks but the way in which they were being applied. A paramount
obstacle for the use of classic surplus production models in the 1960s and part of the
1970s was the equilibrium constraint (see Section 10.6 on fitting models data). At
that time, due to the lack of readily available computers to perform iterative search
algorithms, scientists engaged in surplus production model-fitting were forced to
assume that populations were in equilibrium at all exploitation levels (i.e. that every
catch observed was sustainable) to simplify the process of fitting surplus production
models to data.
The dangerous consequences of this assumption are well known and explicitly
warned against in fishery text books (Pitcher and Hart, 1982; Hilborn and Walters,
1992). However, the personal computer revolution has helped to overcome the
equilibrium constraint through the availability of non-linear optimization routines
which are accessible to virtually any fishery scientist in the world today. The diversity
of approaches this offers for fitting surplus production models has translated into a new
10. Fishery stock assessment models and their application to sharks 155
era of popularity for the utilization of what are presently known as dynamic surplus
production models that have been applied to organisms as slow-growing as whales and
sharks (Punt, 1991; Prager et al., 1994; Polachek et al., 1993; Babcock and Pikitch, 2001).
Perhaps the most interesting outcome of all this re-appraisal of surplus production
models is the view that most of the problems associated with successfully applying
them are due to the quality of the fisheries data (Hilborn, 1979; see also Section 10.3),
and the finding that simple surplus production fishery models can sometimes perform
better than the more elaborate and biologically detailed age-structured approaches
(Ludwig and Walters, 1985, 1989; Ludwig et al., 1988; Punt, 1991).
One of the reasons for the difficulty in applying these models to sharks is that the
data available on shark fisheries and our knowledge about shark biological parameters
may not be adequate. This is expressed clearly in the work of Anderson (1990),
Anderson and Teshima (1990) and Bonfil (1996). In fisheries science, independent of
the species in question, the most common problem is that lack good and sufficient data
that lack contrast in the data when it is available. Another problem often overlooked is
that the more ‘realistic’ age-structured models also pose problems in their application.
Age-structured data are much more difficult and expensive to obtain. Further, the
life cycles of most shark species, even in terms of the basic parameters of age, growth
and reproduction, have just started to be unveiled during the last 20 years, and this
only in the case of a handful of stocks [see Pratt and Casey, (1990) and Cortés, (2000)
for reviews]. In addition, there are some relevant areas of elasmobranch population
dynamics that are still largely unknown. For example: empirically derived stock-
recruitment relationships have never been documented for any elasmobranch, although
a strong relationship is suspected due to the reproductive strategies of the group
(Holden, 1973; Hoff, 1990); the size, structure and spatial dynamics of most stocks
of elasmobranchs are almost totally unknown. Inadequate knowledge of migration
routes, stock delimitation and movement rates amongst them, can seriously undermine
otherwise “solid” assessments and management regimes.
Hoff (1990) favored the use of dynamic surplus-production models for shark
stock assessment for a variety of reasons. Punt (1988, 1991) also reported dynamic
surplus production models to be the most reliable for management of slow-growing
resources with limited reproductive potential such as baleen whales, when tested using
a simulated fully age-structured population. Similar positive results were reported with
a Schaefer model for a swordfish age-structured simulation model (Prager et al., 1994).
The results of Bonfil (1996) suggest that surplus production models are good enough
for shark biomass assessment but less so for management parameter estimation. He
found that although generally inferior to the Deriso-Schnute model (Section 10.4.1
below), surplus production models are capable both of estimating biomass benchmarks
and obtaining good biomass fits for most of the scenarios analysed.
The best advice in regard to model choice for elasmobranch stock assessment is
found in Section 2.2.3. Surplus production models can, and should, be applied to
elasmobranch fisheries as they are one of the easiest to implement, but their results
should be taken as a first and preliminary assessment. A complete and reliable
assessment should not stop there but attempt to apply delay-difference and fully-age
structured models as soon as that is also possible.
