Browsing by Author "Brandão, Anabela"
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- ItemOpen Access2006 assessment of the toothfish (Dissostichus eleginoides) resource in the Prince Edward Islands vicinity(2006) Brandão, Anabela; Butterworth, Doug SThe ASPM assessment of the Prince Edward Islands toothfish resource by Brandão and Butterworth (2005) that permitted annual fluctuations about a deterministic stockrecruitment relationship is updated to take account of further catch, GLM standardised CPUE and catch-at-length information that has become available for the years 2005 and 2006. The assessment allows for a second fleet to accommodate data from a pot fishery that operated in 2004 and 2005. Updated biological parameter values for Subarea 48.3 are incorporated and lead to less optimistic results. The resource is estimated to be at about 40% of its average pre-exploitation level in terms of spawning biomass. It is suggested that it would be prudent to restrict annual legal catches to 500 tonnes or less, unless a large proportion of the catch is to be taken by pots (which avoid the cetacean predation associated with longlining). Specific issues raised at WGFSA-SAM 2006 about this assessment are addressed.
- ItemRestricted2007 assessment of the toothfish (Dissostichus eleginoides) resource in the Prince Edward Islands vicinity(2006) Brandão, Anabela; Butterworth, Doug SThe ASPM assessment of the Prince Edward Islands toothfish resource by Brandão and Butterworth (2006) that permitted annual fluctuations about a deterministic stock-recruitment relationship is updated to take account of further catch, GLM standardised CPUE and catch-at-length information that has become available for the years 2006 and 2007. The assessment allows for a second fleet to accommodate data from a pot fishery that operated in 2004 and 2005. Biological parameter values adopted for Subarea 48.3 are used. The resource is estimated to be at about 37% of its average pre-exploitation level in terms of spawning biomass. It is suggested that it would be prudent to restrict annual legal catches to 500 tonnes or less, unless a large proportion of the catch is to be taken by pots (which avoid the cetacean predation associated with longlining).
- ItemRestrictedAbalone poaching confiscation numbers and trends for Zones A-D updated to include data until 2009(2009) Brandão, AnabelaPoaching confiscation data have been updated using all data currently available until the third quarter of 2009. The data have been reworked in terms of a standard Model year y that is taken to run from October of year y-1 to September of year y. This was necessary for reasons of internal consistency in the assessment process which uses a Model year defined in this manner. The data provided by A. Mackenzie have been reworked in the same way as Plagányi (2008), and the “revised” trend and minimum numbers confiscated are given in this document.
- ItemOpen AccessAge-Structured Production Model (ASPM) assessments of the Alfonsino (Beryx splendens) resource in the SIOFA area of the Southern Indian Ocean(2020) Brandão, Anabela; Butterworth, Doug; Johnston, SusanAn Age-Structured Production Model is applied to assess the Alfonsino (Beryx splendens) resource in the West and East SIOFA areas of the Southern Indian Ocean. Data limitations restrict these applications to deterministic variants, which assume no variation in annual recruitment about the predictions from a stock-recruitment relationship. The models are fitted to the CPUE series and single year of commercial catch length distribution information available. Both West and East stocks are estimated to be at about 60% of their pre-exploitation spawning stock biomass levels, and well above the levels corresponding to MSY (MSYL). These results are insensitive to all sensitivities explored, except for changes in the value assumed for natural mortality (M). For the Base case assumption of M=0.2, projections under constant annual catches up to 40% above the 2018 levels remain above MSYL for the next two decades. However, if a less productive situation is assumed (M=0.15), there are some cases of spawning biomass dropping below MSYL within 10 years for both areas, including even for continuation of the 2018 catch for the East area.
