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FISHERIES BIOLOGY /
STOCK ASSESSMENT
GARDEL XYZA LIBUNAO

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FISHERIES TECHNOLOGISTS 2021 1

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Learning points
What is stock assessment?
Purpose: Why is it done?
Definition: Fish population vs. fish stock
Types of Data needed for stock assessment
Sampling methods
From Data to Estimations : Indicators and biological reference points
Integration into Fisheries Management
Stock assessment models
Fish population dynamics
Holistic and Analytical models
Dynamics of a cohort: Estimating age, growth and mortality
Stock/Recruitment Relationship
Computer Packages for Stock Assessment Studies
2 2

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Tragedy of the commons

• Though countries control their own EEZ, no part of the ocean is private property; this creates the fundamental
aspect of fisheries: they are a common pool resource—meaning they are shared, public, and have no inherent
way to exclude individuals from exploiting it.
• Without governance, a tragedy of the commons emerges, where individuals maximize their own benefit at the
expense of sustainability and others with less power or capital. Combating a commons issue requires collective
stakeholder action or government regulation.

3 3

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Stock Assessment
Purpose: Why is it done?

Are there really plenty of fish in the sea? How do we know?

Stock assessment is the process of collecting, analyzing and

reporting fish population information to determine changes in
the abundance of fishery stocks in response to fishing and,
to the extent possible, predict future trends of stock abundance.

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Stock Assessment
Purpose: Why is it done?

Scenario 1: Stock assessment studies indicate decline in fish stocks

Response: Fishing regulatory measures such as

Restrictions on the expansion of fishing fleet

Restrictions on total amount of catch that could be taken

Closed fishing seasons or No fishing zones

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Stock Assessment
Purpose: Why is it done?

Scenario 2: Stock assessment studies show that there is overfishing

Response: Fishing regulatory measures such as

Mesh size regulations

Harvest size restrictions

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Stock Assessment
Purpose: Why is it done?

Types of overfishing:

Growth Overfishing: Harvesting a fish population at a smaller size which does not
allow for the producing of the maximum yield per recruit. It can be prevented by
reducing fish mortality rates and allowing for full growth.

Recruitment Overfishing: Depleting the older population of fish with overfishing

which prevents proper reproduction. The species can no longer replenish because
there are not enough flourishing adult fish to replicate. This is the most common
form of overfishing.

7 7

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Stock Assessment
Purpose: Why is it done?

Types of overfishing:
Ecosystem Overfishing: Diminishing a fish population by
overfishing it, which in turn shifts the balance of an
environment. This causes predators that can no longer
rely on food sources of smaller fish, smaller fish
populations increasing because of a decline in
predators, etc.

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Stock Assessment
Purpose: Why is it done?

Stock assessments provide a scientific and quantitative basis to the process of developing and
implementing a management plan in several areas.

1) Determine the status of fish stocks

A fishery stock assessment describes the past and current status of a fish stock i.e. how big is the stock? Is
it growing in size or shrinking?

2) Forecast future conditions, including under various potential management actions

A stock assessment also attempts to make predictions about how the stock will respond to current and
future management options. Will a slight increase in fishing pressure have a negative effect on the stock
next year? Ten years from now?

9 9

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Stock Assessment
Purpose: Why is it done?

Maximum Sustainable Yield (MSY)

The objective of fish stock assessment is to predict changes in the size of stock and
the size of yields so that optimum levels of effort and yield could be determined.

Increase in yield with increase in fishing effort up to a

certain level, after which, the renewal of stock
(reproduction + growth) does not compensate the loss
of biomass due to fishing, and hence, further increase
in fishing effort leads to decline in yield.

The MSY is defined as the largest average catch,

which can continuously be taken from a stock.

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Stock Assessment
Purpose: Why is it done?

Maximum Sustainable Yield (MSY)

The MSY is a useful tool for describing the
fish stocks in relation to exploitation. It
explains the fact that more fishing does not
mean more fish and that fishing beyond a
certain point, overfishing can mean less
fish. The fishing effort, which in the long
term gives the highest yield, is indicated as
FMSY.

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Stock Assessment
Purpose: Why is it done?

Maximum Economic Yield (MEY)

• Yield level, which coincides with the level of harvest or
effort that maximized the sustainable net returns from
fishing.
• A MEY harvest is desirable because it is the catch level that
enables society to do the best it can with what nature has
provided
• Relating to MSY, the maximum economic yield (MEY) is the
level of catch that provides the maximum net economic
benefits or profits to society

Yield vs fishing effort – blue line

Cost of fishing (worker wages, vessel maintenance, equipment, fuel etc.) is proportional to fishing effort – red line
(intersects the curved yield line at some point)
Blue shaded area above cost line = yield to cost ratio is greater than 1 = profit!
Point at which cost line and yield curve meet is where yield to cost ratio is equal to 1 = no more profit 1212
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Stock Assessment
What is a fish stock?

Capture fisheries research is usually concerned with the

fish stock exploited by a particular fishery, rather than
with an individual fish or with the total population of a
species

A fish population is a biological unit referring to individuals of

a species living in the same area.

A fish stock is a management unit grouped by genetic

relationship, geographic distribution, and movement patterns.
• defined as much by management concerns – such as
jurisdictional boundaries or harvesting location – as by
biology
• group of fish managed as a single unit

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Stock Assessment
What is a fish stock?
u la
in s
Pen
a nga
bo
Zam

Tuloy from the waters near Dapitan City may be considered a

separate population from those near Isabela City, but both
since Zamboanga Peninsula is managed as a single
management unit, are part of the Zamboanga Peninsula tuloy
fish stock.

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Stock Assessment
What is a fish stock?

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Stock Assessment
What is a fish stock?

A cohort or annual class or a generation, is a group of individuals born in the same

spawning season.
Within a fish stock or population, a cohort is a group of fish all born in the same year. Within the Gulf
of Maine cod stock, all of the cod born in 2004 belong to one cohort and those born in 2005
comprise a second cohort.