Bt (10.2)
Bt +1 = Bt + rBt (1 − ) (10.2)
K
When catch is included in the above equation we obtain the discrete version of the
Schaefer (1954) surplus production model:
Bt (10.3)
Bt +1 = Bt + rBt (1 − ) − Ct
K (10.3)
where
Ct = qfBt (10.4)
(10.4)
and C is catch, q is the catchability coefficient and f is effort. In the Schaefer model
above, the middle term is known as the surplus production. If the surplus production is
greater than catch, population size increases; if catch equals surplus production, catch is
sustainable and the population size remains constant (Bt+1 = Bt); if catch is greater than
surplus production, population size declines.
Assumptions
The Schaefer model has the following assumptions:
• there are no species interactions
• r is independent of age composition
• no environmental factors affect the population
• r responds instantaneously to changes in B (no time delays)
• q is constant
• there is a single stock unit
• fishing and natural mortality take place simultaneously
• no changes in gear or vessel efficiency have taken place
• catch and effort statistics are accurate
In practice, many of the above assumptions are not met but this does not mean
that the method cannot be used. As long as it is used critically, the Schaefer model is
a powerful tool for an initial assessment of a stock. The management parameters of
importance from the Schaefer model are given by:
MSY = r K/4
BMSY = K/2
Optimum effort (fMSY) = r/2q
MSY = rKe-1/lnK
BMSY = Ke-1
fMSY = r/q lnK
158 Management techniques for elasmobranch fisheries
Pella and Tomlinson (1969) proposed a generalized model that can take any shape,
including that of the Schaefer (m =2) and Fox (m = 1) models.
dB rB m (10.6)
= rB −
dt K (10.6)
However, there is a price to be paid for this ‘improvement’, one must estimate an
additional parameter (m) to fit the model to the data. This model is not much more
useful because despite its ‘flexibility’ the fit will probably be worse than with the
Schaefer or Fox models as there is often an inverse relationship between the number of
parameters to be estimated and the performance of the models (Hilborn and Walters
1992).
10.3.1 Introduction
Beverton and Holt (1957) first developed this model, which provides a steady-state
(static) view of the population that allows determination of the catch or yield relative
to recruitment (catch divided by recruitment, thus the yield per recruit, or Y/R,
name of the technique) that can be obtained from a stock at different levels of fishing
mortality F (which is dependent on effort) and age of entry to the fishery. The method
is described in detail by Pitcher and Hart (1982), Megrey and Wespestad (1988), and
Quinn and Deriso (1999).
The model describes the population in terms of the biological processes of growth,
recruitment and mortality and treats the exploited population as the sum of its
individual members. It has more biological detail than surplus production models but
is not as powerful and detailed as the fully age-structured models treated below. Also,
it is inferior to SPMs in the sense that it is static, assumes that there is no dependence
between stock size and recruitment, and cannot provide estimates of absolute biomass
or be used for making projections of stock size according to different management
strategies. Its main utility is that it indicates if the fishery is catching fish at an age that
is too early or too late to obtain the maximum biomass relative to recruitment and if
the level of fishing mortality is too high or could be higher.
10.3.3 Methodology
This model is based on three equations:
(i) Von Bertalanffy Growth Model (in weight):
Wt = W∞ (1 − e − k ( t −t0 ) ) 3 (10.7)
(10.7)
(ii) Exponential survival model:
N t = R ⋅ e − M (tc −tr ) ⋅ e -(M + F)(t-tc ) (10.8)
(10.8)
where R is the number of recruits, tc is age at first capture and tr is age of recruitment
to the stock.
(iii) General yield equation:
t1
Y = � F ⋅ N tWt dt (10.9)
(10.9)
tc
Y n =3
= F ⋅ W∞ ⋅ e − M (tc −tr ) ⋅ � F + MΩ n+ nK ⋅ e − nK ( tc −t0 ) ⋅ (1 − e -(M + F + nK)(t1-tc ) ) (10.11)
(10.11)
R n =0
The model predicts the level of yield (catch) that can be obtained depending on
the age of entry and maximum age in the stock and the level of natural and fishing
mortality.
