Distinct Yellown Tuna (Thunnus albacares) Stocks Detected in

Western and Central Pacic Ocean (WCPO) Using DNA

Microsatellites
RoselynD.Aguila

, SweedyKayL.Perez, BillyJoelN.Catacutan, GraceV.Lopez, NoelC.Barut,

MudjekeewisD.Santos
Published:September22,2015

http://dx.doi.org/10.1371/journal.pone.0138292

Correction
3Dec2015:AguilaRD,PerezSKL,CatacutanBJN,LopezGV,BarutNC,etal.(2015)Correction:DistinctYellowfinTuna
(Thunnusalbacares)StocksDetectedinWesternandCentralPacificOcean(WCPO)UsingDNAMicrosatellites.PLOSONE
10(12):e0144568.doi:10.1371/journal.pone.0144568|Viewcorrection

Abstract
Theyellowfintuna,Thunnusalbacares(Bonnaterre,1788),coversmajorityofthePhilippinestunacatch,oneofthemajorfisheries
commoditiesinthecountry.Duetoitshigheconomicimportancesustainablemanagementofthesetunashasbecomean
imperativemeasuretopreventstockdepletion.Currently,thePhilippineyellowfintunaisbelievedtobepartofasinglestockofthe
greaterWCPOthoughsomereportssuggestotherwise.Thisstudythereforeaimstoestablishthegeneticstockstructureofthe
saidspeciesinthePhilippinesascomparedtoBismarckSea,PapuaNewGuineausingnine(9)DNAmicrosatellitemarkers.
DNAmicrosatellitedatarevealedsignificantgeneticdifferentiationbetweenthePhilippineandBismarckSea,PapuaNewGuinea
yellowfintunasamples.(FST=0.034,P=0.016),whichisfurthersupportedbymultilocusdistancematrixtesting(PCoA)and
modelbasedclustering(STRUCTURE2.2).Withthesefindings,thisstudypositsthattheyellowfintunapopulationinthe
PhilippinesisaseparatestockfromtheBismarckSeapopulation.Thesefindingsaddevidencetothealternativehypothesisof
havingatleast2subpopulationsofyellowfintunaintheWCPOandcallsforadditionalscientificstudiesusingotherparametersto
investigatethis.Accuratepopulationinformationisnecessaryinformulatingamoreappropriatemanagementstrategyforthe
sustainabilityoftheyellowfintunanotonlyinthePhilippinesbutalsointheWCPO.
Citation:AguilaRD,PerezSKL,CatacutanBJN,LopezGV,BarutNC,SantosMD(2015)DistinctYellowfinTuna(Thunnus
albacares)StocksDetectedinWesternandCentralPacificOcean(WCPO)UsingDNAMicrosatellites.PLoSONE10(9):
e0138292.doi:10.1371/journal.pone.0138292
Editor:DirkSteinke,BiodiversityInsituteofOntarioUniversityofGuelph,CANADA
Received:April29,2014Accepted:August29,2015Published:September22,2015
Copyright:2015Aguilaetal.ThisisanopenaccessarticledistributedunderthetermsoftheCreativeCommons
AttributionLicense,whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthor
andsourcearecredited
DataAvailability:AllrelevantdataarewithinthepaperanditsSupportingInformationfiles.
Funding:TheDepartmentofScienceandTechnologyPhilippineCouncilforAgriculture,AquaticandNaturalResources
ResearchandDevelopmentgrantedfundingtoMDS,NCB,andGVLforthestudy.Thefundershadnoroleinthestudy
design,datacollectionandanalysis,decisiontopublish,orpreparationofthemanuscript.
Competinginterests:Theauthorshavedeclaredthatnocompetinginterestsexist.