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Stock Assessment
Data needed

Stock assessment scientists will estimate the current status of the stock
relative to management targets and predict the future status of the stock
given a range of management options.

Fishery-dependent data
1. Landing records
2. Portside sampling
3. Onboard observers
4. Log books and vessel trip records

Fishery-independent data
1. Swept area method
2. Acoustic surveys
3. Underwater visual fish census surveys
4. Capture-Mark-Recapture
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Stock Assessment
Data needed

Fishery-dependent data
Sources: Derived from the fishing process itself
• From commercial sources (fishermen or dealer reports) and recreational sources
(individual anglers, party or charter boats)

Data collected: Total amount of fish removed from the ocean (landings and dead discards)
and the level of fishing participation (effort)
• who, what (target species), when (season), where (location) and how (gear type); related
economic information (the cost of fishing trips, the value of fish sold); and biological
information (species, age, length, weight, maturity of fish caught in a fishery)
Collection method: Self-reporting, onboard observers, portside surveys, telephone surveys
or vessel-monitoring systems

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Stock Assessment
Data needed

Fishery-dependent data:
1. Landing records – records which result directly from the sale of caught fish
2. Portside sampling - some portion of both recreational and commercial catch is sampled on
the docks for size (length) and age by government scientists known as portside observers or
port agents
• Length is measured on site. Determining a fish’s age, however, requires taking biological
samples to be evaluated in a lab. Scientists can determine a fish’s age by counting the
growth rings in a scale or an otolith (ear bone), much like counting the rings of a tree
3. Onboard observers - government personnel known as onboard observers sometimes
accompany fishing vessels. Observers are trained to sample catch for size, and sometimes age,
and to estimate bycatch and discards.
4. Log books and vessel trip records - fishermen keep their own records, called log books or
vessel trip reports, which they pass on to government officials.

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Stock Assessment
Data needed

Fishery-independent data: Collected by scientists conducting long-term resource

monitoring projects known as fishery-independent surveys. These do not rely from actual
fishery data but rather from research programs/experiments at sea carried out over
relatively short periods of time.

1. Swept area method for demersal fishes

2. Acoustic surveys for pelagic fishes
3. Underwater visual fish census surveys
4. Capture-Mark-Recapture

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Stock Assessment
Data needed

Fishery-independent data:
1. Swept area method for demersal fishes
Bottom trawl surveys are widely used for monitoring
demersal stocks when a simple index of abundance is
required for scientific and related work.

The objectives of bottom trawl survey are:

• Estimation of the total biomass and catch rates.
• Estimation of biomass of selected species.
• Collection of biological data such as length frequency
data for estimation of growth and mortality parameters.
• Collection of environmental data.

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Stock Assessment
Data needed

Fishery-independent data:
1. Swept area method for demersal fishes
Catch per unit area (estimates biomass)
= catch / swept area

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Stock Assessment
Data needed

Fishery-independent data

2. Acoustic surveys for pelagic fishes

• multi-frequency, wide band, multibeam, vertical and
horizontal echosounding

• Aim To determine the relative abundance of the target

species. This information is then used to determine catch
rates and management advice for the following year.

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Stock Assessment
Data needed

Fishery-independent data

2. Acoustic surveys for pelagic fishes

• How: These surveys use sound waves emitted from a
"transducer" to estimate the density of plankton and fish
shoals. The survey vessel tows the transducer under water,
which is linked to an echo sounder in the vessel which
records the shoals of fish as "marks" on a screen or paper
trace.

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Stock Assessment
Data needed

Fishery-independent data
3. Underwater visual fish census surveys
• These are based on on-site visual counts of organisms.
• Census methods can be done by either snorkeling or
scuba diving. In certain instances, cameras, video cameras
or submersible gear can be used to get around the constraints
linked to sampling by divers
• Snorkeling or scuba are best carried out in clear,
calm and shallow water (generally between the surface
and a depth of 20 m).

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Stock Assessment
Data needed

Fishery-independent data
3. Underwater visual fish census surveys are conducted:
a. Along random paths (chosen by chance)
b. Using quadrats (grids moved along a transect by divers) or transects
• Rectangular area whose length and width is clearly defined. The census, or count, is
carried out within the boundaries of the transect, which is generally denoted out by a
flexible graduated tape measure, which is rolled out on the seafloor

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k164xlkuLYh5qRPbPXmkqOPcUmVkZb4RVMMdRAVJIuE8p_v9_Q#f0005

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Stock Assessment
Data needed

Fishery-independent data
3. Underwater visual fish census surveys are conducted:
a. Along random paths (chosen by chance)
b. Using quadrats (grids moved along a transect by divers) or transects
c. From stationary points.
• Observer begins counting from a determined point while slowly turning in a circle. This method is
quicker than laying a transect. It is particularly recommended for studying a species or small group
of species, especially in very heterogeneous environments, and for isolated complex structures or
large-size formations (coral heads, large boulders).

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Stock Assessment
Data needed

Fishery-independent data
3. Underwater visual fish census surveys
• Data taken: Status of fish stocks
a. Identifying and counting species - an estimate of species richness (i.e. the number of
species), particularly for environmental inventories.
b. Counting individuals - individuals are counted to estimate abundance (number of fish) and
density (the number of fish per surface area unit) (e.g. individuals per square meter).

