Numerical Taxonomy & Biometrics.pdf

This PPT wants to explore the road of numerical taxonomy and its potential in Cladestics & Phenetics in Plant taxonomy.

1. PLANT TAXONOMY
NUMERICAL TAXONOMY &
BIOMETRICS

2. WELCOME TO THIS DOMAIN
Biometrics,NumericalTaxonomy and
Cladistics,Characters;Variations;OTUs,
CharacterWeightingandCoding;Cluster
Analysis;Phenograms,Cladograms–ABird’s
eyeViewoftheissue
APresentationBy
Dr.N.Sannigrahi,AssociateProfessor,
DepartmentofBotany,
NistariniCollege,Purulia,
D.B.Road,Purulia(W.B)India723101

3. BIOMETRICS
Increasingly,quantitativeapproachestoplantmorphologyare
changingthelandscapeofresearchforplantecology,physiology,and
evolution.Advancesinmicroscopy,imaging,andcomputational
analysespotentiallyallowmoredetailedinvestigationsthanhave
previouslybeenpossible.Thishasincreasedthevarietyandquantity
ofdataavailableforphenotypicanalysis,andisstimulatingnew
directionsandapplicationsinthestudyofplantmorphology.The
increasedspeedanddetailthatcanbecapturedbythesenew
technologiesalsomeansthattheinformationrepresentedbyshape
andformcanpotentiallybeasrichabioinformaticsdatasourceas
geneticdata.Theobjectofthescienceistobringtogetherplant
morphologists,systematists,andpaleobotanists,alongsidecomputer
scientists,appliedmathematicians,andinformaticians,whowere
unitedintheirinterestindevelopingorapplyingnovelbiometricor
bio-informaticsmethodstotheformandfunctionofplants.
Biometricsthusanapproachtopaylightontheunitcharacterswhich
likelytobetwostatesthatcannotbesubdividedlogically.

4. BIOMETRICS
Verificationsystemseitherrejectoracceptthesubmittedclaimofidentity
bycomparingitwiththepre-storedbiometricsofthesameindividual
whileidentificationsystemsrecognizeanindividualbysearchingthe
matchingqueriedbiometricintheentiredatabase.Biometricidentification
isapatternrecognitionbasedclassificationsystemthatrecognizesan
individualbydeterminingitsauthenticityusingaspecificphysiologicalor
behavioralcharacteristic.Biometricauthenticationsystemsgenerallyusea
patternrecognitionapproachthatverifiesoridentifiesanindividual’s
authenticityofitsuniquelyidentifiablephysiologicalorbehavioral
characteristic,whichiscalledabiometric.
Therearetwomethodsusedtoestablishingtherelationshipsbetweenthe
organisms-Pheneticmethod&PhylogeneticorCladisticsmethod.
PHENETIC-Hereoverallsimilarityoftaxabasedontheoverall
similarityoftaxaregardlesswhethertheirsimilaritiesare
symplesiomorphies(Sharedprimitivecharacters)orSynapomorphies(
sharedderivedcharacters)inapohylogeneticsense.
CLADISTIC-Strictlyphylogeneticandonlysynapomorphiesareusedto
assessthephylogeneticrelationshipwhilesharedsymplesiomorphieshave
nouse.AphylogenetictreeorCladogramisdevelopedandtheapproachis
calledCladistics.

5. NUMERICAL TAXONOMY
Numericaltaxonomyortaximetrics,nowadaysfrequentlyandperhaps
moreappropriatelyreferredtoasphenetics,referstotheapplicationof
variousmathematicalprocedurestonumericallyencodedcharacter
statedatafororganismsunderstudy.
Thus,itistheanalysisofvarioustypesoftaxonomicdataby
mathematicalorcomputerizedmethodsandnumericalevaluationof
thesimilaritiesoraffinitiesbetweentaxonomicunits,whicharethen
arrangedintotaxaonthebasisoftheiraffinities.
AccordingtoHeywoodthenumericaltaxonomymaybedefinedasthe
numericalevaluationofthesimilaritybetweengroupsoforganisms
andtheorderingofthesegroupsintohigherrankingtaxaonthebasis
ofthesesimilarities.
Numericaltaxonomyinvolvestwoaspects-
i.Constructionoftaxonomicgroupsbyinvolvingthelargernumberof
charactersandtheresemblanceonthebasisofclusteranalysis,
Ii.Discriminationofthetaxonomicgroupstoshowtheoverlappingof
charactersandthediscriminationisusedtoselectthem.