Introduction
Globally,tunaproductionhasconstantlybeenanimportantsourceofannualtotalmarineproductionforcoastalcountries.Inthe
WesternandCentralPacificOcean(WCPO),tunaspecies,primarilyskipjack,yellowfinandbigeyetunas,havebeentheleading
sourceoffisherycatchandproduction.Thesethreespeciesalonecontributedanapproximate2.2millionmtintheregionsfishery
catchin2011,representing79%ofthetotalPacificOceancatch[1].InthePhilippines,ithascontributed30%ofthetotalannual
marineproductionand42%exportshareamountingtoUS$10million[2],makingitoneofthecountrysmajorfisheries
commodities[3].
SustainingtunaresourcesintheWCPOandinthePhilippinesisnotonlyimportanteconomicallybutmoresototheecosystem.
TheCoralTriangle,aregionconsideredtobetheglobalcenterofmarinebiodiversityandoneoftheworldstopprioritiesformarine
conservation,spanningeasternIndonesia,Malaysia,PapuaNewGuinea,TimorLesteandtheSolomonIslands,andthe
Philippines,hasbecomeapriorityformonitoringandconservation,especiallythemarineenvironment[4].Conservingthisregion
requiresthatthespeciesinitareadequatelysustainedtopreventimbalancesthatcouldresulttostockdepletion,whichcouldhave
devastatingeffectsonbothbiodiversityandfisheries.Thus,studiesthatcouldfurtheridentifybothpopulationconnectivityand
structuringareusefulinimprovingmanagementandconservingtheregionsmarineresources[5].
Thoughyellowfintunaisnot,asofyet,inanoverfishedstate,ithasbeenhugelyexploitedacrossthewesternequatorialPacific
thusalimitonitscatchatcurrentlevelshavebeenrecommended[6,7].AnymeaningfultunamanagementintheWCPOrequires
thatthetunapopulationstock(s)intheareabefullyidentifiedanddescribed.Identificationofexistingpopulationstructuresand
boundariesdelineatedbyagreeingphylogeographicdistributionpatternscanbeusedinestablishingfisheriesmanagementunitsas
wellasplansformarineprotectedareas[5].Yellowfintuna(YFT),Thunnusalbacares(Bonnaterre,1788),iswidelybelievedtobe
panmicticwithinandbetweenoceans.YFTpopulationbetweentheAtlanticandthePacificOceansshowlowlevelsofgenetic
differentiationindicatingaveryslowgeneticdriftduetothespecieslargepopulationsize[8].Similarly,YFTsintheWesternPacific
andinWesternIndianOceansshowednogeneticdifferentiationbasedonnonsignificantpairwiseFSTvaluesrevealingan
extensivegeneflowbetweentheseoceanbasins[9].BecauseYFTsareoceanicandarethereforehighlymigratory,theyare
believedtobeasinglestockinthewesternandcentralPacificregion[9,10].
Incontrast,otherreportssuggestthattherearedifferentYFTstockswithinthePacificOcean.Forexample,intheEasternPacific
region,thestockstructureoftheYFThasexhibitedlimitedmixingbetweenthenorthernandsouthernregionsusingtaggingand
nitrogenisotopeanalysis[11].IntheWesternPacificOcean,theYFTstockhasbeenfoundtohaveverylimitedheterogeneityusing
microsatellitemarkers,similarwiththeearlierfindingsusingallozymeandmitochondrialDNAmarkers[10].Moreover,YFTcatch
dataasearlyasthe1990sintheWCPOshowedaslowergrowthratealongthePhilippineandIndonesianwatersindicatinga
probablepopulationstructuring[6].

Here,wecomparedthepopulationoftheYFTcaughtinthePhilippinewaterstotheYFTpopulationcaughtinBismarckSea,Papua
NewGuineausingnine(9)DNAmicrosatellitelociasgeneticmarkers.YFTsinBismarckSeashowedsignificantgenetic
heterogeneityascomparedtothePhilippineYFTssuggestingaseparationinstocksofthetwoareasandtheexistenceofatleast
twostocksofYFTintheWCPO.

MaterialsandMethods
TissueSampling,DNAExtraction,andAmplification

Tissuesampleswereextractedfrom310YFTindividualscollectedinthecourseoftwoyearsfromMay2010toMay2012fromfour
tunalandingsitesselectedacrossthePhilippineshoresandasiteintheWCPOoutsidethePhilippines(Fig1)[12].Thesample
collectionsitesweremunicipalfishlandingsitesandnearbyfishmarketslocatedinSubic,ZambalesforWestPhilippineSea,
PuertoPrincesa,PalawanforSuluSea,EasternSamarforEastPhilippineSeaandGeneralSantosforCelebesSea.
RepresentativeYFTsampleswerecollectedintheBismarckSea,PapuaNewGuinea(41760S1491858E).ThePhilippine
sampleswerepersonallycollectedbytheauthors.TheBismarckSeatunasampleswerecollectedbyFilipinofishingboatcaptains
fromFrabelleFishingCorporationtrainedinmuscletissuecollectionandstorageimmediatelyafterthetunacatch.Nospecific
permitswererequiredduringsamplecollectionsincethesamplesareneitherendangerednorprotectedspeciesandthesamples
werecollectedfromfishingboatsandfishmarkets.Initialidentificationofthesampleswasbasedonthehandbookforidentifying
yellowfinandbigeyetunasinfreshcondition[13].

