Impact de La Dégradation Des Habitats Côtiers Et Estuariens Sur La Dynamique Des Stocks Nourriceries Dépendants de Manche Est
Impact de La Dégradation Des Habitats Côtiers Et Estuariens Sur La Dynamique Des Stocks Nourriceries Dépendants de Manche Est
Impact de La Dégradation Des Habitats Côtiers Et Estuariens Sur La Dynamique Des Stocks Nourriceries Dépendants de Manche Est
Maître de stage : Juliette CHAMPAGNAT, Etienne Jérémy LOBRY- Directeur de Recherche, INRAE
RIVOT, Olivier LE PAPE Pablo BROSSET- Enseignant-chercheur,
Enseignant référent : Hervé LE BRIS DECOD-Institut Agro
Les analyses et les conclusions de ce travail d'étudiant n'engagent que la responsabilité de son auteur et non celle de l’Institut Agro Rennes-Angers
Je tiens tout d’abord à remercier Jérémy Lobry, Pablo Brosset et Hervé Le Bris d’être membres de
mon jury et d’avoir accepté d’évaluer mon travail.
Je tiens également à remercier très chaleureusement mes encadrants: Juliette Champagnat, Etienne
Rivot et Olivier Le Pape, pour leur aide très précieuse durant cette période. Vous m’avez apporté un
excellent encadrement qui m’a permis de réaliser ce stage dans les meilleures conditions.
Je souhaite remercier l’ensemble de l’équipe du pôle halieutique pour leur excellent accueil et leur
bonne humeur. C’était un véritable plaisir de venir travailler chaque jour dans votre équipe. Merci
pour les super échanges pendant les pauses café, les repas, les apéros et la plongée !
Un très grand merci au journal club, ou plutôt au Mickey club, pour l’animation scientifique du
mercredi soir, mais surtout pour les super moments en after work. C’est vraiment génial de sortir
avec vous le mercredi. Un grand merci tout particulier à l’organisateur en chef Quentin Queros.
Je remercie également très fortement les participants de l’AFH et les organisateurs. Un super
moment passé avec les halieutes de toute la France. Cette semaine était vraiment géniale
scientifiquement, et les soirées organisées après ont vraiment prouvé que les halieutes étaient une
grande famille, merci de m’avoir permis d’en faire partie. Pour le reste, ce qui se passe à Brest reste
à Brest !
Je tiens à remercier Aurélien, fidèle partenaire de bureau toujours là même quand le labo était
presque vide, ces 6 mois de co-bureau ont vraiment été drôles et sans toi ça aurait été beaucoup
moins fun.
Un très grand merci à tous mes copains que j’ai rencontrés depuis le début des études supérieures,
chacun a votre niveau vous m’avez tous permis d’en arriver là et surtout d’avoir vraiment profité de
ces cinq années et c’est bien l’essentiel. Alors un très grand merci à Clément, Clarisse, Marina,
Garance, Aurélien, Lucas, Victor, Cyriac, Lucille, Fanny, Marie, bref vous êtes beaucoup trop
nombreux … tout ceux du CENB, de l’IUEM et d’ACO !
Enfin, nous remercions le projet Hapomax (Office Français de la Biodiversité) et le projet Seawise
(Union Européenne) qui ont financé ce travail.
i
Table of contents
1. Introduction 1
ii
List of abbreviations
EEC : Eastern English Channel
ICES : International Council for the Exploration of the Sea
SSB : Spawning Stock Biomass
List of figures
Figure 1. Schematic diagram of the simulation framework
Figure 2. Map of ICES divisions 7.d
Figure 3. Habitat loss in the three areas of interest since 1870.
Figure 4. Fit between data (Obs) and model prediction (Pred) of seabass for SSB (left) and catch
(right).
Figure 5. Production curves according to habitat scenarios as function of SSB (A) or fishing
mortality (B) for seabass.
Figure 6. Effects of habitat scenarios on SSB (A) and Catch (B) gain at MSY by species.
Figure 7. Difference in catch gain per species according to the assumption made for quality
scenarios. Quality band for the scenario apply restoration only on the juveniles in shallow habitats
and Quality all for the restoration on all the juveniles.
List of tables
Table 1. Data for model parameterization.
Table 2. Percentage of juveniles present in habitats under 5 m and associated restoration factor.
List of appendices
Appendix 1. Age structured model.
Appendix 2. Data and equation to calculate fecundity and associated values for each species.
Appendix 3. Proportion of catches in division 7.d for whiting (4 and 7.d) and seabass (4.b–c, 7.a,
and 7.d–h).
Appendix 4. Nursery maps for each species.
Appendix 5. Complementary equations for parameterization of quality multipliers.
Appendix 6. Fit plot for each species.
Appendix 7. Comparison between K value, reference points, MSY related indicators from the
estimation of our model and ICES prediction.
Appendix 8. Production curves for each species.
iii
1. Introduction
Estuaries and coastal areas are highly productive ecosystems (Costanza et al., 1997), and are
essential habitats for many fish species (Seitz et al., 2014). Essential habitats are defined as habitats
that support at least one phase of the life cycle of fish (Delage et Le Pape, 2016). They are
described in the Magnuson-Stevens Fishery Act (2007) as "the waters and substrates necessary for
fish to spawn, reproduce, feed, and grow to maturity". Estuaries and coastal areas are essential
habitats as they act as nurseries for a large proportion of fisheries resources (Miller et al., 1984;
Minello, 1999; Beck et al., 2001). A high density of juveniles, presence of prey that allows stronger
growth, conditions that enhance survival of juveniles, and migration of subadults to adult habitats
are the four criteria proposed by Beck et al., (2001) to characterize nurseries. These habitats have a
major role in the renewal of nursery-dependent species (Rijnsdorp et al., 1992; Gibson, 1994; Le
Pape et al., 2007). These nursery-dependent species are also of great importance to fisheries, for
example two-thirds of commercial landings in the North-East Atlantic come from species using
coastal and estuarine systems as nursery habitat (Brown et al., 2018).
However, the coastal location of these nurseries makes them particularly vulnerable to human
activities, which are highly concentrated on the coast (Lotze et al., 2006; Airoldi and Beck, 2007).
These anthropogenic pressures can lead to habitat losses but also to the degradation of the quality of
the remaining habitats. Brown et al. (2018), showed that 92% of species that use coastal habitats are
impacted by human pressures, which can be related to pollutants, eutrophication, anoxia, invasive
species and physical development of the coastline. These pressures can have important
consequences on both size and quality of these habitats that are key features for stock renewal as
well as for fisheries management (Johnson et al., 1998; Peterson et al., 2000; Rochette et al., 2010;
Le Pape and Bonhommeau, 2015; Champagnat et al., 2021). For example, studies have shown the
toxic effects of exposure to pollutants (Davoodi and Claireaux, 2007; Foekema et al., 2008; Wessel
et al., 2010). Other general lab studies have demonstrated that the future reproductive success of
fish exposed to pollutants at the juvenile stage can be altered through decrease in fecundity, egg
viability, and survival (Fonds et al., 1995; Daouk et al., 2011; Horri et al., 2018). Due to the
complexity of the life cycle of fish and the multiple sources of natural variation in their abundance,
the quantification of the effects of exposure to pollutants on their survival and future fecundity in
the wild remains unknown (Hamilton et al., 2016). Consequences for demographic rates and
population dynamics are generally unknown (Rose et al., 2003; Ono et al., 2019), but these
estimates are necessary to predict the effects of coastal habitat degradation on the dynamics of
1
exploited marine populations (Vasconcelos et al., 2014; Boyd et al., 2018). The impacts of local
anthropogenic disturbance on juveniles of nearshore nursery-dependent species are thus well
documented (Brown et al., 2018), but the consequences of these mortalities for population renewal
are still poorly quantified (Lotze et al., 2006; Sundblad and Bergström, 2014; Vasconcelos et al.,
2014).