- ItemRestrictedAge-structured production model assessments and projections including updated parameters to model the intermittent aggregation of Namibian orange roughy(2007) Brandão, Anabela; Butterworth, Doug SUpdated assessments of the four orange roughy aggregations off Namibia, based upon a maximum penalised likelihood approach which uses all available indices of abundance and reflects the proportion of a stock present at the fishing aggregation each year, are presented, and projections under constant catch levels reported. Further abundance data now available for Frankies allow the parameters of the beta distribution used to reflect the proportion aggregating to spawn each year to be updated. This leads to more optimistic results for stock status, slightly so for Frankies and Rix for which estimates of the ratio of current to preexploration levels increase from the 60%’s to the 70%’s, but substantially so for Johnies which is no longer estimated to be heavily depleted. With no new standardised CPUE values available, Hotspot remains estimated as highly depleted. The range of variable aggregation levels estimated are not qualitatively incompatible with information for Australian orange roughy aggregations. Changing from the earlier to the updated beta distribution parameters increases medium term annual sustainable yield estimates for the resource as a whole from 1 850 to 4 400 tons, though the latter figure needs to be considered with caution as it is particularly dependent on the assumption that the beta distribution estimated for proportions aggregating at Frankies applies also to Johnies. Broadly speaking, MSY estimates at 1 600 to 3 500 tons are some 5–60% more than estimated a year previously. However, the varying proportions of abundance present at aggregations from year to year would lead to difficulties in making a catch of this size every year.
- ItemRestrictedAlternative structural models for the Northeast Chatham Rise orange roughy fishery(2006) Butterworth, Doug S; Brandão, AnabelaA particular difficulty with assessments of the Orange Roughy resource on the Northeast Chatham Rise is the seeming inability of standard population models, with their standard assumptions of a linear relationship between CPUE and survey indices to abundance, to simultaneously reflect the trends of all these indices. Especially concerning is that while the outputs from these models suggest a recovery in abundance for the Spawning Box after about 1992, the CPUE and hydroacoustic survey results for that period indicate the reverse. A number of mechanisms have been suggested that might be able to resolve these inconsistencies: resident-and-transient fish (related perhaps to spawning migrations), seasonal patterns, hyperdepletion, disturbance, intermittent aggregation, effort saturation and fishing behaviour (Anon. 2005). The purpose of this paper (following a proposal in Anon. 2005) is to investigate this using a simple age-aggregated population model as a basis.
- ItemRestrictedAnalyses of the fisheries independent monitoring survey data of the rock lobster resource of South Africa to include the 2011/12 season(University of Cape Town, 2012) Brandão, Anabela; Butterworth, Doug SAnalyses of FIMS data are updated to include data for the 2011/12 season. Results show a drop in the last season’s index for the FIMS relative abundance indices in the Dassen and Lambert’s Bay Zones but there is an increase for Cape Point and Saldanha Bay. For Dassen Island this continues a fairly steady downward trend since 2002. The percentage of females in the last season has increased in the Cape Point and Dassen Zones, but has decreased for Saldanha Bay and Lambert’s Bay.
- ItemOpen AccessAnalyses of the Fisheries Independent Monitoring Survey data of the rock lobster resource of South Africa to include the 2012/13 season(MARAM, University of Cape Town, 2013) Brandão, Anabela; Butterworth, Doug SAnalyses of FIMS data are updated to include data for the 2012/13 season. Results show a drop in the last season’s index for the FIMS relative abundance indices in the Dassen, Lambert’s Bay and Saldanha Bay Zones. Although the index for Saldanha Bay is lower than that of the previous season, it is still at a higher level than most indices for other seasons but there is a very large standard error associated with this estimate. There is a large increase for Cape Point, although this estimate has a large standard error. For Dassen Island this continues a fairly steady downward trend since 2002. The percentage of females in the last season has increased in all Zones.
- ItemOpen AccessAnalysis of tagging data of the toothfish (Dissostichus eleginoides) resource in the Prince Edward Islands vicinity(2018-03) Brandão, Anabela; Butterworth, Doug SSome simple analyses of the tag-recapture data available for the PEI toothfish resource are undertaken. Somatic growth rate seems to be less than that in Subarea 48.3 which has previously been assumed for assessments of the PEI resource. If the first two years of data for each vessel are excluded, broad indications are that the tag recovery efficiency on the two vessels operating in the fishery are about the same and not changing over time.