Fig1.MapofWesternandCentralPacificOcean(WCPO)showingyellowfintuna(Thunnusalbacares)collectionsites.

1Zambales2Palawan3EasternSamar4GeneralSantos5BismarckSea,PapuaNewGuinea.QuantumGIS
package[12]wasusedinthemaplayoutofWCPO.
http://dx.doi.org/10.1371/journal.pone.0138292.g001
MuscletissueswereextractedfromtheleftposteriorpartofthefreshorfrozenYFTsamplesofvarioussizesrangingfrom15to89
cminforklength(S1Table).Themuscleextractswerepreservedinabsoluteethanolandstoredat20C.DNAwasextractedusing
theCTABextractionprotocolwithmodifications[14,15].Ninemicrosatelliteloci(Obe231,Obe294,Obe652,Obe467,Obe157,
Obe674,Obe527,Obe237,Obe218,andObe236)isolatedfrombigeyetunawerecrossamplifiedusingtheprescribedprotocol
[16].PrimerpairsusedforPCRarelistedinTable1.Eachforwardprimerwaslabeledwitheither6FAMorHEXfluorescentdyeat
the5end.ThePCRcocktailmixconsistedof0.13mMdNTPs(KAPA),0.67Mforwardandreverseprimers(1stBASE),0.08U
standardTaqpolymerase(KAPA),and1lDNAtemplate.Themixwasaliquotedtoa12lreactionandwasrunusingthefollowing
PCRparameters:initialdenaturationat95Cfor2min30and35cyclesofamplificationwithdenaturationat94Cfor30s,
annealingat58Cfor30s,andextensionat72Cfor30sandafinalextensionat72Cfor2min.ResultingPCRproductswere
confirmedbyrunningthemingelelectrophoresisusing3%agarosegel.Fragmentlengthanalysisofthesampleswasoutsourced
toMacrogenInc.,Koreausingthe3730XLDNAanalyzer(AppliedBiosystems,USA)andBigDyeTerminatorv3.1Cycle
SequencingKit(AppliedBiosystems,USA)withsizestandards400HDand500LIZ.

Table1.Forwardandreverse5'3'primersequencesusedinPCRamplificationoftenDNAmicrosatellitemarkers[15].

http://dx.doi.org/10.1371/journal.pone.0138292.t001
GeneticAnalysis

Priortostatisticalanalyses,thesampleswereidentifiedasYFTsbyrunningphylogenetictrees(NeighborJoiningandmaximum
likelihoodusingtheTamuraNeimodelwithgammavalue=0.576)inMEGA5[17]usingpartialfragmentsequencesofthemtDNA
DloopcontrolregionagainsttheYFTsequences(GenBankaccessionnumbersJN988636.1JN988641.1)ofPedrosaGerasmio
etal.[18].Representativebigeyesequences(GenBankaccessionnumbersJN988645.1JN988649.1)fromthesamestudywere
includedasoutgroup(S1andS2Figs).CallingallelesobtainedfromfragmentanalysiswasdoneusingPeakScannersoftware
v1.0fromAppliedBiosystemsbyLifeTechnologies[19](S2Table).AllelesizefrequencieswerecomputedusingExcel
MicrosatelliteToolkitv.31[20].Geneticvariationinmicrosatellitelociinthefivepopulationswasanalyzedbydeterminingthe
numberofallelesperlocus(a),allelicrichness(Rs),observedheterozygosity(Ho),andexpectedheterozygosity(He)foreach
locusfromeachsiteusingGENEPOPv4[21].ThesameprogramwasalsousedtocheckfordeviationsfromtheHardyWeinberg
equilibrium(HWE)andlinkagedisequilibriumofeachlocuswithineachsite(exacttests[21]).TheestimatesofWrightsFSTto
evaluatesignificantgeneticvariationbetweenthepopulationsbeingobservedwerecalculatedusingARLEQUINv3.5.1.2[2225].
ThesignificanceofallstatisticalanalyseswasassessedusinganadjustedalphabythesequentialBonferroniprocedure[26].
PrincipalCoordinatesAnalysisofthemultilocusdataamongthefivesamplinglocationswascalculatedandgraphedusingGenAlex
6.5[27,28].AmodelbasedclusteringmethodforinferringpopulationstructureofyellowfintunawasimplementedinSTRUCTURE
2.2[29].Thesamplesweretestedwith10valuesofK(K=1toK=10)eachforteniterationsusingtheAdmixturemodelwith
inferredalphaandcorrelatedallelefrequenciesatsetlambda=1.ThemostsuitableKwasinferredusingtheEvannomethod[30]
employedintheprogramStructureHarvester[31].