For a given species, the estimate of the mean density D on a transect of

width d and length L is expressed as In the case of stationary points, density is expressed as

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Stock Assessment
Data needed

Fishery-independent data
3. Underwater visual fish census surveys
• Data taken: Status of fish stocks
• Data taken: Environmental factors – morphology of study site

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Stock Assessment
Data needed

Fishery-independent data
4. Capture-Mark-Recapture
• The method involves capturing a number of animals, marking them, releasing them back into the
population, and then determining the ratio of marked to unmarked animals in the population.
• It is based on the principle that if a proportion of the population was marked in some way, returned to
the original population and then, after complete mixing, a second sample was taken, the proportion of
marked individuals in the second sample would be the same as was marked initially in the total
population

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Stock Assessment
Data needed

Fishery-independent data
4. Capture-Mark-Recapture
• For example, suppose you took 200 fish out of a lake having an unknown number of fish, put PIT tags on
them, return them to the lake and let them mix thoroughly. If you then take 250 fish from the lake and
find 50 of them to have PIT tags, then M = 200, T = 250, R = 50, and the unknown total number of fish in
the lake (N) could be estimated as:

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Stock Assessment
Data needed

Fishery-independent data
4. Capture-Mark-Recapture
Solve this à

Considerations:
• What are the possible caveats when
studying open areas? Closed areas?
• How do we mark different species?
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Stock Assessment
Data needed

Fishery-independent data
4. Capture-Mark-Recapture: Peterson method (also known as the
Lincoln-Peterson index)
• A “closed system,” meaning no fish are entering (also no births)
or leaving the pond (and no deaths) during the study.
• Marks: external tag, fin clip, dye, PIT tag, etc
• In the United States, conservation measure for lobsters require
fishers to return berried lobsters to the sea after V-notching
• Oxytetracycline – an antibiotic which is injected in a fish to leave
a mark on its skeletal structures such as otoliths

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Stock Assessment
Data needed

Stock assessments require three primary categories of information:

1. Catch Data (The amount of fish removed from a stock by fishing):
• Commercial catch monitoring, Logbooks, Observers
2. Abundance Data (A measure, or relative index of the number or weight of fish in the
stock):
• Data from a statistically-designed, fishery-independent survey (systematic sampling carried out by research or
contracted commercial fishing vessels separately from commercial fishing operations) that samples fish at
hundreds of locations throughout the stock’s range. Most surveys are conducted annually and collect data on all
ecosystem components.
3. Biology Data (Provides information on fish growth rates and natural mortality):
• information on fish size, age, reproductive rates, and movement.

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Stock Assessment
Data needed

Sampling methods:
• The ideal basis for fish stock assessment is data that fully represent a stock.
• It should be the aim of any program for the collection of data on a fishery, to obtain samples that fully represent the
population under investigation

1. Simple random sampling – any fish from the stock should have the same probability of being sampled
2. Stratified random sampling – population is first divided into strata

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Stock Assessment
Data needed

1. Simple random sampling – any fish from the stock should have the same probability of being sampled
2. Stratified random sampling – population is first divided into strata

3. Proportional sampling – allocate samples in proportion to stratum size

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Stock Assessment
From data to estimations

Different stock assessment tools can be used to estimate different

reference points and performance indicators:
1. Performance indicators are measures of some attribute of the fishery, including:
• quantitative and qualitative empirical indicators (e.g., mean size of fish in the catch)
•statistically derived indicators using a model (e.g., biomass estimated using a stock assessment model)
•proxy indicators for biomass (e.g., catch rates or density estimates)
•fishing mortality (e.g., spawning potential ratios or length composition of the catch)
•indirect indicators (e.g., increased travel time as an indication of declining local stocks).

37

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Stock Assessment
From data to estimations

Different stock assessment tools can be used to estimate different

reference points and performance indicators:
2. Reference points are predetermined levels for indicators that allow for analysis of the relationship between
performance indicators and the objectives of the fishery.
• There are typically two types of reference points:
a. a target reference point is an indicator value that corresponds to the condition of the fishery being at a
desirable level
b. a limit (or threshold) reference point is an indicator value that corresponds to the condition of the fishery
being undesirable (e.g., overfished).

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Stock Assessment
From data to estimations

How is the fishery performing?

Collect data and from the data estimate indicators.
Use indicators to measure the social, biological,
economic, and operational performance of a
fishery

Do I establish harvest control rules as part of

fisheries management?
Are indicators at the Target Reference Points
(orange) or at the Limit Reference Points (purple)?
If Limit reference threshold is not achieved, restrict
harvest.

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Stock Assessment
Integration into Management

Reference points typically allow managers to make at least two

statements about stock status, namely overfishing and overfished declarations:

Overfished refers to the biomass (B) of a population, or stock, of fish (amount of fish in the water).
• There is some amount of biomass, B, that will produce MSY—this is BMSY.
• Biomass of fish in the water < BMSY, the stock is overfished, or depleted. If the amount of fish in the water is
more than would produce MSY it is underfished. The ratio of B/ BMSY is commonly used, though the number of
demarcation varies by governing body (B may represent spawning biomass, vulnerable biomass, or total stock
biomass). USA typically defines an overfished fishery as any with B/ BMSY below 0.5

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Stock Assessment
Integration into Management

The MSY biomass (BMSY) is the stock

biomass that can support harvest of
the maximum sustainable yield.

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Stock Assessment
Integration into Management

Reference points typically allow managers to make at least two

statements about stock status, namely overfishing and overfished declarations:

Overfished refers to the biomass (B) of a population, or stock, of fish (amount of fish in the water).
• There is some amount of biomass, B, that will produce MSY—this is BMSY.
• Biomass of fish in the water < BMSY, the stock is overfished, or depleted. If the amount of fish in the water is
more than would produce MSY it is underfished. The ratio of B/ BMSY is commonly used, though the number of
demarcation varies by governing body (B may represent spawning biomass, vulnerable biomass, or total stock
biomass). USA typically defines an overfished fishery as any with B/ BMSY below 0.5

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Stock Assessment
Integration into Management

Reference points typically allow managers to make at least two

statements about stock status, namely overfishing and overfished declarations:

Overfishing refers to fishing mortality (F), or the rate of fish killed by catching them (just think of this as
the proportion of fish caught).
• There is an ideal proportion of fish to catch that will produce MSY—this is called FMSY.
• Fish caught (F) > FMSY = overfishing
• Fish caught (F) < FMSY = underfishing
• Fishing mortality = F/ FMSY > 1 = overfishing.

