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PopulationandDPSOriginofSubadultAtlanticSturgeonintheHudsonRiver

FinalReportSubmittedtotheWaterResourcesInstituteMay27,2016

IsaacWirginDepartmentofEnvironmentalMedicine

NYUSchoolofMedicine57OldForgeRoad

Tuxedo,NewYork10987

Voice:845-731-3548Fax:845-351-5472

Email:Isaac.wirgin@nyumc.org

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Abstract:Atonetime,AtlanticsturgeonsupportedasignaturefisheryintheHudsonRiverEstuaryandidentificationofitsmigratorypatternsislistedasapriorityunderLongRangeTarget1oftheActionsPlannedfor2010-2014(EffectivelyManagingMigratoryFish).ThisstudyprovidedimportantnewinformationthatwillbeusedbytheNYSDECandNOAA’sOfficeofProtectedResourcestomanageAtlanticsturgeonintheHudsonRiverecosystemandcoastwide.AtlanticsturgeonisfederallylistedundertheU.S.EndangeredSpeciesAct(ESA)asfiveDistinctPopulationSegments(DPS),ofwhichfourweredesignatedas“endangered”andoneas“threatened.”TheNewYorkBightDPSiscomprisedoftheHudsonandDelawareRiverpopulationsandislistedas“endangered.”SubadultAtlanticsturgeonareknowntoexittheirnatalestuariestocoastalwatersandnon-natalestuarieswheretheyarevulnerabletodistantanthropogenicthreats.Infact,duringthewarmermonths,theHudsonRiverhostslargenumbersofsubadults,buttheirpopulationandDPSoriginislargelyunknownalthoughSection7oftheESAdemandsthatoriginofindividualspecimensbedetermined.WeusedmicrosatelliteDNAanalysisat11lociandsequenceanalysisofthemitochondrialDNA(mtDNA)controlregiontodeterminetheDPSandpopulationoriginof106subadultAtlanticsturgeoncollectedinthelowertidalHudsonRiverestuary.Wefoundthat101ofthe106subadultsassignedtotheHudsonRiverwithatleast95%andusually100%probability.Ofthose5specimensthatdidnotassigntotheHudson,2assignedtotheJamesRiver,VA,2assignedtotheKennebecRiver,ME,and1assignedtotheSaintJohnRiver,NB.Thus,fourspecimensassignedtoDPSotherthantheNewYorkBightDPSandonetotheCanadianManagementUnit.ThisanalysiswillpermitthequantificationoftheeffectsofanthropogenicthreatsindifferentlocalesoracrossseasonsintheHudsonRiverEstuaryonindividualpopulationsorDPSofAtlanticsturgeonandwillserveasamodelforsimilarpopulationcompositionanalysisforotherestuariescoastwide.SummaryPointsofInterest

A. Greaterthan95%ofsubadultAtlanticsturgeonintheHudsonRiverareofHudsonRiverorigin.

B. However,theHudsonRiverishosttoanumberofsubadultAtlanticsturgeonthatwerespawnedinotherpopulationsandsometimesotherDistinctPopulationSegments.

C. TheHudsonRiverharborsthepopulationofAtlanticsturgeonwiththelargestEffectivePopulationSize(Ne)coastwide.

KeywordsMicrosatelliteDNAanalysis,mitochondrialDNAcontrolregion,IndividualBasedAssignmentTesting,MixedStockAnalysis,DistinctPopulationSegments

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Background:AtlanticsturgeonAcipenseroxyrinchusoxyrinchusistheposterchildfortheHudsonRiverestuarywithitsimageservingasthelogofortheHudsonRiverprominentlydisplayedonbridgescrossingthemain-stemriveranditsmajortributaries.Historically,AtlanticsturgeonsupportedoneofthethreesignaturefisherieswithintheHudsonRiverEstuary.SpawningpopulationsofAtlanticsturgeonextendfromtheSt.LawrenceRiver,Quebec,toatleasttheAltamahaRiver,Georgia.Historically,therewerecloseto30spawningpopulationscoastwide(ASSRT2007),butthatnumberhasdwindledinrecentyearsto15-20rivers(Wirginetal.2015b).Atlanticsturgeonareanadromousandtheirspawninglocationswithinnatalriversareabovethesaltfrontandusuallyovergravel,cobble,orboulderbottom.IntheHudsonRiver,theyareknowntospawnfromearlyJunetoearlyJulyindeepwaterinanareaextendingfromHydeParktoCatskill,NewYorkandperhapsevenfurtherupriver.Theireggsaredemersalandhatchwithin4-6dayspost-fertilization;theexactdurationistemperaturedependent.JuvenileAtlanticsturgeonareresidentwithintheirnatalriversfor2-6yearsbeforemigratingassubadultsintocoastalwaters.Theirdurationofriverresidencyispopulationdependentandisshorterinsoutherncomparedtonorthernrivers.SubadultAtlanticsturgeonarehighlymigratoryincoastalwaters,thedurationofmigrationcanbeprolonged,ispopulationdependent,andutilizesunknownmigratorycorridors.MatureadultAtlanticsturgeonreturntonatalriverstospawn,theirageatmaturityisonceagainhighlyvariableandpopulationdependent.Forexample,femalesinSouthCarolinaspawnat7-19years(Smithetal.1982),age15andolderintheHudsonRiver(Bain,1997),andat27-28yearsintheSt.LawrenceRiver(ScottandCrossman1973).Incomparison,malesspawnintheSuwaneeRiver,Florida,at7-9years(Huff1975),intheHudsonRiveratage12andolder(Bain1997),and16-24yearsintheSt.LawrenceRiver(Caronetal.2002).Postspawningadultsexittheirnatalestuaries,weekstomonthsafterspawning,andresumetheircoastalmovements.Theabsenceofadultsfromspawningriversformanyyearsandthedifficultyincollectingearlylife-stagesmakecensusingofpopulationsandevaluationoftemporaltrendsintheirabundancesproblematic.

