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Evidence Project Final Report
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Project identification
1.
Defra Project code
2.
Project title
MF1204
Improved Understanding and Management of Shellfish
Fisheries
3.
Contractor
organisation(s)
The Centre for Environment, Fisheries
and Aquaculture Science
Lowestoft Laboratory
Pakefield Road
Lowestoft
NR33 0HT
54. Total Defra project costs
(agreed fixed price)
5. Project:
EVID4 Evidence Project Final Report (Rev. 06/11) Page 1 of 29
£
428911
start date ................
01/04/2007
end date .................
31/3/2012
6. It is Defra’s intention to publish this form.
Please confirm your agreement to do so. ................................................................................... YES
NO
(a) When preparing Evidence Project Final Reports contractors should bear in mind that Defra intends that
they be made public. They should be written in a clear and concise manner and represent a full account
of the research project which someone not closely associated with the project can follow.
Defra recognises that in a small minority of cases there may be information, such as intellectual property
or commercially confidential data, used in or generated by the research project, which should not be
disclosed. In these cases, such information should be detailed in a separate annex (not to be published)
so that the Evidence Project Final Report can be placed in the public domain. Where it is impossible to
complete the Final Report without including references to any sensitive or confidential data, the
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Executive Summary
7.
The executive summary must not exceed 2 sides in total of A4 and should be understandable to the
intelligent non-scientist. It should cover the main objectives, methods and findings of the research, together
with any other significant events and options for new work.
Shellfish fisheries are becoming an increasingly important component of the UK marine fisheries,
particularly so for England. The first sale value Scallops, Crabs and Lobsters alone amounted to nearly
40% of the total for wild capture marine fish in 2010. Despite their economic importance, the scientific
understanding of both the biology and fisheries of these stocks lags well behind their fin-fish counterparts.
Many of the techniques previously used for the assessment of shellfish stocks have been derived from the
world of fin-fish stock assessment and whilst they are a useful starting point, many of the assumptions
regarding biology and fishery actions which are made when using fin-fish models are violated when
applied to shellfish. In particular there are major differences in the way that animals grow (i.e. fish grow
more or less continuously whereas crustaceans grow by increments each time the shell is shed), and the
mobility of many shellfish is vastly reduced compared to fin-fish. Shellfish fisheries are significantly
different to most fin-fish fisheries, a much wider range of gears are deployed, much of the landings in
some areas are taken by small vessels and many gears involve attracting individuals to baited traps rather
than using active, mobile gears. Even where mobile gears are used (e.g. scallop dredges), the species
are essentially sessile and therefore fishing can locate and target high areas with the highest densities.
The project therefore sets out to address some of these issues by creating models to specifically simulate
and assess shellfish stocks. Along the way we have made a critical review of the available data and
techniques for determining growth rates of crabs and lobsters which is one of our key areas of uncertainty
in stock assessment. This project has also benefited from being aligned with EU funded projects, enabling
us to expand the depth to which we have explored the use of models in data-poor situations.
In the original plan there were five main objectives, each with sub-objectives. Two of these main
objectives were dropped in agreement with Defra as the project progressed. The remaining top level
objectives are given below, each top level objective having several objectives within.
Objective 1.
To model the potential responses of shellfish stocks to different management options
through incorporation of life-history modelling.
Objective 3.
To evaluate relationships between inshore and offshore shellfish populations and their
response to exploitation using metapopulation and hydrographic modelling including data
EVID4 Evidence Project Final Report (Rev. 06/11) Page 2 of 29
collated under objective 2
Objective 5.
To evaluate the impact on reproductive potential of crustacean stocks of exploitation
patterns which differ between sexes
Some of the modelling techniques developed within the project have been able to address multiple
objectives simultaneously and the project has resulted in a significant improvement in the modelling
arsenal of Cefas which is now being used to help evaluate and support Defra policy questions.




We have investigated the merits of modelling growth in a more biologically realistic manner.
o this enables us to capture moult-based events such as mating and mortality more
accurately
o
It also makes investigation into seasonal fishery management more realistic (i.e. the
timing of management measures with likely periods of growth.
o
The availability of reliable data regarding growth and natural mortality is key to the
assessment of crustacean fisheries.
We have reviewed the available data regarding growth rates of crabs and lobsters
o Historical growth data have been re-captured from paper documents and re-analysed for
moult timing and moult frequency as well as fitting traditional continuous growth models.
o
The Lipofuscin ageing technique is reviewed and the implications of using the growth &
natural mortality rates in assessments are explored. The disparity between traditional
and Lipofuscin growth and mortality rates is variable depending upon the species
concerned. Whilst Lipofuscin accumulation rates are to an extent dependent upon local
environmental conditions they have been shown to be good estimators of age in some
circumstances. The cost of performing such analyses are, however, such that the
information gathered from traditional sources is likely to be more appropriate for routine
assessments.
o
Cefas is aware of a very recent development in ageing techniques through the analysis of
eye stalks and stomach parts of crustaceans (Kilada et al 2012 ). Such direct approaches,
if verified for European crustaceans, are likely to be more cost effective and logistically
tractable than lipofuscin assays and could open acces to apply age structured
methodology routinely. Whilst beyond the scope of this report, Cefas is investigating the
application of these techniques to crabs through its Seedcorn programme.
We have created a flexible modelling tool to examine the effects of spatial management and subpopulation structure. This model can also be used to explore different management options by
sex.
o
Migration between sub-stock units, even at relatively low levels can rapidly mitigate the
intended effects of management.
o
The development of spatially structured management systems therefore needs careful
consideration if conservation targets (e.g MSY) are to be met.
Previous assertions that sperm-limitation in Nephrops stocks is unlikely were questioned.
o
Analyses show that under some, not implausible circumstances, the possibility of spermlimitation is possible.
o
In order to ascertain the likelihood of the particular circumstances it will be necessary to
gather information on individual spawning behaviour.
o
Although the model was parameterised in this instance for Nephrops in the Farn Deeps,
the approach can be applied to other crustaceans with limited dispersal behaviours.
Project Report to Defra
8.
As a guide this report should be no longer than 20 sides of A4. This report is to provide Defra with details of
the outputs of the research project for internal purposes; to meet the terms of the contract; and to allow Defra
to publish details of the outputs to meet Environmental Information Regulation or Freedom of Information
obligations. This short report to Defra does not preclude contractors from also seeking to publish a full,
formal scientific report/paper in an appropriate scientific or other journal/publication. Indeed, Defra actively
encourages such publications as part of the contract terms. The report to Defra should include:
EVID4 Evidence Project Final Report (Rev. 06/11) Page 3 of 29







the objectives as set out in the contract;
the extent to which the objectives set out in the contract have been met;
details of methods used and the results obtained, including statistical analysis (if appropriate);
a discussion of the results and their reliability;
the main implications of the findings;
possible future work; and
any action resulting from the research (e.g. IP, Knowledge Exchange).
EVID4 Evidence Project Final Report (Rev. 06/11) Page 4 of 29
Scientific objectives set out in the contract
The primary objective of this project is to undertake modelling studies to provide a better understanding of
the way in which shellfish stocks and fleets respond to exploitation, and hence to improve the evidence
base on which advice on the sustainable management of shellfish stocks is given.
Key objectives of the project are:
Objective 1.
To model the potential responses of shellfish stocks to different management
options through incorporation of life-history modelling
1.1 Develop models for pot fisheries that explicitly model growth by moult in crustaceans
1.2 Link these sized-based models with new information on the size-age relationship and growth
curves for lobsters and crabs
1.3 Extend models for pot fisheries to include variable catchability and vulnerability of crabs and
lobsters
1.4 Develop simple models of exploitation of shellfish stocks using life history modelling approaches
– Dropped by agreement with Defra
Objective 2. To evaluate the potential responses of shellfish fishing fleets to different management
options through analysis of satellite monitoring data and catch and effort returns
from the shellfish licensing scheme, and to present this information in a GIS
framework
2.1 Use a GIS framework to describe the pattern of fishing effort for various shellfish fleets
2.2 Use GIS framework of fishing effort data over multiple years to predict response of fishing fleets
to different management options
– Dropped by agreement with Defra although some work done and presented in annual
reports
Objective 3.
To evaluate relationships between inshore and offshore shellfish populations and
their response to exploitation using metapopulation and hydrographic modelling including data
collated under objective 2
3.1 Review of historical tagging data for crustacean fisheries and links between inshore and
offshore stocks
3.2 Develop framework for the metapopulation modelling for crustacean fisheries
3.3 Evaluate various scenarios of links between inshore and offshore stocks of crabs and lobsters
and the implications for management
Objective 4.