Some studies have quantified the impact of nursery habitat degradation for specific populations
with models spatially structured by stages and ages (Rose et al., 2018; Archambault et al., 2018;
Camp et al., 2020; Champagnat et al., 2021). These models are very case-specific due to the
complex parameterisation and the large amount of data and knowledge required (Lipcius et al.,
2019). Consequently, their application to other case studies is difficult, although necessary for
management orientation (Brown et al., 2018). In this context a more generic model would be
beneficial for application to more species.
In this work, we build on a generic age and stage structured model developed by Champagnat et al.
(in prep) to quantify the importance of nursery degradation/restoration on stock dynamics and
productivity. In this model, survival in nursery area is described by a Beverton-Holt relationship
which underlies competition mechanism between juveniles in nursery (Beverton and Holt, 1957).
This relationship is parametrized in terms of steepness and carrying capacity.
Steepness is the proportion of unfished equilibrium recruitment produced when the spawning stock
biomass is reduced to 20% of its unfished level (Mace and Doonan, 1988). It characterizes the drop
off in recruitment when the reproductive potential is reduced. This parameter is dimensionless and
can therefore be compared between different species. The value of steepness can vary from 0.2, for
a linear stock-recruitment relationship, to 1, for a constant recruitment above 20% of pristine
biomass (Myers et al., 1999). When steepness is close to 1, the density-dependent mortality between
eggs and recruits is very high, while conversely, it is low for a low steepness value (Mangel et al.,
2013). Steepness is an indicator of the resilience of a stock to fishing: if steepness is high, the stock
will be able to maintain high productivity even in a state of overexploitation (Mangel et al., 2013).
The shape of eggs-recruit density dependent survival relationship is therefore very important as it
determines the resilience to fishing and therefore the management reference points associated with
the stock (Brodziak and Legault, 2005; Punt and Dorn, 2014; Rindorf et al., 2022). However,
parameterizing a relationship between the spawning stock biomass and the number of recruits, a
stock-recruitment relationship, is very complex due to the limited availability of data and the
imprecision of parameter estimates (Haltuch et al., 2008; Conn et al., 2010). Hierarchical analysis
2
approaches have been used to estimate stock-recruitment relationship patterns, ad to relate estimates
to the life history traits of species in a generic way (Myers and Mertz, 1998; Myers et al., 1999;
Hilborn, 2003). In particular, this approach has been used to estimate steepness for all fish in
Thorson’s model (2019).
The Beverton-holt relationship is also parameterized by an asymptote, linked to the carrying
capacity of the nursery. Carrying capacity is defined as the maximal population size of a given
species that an area can support (Daily and Ehrlich, 1992). The carrying capacity tends to be higher
for wider and more productive nurseries areas, but vary depending on the species; species that have
lower resource requirements can be more easily supported in areas of lower productivity or resource
availability (Seitz et al., 2008). One hypothesis, supported by several studies, is that the main
mechanism controling carrying capacity is competition for food due to a limited number of prey (Le
Pape and Bonhommeau, 2015; Saulnier, 2019; Day, 2020). But other mechanisms can also affect
this carrying capacity of nursery areas such as predation, competition for space, parasitism, or
environmental variability (Day, 2020).
The previous use of the model by Champagnat et al., (in prep) remained conceptual with application
to theoretical populations and scenarios based on hypothetic values. It evidences the sensitivity of
population response to species life history traits, and especially steepness. The objective of our
study is to develop practical applications by applying this model to a group of species at the stock
level and for a given management unit. The Eastern English Channel, ICES division 7.d, is
fisheries area of main interest but also highly anthropized. It includes in particular the Seine estuary,
which has very high levels of degradation (Le Pape et al., 2007; Archambault et al., 2018). Seine
estuary has experienced important morphological changes from channel dredging and the building
of dikes and harbors, with a resulting substantial reduction in suitable shallow muddy nursery areas
(Rochette et al., 2010; Champagnat et al., 2021). In addition, this area has been facing high levels of
chemical contamination for decades (Barjhoux et al., 2018), causing reductions in habitat quality for
juveniles (Gilliers et al., 2006; Amara et al., 2007; Courrat et al., 2009). Other nurseries in the
Eastern English Channel have also suffered from degradation of both surface area and quality. Four
species of high fisheries interest were accounted for this analysis: sole (Solea solea), plaice
(Pleuronectes platessa), whiting (Merlangius merlangus) and seabass (Dicentrarchus labrax).
These species have similar life cycle with juveniles dependent to estuaries and coastal habitats.
Adults of these species spawn on large spawning grounds, mostly outside the coast (Pawson et al.,
2007, Rochette et al., 2013). The fertilized eggs released into the water column became larvae then
3
drift with the current (Rochette et al., 2012; Dambrine, 2020). Some of these larvae reach the
coastal and/or estuarine areas and metamorphose into juveniles that settle in nurseries. For a
species-specific period of time, juveniles grow in these habitats, which offer protection against
predators and conditions that maximize their survival (Gibson, 1994; Beck et al., 2001; Parlier,
2006; Carpentier et al., 2009). Around sexual maturity, fish leave the coastal nursery areas to move
to adult habitats and subsequently participate in reproduction. While sharing dependency to nursery
areas, the juveniles of these species are not distributed over the same areas. Their distribution of
juveniles stage depends on habitats features such as depth, salinity and prey, with optimum that
differs between species (Morin et al., 1999; Amara et al., 2001; Day, 2021), which leads to a distinct
distribution at juveniles stage (Ysebaert et al., 2003). This group of species is therefore particularly
interesting for studying the degradation of nurseries in a highly anthropized area.
The present study aims to quantify the effects of human disturbance on nurseries in the Eastern
Channel and establish their consequences on this four population of interest. A two step approach
was used: (i) Parameterize the generic stage-based life cycle model of Champagnat et al. (in prep)
for four populations of interest in the Eastern Channel based on available literature and on the most
recent results of stock assessment. (ii) Combine the model with scenarios of habitat degradation to
assess the effect of nursery habitat degradation on the four species. For this purpose, the area loss in
Eastern English Channel nursery was quantified since 1870 and the effects of quality degradation
were estimated. A quantification of the effects of the restoration of both surface and quality of these
habitats on the population dynamics was carried out and compared between species.
A schematic diagram of the simulation framework is summarized in figure 1. To quantify the effects
of the degradation of common nurseries the model has been parametrized with literature and stock
assessment and the carrying capacity has been calibrated. Then, habitat scenarios has been built
with historical data and literature. Finally, the model outputs were used to simulate the population
dynamics and estimate the equilibrium reference points. The effects of nursery restoration could
finally be compared between species.
