elasmobranch bycatch in the canadian northwest atlantic and arctic adjacent seas

164 Pages·2015·22.74 MB·English

by  Aurelie Cosandey Godin

ELASMOBRANCH BYCATCH IN THE CANADIAN NORTHWEST
ATLANTIC AND ARCTIC ADJACENT SEAS: COMPOSITION,
BIOGEOGRAPHY, AND MITIGATION
by
Aure´lieCosandey-Godin
Submittedinpartialfulfillmentoftherequirements
forthedegreeofDoctorofPhilosophy
at
DalhousieUniversity
Halifax,NovaScotia
March2015
©CopyrightbyAure´lieCosandey-Godin,2015
T C
ABLE OF ONTENTS
ListofTables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
ListofFigures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vi
Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii
ListofAbbreviationsandSymbolsUsed . . . . . . . . . . . . . . . . . . . . . . ix
Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi
Chapter1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1 GlobalFisheries,Bycatch,andElasmobranchConservation . . . . . . . . 1
1.2 Elasmobranch Species in the Canadian Northwest Atlantic and Arctic
AdjacentSeas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.3 StructureoftheDissertationandStatementofCo-Authorship . . . . . . . 4
1.3.1 DataAccessibility . . . . . . . . . . . . . . . . . . . . . . . . . 6
Chapter2 ApplyingBayesianSpatio-temporalModelstoFisheriesBycatch
intheCanadianArctic . . . . . . . . . . . . . . . . . . . . . . . 7
2.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.3 MaterialsandMethods . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.3.1 GreenlandSharkBycatchDataset . . . . . . . . . . . . . . . . . 11
2.4 HierarchicalSpatio-temporalModelStructure . . . . . . . . . . . . . . . 14
2.5 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.5.1 ModelSelection . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.5.2 InferenceandPrediction . . . . . . . . . . . . . . . . . . . . . . 21
2.6 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Chapter3 PredictingSharkBycatchHotspotsinaPelagicLonglineFishery 29
3.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
3.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
3.3 MaterialsandMethods . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
ii
3.3.1 Datasets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
3.3.2 BycatchperUnitofEffortStandardizationModelsoftheObserver
Dataset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
3.3.3 PredictionontheTotalFishingEffortUsingtheLogbookData . . 39
3.3.4 HotspotsandExcursionMaps . . . . . . . . . . . . . . . . . . . 39
3.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.4.1 ModelSelection . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.4.2 InferenceandPrediction . . . . . . . . . . . . . . . . . . . . . . 42
3.4.3 HotspotRegionsandExcursionMaps . . . . . . . . . . . . . . . 44
3.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Chapter4 ElasmobranchDiscardsintheCanadianNorthwestAtlanticand
ArcticAdjacentSeas: CompositionandBiogeography . . . . . 55
4.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
4.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
4.3 MaterialsandMethods . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
4.3.1 Datasources . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
4.3.2 Datapreparation . . . . . . . . . . . . . . . . . . . . . . . . . . 58
4.3.3 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
4.3.4 EstimatesofDiscardsonTotalFishingEffort . . . . . . . . . . . 61
4.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
4.4.1 Descriptiveanalysis . . . . . . . . . . . . . . . . . . . . . . . . 62
4.4.2 Predictions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
4.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
4.5.1 KeyareasofcumulativeimpactsinScotia-Fundy . . . . . . . . . 71
4.5.2 Deepwaterandnorthernelasmobranchspecies . . . . . . . . . . 79
4.5.3 Geostatisticalmodelsforat-seaobserverdata . . . . . . . . . . . 81
4.5.4 ConcludingRemarks . . . . . . . . . . . . . . . . . . . . . . . . 84
Chapter5 The Effect of Circle Hooks on Shark Catchability and At-Vessel
MortalityRatesinLonglineFisheries . . . . . . . . . . . . . . 85
5.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
5.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
5.3 MaterialsandMethods . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
5.3.1 DataSelectionandManipulation . . . . . . . . . . . . . . . . . . 87
5.3.2 Meta-Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
5.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
iii
5.4.1 Catchability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
5.4.2 At-VesselMortality . . . . . . . . . . . . . . . . . . . . . . . . . 92
5.4.3 HookingLocation . . . . . . . . . . . . . . . . . . . . . . . . . 94
5.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
5.5.1 Catchability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
5.5.2 At-VesselMortalityandHookingLocation . . . . . . . . . . . . 97
Chapter6 No Effect from Rare-Earth Metal Deterrent on Shark Bycatch
inaCommercialPelagicLonglineTrial . . . . . . . . . . . . . 99
6.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
6.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
6.3 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
6.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
6.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
Chapter7 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