To extend spatial modelling frameworks currently being developed (under M0229)
and apply generic lessons to specific case studies on Nephrops and crabs using data collated
under objective 2
Dropped by agreement with Defra
Objective 5.
To evaluate the impact on reproductive potential of crustacean stocks of exploitation
patterns which differ between sexes
5.1 Develop further initial models to investigate the potential for sperm competition in Nephrops
5.2 Examine the likelihood of impact on the reproductive potential of crab and lobster stocks of
differential minimum size limits for males and females
5.3 Examine the likelihood of impact on the reproductive potential of lobster (and crab) stocks of
management measures that provide increased protection of the female component of the stock only
5.4 Evaluation of potential impact of differences in exploitation rates between sexes
General Introduction
This project represented an ambitious drive to develop and improve the range of modelling techniques used
for the assessment of shellfish stocks. Many of the techniques previously used have been derived from the
world of fin-fish stock assessment and whilst they are a useful starting point, many of the assumptions
regarding biology and fishery actions which are made when using fin-fish models are violated when applied
to shellfish. In particular there are major differences in the way that animals grow (i.e. fish grow more or
less continuously whereas crustaceans grow by increments each time the shell is shed), and the mobility of
EVID4 Evidence Project Final Report (Rev. 06/11) Page 5 of 29
many shellfish is vastly reduced compared to fin-fish. Shellfish fisheries are significantly different to most
fin-fish fisheries, a much wider range of gears are deployed, much of the landings in some areas are taken
by small vessels and many gears involve attracting individuals to baited traps rather than using active,
mobile gears. Even where mobile gears are used (e.g. scallop dredges), the species are essentially sessile
and therefore more easy to target.
The project therefore sets out to address some of these issues by creating models to specifically simulate
and assess shellfish stocks. Along the way we have made a critical review of the available data and
techniques for determining growth rates of crabs and lobsters which is one of our key areas of uncertainty in
stock assessment. This project has also benefited from being aligned with EU funded projects, enabling us
to expand the depth to which we have explored the use of models in data-poor situations.
Some of the modelling techniques developed within the project have been able to address multiple
objectives simultaneously and the project has resulted in a significant improvement in the modelling arsenal
of Cefas which is now being used to help evaluate and support Defra policy questions.
1. Objective 1. To model the potential responses of shellfish stocks to different management
options through incorporation of life-history modelling
Many stock assessment and modelling methodologies applied to shellfish stocks were developed for finfish
species, and little account has been taken of specific life histories of shellfish (Smith & Addison, 2003).
However, the biology, life cycle and behaviour of shellfish, and crustaceans in particular, is complex and this
is frequently reflected in fishery catch rates that vary widely in space, time and between sexes. Further,
crustaceans grow by moulting so the use of continuous growth models could be inappropriate at times.
Biologically based models provide a means to explicitly account for, and evaluate the importance of these
biological processes to stock assessment and management.
Models developed under this objective typically use short time scales to take account of seasonality in the
crustacean life-cycles and subsequently catchability effects and discrete time moult increment and moult
frequency models that probabilistically model the discontinuous crustacean growth process. They may also
incorporate spatial dimensions for animals such as crabs that also exhibit large scale migratory behaviour.
1.1 Objective 1.1 Develop models for pot fisheries that explicitly model growth by moult in
crustaceans
Models developed under this objective include:
1.1.1 A size-structured yield per recruit model for lobsters
This biological-based model for lobsters was developed and programmed using Visual Basic for
Applications (VBA), interfacing through MS Excel and was parameterised to represent a UK inshore lobster
fishery. The model incorporates probabilistic growth which explicitly includes moult probability and moult
increment. Growth was modelled with three size dependent growth ‘stanzas’, and for each stanza a
minimum moult increment and a vector of probabilities for growth increments at one-millimetre intervals
starting with the minimum were specified according to suggestions from unpublished notes of Idoine and
Addison. The timing of moulting was varied for different components of the population. Maturity was
modelled using a logistic curve, parameterised using data from UK populations. Spawning took place three
months after moulting (and mating) and ovigerous females were then transferred to a ‘berried’ component of
the population for nine months until their eggs hatched and they were reassigned to the general population.
Natural mortality was separated into an annual rate and an instantaneous moulting mortality allowing an
additional moulting mortality to be applied in the month when moulting took place. Fishing mortalities were
separable, consisting of a selection pattern at length and F multiplier. Selection at length was specified to
take account of both trap selectivity and discard practice. Males and females were modelled separately.
The model has been applied through experimental scenarios to evaluate the implications of a range of
potential changes in management including: changing fishing effort levels (by F multiplier), changing MLS
from 87mm to 90mm, prohibiting the landing of ovigerous females, voluntary V-notching of ovigerous
females and voluntary V-notching of undersized lobsters. Measures have been considered in isolation and
in combination. Subsequently, maximum and slot size limits have also been investigated generically, but in
the context of an inshore lobster fishery, but temporal closures to the fishery have not been investigated
although the model would readily facilitate evaluation of these.
Sensitivity to alternative natural mortality regimes was investigated through scenarios for continuous natural
mortality that is constant over size verses a combination of continuous and instantaneous moult related (and
therefore size structured) natural mortality. Sensitivity to different rates of V-notching take up was also
investigated.
EVID4 Evidence Project Final Report (Rev. 06/11) Page 6 of 29
These investigations amount to simulation of over 50 different scenarios in all (Appendix 1a).
Figure 1.1.1. Schematic summarising the structure and processes of the lobster per recruit model (continuous and growth linked
natural mortality not shown)
Initial parameterisations of the model for a heavily exploited inshore fishery were broadly consistent with
conventional assessments (employing continuous growth models) indicative of growth overfishing and
spawning potential reduced to relatively low levels.
Small to moderate gains in long term yield were suggested by substantial reductions in fishing mortality
(>15%), a 3mm increase in the MLS (5%) and V-notching of undersized lobsters (6%), with generally
smaller gains in YPR for measures aimed at ovigerous females (banning landing (2%) and this plus Vnotching (2%) ovigerous females). Slot and maximum size limits had no or small negative effects on yield at
current levels of fishing mortality.
Substantial reductions in fishing mortality had a major impact on relative spawning potential (EPR), with
technical measures directed at ovigerous females (banning landing [3-fold increase] and this plus Vnotching ovigerous females [5-fold increase]) having more impact on spawning potential than those
focussed on the MLS (increasing MLS [50% increase and V-notching undersized lobsters [doubling]).
Combinations of measures were often synergistic when applied at current fishing mortality levels, but these
synergies were lost as fishing mortality was reduced and redundancy introduced as more than one
protective measure applied to the same individuals. Slot and maximum size limits had little effect on
spawning potential at current or higher fishing mortalities, but resulted in increases in spawning potential as
fishing mortality was reduced. These results concur broadly with expectations assuming continuous growth,
but the explicit modelling of discontinuous approach permits evaluation of V-notching, something which
would be more difficult (and indirect) using continuous growth models.
Change relative to status quo (%)
YPR
EPR
Management option \
1
2
3
4
5
6
7
8
9
10
Relative fishing pressure (F multiplier) ->
Baseline
Ban on landing ovigerous females
Ban on landing ovigerous and V-notching
ovigerous
V-notching of undersized
Ban on landing ovigerous and V-notching
ovigerous and undersized
Increasing MLS from 87mm to 90mm
Increasing MLS from 87mm to 90mm and
ban on landing ovigerous
Increasing MLS from 87mm to 90mm, ban on
landing ovigerous and V-notching ovigerous
Increasing MLS from 87mm to 90mm and Vnotching of undersized
Increasing MLS from 87mm to 90mm, ban on
landing ovigerous, V-notching ovigerous and
0.25
14.0
0.5
6.7
1.0
0.0
1.5
-2.5
0.25
932
14.4
9.5
2.0
-1.2
8.7
7.5
2.2
-0.8
14.8
9.4
6.2
6.7
9.5
10.3
8.6
8.3
16.5
10.4
4.6
2.6
1037
320
47
-6
16.8
13.5
7.1
4.3
1905
820
291
147
10.6
11.0
7.1
4.8
2413
1239
547
316
17.3
13.6
12.5
14.7
1130
465
229
199
11.4
14.1
14.0
14.2
2586
1549
981
771
EVID4 Evidence Project Final Report (Rev. 06/11) Page 7 of 29
0.5
245
1.0
0
1.5
-44
1739
676
186
62
2209
1037
379
178
998
342
115
80
2339
1277
730
555
17
22
27
undersized
Slot size limit - prohibition on landing 120129mm
Maximum size limit 130mm
Maximum size limit 120mm
12.4
6.5
0.0
-2.5
1170
311
7
-43
0.0
4.3
-0.1
-2.5
1572
361
6
-43
-12.5
-0.3
-0.7
-2.6
2305
631
38
-39
Table 1.1 Relative change in long term yield and egg production (per recruit) implied by changes in fishing mortality and combinations
of technical measures compared with the status quo situation for female lobsters
Negative values in red and italicised
1.1.2 A size structured simulation model for crabs
This model was developed in collaboration with colleagues from IFREMER (France) in conjunction with an
EU funded project, POORFISH, aimed at developing methodologies for data poor fisheries. It was
implemented using the FLR software package for R (R Development Core Team, 2009) and simulates crab
stocks and fisheries in the English Channel, Western Approaches, Celtic Sea and northern Biscay. It
includes discontinuous growth, spatially structured populations and fisheries with the potential for migration,
seasonally structured populations that capture the effects of biology and behaviour on catchability and the
potential to link natural mortality with moulting (thereby introducing size structured natural mortality).
