Taxonomy and classification Implications for avian identification
- 1. Taxonomy and classification: Implications for avian identification There are overone millionknownspeciesglobally,of whichapproximatelyjustover10,000 are birds (Reddingetal. 2015). Knowingthis, asystemof classification andidentification isessential forthe purpose of distinguishing phylogeneticlineagesandmorphologicalrelationshipscomparatively betweenorganisms. Withoutsuchasystem,identificationof anorganismwouldbe dependenton the observer’sdescriptionof itsfeatures,whilstunderstandingthe organism’srelationshiptoits surroundingcommunitywouldbe increasinglydifficultwhentryingtodifferentiate between organismswithsimilarmorphology.The taxonomicsystemprovidesastandardised phylogenetic pointof reference whenestablishingthe identityof anorganism. Currently,the moderntaxonomic systemisderivedfromthe “SystemaNaturae”developedbyCarl Linnaeusinthe 1700’s (Harris 2005). This systemoperatesonthe basisthatorganismclassificationoccursacrosslevelswhereby organismsare groupednotjust tospecieslevel,butalsoinaccordance to theirrelationtoother organismsacrossall levelsof life. The systemapproachesclassification basedon phylogenetic similaritiesandexternal morphologywithin apopulation.Morphologictraits whichdemonstrate relationshipsbetween individualtaxaare groupedintoa hierarchy fromspecies todomain(Harris 2005). Each identifiedspeciesisthenformallydescribedinascientificjournal andgivenaLatin binominal,withspecimentypesavailable forexaminationbypeers(ICZN 2000). ThoughLinnaeus’smethodsformthe foundationsof taxonomicmethodsusedtoday,fundamentally the basisof itscreationisflawed.Linnaeuslackedanyunderstandingof evolutionandnever acknowledgedthe findingsof Darwin(Ereshfsky2001).Thus manyof histaxonomicclassifications couldnot distinguishconvergentevolutionarytraits fromspeciesspecifictraits.The simple principle of groupingspeciesbasedonexternal morphology hasledtounnatural taxaclassification(Jensen 2009) whichinmanycases is merelyseparate speciesthatshare asimilarconvergent,morphological trait (Dornburger al. 2015). Consequently,due tothe identifiedfailingsof Linnaeus’shierarchy,a numberof alternative classificationmethods weredeveloped. In an attemptto resolve the issueof misidentifiedspecieswhichshare aphylogenetictrait,Willi HenningdevelopedCladisticsclassification in1979. The method operatesonthe principlesof classificationbasedoncommonancestryof an organism (Schmitt2003). Thismethodallowsfor clear,visual indicationinphylogeneticdivergence of anevolutionarytrait asdemonstratedby Noriegaetal. (2011) who successfullyreclassified Thegornismicrastur(asmall falconlikebird) based on theircommonancestral traitsof the falconidfamily.Howevercladisticidentificationisflawed whenpaleoenvironmentsare consideredforthis speciesashistoricmorphologylinksthisfalcontoa temporal forestenvironmentyetcurrentlyitispredominantinthe Antarctic. ThoughCladistics utilisesphylogenytoestablishanevolutionarytree relatingtraitsbetweenspecies,itfailsto considerenvironmental factorslimitingaspecies developmentbyonlyfocusingonone morphologic trait. Numerical taxonomywasestablishedbySneathandSokal in1973 as statistical ecology’spopularity grewand computertechnologybecame more advanced. Thismethodhopedtoeliminate observer biasand taxonomicerrorbyimplementing astatistical andsystematicapproachto identification. A numberof measurementswouldbe takenfromanorganismandmultivariate analysisperformedto groupindividualsonthe basisof archivedmeasurementsof matchingorganisms (Sneath&Sokal
- 2. 