Atvaryingtimes,manyriverscoastwide,includingtheHudsonandparticularlytheproximalDelaware,hostedlargefisheriesforAtlanticsturgeonprimarilytargetingcaviar-ladenfemales.Manyofthesefisheriescrashed,includingthatintheHudson,inthelate1890s,tolevelsthatwerelessthan10%oftheirhistoricalhighs.Asfisheriesinnorthernandmid-Atlanticriversdeclined,thefisheriesshiftedtomoresouthernrivers,particularlyinSouthCarolinaandGeorgia,butthesetoosufferedasimilarfateasthoseintheHudsonandDelaware.By1998afederalcoastwide40-yearharvestmoratoriumwasimposedonthefisheries.Thiswasfollowedin2012byU.S.federallistingofthespeciesundertheEndangeredSpeciesAct(ESA)asfiveDistinctPopulationSegments(DPS)ofwhichfour(NewYorkBight,ChesapeakeBay,Carolinas,andSouthAtlantic)weredesignatedas“Endangered”andthefifth(GulfofMaine)as“Threatened”(FederalRegister2012ab)Asaresult,federalmanagementofthespeciesunderESAisonaDPSbasis,ratherthanasasinglecoastwideentity.However,becausetheabundanceoftheindividualspawningpopulationsisbelievedtovarybyatleastanorderofmagnitude,itisalsoimportanttoconsiderthevulnerabilitiesofindividualpopulationstothevarietyofanthropogenicstressorsidentifiedinthelistingdocument.Forexample,theHudsonRiverpopulationisconsideredtobethelargestcoastwideandtheDelawareRiverpopulationoneofthesmallest.Thus,theDelaware

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RiverpopulationisconsideredtobemorevulnerabletoextinctionfromanthropogenicstressorsthantheHudsonRiverpopulationdespitebothoftheirlistingswithintheNewYorkBightDPS.

Asmentionedpreviously,subadultAtlanticsturgeonfromallspawningpopulationsmigrateintocoastalwatersforextendeddurations.Besidescoastalwaters,itisknownthatsubadultsmigrateseasonallyintonon-natalestuariessuchasLongIslandSound,theConnecticutRiver(Waldmanetal.2013),andtheinnerMinasBasinoftheBayofFundy(Wirginetal.2012).ThesemayincludeestuariesthatdonotsupportspawningsuchastheConnecticutRiver-LongIslandSoundandestuariesthatdosupportcontemporaryspawningsuchasDelawareBayandChesapeakeBay.Conversely,subadultsspawnedinestuariesotherthantheHudsonarebelievedtoseasonallymoveintothelowerHudsonRiverEstuary.Becauseoftheirhighlymigratorybehavioroutsideoftheirnatalestuaries,specimensfrommultiplepopulationsandDPSarelikelytoco-aggregateincoastalwaters(Wirginetal.2015ab)orotherestuariesdistantfromtheriverinwhichtheywerespawned(Waldmanetal.2013).

ItissometimesimportanttodeterminetheDPSandpopulationoriginofindividualspecimensinthesemixedcoastalandestuarineaggregationsbecauseoftheirvulnerabilitiestoanthropogenicstressorsatlocalesdistantfromtheirnatalestuaries.Forexample,ithasbeendocumentedthatbycatchofAtlanticsturgeonincoastalfisheriestargetedtootherspeciesmaybeanimportantcontributortothedeclineofsomemorevulnerablepopulationsortheirfailuretorebuild(Wirginetal.2015b).Similarly,vesselstrikemortalitiesofAtlanticsturgeonhavebeenshowntofrequentlyoccurintheDelawareRiver(BrownandMurphy2010)andJamesRiver(Balazik2012)andhavebeenproposedtobeasignificantfactorinthedeclineofthosepopulations.MigratorysubadultAtlanticsturgeonmayalsobevulnerabletoavarietyofanthropogenicstressorsintheHudsonRiver,includingexposuretotoxicchemicalssuchasPCBsandaperceivedrecentincreasedfrequencyofvesselstrikemortalities.Thus,thereisaneedtoidentifytheoriginofindividualsturgeonspecimenstoquantifythevulnerabilitiesofindividualpopulationsandDPStostressorsatlocalesdistantfromtheirnatalestuaries.