Although the model includes a stock recruitment relationship, in the absence of meaningful data to
parameterise this, simulations carried out to date were run for constant recruitment (i.e. per recruit). The
model was applied to evaluate the potential protection to spawning potential offered by spatially variable
MLS regime in the English Channel, Western Approaches, Celtic Sea and northern Biscay. Results
explored the sensitivity of proportions of SSB below the MLS under a range of fishing mortalities to
alternative assumptions regarding biological parameters including growth, natural mortality and maturity. In
area VIIe (the main UK crab fishery) at current fishing mortalities around 3.3% of female virgin SPR was
below the MLS, equating to around 20% of SPR at this fishing rate. However this result was sensitive to
biological assumptions, with an alternative moult frequency model reducing these proportions in all cases.
The alternative natural mortality assumptions made substantial differences to the proportions expressed as
%VirginSPR, but had much less impact in terms of %CurrentSPR. This difference reflects very low natural
mortalities for larger crabs which boost virginSPR when continuous natural mortality is replaced by moult
linked natural mortality. A conventional length based yield per recruit analysis also yielded lower proportions
of both Virgin and current SPR at current F, this most likely reflecting differences in effective growth rate due
to the alternative models. The seasonal population structure incorporated simulates variable catchability
observed in crabs, fulfilling objective 1.3 and this model is therefore discussed further in that section,
although it also falls under objective 1.1. in many aspects of its biological realism. A schematic summarises
some aspects of the model (Figure 1.1.2) and more details are available in appendices 1d & 1e.
Figure 2. Schematic summarising the structure of the seasonally and spatially structured simulation model for edible crabs
1.2 Objective 1.2 Link these sized-based models with new information on the size-age
relationship and growth curves for lobsters and crabs
Models developed under objective 1.1 (and 1.3) utilise the best available information on growth by moult
and other biological process that is available for crustaceans, whether this be historic or new. It had been
envisaged that they would provide a basis with which to evaluate new age and growth data, in particular
data generated by recent Defra funded studies using lipofuscin analyses for lobsters and crabs (Defra
funded R & D projects MF0215 and MF0225). However, MF0215 and MF0225 generated results in terms of
continuous growth models rather than discrete moult based models, because the lipofuscin method is
considered indicative of age directly rather than providing a record of moult history. It is therefore more
relevant to evaluate growth parameters from lipofuscin based studies and their implications for assessment
and management in the context of continuous growth models and assessment methods incorporating these
EVID4 Evidence Project Final Report (Rev. 06/11) Page 8 of 29
(e.g. length based VPA and or length converted catch curves).
Therefore, in order to fulfil this objective:
 available growth data for crustaceans were reviewed, considering both continuous and discrete
growth models and conventional (primarily aquarium or tagging studies) and lipofuscin based
studies (Appendix 1b),
 growth data obtained from conventional means (tagging studies and/or aquaria experiments) were
compared with data and parameters obtained from the lipofuscin studies and comparative stock
assessments using existing parameters and alternatives based on the lipofuscin work (Appendix 1c)
were implemented and described.
1.2.1
General review of growth data for European lobsters and edible crabs
A review of literature on growth of European lobsters and edible crabs identified a number of historic
datasets, often available in paper copy or graphical format that could potentially be digitised and reanalysed (independently or in-combination) using more modern statistical methods. Given the high
influence to stock assessment of uncertainties in growth parameters and the very high costs of field
programmes to obtain such data, we would recommend that the digitisation and joint compilation/analysis of
available historic datasets is carried out whenever possible. Many historic data for crabs in the English
Channel were digitised and analysed together with new data in the recently completed MF1103 (crab
tagging) project, but there are further historic datasets for crabs and lobsters that have not yet been
captured.
In the literature, crustacean growth data are presented and analysed in terms of moult increment, moult
frequency and continuous models, although not all of these have been carried out in each case. When
considering discontinuous growth models, more data are generally available for moult increment than moult
frequency, although the latter may have more influence on population growth rates and may also be linked
with natural mortality (through increased vulnerability during the moult process). Growth data for the older
part of crustacean populations are particularly lacking, because intermoult periods are long and this causes
additional problems for both tagging and aquarium experiments. The key problems with data obtained from
aquarium studies relate to the artificial environment and whether observed growth reflects what would occur
under natural conditions, while differential tag loss during moulting and tag loss and over extended
intermoult periods (where variable reporting rates may also occur) are critical difficulties with tagging
programmes.
A range of models have been used, particularly for moult frequency, where historically linear models,
sometimes with a log or power transform have been applied (Figure 1.2.1). Modern statistical methods
permit more complex models to be fitted and more appropriate treatment of the error distributions. Logistic
models are frequently used for binomial population processes such are the proportion moulting annually (or
maturing) against size (or age). For the lobster modelling described in objective 1.1, we used a logistic
model actually parameterised for American lobsters, but considered more suitable than the alternative linear
and transformed linear models available historically. The logistic model constrains moult frequency between
0 and 1 and small lobsters and crabs moult more than once per year. However, double moulting was
modelled as a separate process in the lobster per recruit model which overcomes this problem.
Figure 1.2.1 Moult frequency models for European lobsters (except Fogarty & Idoine – H. americanus) presented by various authors
Parameters for continuous growth models, usually the von Bertalanffy equation, have been estimated and
presented by a number of authors, for both crabs and lobsters and these often vary quite widely (Figures
1.2.2 and 1.2.3) Parameters of the von Bertalanffy model are negatively correlated which can cause
problems during estimation and some authors have fixed L∞ a priori on the basis of observations of large
animals in the regional fishery concerned and only fitted the other von Bertalanffy parameter (K).
EVID4 Evidence Project Final Report (Rev. 06/11) Page 9 of 29
Parameters fitted in this way include those currently used by Cefas for crab and lobster stock assessments.
It is not clear whether this is appropriate or whether observed differences in regional population size
structures reflect quite widely differing growth characteristics or if these are localised sub-populations
(influenced by selective environmental pressures, including fishing) of larger populations with broadly similar
growth characteristics.
Figure 1.2.2 Von Bertalanffy growth curves for lobsters estimated by a range of authors
Figure 1.2.3 Comparison of von Bertalanffy growth curves for male (left/blue) and female (right/red) crabs. Curves where L ∞ has been
constrained are shown by dashed lines
1.2.2
Review of lipofuscin based studies on crustacean age and growth
As noted above, most growth data for lobsters and crabs have been obtained from aquarium or tagging
studies, but in recent years a number of authors have also used lipofuscin pigment accumulation as a proxy
for age and we briefly reviewed a number of papers relating to these, including some based on Defra R & D
projects (MF0215 and MF0225). Further detail is available in Appendix 1c.
Several authors have presented lipofuscin based age and growth studies for European lobsters and the
consensus is that lipofuscin concentration is a relatively accurate age predictor for European lobsters and
more accurate than using carapace length. Sheehy et al., (1999) suggested that carapace length was a
poor predictor of age, but sampling biases due to high fishing pressure and the way these reference age
data were collected are likely to have reduced contrast in size and they are acknowledged as not being
representative of the population as a whole. Other authors noted that there was also a good relationship
between size and age, with Uglem et al., (2005) concluding ‘that using carapace length is not necessarily an
inferior method’ and ‘that the choice of method for age determination should be evaluated on the basis of
the desired precision of ageing and that in some situations carapace length may provide a sufficiently
accurate estimate of age in a considerably more time- and cost-effective manner than quantification of
lipofuscin’. Although reference aged data for lobsters were available, these are generally limited to
relatively young lobsters, so extrapolation well beyond the range of the data is used to predict the age of
EVID4 Evidence Project Final Report (Rev. 06/11) Page 10 of 29
older animals. Sheehy acknowledges this as a concern in the final report for Defra project MF0215.