4
1. Parameters Calibration of carrying capacity (K)
• Recrutement and minimizing
Carrying Model - ICES
maximum age capacity SSBpred SSBobs
• Natural mortality (K) Catchpred Catchobs
• Larvae mortality
• Fecondity
• Steepness (h)
2. Habitat scenarios
Es=ma=on of surface loss
Habitats < 5m:
1870
Model
2020
Eggs
Quality effects
Beverton-holt relationship with !"#$%& Decrease of
steepness (h) and carrying capacity (K) On average : =
'((# juveniles density
(Courrat et al., 2009)
3. Model outputs
Outputs at equilibrium
SSB & Catches
Es=ma=on of
Catches
CRMD, SSBRMD
and FRMD, for
each species
F
Produc,on curves
The impact of the degradation of nursery areas on stock productivity was simulated with a
deterministic life cycle model, structured by stage and age (Champagnat et al., in prep). This model
considers a single closed population and a unique nursery area. After recruitment age (arec), fish
undergo natural mortality and fishing mortality, and population abundance (Na,y) at age a for year y
is described by the classical population dynamics equation :
For the last age group amax, the population abundance is described as :
(2) Nama x ,y+1 = Nama x ,y × e −(Mama x ,y+Fama x ,y ) + Nama x−1,y × e −(Mama x −1,y+Fama x −1,y )
Recruitment, defined as the number of juveniles arriving in nurseries, is the critical component of
this model. It must account for the habitat-mediated mortalities during juvenile stage while
remaining generic for parametrization.
The recruitment Narec,y is computed from eggs numbers produced in a year, ωy, defined by equation
(3):
a ma x
∑
(3) ωy = Na,y × Mata,y × pfa,y × Feca,y
a=arec
with, Mata the probability of being mature at age a, pfa the female proportion at age a, and Feca the
fecundity at age a.
The mortality from eggs to recruited juveniles was assumed to follow a compensatory density
dependent mortality process resulting from intra-cohort competition for trophic resources and/or
space (Beverton and Holt, 1957). Recruitment (Narec,y) is modelled by a Beverton-holt relationship
but reparametrized in terms of its asymptote, K, interpreted as the carrying capacity of the nursery,
and steepness (h) according to the equation (4):
6
4hω(y−1)
(4) Narec,y = 4hω( y−1)
W̄(1 − h) + K
with W̄ the average number of eggs produced by a recruit during its lifetime in the absence of
fishing, equation (5):
a ma x
∑
(5) W̄ = Sa × Mata × pfa × Feca
a=arec
with Sa the cumulative survival at age a without fishing (equation in appendix 1).
M di × S 1
(7) K = limω−>+∞ Narec = ×
M dd e Mdi ×arec − 1
With Mlarvae the larvae mortality occurring during larvae drift which is only density independent.
Once parameterized (see next section), the model is used to simulate equilibrium states by exploring
a wide range of fishing mortality rate (F, from 0 to 1). Results obtained were used to empirically
construct the equilibrium curve for Catch (C) and Spawning Stock Biomass (SSB), therefore
enabling the estimation of management reference points such as SSBMSY, CMSY and FMSY (MSY,
Maximum Sustainable Yield) (equations for catch and SSB are available in appendix 1).
2. 2. Case study
The analysis explored the impact of disturbance of common nursery areas for a group of species of
fisheries interest. Our case study focuses on the Eastern English Channel (EEC; ICES Division 7.d.,
figure 2) management unit. The study area include (i) coastal nursery dependent species with (ii)
7
analytical stock assessments data and outputs, (iii) quantitative knowledge on juvenile distribution.
In Eastern English Channel, the four selected species fulfill these requirements: Sole (Solea solea),
Plaice (Pleuronectes platessa), Whiting (Merlangius merlangus), and Seabass (Dicentrarchus
labrax).
Source: ICES
Parameterization use a combination of parameters extracted from stock assessments and literature
and a calibration of carrying capacity (K).
To parametrize the model, the data used were taken from stock assessments and literature.
Recruitment age, maximum age, weights at ages, maturity ogive, and fishing and natural mortality
were taken from stock assessment reports (ICES. WGNSSK., 2021 and ICES. WGCSE., 2021).
In addition to stock assessment outputs, fecundity equations, larvae mortality, and length at ages
were necessary; they were collated from literature. Steepness was extracted from the Fishlife
package (Thorson, 2019) which analyzes stock-recruitment series from the RAM database (Myers
et al., 1995) based on a multivariate hierarchical Bayesian model with taxonomic structure extracted
8
from Fishbase (Froese and Pauly, 2022). The taxonomic structure embedded within the hierarchical
structure of the model strengthens the estimate for taxa for which data are insufficient, we extracted
the values at the taxonomic level of the Order to obtain a robust estimate. The different data needed
for parametrization and their sources for each species are presented in Table 1, all the data used to
calculate the parameters ω, W̄ and the fecundity equations are available in appendix 2.
2 11 0.1
Sole (ICES. (ICES. 0.771 (ICES. 3×log(10)
WGNSSK, Stock WGNSSK., WGNSSK.,
Annex, 2021) 2021) 2021)
Vector
2 7 (see appendix 2)
Plaice (ICES. (ICES. 0.771 (ICES. 3×log(10)
WGNSSK, Stock WGNSSK., WGNSSK.,
Annex, 2021) 2021) 2021)
8 Matrix
1
Whiting (Henderson and (ICES. 0.626 (ICES. 3×log(10)
WGNSSK., WGNSSK.,
Holmes, 1989) 2021) 2021)
4 16 0.24
Seabass (ICES. WGCSE., (ICES. WGCSE., 0.736 (ICES. WGCSE., 3×log(10)
2021) 2021) 2021)
Given the information available, only the parameter K, the carrying capacity of the nursery areas,
which ultimately determines the population size, requires calibration.
Calibration of K
For each species, the carrying capacity K was calibrated from stock assessment outputs. The value
of K was estimated by minimizing the difference between the SSB and catches simulated by our
9
model with thus of the stock assessment outputs. Estimates of K were obtained by minimizing the
following objective function:
yma x
(log(SSBpred,y ) − log(SSBICES,y ))2 + (log(Cpred,y ) − log(CICES,y ))2
∑
(8)
y=ymin
with ymin and yma x the first and the last year of the stock assessments respectively, SSBpred the model
predictions of SSB, SSBICES the SSB provided by ICES, Cpred the model predictions of catches and
CICES the catches provided by ICES.
Spawning stock biomass and catches are taken from the stock assessments for sole and plaice.
While for whiting and seabass, SSB and catches were derived from stock assessments covering a
wider area and were therefore scaled to the EEC proportionally to the relative landings in this area.
Landings data by area are taken from the historical catch database. For seabass, the landings data
covered the entire stock assessment period. For whiting, the first twelve years of the stock
assessment period did not have landings data by area, for this period, the proportion of catches was
calculated as the average proportion for the first 5 years with spatialized data. The proportion of
catches in divisons 7.d for seabass and whiting are available in appendix 3.