1973). This methodallowsforanyscientist,regardlessof taxonomictraining,toadequatelyidentify an organism.Though,ashighlightedbyBlackwelder(1967) knowingwhatcharactermeasurements to take is dependentonexperience of taxonomyandthusmeasurementscannotbe performedby statisticiansastheirknowledge of anorganism’senvironmentalrange andpotential environmental regulatorsonitsdevelopment,islimited. Astechnologycontinuedtoevolve, SibleyandAhlquist in 1986, developedthe firstmethodof identificationtouse DNA analysisasan indicatorof species. DNA-DNA hybridisation determinedspeciesclassificationbasedonthe meltingpointsof hybridDNA comprisedfromtwo separate dissociatedandrealignedbase pairstrandsfromtwoseparate organisms (Gibson1987). However,thismethodhasnotaddressedmeltingpointvariationbetween genomesandpossibleeffectsof “junkDNA”,consequentlymoderntechniqueshave since reversed some of the taxonomicclassificationsprovidedbythismethod. Asanexample Houde (1986) assessed variouslineagesof ratite birdsinconjunctionwithanalysisof fossilsrecordsand determinedthatancestorsof ostrichesshouldbe groupedwithNorthAmericanandEuropeanbirds. Thishas since beenproventoincorrect. To date,DNA sequencinghasbecome the dominantmethodof choice foridentification. DNA barcodingor Mitochondrial gene sequencing,utilisesa648 base pairfragmentlocatedinthe mitochondrial cytochrome coxidase subunitIgene asa geneticmarkerinall organisms (Herbertet al. 2003). Mitochondrial DNA isabundantthroughoutmanycells thuscaneasilybe extracted, itis alsoinheritedviathe maternal gamete sogeneticlineage istraceablethroughoutgenerations (Lefevre 2008).Identification isperformedonanorganismviaPCR analysis of theirmtDNA to establishthe codingsequence withintheirmitochondrialcytochrome coxidase subunitI(COI) sample. The sequence inwhichtheirbase pairsoccuris speciesspecificthusisused toidentifythe organismviacomparisonto archivesof knownspeciessequences inpublicdatabases. Species separationisdependantof howfarapart the evolutionarydivergenceoccurredbetweenthe two speciesbeingcompared andwhetherthe sampledgenesare paralogousororthologous.Thisisdue to levelsof functional andnon-functional sequencingchanginginaccordance to the sequences responsible fortraitexpression unique tothe species(Frazer etal. 2003). Molecularclockshave demonstratedthatmodern organismscontaincomplex sequence variationsof more primitive ancestors thusdependingon the pointof mutationorcreationof a paralogous/orthologousgene, the similaritiesbetweensequencedDNA intwoseparate specieswillbecome increasinglyless pronouncedwithincreaseddistance andtime betweensharedcommonancestors (Wiemer& Fiedler2007). Goncalves etal (2015) successfullyutilised DNA barcoding,inconjunctionwiththe GenBankdatabase, inthe identificationof Graydidascalusbrachyurus eggsconfiscatedfromthe illegal pettrade. Goncalves demonstrated the importance of thismethodinthe identificationof specieswhenmorphological traitsare unclearorunavailable,aswellashighlighting itsuse in identifyingothercrypticspecies (Burns etal.2007). Techniqueshave alsobeendevelopedtobetterunderstandthe originsof phylogenetictraits.One such technique utilisesmicrosatellites whichconsistsof arepetitive base pairsequence knownasa short tandemrepeat(STR).STRmarkerscan be usedto produce higherresolutionof anorganism’s allelicdiversityandphylogenybyperformingPCRanalysiswithprimersbyflankingthe repetitive sequence of the microsatellites.The numberof times asequence wasrepeatedwithina microsatellite locus,determinesthe size of the amplicons producedbythe PCR,whichinturnis measuredandthenassessedagainstrecordedco-dominantalleles(Guichoux etal. 2011). Allentoft et al (2009) were successfullyable use microsatellite 454 sequencing toidentifyanew setof genetic
- 3. markersfor an extinctspeciesof moa. The studyidentifiedthatmicrosatelliteloci notonly demonstratedallelicdiversitybetweenspecies,itcouldbe usedtotrace inheritedlineagesof an organism’smorphology. Due to the popularityof DNA (mtDNA) sequencingin identificationandthe belief of some thatDNA sequencingwill replace the morphological basedtaxonomy(Herbert etal. 2003), the appeal and continuedpractice of taxonomyasa skill;hasreducedsignificantlyinnumber. However,the use of molecularmethodssuchDNA barcodingasa replacementformoderntaxonomyisn’tnecessarilythe stepforwardinidentificationandclassification. ThoughDNA sequencinghasitsadvantages,for example whenassessingcloselyrelatedspecies,sequence divergenceif oftensignificantlylowerand thusdifferentiation of speciescanbe doesso more accurately(Herbert etal. 2004); DNA sequencing doeshave itsweaknesses. The understandingthatinterspecificvariationinthe COIgene exceedsthe variationseeninintraspecific(the barcode gap) isnot alwaystrue.Wiemers&Fiedler(2007) found that the utilisationof onlythe