Click and Learn CSI Wildlife: Using genetics to hunt...

www.BioInteractive.org PublishedSeptember2016

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.”

Student Worksheet

3. Yourcolleaguesinthelegaldepartmentarepreparingtotakeacasetotrial.Tohelpthem,rewriteyourdescriptionoftheprocessofDNAfingerprintingsoajurycouldunderstandit.

Nowyouarereadyforyourfirstmajorassignment.Yourcolleaguesareinvestigatinganewlyseizedtuskandwonderifthetuskisfromarecentlydiscoveredcrimewhere10elephantsfromthesamepopulationwerefounddeadwiththeirtusksremoved.Thegenotypeoftheseizedtuskforfiveshorttandemrepeat(STR)lociisshowninTable1.AllelenamesforeachoftheSTRlocicorrespondtotheirsizeinbasepairs(bp).Table2liststhegenotypesofthesamefiveSTRlocifor10recentlyslaughteredelephants.

SeizedtuskFH19 FH60 FH67 FH71 FH129193193

147147

152160

Table1:GenotypeforfiveSTRlocirecoveredfromaseizedelephanttusk.

FH19 FH60 FH67 FH71 FH129

Elephant1 189193

147147

152154

Elephant2 185193

147147

152152

Elephant3 183185

147147

152162

Elephant4 193193

147147

152152

Elephant5 187187

145147

152160

Elephant6 187193

145147

152160

Elephant7 193193

149151

156160

Elephant8 193193

147147

152160

Elephant9 193193

147147

160160

Elephant10 189193

147147

152156

Table2:GenotypesusingfiveSTRlocifor10slaughteredelephants.

4. Didtheseizedtuskcomefromoneoftherecentlyslaughteredelephants?________Whatevidencesupportsyourfinding?

Student Worksheet

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

Student Worksheet

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).

Student Worksheet

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.

Student Worksheet

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

Student Worksheet

Part3:Lateonenight,rangersinaparkhearagunshotandquicklymovetoinvestigate.Oneelephanthasbeenslain,butthequickactionsoftherangersmakethepoacherflee,whichsavesthelivesofmanyelephants.Eventually,asuspectiscapturedwithonepairofelephanttusks.Yourbossgivesyouthetuskandabloodsamplefromthekilledelephant.Sheasksyoutodeterminewhetherthetuskscamefromtheelephantthatwaskilled.YouanalyzethesamplesandtheresultsareshowninFigure1.EachSTRlocusisshowninadifferentcolor.

Figure1.ThegelwiththeallelesforfourdifferentSTRlocifortheelephanttuskandthekilledelephant.

9. UsetheevidenceinFigure1todeterminewhetherthetuskcamefromtheslainelephant.Writeabrief

summaryofyourfindingsforthecasefile.

Student Worksheet

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.

Click and Learn CSI Wildlife: Using genetics to hunt...

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