Once calibrated, the realism of baseline population dynamic was assessed by looking at the values
CMSY SSBMSY
of FMSY , and (SSB0 is the unfished spawning biomass at equilibrium). Realism of
SSBMSY SSB0
CMSY SSBMSY
FMSY and values will be assessed by comparing to stock assessment outputs and will
SSBMSY SSB0
10
The stock-recruitment relationship depends directly on the surface of the nursery habitats (Eq (4)
and Eq (7)). This surface can be modified: a multiplier (λsur face) is applied on the S factor of the
parameter K.
It is assumed that the alteration of the quality of juvenile habitats induces change in mortality rates
Mdd and Mdi. To represent this change in mortality, in relation to the modification of the
environmental quality, a multiplier (λqualit y) is applied to Mdd and Mdi which modifies the h and K
values (Eq (6) and Eq (7)). No information was available to define how a quality scenario would
impact Mdd and Mdi. Thus we assumed a common multiplier (λqualit y). To have quality and surface
scenarios with similar meaning we used λqualit y and λsur face with values < 1 represent habitat
restoration. The expression of parameters h and K can therefore be rewritten from Eq (6) and (7) as:
di ×a
e −λqualit y ×M rec × e −Mlar vae × W̄
(9) h= di ×a
4 + e −λqualit y ×M rec × e −Mlar vae × W̄
M di S 1
(10) K = dd × ×
M λsurface e λqualit y ×Mdi ×arec − 1
These formulations of h and K as a function of quality and surface make it possible to easily
simulate habitat restoration scenarios and thus study their impact on population dynamics.
The construction of the surface scenarios was based on estimation of surface losses since 1870. This
estimation was derived from bathymetry data in three coastal sectors of the French EEC coastline in
1870 (Bay of Veys, Seine Estuary, Somme Bay and Canche) available on the EMODnet
Bathymetrie website. The sectors selected were of major interest for our study as they cover areas
identified as common nursery for the four studied species (Riou et al., 2001; Rochette et al., 2010;
Carpentier et al., 2009; Bacq et al., 2013). To our best knowledge, no similar data were available for
the English coast. The sampled points were transformed into maps using a universal kriging
method. In a first step, a semi-variogram was constructed with a spherical model, without nugget
11
effect. Then, spatial interpolation by kriging was realized on the area covered by the sampling. The
resulting maps were compared with the 2020 bathymetry map, with the same spatial coverage. The
loss of habitats of less than 5 meters bathymetry (in relation to the 0 of the maps) was estimated in
each sector. This depth was chosen because it concentrates anthropic pressures and surfaces loss in
coastal nursery areas (Rochette et al., 2010). Finally, habitat loss at the EEC scale (Sloss) was
estimated as the sum of the areas lost in each sector between 1870 and 2020 divided by the total
EEC area above 5 meters in 2020. For the other areas for which we had no information, it was
assumed that no change had occurred. A surface restoration multiplier is calculated according to the
equation:
1
(11) Srestoration =
1 − Sloss
The juveniles of the different species have different bathymetric distributions, and especially in
shallow areas (i.e. less than 5m). Those differences in concentration is shallow areas will therefore
induce differences in the way species are impacted by surface loss and quality degradation in
shallow areas. The proportion of juveniles present in less than 5 meters depth was therefore
estimated from the nursery and bathymetric maps. The nursery maps for each species were
available on Sextant (appendix 4). A fine-scale bathymetric map of the EEC was downloaded from
the Emodnet bathymetry site. The resolution of the bathymetry map was first degraded, with
bilinear interpolation method, to match that of the nursery. The two maps were then coupled to
obtain the proportion (Prop) of juveniles present in the band above 5 meters depth.
The proportion of juveniles (henceforward called Prop, see 2.3.1) was used to calculate a surface
restoration factor (λsur face) which we apply to S, to simulate a restoration of the nursery area as in
1870. The area lost was only applied to the proportion of juveniles present in this area according to
the equation:
1
Total Densit y + (Prop × Srestoration ) − Prop
(12) λsurface =
Total densit y
12
2. 3.3. Parameterization of quality effects
Despite the numerous studies of the impact of toxic pollution carried out at the individual fish level
(Davoodi and Claireaux, 2007; Foekema et al., 2008; Wessel et al., 2010), the quantitative effects
on density dependent survival are not known (Lotze et al., 2006; Sundblad and Bergström, 2014;
Vasconcelos et al., 2014). Here we rely on previous work by Courrat et al. (2009) who measure the
density of marine juvenile fish in the different English Channel estuaries and correlated the spatial
variations to anthropogenic pressures to estimate the ecological status of transitional waters based
on fish for the EU (European Union) water framework directive (Delpech et al., 2010). Three
categories of ecological status of the estuaries were identified according to the density of juveniles:
good, average and poor quality status. The estuaries with a good ecological status had a density of
juveniles 20% higher than estuaries of average quality and 40% higher than estuaries of poor
quality.
In our model the different estuaries cannot be treated separately. The quality scenarios have
therefore been constructed by considering a homogeneous quality status of the nursery areas for all
the nursery sectors (i.e., a single parameter λqualit y for the whole EEC). An assumption of the
ecological status of the different estuaries in the EEC has been made: on average, all estuaries are
considered to be in average condition. Our scenarios will therefore seek to restore these estuaries to
a good ecological status. We derive two different scenarios for habitat quality restoration. A first one
where the restoration is applied to all juveniles (quality all). A second one where the restoration is
applied to the most coastal juveniles only (quality band) (i.e. < 5m). This assumption was made to
differentiate juveniles present in very coastal areas, a priori subject to high levels of contamination,
and juveniles present in more offshore waters less affected by the degradation of shallow habitat
quality.
The first restoration scenario (quality all) was based on a new K (Kscenario all) calculated to simulate a
value of K increased by 20% according to the equation:
13
The second restoration scenario (quality band) is only applied to the proportion of juveniles present
in less than 5 meters (Prop) (see 2.3.1). In this case, Kscenario band is calculated according to the
equation:
In a first step, we calculate Mdi and Mdd according to the equations available in appendix 5. In a
second step, we calculate the multiplier λqualit y that will be applied to Mdi and Mdd to simulate an
increase in juveniles density linked to a quality restoration. The equation of λqualit y can be deduced
M di
( Kscenario )
M dd
log +1
(15) λqualit y =
M di
The estimates of surface losses and quality effects lead us to obtain four scenarios: (i) surface
restoration, (ii) quality restoration applied to all juveniles (quality all), (iii) quality restoration
applied to the most coastal juveniles (quality band) and finally (iv) a scenario that combines surface
and quality band restoration.
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3. Results
The loss of the surface areas in the three coastal sectors under 5 m was estimated to 12.93%
between 1870 and 2020 at the EEC scale (figure 3). The proportions of juveniles present in habitats
above 5 m were calculated, and then the surface and quality restoration factors were estimated for
each species (table 2). Seabass was the species with the most coastal distribution with 80% of his
juveniles concentrated in less than 5 m, followed by sole with almost 50%. Due to highly
concentrated, these two species are the most affected by surface loss since 1870 and quality
degradation. Thus they will be associated with a higher restoration factor than the others (i.e., a
lower λsur face and λqualit y). In contrast, plaice and whiting have a very low restoration factor due to
15
Table 2. Percentage of juveniles present in habitats under 5 m and associated restoration factor.