- ItemOpen AccessApplication of a photo-identification based assessment model to southern right whales in South African waters(2012) Brandão, Anabela; Butterworth, Doug S; Müller, Andrea; Best, Peter BThe three-mature-stages (receptive, calving and resting) model of Cooke et al. (2003) is applied to photo-identification data available from 1979 to 2010 for southern right whales in South African waters. The 2010 number of females having reached the age at first parturition is estimated to be 1 205, the total population (including males and calves) 4 725, and the annual population growth rate 6.8%. The probability (average 11%) that a resting mature whale rests for a further year appears to vary annually, whereas the probability (7%) that a receptive whale rest (or aborts) rather than calves the next year appears to be constant. Information from resightings of grey blazed calves as adults with calves allows estimation of first year survival rate of 0.914 (compared to a subsequent annual rate of 0.987, and an age at 50% maturity of 6.4 years. However this suggests also that 27% (s.e. 6%) of grey blazed calves lose their marking before becoming adults. In contrast, the relative proportions of grey blazed animals amongst calves and amongst calving adults suggest rather a value of 10% (s.e. 8%). If the proportion losing markings is in fact 10%, first year survival rates estimate drops to 0.837 and the population growth rate to 6.4% pa.
- ItemOpen AccessApplication of a photo-identification based assessment model to southern right whales in South African waters, now including data up to 2012(2013) Brandão, Anabela; Butterworth, Doug S; Ross-Gillespie, Andrea; Best, Peter BThis paper extends the analyses of Brandão et al. (2012) which applied the three-mature-stages (receptive, calving and resting) model of Cooke et al. (2003) to photo-identification data available from 1979 to 2010 for southern right whales in South African waters, by taking two further years of data into account. The 2012 number of parous females is estimated to be 1 321, the total population (including males and calves) 5 062, and the annual population growth rate 6.6%. This reflects a small reduction to the 6.8% increase rate estimated previously; this is a result of slightly lesser numbers in recent years than estimated previously. Information from resightings of grey blazed calves as adults with calves allows estimation of first year survival rate of 0.850, compared to a subsequent annual rate of 0.988. This information also suggests that 7% (s.e. 6%) of grey blazed calves are not recognised as such when adults; this estimate is much less than that of 27% obtained previously by Brandão et al. (2012), and is more compatible with the relative proportions of grey blazed animals amongst calves and amongst calving adults which suggest a value of 10% (s.e. 8%).
- ItemRestrictedApplication of lognormal and delta-lognormal linear models to standardise CPUE abundance indices (1994 to 2002) for orange roughy off Namibia(2003) Brandão, Anabela; Butterworth, Doug SGLM analyses are used to standardise the CPUE data for Namibian orange roughy. The possibility of there being a “learning” period of lower CPUE for a new vessel when it enters the fishery is taken into account. Alternative statistical approaches to deal with tows that record zero catch of orange roughy are considered. Further, to allow for areal expansion of the fishery at each aggregation, sub-aggregations are defined and CPUE trends estimated separately for each. Different methods for combining the results for the various sub-aggregations to provide a single index for an aggregation are considered. In broad terms standardised CPUE values for 2002 appear similar (with some slightly lower) to those for the previous year.
- ItemOpen AccessAssessment of the toothfish (Dissostichus eleginoides) resource in the Prince Edward Islands vicinity to include data from 1997 to 2013(2013) Brandão, Anabela; Butterworth, Doug SThe ASPM assessment of the Prince Edward Islands toothfish resource by Brandão and Butterworth (2007) that permitted annual fluctuations about a deterministic stockrecruitment relationship is updated to take account of further catch, GLMM standardised CPUE and catch-at-length information that has become available for the years 2007 to 2013. The assessment allows for three fleets to accommodate data from a pot fishery that operated in 2004 and 2005 and a trotline fishery since 2008 in addition to the Spanish longline operations. Biological parameter values adopted for Subarea 48.3 are used. The resource is estimated to be at a depletion of about 87% of its average pre-exploitation level in terms of spawning biomass, but this requires large recruitment pulses in the 1990s and does not reflect the large CPUE decline when the fishery commenced. Imposing alternative constraints lead to a depletion of about 43%. These different assessments imply rather different sustainable yields, though all suggest medium term abundance increases for a TAC of 500 t.