Becausetheyarehighlymigratoryoutsideoftheirnatalestuaries,determinationoftheabundanceofsubadultsandadultsofindividualpopulationsandDPSandtrackingtheirmovementsincoastalwatersandnon-natalestuariesisproblematic.GeneticanalysishasproventobeaneffectivetooltoidentifythepopulationandDPSoriginofindividualAtlanticsturgeonandtheirmixedaggregations.Briefly,thegenotypesoffishofunknownoriginarecomparedtothoseinreferencecollectionsfromknownspawningpopulations.Theoriginofindividualspecimensofunknownancestryisthenassignedtothereferencecollectionwhosegenotypesbestmatchthoseoftheunknownindividualsortheiraggregations.Inpractice,thishasinvolvedusingmicrosatelliteDNAanalysisat11independentlociandsequenceanalysisofthemitochondrialDNA(mtDNA)controlregiontocharacterizespawningadultsandpre-migratoryjuvenilesfromreferencespawningpopulations(Wirginetal.2012;Waldmanetal.2013;Wirginetal.2015ab).Collectionsofspecimensofunknownoriginarethencharacterizedatthesame11microsatellitelociandmtDNAsequenceandcomparedtothoseinthereferencecollections.Usinganapproachtermed,IndividualBasedAssignment(IBA)testing,thepopulationandDPSoriginofeachindividualspecimeninamixedaggregationcanbeassignedwithdeterminedprobabilitiesofaccuracy.Asecondapproach,MixedStockAnalysis(MSA),canbeusedtodeterminetheproportionof

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individualsinamixedaggregationthatassigntoeachreferencepopulationandDPS.Inthisandpaststudies,wehavegeneticallycharacterized1,3497individualsfrom11referencespawningpopulationsofAtlanticsturgeonatthese11microsatellitelociandthemtDNAcontrolregion.ThisreferencedataallowsustodeterminetheoriginofsubadultAtlanticsturgeonofunknownorigininthecurrentstudy.

Ourobjectivesinthisstudyasdescribedinourproposalwereseveralfold:

1- Estimatetheoverallproportionofnon-natalsubadultAtlanticsturgeonwithinthelowertidalHudsonRiverestuaryseasonallyandidentifytheirpopulationandDPSoforigin.

2- Definetheoverallspatialboundariesoftheincursionofnon-natalsubadultAtlanticsturgeonwithinthetidalHudsonRiverestuaryandtheirminimumandmaximumlengthrange.

Althoughnotidentifiedintheoriginalproposal,wealsofeltthatitwasprudenttoaddresstwoadditionalobjectiveswiththisdata

1- IncreasethenumberofsamplesinourreferenceHudsonRivercollectionbyaddingadditionalyearsofjuvenileandadultcollections.

2- Identifyeffectivepopulationsize(Ne)ofHudsonRiverAtlanticsturgeonbasedon3yearsofjuvenilecollections.

Methods

Samplecollections

Intotal,wewereabletosecure106subadultjuvenilesamplesfromtheHudsonRiverthatwerecollectedbetweenearlyJuneandmid-November.Wetargetedspecimensthatwere>600mmtotallength(TL)and<1300mm(TL).Specimenswerecollectedbetween2009and2014,withthevastmajoritybeingcollectedin2014.Additionally,almostallofthesampleswerecollectedbyNormandeauAssociatesbygillnetswithasmallernumbercomingfromtrawling.AllsamplesweredepositedbyNormandeauinthetissuerepositoryhousedbytheNationalOceanServiceinCharleston,SC.Unfortunately,anumberofsamplesthatNormandeaurecordsshowedweredepositedwiththeNOSrepositorywereneverlocateddecreasingthenumberofsamplesthatcouldbeanalyzedinthisstudy.Also,duringthistime(2015),thetissuerepositorywasmovedfromCharleston,SCtotheUSGSfacilityinLeetown,WVwhichexacerbatedtheproblem.Additionally,111specimenswereanalyzedfromthreeyear-classesofjuvenileHudsonRiverspecimens(<500mmTL)(2011(n=30),2013(n=35),2014(n=46))tobolsterourHudsonRiverreferencecollectionsamplesize.Thiswouldprovideuswithmoreconfidenceinourassignmenttestingandmixedstockanalysis.ThesereferencesampleswereobtainedfromtheNYSDECspringtimecollectionsfromtheHaverstrawBay,NYarea.DNAIsolations

FinclipswerethesourceofDNAfromallsamplesanalyzedinthisstudy.Finclipswerewashedwithphosphate-bufferedsaline,andincubatedincetyltrimethylammoniumbromide(C-Tab)buffer(Saghai-Maroofetal.1984)anddigestedat65oCwithproteinaseK(RocheDiagnostics,Indianapolis,IN).DNAs

