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Methods Ecol Evol. 2019;1–7. wileyonlinelibrary.com/journal/mee3 | 1© 2019 The Authors. Methods in Ecology and Evolution © 2019 British Ecological Society
Received:1August2018 | Accepted:21February2019DOI: 10.1111/2041-210X.13173
P R A C T I C A L T O O L S
Empowering conservation practice with efficient and economical genotyping from poor quality samples
Meghana Natesh1,2* | Ryan W. Taylor3,4* | Nathan K. Truelove5 | Elizabeth A. Hadly3 | Stephen R. Palumbi3,5 | Dmitri A. Petrov3* | Uma Ramakrishnan1*
*Equal contribution.
1National Centre for Biological Sciences,TIFR,Bangalore,India2Sastra University, Tirumalaisamudram, Thanjavur, India3DepartmentofBiology,StanfordUniversity, Stanford, California4End2End Genomics LLC, Davis, California5HopkinsMarineStation,StanfordUniversity, Pacific Grove, California
CorrespondenceDmitri PetrovEmail:[email protected]:[email protected]
Funding informationR43HG009482, Wildlife Conservation Trust grant(UR),FulbrightNehrugrant(2092/F-NAPE/2015, UR) and Wellcome Trust/DBT India Alliance (UR, IA/S/16/2/502714), SummitFoundationandGlobalGenomeInitiative at the Smithsonian Institution (NT, SRP,SteveBox)supportedconchwork.
Handling Editor: Douglas Yu
Abstract1. Moderate-tohigh-densitygenotyping(100+SNPs)iswidelyusedtodetermineand measure individual identity, relatedness, fitness, population structure andmigrationinwildpopulations.
2. However,theseimportanttoolsaredifficulttoapplywhenhigh-qualitygeneticmaterial isunavailable.Mostgenomictoolsaredevelopedforhigh-qualityDNAsources from laboratory or medical settings. As a result, most genetic data from marketorfieldsettingsislimitedtoeasilyamplifiedmitochondrialDNAorafewmicrosatellites.
3. To enable genotyping in conservation contexts, we used next-generation se-quencingofmultiplexPCRproductsfromverylow-qualityDNAextractedfromfaeces,hairandcookedsamples.Wedemonstratedutilityandwide-rangingpo-tential application in endangered wild tigers and tracking commercial trade inCaribbean queen conch.
4. We genotyped 100 SNPs from degraded tiger samples to identify individuals,discerncloserelativesanddetectpopulationdifferentiation.Co-occurringcarni-voresdonotamplify(e.g.Indianwilddog/dhole)oraremonomorphic(e.g.leop-ard).Sixty-twoSNPsfromconchfrittersandfield-collectedsampleswereusedtotestrelatednessanddetectpopulationstructure.
5. We provide proof of concept for a rapid, simple, cost-effective and scalablemethod(forbothsamplesandnumberofloci),aframeworkthatcanbeappliedtoother conservation scenarios previously limited by low-quality DNA samples.Theseapproachesprovideacriticaladvanceforwildlifemonitoringandforensics,open thedoor to field-ready testing, andwill strengthen theuseof science inpolicydecisionsandwildlifetrade.
K E Y W O R D S
conch,conservationgenetics,endangeredspeciesmonitoringgenotyping,multiplexPCR,noninvasivesamples,SNPs,tigers
2 | Methods in Ecology and Evolu on NATESH ET Al.
1 | INTRODUC TION
Stemming the tide of global species decline requires continuousmonitoring and nimble, adaptivemanagement to promote speciesrecovery.Effectivemonitoringreliesonidentifyingspeciespresenceand the ability to track specific individuals and their familial rela-tionships.Whilespeciesrecoveryiscriticallydependentontrackingindividuals and their dynamics locally, integrating data across the speciesrangeallowsmonitoringofgloballarge-scalethreatsinclud-ingpopulationrangereductionandillegalwildlifetrade.