- ItemOpen AccessAssessment of the toothfish (Dissostichus eleginoides) resource in the Prince Edward Islands vicinity to include data from 1997 to 2013, including tag-recapture data(2014) Brandão, Anabela; Butterworth, Doug SThe assessment of the Prince Edward Islands (PEI) toothfish (Dissostichus eleginoides) resource carried out by Brandão and Butterworth (2013) is updated to take into account further data available for 2013 and a revised CPUE standardisation in which several desirable improvements have been made. This update also incorporates tag-recapture data and a new basis to estimate the extent of cetacean depredation. For the Base Case and many of the assessment sensitivities the resource is estimated to be at a depletion (in relation to its average pre-exploitation level in terms of spawning biomass) in the 55-60% range. Introduction of the tag-recapture data hardly changes point estimates but does reduce estimation variance. Projections suggest that the resource would increase slowly under constant annual future catches of 500 t. This would remain the case for somewhat higher catches as well, but it remains a concern that for the last three years the longline CPUE is well below model predictions. In these circumstances, perhaps recommendations to increase the TAC beyond 500 t should first await further trotline CPUE data.
- ItemOpen AccessAssessment of the toothfish (Dissostichus eleginoides) resource in the Prince Edward Islands vicinity to include data from 1997 to 2017(2018-10) Brandão, Anabela; Butterworth, Doug SThe assessment of the Prince Edward Islands (PEI) toothfish (Dissostichus eleginoides) resource carried out by Brandão and Butterworth (2017) is updated to take further data now available for 2017 into account. This update also incorporates tag-recapture data and a new basis to estimate the extent of cetacean depredation. For the Base case and many of the assessment sensitivities, the resource is estimated to be at a depletion (in relation to its average pre-exploitation level in terms of spawning biomass) in the 36-42% range. If the model is forced to fit the trotline CPUE indices and the tag-recapture data as well, the estimated average pre-exploitation level in terms of spawning biomass is in the range of 12-26%, but this requires an assumption of very high levels of tag loss.
- ItemOpen AccessBack-tracking biomass estimates to 1932 using results from a "Replacement Yield" model fit to catch and survey data for the South Coast kingklip resource off South Africa for estimates of current status relative to MSY-related reference points(2014) Brandão, Anabela; Butterworth, Doug SBack-tracking biomass values to 1932 for each posterior replicate of a Bayesian “Replacement Yield” model applied to the total annual catches and the survey abundance estimates for the South African kingklip resource off the South coast by Brandão and Butterworth (2013) results in both a mean and median current (2012) depletion of about 40%. This suggests current status close to BMSY, which taken together with the recent increasing trend in survey abundance estimates suggests a current fishing mortality less than FMSY.
- ItemRestrictedBiopsying Southern right whales: their reactions and effects on reproduction(Wiley, 2005) Best, Peter B; Reeb, Desray; Rew, Mary Beth; Palsbøll, Per J; Schaeff, Cathy; Brandão, AnabelaCollecting skin biopsies from large whales for genetic analysis is often subject to national permit, and in the case of cow-calf pairs, it may be prohibited. We present results of 906 biopsy attempts on southern right whales (Eubalaenaustralis) in South African waters between 1995 and 1997, including 147 cow-calf pairs. Our sampling success was higher for biopsy darts with a bore of 4 mm compared to 4.6 mm. Contact periods averaged 17.7 min for cow-calf pairs and 25.4 min for whales unaccompanied by calves. There were no significant differences in the short-term reactions of males and females to biopsying, but the reaction of single animals of either sex was greater than for larger groups. Cows accompanied by calves had the strongest reactions, which were significantly greater than even single females. We found evidence of sensitization to repeat biopsying (over periods of hours to 65 days) for cows but not calves (n = 20). We compared the subsequent reproductive history of 117 biopsied cows with that of 163 unbiopsied cows from the same years, and we compared the distribution of calving intervals for biopsied animals with 829 intervals recorded from 1985 to 1995. We did not detect any adverse effects on the proportion of successful reproductive cycles, and hence calf survival, or the proportion of longer-than-normal cycles, although the power of all the statistical tests was low. We concluded that any prohibition on the biopsy sampling of cow-calf pairs should be carefully reconsidered in the light of the valuable genetic insights such sampling could achieve.