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werepurifiedbyphenol-chloroformextractions,alcoholprecipitated,airdriedandresuspendedinTEbuffer.ConcentrationsandpuritiesofDNAswereevaluatedusingaNanodropND-1000Spectrophotometer(NanoDropTechnologies,Wilmington,DE).DNAconcentrationswereadjustedto50ng/µlforstandardizationofsubsequentanalyses.MitochondrialDNAControlRegionSequenceAnalysisA560basepair(bp)portionofthemtDNAcontrolregionwasamplifiedwithderivedAtlanticSturgeon-specificprimersS1(5'-ACATTAAACTATTCTCTGGC-3')andG1(5'-GAATGATATACTGTTCTACC-3')(Ongetal.1996).Thesameprimerswereusedtosequenceaportionofthe560bpamplicon.Wereportheredataononly205bpoftheamplicontoallowforcomparisonofhaplotypesinsubadultHudsonRiverspecimenstopreviouslycharacterizedreferencecollectionsfromotherrivers(Wirginetal.2000;Wirginetal.2007;Petersonetal.2008;Grunwaldetal.2008;Frittsetal.2016).Polymerasechainreactions(PCRs)werein50µlvolumesthatcontained50ngoftemplateDNA,5µlof10xRocheAppliedScience(Indianapolis,IN)reactionbuffer,0.25µlofeachdNTP(25mMstocks)(GEHealthcare,Piscataway,NJ),0.07µlofS1primer(0.1µMstock),0.05µlofG1primer(0.1µMstock)(IntegratedDNATechnologies,Coralville,IA),1unitofTaqDNAPolymerase(RocheAppliedScience)and

43.9µlofH20.Amplificationconditionswere94oCfor5minfollowedby40cyclesat94oCfor45s,56o

Cfor45s,72oCfor60s,followedbyafinalextensionat72oCfor10mininMJResearchPTC-100TMthermalcyclers.AmpliconswerepurifiedwithQIAquickPCRPurificationkits(Qiagen,Valencia,CA).

PurifiedPCRproductswereDye-TerminatorCycleSequencedasrecommendedinGenomeLabMethodsDevelopmentkitsbythemanufacturer(BeckmanCoulter,Inc.,Fullerton,CA).Sequencingconditionswere30cyclesat96oCfor20s,50oCfor20s,and60oCfor240s.SequencingproductswereEtOHprecipitated,re-suspendedin40µlofBeckmanCoulterCEQSampleLoadingBuffer,loadedintoaBeckmanCoulterCEQTM8000automatedcapillary-basedDNAsequencer,runusingthestandardlongfastreadmethod(LFR-1),andanalyzedwiththeSequenceAnalysisModuleoftheCEQTM8000GeneticAnalysisSystem.

MicrosatelliteAnalysisElevenmicrosatellitelociwerescoredthatwerepreviouslyshowntobeeffectiveindistinguishingreferencespecimensfromspawningpopulations(Kingetal.2001;Wirginetal.2015ab).TheselociincludedLS19,LS39,LS54,LS68(Mayetal.1997),Aox23,AoxD45(Kingetal.2001),andAox44,AoxD165,AoxD170,AoxD188,AoxD24(Henderson-ArzapaloandKing2002).MicrosatellitegenotypesweredeterminedusingtheBeckmanCoultersequencer.IndividualPCRreactionsweremulti-pooled,dilutedupto1:3withSampleLoadingSolution(BeckmanCoulter),0.5-2.0μlofreactionswereloadedonto96wellplatesalongwith0.5μlofCEQDNASizeStandard-400and40µlofSampleLoadingSolution(BeckmanCoulter),andrunwiththeFRAG1program(BeckmanCoulter).

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StatisticalAnalysesMicrosatellitedatawasinitiallyexaminedusingMicroChecker(VanOosterhoutetal.2004)toidentifythepresenceofnullalleles,scoringerrors,and/orlargealleledrop-out.Individual-basedassignment(IBA)testsandmixed-stockanalysis(MSA)wereusedtoestimatetheDPSandpopulationoriginofAtlanticSturgeoninourcollectionofHudsonRiversubadultsusingtheONCORprogram(Kalinowskietal.2008).ONCORusedgeneticdatatoestimatethepopulationoforiginofindividualsbyperformingdataanalysisandsimulationsformixtureanalysisandassignmenttests.Inmixtureanalysis,areferencebaselinegeneticdatasetwasusedtoestimatethepopulationcompositionofamixedcollectionusingconditionalmaximumlikelihoodtoestimatemixtureproportions.Individual-basedassignmenttests,usingmulti-locuslikelihoodfunctions,wereusedtoassignindividualsinamixedcollectiontothereferencecollectionthatwouldhavethehighestprobabilityofproducingthegivengenotypeinthemixedcollection.ONCORusedthemethodsofRannalaandMountain(1997)toestimatetheprobability.ItshouldbenotedthatouranalysisofacombinationofdiploidandhaploidmtDNAdataviolatesanassumptionofthisMonteCarloresamplingmethod.Weestimatedmixtureproportionswith95%confidencelimitsbasedon10,000bootstraps.ResultswerereportedforeachpopulationinthereferencebaselinecollectionaswellasforeachDPS.Additionally,leave-one-out-testswereperformedinONCORtoevaluatehowwellindividualspecimenscouldbeassignedtotheDPSorpopulationfromwhichtheywerecollected.Inthistest,eachindividualineachreferencecollectionwassequentiallyremovedfromthebaselineanditsoriginestimatedusingtherestofthatreferencecollection.ThistestprovidesaquantitativemeasureoftheaccuracyofassignmentstoeachreferenceorDPScollection.NeEstimator(Doetal.2014)wasusedtoestimateeffectivepopulationsize(Ne)usingasingle-samplemethod—abias-correctedversionofthemethodbasedonlinkagedisequilibrium(WaplesandDo,2010).ResultsIntotal,wewereabletoobtain106samplesfromtheNOSandUSGStissuerepositoryforouranalysis.Meantotallengthofthespecimenswas990.6mm(range595to1720mm).CollectionsitesintheHudsonRiverrangedfromRiverMile(RM)7toRM77withthevastmajorityofthespecimensbeingtakenbetweenRM48andRM49.Collectiondatesrangedbetweenmid-Juneandmid-Novemberwiththevastmajorityofspecimenstakeninmid-Juneandearlytomid-September.Similarly,most(73%)ofthespecimenswerecollectedin2014,butsomedatedbacktoasearlyas2009.WeweresuccessfulinusingacombinationofmicrosatelliteDNAandmtDNAcontrolregionsequenceanalysestoaccuratelyassignDPSandpopulationorigintoallofthespecimensusingtheONCORprogramwithourreferencedataset.Ourreferencecollectionsusedtomaketheseassignmentsconsistedof1,347specimensfrom11spawningpopulationscoastwide(Table1).AsindicatedinTable2,ourassignmentaccuracyusingleave-one-outtestswasveryhightothefiveindividualDPS(andCanadianpopulations)andlesssototheindividualpopulations(Table3).Forexample,wewere92.1%accurateinassignmentsattheDPSlevelandourmeanaccuracyinassignmentsatthepopulationlevel