Inprinciple, all of thesegoals canbeachievedviagenotypingamodestnumberoflocisuchasmicrosatellitesorsinglenucleotidepoly-morphisms(SNPs).Tostudyendangeredspeciesthatarerareandelu-sive,approachesmustbeabletoaccommodatenoninvasivesourcesofDNAsuchasfaeces,shell,feathers,hairandsaliva,whichyieldimpure,mixedand/orextremelysmallamountsofdegradedDNA.Moreover,marketsamplesgeneratedbywildlifetrademaybeprocessed,cooked,dried ormixedwith other species, again providing low-quality andoftenmixedDNA.Currentapproachestendtorequirerelativelylargeamounts of DNA (Carroll et al., 2018, nanograms of DNA) from the targetspecies,ordemandexpensiveandgenerallyinefficientenrich-mentstrategies(Snyder-Mackleretal.,2016;Chiou&Bergey,2018).Approaches designed for lower concentrationDNA samples (Krausetal.,2015)requireexpensiveandspecializedequipment.
HerewedemonstratethatamultiplexPCRapproachfollowedbynext- generation sequencing satisfies all the requirements necessary for inexpensive,fast,andeasygenotypingoflow-qualitysamples.Ourap-proachissimilartoGT-seq(Campbell,Harmon,&Narum,2014)butcanusepubliclyavailablesoftwarefordesigningprimersandcallingSNPsand targets only short fragments in order to succeed with degraded DNA.Weillustratethepowerofthismethodfortwoendangeredspe-ciesindivergentconservationcontextsandreal-lifesettings:genotypesfromfaeces,shedhairandsalivafoundonkilledpreyfromwildIndianti-gersandfromCITES-regulatedCaribbeanqueenconchimportedtotheUSandsoldinfriedfritters(methodschematicFigure1a,b).Methodsin-cludeDNAextraction,multiplexPCR,asecondbarcodingPCR,IlluminaMiSeqsequencingandbioinformaticsforSNPgenotyping.
The tiger Panthera tigris, a charismatic carnivore, is classified as endangered by the IUCN red list. Distribution across 14 countries (Goodrichetal.,2015)makesitcriticalthatlocallycollecteddatabecomparableacrosstigerrange.Genotypingofscatorhair,alongwithrapidforensictestingofconfiscatedskinsorothertradedpartscanverifyspecies,individualidentityandsourcepopulations.Wedevel-opedamultiplexprimersetfor192SNPlociandtestedthemonfae-cal,tissue,salivaandhairsamplesfromcaptiveandwildtigers.Wealsogenotypedtwosympatriccarnivores,thedhole(Cuon alpinus), andtheleopard(Panthera pardus), that may be confused with tigers whentargetingnoninvasivesamples.
Our second example illustrates the use of this approach evenwhen reference genomes are unavailable, and again highlights use in difficultsamples:inthiscasefriedconchfritters.Althoughformerlyabundant, the queen conch (Strombus gigas) was listed in CITES Appendix II in 1990, which allows for control of trade to reduce
over-exploitation.IdentifyinggeographicancestryofillegallytradedqueenconchproductsinFloridamarketswillaidconservationactionthat will allow recovery of this formerly lucrative fishery. Because themostdirectaccessto importedconch is fromthehundredsofrestaurants inFlorida,wesought techniques thatwouldallowge-notypingfromthemostabundantmenuitem,friedconchfritters.
2 | MATERIAL S AND METHODS
2.1 | Sample collection
Fortigers,multiplesamplesfrom13captivetigers(USAzoos)repre-sentingdifferentscenarioswereusedforstandardization(SupportingInformation,TableS1).Bloodandcorrespondingfaecalswabsfromcaptivetigers, (includingoneparent–offspringandonesiblingpair)werecollectedinIndia.WildtigersweresamplednoninvasivelyfromprotectedareasacrossIndia(SupportingInformation,TableS2).