7.1 ElasmobranchBycatchandDiscardsintheNorthwestAtlanticandArctic
AdjacentSeas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
7.2 BycatchMitigation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
7.3 GeostatisticalModelsandNewStatisticalDevelopmentsforBycatchStudies113
7.4 NextSteps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
AppendixA BayesianHierarchicalModel . . . . . . . . . . . . . . . . . . . 138
A.1 ModelStructure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
A.2 Priors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
AppendixB ExcursionFunctionsMaps . . . . . . . . . . . . . . . . . . . . 141
AppendixC Dataspecifications . . . . . . . . . . . . . . . . . . . . . . . . . 145
iv
L T
IST OF ABLES
2.1 Datasummary . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.2 Spatio-temporalcorrelationstructuresconsidered. . . . . . . . . . . 16
2.3 DICvaluesforallmodelstested. . . . . . . . . . . . . . . . . . . . 19
3.1 Listofcovariates. . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
3.2 Listofbycatch-per-unit-of-effort(BPUE)modelsconsidered. . . . 38
3.3 Posterior estimates, mean and 95% credibility interval, of model
parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
5.1 Listofstudies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
5.2 Summaryoftheresultsofthemeta-analysisoncatchability. . . . . 92
5.3 ANCOVAresults . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
5.4 Summaryoftheresultsofthemeta-analysisonat-vesselmortality. . 93
6.1 Speciescaughtintheexperiment. . . . . . . . . . . . . . . . . . . 105
6.2 Estimated parameter values, standard error, degrees of freedom,
t-values,andp-valuesfromthegeneralizedlinearmixedmodels. . . 107
A.1 Summaryofthedefaultpriorsusedinthemodeltested. . . . . . . . 140
C.1 Listoffishinggear. . . . . . . . . . . . . . . . . . . . . . . . . . . 145
v
L F
IST OF IGURES
1.1 MapsoftheNorthwestAtlanticandArcticAdjacentSeas. . . . . . 5
2.1 Map of Baffin Bay and picture of Greenland shark, Somniosus
microcephalus . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.2 Covariatesofinterest . . . . . . . . . . . . . . . . . . . . . . . . 15
2.3 Modelevaluationandselection. . . . . . . . . . . . . . . . . . . . 20
2.4 Meanandthe2.5%and97.5%quantilesfortheposteriordistribu-
tionofthebathymetrysmoothedregressioneffect. . . . . . . . . . 22
2.5 Observed versus predicted values (counts) of Greenland shark by-
catch. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.6 Summaryofthespatialrandomeffect. . . . . . . . . . . . . . . . 24
2.7 Hotspotmap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
3.1 Map of observed and logged pelagic longline fishing effort and
spatialmeshusedinmodels. . . . . . . . . . . . . . . . . . . . . 34
3.2 Goodnessoffit. . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
3.3 Modelpredictions. . . . . . . . . . . . . . . . . . . . . . . . . . . 51
3.4 Mapsofthemeanexpectedsharkbycatch. . . . . . . . . . . . . . 52
3.5 Mapsofthestandarddeviationoftheexpectedsharkbycatch. . . . 53
3.6 Excursionfunctionsmaps. . . . . . . . . . . . . . . . . . . . . . 54
4.1 Totalobservedweightofelasmobranchdiscards,1996-2012 . . . 63
4.2 fleet-selectivityforelasmobranchdiscards. . . . . . . . . . . . . . 64
4.3 Bathymetryeffectonelasmobranchdiscards. . . . . . . . . . . . . 66
4.4 Temporaltrendsofelasmobranchdiscards. . . . . . . . . . . . . . 67
4.5 Temporaltrendsofelasmobranchdiscardsweight. . . . . . . . . . 68
4.6 Spatialrandomfieldsincludedintheoccurrencemodels. . . . . . 69
4.7 Spatialrandomfieldsincludedintheweightmodels. . . . . . . . . 70
vi
4.8 Total estimates of discards for selachii and batoid by fleet sector
andyear. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
4.9 Totalestimatesofdiscardsperspeciesperfleetsector,1996-2012. 72
4.10 Seasonaltrendsintotaldiscardsforselachiiandbatoids. . . . . . 73
4.11 Mapsoftotaldiscardsforselachiiandbatoids. . . . . . . . . . . . 74
4.12 MapsoftotaldiscardsfortheScotia-Fundyareabyselachiispecies. 75
4.13 MapsoftotaldiscardsfortheScotia-Fundyareabybatoidspecies. 76
4.14 Mapsoftotaldiscardsfordeep-waterspecies. . . . . . . . . . . . 77
5.1 Worldmapshowingthelocationsofallstudies. . . . . . . . . . . 89
5.2 Meta-analysisoncatchability. . . . . . . . . . . . . . . . . . . . . 91
5.3 Meta-analysisonat-vesselmortality. . . . . . . . . . . . . . . . . 94
6.2 PictureofNd/Pralloy. . . . . . . . . . . . . . . . . . . . . . . . . 103
6.3 Meancatch-per-uniteffortintheexperimentallonglinetrial. . . . 106
B.1 Excursionsfunctionsforbluesharks. . . . . . . . . . . . . . . . . 142
B.2 Excursionsfunctionsforporbeaglesharks. . . . . . . . . . . . . . 143
B.3 Excursionsfunctionsforshortfinmakosharks. . . . . . . . . . . . 144
C.1 Example ofthe mesh andDirichlet tessellation usedin the Selachii
models. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
C.2 Observeddistributionofdiscardsforeachelasmobranchspecies,
1996-2012. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
vii
A
BSTRACT
BACKGROUND: Industrial fishinghas profoundly changedthe biological stateof oceans
andseas. Whilethedirectimpactsofoverfishingontargetstocksarebeingincreasingly
addressed,unwantedbycatchanddiscardingofnon-targetspeciesremainsakeychallenge
ofcontemporaryfisheriesmanagement. Excessbycatchmortalityisparticularlythreatening
forintrinsicallyvulnerablespecies,suchassharks,skates,andrays(ClassChondrichthyes).