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was85.8%.Specifically,wewere90.3%accurateinassigningHudsonRivercollectedspecimensbacktotheHudsonwiththevastmajorityofthemisassignmentsgoingtotheDelawareRiver(6.5%)UsingMixedStockAnalysisinONCOR,weinitiallydeterminedtheproportionsofspecimensfromthe11referencecollectionscontributingtoourcollectionofsubadultsofunknownoriginfromtheHudsonRiver(Table4).Asexpected,thevastmajorityofspecimenswerecontributedbytheHudsonRiver(95%)withsmallerproportionsnotedfromtheKennebecRiver(2%),JamesRiver(1.8%),andSaintJohnRiver(<1%).Giventheassignmentaccuraciesdescribedabove,wefeltconfidentinusingthesereferencecollectionstoassignourjuvenileHudsonRivercollectiontoindividualDPSandspawningpopulations.Intotal,101(95.3%)specimensassignedtotheHudsonRiver,inmostcaseswith100%probability(seeAppendixfordataoneachindividualspecimen).However,9ofthe101HudsonRiver-assignedspecimensdidsowithlessthan100%probability,butinallcasesthesespecimenswereassignedtotheHudsonwith>95%probability.FivespecimensassignedtospawningpopulationsotherthantheHudson.Theseincluded2specimensthatassignedtotheJamesRiver,VA,2specimensthatassignedtotheKennebecRiver,ME,and1specimenthatassignedtotheSaintJohnRiver,NB,Canada.Ofthese5non-Hudsonassignedspecimens,onlyoneoftheJamesRiverspecimenassignedwith100%probabilitywiththeother4specimens’assignmentprobabilitiesrangingbetween82.7%to94.8%.Surprisingly,these5specimensassignedtopopulationsinotherthantheNewYorkBightDPS,with2assigningtotheChesapeakeBayDPS,2assigningtotheGulfofMaineDPS,andoneassigningtotheCanadianmanagementunit.GiventhenewreferencecollectiondatafromthreeyearscollectionofHudsonRiverjuvenilesgeneratedforthisstudy,wecalculatedeffectivepopulationsize(Ne)estimatesfortheHudsonRiverandcomparedthesetoourotherreferencecollectionscoastwide(Table5).Notsurprisingly,wefoundthattheHudsonRiverhadthelargestNecoastwide(217.4;95%CI156.8-337)followedbytheAltamahaRiver,GA(138.7;95%CI103.5-201),andtheSavannahRiver,SC-GA(138.1;95%CI109.3-182.7).Also,theDelawareRiver,thesecondpopulationintheNewYorkBightDPS,hadoneofthesmallestNe(41.6;95%CI36.6-47.5).DiscussionSubadultAtlanticsturgeonareknowntomigrateintocoastalwaters(Wirginetal.2015ab)andsubsequentlyintonon-natalestuaries,someofwhichhostnaturalreproductionandotherswhichdonot(Waldmanetal.2013).Duringtheseseasonalforays,subadultsmaybeexposedtoavarietyofanthropogenicstressorsinthesenon-natalestuarieswhichmayacutelyjeopardizetheirsurvivalorcausesublethaleffects.EstuarinestressorsthatwereidentifiedintheU.S.federallistingdocuments(FederalRegister2012ab)includedvesselstrikes,bycatch,dredging,chemicalpollution,compromisedwaterquality,andotherenvironmentalperturbations.ManyofthesestressorstosturgeonsareknowntooccurregularlyinthetidalHudsonRiverestuary.BecauseAtlanticsturgeonarefederallylistedandmanagedas5DPS,itisimportantforProtectedResourcesmanagerstoevaluateandquantifythepotentialeffectsofthesestressorsonrepresentativesoftheindividualDPSandperhapspopulationsthatmayhavemigratedtonon-natalestuaries(Damon-Randalletal.2013).However,therewasan