This model allows managers to investigate the effects of varying fishing mortality
(F) or age of first entry (tc) on yield. One disadvantage of the model is that the shape
of yield is completely determined by growth and mortality. If the stock has a low rate
of growth and high M the yield curve is asymptotic (this wrongly suggests yield does
not decrease as you fish harder and harder). Conversely, if the stock has rapid growth
rate and a low M the yield curve is dome-shaped.
The main disadvantages are that the method provides no estimate of the absolute
biomass of the stock and gives only limited advice on management actions. As with life
tables, a disadvantage of this method is that it is not dynamic (there is no time variable)
and therefore cannot be used to make predictions. Nor does it incorporate density-
dependent processes such as stock-recruitment relationships. Other disadvantages of
the model are that it unrealistically assumes constant growth and mortality rates; it
is more expensive to implement than SPMs as age needs to be frequently determined
requiring large samples of fish; the curve shape is predetermined and inflexible; the
model predicts yield even at infinite effort, which is unrealistic; and yield is not
expressed in absolute terms so the real magnitude of the catch cannot be known.
Using the Y/R method alone can be misleading as pointed by Grant et al. (1979).
These authors suggested that the recommended 10-fold increases in fishing mortality
from their Y/R assessment was a bad advice as only a 2-fold increase could already
reduce the reproductive stock of school sharks to less than half of its original
abundance. Using a modified demographic method Au and Smith (1997) showed that
the estimates of Y/R obtained by Smith and Abramson (1990) for the leopard shark
(Triakis semifasciata) were considerably lower after adjusting for the effect of reduction
in recruitment due to fishing. Also, Rago et al. (1998) found that the optimum age of
entry predicted by the Y/R model would lead to recruitment failure and stock collapse
in spiny dogfish (Squalus acanthias) because of the late age of maturity in this species.
Another problem of the Y/R method is that a poor estimation of growth or mortality
can strongly influence conclusions and lead to decisions that could put the stock in
jeopardy.
10.3.5 Applications
The Y/R method has been used for stock assessment of school sharks (Grant et al.,
1979), for little skate (Waring, 1984), for leopard shark (Smith and Abramson, 1990),
for silky sharks (Bonfil, 1990), for sandbar sharks (Cortés, 1998) and for porbeagle
(Campana et al., 1999, 2001). To my knowledge this method has not been used as the
main basis for the management of any elasmobranch species.
the gear) to available biomass and population numbers from the previous year. The
advantage of the model lies on several simplifications that allow the incorporation of
important population dynamics processes into a simple equation. However, perhaps
its more important characteristic is that the model allows for time-lags in the dynamics
of the stock, such as are found in species with slow growth and late age of entry to the
fishery. This ability to take into account time-delay is what gives the model its name
of ‘delay-difference’ model. The derivation of the delay-difference model here is taken
from Hilborn and Walters (1992).
The model assumes that body growth of the exploitable stock can be represented by
a linear function (the Brody equation):
(10.12)
wa = α + ρwa +1
where wa is body weight at age a, andwα α + ρware
a =and
(10.12)
a +1 constants. This equation states that
after a certain age, the typical von Bertalanffy model of growth in weight(10.12)
shown in
Figure 10.2 can be represented by a linear equation of weight at age a against weight
at age a+1.
FIGURE 10.2
Individual growth in weight according to the von Bertalanffy Growth Model.
1.2
0.8
weight
0.6
0.4
0.2
0
0 2 4 6 8 10 12 14 16 18 20 22 24
age
FIGURE 10.3
Ford-Walford plot of weights at age. Solid diamonds represent the
original data points and each straight line is a linear regression using a
different starting age (0, 2, 4, 6, and 7).