6. WHAT IS NUMERICAL TAXONOMY?
Theperiodfrom1957to1961sawthedevelopmentoffirstmethodsand
oftheoryofnumericaltaxonomy.Plantsasweallknowareclassified
basedontheircharacters.ItwasMichelAdanson,aFrenchbotanist,who
forthefirsttimeputforwardaplanforassigningnumericalvaluestothe
similaritybetweenorganismsandproposedthatequalweightageshould
begiventoallthecharacterswhileclassifyingplants.
Heusedasmanycharactersaspossiblefortheclassification,andsuch
classificationscametobeknownasAdansonianclassifications.
Numericaltaxonomywashoweverlargelydevelopedandpopularizedby
SneathandSokal.
TheapplicationofAdansonianprinciplesanduseofmodernmethodsand
electronicdata-processingtechniques,havehelpedintheevolutionof
severalnewclassificationsofplantsduringthepastfewdecades.
Phylogeneticconclusionscanbedrawnfromthetaxonomicstructureofa
groupandfromcharactercorrelationsassumingsomeevolutionary
mechanismsandpathways.
Thescienceoftaxonomyisviewedandpracticedasanempiricalscience

7. PRINCIPLES OF NUMERICAL TAXONOMY
PRINCIPLES:
i.Themoretheselectionofcharacters,themoretheclarity&authentic
theclassification,
ii.EveryCharactersshouldbegivenequalweightage,
iii.Theentireclassificationbasicallyshouldbedoneontheirbasisof
pheneticapproach.
(a)ConstructionofTaxonomicGroups:
i.Anysample,item,individualisselectedtoanalyzeOUTwhichisthe
basicunitofNumericalTaxonomy
ii.Innumericaltaxonomy,first,individualsareselectedandtheir
charactersspottedout.Thereisnolimitationtothenumberofcharacters
tobeconsidered.However,thelargerthenumberofcharacters,betteris
theapproachforgeneralizationofthetaxa.
ii.Theresemblancesamongtheindividualsarethenestablishedonthe
basisofcharacteranalysis,whichcanoftenbeworkedoutwiththehelp
ofcomputers,theaccuracyofwhichdependsontheappropriatenessin
character.Thebestwaytodelimitatetaxais,toutilizemaximumnumber
ofcharacters,withsimilarweightagegiventoallofthem.

8. PRINCIPLES OF NUMERICAL TAXONOMY
(b)DiscriminationoftheTaxonomicGroups:
Whenthetaxonomicgroupschosenforthestudyshowoverlappingof
characters,discriminationshouldbeusedtoselectthem.
Discriminationanalysiscanbedonebyvarioustechniques,specially
devisedforsuchpurposes.Numericaltaxonomyisthus,basedon
certainprinciples,alsocalledneoAdansonianprinciples.
Principles of numerical taxonomy have been enumerated by
Sneath and Sokal:
(i) The greater the content of information in the taxa, and more the
characters taken into consideration, the better a given classification
system will be.
(ii) Every character should be given equal weightage in creating new
taxa.
(iii) The overall similarity between any two entities is a function of
the individual similarities in each of the many characters, which are
considered for comparison.

9. PRINCIPLES OF NUMERICAL TAXONOMY
(iv)Correlationofcharactersdifferinthegroupsoforganismsunder
study.Thusdistincttaxacanberecognized.
(v)Phylogeneticconclusionscanbedrawnfromthetaxonomicstructure
ofagroupandfromcharactercorrelations,assumingsomeevolutionary
mechanismsandpathways.
(vi)Thescienceoftaxonomyisviewedandpracticedasanempirical
science.
(vii)Pheneticsimilarityisthebaseofclassifications.
SLECTIONOFCHARACTERS:
Theunitcharactersmaybetwoormorestatesdependinguponthenature
ofthecharacterstakenintoaccountsuccessiveweightageshouldbe
employedforhomoplasywhichartebasicallyuniqueinallrespect.
A.BinaryCharacters:Thischaractersbasicallydenoteonlytwostates-
presentorabsentdenotedby+/-or1/0,ifmissingdenotedwithNC
B.MultistateCharacters:Moredifferentstatesofcharactersareexplored
eitherqualitativeorquantitative.Itisdenotedwith0,1,2,3,4,5,6,7etc.
Forexamplecoloroftheflowertobedenotedbydifferentassigned
valuesforeachcolor.

