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