comparing dna sequences to understand evolutionary...

ComparingDNASequencestoUnderstandEvolutionaryRelationshipswithBLAST

INVESTIGATION3BIGIDEA1

AdaptedbyC.Hollinger fromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard ©,revised2015,2017.

LabInvestigation3:BLASTPre-Lab

EssentialQuestion:Howcanbioinformaticsbeusedasatooltodetermineevolutionaryrelationshipsandtobetterunderstandgeneticdiseases?

1AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

LabInvestigation3:BLASTPre-Lab

LearningObjectives:Youwillbeableto-• createcladogramsthatdepictevolutionaryrelationships

• analyzebiologicaldatawithasophisticatedbioinformaticsonlinetool

• usecladogramsandbioinformaticstoolstoaskotherquestionsofyourownandtotestyourabilitytoapplyconceptsyouknowrelatingtogeneticsandevolution

2AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

LabInvestigation3:Pre-LabBackgroundInformation:ReadpagesS41toS44.

Answerthefollowingonyourpre-labhandout.1. Explainwhybeingabletoidentifythelocationand

sequenceofgenesisimportant.2. Whyisbioinformaticsconsideredapowerfultool?

Provide2piecesofevidencetosupportyourclaim.3. Whatisacladogram?Howarecladogramsused?4. Drawacladogramthatdepictstheevolutionary

relationshipamonghumans,chimpanzees,fruitflies,andmosses.

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LabInvestigation3:Pre-Lab5.UsedatainTable1toconstructacladogramofthemajor

plantgroups.(pageS43)6. LookatTable2.PercentageSimilarityBetweentheGAPDH

GeneandProteininHumansandOtherSpecies onpageS44thatcomparesthe%similaritybetweentheGAPDHgeneandproteininhumanswiththeotherspeciesinthetable.a. Whyisthepercentagesimilarityinthegenealwayslowerthan

thepercentagesimilarityintheproteinforeachofthespecies?(Hint:Thinkabouthowageneisexpressedtoproduceafunctionalgeneproduct,inthiscaseaprotein.)

b. Drawacladogramdepictingevolutionaryrelationshipsamongthe5speciesaccordingtopercentsimilarity

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AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017. 5

ComparingDNASequencestoUnderstandEvolutionaryRelationshipswithBLAST

INVESTIGATION3BIGIDEA1

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LabInvestigation3:BLASTLabProcedure–ReadtheparagraphsatthebottomofpageS44.ThisisanenlargedphotoofFigure3.ThisfossilspecimenwasfoundneartheLiaoningProvinceinChina.Itisanewlydiscoveredspecies.

(Remember:DNAnucleotidesequenceswereextractedfromsofttissueinthisfossil.)

Source:AmericanMuseumofNaturalHistory,MickEllison

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LabInvestigation3:BLASTLab

• Procedure– It’suncommonforanysofttissuetosurvivefossilization,butDNAnucleotideswereextractedfromsmallamountsofsofttissueinthisfossil.Scientistsusedthatinformationtosequenceseveralgenes.

– YourtaskistouseBLASTn toanalyzethesegenesanddeterminetheplacewherethefossilspeciesismostlikelytobeplacedonthecladogram.

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LabInvestigation3:BLASTLabSTEP1:UsingFigure4.FossilCladogram,formaninitialhypothesisastowhereyouthinkthefossilspecimenshouldbeplacedonthecladogrambasedonthemorphology(formandstructureofanorganism)youmadeearlier.• Writeyourhypothesistotherightofthecladogram.• RemembertodrawwhereyouthinkthefossilspecimenshouldbeonthecladograminFigure4onpage2ofyourlabhandout.

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LabInvestigation3:BLASTLab

STEP2:Highlightandcopyoneofthe4genes*onthehandoutprovided.STEP3:Uploadone ofthegenesequencesintoBLASTbygoingtotheBLASThomepage.https://blast.ncbi.nlm.nih.gov/Blast.cgi

*4differentDNAnucleotidesequencesextractedfromsofttissueinthefossil.

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HomepageforBLAST atNCBI

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HomepageforBLAST atNCBI

BEGINbyClickingonNucleotideBLAST.

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Thisisthenextpageyou’llsee.

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UploadingaGeneSequence

Chooseyourfirstgene.Copyandpastethenucleotidesequenceofthatgene(1,2,3,or4)intotheEnterQuerySequencebox.

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UploadingaGeneSequence

* Besuretoaddajobtitlesoyouknowwhichgenenucleotidesequenceyouuploaded.

Here’sthenucleotidesequence.

*

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ClickonBLASTScrolltothebottomofthepage.ClickonBLASTbutton.

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ResultsYou’llseetheresultsin2forms– asaDiagram,whichyouseebelow,andaTable.ClickonGraphicSummarytoseetheTableofyourBLASTresults.

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Results

Thelistofspeciesthatappearsinthissectionarethosewithsequencesidenticalto ormostsimilar, tothegeneyouuploaded.ThesequencesbecomeLESSsimilarareyougodownthelist.

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ResultsClickonaparticularspeciestofindoutmorespecificinformation,includingtheclassificationscheme(scientificname),theproteinthatthesequencecodesfor,andthesequenceofbasesthatappeartoalignwithyourgeneofinterest.

Copyandpastethescientificnameofthatspeciesandgoogleittofindoutthecommonname.

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ResultsYoumustclickontheboxofthespeciesyouwanttousetocreatethe“DistanceTreeofResults.”Seethenextslide.

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MakeaDistanceTreeofResults

ScrollbacktothetopofthepageandclickonDistancetreeofresults.Watchwhathappens!

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TheCladogram

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Thisisthegeneyouuploaded.

TheLegendYouwillbeprovidedwithalegendwiththatincludesa“LabelColorMap”anda“BLASTnamescolormap”sothatyoucanbetterunderstandthecladogramyoursearchproduced.

Thisisthegeneyouuploaded.

23AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

ModifyingtheView

ChangetheMaxSeqDifferencefrom

ChangetheMaxSeq Differencefrom0.75to0.15toseeaclose-upofthetree.Yourgeneishighlightedinyellowbelow.

Usingthelegend,youcandetermineevolutionaryrelationships.24

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What’snext?• Youwill– Repeatthisprocessfor2othergenesofinterest.– Analyzeyourresults.– DecidewhetherornotthedatafromtheBLASTsearchsupportsyourhypothesisabouttheplacementofthefossilspeciesonthecladogram.

– Compareanddiscussyourcladogramwithotherstudents.

25AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

DesignandConductInvestigation

• Youwill– FindandBLASTyourowngenesofinterest.– Useexampleprocedureprovided.– Possiblyuseoneormoreofthesuggestedgenestoexplore.

26AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.27

FOR TEACHERS:YoucanuseotherresourceslikethosefoundattheENSI,UCMP,andBioInteractive sitesbeforeorafterdoingthislab.

28AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,

2017.