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    Biological traits of marine benthic invertebrates in Northwest Europe

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    Composition and decomposition of rhizoma peanut (Arachis glabrata Benth.) belowground biomass

    Experimental siteAll procedures for the experiment involving animals were carried out in accordance with relevant guidelines and regulations and they were approved by the Institutional Animal Care and Use Committee (IACUC) of the University of Florida (protocol #201509019). The experiment was conducted at the University of Florida North Florida Research and Education Center (NFREC) located in Marianna, FL (30° 52ʹ N, 85° 11ʹ W, 35 m asl) during 2018 and 2019.The study site was an existing mixed RP-bahiagrass grazing study where ‘Ecoturf’ RP was strip-planted into ‘Argentine’ bahiagrass on 12 June 2014. Rhizoma peanut strips were approximately 2-m wide, making it possible to harvest RP forage, roots, and rhizomes free of bahiagrass contamination3,4. The RP was collected from a nursery at the University of Florida—NFREC, whereas the bahiagrass seeds were bought from a seed company. All plants were collected, purchased, managed, and the research was conducted in compliance with relevant institutional, the corresponding national, and international guidelines and legislation.Soils at the experimental site were classified as Orangeburg loamy sand (fine-loamy, kaolinitic, thermic Typic Kandiudults24. At the beginning of the study, soil pH was 5.7 and soil OM was 15.4 g kg−1. Additionally, Mehlich-I extractable soil P, K, Mg, and Ca concentrations at the beginning of the experiment were 26, 99, 43, and 224 mg kg−1, respectively. Total annual rainfall and average annual temperature at the experimental site were 1889 and 602 mm, and 19 and 21 °C, for 2018 and 2019, respectively, and their monthly averages are shown in Fig. 5.Figure 5Monthly weather conditions at North Florida Research and Education Center (NFREC) Marianna, FL, during the experimental years.Full size imageTreatments and experimental designTreatments were two defoliation regimes applied to RP, continuously stocking and 56-days interval between clipping harvests. At the continuous stocking, stocking rates were variable to maintain similar herbage allowance among pastures, which was assessed every 14 days as described by Sollenberger et al.25. Two tester Angus crossbred steers (Bos spp.) remained on each pasture throughout the experimental period. Put-and-take cattle were allocated as needed to maintain a target herbage allowance of 1.5 kg DM kg−1 bodyweight3. Treatments were situated adjacent to each other (i.e., paired sites) in monoculture strips of RP within each of three 0.85-ha pastures. Each pasture was considered a block, thus the experiment consisted of three replicates of each treatment in a randomized complete block design. Within each replicate, treatments had three repetitions (pseudo replicates). To prohibit animal access to the non-grazed treatment, three 2 × 2-m exclusion cages were placed on RP strips in each pasture. Rhizoma peanut herbage mass was determined at both the grazed and non-grazed sites three times each year, at days 56, 112, and 168 of the experimental period by using a 0.25-m−2 quadrat. Two quadrats were collected in each repetition by clipping all the biomass within each quadrat at 2-cm stubble height. After each herbage mass sampling, the non-grazed residual dry matter inside the cages was clipped to a 2-cm stubble height using a weed eater and the herbage removed by raking. On average, across sampling dates and years, herbage mass at the grazed and non-grazed sites was 1050 and 1810 kg of organic matter (OM) ha−1, respectively.Long-term and short-term decomposition studiesThere were two types of root-rhizome decomposition trials. The first is referred to as the long-term decomposition study, and the second is the short-term decomposition study. The long-term study had an incubation period of 168 days, with a single in-situ incubation per year starting in May. The short-term study had in-situ incubation periods of 56 days and there were three incubations per year, occurring in May, June, and August. In all cases, only roots and rhizomes attached to the plant were used in both trials.Long-term studyOn 26 Apr. 2018 and on 23 Apr. 2019, right after RP emergence after breaking dormancy, RP roots and rhizomes were collected from an existing mixed RP-bahiagrass grazing study where RP had been planted in strips into bahiagrass (Paspalum notatum Flüggé) in 2014. Rhizoma peanut strips were approximately 2.75-m wide, alternating with similar wide bahiagrass strips. A pure stand of RP had been maintained in the strips during previous years using herbicides3, making it possible to harvest RP roots and rhizomes free of bahiagrass contamination. Roots and rhizomes were collected at 24 different points in each of three blocks of the original experiment. Roots and rhizomes were collected at 20-cm depth using shovels. As defoliation treatments had not being applied at this time of the year, the same material was used to perform the incubation inside and outside the exclusion cages. After harvesting, excess soil was removed by shaking from the