43

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Stock Assessment
Integration into Management

FMSY is the rate of fishing mortality (the

proportion of a fish stock caught and
removed by fishing) resulting, in a
population size of BMSY

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Stock Assessment
Integration into Management

Reference points typically allow managers to make at least two

statements about stock status, namely overfishing and overfished declarations:

Overfishing refers to fishing mortality (F), or the rate of fish killed by catching them (just think of this as
the proportion of fish caught).
• There is an ideal proportion of fish to catch that will produce MSY—this is called FMSY.
• Fish caught (F) > FMSY = overfishing
• Fish caught (F) < FMSY = underfishing
• Fishing mortality = F/ FMSY > 1 = overfishing.

45

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Stock Assessment
Integration into Management

“Kobe plots”
• F/ FMSY ratio against the B/ BMSY ratio to
get a sense of the sustainability of a
fishery.

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Stock Assessment
Fish population dynamics

BUT How will you know the present biomass (total

weight of the stock)?
Fish population dynamics describe how a stock or a
combination of them changes over time as a function of growth,
recruitment, mortality, immigration and emigration.
• It is the basis for understanding fish populations and associated
fisheries.
• It is the central component of any effort to assess the population
dynamics so as to provide quantitative advice for fishery
management.

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Stock Assessment
Fish population dynamics

Many fish populations follow a logistic pattern

(sigmoid curve) of density-dependent growth.
Beginning with a population size where space
and food are not limiting, the population
grows rapidly in an exponential pattern; at a
certain population density, population growth
slows and stabilizes at a given carrying
capacity, K. (Carrying capacity is the maximum
number, density, or biomass of a population
that a specific area can support sustainably.)

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carrying-capacity-K_fig1_325275123

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Stock Assessment
Fish population dynamics

Fish population dynamics is the study of change in a fish

population over time.
• Equates to the population size plus births (i.e., recruitment)
and immigration and minus mortality and emigration.

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HOW DO YOU ESTIMATE THESE PARAMETERS?

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Stock Assessment
Deterministic models

1. Micro-analytical/Analytical models otherwise known as dynamic pool models take into

account recruitment, mortality, age, growth and all other factors affecting stock
2. Macro/Holistic/Global/Synthetic models are used for rough approximation of the
existing status of the stocks and these models are simple, require only catch and effort
data for different years/time and analysis is straight forward.
• They do not consider the events within a population, and particularly ignore the growth
and mortality of the individuals forming the population.
• These models view population as one unit of biomass, with all individuals having the same
growth and mortality rates.

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Macro/Holistic/Global/Synthetic models

1. Swept area method

2. Surplus production method - use catch per unit effort (CPUE) as input. The data, which
represent a time series of years, are usually collected from commercial fishery (i.e.
records of landed catches)
• Assumption: Biomass of the fish in the sea is proportional to the CPUE.

Yield per unit effort (Y/f) is also CPUE in weight:

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Stock Assessment
Macro/Holistic/Global/Synthetic models

1. Swept area method

2. Surplus production method - use catch per unit effort (CPUE) as input. The data, which
represent a time series of years, are usually collected from commercial fishery (i.e.
records of landed catches)
• Assumption: Biomass of the fish in the sea is proportional to the CPUE.

Yield per unit effort (Y/f) is also CPUE in weight:

52
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Stock Assessment
Macro/Holistic/Global/Synthetic models

CPUE
• Catch per unit of fishing effort (CPUE) is the total catch divided by the total amount of effort used
to harvest the catch.
• an indirect measure of the abundance of a target species: A decreasing CPUE indicates
overexploitation, while an unchanging CPUE indicates sustainable harvesting.

What do you mean by effort?

• Does effort change depending on fishing gear?

53

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Stock Assessment
Macro/Holistic/Global/Synthetic models

What do you mean by effort?

54

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Macro/Holistic/Global/Synthetic models

What do you mean by effort?

55

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Stock Assessment
Macro/Holistic/Global/Synthetic models

CPUE
What do you mean by catchability coefficient q?
• Portion of stock captured by one unit of effort
• How efficient is your fishing effort? Depends on:
1. Directly proportional to efficiency of fishing fleet – efficiency will increase if fishers know more about the
location and behavior of fish. Example: CPUE of bigeye tuna by purse seiners increased with introduction
of FADs. Why?
2. When a fleet targets a specific species. Example: The increase in depth of longline gear to target bigeye
tuna increased the catchability for that species, but decreased the catchability of yellowfin tuna.
3. Environmental factors - the 1981–1983 El Niño reduced catchability of yellowfin tuna to the purse-seine
fisheries of the eastern Pacific Ocean (EPO) to such an extent that many vessels transferred their
operations to the western Pacific

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Stock Assessment
Macro/Holistic/Global/Synthetic models

1. Swept area method

2. Surplus production method - use catch per unit effort (CPUE) as input. The data, which
represent a time series of years, are usually collected from commercial fishery (i.e.
records of landed catches)
• Assumption: Biomass of the fish in the sea is proportional to the CPUE.

Both models of Schaefer conform the assumption that Y/f

declines as effort increases.
Straight line of Schaefer model – implies that Y/f reaches
zero for certain f value
Curved line in Fox model – implies that Y/f never approaches
zero, even at very high levels of effort

57

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Stock Assessment
Micro-analytical/Analytical models

• Take into account recruitment, mortality, age, growth and all

other factors affecting stock
• They require the age composition of catches to be known. For
example: How many of the fish caught are 1 year old? 2 years old?
• They are “age-structured models” working with concepts such as
mortality rates and individual body growth rates.
• The basic concept in age-structured models is that of a cohort – a
group of fish all of the same age belonging to the same stock.