Results
DNAMicrosatelliteVariation

Yellowfintunasamplesofsizesrangingfrom15to89cminforklength(S1Table)werecollectedfrompublicmarketsandmunicipal
landingsitesalongthefourmajorseaboardsofthePhilippinesandfromBismarckSea,PapuaNewGuineawiththecooperationof
FrabelleFishingCorporation,aPhilippinefleetfishinginthehighseas.Tenmicrosatellitelociwereanalyzedforsignificantvariation
amongtheyellowfintunasamples.TheselociweretestedfordeviationagainsttheHardyWeinbergEquilibrium(HWE)toavoidthe
useofnonneutrallocus.Oneofthesetenloci,Obe652,wasfoundtosignificantlydeviatefromHWE,thuswasnotusedintherest
oftheanalysis.Theallelicrichnessobservedfromeachsamplesiteusingtheseninelocirangesfromtwoto13alleles.Observed

heterozygositiesrangefrom0.182to0.867ascomparedtothesamplepopulationsexpectedheterozygositiesrangingfrom0.355
to0.861.BasicdescriptivestatisticsofeachlocusineachsamplesiteareshowninTable2.Allelefrequenciesofeachlocus
globallyandineachsamplesiteareshowninTablesAJofS1File.

Table2.DescriptivestatisticsofninemicrosatellitesinThunnusalbacares.

http://dx.doi.org/10.1371/journal.pone.0138292.t002
Hierarchicalvariationsusingdistancemethodbasedonthenumberofdifferentallelesforthewholepopulationarepresentedin
Table3.Nosignificantgeneticdifferentiationwasobservedinallhierarchies.ThesinglestockassumptionofthePhilippinesites
wasinferredfromthisdataalbeitinconclusivesincethesamplesweremostlyjuvenilecollectedfrommarketsandmunicipallanding
sitesanddonotaccountforadultsthatcouldbemigratingaroundthePhilippinewaters.TheYFTsampleswerethentreateda
prioriastwogroups,thepooledPhilippinesitesandtheBismarckSea,PapuaNewGuineasite.Significantgeneticdifferentiation
wasobservedbetweenthesetwogroupswithFST=0.034(P=0.016).ThisfindingbetweenthepooledPhilippinesamplesandthe
BismarckSeasamplesisconsideredmoderatevariationbasedonWrightsqualitativeguideline[32].

Table3.AnalysisofMolecularVariance(AMOVA)ofgeneticvariationofyellowfintunafromfivelocations.

http://dx.doi.org/10.1371/journal.pone.0138292.t003
Geneticdifferentiationestimateswerealsodeterminedbetweenpairsofsitesusingdistancemethodbasedonthenumberof
differentalleles.SamplesfromthePhilippinesiteswerecomparedtothosefromBismarckSea,PapuaNewGuineatoconfirm
whetherthesesitesexhibitstructuring,inanattempttosupportthevariationobservedbetweenthetwogroups.
Ontheotherhand,SignificantFSTswereobservedinBismarckSea,PapuaNewGuineawhenpairedtothefourPhilippinesites
withFSTrangingfrom0.2233to0.2582,exhibitingmoderatetogreatvariation(P=0.00000Table4).Amongthesignificant
pairwiseestimates,theZambalesBismarckSeapairpresentedthehighestdegreeofdifferentiationatFST=0.2382(P=0.00000).