1
0.9
Wa+1
all
0.8
2
4
0.7
6
0.6 7
Wa+1
0.5
0.4
0.3
0.2
0.1
0
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1 1.1
Wa
St = ψ (1 − ht ) (10.14)
(10.14)
where Ψ is the natural survival rate and h is the harvest rate in year t. This assumes that
harvest (fishing) takes place in a short time during the beginning or end of the year.
Biomass Biomass
at age canatbeage
represented as numbers atasage
can be represented times average
numbers at ageweight
times at age: weight at age:
average
_
Ba = N a wa (10.15) (10.15)
This can be extended for the whole exploited population plus the recruitment R:
� a max _
�
Bt = � � N t ,a wa � + wk R t (10.16)
(10.16)
� a =k �
where k is the age of recruitment (to the gear or fishery). Population number N, can
be expressed as survivors from last year at age a-1, and all the weights at age a can be
expressed using the Brody equation, thus arriving at the following formula:
� �
� a max a max _ �
Bt = St −1 �α � N t −1,a −1 + ρ � N t −1,a −1 wa −1 � + wk R t (10.17)
(10.17)
� a = k +1 a = k +1 �
�� ��
Factoring out terms that do not depend on age results in sums over age k and older for
year t-1:
B = S αN + S ρB + w R (10.18)
t t −1 t −1 t −1 t −1 k t
(10.18)
and total numbers in the population are
N t = St −1 N t −1 + R t (10.19)
(10.19)
164 Management techniques for elasmobranch fisheries
( R0 ) (10.24)
a ' = ln + B0b'
(10.23) , b' (10.24)
For the Beverton and Holt recruitment model the equations are:
aSt − k +1 (10.25)
Rt +1 = (10.25) , (10.26)
b + St − k +1
(b + B0 ) (10.26)
(10.25) , a = R0 (10.26)
B0
Other parameters needed to fit the delay-difference model can be estimated
externally or internally with the following assumptions:
• ρ and wk are estimated directly from growth data and
• ψ depends on external estimates of natural mortality, M.
This leaves us with only 3 parameters to be estimated during model fitting by non-
linear methods:
(i) b or b’ for the stock recruitment relationship
(ii) B0 stock size at the beginning of the fishery
(iii) q the catchability coefficient for the catch equation
Thus, the delay-difference model can be simplified by fixing values for the first
3 parameters listed above and fitted to the catch and effort data by finding the values
of the last 3 parameters using nonlinear iterative methods such as those included in
spreadsheet software. The parameter a or a' of the recruitment model is eliminated by
the assumptions above.
10. Fishery stock assessment models and their application to sharks 165
FIGURE 10.4
Diagrammatic representation of the 1960 cohort of humans (all individuals born in 1960). N
represents the numbers of age A alive each year for cohort 1960.
VPA and CAGEAN are recursive algorithms that track the history of each cohort
in the exploited population back in time from the present to the time when each cohort
was born or more commonly to the time it recruited to the fishery, i.e. they calculate
the number of fish alive in each cohort for each past year, following each cohort
through time. They are used to reconstruct the entire exploited population to estimate
fishing mortality and numbers at age for each age class in each year.
of natural causes) and if we know the instantaneous natural mortality rate then, for
fisheries where the fishing period is short it can be assumed that there is no natural
mortality during the short fishing period so that:
Nt = Nt+1 + Ct +Dt (10.27)
where
Dt = Nt (1-S) (10.28)
so that
Nt - Dt = Nt+1 + C (10.29)
Nt - Nt + Nt S = Nt+1 + Ct (10.31)
Nt S = Nt+1 + Ct (10.32)
TABLE 10.1
Hypothetical example of data required and the results of a cohort analysis for a short-lived
elasmobranch, loosely based on the life history of Rhizoprionodon terraenovae. See text for
methods used to calculate each column.
Nt’ = Nt S (10.35)
Ft = - ln (1-ht) (10.37)
Table 10.1 shows the results of the calculations for the cohort born in 1980; but
other cohorts can be treated in the same way for a full VPA. For the last cohort in
the last year of data we assume there are no fish left, they all die after age 10 in 1990.