Only the work of Sheehy and co-workers was identified with respect to the use of lipofuscin for ageing
crabs, and unlike lobsters there were no reference aged crabs available to calibrate the regression with
lipofuscin. To overcome this Sheehy and Prior (2008) carried out modal frequency analysis on frequency
distributions of lipofuscin concentration and carapace width. These distributions were obtained according to
a weight stratified sampling programme, which accentuates minor peaks and although the authors justify
this by arguing that sampling was random within broad strata, we have concerns with regards to the validity
of fitting Gaussian distributions that may straddle differently weighted sampling strata. Since weight, width,
age and lipofuscin concentration are all correlated, then the weight stratified sampling protocol will influence
both modal analyses of lipofuscin and width, although the latter more strongly. There was also a
discontinuity in the sizes of crabs obtained by sampling the littoral and the commercial fishery, which may
have resulted in the omission of a mode and results in a slight disjunction between the sampled data in a
plot of width against age. Given the lack of reference data and some concerns regarding the analysis there
remains a higher degree of uncertainty regarding the results of lipofuscin studies relating to crabs than for
lobsters.
In summary, lipofuscin concentrations can provide an accurate method for aging crustaceans, although
accumulation rates vary in response to environmental factors, in particular temperature and may therefore
require calibration on a regional scale (e.g. accounting for local temperature history. Size may be less well
correlated with age, but has also been shown by some authors to be a good predictor of age and is
considerably more time and cost effective to collect, if accuracy can be foregone. A further disadvantage of
the lipofuscin concentration methodology is that sampling requires the destruction of (or severe damage to)
the animal, which means it cannot be calibrated by taking samples from individual animals at times of
release and recapture during tagging programmes.
1.2.3
Comparison of lipofuscin derived growth parameters and their implications for stock
assessment
Length based virtual population analysis (LVPA), followed by per recruit analysis was carried out for lobsters
using length frequency data from the Yorkshire Humber fishery unit and for crabs using length frequency
data from the western Channel fishery unit, these areas corresponding to the areas from which alternative
growth parameters based on lipofuscin concentrations had been estimated. In each case 3 alternative
scenarios were undertaken:
 growth and natural mortality parameters obtained from historic literature and currently used in Cefas
stock assessments,
 growth parameters estimated by Sheehy and co-workers using lipofuscin based methodology,
 growth parameters from 2) and empirically derived natural mortality rates (Hoenig, 1983) based on
longevity estimates from lipofuscin studies.
LVPA for lobsters using historic growth curves suggests that fishing mortality for lobsters of both sexes is
similar and very high, peaking above 1.5, whilst fishing mortality for both sexes is considerably reduced
when the lipofuscin based growth parameters are used (Figure 1.2.4), reflecting slower growth rates, older
age at size and therefore reduced rate of decline in numbers with age obtained using the lipofuscin based
growth curves. Natural mortality rates obtained from lipofuscin based longevity estimates were not
substantially different from those currently used, so applying these had little additional effect.
Figure 1.2.4. Comparison of fishing mortality for Yorkshire Humber lobsters estimated by LVPA using current estimates of growth and
natural mortality (left), Sheehy et al. lipofuscin estimated growth (centre) and Sheehy et al. estimated growth and natural mortality rates
(right). Blue: males, red: females
Per recruit analyses for Yorkshire Humber lobsters (Figure 1.2.5) taken from the 2011 Cefas stock
assessments suggest the stock is growth overfished, with fishing mortality above F max for both sexes and
relative spawning potential reduced below 10% of unexploited levels. The use of lipofuscin based growth
EVID4 Evidence Project Final Report (Rev. 06/11) Page 11 of 29
curves, implies that females are not growth overfished and there are slightly higher levels of relative
spawning potential, although these are still below target levels. Including the lipofuscin based natural
mortality rates result in both sexes being fished below F max (i.e. not growth overfished), and relative
spawning potential levels are above the potential limit reference of 10%, but below candidate target levels of
25% and 35% EPR. The lipofuscin based parameters also imply reduced levels of absolute yield per recruit.
The slower growth rates based on the lipofuscin studies are the principal driver of the results, with the
slightly higher natural mortality rate for males also having a small effect.
Figure 1.2.5. YPR and % of virgin SPR (or EPR) curves for lobsters in the Yorkshire Humber fishery. Top row: using historic growth
curves and natural mortality estimates, middle row: using growth curves from Sheehy et al., 1999, bottom row: using growth
parameters and natural mortality rates from Sheehy et al., 1999. Blue: males, red: females, solid lines: YPR or %VirginSPR, dashed
lines: %VirginEPR
EVID4 Evidence Project Final Report (Rev. 06/11) Page 12 of 29
LVPA for edible crabs under the same assumptions regarding growth and natural mortality as were used in
Cefas assessments prior to 2012 (Figure 1.2.6) indicates high fishing mortality for females and low to
moderate fishing mortality for males . Using the lipofuscin based growth curves changes this perception,
reducing the F on females, but dramatically increasing it for males. This reflects the faster growth estimated
for males, reducing the age of larger males and therefore increasing the rate of decrease in numbers.
Changing to the natural mortality rates based on the lipofuscin longevity estimates has a very large effect,
with much higher natural mortality rates for both sexes resulting in a substantial downward scaling of fishing
mortality to relatively low levels for both sexes, especially females.
Figure 1.2.6. Comparison of fishing mortality for western Channel crabs estimated by LVPA using current estimates of growth and
natural mortality (left), Sheehy and Prior (2008) lipofuscin estimated growth (centre) and Sheehy and Prior estimated growth and
natural mortality rates (right). Blue: males, red: females
Per recruit analyses for edible crabs (Figure 7) show that under current growth and nautral mortality
parameters, the stock is considered growth overfished for females (although F is at F max for males) and
spawning potential is reduced to (just below) the 10% reference EPR limit. Using lipofuscin based growth
curves results in males being growth overfished, with females exploited at or just below F max and spawning
potential just above the limit reference, but well below candidate target levels. The use of natural mortality
rates based on lipofuscin study estimates for longevity radically changes the perception with YPR being
fished well below maximum levels and relative spawing potential far above target levels. However this latter
perception is not borne out by recent catch and effort data where landings and catch rates have declined in
a number of areas after increases in effort and peaks in landings (e.g. western Channel, North Norfolk,
Humber fishery).
EVID4 Evidence Project Final Report (Rev. 06/11) Page 13 of 29
Figure 1.2.7. Comparison of per recruit analysis for crabs in the Western Channel estimated by LVPA and using current estimates of
growth and natural mortality (above), Sheehy and Prior lipofuscin estimated growth (centre) and Sheehy and Prior estimated growth
and natural mortality rates (below)
Summary.
The impacts of new parameters estimates based on lipofuscin studies differ for lobsters and crabs. For
lobsters lipofuscin studies have suggested slower growth rates and broadly similar natural mortality rates.
The assessment results using these alternative growth rates show a lower fishing rate than currently
estimated although target spawning potential references are generally still not met. For crabs faster growth
rates are implied for males resulting in a worsening prognosis, while that for females is slightly improved,
but the major effect is due to hugely increased natural mortality rates which suggest this crabs stocks is
heavily under-exploited. Although we have some concerns that the currently used natural mortality
parameters for crabs may be low, and imminently plan to investigate this in future work, the very optimistic
perception provided by these high natural mortality rates seems at odds with recent catch and effort data
from the fisheries as well result s based on recent tagging studies that were suggestive of high rates of
fishing mortality. Further details of these comparative assessments are provided in Appendix 1c.
