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)

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