From faecesto foxes: using genetics to manage an invasive ... · From faecesto foxes: using...
Transcript of From faecesto foxes: using genetics to manage an invasive ... · From faecesto foxes: using...
Fromfaeces tofoxes:usinggeneticstomanageaninvasivepredatorforwildlifeconservation
AnnaJMacDonald,AaronAdamack,CatrionaDCampbell,EliseFDewar,BerndGruber,ElodieModave,Sumaiya Quasim &StephenDSarre
Photo DPIPWE Photo by Felicity Hatton
FoxeswereintroducedtoAustraliamid-late1800s
• Foxeswereintroducedfrom
Europe- sourcepopulation
uncertainbutthoughttobe
fromtheUK
• Likelyverysmallnumberof
foundersAustralianfoxdistributionin2007
FoxesinTasmania… uncertainty&debate…• 1864-1990s:historicalintroductions,littleevidenceforestablishedpopulation
• 1998:reportoffoxleavingashipinBurnie
• 1999:allegeddeliberateintroductionoffoxes
• 2001:foxprints,foxcarcass(shot)
• 2002:foxscatnearBurnie (IDfromhair),FoxFreeTasmaniataskforce
• 2003-2011:foxcarcasses,sightingreports,foxscats(DNA)…
WhatcangeneticstellusaboutfoxesinTasmania?
Hardevidenceoffoxpresence
2-stageDNAtest:1)PCRtodetectmammal/foxDNA2)SequencingtoconfirmfoxIDs
DetectionoffoxesinTasmaniafromscatDNA
MammalDNA
Fox-specificDNABerryetal. (2007)WildlifeResearch
devil e.quoll s.quoll fox
Sarre,etal (2013)JournalofAppliedEcology
2007-2012• >11,000scats• DNAfrom~80%ofscats• FoxDNAdetectedfrom61scats2014• >2,500scatstested• NofoxDNAdetected
Whatistheriskoffalse+ves using“thefoxtest”?
Gonçalves etal.(2014)ForensicSci.Int.Genet.
…
…
CTGGAAGGGCGTGGTAGTTTATA
AGACTGTGTCGATGACGAAAG
1)“Fox”primerswouldneedtoamplifynon-foxDNA
ThisdependsonprimerspecificityANDthestringencyofthePCRconditions
2)Non-foxDNAsequences wouldneedtobemistakenforfox
MammalDNA
Fox-specificDNABerryetal. (2007)WildlifeResearch
devil e.quoll s.quoll fox???
CannotdistinguishfoxDNAfromnon-specificamplificationusing
gelelectrophoresis
BUTwecanusingDNAsequences!
Blindtrialsincluded208non-foxscats:
• 9putativefoxresultsbasedonPCRtestalone
• 0confirmedfoxresultsbasedonPCR+DNAsequencing
• Nofalsepositivesobserved
149knownfoxscatsalsotested:
• 127scoredasfoxpositive
• 22falsenegatives,i.e.nofoxDNAdetected
How confident can we be in the fox test?
Ramseyetal (2015)JournalofAppliedEcology
How confident can we be in the fox test?
BioinformaticanalysisofspeciesassignmentusingDNAsequencesfrom74Australian(includingintroduced)vertebratespecies:
• Nonon-foxsequencesweremistakenlyassignedtofox=nofalsepositives
• Nogenuinefoxsequencesweremisidentified=nofalsenegatives
• ThissequencingtestcanreliablydistinguishfoxDNAinAustralia
MacDonald&Sarre(2015)JournalofAppliedEcology
• FoxDNAdetectedfrom61Tasmanianscatsfrommultiplelocations
• LimitationsofthisfoxDNAtestarerelativelywellunderstood
• Lowriskoffalsepositives
• Higherriskoffalsenegatives
What we can say from the fox DNA test:
What we can’t say from the fox DNA test:
• Howmanyindividuals?
• Relatedness?
• Sexoffoxes/sexratio?
• Originsoffoxes?
• Provenanceoffoxpositivesamples?We can use other genetic methods to tackle these questions
– but we need appropriate markers and reference data
What do we need to tackle these questions with DNA:population genetics?
• Howmanyindividuals?
