Comparing DNA Sequences to Understand Evolutionary...

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Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST INVESTIGATION 3 BIG IDEA 1 Adapted by C. Hollinger from AP © Biology Investigative Labs: An Inquiry-Based Approach. Copyright 2012 by The College Board © , revised 2015, 2017.

Transcript of Comparing DNA Sequences to Understand Evolutionary...

Page 1: Comparing DNA Sequences to Understand Evolutionary ...harenberg.weebly.com/uploads/4/7/5/4/47544635/2017_blast_lab_ppt.pdfFossil Cladogram, form an initial hypothesis as to where you

ComparingDNASequencestoUnderstandEvolutionaryRelationshipswithBLAST

INVESTIGATION3BIGIDEA1

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

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LabInvestigation3:BLASTPre-Lab

EssentialQuestion:Howcanbioinformaticsbeusedasatooltodetermineevolutionaryrelationshipsandtobetterunderstandgeneticdiseases?

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

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LabInvestigation3:BLASTPre-Lab

LearningObjectives:Youwillbeableto-• createcladogramsthatdepictevolutionaryrelationships

• analyzebiologicaldatawithasophisticatedbioinformaticsonlinetool

• usecladogramsandbioinformaticstoolstoaskotherquestionsofyourownandtotestyourabilitytoapplyconceptsyouknowrelatingtogeneticsandevolution

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

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LabInvestigation3:Pre-LabBackgroundInformation:ReadpagesS41toS44.

Answerthefollowingonyourpre-labhandout.1. Explainwhybeingabletoidentifythelocationand

sequenceofgenesisimportant.2. Whyisbioinformaticsconsideredapowerfultool?

Provide2piecesofevidencetosupportyourclaim.3. Whatisacladogram?Howarecladogramsused?4. Drawacladogramthatdepictstheevolutionary

relationshipamonghumans,chimpanzees,fruitflies,andmosses.

3AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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LabInvestigation3:Pre-Lab5.UsedatainTable1toconstructacladogramofthemajor

plantgroups.(pageS43)6. LookatTable2.PercentageSimilarityBetweentheGAPDH

GeneandProteininHumansandOtherSpecies onpageS44thatcomparesthe%similaritybetweentheGAPDHgeneandproteininhumanswiththeotherspeciesinthetable.a. Whyisthepercentagesimilarityinthegenealwayslowerthan

thepercentagesimilarityintheproteinforeachofthespecies?(Hint:Thinkabouthowageneisexpressedtoproduceafunctionalgeneproduct,inthiscaseaprotein.)

b. Drawacladogramdepictingevolutionaryrelationshipsamongthe5speciesaccordingtopercentsimilarity

4AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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

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ComparingDNASequencestoUnderstandEvolutionaryRelationshipswithBLAST

INVESTIGATION3BIGIDEA1

AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard ©,revised2015,2017. 6

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

(Remember:DNAnucleotidesequenceswereextractedfromsofttissueinthisfossil.)

Source:AmericanMuseumofNaturalHistory,MickEllison

7AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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LabInvestigation3:BLASTLab

• Procedure– It’suncommonforanysofttissuetosurvivefossilization,butDNAnucleotideswereextractedfromsmallamountsofsofttissueinthisfossil.Scientistsusedthatinformationtosequenceseveralgenes.

– YourtaskistouseBLASTn toanalyzethesegenesanddeterminetheplacewherethefossilspeciesismostlikelytobeplacedonthecladogram.

AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017. 8

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

9AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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LabInvestigation3:BLASTLab

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

*4differentDNAnucleotidesequencesextractedfromsofttissueinthefossil.

10AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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HomepageforBLAST atNCBI

THISISWHATTHEBLASTHOMEPAGELOOKSLIKE.11AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard ©,revised2015,2017.

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HomepageforBLAST atNCBI

BEGINbyClickingonNucleotideBLAST.

12AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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Thisisthenextpageyou’llsee.

13AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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UploadingaGeneSequence

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

14AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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UploadingaGeneSequence

* Besuretoaddajobtitlesoyouknowwhichgenenucleotidesequenceyouuploaded.

Here’sthenucleotidesequence.

*

15AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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ClickonBLASTScrolltothebottomofthepage.ClickonBLASTbutton.

16AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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

17AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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Results

Thelistofspeciesthatappearsinthissectionarethosewithsequencesidenticalto ormostsimilar, tothegeneyouuploaded.ThesequencesbecomeLESSsimilarareyougodownthelist.

18AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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ResultsClickonaparticularspeciestofindoutmorespecificinformation,includingtheclassificationscheme(scientificname),theproteinthatthesequencecodesfor,andthesequenceofbasesthatappeartoalignwithyourgeneofinterest.

Copyandpastethescientificnameofthatspeciesandgoogleittofindoutthecommonname.

19AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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ResultsYoumustclickontheboxofthespeciesyouwanttousetocreatethe“DistanceTreeofResults.”Seethenextslide.

20AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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MakeaDistanceTreeofResults

ScrollbacktothetopofthepageandclickonDistancetreeofresults.Watchwhathappens!

21AdaptedbyC.HollingerfromAP© BiologyInvestigativeLabs:AnInquiry-BasedApproach.Copyright2012byTheCollegeBoard©,revised2015,2017.

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TheCladogram

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

Thisisthegeneyouuploaded.

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TheLegendYouwillbeprovidedwithalegendwiththatincludesa“LabelColorMap”anda“BLASTnamescolormap”sothatyoucanbetterunderstandthecladogramyoursearchproduced.

Thisisthegeneyouuploaded.

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

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ModifyingtheView

ChangetheMaxSeqDifferencefrom

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

Usingthelegend,youcandetermineevolutionaryrelationships.24

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

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

– Compareanddiscussyourcladogramwithotherstudents.

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

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DesignandConductInvestigation

• Youwill– FindandBLASTyourowngenesofinterest.– Useexampleprocedureprovided.– Possiblyuseoneormoreofthesuggestedgenestoexplore.

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

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

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FOR TEACHERS:YoucanuseotherresourceslikethosefoundattheENSI,UCMP,andBioInteractive sitesbeforeorafterdoingthislab.

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

2017.


Classification of Living Things Eubacteria Archaebacteria Protista Plantae Fungi Animalia DOMAIN BACTERIA DOMAIN ARCHAEA DOMAIN EUKARYA Cladogram of Six.

Classification of Living Things Eubacteria Archaebacteria Protista Plantae Fungi Animalia DOMAIN BACTERIA DOMAIN ARCHAEA DOMAIN EUKARYA Cladogram of Six.

What is a synapomorphy?. Terms systematics [taxonomy, phylogenetics] phylogeny/phylogenetic tree cladogram tips, branches, nodes homology apomorphy synapomorhy.

What is a synapomorphy?. Terms systematics [taxonomy, phylogenetics] phylogeny/phylogenetic tree cladogram tips, branches, nodes homology apomorphy synapomorhy.

SCIENCE: BIOLOGYharenberg.weebly.com/uploads/4/7/5/4/47544635/biology... · 2018-04-25 · NMPED Biology EOC Blueprint Project Management by 2 Purpose Statement Biology The Biology

SCIENCE: BIOLOGYharenberg.weebly.com/uploads/4/7/5/4/47544635/biology... · 2018-04-25 · NMPED Biology EOC Blueprint Project Management by 2 Purpose Statement Biology The Biology

Supplementary Figure S1. Cladogram for the …...Supplementary Figure S1. Cladogram for the Poaceae. Based on the combined Bayesian phylogenetic analysis of molecular and morphological

Supplementary Figure S1. Cladogram for the …...Supplementary Figure S1. Cladogram for the Poaceae. Based on the combined Bayesian phylogenetic analysis of molecular and morphological

Dispatch—Explain this cladogram Practice Evolution Quiz .

Dispatch—Explain this cladogram Practice Evolution Quiz .

Reading and Making a Cladogram

Reading and Making a Cladogram

3/15/19 Chapter 15 · Broughton High School 23 | P a g e Academic Biology Chapter 15 – Evolution Carson /Davis Reading a Cladogram A cladogram is a diagram used in cladistics which

3/15/19 Chapter 15 · Broughton High School 23 | P a g e Academic Biology Chapter 15 – Evolution Carson /Davis Reading a Cladogram A cladogram is a diagram used in cladistics which

A Cladogram of Plant Groups – shows evolutionary relationships of plants

A Cladogram of Plant Groups – shows evolutionary relationships of plants

A Cladistic Analysis of Phenotypic Associations …sented by the cladogram. Obviously, the power of the cladistic approach de- pends upon the confidence one has in the cladogram and