In a first step, the results will be illustrated only with the second quality scenario applied to inshore
juveniles (quality band). Finally, a sensitivity analysis of the assumptions on the quality scenario
will be conducted in order to compare the results of the two quality scenarios.
3. 2. Seabass
A detailed interpretation of both calibration and results of the habitat scenarios is presented for
seabass. For the other species, fit plots was available at appendix 6, value of K, reference points,
MSY related indicators and average SSB and catch values at appendix 7, and production curves in
appendix 8. Note the results for seabass are expressed as a percentage of SSB or catch reallocated to
area 7.d and not in relation to the management unit used by ICES
The calibration of the model estimates K at 1.1x107 juveniles. Model predictions of catches and
SSB do not fit perfectly with annual ICES data (figure 4). But the average SSB values estimated by
ICES and the average SSB values predicted by our model are similar with 5.8 × 106 and 5.6 × 106
Kg respectively for this period. The same conclusion can be made for catches with ICES values at
1.4 × 106 Kg and our model predictions at 1.2 × 106 Kg.
16
Figure 4. Fit between data (Obs) and model prediction (Pred) of seabass for SSB (left) and catch
(right).
SSBMSY
0.25 (0.35 for ICES estimate) and ratio estimated at 0.27.
SSB0
The population dynamics and productivity were represented by the construction of equilibrium
curves for catch as a function of SSB and F under a wide range of fishing mortality for the reference
and the 3 scenarios of habitat restoration (figure 5). Restoring the surface of juvenile habitat only
impacts K (equation (10)), and hence only impacts the scale of the productivity curve, with
increased catches, and increased level of biomass at MSY (figure 5 A), but FMSY remains unchanged
(figure 5 b). By contrast, restoring habitat quality affects both K and h parameters (equation (9) and
(10)), and hence not only increases catches and SSBMSY but also increases FMSY (+ 0.01) which
maximizes the catch.
17
A B
Figure 5. Production curves according to habitat scenarios as function of SSB (A) or fishing
mortality (B) for seabass in divisions 7.d.
The effects of habitat restoration scenarios were compared across that species, by estimating
relative gains in SSB and catches at MSY equilibrium state (figure 6). As for the seabass, whiting
are expressed as a percentage of SSB or catch reallocated to area 7.d and not in relation to the
management unit used by ICES. The surface scenario has the least impact on SSB with gains
ranging from 0.6% for whiting to 11.9% for seabass (figure 6 A). This great heterogeneity between
species is also found in the gains linked to the restoration of quality with an increase in SSB ranging
from 1.3% for whiting to 16.5% for seabass. Finally, when the two restoration scenarios are
combined the effects of separate restoration measures become synergistic, and two groups of
species emerge. Whiting and plaice are the species for which the combined restoration has the least
effect with gains of 1.9% and 7%, respectively, whereas sole and seabass have a strong increase in
SSB with gains of 22.7% and 30.3%, respectively.
In a similar way, the gain of catch at MSY follows those of the SSB (figure 6 B). However, the
catch gains for seabass are even greater than for SSB because the MSY state is attained for a higher
fishing mortality (FMSY + 0.01) which therefore increases the catch. For the combined scenario, the
gains represent an increase of 1.9, 7, 22.7 and 40.4 % for whiting, plaice, sole and seabass
respectively. In terms of tons, the restoration of habitat surface and quality under our scenarios
18
represents an increase of 250, 480, 1015 and 510 tons for whiting, plaice, sole and seabass
respectively.
40
30
A
20
Increase at MSY (in %)
10
40
B
30
20
10
0
Surface Quality Combined
Scenarios
Figure 6. Effects of habitat scenarios on SSB (A) and Catch (B) gain at MSY by species.
When we conceptualize the quality scenario, we assumed that only the juveniles present in less than
5 m were impacted by the quality. This assumption has been formulated by experts knowledge, but
no quantitative data can really support it. We tested another assumption in which nursery quality
would impact all juveniles present in the EEC with no restriction to the shallow areas below 5m. To
19
illustrate the differences generated by these two hypotheses, the model was run with this second
scenario and difference was compared in a histogram of catch gains at MSY by species (figure 7).
Large differences emerge from these two quality scenarios. Firstly, as expected, the restoration of
quality for all juveniles in the EEC leads to a greater homogeneity in the gains than when the
restoration was carried out according to the bathymetric distribution of juveniles. The differences
found between this species are therefore only related to demographic parameters, and especially h
and fecundity, which strongly differ between species. This scenario shows a higher sensitivity to
quality restoration for species with lower steepness (whiting, figure 7). Moreover, all species have
greater catch gains in this “global” restoration scenario due to a larger quantity of juveniles
impacted by the restoration. This scenario generates an increase of 31, 22, 14 and 6 percentage units
compared to the partial scenario (figure 6 and 7), for whiting, plaice, sole and seabass respectively.
The results of our model are thus very sensitive to the assumptions made regarding nursery habitat
quality restoration scenarios.
Figure 7. Difference in catch gain per species according to the assumption made for
quality scenarios. Quality band for the scenario apply restoration only on the
juveniles in shallow habitats and Quality all for the restoration on all the juveniles.
20
4. Discussion
In that study, we assessed the consequences of nursery restoration through an age and stage
structured model. We developed a generic model with a stock-recruitment relationship directly
related to the quality and surface of the nursery habitat. The model was parameterized from the
literature and stock assessments and the carrying capacity was calibrated on stock assessments
output to simulate realistic population size and dynamics. The model was applied to four nursery-
dependent EEC species characterized by various life history traits and various degrees of
concentration on the same coastal nursery habitats. The model was used to simulate equilibrium
catch curves obtained under different scenarios of nursery quality and surface restoration for the
four species. Surface restoration increased the catches and biomass at MSY. The restoration of
quality lead to a stronger increase in catches and biomass at MSY, but also an increase of fishing
mortality at MSY. Overall, the species with the higher level of concentration on shallow nursery
areas were the most sensitive to the habitat restoration scenarios. The response also depends to other
life history traits. Species with lower steepness exhibit a stronger response to habitat scenarios.
Thus, seabass was the species for which habitat restoration had the greatest impact, while whiting
was the least affected.
4. 1. Model calibration
Our study was based on a model parameterized with data from stock assessments and literature.
Of course, a limit of the method is that it directly depends upon the estimates made by ICES and
therefore cannot be applied to stocks that are not assessed, or for which the assessments do not
estimate the necessary data.
Beyond those limits, an advantage of the method is that only one parameter, the carrying capacity
(K), remained to be calibrated from stock assessment outputs. This makes it very easy to use and
greatly limits the calibration time. The calibration of K implies two ecological assumptions, the first
being that the carrying capacity of the nursery habitat is reached and limiting. This assumption is
still debated, although recent studies tend to validate a seasonally limiting capacity (Le Pape and
Bonhommeau, 2015; Saulnier, 2019; Day, 2020). Then, the output of our model were fitted to catch
and SSB data from ICES working groups. For whiting and seabass, as the assessment unit of the
stock is larger than area 7.d, a biomass reallocation was made according to the proportion of catches
in this area. This reallocation adds uncertainty to the data, particularly in relation to fishermen's
21
behaviour, which may differ from one year to the next, or due to changes in fishing regulations.