root-rhizome mat using a 1.4-cm diameter sieve. Thereafter, the existing aboveground material was clipped, and the roots and rhizomes were then washed over the same sieve to remove the remaining soil. After washing, roots and rhizomes were dried to constant weight in a forced-air drying oven at 55 °C.To perform the decomposition study, approximately 12 g of dry roots and rhizomes were placed in Ankom bags (10 by 20 cm, 50 µm porosity; ANKOM Technology) and sealed17. Roots and rhizomes were aimed to be placed intact into Ankom bags, nonetheless, when they could not fit inside the bags, they were cut in the middle before being placed. On 2 May 2018 and 1 May 2019, the incubation period began. For each treatment, bags were incubated in situ in the field at 10-cm depth in the same blocks from which they were collected. Bags were removed from the field after 0, 3, 7, 14, 28, 56, 112, and 168 days. For each treatment within each block, three bags were incubated for each incubation time. Additionally, empty bags (one bag per treatment per time per block) were placed in the field. After removal of the in-situ bags from the field, samples and empty bags were dried at 55 °C for 72 h, cleaned with a brush, and weighed. Thereafter, samples were ground to pass a 2-mm screen using a Wiley Mill (Model 4, Thomas-Wiley Laboratory Mill, Thomas Scientific) and analyzed for DM and OM. Subsamples of the 2-mm ground samples were ball milled in a Mixer Mill (MM 400, Retsch) at 25 Hz for 9 min. Ball-milled samples were analyzed for C and N by dry combustion using an elemental analyzer (Vario Micro cube, Elementar). Additionally, samples ground at 2-mm were used to determine ADF in aboveground samples26. The N concentration in the ADF was determined using the above protocol to obtain the ADIN.Short-term studiesThe short-term studies were performed following the same procedures as the long-term study, except that the incubation period was only 56 days, and these studies were repeated three times each year. Roots and rhizomes were incubated in situ on 2 May, 27 June, and 23 Aug. 2018 and on 1 May, 26 June, and 21 Aug. 2019, following the same protocol as described above, except that bags were removed from the field after 0, 3, 7, 14, 28, and 56 days of incubation. The incubations occurring in May, June, and August will be referred as early, middle, and late season, respectively.The early-season incubation period uses the data from the first 56 days of the long-term study described above. For the middle- and late-season incubations each year, roots and rhizomes were harvested approximately 7 days days prior to incubation. Approximately six points in each repetition were collected at 20-cm depth using shovels. For the grazed treatment, roots and rhizomes were collected in the grazed area nearby the exclusion cages, whereas for the non-grazed treatment, the material was collected inside the exclusion cages. After removal of the bags from the field, they were processed and analyzed for DM, OM, C, and N following the protocol described above.Statistical analysesLong-term studyRemaining biomass, remaining N, C:N ratio, ADF, and ADIN were analyzed using the PROC GLIMMIX from SAS27, with treatment and days of incubation as fixed effects, and years and blocks as random effects. Days of incubation were considered repeated measures. Means were compared using the PDIFF procedure at the 5% significance level. When treatment or the interaction of treatment × day of incubation were statistically significant in the ANOVA, nonlinear models were tested to fit the data for each variable and treatment. Nonlinear models were selected for a given response based on data distribution and type of response. If only days of incubation was significant, the same model was applied for all treatments.Remaining biomass (OM basis), remaining N, and C:N ratio were explained by the single exponential decay model14,17,28. The equation describing this process is:$$X=B0, {exp}^{-kt},$$
    (1)
    where X is the remaining biomass, remaining N, or C:N ratio at day t, B0 is the disappearance coefficient, and k is the relative decay rate (g g−1 day−1). The model used to describe ADF and ADIN was the two-stage model “linear plateau”15,29. The equation describing this process is:$$begin{gathered} Xt = A + b1 times t, {text{if t }} le {text{ T}}, hfill \ {text{and}},{ } Xt = A + b1 times T, {text{if t }} > {text{ T}}, hfill \ end{gathered}$$
    (2)
    where X is the concentration of ADIN, t is the day of incubation, A is the initial concentration, b1 is the rate of increase in concentration from the beginning of incubation until plateau is reached; and T is the day in which concentration reaches the plateau.Short-term studiesThe single exponential model was applied in the remaining OM and remaining N, for each experimental unit, to obtain individual values for B0 and k. The data for initial N concentration, initial C:N ratio, and B0 and k for remaining OM and remaining N were analyzed using the PROC GLIMMIX from SAS27, with treatment and period as fixed effects, and years and blocks as random effects. Means were compared using the PDIFF procedure at the 5% significance level.Arrive guidelinesThis is study is reported in accordance to ARRIVE guidelines. More