1.3 Objective 1.3 Extend models for pot fisheries to include variable catchability and vulnerability of
crabs and lobsters
Work carried out under the EU (and matched Defra) funded POORFISH project was dovetailed with the
objectives for MF1204 with regards to the development of a spatially structured simulation model for crabs
with seasonal time steps and incorporating movement and alternative continuous or moult related natural
mortality rates. The model included 3 seasons, which was considered the simplest structure that would
adequately capture the seasonal variation catchability for crabs. These were winter, during which time most
EVID4 Evidence Project Final Report (Rev. 06/11) Page 14 of 29
female crabs are ovigerous, largely inactive and therefore rarely caught by baited traps (Bennett, 1995),
spring/summer, including the moulting season for females when crabs are caught, but catchability may be
lowered due to moulting by females, mating (both sexes) and subsequent discarding of ‘soft’ crabs and
autumn, the most important season for crab fisheries with voraciously feeding pre-spawning females highly
catchable on the main fishing grounds.
1.3.1
Preliminary simulations
Simulations were carried out to explore the impacts of increasing fishing effort on the western Channel and
associated crab fisheries. These were documented in POORFISH deliverable 4s (Appendix 1d, section i).
Equilibrium landings from the base run projection were in broad agreement with levels of landings observed
in the fisheries, with substantial UK landings from VIIe and substantial French landings from VIIh & VIIIab,
while the VIId and VIIfg fisheries were considerably smaller.
Increasing fishing mortality resulted in reductions in the level mature biomasses for both sexes and
generally did not increase yields. Where increases in yield were noted, they were slight and an increase for
one fleet was usually offset by a decrease for another. It was concluded that increasing F will result in
reductions to mature biomass and provide no benefits in terms of yield.
Constant recruitment levels were applied during these simulations because insufficient evidence was
available to meaningfully parameterise a stock recruitment relationship. However different levels of
recruitment were explored and as would be expected reduced recruitment resulted in lower levels of mature
biomass and yield. New equilibria were reached quite quickly (4-6 years) indicating that stocks and fisheries
were quite recruitment dependent and that the implications of any systematic recruitment failures would
manifest themselves in the short to medium term. However, the ubiquitous distribution, high fecundity and
significant larval dispersal of crabs are all factors which suggest that crabs should be relatively resilient and
in the event of local depletion recovery could be quite rapid assuming that no species replacement took
place.
Introducing a two stage model for natural mortality, consisting of instantaneous moult mortality and reduced
continuous natural mortality tended to result in slightly lower natural mortality overall. This is because not all
crabs moult every year, so natural mortality is reduced and especially so for the larger crabs, which moult
less frequently.
The movement parameters used here were estimated from historic data and implied minimal transfer of
crabs between ‘stock/fishery units’. Significant movements by crabs have been demonstrated, but are not
easily quantified at the stock level. This model provides a preliminary basis to consider the impacts of largescale adult stock movements on stocks and fisheries. Subsequent work (Defra project MF1103) has
confirmed large scale movements by crabs in the English Channel and analyses to quantify these were
carried out, which may provide improved information with which to parameterise this or other similarly
spatially structured models.
1.3.2 Secondary simulations
Further simulations were subsequently carried out to evaluate the contribution to spawning stock of
protection provided by the different MLS regimes of the western Channel and associated fisheries. These
analyses were couched in terms of percentage of unexploited spawning biomass which entailed extending
the size ranges considered to smaller size classes to take account of all potentially spawning animals. As a
result growth models that would permit double moulting were required. An experimental design was
implemented to compare the effects of: 2 moult frequency models, 2 moult increment models, 2 natural
mortality models and 2 maturity ogives. Rather than carrying out the full range of potential permutations,
pairs of runs were compared, reducing both computer run-time and time required for interpretation and
documentation. These simulations were documented in a manuscript (Appendix 1e) intended for publication
in the proceedings of an international conference on data poor fisheries where the work was presented,
although to date this special volume proceedings has not been published.
SSB trajectories equilibrated within 15 years for fishing mortality multipliers of 0.4 and above, but the run
duration needed to be extended to 50 years to permit equilibration for the unexploited scenarios. Spawner
per recruit curves (Figure 1.3.1) were similar in form between area and sex, but showed two distinct
patterns, with scenarios based on the two stage (moult dependent) model for natural mortality declining
more rapidly from virgin SPR, as increasing fishing mortality was applied, than the remaining scenarios.
Differences due to the alternative maturity ogives and growth models, both moult frequency and moult
increment, were small, i.e. results were relatively robust to these alternatives.
EVID4 Evidence Project Final Report (Rev. 06/11) Page 15 of 29
Figure 1.3.1. Spawner per recruit curves derived (as final year SSB) from the simulations, by sex, area and run
Percentage virgin SPR at Fsq was higher in the western Channel and Western Approaches and northern
Biscay (depending on which sex was considered) and lower for the eastern Channel and Celtic Sea,
consistent with results for standard SPR curves based on continuous growth models.
Levels of female SSB below the MLS were 0.3-3.3% virgin SPR for continuous natural mortality and 0.21.6% virgin SPR for moult related (size dependent) natural mortality, depending on fishery unit. The
proportion of virgin SPR below the size limit reflected the MLS regime of the areas, being highest in the
Western Channel or Celtic Sea where the UK Government (males 160mm, females 140mm) and Cornwall
SFC (males 160mm, females 150mm) apply higher limits and lowest in Northern Biscay where the smallest
size limit was in place (130mm both sexes). The levels of % virgin SPR may be artificially lowered by overestimation of the virgin spawner per recruit levels, as there was some evidence for accumulation of
individuals in the plus group in these cases, particularly for the moult related natural mortality scenarios,
where M was very low for larger crabs.
Expressing the SSB below the MLS as a percentage of current SSB provides a measure of the importance
of the MLS under current conditions, but some caution with this metric is needed because it also reflects the
level of fishing mortality being applied. For example, if fishing was so high it captured all animals above the
MLS, 100% of SSB would be below this size. Taking account of issues with the data available, the level of
protection to current SSB afforded by the MLS was estimated to be in the region of 6%-25% in the Western
Channel and Celtic Sea where the highest MLS regime is in place, but this could be lower if F has been
overestimated. In the Eastern Channel the level of protection was estimated to be in the region of 4%-17%,
while in Northern Biscay, where the lowest MLS regime in the study area is found it was estimated to be in
the range 1.5%-9%, but this could be higher if F was underestimated. An important conclusion was that
MLS regimes play a small, but significant role in protecting spawning potential and their importance is
increased as fishing pressure increases.
A considerable amount of time was invested in collating data, estimating parameters and investigating the
behaviour of certain models, even though crab fisheries are considered data poor. However, this case study
highlighted the dependence of results on biological parameters and the need for better biological data and
quantification of the key life processes for crabs, such as growth, natural mortality and the relationship
between stock size and recruitment. Conclusions were drawn from the initial simulations regarding the
implications of increasing fishing effort for SSB and yield and the importance of recruitment to the fishery
and the secondary simulations provided some quantification of the importance of the MLS regimes for
spawning potential.
2. Objective 2. Evaluate the potential responses of shellfish fishing fleets to different
management options through analysis of satellite monitoring data and catch and effort
returns from the shellfish licensing scheme, and to present this information in a GIS
framework
Fishing effort data for vessels included in the Vessel Monitoring System (VMS) were collated for Nephrops
in the Irish Sea and edible crabs in the North Sea, English Channel and Celtic Sea were collated with
landings information. The crab data were screened to remove steaming and other non-fishing time and
presented using Geographical Information Systems (GIS) to highlight seasonal and annual trends in fishing
activity, while the Nephrops data were classified by the proportion of Nephrops in the catch as a means of
determining the extent of grounds where Nephrops are abundant (Figure 2.1). This has is relevant to both
fisheries management and spatial planning.
EVID4 Evidence Project Final Report (Rev. 06/11) Page 16 of 29
Figure 2.1. Proportion of Nephrops by weight in landings collated with VMS data for the Eastern Irish Sea
Following discussion with Defra this objective was removed to permit greater focus on completion of the
modelling work.
3. Objective 3. To evaluate relationships between inshore and offshore shellfish populations
and their response to exploitation using metapopulation and hydrographic modelling
including data collated under objective 2
3.1 Introduction
The macro-crustacean fisheries of England are two of the most valuable, eclipsed in recent years only by
scallops. Lobster fisheries tend to be more coastal in nature although some fisheries extend several miles
offshore. Crab fisheries tend to have an even wider spatial distribution than lobsters although the extent to
which potting is feasibly depends upon areas where mobile gears are absent. The stocks upon which
fisheries operate are considered to be widespread, defined by the potential for larval transport as well as the
ability of the larger animals to undertake migrations. Within these larger stock regions there are often areas
frequented by larger, and smaller classes of individual and these in turn attract different portions of the fleet.