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absenceofempiricalquantitativedatatoaddresstheDPSandpopulationoriginofsubadultAtlanticsturgeoninanynon-natalestuary.Therefore,thisstudywasdesignedtofillthisvoidanddeterminetheDPSandpopulationoriginofsubadultsinthetidalHudsonRiverestuary.OuroverallhypothesisinthisprojectwasthatallsubadultAtlanticsturgeonintheHudsonRiverseasonallywerespawnedintheHudsonRiver.WetestedthishypothesisusingtwoDNAapproaches,microsatelliteandmtDNAanalyses,thatplayedamajorroleintheinitialdelineationofthe5DPSandintheirsubsequentmanagementbyNOAA(FederalRegister2012ab).Thisstudywasdesignedtooptimizethelikelihoodofdetectingnon-natalspecimensintheHudsonRiverbyfocusingouranalysison;1)subadultsthatrangedinsizefrom600to1300mmTL,2)specimensthatwerecollectedinsummerandfallafterthecompletionofspawning,and3)weresampledinthelowerriverwheresubadultsfromelsewhereweremostlikelytoaggregate.Although,thesewereourgoals,theywerenotmetasstringentlyaswewouldhavehoped.Thatisbecauseouranalysiswasrestrictedtospecimensthathadbeenpreviouslycollectedinprogramsdesignedforotherobjectives.Thus,wefeelthatmayhaveunderestimatedtheproportionofnon-natalsubadultsthatseasonallymigrateintotheHudsonRiver.OurmajorfindingwasthattheHudsonRiverestuarydoesseasonallyhostsubadultAtlanticsturgeonthatwerespawnedelsewhere.Infact,approximately5%ofoursubadultspecimenswerespawnedinotherpopulations-inallcasesnotevenwithintheNewYorkBightDPS.OfthefivespecimensnotspawnedintheHudsonRiver,2assignedtotheChesapeakeBayDPS(JamesRiver,VA),2assignedtotheGulfofMaineDPS(KennebecRiver,ME),andoneassignedtotheSaintJohnRiverwithintheCanadianmanagementunit.Thus,migrationsofsubadultsfromotherDPSandpopulationsmaysubjectthemtoanumberofstressorsthatarecommonintheHudsonRiverandmaynotbeencounteredintheirnatalrivers.WefeelthatourassignmentsofthesesubadultstootherthantheNewYorkBightDPSisaccurategiventheresultsofourleave-one-outtests.Thesetestsdemonstratedthatacrossallreferencecollectionscoastwide,ourmeanassignmentaccuracytothe5DPSwas92.1%withveryfewmisassignmentsofHudsonRiverspecimenstotheGulfofMaineorChesapeakeBayDPS.Forexample,only2.2%ofHudsonRivercollectedreferencespecimensmisassignedtotheGulfofMaineDPS.Oneadditionaloutgrowthofourstudywasourabilitytoestimateeffectivepopulationsize(Ne)ofAtlanticsturgeonfromtheHudsonRiveraswellasotherpopulationscoastwide.AlthoughtheratioofNetocensussizeforAtlanticsturgeonisunknown,itcanprovidearelativemeasureofthesizesofindividualpopulationsandoveralltrendsintheirabundances.Notsurprisingly,NeoftheHudsonRiverpopulationwasbyfarthelargestcoastwide,farexceedingthatoftheDelawareRiver,thesecondpopulationintheNewYorkBightDPS.OurNeresultsareconsistentwiththoughtsexpressedinthemostrecentAtlanticsturgeonreview(ASSRT2007)inwhichtheHudsonRiverpopulationwasviewedasthemostrobustcoastwide.However,forthefirsttimeweprovideaquantitativecomparativeindexofthesizeofAtlanticsturgeonpopulationscoastwide.PolicyImplications

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OurresultswillinformNOAAmanagersfortheirSection7consultationstoevaluatethelikelihoodofproposedprojectstonegativelyimpactAtlanticsturgeonfromeachofthe5DPS.Priortoourstudy,therewasanabsenceofempiricalquantitativedataonthemovementsofsubadultAtlanticsturgeontonon-natalestuariesandthelikelihoodoftheirencounteringstressorsthere.OurestimatesofNealsoprovidedresourcemanagerswiththefirstrelativemeasuresofpopulationabundanceforeachofthesespawningpopulationscoastwide,includingtheHudsonRiver.OutreachCommentsResultsfromthisstudywererecentlypresentedbyDr.WirginonMay17,2016,toUSGSandNOAAOfficeofProtectedResourcesManagersattheAtlanticandShortnoseSturgeonResearchandManagement:Past,Present,andFutureworkshopinLeetown,WestVirginia.Thetitleofhistalkwas:UseofIndividualBasedAssignmentTestsintheCoastwideManagementofAtlanticSturgeonbyWirgin,I.,D.Fox,T.Savoy,andM.Stokesbury.Dr.WirginalsoplanstodiscusshisresultsandtheirimplicationsforsturgeonmanagementlocallywithAmandaHiggs,RobertAdams,andGregKinneyoftheNYSDECHudsonRiverFisheriesUnitattheirNewPaltz,NYoffice.Asusual,Dr.WirginintendstopublishtheseresultsinapeerreviewedjournalaspartofalargermanuscriptontheuseofDNAanalysisinthemanagementofAtlanticsturgeon.StudentTrainingMs.MelissaDellaTorre,aspring2016graduateoftheMSprogramintheDepartmentoftheEnvironmentalMedicineoftheNYUSchoolofMedicine,participatedinconductingresearchforthisproject.Init,shewastrainedinDNAisolations,PCR,mtDNAsequencing,microsatelliteDNAanalysis,andstatisticalanalysisofpopulationgeneticsdata.ShepresentedaposteronherstudiesofAtlanticandshortnosesturgeonbiologyatNewYorkMarineSciencesConsortiumannualmeeting(Oct,2015)atwhichshewasawardedaprizeforbestgraduatestudentposter.