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Stock Assessment
Micro-analytical/Analytical models

Dynamics of a cohort:
• Curve A – Decay in the number of survivors as a function of age of the
cohort.
• Curve B – Average body length increases as the cohort grows older
• Curve C – Corresponding body weights
• Curve D – Plot of total biomass = Number of survivors * average body
weight against the age of the cohort

Two major elements in describing the dynamics of a cohort:

1. The average body growth in length and weight
2. The death process

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Stock Assessment
Estimating age

Cohort – batch of fish all of approximately the same age and

belonging to the same stock.
Age – not an individual level but the average age of a cohort.
“Birthday” = day larva hatches from the egg
Larvae (or juveniles) – little influenced by fishery (unexploited
phase of life)
Tr – youngest age at which the fish may be vulnerable to fishing
gears. A fish at age Tr is called a “recruit”.
• Recruitment = number of fish that have attained age Tr during a
recruitment season
• Recruitment intensity = number of recruits per time unit
• Recruitment pattern = “autumn cohort”, “spring cohort”

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Stock Assessment
Estimating age

Otoliths, commonly known as "earstones," are hard, calcium carbonate

structures located directly behind the brain of bony fishes. Annual growth rings
in fish ear bones (otoliths) are read by biologists in laboratories.
• The samples may be collected during fishery-independent surveys or be
obtained from observers and other fishery sampling programs.

There are three types of otoliths, all of which aid fish in balance and hearing:
1. Sagitta: The largest of the 3 pairs of otoliths, sagitta is involved in the detection of
sound and the process of hearing, or converting sound waves into electrical signals
2. Asteriscus: This type of otolith is involved in the detection of sound and the process
of hearing.
3. Lapillus: This type of otolith is involved in the detection of gravitational force and
sound

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Stock Assessment
Estimating age

The dark translucent zone represents a period of fast growth. The white opaque
zone represents a period of slower growth. Biologists estimate fish age by
counting these opaque zones, called annuli.

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Stock Assessment
Length-weight relationship

W(i) – body weight of fish number i

L(i) – total length of fish number i
q and b are parameters – depends on data

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Stock Assessment
Length-weight relationship

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Stock Assessment
Estimation of growth parameters

The study of growth means basically the determination of the

body size as a function of age. Therefore all stock assessment
methods work with age composition data.

Growth model: a depiction of length or weight of animals as a

function of age.

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Stock Assessment
Estimation of growth parameters

The study of growth is to determine the body size as a function

of its age.
1. Gompertz curve (sigmoid function) – growth is slowest at
the start and end of a time period
2. Von Bertalanffy – expresses length as a function of age of
the animal. Fish increases in length as they grow older but
their growth rate (change in length per unit time)

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Doll/publication/337806909/figure/fig2/AS:833289250164736@1575683047780/Theoretical-growth-
curves-generated-from-the-von-Bertalanffy-and-Gompertz-growth-models.png

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Stock Assessment
Estimation of growth parameters

Von Bertalanffy growth function (VBGF) : describe the total

length of the average individual at any given age.
Rate of growth versus length – straight descending line. This line will
cut the x-axis at a point at which the rate of growth is zero. This is the
point beyond which the fish will not grow further and the length of
the fish at
this point is known as the asymptotic length denoted by L∞.

L (t) – length of fish at time t

Parameters:
L∞ - the maximum length of the infinitely old fish called the
asymptotic length, K - the growth or curvature parameter and t0 -
theoretical age at L=0

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Stock Assessment
Estimation of growth parameters

Von Bertalanffy growth function (VBGF)

Assume that these parameters are estimated:

The length in cm at a given age of an average fish of the stock can be

calculated by inserting a value for t, ex: t=2 years.

Thus knowing the parameters, we can calculate the length at any age
of the fish and from there we can calculate the growth rate
(cm/year).
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Stock Assessment
Estimation of growth parameters

Von Bertalanffy growth function (VBGF) :

BUT HOW DO YOU ESTIMATE PARAMETERS?

For example: you have age reading and length measurements data from resource surveys with a research
vessel. Suppose that we have observed two annual peak recruitment seasons and have decided to define 2
cohorts per year:
1. Spring cohort – fish recruited from January to June
2. Autumn cohort – fish recruited from July to December

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Estimation of growth parameters

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Estimation of growth parameters (K and L∞)– Gulland and Holt plot

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Estimation of growth parameters (K and t0)– von Bertalanffy plot

Difference of von Bertalanffy and Gulland and Holt plot:

• Von Bertalanffy requires an estimate of L∞ (average length
of very old fish (short cut method) à 1) In small samples you
may simply use the length of the largest fish or 2) In a very
large sample you take the average of 10 largest fish or 3) Use
Powell-Wetherall method

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Estimation of growth parameters (K and t0)– von Bertalanffy plot

Ford- Walford plot – method in use in the estimation of parameters of the VBGE if you
are provided the length at each data or modal length measured at regular time intervals
for a single age class or cohort
• Plot could be used to obtain a quick estimate of K and L∞ . From VBG equation,
growth parameters are equal to:

• Note the constant time interval of one year. 74

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Estimation of growth parameters

The use of age/length keys:

• A table showing, for each length class of fish of a
particular stock, the percentage or fractional age-
frequency distribution.
• To estimate the age composition of the catch from a
particular stock, we only need to determine an
age/length key based on a small sample of age readings.
• Lengths are converted to ages by means of the key. The
same key may be used in consecutive years as long as
there is no suspicion of major changes in the age
composition of the stock.

Example: Age/length key could be based on 182 randomly

drawn fish with the following distribution.

To get key: Divide each row entry by the row total for each
length group
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Estimation of growth parameters

Age/length key could be used to assign ages to a much

larger length-frequency sample of the same stock.

Formula = Frequency observed * Value in key

Example: Length group 10-15 cm is estimated to consist of 7035*0.25 = 1759 age group 0 fish and
7035*0.75 = 5276 1-group fish. How about for 15-20 cm fish?

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Estimation of growth parameters

Age/length key could be used to assign ages to a much

larger length-frequency sample of the same stock.

Formula
= Frequency observed * Value in key
How about for 15-20 cm fish?

