DNA Barcoding

DNAbarcoding:anewdiagnostictoolforrapidspeciesrecognition,identification,anddiscoveryJamesHankenMuseumofComparativeZoologyHarvardUniversity,USAWhatisDNAbarcoding?•Definition:DerivationofashortDNAsequence(s)thatenablesspeciesidentificationorrecognitioninaparticulardomainoflife(eucaryotes).•Focustodate—inanimals—hasbeenona658base-pair(bp)fragmentofthemitochondrialgene,cytochromeoxidasesubunitI(COI).•TheBarcodeofLifeInitiative(BOLI)wouldresolvebarcodesfornamedspeciesanduseabarcodingapproachtoassessundescribedbiologicaldiversity.•Verycontroversial!Whatisn’tDNAbarcoding?•Itisnotintendedto,inanyway,supplantorinvalidateexistingtaxonomicpractice.•ItisnotDNA-taxonomy;itdoesnotequatespeciesidentity,formallyorinformally,withaparticularDNAsequence.•Itisnotintendedtoduplicateorcompetewitheffortstoresolvedeepphylogeny,e.g.,AssemblingtheTreeofLife(ATOL).“theroleofanymoleculardiagnosticistoaidresearch,nottoserveasanendinitself.Barcoding…isindependentofquestionsastowhetherindividualtaxaarespecies,whatspeciesare(orshouldbe),andwheretheyfitinaunifiedtreeoflife….Barcodingisnotanendinitself,butwillboosttherateofdiscovery.TheuniquecontributionofDNAbarcodingto…taxonomyandsystematicsisacompressedtimelinefortheexplorationandanalysisofbiodiversity.”Potentialapplications1)Facilitatingidentificationandrecognitionofnamed(described)species:•linkinglifehistorystages,genders;•differentiatingcrypticspecies;•identifyinggutcontents;•humandiseasevectors;•agriculturalpests;•biosecurity(?).2)Surveyingandinventoryingbiodiversity;e.g.,flaggingpotentiallynew(undescribed)species.Differentiatingcrypticspecies•Astraptesfulgerator,skipperbutterfly.•Wide-ranging;southernU.S.tonorthernArgentina.•InnorthwesternCostaRica,comprisescomplexof10sympatricspeciesthataredistinctinDNAsequence(COI),larvalcoloration,foodplants,andsubtlemorphologicaltraits.D.Janzen,etal.,submittedSympatriclarvaeofAstraptesfulgeratorFoodplant:CeltisiguanaeaFoodplant:Trigonia(2species);larvaewillstarveifrearedonplantsusedbyotherlarvaltypes.Strengths•Offersalternativetaxonomicidentificationtoolforsituationsinwhichmorphologyisinconclusive.•Focusononeorasmallnumberofgenesprovidesgreaterefficiencyofeffort.•CostofDNAsequencingisdroppingrapidlyduetotechnicaladvances.•Potentialcapacityforhighthroughputandprocessinglargenumbersofsamples.•Oncereferencedatabaseisestablished,canbeappliedbynon-specialist.Weaknesses•Assumesintraspecificvariationisnegligible,oratleastlowerthaninterspecificvalues.•Nosinglegenewillworkforalltaxa(e.g.,COIisnotappropriateforvascularplants,orevenforsomeanimals).•Single-geneapproachislessprecisethanusingmultiplegenes;mayintroduceunacceptableerror.•Someofthemostattractiveaspectsrelyonfuturetechnology,e.g.,handheldsequencer.00.20.40.60.81.0248163264%Proportionofspeciespairs00.20.40.60.81.0248163264%n=13,320n=17Annelida,Arthropoda,Chordata,Mollusca,Echinodermata,Nematoda,PlatyhelminthesCnidaria(corals,anemones,jellyfish,seapens,etc.)Between-speciessequencedivergenceinCOI(%)COIsequencedivergenceamongNorthAmericanbirdsK2P(%)SequencedataBarcodingmustadheretostandardsforspecimenanddatamanagementVoucherspecimensandelectronicdatabasesDigitalimagesPilotprojects2)Possibletargets:•“Alltaxa”—primates,turtles,mosquitoes,tephritidfruitflies,birds,sphinxmoths,salamanders,etc.•Regionalfaunas,e.g.,GulfofMainemegafauna.•Existinginventories,e.g.,INBioandACG(CostaRica).1)Goalsandobjectives:•Validatebarcodingapproach,ingeneral,andtheuseofCOI,inparticular(foranimals);i.e.,proofofprinciple.•Assessfeasibilityoflarge-scaleeffort,e.g.,identifybottlenecks,cost,logisticissues.3)Wouldrelyprincipallyonmuseumspecimens.•Barcodingmustvalidateexistingtaxonomybeforeitcanbeofferedasanidentificationtool,andespeciallybeforeitcanbeusedtodiscovernewspecies.•Pilotprojectswillutilizemuseumspecimens.•Newinventoryeffortswillyieldlargenumbersofvouchers,whichmustbeproperlyaccessioned,databased,andstored.•Resultswillflagmanynewspeciesrequiringformaldescription.•Additionalburdenonmuseums,herbaria,etc.,butmayalsooffernewsourcesofsupport.Roleofmuseums(andimpact)DNAbarcodingisunderway…SeealsoNature426:514(4Dec2003)andappealstothebiotechsectorAnticipatednextsteps(2004)•January:WorkinggroupsubmitsagrantproposaltofoundacoordinatingSecretariattodevelopaBarcodeofLifeInitiative(BOLI)basedinWashington,DC;decisionexpectedlateMarch.•May:FoundingmeetingoftheBOLIConsortium(museumsandherbaria)atU.S.SmithsonianInstitution(NMNH).•Latefall:FirstInternationalBarcodeofLifeConference;venueTBD.