The combined effect of fishery and biological processes working on different scales is that over the spatial
range of the entire stock we may encounter different biological characteristics, different fleet components
and different local management regimes. As a case in point there has been considerable debate as to
whether the crab fishery off the North Norfolk coastline, where the individuals appeart to be smaller, is
actually a fishery on a juvenile (i.e. nursery) area with the larger individuals moving offshore.
In this modelling approach we undertook to construct a scenario testing model with which we could explore
the consequences of different management regimes on different sub-components of a stock. The
application of the model could then help managers determine which course of action was more likely to
succeed in a spatially complex environment.
3.2 Model description
A spatially structured model was constructed in which linked populations of shellfish could exist with
potentially different management regimes operating on the different components. The model, written in C++
was structured such that the number of populations was unlimited and could therefore cope with any mosaic
of population structure. Time was also handled flexibly and years could be sub-divided into any number of
different periods in order to explore the interplay between seasonal management and seasonal biological
events such as migration or spawning.
Each population was structured by both size and weight and had its own parameter set governing biological
functions such as growth, natural mortality, weight-length, maturity rates and spawning seasons. Growth
was modelled as a continuous function but allowed for each cohort to be represented by a distribution of
EVID4 Evidence Project Final Report (Rev. 06/11) Page 17 of 29
sizes at any one time. Natural mortality could be specified as constant over age/size (as is currently
assumed in assessments), or variable with size and or age therefore giving flexibility to utilise new data as
they became available. The recruitment process can be parameterised as either a Ricker or Beverton-Holt
function. Linkages were specified for each potential movement, the probability of moving in any one period
being governed by either age or size of animal. Seasonal movements were enabled by specifying a time
window in which movements could take place and movements could be for combined sexes or single sexes.
The probability of moving from one population to another was therefore determined by a sigmoid function
governed by either age or size, the season in relation to any seasonal window, the sex and an overall
probability parameter. Recruitment was initially to the local population but larval dispersion could be
mimicked using linkage functions operating on the smallest sizes. There is no explicit requirement that
individuals have to pass sequentially through linkages (e.g. A -> B -> C rather than A->C directly), however
biological realism would suggest that this should be the norm and therefore the combination of spatial and
temporal resolution should be such that individuals can only move through one stock unit in any given
period.
Fishery management on the different populations was independent and many forms of input and output
control were enabled, with the possibility of several management options acting simultaneously. It was also
possible to define multiple fisheries on the same stock unit, each with different management restrictions and
therefore it was possible to mimic different fleet segments. The only mandatory management parameter
required for each defined fishery was the specification of either a landings quota or effort control (fishing
mortality) value. Closed areas could be defined by giving a zero TAC. Selectivity of the fishery was
controlled through a sigmoid function, thereby allowing for the potential of different levels of compliance with
a minimum landing size. Fisheries could be specified to be single sex or combined sex. In addition to this a
closed season could be specified along with v-notching and berried ban schemes all of which could be
independently enabled.
3.3 Model implementation
In order to demonstrate the performance of the model, a series of lobster-like populations were constructed
using the same parameter sets as defined for the Northumberland lobster stock assessment. The use of
these particular parameters in the following model description was not supposed to represent any real-world
understanding of the specific stock structuring and was used purely for demonstration purposes. Five
different stock components were created, all with the same biological parameters governing growth,
maturity, recruitment (including seasonality of berried and natural mortality. Two sets of runs were
performed, firstly exploring the effects of different fishing mortalities with no connectivity between the stocks
and secondly to explore the effects of differing levels of larval connectivity between the stocks with a fixed
fishing mortality of 0.3. Both sets of runs used the same basic set of management strategies which were
defined according to the schedule in the table below.
Stock Unit
MLS
Berried Ban
Fishing effort
A
87mm
N
Constant
B
87mm
Y
Constant
C
90mm
Y
Constant
D
90mm
Y
Constant
E
NA
NA
CLOSED
The range of fishing mortalities tested was 0.15, 0.3, 0.5 and 1.0. A fishing mortality (F) of 0.15 is the same
rate as assumed for natural mortality (M) and F=M is often considered a reasonably proxy for a fishing rate
likely to deliver Maximum Sustainable Yield. There are several lobster fisheries currently assessed to have
fishing mortality rates around the 1.0 level.
Differing levels of larval linkage were explored, in which 5%, 10%, 25%, 50% and 75% of larval production
was transported from stock units B-E inclusive to unit A. For each of these runs there was also a migration
of later-stage individuals from A to units B-E. This was controlled by a sigmoid probability function with a
50% probability of moving occurring at 80mm. The redistribution occurred equally from A to B-. Following
these investigations, a further simulation was undertaken to explore the implications of closing area A (the
nursery grounds) with a 25% larval redistribution rate and a fixed fishing mortality of 0.3.
Each scenario was run on a quarterly basis for 40 years at which point all the populations appeared to have
reached equilibrium conditions.
3.4 Results.
Three metrics are presented for each scenario representing the stock at final equilibrium (i.e. long term
expectations). These metrics are the Spawner per Recruit (SpR), the Spawning stock biomass (SSB) and
the projected landings. SPR is the weight of spawning stock expected to be derived from each recruit and
is expressed here as the percentage of SpR expected from an unfished stock. 35% is commonly used as a
EVID4 Evidence Project Final Report (Rev. 06/11) Page 18 of 29
proxy for MSY.
Run set 1.
F = 0.15
F = 0.3
F = 0.5
F = 1.0
A (constant F)
41%
22%
12%
6%
B (as A and Berried ban)
42%
22%
12%
6%
C (as A and MLS=90)
43%
23%
13%
7%
D (all)
43%
24%
14%
7%
100%
100%
100%
100%
E (closed)
Table 3.1.1 Spawner pre recruit expressed as a percentage of Virgin levels under different Fishing mortality assumptions.
F = 0.15
F = 0.3
F = 0.5
F = 1.0
A (constant F)
10,908
5,699
3,148
1,442
B (as A and Berried ban)
11,072
5,820
3,224
1,477
C (as A and MLS=90)
11,353
6,146
3,540
1,754
D (all)
11,518
6,272
3,620
1,792
E (closed)
26,634
26,634
26,634
26,634
Total
71,486
50,571
40,165
33,099
Table 3.1.2. Equilibrium Spawning Biomass under different Fishing mortality assumptions
F = 0.15
416
F = 0.3
431
F = 0.5
387
F = 1.0
322
B (as A and Berried ban)
414
431
389
324
C (as A and MLS=90)
422
444
404
340
D (all)
420
445
405
341
0
0
0
0
1,671
1,751
1,584
1,326
A (constant F)
E (closed)
Total
Table 3.1.3 Equilibrium Landings under different Fishing mortality assumptions
The results of the first set of runs (with no migration) gives broadly similar results to those in section 1.1.
The major difference between the two modelling approaches is the measure of spawning potential used as
the model described in section 1.1 measured spawning potential in terms of egg production whereas the
model here measures ability of recruits to eventually join the spawning population. The number of eggs
produced is a reasonable measure of stock resilience (more eggs should mean a better chance of good
recruitment), whereas the measure of actual recruits on the ground reflects the fact that habitat and
resources are a limiting factor and more eggs will not necessarily mean more recruits.
At high levels of fishing mortality (F=1.0,typical of a number of Lobster stocks in recent assessments),
neither the introduction of a ban on the landing of berried females or an increase in the minimum landing
size has an appreciable effect upon the spawning potential of the stocks, their spawning biomass or the
potential landings. Of these two measures an increase in MLS increase delivers slightly more benefits but
the difference is small. In combination, the benefits of the two measures are compounded. Of all the
measures explored here, only a reduction in overall fishing rate makes any significant movement towards
achieving stock status which would be commensurate with estimates of MSY.
Run set 2.
F = 0.3
Proportion of recruits
exported to A
5%
10%
25%
50%
75%
A (constant F)
20%
48%
278%
2268%
B (as A and Berried ban)
26%
30%
44%
C (as A and MLS=90)
27%
32%
46%
D(all)
28%
32%
100%
100%
E (closed)
25% (closing
A instead of
E)
2220%
100%
67%
95%
12%
70%
112%
13%
47%
70%
95%
13%
100%
100%
100%
12%
Table 3.2.1. Spawner pre recruit under different migration assumptions expressed as a percentage of levels observed in the closed
population.