• Relatedness
• Sexoffoxes/sexratio
• Originsoffoxes
Populationgeneticmarkersþ
Probabilityofidentity☐
Sex-specificmarkers☐
Populationdiagnosticmarkersý
Needgoodunderstandingofgeneticdiversity&allelefrequenciesofmainlandAustralianfoxpopulation
~
~
What do we need to tackle these questions with DNA:DNA metabarcoding of diet?
• Provenanceoffoxpositivesamples
GoodreferenceDNAdatabase☐Diagnosticgeneticmarkers☐SufficientDNA☐
Needgoodunderstandingofgeographicdistributionofgeneticdiversityineachpotentialpreyspecies
~~
~
MicrosatellitemarkersforindividualID:• 16scats&4carcassessuccessfullygenotyped• Eachhasauniquegenotype=atleast20individualfoxes
How many individual foxes?
• Remnantsofhistoricintroductions?– expectTasmanianfoxestobegeneticallydistinctfrommainlandAustralianfoxes
• Recentintroductionoflitter(s)?- expectTasmanianfoxestobesiblings/havesamemainlandorigin
• Multiplerecentintroductions?- expectTasmanianfoxestonotbecloselyrelated,havedifferentmainlandorigins
What are the origins of Tasmanian foxes?
• Australia-widemicrosat studywith>3000samples(OliverBerry,AaronAdamack)• Microsatellitesproviderelativelypoorresolutionoffoxpopulationstructurein
Australia,butcandistinguisheastfromwest
Tasmaniansamples(fromfoxcarcasses)areindistinguishablefromeasternmainlandAustralian
samples
RulesoutremnanthistoricTasmanianpopulation
Tasmanianfoxesarenotgeneticallydistinct
Basedon30microsatellitemarkers
Canweimproveresolutionusingnewmarkers?
Largernumberofgeneticmarkersmayprovidebetterresolution?160foxsamplesfromacrossAustraliaanalysed withDArTseq
110.0 119.0 128.0 137.0 146.0 155.0
-35
-30
-25
-20
goodinds$long
goodinds$lat
NewSouthWales
Queensland
SouthAustraliaVictoria
WesternAustralia
-5
0
5
-4 0 4PCoAAxis1(2%)
PCoA
Axis2
(1.2%)
SNPsalsoshowlittlegeographicstructureinAustralianfoxes=likelyinsufficientresolutiontoassignoriginsofTas foxes
Basedon5000SNPs
Tasmania
• Needcautionwhenconclusionsinfluencemanagement
• Problemswithincompletereferencedatabases:
• Problemswithpoorgeographiccoverage:
DNA diet analysis may help determine provenance
Conclusions1• Needtounderstandlimitsofdetectionandreal risksoffalsepositives/
negativestomakeeffectiveuseofDNAdetectioninwildlifemanagement.
• Implicationsoffalsepositives/negativeswillvarywithmanagementcontext.
• DNAmayextendourunderstandingofTasmanianfoxorigins– butweneedbetterunderstandingofgeneticdiversityinmainlandfoxpopulationstounderstandwhatispossible.
• DNAdietanalysishaspotentialtodetermineprovenanceofTasmanianscats– butweneedconcertedefforttobuildreferenceDNAdatabasesandIDdiagnosticmarkersforAustralian fauna.
Conclusions2
• Whateveryourinterpretationofrecentevidence,vigilanceisessentialtopreventfutureincursions/establishmentoffoxesinTasmania.
• ThereismuchwecanlearnfromthelastdecadeoffoxDNAdetectiontodevelopmoreeffectivegenetictoolsforbiosecurity&pestmanagement.
• RachelAnnetts• ValCaron• DianneGleeson• MaxPowell• Nur Iylani Ramlee• SamRyan• PiaSalgado• KristinStewardson• Kejun Wei• MattYoung• MikeBunce&theTrEnD LabteamatCurtin• AustralianNationalWildlifeCollection• QueenVictoriaMuseumandArtGallery• SouthAustralianMuseum• TasmanianMuseumandArtGallery• IlluminaMiSeqPilotProjectfunding&AGRF• DiversityArraysTechnologies
• CandidaBarclay• OliverBerry• PeterCremasco• CraigElliot• SimonFearn• StephenHarris• TomPriestley• DavidRamsey• InvasiveSpeciesBranchstaff• Scatsurveyvolunteers
Acknowledgements