Table4.PopulationpairwiseFSTs(lowerdiagonal)andPvalues(upperdiagonal)ofT.albacaresusingbetweenthefivelocations.

http://dx.doi.org/10.1371/journal.pone.0138292.t004
GeneticStructuring

DNAmicrosatellitevariationissupportedbytheseparationofthesamplesintotwodistinctgroupsasobservedinthePrincipal
CoordinatesAnalysis(PCoA)usingamultilocusdistancematrixasrepresentedinFig2.Eachcoloreddotrepresentsayellowfin
individualcollectedinacorrespondingsamplingsiteasindicatedbyitscorrespondingcolor.TheYFTsamplescollectedfrom
BismarckSea,PapuaNewGuinea(purpledots)formedadistinctgroupontherightaxisoftheplot,separatefromsamples
collectedinthePhilippinesites.ThissuggestsadistinctclusteringbetweentheYFTsamplescaughtinthePhilippinesitesand
BismarckSea,PapuaNewGuinea.

Fig2.PrincipalCoordinatesAnalysisofT.albacaresexhibitingtwoseparateclustersbasedondistrictmatrixusingnineDNAmicrosatellite
loci.

RedGeneralSantosGreenEasternSamarBlueZambalesYellowPalawanPurpleBismarckSea,PapuaNewGuinea.
http://dx.doi.org/10.1371/journal.pone.0138292.g002
FurthersupportonthedistinctclusteringofYFTwasobtaineduponusingthemodelbasedclusteringmethod,STRUCTURE,on
ourmultilocusgenotypedata.TenvaluesofK(S3Fig),with10iterationsforeachKvalue,weretestedasshowninFig3.Themost
suitablevalueofKwasassessedusingDeltaK,astatisticthatisbasedontherateofchangeinthelogprobabilityofdataina
seriesofKvalues[30].ThemostsuitablevalueofKisK=2(Fig4)andwasthususedininterpretingtheclusteringresultofthe
analysis.Thenumbersinthebarplot(Fig3,K=2)correspondstothesamplingsitefromwhichtheindividualswerecollected.All

fourplotsrepresentingPhilippinesites,14,weremarkedred,indicatingonestock.Meanwhile,theplotrepresentingtheBismarck
Seasamples,site5,wasmarkedgreen.ThisindicatesdifferenceinstructurecomparedtotheYFTsamplesfromthePhilippine
siteswhichweremarkedred.

Fig3.Barplotsofdifferentassumptionsofclusters,KinT.albacaresbasedonmultilocusdata.

PlotsforvaluesofK=1toK=10wereconstructedinSTRUCTURE2.2,with10replicaterunsforeachKvalue.Plotsforthe
mostsignificantKvalues,K=2toK=4,areshown.
http://dx.doi.org/10.1371/journal.pone.0138292.g003

Fig4.DeltaKandthemeanofestimatenaturallogprobabilityofSTRUCTURErunsofT.albacaressamplesusingvaluesofK=1toK=10.