10. PRINCIPLES OF NUMERICAL TAXONOMY
RULES:
Therearenumberofrulesarefollowedinthisregardasstatedbelow.
i.Thecharactersmusttobechosenalmostallpartsoftheorganism
irrespectiveoftheoccurrence,
Ii.Notlessthan50charactersaretobeconsideredinthisanalysis,
Thecharactersmustcomprisealmostallthestagesofthelifecycleof
theplants,
Attentiontobegiveninalltherespectswithspecialreferenceto
morphology,physiology,ecologyetc.
CHARACTERS WEIGHTING:
1.Equalweightage–Allthecharactersshouldbegivenequalweightage
asthenumericaltaxonomydeservesequalimportanceofallthe
measurableunits,
Ii.SuccessiveWeightage-Homoplasycharacterswhichareuniquein
realsenselikethorns,spinesetcshouldbegivenmoreweightagefor
consideration

11. CLUSTER ANALYSIS
Itisastatisticaltoolinwhichmoresimilarelementsareplacedinone
groupratherdifferentfromobjectsbelongingtoothergroupsusedfor
theexploratorydataanalysis.Here,mostlycomputerdrivensoftware
sortouttheOTUsaccordingtotheiroverallsimilarityandproducesa
phenogram,akindofdendogramwhichshowsthetaxonomic
relationshipbetweenthetwoorganisms.
Itcanbedonebytwocategoriesmethods-
A.Hierarchicalclusteranalysismethod-twotypes.Agglomerativeand
divisivemethod.Intheagglomerativemethod,allobjectsstartin
separateclusterstillslowlythesimilarobjectsarecombinedandthe
optimumnumberischosenfromamongalloptions.
Indivisivemethod,allobjectsstartinthesameclusteranditisreverse
ofagglomerativemethod
B.Non-hierarchicalclusteranalysismethod.

12. CLUSTERING METHODS
Clusteringcanbedonebytwomethods-
Monolethicsystem-thissystememploystheattributesoneatatime.
Thismethodleadstotheartificialclustering.
Consideringalltheirattributessimultaneously,thismethodgivesa
naturalgrouping.Oneclustergroupisseparatedfromtheotherby
dividinglinewhichindicatesadistinctgapbetweenthetwo.
PheneticClusteringmethods:
Itismostlypheneticapproachesandisnowrarelyemployedin
taxonomyastheyoftenleadtosubstantiallydifferentclusterswhen
appliedtorealdata.Thefollowingmethodismostlyusedinthiscase.
Nearestneighborclusteringmethod:Itiscalledasinglelinkage
clustering.HerephenogramsareconstructedbyjoiningOTUsand
groupsonthebasisoftheirsimilarmembersi.ealmostshortest
distance.WhetheranOUTwilljoinanexistingclusterdependsonits
maximumsimilarity(orminimumdistancefrom)anymemberofthat
cluster.APhenogramisinitiatedbyjoiningthetwomostsimilarOTUs.
Thefollowingexamplecanimpregnatetheconcept.

13. SIMILARITY MATRIX
C B A
A 0.40 0.63 1.0
B 0.53 1.0
C 1.0

14. Sequence Procedure involved in the Phenetic Clustering of the
aforesaid three taxa:
STEP ACTION RESULT ACTION TREE
1. Find greatest
similarity less
than unity
0.63( A-B)Join A to B at
level 0.63
See on the
next page
2. Find the next
highest
similarity
0.53 ( B-C) Join C to
A+B Cluster
at level 0.53
See on the
next page

15. Sequence Procedure involved in the Phenetic Clustering of the aforesaid
three taxa.

16. I-Cladograms, II-Phylogram, III-Dendrogram

17. ADVANTAGES
a.Thedataofconventionaltaxonomyisimprovedbynumerical
taxonomyasitutilizesbetterandmorenumberofdescribed
characters.Thedataarecollectedfromavarietyofsources,suchas
morphology,chemistry,physiology,etc.
b.Asnumericalmethodsaremoresensitiveindelimitingtaxa,the
dataobtainedcanbeefficientlyusedintheconstructionofbetterkeys
andclassificationsystems,creationofmaps,descriptions,catalogues,
etc.withthehelpofelectronicdataprocessingsystems.Numerical
taxonomyhasinfactsuggestedseveralfundamentalchangesinthe
conventionalclassificationsystems.c.Thenumberofexisting
biologicalconceptshavebeenreinterpretedinthelightofnumerical
taxonomy.
C.
d.Numericaltaxonomyallowsmoretaxonomicworktobedoneby
lesshighlyskilledworkers.

18. DISADVANTAGES
a.Thenumericalmethodsareusefulinpheneticclassifications
andnotphylogeneticclassifications.
b.Theproponentsof“biological”speciesconcept,maynot
acceptthespecificlimitsboundbythesemethods.
c.Characterselectionisthegreatestdisadvantageinthis
approach.Ifcharacterschosenforcomparisonareinadequate,
thestatisticalmethodsmaygivelesssatisfactorysolution.
d.AccordingtoSteam,differenttaxonometricproceduresmay
yielddifferentresults.Amajordifficultyistochoosea
procedureforthepurposeandthenumberofcharactersneeded
inordertoobtainsatisfactoryresultsbythesemechanicalaids.
Itisnecessarytoascertainwhetheralargenumberof
characterswouldreallygivesatisfactoryresultsthanthose
usingasmallernumber.