77

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Stock Assessment
Estimation of mortality

The key parameters used when describing death are called

the mortality rates.
• The mortality rate (chance of dying as a function of
time), is, closely correlated to the predictability of the
environment, i.e. the frequency of random fluctuations
that somehow endangers the survival of the population.

Z (instantaneous rate of total mortality, the total mortality

coefficient, or simply the total mortality rate)
= F (fishing mortality) +M (sum of natural mortality)

Natural mortality is due to predation, disease and deaths due to old

age.
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Stock Assessment
Estimating mortality

N(t) – number of survivors from a cohort attaining age, t

Tr – youngest age at which the fish may be vulnerable to

fishing gears. A fish at age Tr is called a “recruit”.

N(Tr) = number of recruits

Tc – “age at first capture” – age at which they actually

enter the fishery (dependent on mesh size) – marks the
beginning of the exploited phase

Age 0 to Tr = “pre-recruitment phase”

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Stock Assessment
Estimating mortality

Exponential decay model

Z (instantaneous rate of total mortality, the total mortality coefficient, or simply the total mortality rate) =
F (fishing mortality) +M (sum of natural mortality)

The following table gives the percentages of survivors after one and two years respectively of two
populations subject to two different total mortality rates, Z=0.5 and Z=2.0.

The higher the Z, mortality rate is

higher and a cohort subjected to
such a high rate of total mortality
will have been practically
exterminated in 2 years.

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Stock Assessment
Estimating mortality

Exponential decay model

The higher the Z, mortality rate is higher and a cohort subjected

to such a high rate of total mortality will have been practically
exterminated in 2 years.

The dynamics of similarly aged fish of a stock are assumed to

follow the model of natural decay, whereby the reduction in
numbers due to total mortality is an exponential
function of the number of cohorts at the beginning of the period.

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Stock Assessment
Estimating mortality

Z=F+M
The total number of deaths can be split into a number dying due to fishing or the catch (C) and a number dying
due to natural causes (D).
Baranov’s equation or catch equation (one of the most important mathematical expressions in fisheries
biology): number dying due to fishing, the catch, during the time period from t1 to t2 is:

The fraction of deaths caused by fishing, F/Z, is called the

“exploitation rate”.

The number dying due to natural causes is: In real life, mortalities vary with the age of cohort. Small (young)
fish are exposed to greater natural mortality (M) because more
predators can eat them. Small fish suffer less fishing mortality (F)
than large (old) fish because they have not yet migrated to the
fishing grounds or they escape the meshes of the gear.
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Stock Assessment
Estimating mortality

Example of dynamics of cohort with different mortality rates during its life span

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Stock Assessment
Estimating mortality

How do you estimate total mortality coefficient, Z?

• The total mortality coefficient Z can be estimated when estimates of the number
of fish in the cohort are available for two different moments during its exploited phase, t1 and t2.

1. CPUE (the numbers caught per trawl hour) is a quantity which can be assumed proportional to the number
of fish in the sea, N.

Parameter q is the “catchability coefficient”: the more efficient the gear is, the higher the value of q because q is
a measure of the ability of the gear to catch fish. 84

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Stock Assessment
Estimating mortality

How do you estimate total mortality coefficient, Z?

2. Heincke’s method
• CPUE of oldest age groups is lumped
since it is difficult to separate the older age groups
• Youngest age group is excluded since it is not yet exploited by the fishery.
3. Robson and Chapman’s method

4. Beverton and Holt’s Z- equation based on length data

• There exists a functional relationship between Z and the average length of the fish, L
• L’ is some length for which all fish of that length and longer are under full exploitation.

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Stock Assessment
Estimating mortality

Beverton and Holt’s Z- equation based on length data

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Stock Assessment
Estimating mortality

Z=F+M
How do you estimate natural mortality coefficient, M?
1. Analysis of catch data from commercial fisheries, sampling programs, or mark and recapture experiments.
2. Correlation with other life history parameters.
3. Estimation of predation from stomach content analysis and consumption experiments
4. Pauly’s empirical equation for Natural Mortality Estimation
• Regression analysis to functionally link natural mortality M with VBGF parameters and climatic
parameters

• VBGF parameters: K (per year), L (TL in cm)

• Annual average habitat temperature of the surface in degrees centigrade, T
• 0.8 is an adjustment factor used for schooling species
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Stock Assessment
Estimating mortality

How does M relate to K (von Bertalanffy curvature parameter)?

• K is related to longevity of fish and longevity is related to mortality.

• A slow growing species (low K) cannot bear high natural mortality (M) – if it did ot would soon become
extinct.
• As a generalization: Fish species with a high K-value have a high M-value and species with low K-value have
a low natural mortality.

How does M relate to L∞?

• Natural mortality is linked to L∞ since large fish have fewer predators than small fish.
• Fish with high natural mortality mature early in life. Why?

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Stock Assessment
Estimating mortality

How does M relate to K (von Bertalanffy curvature parameter)?

• K is related to longevity of fish and longevity is related to mortality.

• A slow growing species (low K) cannot bear high natural mortality (M) – if it did ot would soon become
extinct.
• As a generalization: Fish species with a high K-value have a high M-value and species with low K-value have
a low natural mortality.

How does M relate to L∞?

