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Student Worksheet
ClickandLearnCSIWildlife:Usinggeneticstohuntelephantpoachers
ABOUTTHISWORKSHEETForensicscientistscollectandanalyzescientificevidencetosolvecrimes.Onetypeofevidencetheyuseisgeneticdata.Inthisactivity,youwilluseDNAanalysistosolveseveralcrimesrelatedtoelephantconservation,afieldofscienceknownaswildlifeforensics.ThisworksheetcomplementstheClickandLearn“CSIWildlife.”(http://www.hhmi.org/biointeractive/csi-wildlife).
MATERIALS
• AccesstoHHMIBioInteractive’sClickandLearn“CSIWildlife”• 1copyofthedatahandout• Four-functioncalculator
PROCEDURE
Congratulations!Youhavejustbeenhiredbyaninternationalpoliceforcetoworkasaforensicscientistdedicatedtoprotectingwildlifeandinvestigatingillegalactivitywhereprotectedanimalsareinvolved.Inparticular,youwillbefocusedontheprotectionofAfricanelephants.Youareexcitedtoputyourscientificskillstowork.Tohelpyoulearnmoreaboutwhatyouwilldoinyournewposition,yourbossasksyoutocompleteHHMIBioInteractive’sClickandLearn“CSIWildlife.”Butbeforeyoubegin,sheasksyoutoanswerthefollowingquestions.
1. Elephantsareakeystonespeciesandplayapivotalroleinshapingtheforestsandsavannasinwhichtheylive.Knowingtheimportanceofelephants,aninternationalgroupofscientistsconductedacensustoestimatethenumberofAfricanelephants.TheGreatElephantCensusdatawasreleasedinAugust2016,andunfortunately,theresultsrevealthatAfricanelephantshavedecreasedby30%injustthepastsevenyears.Whatideasdoyouhaveforwhythenumberofelephantsisdeclining?
2. YouhavelikelyheardofinvestigatorsusingDNAfingerprintingtoidentifyindividualsincrimesceneinvestigations.BrieflydescribeyourcurrentunderstandingoftheprocessofDNAfingerprinting.
Part1:Nowthatyouhavesharedwithyourbosswhatyoualreadyknow,sheisreadytosendyoufortraining.CompletetheactivitiesthatareinCaseOneinHHMIBioInteractive’sClickandLearn“CSIWildlife.”
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Student Worksheet
ClickandLearnCSIWildlife:Usinggeneticstohuntelephantpoachers
3. Yourcolleaguesinthelegaldepartmentarepreparingtotakeacasetotrial.Tohelpthem,rewriteyourdescriptionoftheprocessofDNAfingerprintingsoajurycouldunderstandit.
Nowyouarereadyforyourfirstmajorassignment.Yourcolleaguesareinvestigatinganewlyseizedtuskandwonderifthetuskisfromarecentlydiscoveredcrimewhere10elephantsfromthesamepopulationwerefounddeadwiththeirtusksremoved.Thegenotypeoftheseizedtuskforfiveshorttandemrepeat(STR)lociisshowninTable1.AllelenamesforeachoftheSTRlocicorrespondtotheirsizeinbasepairs(bp).Table2liststhegenotypesofthesamefiveSTRlocifor10recentlyslaughteredelephants.
SeizedtuskFH19 FH60 FH67 FH71 FH129193193
147147
97103
6262
152160
Table1:GenotypeforfiveSTRlocirecoveredfromaseizedelephanttusk.
FH19 FH60 FH67 FH71 FH129
Elephant1 189193
147147
9797
6264
152154
Elephant2 185193
147147
95103
6262
152152
Elephant3 183185
147147
9597
6264
152162
Elephant4 193193
147147
91105
6264
152152
Elephant5 187187
145147
9595
6264
152160
Elephant6 187193
145147
9197
6464
152160
Elephant7 193193
149151
9797
6062
156160
Elephant8 193193
147147
97103
6262
152160
Elephant9 193193
147147
9797
6262
160160
Elephant10 189193
147147
95105
6262
152156
Table2:GenotypesusingfiveSTRlocifor10slaughteredelephants.
4. Didtheseizedtuskcomefromoneoftherecentlyslaughteredelephants?________Whatevidencesupportsyourfinding?
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Student Worksheet
ClickandLearnCSIWildlife:Usinggeneticstohuntelephantpoachers
5. Drawtheexpectedpatternofbandsonagelthatshowstheallelesfortheseizedtuskandtheelephantyouidentifiedasapotentialmatch,forSTRlociFH60andFH129.IncludeaDNAladderthathasDNAfragmentsthatare125,150,and175basepairs(bp)insize.