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    Drivers of parasite communities in three sympatric benthic sharks in the Gulf of Naples (central Mediterranean Sea)

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    Dispersal and oviposition patterns of Lycorma delicatula (Hemiptera: Fulgoridae) during the oviposition period in Ailanthus altissima (Simaroubaceae)

    Fluorescent markingDispersal of SLF adults was tracked using a fluorescent marking system (FMS), which has been demonstrated to be applicable for multiple insect species including SLF nymphs21,22,24. To mark the SLF, either red, yellow, or blue fluorescent paint (#1166R, #1166Y, #1166B, BioQuip Products, USA) was diluted with distilled water (1:4). The mixture was then gently sprayed three times (ca. 20 mg each time) on each SLF individual using a mist sprayer from a distance of 30–50 cm (SI 2). Throughout the field survey, a handheld ultraviolet (UV) laser (PX 600 mW, class IIIB purple laser, 405 nm, Big Lasers, USA) was used to detect fluorescent-marked SLF individuals25.Effect of fluorescent marking on SLFPrior to field survey, the potential effects of fluorescent marking on the survivorship and flight behavior of SLF adults (sex ratio 1:1) were evaluated. SLF adults were collected using sweeping nets (BioQuip Products, USA) from Gyeonggi-do, South Korea (37°47′85.95″ N, 127°11′64.58″E) in September 2020. Two hours after fluorescent marking of SLF, both fluorescent-marked and unmarked SLF were subjected to survivorship and flight behavior assessment.Survivorship of insects was measured on two A. altissima trees (ca. 2 m in height) located in Gachon University, South Korea (37°45′38.50″N, 127°13′37.75″E). Two fluorescent-marked and two unmarked insects were placed in a cylindrical mesh cage [25 × 30 cm (radius × height)] enclosing a tree branch; a total of 20 groups were tested (n = 40). Then, survivorship of SLF was determined once every two days until no individuals were alive. Survivorship was compared between fluorescent-marked and unmarked SLF using Kaplan-Meir survivorship analysis (JMP 12, SAS Institute Inc., USA).The effects of fluorescent marking on flight behavior were evaluated in an open space (986 m2) in Gachon University, South Korea (37°45′08.37″N, 127°12′79.69″E) at 26 ± 1 °C and a relative humidity of 30 ± 5%. To induce flight of SLF adults, a wooden square rod [3 × 3 × 100 cm (width × length × height)] was established upright at the center of the arena. The SLF adult was placed individually 10 cm away from the top on the wooden square rod. To minimize any unnecessary stimuli from experimenter, SLF flight was induced by following the same sequence: once the insect climbed up the rod and oriented itself staying still to a random direction, then an experimenter carefully positioned at the back of the insect and gently pecked the forewings using tweezers to initiate its flight33,34. Pecking was intended to mimic predatory behavior of birds. Once the insect jumped away, an operator followed the individual until it landed on the ground (n = 30). The experiment was conducted for 2 h between 13:00–15:00 and marked and unmarked SLF were randomly tested during the evaluation. The number of pecks to initiate the flight, flight duration, and flight distance of SLF were compared using t-test (JMP 12, SAS Institute Inc., USA).Field study sitesDispersal patterns of SLF adults in A. altissima patches and their oviposition patterns were investigated in multiple A. altissima patches located along two streams in Gyeonggi-do, South Korea: Tan stream in Seongnam-si (37°48′01.80″N, 127°11′56.03″E) and Gyeongan stream in Gwangju-si (37°41′54.21″N, 127°27′12.37″E). Both Tan and Gyeongan streams run along suburban residential areas in their respective cities, with pedestrian lanes built along the streams. We selected seven A. altissima patches as study patches when more than 10 SLF adults were found per patch (Fig. 3). In the study patch, all SLF individuals or ca. up to 30 adults were florescent-marked. In addition, when the number of SLF adults was less than 10 from an A. altissima patch, those patches were designated as neighboring patches (Fig. 3). Dispersal and oviposition of SLF adults were monitored from both study and neighboring patches during the study.In Tan stream, four study patches (patches A–D) and one neighboring patch, which were distributed over ca. 1760 m, were selected (Fig. 3a). Areas around the patches were generally covered with grass and shrubs, and the areas were occasionally managed by local administration. Deciduous trees were regularly planted along the pedestrian