• Natural mortality is linked to L∞ since large fish have fewer predators than small fish.
• Fish with high natural mortality mature early in life, compensating for the high M by starting to reproduce
earlier .There is a direct relationship of M with the ratio of gonad weight to somatic weight (Fish with high
mortality may compensate by producing more eggs)
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Stock Assessment
Estimating mortality

Z=F+M
How do you estimate natural mortality coefficient, M?
1. Analysis of catch data from commercial fisheries, sampling programs, or mark and recapture experiments.
2. Correlation with other life history parameters.
3. Estimation of predation from stomach content analysis and consumption experiments
4. Pauly’s empirical equation for Natural Mortality Estimation
5. Rikhter and Efanov’s formula
• They showed a close association between M and Tm50% (age when 50% of the population is mature –
“age of massive maturation”)

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Stock Assessment
Estimating mortality

Gear selectivity
• Complete length (or age) ranges of fish or shellfish are not always under full exploitation.
• Most fishing gears are selective for a certain length range only, excluding the capture of very small and
very large fish. Gear selectivity is strongly related to the estimation of Z (total mortality)

• Determined by “covered codend method” – determine the amount and sizes of fish that escape through
the meshes of the codend by covering the codend with a much larger bag with much finer meshes. The
selectivity of the gear can then be determined by comparing the sizes of the fish in the codend with
those of the fish in the cover

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Stock Assessment
Estimating mortality

Gear selectivity

a and b are parameters of the regression line

yi is the proportion of fish retained in the codend for the ith length class
xi is the mid-length of the ith class

The length range from L25% to L50% is called as the selection range.
As the probability that a fish will escape through a mesh depends on its shape and in particular on its body
depth compared to the mesh size it is assumed that the body depth at which 50% of the fish are retained is
proportional to the mesh size. As body depth is proportional to body length it implies that similar expression
holds for length of the fish also.

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Stock Assessment
Estimating mortality

The following data is from an

experiment that deals with threadfin
breams (Nemipterus
japonicus) that are caught with a
trawl net with codend mesh size 4
cm and a cover of much small
meshes.

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Stock Assessment
Estimating mortality

Regression analysis done with x on y

gave the following results

The selection factor for the trawl net used with mesh size 4 cm is 3.292. 94

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Stock Assessment
Estimating mortality

Virtual Population Analysis (VPA) or cohort analysis

• Previous methods can be applied to data sets originating from small samples of the commercial
catch or from research vessel catches while VPA estimates the total numbers caught by
commercial fishing
• Look at the past using historic data to analyze the effect that a fishery had on a particular year
class of a stock. (VS: Predictive methods or Thompson and Bell methods (used to predict the
effect of different levels of fishing effort in the future).
• An analysis of the catches of commercial fisheries, obtained through fishery statistics,
combined with detailed information on the contribution of each cohort to the catch, which is
usually obtained through sampling programs and age readings)
• Virtual population – population created by the method, based on real total catch data and
assumptions of the level of natural mortality and terminal fisheries mortality

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Stock Assessment
Estimating mortality

Virtual Population Analysis (VPA) or cohort analysis

• Looks at a population in a historic perspective
• Once history is known, it becomes easier to predict future
catches
• The total landings from a cohort is the first estimate of the
numbers of recruits from that cohort. Given an estimate of
M (fish that died from natural causes) and those that died
from fishing mortality (F) we can do a backwards
calculation and find out how many fish belonging to the
cohort were alive year by year and ultimately, how many
recruits there were.

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Stock Assessment
Estimating mortality

Jones’ Length-based cohort analysis

• Situation when only length composition data for the total fishery are available for one year or when
only the average length composition is available for a sequence of years.
• Uses “pseudo-cohort” – decomposes size groups into ages using a growth model (VBGF)
• Deterministic model that assumes that the picture presented by all length (or age) classes caught
during one year reflects that of a single cohort during its entire life span

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Stock Assessment
Prediction models

Beverton and Holt’s Yield per Recruit (Y/R) model

• expected life time yield per fish recruited into the stock at a specified age
• used by fishery managers to understand the biological / economical effect of fishing on the stocks and helps
them to take suitable measures to ensure sustainable yields from the fishery
• Maximum yield from a cohort can be realised only by exploiting it at an age or size (optimum age or length) at
which the cohort’s biomass reaches its maximum (prevent growth or recruitment overfishing)
• response of a population to fishing mortality on a per-recruit basis depends on:
1. Natural mortality (M),
2. Fishing mortality (F)
3. Growth rate (K, from the von Bertalanffy growth equation)
4. Age (tc) at first capture (depends on gear selectivity)

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Stock Assessment
Prediction models

Beverton and Holt’s Yield per Recruit (Y/R) model

In the Y/R model the yields are relative to recruitment and it is possible to
calculate Y/R by varying the input parameters such as F (proportional to
effort) and Tc (function of gear selectivity) which are possible to be
controlled by a fishery resource manager. Change in mesh size leads to
increase or decrease in Tc.

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Stock Assessment
Prediction models

Beverton and Holt’s Yield per Recruit (Y/R) model

• The Y/R curve has a maximum point known as the ‘
Maximum Sustainable Yield’ which depends on the age at
first capture (Tc) which in turn is influenced by the mesh
size of the gear (related to F).
• By combining a range of values of Tc and F and assuming
that other conditions operating in the fishery are not
changing, the long term sustainable yield is arrived.
• Fishing effort above FMSY lead to a severe reduction of the
total yield.

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Stock Assessment
Prediction models

Thompson and Bell model

• widely used prediction model in assessing the optimum factor for increase or
decrease of fishing effort to achieve maximum sustainable and economic yield
of a commercially exploited species
• The output of the Thompson & Bell analysis are the predictions of catch in
numbers, total deaths in numbers, the mean biomass and yield for a
combination of different F and M values.
• Opposite of VPA: VPA and cohort analysis are historic or retrospective models
while Thompson and Bell model is predictive.
• Two main stages:
1. Provision of inputs:
2. Calculation of outputs in the form of predictions of future yields, biomass
levels and even value of the future yields

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Stock Assessment
Prediction models

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Stock Assessment
Prediction models

Step 1 Estimate Value of yield for

each length class from per
unit price data:

F-factor = 1

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Stock Assessment
Prediction models

Step 2
Estimate the yield, biomass & value
for varying Fishing mortality factors
(F-factor). The output for F-factor =
0.5 (obtained by multiplying the
fishing mortality of all length classes
with 0.5).

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Stock Assessment
Prediction models

Step 2
For F-factor = 1.5 (obtained by
multiplying the fishing mortality of
all length classes with 1.5).