EVID4 Evidence Project Final Report (Rev. 06/11) Page 19 of 29
F = 0.3
Proportion of recruits
exported to A
5%
10%
25%
50%
25% (closing
A instead of
E)
75%
A (constant F)
2,965
3,946
4,589
2,961
901
6,015
B (as A and Berried ban)
3,737
2,414
652
40
0
652
C (as A and MLS=90)
3,945
2,546
684
42
0
684
4,014
2,586
693
44
0
693
E (closed)
14,598
8,143
1,531
76
0
642
Total
29,259
19,635
8,148
3,163
901
8,685
D(all)
Table 3.2.2. Equilibrium Spawning Biomass under different migration assumptions
F = 0.3
A (constant F)
202
268
455
183
82
25% (closing A
instead of E)
0
B (as A and Berried ban)
274
175
45
2
0
45
C (as A and MLS=90)
280
177
44
2
0
44
D (all)
280
177
44
2
0
44
0
0
0
0
0
45
1,037
797
589
190
82
179
5%
E (closed)
Total
10%
25%
50%
75%
Table 3.2.3. Equilibrium Landings under different migration assumptions
Once linkages between stock units are operational, the "true" SpR measure (i.e. % of virgin SpR) is
impossible to determine as the movement of individuals between fished and unfished portions of stock
means that there is no "virgin" basis upon which to make the determination. The presentation of SpR as a
fraction of the that observed in the unfished area is an approximation to the "virgin" state but is technically
flawed.
The introduction of migration between the stock units makes a vast difference to the stock metrics. The
flawed nature of using the SpR from the closed area as a metric is shown by the increasing skewness of the
results with increasing levels of migration (table 3.2.1). The more migration occurring in the larval phase the
greater the apparent health of the stock (increasing SpR compared to the unfished stock), whilst the SSB
and landings drop away steeply (tables 3.2.2 and 3.2.3). There was surprisingly little effect on either
recruitment or SSB when the closed area was changed from E to A (the nursery ground). SSB increased by
only 6% but total landings fell by a dramatic 70%.
The relative merits of berried bans or increases in MLS remain the same (i.e. a move to 90mm gives
marginally more protection to the stock) irrespective of the level of migration given the scenarios presented
here.
3.5 Discussion.
The use of the two different measures of spawning potential, Eggs Per Recruit (as used in section 1.1) and
Spawner per Recruit give quite different prognoses for the similar management approaches. Under the
assumption of fishing mortality equal to 0.5 (moderately high), the introduction of a ban on the landing of
berried females is forecast to increase egg production by 86% whereas the level of spawning stock resulting
from those eggs is forecast to only increase by 2%. In order to improve the robustness of the evaluation of
potential management plans for crustaceans to it is therefore highly important that the nature of the
relationship between spawning stock and the resulting recruitment is ascertained.
It is clear from these relatively simple tests, that the success of local scale management upon
interconnected stock units can vary considerably depending upon where and how management is targeted.
Most importantly we have demonstrated that what might seem an obvious management measure for stock
protection (i.e. a ban on fishing on nursery grounds) will not necessarily deliver the benefits to the stock
which might be expected given the large impact upon the fishery.
The development of this scenario modelling tool has provided Cefas with the facility to test a wide range of
potential management scenarios. The model has been constructed in such a way as to be able to
incorporate more complex understanding of biological processes as data become available in the future.
Evaluations using this type of modelling approach are likely to become increasingly useful as the various
fishery managers operating on different portions of a single stock instigate local management measures as
they move towards compliance with the Marine Strategy Framework Directive. The complexity and flexibility
built into this particular model means that the modelling requirements have been met for not only objectives
EVID4 Evidence Project Final Report (Rev. 06/11) Page 20 of 29
3.2 and 3.3, but also 5.2, 5.3 and 5.4.
4. Objective 4. To extend spatial modelling frameworks currently being developed (under
M0229) and apply generic lessons to specific case studies on Nephrops and crabs using data
collated under objective 2
Preliminary work undertaken, but eventually dropped in agreement with Defra. Now that the model has
been fully developed in M1104 and some of the problem areas sorted, changing from a single-sex to a
multi-sex model would be relatively straight-forward.
5. Objective 5.To evaluate the impact on reproductive potential of crustacean stocks of
exploitation patterns which differ between sexes
5.1 Develop further initial models to investigate the potential for sperm competition in Nephrops
5.1.1
Introduction
The sex ratio in commercial landings of Nephrops norvegicus typically exhibit an annual cycle with males
predominating during the period the females are brooding eggs (the “Berried” stage) as during this time the
berried females spend the majority of time within their burrow. The period immediately after egg release
can see the females dominate the catches as the male density has been reduced by the fishery in addition
to the females having an increased requirement to feed having been largely burrow-bound over the
preceding months. A raised proportion of female Nephrops in commercial catches at a time where males
were expected to dominate the landings have been noted to precede sharp declines in estimates of stock
abundance (WGNSSK 2008, plus wherever the Portuguese example is reported). One hypothesis
suggested for this phenomenon is that the fishery had reduced the abundance of mature males below the
level required for successful fertilisation at the population scale. Mature females, which would usually be
sheltering within their burrows to protect their eggs, would therefore have no need to remain within the
burrows and were therefore foraging on the surface and therefore available to trawl gear.
Only as planktonic larvae do Nephrops redistribute between mud patches and once recruited to a patch
individuals undergo relatively limited movements(Chapman and Rice, 1971). It can be envisaged that in
situations where male density is reduced to a low level and the search radius of individuals is limited, it is
conceivable that females may not encounter males.
For a clumped distribution of individuals there will be a range of search areas experienced by the males
within the population and the probability of encounter between males and females becomes dependent
upon no only the relative densities of the individuals but upon the degree of clustering.
5.1.2 Model description
The encounter rate of male and female Nephrops was explored for a variety of sex-ratios and spatial
patterns. Population density will, obviously, impact the encounter rate between individuals and to restrict
the analyses to plausible densities, data from the annual TV survey of the Farn Deeps stock undertaken by
Cefas were analysed to determine typical stock densities. Over the period 2006 to 2010 stock density was
determined to be 0.3 per metre squared. The models explored here represent the encounter and mating
probabilities over an entire breeding season. It was assumed that in any given year a male Nephrops will
have 100% probability of encountering and fertilising an available, mature female whose burrow lies within
his search radius. It was therefore implicitly assumed that only males actively search for mates.
The fertilisation rate where the spatial distribution of individuals is either uniform or uniform-random can be
readily determined analytically. Let r be the search radius of a male Nephrops, Dm and Df be the density of
males and females respectively.
If the density of males is such that their search radii overlap then the effective search radius of an individual
can be approximated to be the mid point of the mean distance between individuals.
r
0.5
Dm
The area searched by each male is simply the equation for the area of a circle and the number of females
within this circle therefore becomes
N f    r 2  Df
Assuming that each male will fertilise all the females within his each search radius, the proportion of females
fertilised becomes
Pf 
N f  Dm
Df
EVID4 Evidence Project Final Report (Rev. 06/11) Page 21 of 29
If males are limited in the number of females with which they can mate in any one season (Limf) then above
equation becomes
Pf 
min N f , Lim f  Dm
Df
If we consider the possibility that females may accept multiple matings then the analytical solution becomes
considerably more complex, particularly if we allow the search radius to be non-constant (i.e. related to body
size) and it is more practical to use the approach taken for assessing clumped distributions as described
below.
Clumped distributions of Nephrops were simulated in an individual based model using a Matern procedure
to generate the locations of the individuals. For any given realisation, the number of clusters (parents) was
specified and the coordinates of each parent was selected using a uniform random function. Each
individual was allocated a “parent” location using a random poisson process (to generate clusters of
different magnitude). From this parental location, the coordinates of the child were randomly generated
using a normal distribution with the parent’s coordinates defining the mean. The degree of clustering was
controlled using the number of parents and the variance around the parent location. Random-uniform
distributions can be effectively achieved by specifying a greater number of parents than children. In
addition to specifying the number of parents, the dimensions of the simulated space, total number of
individuals, maximum number of matings per individual, and proportion of male to female children were
input to the program.
For each male Nephrops, a search was made to locate females within his search radius. When a male
encountered a female a fertilisation event took place provided that the maximum number of matings for
either male or female were not exceeded.
The influence of relative densities of the sexes, number of matings per sex and male search radius were
explored. For each combination of input parameters, the proportion of females experiencing at least one
mating event was recorded.
In order to simulate spatial patterns similar to those observed in natural populations, the spatial
characteristics of natural populations were characterised by fitting semi-variograms to the burrow count data
from the Farn Deeps TV survey. Realisations of simulated distributions were then created with the IBM and
semi-variograms were determined for these realisations. By varying the parameters for overall stock
density, number of parent clusters and the variance around them and then comparing the resulting semivariograms of the simulated populations with those of the natural populations, it was possible to derive a
parameter set which produced similar spatial patterning to the natural stocks.