6. Yournextchallengeistocalculatetheprobabilitythatanotherelephantfromthesamepopulationwould
havethesamegenotypeastheonefromtheseizedivorysample.
a. Calculatethefrequencyofeachoftheallelesfoundintheivorysampleusingdatafromthe10slaughteredelephants.StartbyexaminingthedatainTable2forSTRlocusFH19.Theivorysamplewashomozygousforthe193-bpallele.Inthesampleof10elephants,12alleleswerealso193bpinsize,outofatotalof20alleles.LookathowthesedataareusedtodeterminethefrequencyofthealleleinTable3.UsethesameapproachtocalculatethefrequencyoftheotherfourSTRlociinthetableonthefollowingpage.Someofthedataisprovidedforyou.
Table3.Frequencyofallelesfoundintheseizedtuskintheslaughteredelephants’populationforfivedifferentSTRloci.
STRlocus FH19 FH60 FH67 FH71 FH129#ofcopiesofAllele1inthegroupof10elephantsstudied 12 16 9
Totalnumberofallelesinthegroupof10elephantsstudied 20 20
FrequencyofAllele1 12/20=0.60
NumberofcopiesofAllele2inthegroupof10elephantsstudied 12 2
Totalnumberofallelesinthegroupof10elephantsstudied 20 20
FrequencyofAllele2
12/20=0.60
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Student Worksheet
ClickandLearnCSIWildlife:Usinggeneticstohuntelephantpoachers
b. Usetheformulasbelowtocalculatetheprobabilityofanotherindividualhavingthesamegenotypeforeachindividuallocus.EntertheformulasandprobabilityinTable4.
• IftheivorysampleishomozygousforanSTRlocus,theprobability(P(genotypeforlocusX))thatanotherindividualhasthesamegenotypefortheSTRlocusis:
P(genotypeforlocusX)=(frequencyofAllele1)2
• IftheivorysampleisheterozygousforanSTRlocus,theprobability(P(genotypeforlocusX))thatanotherindividualhasthesamegenotypefortheSTRlocusis:
P(genotypeforlocusX)=2×(frequencyofAllele1)×(frequencyofAllele2) STRlocus FH19 FH60 FH67 FH71 FH129Formulawithfilled-invaluesfortheprobability (0.60)2
Calculatedprobabilityforeachlocus 0.36
Table4.TheprobabilitythatanotherelephantinthesamepopulationhasthesamegenotypeateachindividualSTRlocus.
c. TodeterminetheprobabilitythatanotherindividualhasthesamegenotypeforeachofthefiveSTRloci(inotherwords,thesamegeneticfingerprint),multiplyalltheindividualprobabilitiestogether.
Whatistheprobabilitythatallfivematch?__________
7. Impressedwithyourwork,yourbossnowasksyoutoapplywhatyouhavelearnedtothegenotypefortheivorysampleforall16STRloci,listedinTable5below.ThefirstfiveSTRlociarethesameastheoneslistedinTable4.Inaddition,yourcolleaguehasbeenabletocollectadditionalsamplesofelephantsfromthesamepopulationastheonesshowninTable2.Henowhasallelefrequencydatabasedon80alleles,showninthetablebelow.
STRlocus FH19 FH60 FH67 FH71 FH129 FH39 FH40 FH48Allele1size(bp) 193 147 97 62 152 239 242 170Allele1frequency 0.28 0.66 0.36 0.51 0.39 0.31 0.68 0.05Allele2size 193 147 103 62 160 243 242 172Allele2frequency 0.28 0.66 0.10 0.51 0.25 0.41 0.68 0.38STRlocus FH94 FH102 FH103 FH126 FH127 FH153 S03 S04Allele1size(bp) 225 177 149 94 247 169 141 154Allele1frequency 0.65 0.64 0.13 0.18 0.04 0.011 0.55 0.8Allele2size 225 181 151 110 247 171 143 154Allele2frequency 0.65 0.14 0.61 0.11 0.04 0.08 0.39 0.8
Table5.Theivorysampleallelesizeandtheirassociatedallelefrequencyinthepopulationforall16STRlocifromasampleof40elephants(80alleles).