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Stock Assessment
Prediction models

Step 3
Tabulate the predicted total yield,
mean biomass and value obtained
for a range of F-factors, starting
from F-factor = 0. The yield and
value will show continuous increase
and then a steady decline, while the
biomass will show a decline in
quantity for increasing F-factors.

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Stock Assessment
Prediction models

Step 4
Graph the data
MEY obtained at
F-factor 0.75

MSY at current fishing

mortality factor

Interpretation:
Present fishing level (F factor = 1.0) provides the
MSY: increase in fishing effort à decrease the
yield and reduce the biomass. MEY is obtained at
75% of the present fishing effort (F factor =0.75) ,
it is advisable to reduce the fishing effort to that
level to realize better revenue.
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Stock Assessment
Stock/ Recruitment Relationship

The search for the relationship between parental stock size and the subsequent
recruitment in numbers or the year class strength.
• There can be no recruits if no adult fish are left to mature, spawn and produce eggs which
hatch and grow to become recruits.
• Exemplified by recruitment overfishing
• Stock-recruitment models are used to define the relationship between the number of
reproductively mature adults and the number of recruits in a stock

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Stock Assessment
Stock/ Recruitment Relationship

Stock/Recruitment Models:

1. Beverton and Holt model assumes that the number of recruits increases as the mature population gets larger,
then levels off. Above that point, the number of recruits holds constant even as the reproductively mature
population increases, because the habitat simply cannot support any more recruits. This pattern is known as
perfect compensation

2. Ricker model assumes that when the reproductively mature population reaches a certain level, the number of
recruits actually decreases rather than remaining constant. This process is called overcompensation.
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Stock Assessment
Stock/ Recruitment Relationship

Beverton and Holt model

“Above a certain level of spawning stock

(Rmax), there is no relationship between
parent stock and recruitment”

g is a parameter
R – number of recruits increases towards asymptotic level, Rmax when egg production, E = number of females*
average production increases.

Density dependent mortality model – number of recruits levels off due to food competition. If food is limited the
number of starvation deaths becomes a function of the number of specimens which have to share food.
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Stock Assessment
Stock/ Recruitment Relationship

Ricker model

“There is a relationship between all sizes of

parent stock and recruitment and there is
an optimum stock size”

R1 and R2 are parameters.

The number of recruits decreases from a maximum level towards zero as the production of eggs, E increases. The
recruitment decline is explained by cannibalism of the young by the adults.

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Stock Assessment
Computer packages for stock assessment studies

1. LFSA Package - Length – based Fish Stock Assessment

• It requires only length frequency data as input. This package was
specially designed for tropical waters divided into four subpackages
according to the type of input data.
• Available to calculate various growth parameters, mortality
parameters, analysis, Y/R models etc. It requires length frequency,
effort, total catch, position in terms of latitude and longitude, depth,
gear type as inputs.

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Stock Assessment
Computer packages for stock assessment studies

2. ELEFAN Packages - Electronic length Frequency Analysis

• ELEFAN O is the basic system used to create and modify length frequency data files for the use of other four
programmes. ELEFAN I to IV will be using length frequency data created by ELEFAN-O.

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Stock Assessment
Computer packages for stock assessment studies

3. FiSAT - FAO-ICLARM Stock Assessment Tools

• This length assessment tool was developed to analyse
L/F data –at age, catch – at – age, selection and other
data typically collected for tropical fish stock
assessment. It takes advantage of the high resolution
graphic capabilities of micro computer.
• The package is structured around integration of
routines incorporated in LFSA and ELEFAN packages
and a number of new routines

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Stock Assessment
Computer packages for stock assessment studies

4. ANALEN
• Used for analysis of catch-at-length data for the
simulation of multi-gear fisheries with sensitivity
analysis
• Four programs: ANALEN, ANAJON, SENJON,
MONOJO
5. ANACO
• Consists of 2 sets of programs related to VPA:
SIMUCO and VPBAS
6. NAN-SIS – NANSEN Survey Information System
• For logging, editing and analysis of scientific trawl
data

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Stock Assessment
Computer packages for stock assessment studies

7. BEAM
• Bio economic modelling of artisanal and industrial shrimp fisheries based on
age-based Thompson and Bell yield per recruit model
8. CLIMPROD
• Combines environmental variables with surplus production models.
9. VIT
• Designed to analyse exploited marine populations based on catch data, structured by age or size and by
type of gear.
10. POPDYN
• A population dynamics database allows to user the store stock based information on the characteristic of
fisheries system.
11. SPATIAL
• A simulation package developed to model the space/time distribution of fishing intensity using
alternative approaches.

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Stock Assessment
Computer packages for stock assessment studies - FMSP

Fisheries stock assessment by Fisheries Management Science Program (FMSP)

1. CEDA - Catch Effort Data Analysis
• Analyzing catch, effort and abundance data
2. LFDA - Length Frequency Distribution Analysis
• estimates growth parameters and total mortality from fish length frequency distributions
3. Yield software
• estimates yield and biomass-based indicators and reference points, allowing for uncertainty in parameter
inputs
4. ParFish - Participatory Fisheries Stock Assessment
• Fits production model to standard fisheries and/or other data, using a Bayesian statistics and decision
theory to assess the state of a fishery stock and estimate limit and target control levels

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Stock Assessment
Computer packages for stock assessment studies - FMSP

Fisheries stock assessment by Fisheries Management Science Program (FMSP)

5. RAPFISH- A Rapid Analysis Tool for Fishery Sustainability
• Multi Dimensional Scaling, a multivariate statistical dimension reduction tool, has been put to use to rank
fisheries simultaneously on biological, technological, economic, ethical and sociological fronts by ranking
different fisheries under various contributory aspects falling under these five dimensions
6. TropFishR
• Improves on data import and automated analyses offered by FiSAT
7. CatDyn – Catch Dynamics
• Recourse to viewing the stock dynamics through catch rather than the population

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Summary

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