19. APPLICATIONS OF NT
a.Studyofsimilaritiesanddifferencesinbacteria,othermicro-
organismsandseveralanimalgroups.
b.DelimitationofseveralangiospermicgeneralikeOryza,
SarcostemmaSolarium,andothergroupsincludingFarinosaeof
Englerandafewothers.
c.Inthestudyofseveralotherangiospermgeneraincluding
Apocynum,Chenopodium,Crotalaria,Cucurbita,Oenothera,Salix,
Zinnia,wheatcultivars,Maizecultivars,etc.
d.Phyto-chemicaldatafromseedproteinandmitochondrialDNA
RELPstudieshasbeennumericallyanalyzedbyMondaletal.tostudy
theinter-specificvariationsamongeightspeciesofcassiaL.Basedon
theresultsofelectrophoresispatterns,thedegreeofpairingaffinity
(PA)orsimilarityindexwascalculatedbythefollowingformula,
accordingtothemethodofSokal&SnethandRomeroLopesetal.:

20. PHENOGRAM
Phenogramsatypeofdendrogramwhichisbasedonpheneticdata.
Linescalledphenonlines,drawnatrightanglestothedichotomously
branchingdendrogram,representlinesofpercentagesimilarityof
pheneticfeaturesbetweenorganisms.APhenogramismainlybuiltup
onthedataofthenumericalanalysisofpheneticdata.Duringthe
constructionofdiagram,resultsoflargenumberofcharactersdatafrom
allavailablefieldaretaken.Itincludescalculatingthesimilarity
betweentaxaandconstructingadiagramthroughclusteranalysis.
Phenogramisveryusefulasitinvolvesalargenumberofcharacters.
Further,hierarchicalclassificationcanbeachievedbydecidingupon
thesimilaritybetweentaxaassignedtovariousrank.

21. PHENOGRAM

22. CLADOGRAM
ACladogramisadiagramusedincladisticstoshowrelationships
amongorganisms.Acladogramisnot,however,anevolutionarytree
becauseitdoesnotshowhowancestorsarerelatedtothedescendents,
nordoesitshowhowmuchtheyhavechanged;manyevolutionary
treescanbeinferredfromasinglecladogram.ACladogramuseslines
thatbranchoffindifferentdirectionsendingatclade,agroupof
organismsderivedfromalastcommonancestor.Therearemanyshapes
ofcladogramsbutallhavelinesthatbranchofffromothers.Thelines
canbetracedbacktowheretheybranchoff.Thesebranchingpoint
representsahypotheticalancestorwhichcanbeinferredtoexhibitthe
traitssharedamongtheterminaltaxaaboveit.Thehypothetical
ancestormightthenprovidecluesabouttheorderofevolutionof
variousfeatures,adaptationandotherevolutionarynarrativesaboutthe
ancestor.Primarily,themorphologicaldataaremostlyusedbutwiththe
passageoftime,DNA,RNAsequencingdataarenowcommonlyused
inthegenerationofcladograminadditiontotheconventionaldata.

23. CLADOGRAM

24. DIFFERENCE BETWEEN CLADISTICS & PHENETICS
Cladistics Phenetics
It is the method of the classifying
organisms on the basis of their
ancestry & evolutionary relationships.
It is the method of the classifying
organisms based on the structural &
morphologicalcharacters that are
observable.
Mostly evolutionary relationships,
genetic similarity & ancestry related
characters are taken into account
Structure , morphology and ecological
characters are taken into account .
Cladograms of phylogenetic tree is
considered to describe relationship.
Phenograms areused to describe
relationship
High accuracy & high reproducibilityLow accuracy & low reproducibility.
Taxamaybegroupedtogetherby
sharedgroupcharacterstates
(Synapomorphies)Only
Taxamaybegroupedtogetherby
shared ancestral features
(Symplesiomorphies)aswellshared
derivedcharacterstates(
Synapomorphies)

25. HOPE, YOU HAVE
ENJOYED THE JOURNEY
THANK YOU TO EXPLORE
THE ROAD

26. ACKNOWLEDGEMENT
Googleforimages
CollegeBotany-B.P.Pandey
AdvancedPlantTaxonomybyA.K.Mondal
ATextbookofBotany-Hait,Bhattacharya&Ghosh
PlantTaxonomy–O.P.Sharma
TextBookofPlantSystematics-ChittaranjanMohanty
TaxonomyofVascularplants-H.G.Lawrence.
Disclaimer:
Thispresentationhasbeendevelopedfortheenrichmentofonline
learningwithoutanyfinancialinterest.Theauthorisgratefulforallfor
havingthepleasureofusesofthecontentusedinthispresentation.