The table is constructed for this cohort using equation (1) to calculate cohort size at
the beginning of each year (note that fish age 10 in 1990 were age 9 in 1989, etc.). The
equations for VPA when fishing takes place during the whole year (continuous fishing)
are more complicated and can be found in Hilborn and Walters (1992) and Quinn and
Deriso (1999) Sparre and Venema (1992) describe a length-based VPA method.
The above example of cohort analysis includes only one cohort. For a complete
VPA the same method should be applied for all cohorts that have completely ceased
to exist, which is all cohorts that are no longer present in the fishery. One remaining
problem after doing this is that there is no information to do the analysis for living
cohorts (those still present in the fishery) and these are usually the most important for
managers.
One way to solve the problem of incomplete cohorts is to estimate the fishing
mortality rate of cohorts currently being fished and use this to estimate the sizes of
the incomplete cohorts. Two ways used to estimate the size of current cohorts are: (a)
to obtain population size estimates from surveys or mark recapture methods or (b),
more commonly, to assume a value for the current F and estimate previous values from
there.
This last case, known as the terminal F assumption, comes from the following
equation:
Ct � Ft + M � (10.38)
Nt = �
− zt �
��
(1 − e ) � Ft � (10.38)
There are two ways to estimate F here: (a) from tag-recapture methods or (b), from
effort (f) data while assuming that q can be obtained from the relation F = fq.
The catchability coefficients (q) for each age can be obtained from the complete
cohorts and assuming q is constant over time we can use that together with effort data
to calculate F for each age. Another variation of this approach is known as the ‘tuned’
VPA which first uses the q’s from complete cohorts and this is used to derive a new set
of catchability coefficients for the incomplete cohorts.
Disadvantages of VPAs
A problem of VPA is that using the wrong M estimate can lead to severely overestimated
or underestimated cohort sizes. More worryingly, when catchability increases as the
10. Fishery stock assessment models and their application to sharks 169
stock declines in size, using the assumption that the terminal F has not changed has
been found to introduce great errors, overestimating the stock size and probably
recommending larger catches than can be sustained, which can lead to overfishing of
the stock.
Another problem is that to obtain the necessary catch-at-age data it is essential to
perform routine ageing of large samples of fish from the catch (which is costly) and if
the ages are wrongly estimated this will introduce systematic biases to the assessment.
To use the catch equation to estimate mortality within a single cohort we use a modified
version of the catch curve is used with the following equation:
where j denotes a specific cohort. This allows the estimation of the total mortality and
the relative recruitment ‘strength’ of each cohort. This method assumes that fishing
and natural mortality are constant and that vulnerability to the fishing gear is constant
above a given age. One problem is that these catch curves do not allow an estimate of
the natural mortality rate or vulnerability, so their usefulness is limited. CAGEAN
is a modification of these techniques. An introduction to the CAGEAN methods
explained below is provided by Hilborn and Walters (1992) and is recommended
for beginners: Quinn and Deriso (1999) offer an updated and mathematically more
rigorous treatment of the same topics.
C=N
F
F +M
[
1 − e −( F + M ) ] (10.41)
(10.41)
Second, numbers at age a can be related to recruitment times cumulative fishing and
natural mortality for each previous age by
Na = Re -ΣF-ΣM (10.42)
F = fq (10.43)
The Paloheimo method assumes that M is constant over years and uses a well-known
approximation for the last term (which is valid for values of Z that are no larger than
0.7):
� 1 − e− z � Z (10.46)
ln�� �� ≈ − (10.46)
� Z � 2
where j = year, a = age, and k = the number of years that the cohort has been fished.
Equation 10.47 is a linear multiple regression of the form:
Given the needed data (usually catch by age for several ages and the corresponding
effort that produced the catches), this equation can be solved with standard multiple
regression packages to obtain estimates of Rq, q, and M.
The following example taken from Hilborn and Walters (1992) shows an application
of Paloheimo’s method. Table 10.2 presents the required data on catch at age and
corresponding effort for Lake Erie perch.