However, the objective of the study was not to reproduce annual fluctuations in SSB and catches
but to simulate realistic population dynamics. This poor ability to reproduce the annual fluctuations
is due to the second assumption made in the calibration of K. The carrying capacity does not vary
over time, although studies have shown that this capacity can vary on an inter and intra-annual scale
(Luo et al., 2001; Le Pape et al., 2003), for instance as a response to a trophic cascade from the
supply of nutrients and organic matter that would then support primary and secondary production
(Day, 2020). First, our calibration lead to an average estimate of SSB and catches close to the
average estimate of the ICES over the same period, for all species (appendix 7). In addition to the
calibration on SSB and catches, some indicators characteristics of the dynamics (MSY and related
CMSY SS BMSY
indicators like ratios and , and FMSY ) were used to assess the realism of the
SS BMSY SS B0
CMSY
population dynamics. For sole, whiting and seabass, the indicators and FMSY were relatively
SS BMSY
close to those provided by the ICES (appendix 7). For whiting, the model predictions were higher
SS BMSY
than published values. The ratio was within the expected range for all four species.
SS B0
CMSY
Nevertheless for plaice, estimate of the ratio was very high compared to ICES value (0.63
SS BMSY
SS BMSY
and 0.29 for ICES). In view of the ratio which seems to be a realistic value, this very high
SS B0
value can be explained by a parameterization of the model leading to a very high production of the
stock. This high productivity would explain the very high catches supported by a low biomass.
Discrepancies between the simulated and published values of those indicators for plaice are mainly
explained by the values of steepness and fecundity which are two parameters that have a great
influence on population productivity. The high productivity of the plaice in our model can be
explained by a too high fecundity. Several equations from different studies (Dorel, 1986; Vérin et
al., 2001; Jennings et al., 1998; ICES. WGNSSK. Stock Annex, 2021; for length at age and four
equations from Horwood, 1993 for fecundity at length) have been tested in order to modify the
fecundity and thus obtain a dynamic closer to that of ICES, but none of the tested combinations
allowed for improving the ratio.
To our knowledge, our study is the first that assess the effect of restoration of common nursery
areas for a group of species at the scale of a management unit. This study allowed us to accurately
22
estimate the effect of the loss of nursery areas on the French EEC coastline since 1870 on 4 species
simultaneously (sole, plaice, whiting and seabass). In addition, we applied our model to a group of
species for quantifying the impact of juvenile habitat degradation.
Results show that surface restoration, which leads to an increase in the carrying capacity of the
nursery, increased the catches and biomass at MSY, but to a lesser extent than the restoration of
habitat quality. Indeed, the restoration of quality increases both the carrying capacity and the
steepness, leading to a stronger increase in catches and biomass at MSY, but also an increase of
fishing mortality at MSY. In the case of a combined restoration, the effects are in synergy. Indeed,
the restoration of the surface increases the carrying capacity, and the restoration of the quality
increases the density of juveniles in this new surface, the effects of the combined restoration are
higher than the addition of the effects of both surface and quality restoration.
The difference in gains between species due to surface restoration is mainly due to a different
degree of concentration of juveniles in shallow nursery habitat. The differences in quality
restoration are also due to this difference in distribution, but it is also related to steepness and
demographic parameters. This difference linked to steepness and demographic parameters is
reinforced by results obtained through the sensitivity analysis on the hypotheses on quality scenario.
In a quality scenario that ignores the distribution of juveniles, the species that is the most affected
by habitat restoration is the one with the lowest steepness. In this scenario, the contrast in responses
is only related to the demographic parameters of the stock, especially to the steepness and fecundity,
as demonstrated in Champagnat et al. (in prep).
Previous studies, focusing on sole, have already examined the effect of areas and/or habitat quality
scenarios with more complex and specific models. Rochette et al. (2010) and Archambault et al.
(2018) demonstrated the effects of quality degradation and area loss of sole nursery areas in EEC.
But these study only looked at the restoration of the quality of the Seine estuary and its surface area
as in 1850. Our model therefore provided consistent results with these two studies. But the main
interest result is that the general approach allowed to extract the results of 3 other species.
4. 3. Limitations
Our study has some limitations related to the demographic hypotheses made in the model. First, the
model considered juvenile habitat as a single block whereas coastal and estuarine areas are
23
composed of a multitude of habitats with high heterogeneity that can vary over time («shifting
habitat mosaic», Peterson, 2003; Stanford et al., 2005; Wimberly, 2006; Nagelkerken et al., 2015)
and their accessibility is characterised by transient phases of connectivity (Zeigler and Fagan,
2014). Our model considered nurseries as a single homogeneous habitat but ignored the
connectivity which is of primary importance in the nursery function (Sheaves et al., 2015; Alp and
Le Pichon, 2021). Considering the nursery areas as a single block is limiting, especially for the
construction of realist quality restoration scenarios. However, considering such spatial
heterogeneity would require parameterizing specific Beverton-Holt relationships for each nursery
area with different ecological status and various strengths of density dependence, which is
inaccessible for most of the case studies (but see Rochette et al. (2013) for an example). Moreover,
considering different sector of the EEC nursery area would greatly complicate our model and the
elaboration of restoration scenarios by raising questions about population connectivity
(Archambault et al., 2016) and estimation of steepness (White, 2010). Indeed, diffusion of the
outcomes of local nursery restoration at a metapopulation scale highly depends on the level of
connectivity at different stage of the life cycle (Archambault et al., 2018). Our results should
therefore be treated with caution. The interpretations are made at the metapopulation level without
consideration of its spatial structure, which may lead to a poor estimate of exploitation rates,
especially when based on an MSY approach (Ying et al., 2011). For example, our model does not
consider the connectivity between possible EEC sole subpopulations yet it has been shown that this
can lead to a different estimation of restoration effects (Champagnat et al., 2021; Archambault et al.,
2016).
Another limitation of the model is that the different sources of uncertainty are not considered. The
parameters are considered known without errors, the population dynamics is considered
deterministic and no environmental variations is represented. Yet, environmental variability (Pfister
and Stevens, 2003) is large, especially in the recruitment process. This structural limitation
characteristic has notably led to poor predictions of annual variations in SSB and catches.
Finally, our model considers a density dependence that only takes into account the juveniles of the
recruitment age, but the older age groups can also share some of the same areas. Moreover,
mortality rates considered a single species, but the nursery areas are partly shared by several
species, so an inter-species density-dependent could also occur (Gibson, 1994), as show during a
short period of time, late summer (Amara et al., 2001; Van der Veer et al., 2010; Day, 2020). It
would be interesting to take these characteristics into account, but there are no estimates that would
allow us to integrate them into the model.
