www.BioInteractive.org Published September 2016 Page 1 of 8 Student Worksheet Click and Learn CSI Wildlife: Using genetics to hunt elephant poachers ABOUT THIS WORKSHEET Forensic scientists collect and analyze scientific evidence to solve crimes. One type of evidence they use is genetic data. In this activity, you will use DNA analysis to solve several crimes related to elephant conservation, a field of science known as wildlife forensics. This worksheet complements the Click and Learn “CSI Wildlife.” (http://www.hhmi.org/biointeractive/csi-wildlife). MATERIALS • Access to HHMI BioInteractive’s Click and Learn “CSI Wildlife” • 1 copy of the data handout • Four-function calculator PROCEDURE Congratulations! You have just been hired by an international police force to work as a forensic scientist dedicated to protecting wildlife and investigating illegal activity where protected animals are involved. In particular, you will be focused on the protection of African elephants. You are excited to put your scientific skills to work. To help you learn more about what you will do in your new position, your boss asks you to complete HHMI BioInteractive’s Click and Learn “CSI Wildlife.” But before you begin, she asks you to answer the following questions. 1. Elephants are a keystone species and play a pivotal role in shaping the forests and savannas in which they live. Knowing the importance of elephants, an international group of scientists conducted a census to estimate the number of African elephants. The Great Elephant Census data was released in August 2016, and unfortunately, the results reveal that African elephants have decreased by 30% in just the past seven years. What ideas do you have for why the number of elephants is declining? 2. You have likely heard of investigators using DNA fingerprinting to identify individuals in crime scene investigations. Briefly describe your current understanding of the process of DNA fingerprinting. Part 1: Now that you have shared with your boss what you already know, she is ready to send you for training. Complete the activities that are in Case One in HHMI BioInteractive’s Click and Learn “CSI Wildlife.”
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www.BioInteractive.org PublishedSeptember2016
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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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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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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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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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