http://dx.doi.org/10.1371/journal.pone.0138292.g004

Discussion
FisheriesconservationalmanagementhasbeenamainconcernforcoastalcountrieslikethePhilippinesinthepastfewdecades.
Strategieshavebeenimplementedovertheyearsinsustainingmarinestocksespeciallythecommerciallyimportantorganisms.
Technologieshavealsobeenenhancedinanefforttoaidincreatingandimprovingexistingmanagementstrategiesespeciallyin
thewidermarinesystems.Amongthesetechnologies,theadventofthemorestablegeneticmarkersininferringmarinesystem
connectivitieshasbeenoneofthegreatestbreakthroughsinpopulationstudies.Thoughnotanabsolutedecidingfactorin
delineatingsubpopulationsamongorganisms,identifyinganorganismsgeneticstockstructurehasbecomeakeyindetermining
otherequallyimportantfactorslikegeneflow,migrationanddispersalwithwhichastockmaybeconcretelydetermined.
Specifically,thesegeneticmarkerscanprovidehintsontheconnectivityofstocksofmarineorganismsthatcanbefurtherusedin
designingandredesigningsustainablemanagementstrategies[33].Studieshavebeenconductedovertheyearstolookintothe
stockstructureoftunas,oneofthemostimportantmarinestocks,inoceanbasinsworldwide,employingdifferentmethods
includingallozymes[34,35],restrictionfragmentlengthpolymorphism(RFLP)markers[8,36,37],mitochondrialDNAmarkers
[9,3840]andmicrosatellitemarkers[10,41].
AnalysesofmolecularvarianceusingsuitablegeneticdistancemethodswereconductedtoconfirmwhetherthePhilippinestockis
separatefromthewidelybelievedsingleWCPOstock.TherewasnosignificantdifferentiationobservedamongtheYFTsamples
fromthefourPhilippinesitesbasedonDNAmicrosatellitedataalbeitinconclusiveduetosamplinglimitations.Philippinewasthen
comparedtoBismarckSeaYFTswhichrepresentspartoftheWCPO.Moderategeneticdifferentiationwasobservedbetweenthe
twoareasbasedonbothgeneticdistancesandpairwisedifferences.Similarly,comparisonbetweentheBismarckSeaYFTsand
eachgroupofsamplesfromdifferentPhilippinesitesyieldedsignificantvariationbasedonbothgeneticdistancesandpairwise
differences.TheZambalesBismarckSeapair,whichhasthehighestdegreeofdifferentiationobserved,wasthemostsignificant
amongthepairwiseestimatesdueperhapstotheZambalesfishingsitewhichiswithintheWestPhilippineSeaandis
geographicallyseparatedfromthePacificOceanbythePhilippinearchipelago.Theseevidencesfurtherstrengthenthehypothesis
thatthePhilippinesmighthaveasinglestockthatisseparatefromthegreaterWesternandCentralPacificstock,contrarytothe
currentassumptionthattheregiononlyhasasinglestockofyellowfintuna.Tofurthersupportthisassumption,clusteringintotwo
YFTstockswereobservedinbothPCoAusingdistancematrixandmodelbasedclusteringmethod,STRUCTURE.Bothanalyses
clearlydelineatedthetwodistinctgroupsobservedinbothtestsforgeneticdistancesandpairwisedifferences.
HavingaPhilippinestockofyellowfintunaseparatefromtheWesternandCentralPacificispossiblebecauseofthepresenceof
biogeographicbarrierssuchaseddiesandupwellingsaswellasstrongoceancurrentsliketheNorthEquatorialCurrenton
Philippineborders.Jacksonetal.[42],suggestedthattheMindanaoeddiescouldactasbarrierstolarvaldispersalthatcausesto
maintaingeneticdivergenceamongpelagicfishstocksinthearea.Notsurprisinglytherefore,notmuchmovementwereobserved
intaggedPhilippinetunasgoingouttoadjacentareas[43].ThisrestrictionwasattributedtothePhilippinebathymetry,preventing
thetunastocrosstonearbyareas.Moreover,yellowfintunastockinthethenWCPOregion3inwhichthePhilippinesisincluded,
exhibitedbiologicaldifferences,i.e.havingslowergrowthrates,ascomparedtothetunastockoftherestoftheWCPO[6].Such
variabilityingrowthbetweenstocksmaybeindicativeoftheirdifferenceinadditiontogeneticvariation,ashavebeenobservedin
browntrout[44].
ArecentstudyonyellowfintunaalsoreportedapossibleadmixtureofTaiwanstocktothePhilippineSeastock,althoughonlyone
geographiclocationwassampled[45].Populationstructuringandconcordantbarriersinlarvaldispersalinneritictunaswerealso
observedwithintheIndonesianwatersascausedbyPleistocenevicariance[42].Otherstudiesinanothertunaspecies,the
skipjacktuna(Katsuwonuspelamis),alsosupportthisdivergenttunastocksscenario,astheyrevealedapossiblestockdelineation
intheWesternandCentralPacificOceanusingserumesterase&transferrinsystemallozymes[34,35].

Conclusion
TheanalysisoftheseYFTsamplesusingDNAmicrosatellitemarkersexhibitedmoderatevariationbetweenthepooledPhilippine
samplesandtheBismarckSeasamples.ThisstronglysuggeststheexistenceofadistinctYFTstockinthePhilippinesdifferent
fromtheYFTstockfoundintheBismarckSea,PapuaNewGuinea.

Tofurthersupportthefindingsofthisstudy,itisrecommendedthatfurtherstudiesshouldincludeadditionalsamplingsitesfrom
bothareasofPapuaNewGuineaandthePhilippinesandeventuallytherestoftheWesternandCentralPacificregion.Additionally,
larvalsamplingmaybeaddedasthesourceofgeneticmaterial.Otherparameterstotestthestockstructureoftheyellowfintunain
theWCPOcouldbeincludedsuchastheuseoflengthfrequencies,reproductivebiology,otolith,parasites,taggingetc.The
accuracyofsuchpopulationstructureapproachwillgreatlyhelpinassessingstockstatusanddeterminingthemostsuitable
managementstrategyfortheregionsyellowfintuna.