QUESTION:In orderto addressthesepressing concernswe oughttoknowwhere bycatch
occursintimeandspace,andhowitcanbesolvedthroughspatial-temporalmanagement
andmodificationoffishingtechnique.
METHOD: Thesequestions were addressedby developing novel geostatistical methods to
trackandquantifybycatch“hotspots”intheNorthwestAtlanticandadjacentArcticseas.
Thesetoolswereappliedtoanalyse(i)bycatchpatternsofGreenlandshark(Somniosus
microcephalus),anemergingspeciesofconcerninexpandingArcticfisheries;(ii)bycatch
of large sharks in pelagic longline fisheries; and, (iii) to estimate total discards of all
elasmobranch species in Eastern Canadian fisheries. Additional research also clarified
the role of circle hooks in reducing post-release mortality for sharks and field-tested
electropositivemetalsasbycatchdeterrentsinlonglinefisheries.
RESULTS:AreasofhighbycatchwereconcentratedinsouthernCanadianwatersbordering
theUnitedStates: upperBayofFundy,GeorgesBank,BrownsBank,andEmeraldBasin,
howevernorthernlatitudeswereassociatedwithbycatchofdeep-waterspecies—which
areinneedofgreaterattention. Thesepatternsweredrivenbybothspecies’abundanceand
fishingintensity. In2012,totaldiscardamountswereestimatedat3250mt(2722-3849,
95% credible intervals) for sharks and 1772 mt (1642-1911) for skates and rays. Total
bycatchoflarge sharkswashigherthanpreviouslyassumedinpelagiclonglinefisheries.
For bycatch mitigation circle hooks reduced post-release mortality, but electropositive
sharkrepellentswerenoteffectiveinreducingbycatchinpelagiclonglinefisheries.
CONCLUSION: Thisdissertation clearlydemonstrates thehigh spatiotemporalvariability
and inherent complexity of bycatch and supports the use of geostatistical models and
fine-scalespatialmanagementforelasmobranchconservation.
viii
L A
IST OF BBREVIATIONS AND
S U
YMBOLS SED
Symbol Description
BPUE Bycatch-Per-Unit-Effort
CITES ConventiononInternationalTradeinEndangeredSpeciesofWild
FaunaandFlora
CPUE Catch-Per-Unit-Effort
CRDT ConstrainedRefinedDelaunayTriangulation
CSRS CanadianSpatialReferenceSystem
DFO CanadianDepartmentofFisheriesandOceans
DIC DevianceInformationCriterion
EEZ ExclusiveEconomicZone
GAM GeneralizedAdditiveModel
GAMM GeneralizedAdditiveMixedModel
GLM GeneralizedLinearModel
GLMM GeneralizedLinearMixedModel
GMRF GaussianMarkovRandomField
GRF GaussianRandomField
HMS HighlyMigratorySpecies
ICCAT InternationalCommissionfortheConservationofAtlanticTunas
IUCN InternationalUnionforConservationofNature
INLA IntegratedNestedLaplaceApproximations
MCMC MarkovChainMonteCarlo
MSC MarineStewardshipCouncil
MSE MeanSquaredError
MSY MaximumSustainableYield
MUR MultiscaleUltrahighResolution
NAD83 NorthAmericanDatumof1983
NAFO NorthwestAtlanticFisheriesOrganization
Continuedonnextpage
ix
Continuedfrompreviouspage
Symbol Description
NASA NationalAeronauticsandSpaceAdministration
NOAA NationalOceanicandAtmosphericAdministration
RFMO RegionalFisheriesManagementOrganization
SPDE StochasticPartialDifferentialEquation
SST SeaSurfaceTemperature
UTM UniversalTransverseMercator
x