24
4. 3.2. Quality scenario
The effects of quality degradation have been estimated based on loss of juvenile density in nursery
areas based extracted from Courrat et al. (2009) estimations. Other studies have estimated these
effects as a decrease in survival of juveniles, but also a decrease in their growth rate and future
fecundity (Champagnat et al., 2021). This method was not applicable to our study due to the lack of
knowledge on the impact of quality degradation on the demographic parameters of plaice, whiting
and seabass stocks.
In the parametrization of the quality scenario, we assumed a common multiplier on density-
dependent and density independent mortality rate. This is a strong assumption because both
mortality terms are associated with different processes. The density-dependent mortality rate refers
to interactions between juveniles of the same cohort, mostly competition for food or space (Gibson,
1994). Density-independent mortality may involve other mortality processes linked to a large panel
of environmental stresses (e.g. pollutant, Rose et al., 2003; oxygen, Gibson, 1994) and/or predation
(Gibson, 1994). However, no previous knowledge nor experimental studies were available to build
sensible quantification of how density independent and density-dependent mortality rates should be
impacted separately. The assumption of using a single multiplier may have led to high estimate of
the impact of quality scenarios, and caution should be taken when comparing habitat surface and
quality scenarios (Champagnat et al., in prep).
Also, as shown in the section 3.4, the results of the model are very sensitive to the assumptions
made on which specific sectors of the nursery habitat are affected by habitat restoration/degradation
(i.e. the whole nursery area or the area <5m only). Other methods of separating the juveniles most
affected by the degradation of quality could have been tested. The salinity plume of the estuaries
could have been used as an estimator of the distribution of contaminants, but this hypothesis was
not retained due to the very large interannual variability that may exist. For future studies it would
be interesting to develop a more robust method to apply the quality restoration to the proportion of
juveniles really impacted by the degradation of estuarine quality. However, no such information is
available yet to our best knowledge.
The estimation of surface losses could be made on the basis of a sampling of French nursery areas
in 1870, but no data were available for the English coasts which also have nurseries (Kelley, 1988;
25
Rochette et al., 2010; Carpentier et al., 2009). We chose to estimate surface losses since this date
due to the large proportion of EEC nurseries that could be considered by the data. The inclusion of
this large proportion in our study gives it an original character, as most other studies in the EEC
have focused on the Seine Estuary (Rochette et al., 2010, Rochette et al., 2013, Grasso and Le Hir,
2019). The other data available did not allow us to consider such a large proportion of the nursery
areas for other dates.
In our scenario, the nursery habitat is only defined by depth. Defining an ecological niche by a
single variable is however a very simplifying assumption (Grinnell, 1917; Hutchinson, 1957), and
as many studies have shown, the nursery areas of the species in this study can be defined by other
parameters. Salinity and hydrodynamics can have an effect (Kennedy and Fitzmaurice, 1972;
Kelley, 1988; Le Pape et al., 2003), as well as sediment structure (Riou et al., 2001; Rochette et al.,
2010). The estimation of surface losses is therefore very simplified in this study and could be
refined by using species distribution models integrating these many factors, provided that the
necessary historical data are available. For example, Champagnat et al., (2021) used a distribution
model of sole juveniles based on historical data available for the Seine estuary to quantify habitat
loss based on bathymetry and sediment structure. However, we did not have the data to apply this
method to other species and areas in our study.
Also, only the loss/restoration of habitats less than 5 metres depth were considered. This limit is not
based on any prior study or knowledge. However, this depth is also the one that concentrates the
most anthropic pressures and surface losses (Rochette et al., 2010). The importance of this
assumption can be moderated, if a greater depth had been chosen to define scenarios, the proportion
of juveniles affected would have been greater, but the proportion of surface area lost would have
mathematically decreased, hence balancing the effect on population dynamics. The results of the
scenarios would therefore have been approximately the same. However, analysis based on another
depth threshold could not be carried out because we did not have enough data to make a reliable
estimate of the loss of surface of habitats with a bathymetry higher than 5m.
Overall, the proportion of juveniles impacted by habitat loss that we used is likely to be
underestimated and the effects of surface restoration may be greater. Indeed, this proportion was
calculated on maps representing present habitats. It can be hypothesized that if habitats less than 5
metres depth were of larger surface (i.e. as in 1870), the proportion of juveniles present in this
habitat would also be greater
26
4. 4. Management implications
This study quantified the effects of both surface and quality losses on the dynamics of nursery-
dependent species in the Eastern Channel. The estimates of habitat loss provided by this study give
us information on the historical evolution of the EEC nurseries, but these estimates are difficult to
apply to a management context. Indeed, the loss of surface area is mainly due to human activities
such as land reclamation or the construction of port infrastructures (Ducrotoy and Dauvin, 2008;
Brown et al., 2018). Although we have demonstrated the real impact of these developments on
stocks and fisheries, habitat restoration is unfortunately difficult to apply. The destruction of dykes
and the restoration of intertidal areas would require large financial resources and would be done at
the expense of other activities carried out on the coast (Levin and Stunz, 2005). However, this
evidences the need to protect and even partially restore the remaining essential nursery habitat.
This study also demonstrated the considerable importance of shallow nurseries for species with a
very coastal distribution of juveniles. Furthermore, it demonstrated that the gains from MSY
management could be greatly increased if nursery areas were restored. Restoring both nursery
habitat surface and quality would increase a gain of annual catches of 1015, 250, 480, and 510 tons
for sole, plaice, whiting and seabass respectively. In addition to catch gains, the spawning stock
biomass would also be increased, which could have beneficial consequences for the whole
ecosystem (Froese et al., 2008; Smith et al., 2011; Cury et al., 2011; Froese et al., 2016; Gascuel,
2019).
More broadly, this study supports the need to consider essential fish habitat in the management of
stocks and underlines the interest of an ecosystem-based management of fisheries. Restoring coastal
nurseries may be even more beneficial than regulating fishing pressure (Levin and Stunz, 2005; van
de Wolfshaar et al., 2011). Ongoing management measures to restore the surface area (Ducrotoy and
Dauvin, 2008) and quality of estuarine habitats, with some results already observable, such as
significant decreases in pollutant levels, should therefore be encouraged and continued (Meybeck et
al., 2007; Tappin and Millward, 2015).
27
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Appendices
Population dynamics is simulated by a deterministic life cycle model structured by age (a) with a
year time step (y).
Fish are supposed to recruit at age arec. For all ages classes arec < a < amax, population abundance (N)
is described by:
(b) Nama x ,y+1 = Nama x ,y × e −(Mama x ,y+Fama x ,y ) + Nama x−1,y × e −(Mama x −1,y+Fama x −1,y )
Fishing mortality at age is defined, in a simulation mode, as the product of selectivity at age and a
maximum fishing mortality value:
a ma x
Fa,y
× Na,y × (1 − e −(Fa,y+Ma,y )) × SWa,y
∑ Fa,y + Ma,y
(d) Cy =
a=arec
∑
(e) SSB = Na × SWa × pf × Mata
a=arec
With SWa, the stock weights at age, pf the female proportion, and Mata the maturity ogive, all
available in appendix 2.
The number of eggs spawned in year y is computed based on adult abundance:
a ma x
∑
(f) ωy = Na,y × Mata,y × pfa,y × Feca,y
a=arec
with Mata, the probability of being mature, pfa the female proportion and Feca the fecundity
(number of eggs per female). All values used are available in appendix 2.