TABLE 10.2
Data on catch at age and corresponding effort
for the 1971 cohort of Lake Erie perch
(Hilborn and Walters, 1992).
Age Catch Effort
2 103 15.9
3 59 15.4
4 11 13.5
5 3 12.6
10. Fishery stock assessment models and their application to sharks 171
TABLE 10.3.
Parameter correlations for the CAGEAN analysis based
on the Paloheimo method for the data of Table 10.2.
(from Hilborn and Walters, 1992).
Parameter correlations
Rq q M
Rq 1
q -0.71 1
M -0.69 -1 1
These results are suspicious and suffer from strong parameter correlation. This
occurs because of poor data contrast (see Section 10.6); q is negative, which is
impossible, while M is extremely high. To perform this catch-at-age analysis, not only
the catches at age for each year for this cohort are needed, but also the fishing effort
used to catch them. These efforts are all of the same magnitude and almost constant (i.e.
poor contrast in effort) and this is why there is a strong negative correlation between
q and M.
To simultaneously analyse data for three cohorts of Lake Erie perch using this
method (see Hilborn and Walters 1992 for further details), dummy variables may be
used to form an experimental design table, to perform a multiple linear regression. In
this case, the equation becomes:
The first three coefficients represent the recruitment level of each cohort. The dummy
variables X1-3 take the values 1 or 0 depending on which cohort we are analyzing, so
that the corresponding coefficient b (recruitment) is included or excluded. The last
two terms are the same as before and are the fishing effort and number of years of
accumulated natural mortality. An analysis the results would still not be satisfactory
because there is still poor data contrast in the effort for this set of data despite the fact
that there are data for 3 different cohorts and 4 different years of fishing. It is still
impossible to differentiate between the effects of natural and fishing mortality from
these data. However, it is possible to obtain good estimates of the recruitment levels
because there is good contrast in the relative abundance data (CPUE).
� − Faj
+ ln�
�F +M
[− (F + M )
1 − e aj aj ]��� (10.50) (10.51)
� aj aj �
10.6.1 Assumptions
Some of the models used in fisheries stock assessment are simple but the estimation
of their parameters, which implies fitting the models to the data, is not always simple.
In the case of the surplus production models treated above, there are three main
approaches that are commonly employed for the estimation of their parameters.
First, one might assume equilibrium conditions, that is, that all the catches observed
so far in the fishery are sustainable at the corresponding level of fishing effort. This
assumption is invariably wrong and must be avoided. Equilibrium methods were used
to simplify the computations because of difficulties in calculating parameter values
analytically. However, modern computers allow the use of other methods mentioned
below or even more sophisticated ones and there is no longer any need to assume
equilibrium conditions.
Y = b0 + b1 X 1 + b2 X 2 (10.56)
(10.56)
which can be easily solved using the multiple regression facilities available in most
spreadsheet software programs.
Although regression methods are easily applied to solve fisheries models, it has been
demonstrated that they can give biased answers (Uhler 1979). They can also produce
obviously wrong answers, such as negative values of r or q, which are biologically
impossible. The general corollary is that illogical answers only mean bad data!
∧
ε t = (U t − U t ) 2 (10.57)
(10.57)
This means that r, q, K, and the initial biomass size B0 be estimated. Usually, the
problem of finding the best parameter values while minimizing the difference given
by equation 10.57 is solved by using nonlinear estimation procedures such as those
available in spreadsheets.
parameters themselves, all divided by the sum over all possible parameter values of the
product of (a) and (b):
The left term of the equation is the posterior probability distribution or ‘posterior’.
The right-most terms in the numerator and denominator, imply that previous
knowledge about the shape of the distribution of the parameters is available. This is the
strength of the method as it allows additional ‘external’ information, such as biological
or fisheries information to be included into the estimation process.