- ItemOpen AccessConcerning demographic limitations on the population growth rate of West Australian (breeding stock D) humpback whales(2006) Brandão, Anabela; Butterworth, Doug SThe upper bound of 0.126 on the maximum demographically possible annual population growth rate for humpback whales that is currently imposed on age-aggregated assessment models for this species, is based on an analysis that assumes steady age structure. It is conceivable that transient age-structure effects could admit greater population growth rates than suggested by such a bound for short periods. This possibility is addressed by developing an age-structured population model in which possible density dependent changes in pregnancy rate, age at first parturition and natural mortality are modeled explicitly, and allowance is made for the possibility of senescence. The model is applied to the case of the west Australian humpback whale population (breeding stock D), for which breeding ground surveys over the 1982-1994 period provide a point estimate of 0.10 for the annual population growth rate. Results based upon the breeding population surveys estimate of abundance of 10032 in 1999 suggest that 0.12 is the maximum feasible annual rate of increase for this stock over 1982-1994 if it is closed. This result is based on essentially the same parameter choices as led to the earlier r = 0.126 bound, viz. that in the limit of low population size the age at first parturition approaches 5 years from above, the annual pregnancy rate 0.5 from below, and the annual natural mortality rate 0.01 from above.
- ItemOpen AccessConcerning demographic limitations on the population growth rate of West Australian (breeding stock D) humpback whales(International Whaling Commission, 2011) Brandão, Anabela; Butterworth, Doug SThe upper bound of 0.126 on the maximum demographically possible annual growth rate for humpback whales that has standardly been imposed on recent applications of age-aggregated assessment models for this species in the IWC Scientific Committee, is based on an analysis that assumes steady age structure. It is conceivable that transient age-structure effects could admit greater population growth rates for short periods than suggested by such a bound. This possibility is addressed by developing an age-structured population model in which possible density dependent changes in pregnancy rate, age at first parturition and natural mortality are modelled explicitly, and allowance is made for the possibility of natural mortality increasing at older ages. The model is applied to the case of the west Australian humpback whale population (Breeding Stock D), for which breeding ground surveys over the 1982–1994 period provide a point estimate of 0.10 for the annual population growth rate. Results based upon the breeding population survey estimate of abundance of 10,032 in 1999 suggest that 0.12 is the maximum demographically feasible annual rate of increase for this stock over 1982–1994 if it is a closed population. This result is based on essentially the same parameter choices as led to the earlier r = 0.126 bound, i.e. that in the limit of low population size the age at first parturition approaches five years from above, the annual pregnancy rate 0.5 from below, and the annual natural mortality rate 0.01 from above. Transient effects do not appear able to reconcile the observed rate of increase with less extreme values of demographic parameters than led to the previously imposed upper bound of 0.126 on the maximum possible annual growth rate. Although use of extreme values reported for demographic parameters for Northern Hemisphere humpback whale populations, rather than those considered here, would reduce this suggested maximum rate of 0.12, the conclusion that transient effects have a very limited impact on observed population growth rates would be unlikely to change.
- ItemOpen AccessConditioning of the Reference Set of Operating Models for the toothfish resource in the Prince Edward Islands vicinity(2019) Brandão, Anabela; Butterworth, Doug SConditioning results for the Reference Set of Operating Models identified at a Task Team meeting and described in Brandão et al. (2019) are given. The assumptions that show more marked differences in the conditioning results from those of the Base case OM01 are changes in natural mortality (OM02 and OM03), up-weighting all CPUE data by a factor of 10 (OM10), a change in recruitment residual standard deviation (OM11), alternative von Bertalanffy growth parameters (OM12) and large values of tag loss which are assumed to force good fits to the trotline CPUE (OM16 and OM17).