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Student Worksheet
ClickandLearnCSIWildlife:Usinggeneticstohuntelephantpoachers
a. ComparethefrequencyoftheallelesforSTRlociFH19,FH60,FH67,FH71,andFH129thatyoucompletedinTable3withthevaluesinTable5.Whydoyouthinkthevaluesdiffer?
b. Calculatetheprobabilitythatanotherindividualhasthesamegenotypeatall16STRlocibyusingthesameprocedureasSteps6band6candthenmultiplyalltheindividualprobabilitiestogether.Probabilityofanidenticalmatchwithanotherelephantatall16STR__________________
Part2:Yourcolleaguescantellthatyouhavethenecessaryskillstohelpstopthekillingofelephantsforivoryandtobringpoacherstojustice.Yourbosspromotesyoutoleadanewcase.Tosolvethiscase,youfirstneedtocompleteCaseTwoofHHMIBioInteractive’sClickandLearn“CSIWildlife.”Thedetailsofthecase:Anothershipmentofivoryhasbeenseized.Law-enforcementofficialscapturedoneofthepeopleshippingtheivory.Throughinterviewswiththisindividualandhiscontacts,thepolicedeterminethetimingofthepoachingevent,buttheystilldonotknowthelocation.Atthetimetheivorywascollected,threesuspectswereeachcaughtpoachingelephantsinparksfromthreedifferentpartsofAfrica.SuspectonewaspoachinginthecountryofTanzania,Suspect2inCameroon,andSuspect3inZambia.Yourbosswouldlikeyoutolinkthegenotypeofoneoftheseizedtuskstooneofthethreereferencepopulationstakenfromeachcountry.YoudeterminethegenotypeoftheseizedtuskforfourSTRloci,showninTable6.
FH39 FH67 FH103 FH129
239 97 151 154
241 97 153 160
Table6.ThegenotypeforfourSTRlociofaseizedtusk.
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Student Worksheet
ClickandLearnCSIWildlife:Usinggeneticstohuntelephantpoachers
YourlabassistantsummarizestheallelefrequencydataforthethreepossiblesourcepopulationsinFigure2below.
Table7.ComparisonoftheallelesfromtheivorytusktothereferencepopulationsinTanzania,Zambia,andCameroon.
8. MakeaclaimaboutwhichcountryinAfricaismostlikelytobenearthesourcepopulationoftheseizedtusks.Yourclaimwillbeusedincourt,somakesuretohighlighttheevidenceyouusedtomakeyourclaim.
STRLoci FH39 FH67Allele
frequenciesfromthreeelephant
populations
Allelesinseizedtusk
239,241 97,97
STRLoci FH103 FH129Allele
frequenciesfromthreeelephant
populations
Allelesinseizedtusk
151,153 154,160
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Student Worksheet
ClickandLearnCSIWildlife:Usinggeneticstohuntelephantpoachers
Part3:Lateonenight,rangersinaparkhearagunshotandquicklymovetoinvestigate.Oneelephanthasbeenslain,butthequickactionsoftherangersmakethepoacherflee,whichsavesthelivesofmanyelephants.Eventually,asuspectiscapturedwithonepairofelephanttusks.Yourbossgivesyouthetuskandabloodsamplefromthekilledelephant.Sheasksyoutodeterminewhetherthetuskscamefromtheelephantthatwaskilled.YouanalyzethesamplesandtheresultsareshowninFigure1.EachSTRlocusisshowninadifferentcolor.
Figure1.ThegelwiththeallelesforfourdifferentSTRlocifortheelephanttuskandthekilledelephant.
9. UsetheevidenceinFigure1todeterminewhetherthetuskcamefromtheslainelephant.Writeabrief
summaryofyourfindingsforthecasefile.
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Student Worksheet
ClickandLearnCSIWildlife:Usinggeneticstohuntelephantpoachers
10.Itisveryimportantforscientiststoconsidersourcesoferrorinanexperimentandalternativeexplanations.WhatsourcesoferrororalternativeexplanationsmightchangetheansweryougaveinStep9?
11.Aftercompletingthisactivity,doyoubelievethatDNAfingerprintingisusefulasevidenceincriminalcasesandcanhelpinreducingelephantpoaching?Providethreepiecesofevidencefromthisexperiencetosupportyouranswer.
REFERENCE
ThisactivityisbasedontheannotatedresearchpaperWasser,S.K.,Brown,L.,Mailand,C.,Mondol,S.,Clark,W.,Laurie,C.,&Weir,B.S.(2015).GeneticassignmentoflargeseizuresofelephantivoryrevealsAfrica’smajorpoachinghotspots.Science,349(6243),84-87.TheunderlyingdataareavailableontheDryadDigitalRepository:http://dx.doi.org/10.5061/dryad.435p4.
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