SupportingInformation
S1Fig.NeighborJoiningtreeofT.albacarespartialDloopfragmentsequencesusingTamuraNeimodel(gammavalue=0.576)with500bootstrap
replicationstoconfirmcorrectspeciesidentification.

Asubsample(n=73)wasanalyzedwiththeT.albacarespartialDloopfragmentsequencesofPedrosaGerasmioetal.(2012)to
confirmthecorrectspeciesidentificationofthesampledindividuals.Representativebigeyetunasequencesfromthesamestudy
wereusedasoutgroup.
doi:10.1371/journal.pone.0138292.s001
(TIF)
S2Fig.MaximumlikelihoodtreeofT.albacarespartialDloopfragmentsequencesusingTamuraNeimodel(gammavalue=0.576)with500
bootstrapreplicationstoconfirmcorrectspeciesidentification.

Asubsample(n=73)wasanalyzedwiththeT.albacarespartialDloopfragmentsequencesofPedrosaGerasmioetal.(2012)to
confirmthecorrectspeciesidentificationofthesampledindividuals.Representativebigeyetunasequencesfromthesamestudy
wereusedasoutgroup.
doi:10.1371/journal.pone.0138292.s002
(TIF)
S3Fig.Barplotsofdifferentassumptionsofclusters,KinT.albacaresbasedonmultilocusdata.

PlotsforvaluesofK=1toK=10wereconstructedinSTRUCTURE2.2,with10replicaterunsforeachKvalue.
doi:10.1371/journal.pone.0138292.s003
(TIF)
S1File.AllelesizefrequencytablesforallpopulationsofT.albacaresbylocus.

AllelesizefrequenciesofLocusObe218forallpopulationsofT.albacares(TableA).AllelesizefrequenciesofLocusObe236for
allpopulationsofT.albacares(TableB).AllelesizefrequenciesofLocusObe231forallpopulationsofT.albacares(TableC).
AllelesizefrequenciesofLocusObe294forallpopulationsofT.albacares(TableD).AllelesizefrequenciesofLocusObe652for
allpopulationsofT.albacares(TableE).AllelesizefrequenciesofLocusObe467forallpopulationsofT.albacares(TableF).
AllelesizefrequenciesofLocusObe157forallpopulationsofT.albacares(TableG).AllelesizefrequenciesofLocusObe674for
allpopulationsofT.albacares(TableH).AllelesizefrequenciesofLocusObe527forallpopulationsofT.albacares(TableI).Allele
sizefrequenciesofLocusObe237forallpopulationsofT.albacares(TableJ).
doi:10.1371/journal.pone.0138292.s004
(XLSX)
S1Table.SizesofT.albacaresindividuals.

Forklengthofeachsamplewasmeasuredincm(1.0).
doi:10.1371/journal.pone.0138292.s005
(XLSX)
S2Table.AllelesizesofT.albacaresindividualsperlocus.

AllelesizingwasdoneusingPeakScannersoftwarev1.0.Sampleswerecodedaccordingtotheirsamplinglocationsites:YFG
GeneralSantosYFSSamarYFZZambalesYFPPalawanYFBSBismarckSea,PapuaNewGuinea.
doi:10.1371/journal.pone.0138292.s006
(XLSX)

Acknowledgments
TheauthorswouldliketothankMs.MinervaFatimaeH.VentoleroandtheGeneticFingerprintingLaboratoryfortheirunending
support.WewouldalsoliketothankthestaffoftheregionalofficesoftheBureauofFisheriesandAquaticResourcesaswellas
thefishingboatcaptainsofFrabelleFishingCorporationintakingpart,assisting,and/orcoordinatingtheauthorstothefishlanding
sitesatthecourseofthesamplecollectionandGraceousVonYipinassistingtheauthorsinmaplayouts.Wewouldalsoliketo
extendourutmostgratitudetoMr.ReyC.Thomas,Jr.,Dr.EricCrandallandDr.DemianWilletteinprovidingvaluableinsightson
theanalysisofthisstudy.

AuthorContributions
Conceivedanddesignedtheexperiments:RDAMDSNCBSKLPGVL.Performedtheexperiments:RDASKLPBJNC.Analyzed
thedata:RDASKLPMDS.Contributedreagents/materials/analysistools:NCBMDSRDASKLPGVLBJNC.Wrotethepaper:RDA
MDSSKLPGVLNCB.

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