In the results presented here we have explored the effects of density, sex ratio, search radius and the
maximum number of matings each individual can effectively have. 300 simulations of population distribution
were created for each set of parameter values and the probability of a female failing to achieve a single
mating was determined.
5.1.3 Results
With unlimited mating possibilities and a search radius of 100m, the only time that females have no mating
opportunity is when there are zero males in the population (figure 5.1). Even when the search radius is
reduced to 30m there is still full mating success across the range of densities. Only when the radius is
dropped to 3m does there start to be any impact of low sex ratio upon the fertilisation success when
individuals have unlimited capacity to mate. Once the maximum number of matings becomes limiting, then
search radii also begin to be more critical. With a 30m search radius and only 3 matings, the probability of
fertilisation drops rapidly with low male density.
Proportion of females fertilised
radius= 100m: max matings=unlimited
Proportion of females fertilised
radius= 30m: max matings=unlimited
0.1
0.8
0.6
0.6
0.5
0.5
0.4
0.05
0.3
0.05
Male density
0.1
0.5
0.4
0.05
0.3
0.2
0.2
0.2
0.1
0.1
0.1
0.0
0.0
0
0
Female density
0.7
0.6
0.3
0
0.8
0.7
0.4
0.05
0.1
0.8
0.7
Female density
Female density
0.1
Proportion of females fertilised
radius= 3m: max matings=unlimited
0.0
0
0
0.05
Male density
EVID4 Evidence Project Final Report (Rev. 06/11) Page 22 of 29
0.1
0
0.05
Male density
0.1
Proportion of females fertilised
radius= 30m: max matings=1
Proportion of females fertilised
radius= 30m: max matings=3
0.1
0.8
0.6
0.6
0.5
0.5
0.5
0.4
0.05
0.3
0.05
0.1
Male density
0.4
0.05
0.3
0.2
0.2
0.2
0.1
0.1
0.1
0.0
0.0
0
0
Female density
0.7
0.6
0.3
0
0.8
0.7
0.4
0.05
0.1
0.8
0.7
Female density
Female density
0.1
Proportion of females fertilised
radius= 30m: max matings=8
0.0
0
0
0.05
0.1
Male density
0
0.05
0.1
Male density
Figure 5.1 Fertilisation success probability under a range of search radii, stock density, sex ratio and mating opportunities.
5.1.4 Discussion
The few tagging studies that have taken place with Nephrops have indicated that Nephrops
undergo relatively little movement after the larval phase with a maximum range of a few hundred metres
between release and recapture points (Chapman and Rice, 1971). For a large (20cm) Nephrops, a search
radius of 100m represents 5000 body lengths which, when put into a more human context, would represent
a search radius of ~9km. Now for a human to search this radius for potential mates over a year sounds
entirely plausible except for the requirement to be able to retreat back to base the moment danger looms.
Obviously as the size of Nephrops decreases (and a mature Nephrops can be ~8cm), a 100m search radius
is considerably greater. Successfully patrolling an area 5000 body lengths in all directions (and surviving)
may therefore turn out to be more challenging than would be first expected.
Previous analyses have suggested that sperm limitation is not likely to be a significant issue for
Nephrops stocks and this more complex approach would appear to concur, provided that sex ratios are not
skewed too far and that individuals can manage multiple matings over a reasonable distance from their
"home" burrow. The threshold between full mating success and very low mating success has been
demonstrated here to be potential quite narrow. This presents management with two basic options, one is
to invest in the determination of the missing biological information (search radius, multiple mating capacity)
so as to better understand where a critical threshold might be, and the other is to ensure that fishery
practice does not induce significant skews in the sex-ratio of the population. For Nephrops stocks, where
survivability may not be particularly high, management which involves trying to balance the sex-ratio of the
output would not necessarily deliver the desired results. An alternative approach would be to temporally
limit the fishery to times when the sex ratio of the landings are more balanced, however this might mean
imposing limits on fisheries when they are at their traditional peak.
5.2 Objectives 5.2-5.4
The remaining sub-objectives from this topic (5.2, 5.3 and 5.4) are concerned with modelling the effects
of management regimes which target the sexes differently. The model constructed in section 3 was
specifically constructed in such a manner that all of these issues can be addressed using the same
modelling approach.
6. Summary, conclusions and implications for management
Although this project was reduced in scope from the original objectives, the body of work undertaken within
this project represents a significant improvement in our understanding of the data and processes involved
with stock assessment of crustaceans. There are now a number of new modelling techniques available to
Cefas with which we can investigate the potential implications for both the stock and the fishery of differing
management strategies. We are also now able to better appreciate where weaknesses and shortcomings
exist in both our basic data and understanding of biological/ecological processes in order to target future
research.
6.1 Summary of the work carried out and main findings.

We have investigated the merits of modelling growth in a more biologically realistic manner.
o this enables us to capture moult-based events such as mating and mortality more
accurately
o
It also makes investigation into seasonal fishery management more realistic (i.e. the timing
of management measures with likely periods of growth.
o
The availability of reliable data regarding growth and natural mortality is key to the
assessment of crustacean fisheries.
EVID4 Evidence Project Final Report (Rev. 06/11) Page 23 of 29

we have reviewed the available data regarding growth rates of crabs and lobsters
o Historical growth data have been re-captured from paper documents and re-analysed for
moult timing and moult frequency as well as fitting traditional continuous growth models.
o


The Lipofuscin ageing technique is reviewed and the implications of using the growth &
natural mortality rates in assessments are explored. The disparity between traditional and
Lipofuscin growth and mortality rates is variable depending upon the species concerned.
Whilst Lipofuscin accumulation rates are to an extent dependent upon local environmental
conditions they have been shown to be good estimators of age in some circumstances.
The cost of performing such analyses are, however, such that the information gathered
from traditional sources is likely to be more appropriate for routine assessments.
We have created a flexible modelling tool to examine the effects of spatial management and subpopulation structure. This model can also be used to explore different management options by sex.
o
Migration between sub-stock units, even at relatively low levels can rapidly mitigate the
intended effects of management.
o
The development of spatially structured management systems therefore needs careful
consideration if conservation targets (e.g MSY) are to be met.
Previous assertions that sperm-limitation in Nephrops stocks is unlikely were questioned.
o
Analyses show that under some, not implausible circumstances, the possibility of spermlimitation is possible.
o
In order to ascertain the likelihood of the particular circumstances it will be necessary to
gather information on individual spawning behaviour.
o
Although the model was parameterised in this instance for Nephrops in the Farn Deeps,
the approach can be applied to other crustaceans with limited dispersal behaviours.
6.2 Implications for stock assessment and management

More detailed and more realistic models require additional parameters in order to function as
intended. Some additional historic data regarding growth and natural mortality have been identified
and could usefully be compiled and reanalysed. However, both these biological processes heavily
influence assessment results and further work to obtain better, contemporary parameter estimates
is still required.

The modelling approaches developed here which have been parameterised for Lobster stocks all
indicate that changes to management such as an increase in the minimum landing size, or a ban
on the retention of berried females will only make very modest changes to the productivity and
sustainability of the stocks. A pathway which makes significant reductions to the high fishing efforts
would deliver more tangible benefits to the stock.

Differences in some model outputs suggest that stock recruitment dynamics may substantially
modify per recruit outcomes, but our knowledge of, and ability to quantify, recruitment for
crustaceans in particular is very limited. Our current Defra R & D project (PIECRUST) aims to
investigate the potential for develop indices of recruitment and should be beneficial in this respect.
However, without the means to accurately age crustaceans and thereby follow year-classes, it
remains extremely difficult to obtain any information on stock and recruitment dynamics.

The move towards compliance with the Marine Strategy Framework Directive, coupled to spatial
management of the marine resources will require detailed evaluation of potential actions. The
models created within this project provide Cefas with some of the tools that will be required.
However, in order for these models to be run in a meaningful and robust manner, local scale data
regarding growth, mortality and movements will need to be sourced.
EVID4 Evidence Project Final Report (Rev. 06/11) Page 24 of 29
References to published material
9.
This section should be used to record links (hypertext links where possible) or references to other
published material generated by, or relating to this project.
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Hepper, B.T., 1972. The growth at moulting of lobsters Homarus vulgaris Milne-Edwards in the Menai
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