COIgene isinsufficientinsamplingtaxadue toincreasedsequence variationthe longeraspecieshasbeen establishedseparatelyfromitssharedancestor. Inaddition, our understandingof specificregionsof DNA isstill insufficientin the assessmentof itsexpression and impactson an organismsoverall genome (Moritz&Cicero2004). Consequently,inordertoyield anaccurate and detailedunderstanding of the levelsof biodiversity currentlyseenacrossthe globe due to rapidly decliningspeciespopulations andbiodiversity as anthropogenicimpactsbecome more widespread;the scientificworldneeds acombinationof both phylogenetic/morphologybased taxonomy andmolecularmethods.A socalled“integrative taxonomy”isrequiredtofurtheradvance the identificationandclassificationprocess (Will etal. 2005)(Burns et al. 2007)(Miller2007)
- 4. References Allaby,M.(2004). Oxford dictionary of Ecology.Oxford universitypress,London Allentofy,M.,Schuster,S.,Holdaway,R.,Hale,M.,Mclay, E.,Oskam, C., Gilbert,T.,Spencer,P., Willerslev,E.,Bunce,M.(2009). Identificationof microsatellitesfromanextinctmoaspeciesusing high-throughput(454) sequence data. Biotechniques, Vol 46:195-200 Blackwelder,R.(1967). A critique of numerical taxonomy. Systematiczoology,Vol 16: 64-72 Burns,J., Janzen,D.,Hajbabaei,M.,Hallwachs,W.,Herbert,P.(2007). DNA barcodesand cryptic speciesof skipperbutterfliesinthe genuspericharesinAreade ConservacionGuanacaste,Costa Rica. PNAS, Vol 105: 6350-6355 Dornburg,A.,Friedman,M.,Near,T. (2015). Phylogeneticanalysisof molecularandmorphological data highlightsuncertaintyinthe relationshipof fossilandlivingspeciesof Elopomorpha (Actinopterygii:Teleostei). Molecularphylogeneticsand evolution,Vol 89:205-218 Ereshefsky,M.(2001). The povertyof the Linnaean hierarchy.Cambridge universitypress,Cambridge Gibson,L. (1987). Do DNA distances reveal avianphylogeny?. Geosciencesresearch institute, Vol 14 : 47-76 Goncalves,P.,Oliveira-Marques,A.,Matsumoto,T.,Miyaki,C.(2015). DNA Barcodingidentifies illegal parrottrade. Journalof heredity, Vol 10: 560-564 Guichoux,E.,Lagache,L., Wagner,S., Chasumeil,P.,Leger,P.,Lepais,O.,Lepoittevin,C.,Malausa,T., Revardel,E.,Salin,F.,Petit,R.(2011) Currenttrendsinmicrosatellite genotyping. Molecularecology resources,Vol 11: 591-611 Harris,R. (2005). Attackson Taxonomy.Americanscientist, SigmaXi,NorthCarolina Herbert,P.,CywinskaA.,Ball,S.,Waard,J. (2003). Biological identificationsthroughDNA barcodes. The royalsociety, Vol 270: 313-321 Herbert,P.,Penton,E.,Burns,J.,Janzen,D.,Hallwachs.(2004). Ten speciesinone:DNA barcoding revealscrypticspeciesinthe neotropical skipperbutterflyAstraptesfulgerator. PNAS, vol 101: 14812-14817 Houde,P.(1986). Ostrichancestorsfoundinthe NorthernHemisphere suggestnew hypothesisof rartite origins. Nature, vol 324: 563-565 ICZN.(2000). Internationalcodeof zoologicalnomenclature. The international trustof Zoological nomenclature,London Jensen,R.(2009). Phenetics:revolution,reformornatural consequences?.Taxon,Vol 58:50-60 Lefevre,B. (2008). The nucleolusof the maternal gamete isessential forlife. Bioessays,Vol 7:613- 616 Miller,S.(2007). DNA barcoding andthe renaissance of taxonomy. PNAS, Vol104: 4775-4776
- 5. Moritz,C andCicero,C. (2004). DNA barcoding:Promise andpitfalls. PLoSBiology, Nol 2:279 - 354 Noriega,J.,Areta,J.,Vizcaino,S.,Bargo,M. (2011). Phylogenyandtaxonomyof the Patagonian Miocene falconThegornismusculosusameghino,1895 (Aves:Falconidae). Journalof paleontology, Vol 85 :1089-1104 Redding,D., Mooers,A.,Sekercioglu,C.,Collen,B.(2015). Global evolutionaryisolationmeasures can capture keylocal conservationspeciesinNearcticandNeotropical birdbommunites. PhilosophicaltransactionsB,Vol 370: 1-7 Schmitt,M. (2003). Willi Hennigandthe rise of cladistics. Internationalcongressof zoology, Vol18 : 369- 379 Sneath,Pand Sokal,R. (1973). Numerical taxonomy:Theprinciplesand practice of numerical classification. W.H Freemanandcompany,SanFrancisco Wiemers,Mand Fiedler,K.(2007).Does the DNA barcodinggap exist?A case studyinblue butterflies(Lepidoptera:Lycaenidae). Frontiersin zoology, Vol 4:1-16 Will,K.,Mishler,B.,Wheeler,Q.(2005). The perilsof DNA barcodingand the needforintegrative taxonomy. Systematicbiologists,Vol 54:844-851