lanes. There were a total of four, four, 61, and 47 A. altissima trees in patches A to D, respectively (Table 2). Compared with Tan stream, A. altissima patches were located closely to each other in Gyeongan stream: three study patches (patches E–G) and three neighboring patches were spread over only ca. 90 m (Fig. 3b). Vegetation surrounding A. altissima patches consisted of grasses and small shrubs as well as deciduous trees planted along the border of residential area nearby. There were a total of 69, nine, and 53 A. altissima trees in patches E to G, respectively (Table 2). Unlike Tan stream, 45% of A. altissima trees had trunks having cut off by local administration in Gyeongan stream (Table 2; Fig. 5).Dispersal pattern of SLF on A. altissima
    Three fluorescent paint colors were used to mark SLF individuals in the study patches (Fig. 3; SI 2). Insects that took off during marking were captured and excluded from the experiment. Among the selected study patches, SLF adults were generally distributed throughout each patch, while SLF adults were observed only from one out of 61 A. altissima trees in patch C. As a result, in Tan stream, 15 (color of paint used to fluorescent-marking; red), 31 (yellow), 11 (blue), and 32 (red) adults were marked from patches A to D, respectively, whereas in Gyeongan stream, 30 (red), 30 (blue), and 33 (yellow) adults were marked from patches E to G, respectively. Starting from September 14th, 2020 in Tan stream and September 18th in Gyeongan stream, fluorescent-marked SLF adults on A. altissima trees in both study and neighboring patches were counted with a UV laser twice a week (Fig. 3). Survey continued until no individuals were observed from the study patches.Oviposition pattern of SLF on A. altissima
    Oviposition pattern of SLF was surveyed on all A. altissima trees in the study patches in December in both streams (Table 2). For the survey, SLF egg masses were categorized into three types as follows: egg mass with waxy layer, egg mass without waxy layer, and scattered eggs (SI 3). Eggs that were not covered with waxy layer and did not form aggregates were categorized as scattered (SI 3). In the field, A. altissima trees were visually inspected to identify SLF egg mass, and the number of egg masses and their distances from the ground were recorded. In addition, the number of eggs per egg mass was recorded for egg masses located  5 generally indicates collinearity35,36. VIF between height and DRC was 1.56, and therefore the two variables were included together in the GLMM model.Policy statementExperiments involving Ailanthus altissima were conducted in compliance with relevant institutional, national, and international guidelines and legislation. More

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    Monthly spatial dynamics of the Bay of Biscay hake-sole-Norway lobster fishery: an ISIS-Fish database

    We took as a starting point the hake – sole – Norway lobster Bay of Biscay ISIS-Fish database used for COSELMAR project16,20 (see http://isis-fish.org/download.html section “Bay of Biscay scenario dataset”, Database V0 in Fig. 1). This database was built using 2010 data, and was not calibrated, as it was designed for a geo-foresight study. Since our aim was to describe the system over a decade and simulate realistic dynamics close to available observations to assess management measures, we needed to update the parametrisation and calibrate the database. We took 2010–2012 as the calibration period, and 2013–2020 as the simulation period (grey arrow Fig. 1). The database has a monthly temporal resolution (constrained by the ISIS-Fish framework) and the spatial scale was set to match ICES statistical rectangles (0.5° latitude by 1° longitude rectangles, defined by the International Council for the Exploration of the Sea (ICES) https://www.ices.dk/data/maps/Pages/ICES-statistical-rectangles.aspx), consistent with available knowledge and data.In this section, we firstly describe all the data sources used to update and calibrate the database. Then, for each main component of an ISIS-Fish database – i.e. populations, exploitation and management – we describe this paper’s database parameters and assumptions. We finally describe the calibration procedure (inspired by previous work21,22), of which some results are shown in the Technical Validation section. We summarized this workflow in Fig. 1.Data sourcesData sources, estimates, and literature (including grey literature) were needed to update and calibrate the model. They are marked in Fig. 1 with salmon (data sources and estimates) and mustard (literature) blocks:

    SACROIS23: French landings and effort logbook declarations for 2010 were made available at the log-event*commercial category*ICES statistical rectangle*population scale. It was used to design exploitation features of the database, as well as populations spatial structure.

    LANGOLF survey: 2006–2010 LANGOLF surveys observations for 2006–2010 were made available for Norway lobster. They were used to work on Norway lobster abundance per length class and sex.

    Intercatch: catch observations for 2010–2020 in the Bay of Biscay for hake, at the quarter-métier group scale, and catch observations per class for sole on 2010–2012, and 2010 Norway lobster catch observations per sex and length class24, used to describe the inter-annual effort dynamics, to calibrate and validate the model.

    Estimates of hake abundance per size class in 2010, and hake quarterly estimates of recruitment on 2010–2012 from a northern hake spatial stock assessment model21, used to inform hake biology assumptions (named Other 1 in Fig. 1).

    ICES WGBIE24 2010 estimates of abundance per class (sole and Norway lobster), to inform their abundance at the initial time step; 2010–2012 yearly fishing mortality estimates per age class (sole) to calibrate the database (named Other 2 in Fig. 1).

    Other population, exploitation and management assumptions were informed with scientific literature25 and grey literature26,27 (Literature block in Fig. 1).

    Management assumptions were informed with legal texts2,4,28,29,30,31,32,33,34 and reported quota values in working group reports24.