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Table1

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Table2

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Table3

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Table4MixedstockanalysisofreferencepopulationproportionsofsubadultAtlanticsturgeonintheHudsonRiverPopulationEstimates % 95%Confidence

IntervalsSt.Lawrence 0.000 (0.000,0.013)SaintJohn 0.008 (0.000,0.030)Kennebec 0.020 (0.000,0.075)Hudson 0.954 (0.880,0.991)Delaware 0.000 (0.000,0.025)James 0.018 (0.000,0.047)Albemarle 0.000 (0.000,0.020)Edisto 0.000 (0.000,0.000)Savannah 0.000 (0.000,0.019)Ogeechee 0.000 (0.000,0.000)Altamaha 0.000 (0.000,0.000)

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Table5

Ne estimatesbasedon2or3years(exceptKennebec)ofcollectionscombinedusingthelinkagedisequilibriummethod

Population Ne 95%CI Rank

SaintJohn* 51.5 46.6-57.1 6Kennebec 53.0 40.5-73.2 4Hudson* 217.4 156.8-337 1Delaware 41.6 36.6-47.5 8James 45.5 41.1-50.5 7Albemarle* 21.2 19.1-23.6 10Edisto 52.8 45.1-62.4 5Savannah 138.1 109.3-182.7 3Ogeechee 34 29.7-39.1 9Altamaha 138.7 103.5-201 2

*basedonthreeyearsofcollections

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ReferencesAtlanticSturgeonStatusReviewTeam(ASSRT).2007.StatusreviewofAtlanticsturgeon(Acipenseroxyrinchus

oxyrinchus).ReporttoNationalMarineFisheriesService,NortheastRegionalOffice.February23,2007.Bain,M.B.1997.AtlanticandshortnosesturgeonsoftheHudsonRiver:commonanddivergentlifehistory

attributes.EnvironmentalBiologyofFishes48:347-358.Balazik,M.T.,G.C.Garman,J.P.VanEenennaam,J.Mohler,andL.C.WoodsIII.2012.Empiricalevidenceoffall

spawningbyAtlanticsturgeonintheJamesRiver,Virginia.141:1465-1471.Caron,F..,D.Hatin,andR.Fortin.2002.BiologicalcharacteristicsofadultAtlanticsturgeon(Acipenseroxyrinchus)

intheSt.LawrenceRiverestuaryandtheeffectivenessofmanagementrules.JournalofAppliedIchthyology18:580-585.

Brown,J.J.,andG.W.Murphy.2010.Atlanticsturgeonvessel-strikemortalitiesintheDelawareEstuary.Fisheries35:72-83.

Damon-Randall,K.,M.Colligan,andJ.Crocker.2013.CompositionofAtlanticsturgeoninrivers,estuaries,andinmarinewaters.WhitepaperpreparedbyProtectedResourcesDivisionofNOAA,Gloucester,MA.https://www.google.com/search?q=kim+damon+randall+composition+analysis+atlantic+sturgeon&ie=utf-8&oe=utf-8&aq=t&rls=org.mozilla:en-US:official&client=firefox-a

Do,C.,R.S.Waples,D.Peel,G.M.Macbeth,B.J.Tillett,andJ.R.Ovenden.2014.NeEstimatorV2:re-implementationofsoftwarefortheestimationofcontemporaryeffectivepopulationsize(Ne)fromgeneticdata.MolecularEcologyResources14:209-241.

Dovel,W.L.,andT.J.Berggren.1983.AtlanticsturgeonoftheHudsonEstuary,NewYork.NewYorkStateFishandGameJournal30:140-172.

FederalRegister.2012a.Endangeredandthreatenedwildlifeandplants;threatenedandendangeredstatusfordistinctpopulationsegmentsofAtlanticsturgeonintheNortheastregion.77:5880-5912,February6,2012.

FederalRegister.2012b.Endangeredandthreatenedwildlifeandplants;threatenedandendangeredstatusfortwodistinctpopulationsegmentsofAtlanticsturgeonAcipenseroxyrinchusoxyrinchusinthesoutheast.77:5914-5984,February6,2012.

Fritts,M.W.,C.Grunwald,I.Wirgin,T.L.King,andD.L.Peterson.2016.StatusandgeneticcharacterofAtlanticSturgeonintheSatillaRiver,Georgia.TransactionsoftheAmericanFisheriesSociety(InPress).