A Cladistic Analysis of Phenotypic Associations …sented by the cladogram. Obviously, the power of the cladistic approach de- pends upon the confidence one has in the cladogram and

A Cladogram and Taxonomy for Emotionsscholarpublishing.org/Repository/ASSRJ-16-2204.pdf · A Cladogram and Taxonomy for Emotions Lawrence J. Cookson LJ Cookson Consulting, Warrandyte,

A Cladogram and Taxonomy for Emotionsscholarpublishing.org/Repository/ASSRJ-16-2204.pdf · A Cladogram and Taxonomy for Emotions Lawrence J. Cookson LJ Cookson Consulting, Warrandyte,

Phylum Chordata. Section 30-1 Nonvertebrate chordates Fishes Amphibians Reptiles Birds Mammals Invertebrate ancestor Chordate Cladogram.

Phylum Chordata. Section 30-1 Nonvertebrate chordates Fishes Amphibians Reptiles Birds Mammals Invertebrate ancestor Chordate Cladogram.

mrdoddswebsite.weebly.com · A cladogram shows evolutionary relationships between species. You can think of a cladogram as a type of family tree. Follow the directions to draw a cladogram

mrdoddswebsite.weebly.com · A cladogram shows evolutionary relationships between species. You can think of a cladogram as a type of family tree. Follow the directions to draw a cladogram

Phenetic, cladistic, cladogram, phylogenetics

Phenetic, cladistic, cladogram, phylogenetics

Do Now - Weeblyupegui.weebly.com/uploads/5/0/7/0/5070642/evolution1.pdf · •A cladogram –Is a depiction of patterns of shared characteristics among taxa •A clade within a cladogram

Do Now - Weeblyupegui.weebly.com/uploads/5/0/7/0/5070642/evolution1.pdf · •A cladogram –Is a depiction of patterns of shared characteristics among taxa •A clade within a cladogram

Weeblymarunden.weebly.com/uploads/5/9/7/0/59704741/cladogram.pdf · CLADOGRAM ANALYSIS Date: Hour: What is a cladogram? It is a diagram that depicts evolutionary relationships among

Weeblymarunden.weebly.com/uploads/5/9/7/0/59704741/cladogram.pdf · CLADOGRAM ANALYSIS Date: Hour: What is a cladogram? It is a diagram that depicts evolutionary relationships among

Supplementary figure 1: Bayesian cladogram of MT … · pksr mt acp (ks14) dh acp ks15 acp te mlntedilckmlfaqlqsigfftesksqpvlenfygrwfeesqsilerhqflkrtenghvptrsigtmse

Supplementary figure 1: Bayesian cladogram of MT … · pksr mt acp (ks14) dh acp ks15 acp te mlntedilckmlfaqlqsigfftesksqpvlenfygrwfeesqsilerhqflkrtenghvptrsigtmse

Laois Fitzpatrick Cladogram* v.LFP1a 20170201 Fitzpatrick Cladogram 22... · see 28 YSTR haplotypes with 33 FTDNA loci; ... (1995) when using RM, or Bandelt et al. (1999) when using

Laois Fitzpatrick Cladogram* v.LFP1a 20170201 Fitzpatrick Cladogram 22... · see 28 YSTR haplotypes with 33 FTDNA loci; ... (1995) when using RM, or Bandelt et al. (1999) when using

Reading and Making a Cladogram. Cladogram – What is it? An evolutionary family tree Used to be based on physical appearance Now based on similar DNA sequences,

Reading and Making a Cladogram. Cladogram – What is it? An evolutionary family tree Used to be based on physical appearance Now based on similar DNA sequences,

Biology Essentials - 006waterworthapbiology.weebly.com/uploads/2/2/2/1/...Biology Essentials - 006 bozemanscience.com. Phylogenetics Phylogenetic! Tree Cladogram Speciation Morphological

Biology Essentials - 006waterworthapbiology.weebly.com/uploads/2/2/2/1/...Biology Essentials - 006 bozemanscience.com. Phylogenetics Phylogenetic! Tree Cladogram Speciation Morphological

Tree of Life (Fetal Pig) Cladogram Bailey and Will.

Tree of Life (Fetal Pig) Cladogram Bailey and Will.