Eggs are supposed to first survive to the larval drift with density-independent survival before
settling in nursery areas. The larval mortality during larval drift, Mlarvae, are available in appendix 2.
The number of recruits for year y is computed with a Berverton-Holt relationship based on eggs
numbers of the previous year:
4hω(y−1)
(g) Narec,y = 4hω( y−1)
W̄(1 − h) + K
with h the steepness, W̄ the number of eggs produced on average by a recruit during its lifetime in
the absence of any fishing and K the carrying capacity of the nursery.
The number of eggs produced on average by a recruit during its lifetime in the absence of fishing,
W̄, is defined as:
a ma x
∑
(h) W̄ = Sa × Mata × pfa × Feca
a=arec
a−1
e −Mi
∏
(i) Sa =
i=arec
The parameters h and K of the Beverton-Holt relation are related to the independent density and
dependent density mortality (Mdi and Mdd respectively) according to the equations:
di ×a
e −M rec × e −Mlar vae × W̄
(j) h=
4 + e −Mdi ×arec × e −Mlar vae × W̄
M di × S 1
(k) K = limω−>+∞ Narec = ×
M dd e Mdi ×arec − 1
The expression for Mdi and Mdd can therefore be derived as:
4×h
(l) M di = − log( )
e −Mlar vae × W̄ × (1 − h)
dd M di
(m) M =
K × (e Mdi − 1)
Appendix 2. Data and equation to calculate fecundity and associated values for each species.
For the female proportion (pf) we assumed a value at 0.5 for each species.
Fecundity
(Fec)
e (5.619+1.17×log(SWa×1000)) Anon, 1992
Number of eggs
produced by a recruit
during its lifetime in 662795.9 -
the absence of any
fishing (W̄)
Plaice (Pleuronectes platessa)
Parameters Value Source
Maturity ogive Age 1: 0; Age 2: 0.15; Age 3: 0.53; Age 4: ICES. WGNSSK.,
(Mat) 0.96; Age 5: 1; Age 6: 1; Age 7: 1 2021
ICES. WGNSSK,
Fecundity 2.33 × La3.10
stock Annex., 2021
Number of eggs
produced by a recruit
during its lifetime in
19610.72
the absence of any
fishing
(W̄)
Whiting (Merlangius merlangus)
SWa × 1000 1
Length at age (La) ( ) 3.10286 Dorel, 1986
0.00621
Number of eggs
produced by a recruit
during its lifetime in the 13931.71 -
absence of any fishing
(W̄)
Seabass (Dicentrarchus labrax)
Number of eggs
produced by a recruit
during its lifetime in the 262908.3 -
absence of any fishing
(W̄)
Appendix 3. Proportion of catches in division 7.d for whiting (4 and 7.d) and seabass (4.b–c,
7.a, and 7.d–h).
Map of Eastern English Channel nursery areas for sole (in juveniles/m2). Source : Rochette et al.,
2010. (Modified)
Map of Eastern English Channel nursery areas for plaice (in juveniles/m2). Source : Carpentier et
al., 2009. (Modified)
Map of Eastern English Channel nursery areas for whiting (in juveniles/m2). Source : Carpentier
et al. 2009. (Modified)
Map of Seine nursery areas for seabass (in juveniles/m2). Used as an estimator of the distribution
of juveniles across the EEC nurseries. Source : Bacq et al., 2013. (Modified)
Appendix 5. Complementary equations for parameterization of quality multipliers.
4×h
−log( )
e −Mlar vae × W̄ × (1 − h)
M di =
deltaT
With deltaT = 1
The density dependent mortality (Mdd) is dependent to Mdi according to the equation:
dd M di
M =
K × e (Mdi×deltatT ) − 1
With the values of Mdi and Mdd calculated from the parameters h, K and the value of Mlarvae and W̄,
we can calculate a multiplier to simulate a quality restoration.
Appendix 6. Fit plot for each species
Fit between data (Obs) and model prediction (Pred) of sole for SSB (left) and catch (right).
Fit between data (Obs) and model prediction (Pred) of plaice for SSB (left) and catch (right).
Fit between data (Obs) and model prediction (Pred) of whiting for SSB (left) and catch (right).
Fit between data (Obs) and model prediction (Pred) of seabass for SSB (left) and catch (right).
Appendix 7. Comparison between K value, reference points, MSY related indicators from the
estimation of our model and ICES prediction.
7
0.63 0.33 1.6 × 107 6.8 × 106
Plaice 6.8 × 10 0.19
(ICES=0.29) (ICES= 0.25) (2 × 107) (6.1 × 106)
Production curves according to habitat scenarios as function of fishing mortality or SSB for sole.
Production curves according to habitat scenarios as function of fishing mortality or SSB for plaice.
Production curves according to habitat scenarios as function of fishing mortality or SSB for
whiting.
Production curves according to habitat scenarios as function of fishing mortality or SSB for
seabass.
References
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and VIII.
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MESSCENE : Modélisation des fonctions écologiques de l’Estuaire de la Seine et
ScENarios d’Evolution.70p.
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mer, France. 626 pp.
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10.17895/ICES.PUB.8139.
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labrax) in division 4.b–c, 7.a, and 7.d–h (central and southern North Sea, Irish Sea, English
Channel, Bristol Channel, and Celtic Sea), WGCSE.
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Rochette, S., Rivot, E., Morin, J., Mackinson, S., Riou, P., and Le Pape, O. (2010). Effect of nursery
habitat degradation on flatfish population : Application to Solea solea in the Eastern Channel
(Western Europe). Journal of Sea Research, 64(1-2), 34-44. https://doi.org/10.1016/
j.seares.2009.08.003
Diplôme : Master SML-Biologie
Parcours : Sciences Halieutiques et Aquacoles
Spécialisation / option : Ressources et Ecosystèmes Aquatiques
Enseignant référent : Hervé LE BRIS
Auteur : Maël GERNEZ Organisme d'accueil : Institut Agro - Rennes
Abstract: Estuaries and coastal areas are essential habitats for many fish species. These habitats act as
nurseries for a large proportion of species of fisheries interest. Their coastal distribution at juveniles stage
makes them particularly vulnerable to anthropogenic pressures. However, a comprehensive analysis of
the impacts of nursery habitat degradation for exploited fish species is still lacking. Our study aims at
assessing the effects of degradation/restoration of nursery habitat common to four Eastern English
Channel species of large fisheries interest: sole, plaice, whiting and seabass. A generic simulation model
representing the dynamics of exploited populations and the dependence of recruitment on juvenile
habitats is used. It evaluates the combined effect of nursery degradation and fisheries exploitation on
stock dynamics. The model was calibrated for each species based on the results of stock assessments
complemented by literature. Restoration of both surface and quality for nursery habitats were built using
estimated area losses since 1870 and literature. Surface restoration had a smaller impact than quality
restoration on biomass and catch gains at MSY (Maximum Sustainable Yield) for the four species. The
species with the higher level of concentration on shallow nursery areas were the most sensitive to the
habitat restoration scenarios. The response also depends to life history traits; species with lower steepness
exhibit a stronger response to habitat scenarios.