Depending on the type of ‘external’ information that can be incorporated, different
possible prior distributions can be used for the parameters such as the binomial,
normal, uniform, Poisson, multinomial and others. For more details about the types of
distributions for different types of data users should consult a statistical text book.
A rudimentary, but simple way, to implement Bayesian statistics is to calculate the
“kernel”, which is based on the sum of squares.
− t −21
L( parameters) = SS (10.60)
where L is the likelihood of the parameters and SS, the sum of squared differences (10.60)
between the real data and the estimated data points derived from a given set of model
parameter values for t-1 degrees of freedom.
− t −21
SS (10.61)
Pr( parameters | data ) =
� SS
− t −21
(10.61)
parameters
Bayesian approaches have been applied to elasmobranch fisheries by, e.g. McAllister
and Pikitch (1998a,b), Punt and Walker (1998), Babcock and Pikitch (2001), McAllister
et al. (2001) and Apostolaki et al. (2001, 2002). Berger (1985), Gelman et al. (1995) and
Congdon (2001) provide a comprehensive treatment of Bayesian analysis. Hilborn and
Walters (1992), Quinn and Deriso (1999) and Haddon (2001) provide more detailed
treatment of parameter estimation issues.
Data sets with high contrast have strong variations in data values, with relatively
rapid changes back and forth between high and low effort. In these cases, parameters
can be much more precisely estimated although other factors such as the total number
of points in the time-series of data and the intrinsic variability of the data also influence
the final precision of model parameter estimates.
In summary, when fitting models to fisheries data it is imperative to look at the
uncertainty in the parameter estimates and not only at a single ‘goodness-of-fit’
measure such as the sum of squares. It is always advisable to apply different models to
the same data set and compare the results between models, trying to validate results or
to ask questions about why results might be different and what the implications of this
are. In addition, it is important to learn how to use uncertain (‘bad’) results to improve
the contrast in the data through carefully thought and well planned management
regulations aimed at improving the quality of the data (such as large variations in effort
over short periods of time).
Ct = qftBt ⇒ Ut = qBt
obtain fishery-independent indices of stock abundance (see Section 12), either through
research cruises or by coordinating efforts with fishermen to perform controlled
experiments to fish in other areas or other ways than they usually do, such as following
a systematic sampling design. Quinn and Deriso (1999) summarize different ways to
model non-linear relationships between CPUE and abundance.
Finally, it should be mentioned that generalized linear models (GLMs) are becoming
common methods for standardizing fishery-dependent CPUE data. These methods
take account of the effect of various factors (such as environmental variables or fishery
operational variables) on catch rates.
TABLE 10.4
A referenced selection of real shark fisheries, summarizing their main characteristics, the assessment
methods in use and the state of management and the resource.
Canadian TAC (250 t), Fishing Catch curves, catch Overexploited, under
Campana et al.
Porbeagle shark Lamna nasus 850 t/y licenses plus fishing rate trends, age- severe recovering
restrictions 1999, 2001
fishery structured model regulations
Galeorhinus galeus,
None, quotas
Squalus acanthias,
established through ad Recovered after
New Zealand Callorhinchus milii, Francis and
17,000 t/y ITQs and TACs hoc methods overxploitation or
shark fisheries Mustelus lenticulatus, Shallard 1999
(proportion of past unknown
Raja spp. Hydrolagus spp.
catches)
and other 15 spp
Overexploited, under MacAllister and
East coast of US 39 species mostly Bayesian Surplus
3,500 t/y TAC recovering Pikitch. 1998a, b;
shark fishery Carcharhinus Production Models
regulations Branstetter 1999
5 prohibited
Gulf of Mexico 35 species mostly Unknown, likely Bonfil 1997,
12,000 t/y species and other None
shark fisheries Carcharhinus heavily overexploited Castillo et al. 1998
simple regulations
Mustelus schmitii,
Argentinean Galeorhinus galeus, Unknown, likely
30,000 t/y None None Chiaramonte 1998
shark fisheries Carcharhinus brachyurus heavily overexploited
and other 10 spp
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