Grunwald,C.,L.Maceda,J.Waldman,J.Stabile,andI.Wirgin.2008.ConservationofAtlanticsturgeonAcipenseroxyrinchusoxyrinchus:delineationofstockstructureanddistinctpopulationsegments.ConservationGenetics8:1566-1572.

Henderson-Arzapalo,A,andT.L.King.2002.NovelmicrosatellitemarkersforAtlanticsturgeonpopulationdelineationandbroodstockmanagement.MolecularEcologyNotes2:437-439.

Huff,J.A.1975.LifehistoryofGulfofMexicosturgeon,Acipenseroxyrhynchusdesotoi,inSuwaneeRiver,Florida.FloridaMarineResearchPublication16.

Kalinowski,S.T.,K.R.Manlove,andM.L.Taper.2008.ONCOR:Softwareforgeneticstockidentification.Availableat:http://www.montana.edu/kalinowski/Software.htm.

KingT.L.,B.A.Lubinski,A.P.Spidle.2001.MicrosatelliteDNAvariationinAtlanticsturgeon(Acipenseroxyrinchusoxyrinchus)andcross-speciesamplificationintheAcipenseridae.ConservationGenetics2:103-119.

May,B.,C.C.Krueger,andH.L.Kincaid.1997.Geneticvariationatmicrosatellitelociinsturgeon:primersequencehomologyinAcipenserandScaphirhynchus.CanadianJournalofFisheriesandAquaticSciences54:1542-1547.

Peterson,D.L.,P.Schueller,D.Fleming,andI.Wirgin.2008..PopulationdynamicsandcriticalhabitatsofAtlanticsturgeonintheAltamahaRiver.Trans.Am.Fish.Soc.137:393-401.

Rannala,B.andJ.L.Mountain,J.L.1997.Detectingimmigrationbyusingmultilocusgenotypes.Proceedings

17

NationalAcademyofSciencesUSA94:9197-9221.Saghai-Maroof,M.A.,K.M.Soliman,R.A.Jorgensen,andR.W.Allard.1984.RibosomalDNAspacer-length

polymorphismsinbarley:Mendelianinheritance,chromosomallocation,andpopulationdynamics.ProceedingsNationalAcademyofSciences,USA81:8014-8018.

Scott,W.B.andE.J.Crossman.1973.FreshwaterfishesofCanada.FisheriesResearchBoardCanadaBulletin184,966pp.

Stabile, J., J.R. Waldman, J. Hart, and I. Wirgin. 1996. Stock structure and homing fidelity in Gulf of Mexicosturgeon(Acipenseroxyrinchusdesotoi)basedonrestrictionfragmentlengthpolymorphismandsequenceanalysisofmitochondrialDNA.Genetics144:767-775.

vanOosterhout,C.,W.F.Hutchinson,andD.M.P.Wills.2004.Micro-Checker:softwareforidentifyingandcorrectinggenotypingerrorsinmicrosatellitesdata.MolecularEcologyNotes4:535-538.

Waldman,J.R.,T.King,T.Savoy,L.Maceda,C.Grunwald,andI.Wirgin.2013.StockoriginsofsubadultandadultAtlantic sturgeon,Acipenseroxyrinchus, inanon-natalestuary, Long IslandSound. EstuariesandCoasts36:257-267.

Waples,R.S.andC.Do. 2010. LinkagedisequilbriumestimatesofcontemporaryNeusinghighlyvariablegeneticmarkers: a largely untapped resource for applied conservation andevolution. EvolutionaryApplications3:244-262.

Wirgin,I.,C.Grunwald,J.Stabile,andJ.Waldman.2007.GeneticevidenceforrelictAtlanticsturgeonstocksalongthemid-AtlanticcoastoftheUnitedStates.N.Am.J.Fish.Manage.27:1214-1229.

Wirgin,I.,L.Maceda,J.R.Waldman,S.Wehrell,M.Dadswell,andT.King.2012.StockoriginofmigratoryAtlanticsturgeonintheMinasBasin,InnerBayofFundy,Canada,determinedbymicrosatelliteandmitochondrialDNAanalyses.TransactionsoftheAmericanFisheriesSociety141:1389-1398.

Wirgin,I.,J.R.Waldman,J.Rosko,R.Gross,M.R.Collins,S.G.Rogers,andJ.Stabile.2000.GeneticstructureofAtlanticsturgeonpopulationsbasedonmitochondrialDNAcontrolregionsequences.TransactionsoftheAmericanFisheriesSociety129:476-486.

Wirgin,I.,M.W.Breece,D.A.Fox,L.Maceda,K.W.Wark,andT.King.2015a.OriginofAtlanticsturgeonAcipenseroxyrinchusoxyrinchuscollectedofftheDelawareCoastduringspringmonths.NorthAmericanJournalofFisheriesManagement35:20-30.

Wirgin,I.,L.Maceda,C.Grunwald,andT.King.2015b.PopulationoriginofAtlanticsturgeonbycaughtinU.S.Atlanticcoastfisheries.JournalofFishBiology85:1251-1270.