    About populationsThis section describes for each species the assumptions and parameters values, except for accessibility, which has been calibrated, as described in section Calibration procedure. For all assumptions and values, more details are provided in Supplementary Information’s section 2.2.HakeThe stock size structure was defined with 1 cm size bins for [1;40[cm individuals, 2 cm for [40;100[cm individuals, and 10 cm for [100;130+] cm individuals35. Areas of presence were defined based on 2010 SACROIS French landings data per commercial category and statistical rectangle23, leading to the definition of a presence, a recruitment, an interim recruitment and a spawning area25 (see Supplementary Information’s section 2.2 and Figure S1). These areas allow for the description of intra-Bay of Biscay migrations related to spawning and recruitment processes: mature individuals aggregate at the beginning of the year on the shelf break to spawn, and then disperse on the shelf36,37,38,39,40 (at the beginning of April and July in the model). Also, from age 1 (around 20 cm), individuals in recruitment zone spread in interim recruitment zone, to model a diffusion towards areas neighbouring the nursery area, at the beginning of each time step (see Supplementary Information’s section 2.2 and Table S11). Maturity-at-size and weight-at-length relationships were the same functions as used by ICES working group35,41. Natural mortality was fixed at 0.5, basing on preliminar runs, instead of the commonly used 0.442. Recruitment values were defined prior to the simulation for 2010–2020 using available estimates on the 2010–2015 time series21,27. Deterministic estimates from these sources were allocated to the recruitment area in the Bay of Biscay and the beginning of each month in January-September on the whole time series, of which values are provided in the Supplementary Information’s section 2.2 and Table S3. Growth is modelled through monthly growth increments5,25. However, given the different widths of size bins in the implemented size structure, a correction was provided to values in the transition matrix to eliminate artifacts when growing to a size bin wider than the size bin of origin, as detailed in Supplementary Information’s section 2.2. Abundance at the initial step in each zone was estimated from Bay of Biscay abundance estimates for 201021. Mature individuals over 20 cm were allocated to the spawning area, all individuals strictly shorter than 20 cm were allocated to the recruitment area (as they were assumed to be less than 1 year old), and remaining individuals were allocated to the interim recruitment area. None were allocated to the presence area, in which individuals will go later in the time series, after disaggregating from the spawning area25 (Table S13).SoleThe stock is age structured, with 7 classes going from ages 2 to 7+43 (Table S2). No seasonal variations were implemented. Only a single presence zone was defined (see Supplementary Information’s section 2.2 and Figure S1), as in preliminary runs defining more presence areas for sole did not yield more knowledge in this study. We implemented ICES working group values for natural mortality, weight-at-age (Table S1) and maturity-at-age43. Recruitment occurs at the beginning of each year, individuals being recruited at age 2 (ages 0–1 were not modelled; Table S4). We implemented ICES working group estimates27 for abundance at initial time step (Table S14).Norway lobsterThe stock has a sex-size structure, with 1 mixed recruitment class at 0 cm; 33 length classes for males at 2 carapace length mm intervals, from [10;12[to [72;74[carapace length mm; 23 length classes for females at 2 carapace length mm intervals, from [10;12[to [52;54[carapace length mm. A single presence area was defined: the Great Mudbank21 (see Supplementary Information’s section 2.2 and Figure S1). Several seasonal processes occur for this stock, impacting recruitment, accessibility and growth: 1/ January, begins with the annual recruitment. Females are inside their burrows, less accessible; 2/ February-March females are inside their burrows, less accessible; 3/ April: Spring moulting, females are more accessible; 4–5/ May-August females are more accessible; 6/ September, females are inside their burrows, less accessible; 7/ October: Autumn moulting only for immature females and all males, females are inside their burrows, less accessible; 8/ November-December, females are inside their burrows, less accessible44. We implemented ICES working group values for natural mortality, weight-at-class and maturity-at-class45,46,47. Growth occurs twice a year, when moulting in April and October, and is modelled with growth increments. Recruitment occurs at the beginning of each year, modelled with a Beverton-Holt relationship26, and was assumed to have the same spatial distribution as spawning stock biomass. Abundance at initial step was derived from LANGOLF survey observations and ICES WGBIE estimates25,26 (Table S16).About exploitationThe fishing exploitation structure (fleets, strategies, métiers and gears) were derived following a classification method on SACROIS 2010 landings and effort data13,23 from French fleets, and taken from a TECTAC project (https://cordis.europa.eu/project/id/Q5RS-2002-01291) database for Spanish trawlers. More details on their definition are provided in Supplementary Information’s section 2.3, Tables S5–S9 and S20–S21 and Figure S3. Spanish longliners and gillnetters fleets exploitation was described based on catch (observations from Intercatch48) rather than effort.Hake selectivity and discarding functions (one for each gear) were taken from estimates of a spatial hake stock assessment model21. Parameters values and formulæ are provided in Supplementary Information’s section 2.3 and Tables S6-S7. On top of this, inter-annual fleet dynamics factors were included in equation (21) of ISIS-Fish documentation8 in order to account for observed catch temporal variations. These factors are therefore multiplicative parameters of the target factor of each species for each métier. They are computed using observed catch27 and differ according to the period and targeted species:

    over 2010–2016, it is a ratio of observed catch in weight per year over catch observations for 2010: for hake, one per métier *season*year (left(frac{ObservedCatc{h}_{metier,season,year}}{ObservedCatc{h}_{metier,season,2010}}right)), for sole, one per métier *year (left(frac{ObservedCatc{h}_{metier,year}}{ObservedCatc{h}_{metier,2010}}right)), and for Norway lobster, one per year (identical for each métier catching Norway lobster) (left(frac{ObservedCatc{h}_{year}}{ObservedCatc{h}_{2010}}right));

    over 2017–2020: at the time of writing these assumptions, more recent data was not available, and ratios were deduced from trends on 2014–2016. A linear model was fitted on ratios deduced earlier on 2014–2016. If a significant trend was identified (hake: whitefish trawlers quarters 2 and 4, longliners and gillnetters seasons 2–3; sole and Norway lobster: all métiers), the slope was used to deduce 2017–2020 ratios (the slope was halved for hake whitefish trawlers and sole and Norway lobster values to avoid unrealistic high values of effort). Otherwise, 2016 ratios were used.

    All values are provided in Supplementary Information’s section A.2 Tables S22–S24, and the final values of target factors are derived from the Calibration procedure.About managementWe implemented a set of management rules close to what is currently implemented in the Bay of Biscay.All stocks are managed by TALs (Total Allowable Landings) until 2015 and then by TACs (Total Allowable Catch), except for Norway lobster, managed by TALs on the whole time series, not being under the landings obligation. To favour a better parametrisation, allowing for more reliable dynamics on the following years of the time series, no TALs were implemented during the calibration period (2010–2012; Fig. 1). These regulations were implemented from 2013 using historically TALs and TACs values24.Landings of the three stocks are also constrained by a Minimum Conservation Reference Size regulation that was implemented for all stocks using values currently enforced in the studied fishery28. Likewise, from 2016, the Landings Obligation was implemented, with de minimis exemptions for hake and sole, depending on the year and the gear used to fish them2,31,32,33,34. See Supplementary Information’s sections 2.4 and A.3, Figure S2 and Table S10 for further details on these restrictions.In response to the above management rules, a fishers’ behaviour algorithm has been developed to describe fishermen adaptation. Some métiers may be forbidden, depending on some conditions – the catch quota has been reached, the landings obligation is enforced – but also some values – the proportion of discarded catch, and also catch on previous years. Therefore fishermen change métiers within their strategy métiers set through a re-allocation of fishing effort to the latter set. This re-allocation aims to avoid quota overshooting. Further details about this algorithm are provided in the Supplementary Information’s sections 2.4 and A.3 and Figure S2.Calibration procedureThe model has been calibrated using two parameters (population accessibility and fishing target factor) involved in the catchability process (equation (21) in ISIS-Fish documentation8). The objective of the calibration is to reproduce the dynamics of catch over 2010–2012 at the species*métiers group scale, for each year or quarter depending on available data’s granularity. Calibration is sequentially performed: accessibility parameters for each population were estimated first followed by the target factors. The estimation of each parameter set (parameter type * population) combination was separated, and values were estimated jointly within each parameter set. To account for the specificity of each population model dynamics (global age-based for sole, spatial and size-based for hake, spatial, sex and size-based for Norway lobster), an objective function is defined for each population to calibrate their accessibility. More details on objective functions and procedures are provided in Supplementary Information’s section 2.5, as well as estimated values in Tables S17–S19.Hake accessibilityThe calibration for hake accessibility is based on a procedure developed for a former version of the database25. One parameter was estimated per quarter, all values being equal across length classes. The model outputs were fitted to hake catch observations in weight in the Bay of Biscay in 2010–2012 per length class.Sole accessibilityOne parameter was estimated per age class. The model outputs were fitted to WGBIE fishing mortality per age class for sole27 in 2010–2012.Norway lobster accessibilityOne parameter was calibrated per sex and length class. The model outputs were fitted to catch in numbers per length class and sex in 2010 per quarter provided by WGBIE.About target factorsTarget factors drive how the effort is distributed between populations, métiers and season*year combinations. They were split in 3 components: a fixed component derived from the SACROIS effort dataset analysis (Tables S25–S27), another fixed component driving inter-annual variations of fishing effort (Tables S22–S24), derived from catch observations, and finally an estimated component (Tables S28–S30), allowing to tune the model’s dynamics to observed catch. This section focuses on the estimation of the latter.Hake target factors20 parameters were defined, for each combination of the 5 groups of métiers (longliners, gillnetters, whitefish trawler (coastal), whitefish trawler (not coastal), Norway lobster trawler, see definition Table S8) and 4 quarters. We fitted the model’s outputs to the same data and with the same objective function as for hake’s accessibilities estimation.Sole target factors1 estimated component per group of métiers (gillnetters, Norway lobster trawlers and whitefish trawlers) and quarter. We fitted the model’s outputs to sole catch in weight on 2010–2012 for each métier and quarter.Norway lobster target factors1 estimated component per group of métiers (Norway lobster trawlers and whitefish trawlers). We fitted the model’s outputs to monthly Norway lobster landings data per length and sex class for 2010.Base simulationThe base simulation ran from January 2010 to December 2020 inclusive, with a monthly time step, using the database and parameters values described in this document. Several outputs of interest may be explored after a run: catch (discards and landings), as done in several figures in this paper, but also biomass (total biomass or mature biomass), fishing mortality values, or effort, all at a fine spatio-temporal scale. More

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    Population structure of blackfin tuna (Thunnus atlanticus) in the western Atlantic Ocean inferred from microsatellite loci

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