Scatandsaliva(frompredatorbitesontheprey)weresampledby swabbing the sample surface withmoistened synthetic swabs(Ramón-Laca, Soriano,Gleeson,&Godoy, 2015); tipswere storedinlysisbufferin2mlmicrocentrifugetubes.Hairwassampledusingforcepsandstoredinziplockbags.DNAfromlegacyfaecalsamples(collected in alcohol in 2014) was also tested. DNA extraction (first stepinFigure1a)andquantificationaredescribedinSM1.Twoleop-ardsandonedholewere included.Mostsamplesweregenotypedintriplicate.
TissuesamplesfromlivecaughtQueenConchmantlewerecol-lectedusingasterilizedbiopsyforcepswerepreservedinRNALater.SamplesfromconchfritterspurchasedfromMiamirestaurantswerefrozenuntildissectedtoisolateanimaltissuefragments(SM3a).
2.2 | SNP Identification and filtering
2.2.1 | Tigers
We identified SNPs from whole genome sequencing of 75 tigers of wildandcaptiveoriginfromP. t. tigris, P. t. jacksoni, P. t. altaica and P. t. sumatrae subspecies (SM1a).Alignment, filteringandpruningwereusedtoidentifySNPs(SM1a).Wecalculatedminorallelefre-quencies(MAF)foreachSNPwithineachsubspecies,andretainedSNPswithMAF10,15,20,25and30%.WeidentifiedfixedSNPsthatdifferentiatedpopulations.WeprioritizedSNPswithincontigs>10,5and1MBrespectively.Weselected10differentiatingSNPsfromeachsubpopulation,and9992polymorphicSNPsfromeachoftheaforementionedMAFcut-offs,foratotalof50,000SNPs.
2.2.2 | Conch
We extracted RNA from 96 L. gigas individuals(SM3a,SupportingInformation,TableS3).Fourqueenconchindividuals(oneeachfromAruba,Belize,FloridaandSt.Eustatius)wereimportedintoTRINITYv2.2.0(Grabherretal.,2013)toassembleadenovotranscriptome(SM3a).
| 3Methods in Ecology and Evolu onNATESH ET Al.
480,962 SNPs were discovered by aligning 96 conch sequences fromsixpopulationsintheCaribbeantotheassembledtranscriptome(SFGpipeline-https://github.com/bethsheets/Population-Genomics-via-RNAseq/blob/docs/guide-to-assembly-scripts.md,SM3a).
2.3 | Primer design
Publically available Primer3 (Untergasser etal., 2012; amplicon size50–90bp,primersize17–25bpandTm of 60–61°C) was used to design primers for tigerSNPs.Conchprimersweresimilarlydesignedwiththesamecriteriaasabove.Noattemptwasmadetoidentifyincom-patibilitiesbetweenprimerpairs;192primerpairswereshortlistedforbothspecies(SM1b,3b).GT-seqindexesandadapterswereused.
2.4 | PCR amplification and sequencing
LibrarypreparationconsistedofaninitialmultiplexPCRreaction,asecondPCRreactiontoaddsequencingadaptersandindexes,andsamplepooling.Sample inputDNAvolumewasadjustedtoamaximumof1ngper reaction.ThemultiplexPCR simultane-ouslyamplifiedalltargetregionsforeachsampleseparately(ina96-wellplate).ThesecondPCRreactionaddedacombinationofforward (i5) and reverse (i7) Illumina indexes to uniquely identify eachsample.Thesequencinglibrarycontainedequalvolumesofeach sample'sbarcodedproduct andwas cleanedwithAmpurebeads. Sequencing of single 150bp reads was performed onIlluminaMiSeq(SM1f).Alignmentandgenotypecallingfollowed
F IGURE 1 (a)Aschematicforprotocolandapproximatetimetaken.Detailsinthemainandsupplementarytext.(b)Ontheleft,atigerdefecating(photo:HimanushuChhattani),ascrapemark(andassociatedhairsamples,photo:KaushalPatel)andatigerhunting(photo:ShantanuPrasad,associatedlickmarks).Ontheright,aconchemergingfromitsshell,afishermanholdinghiscatchandafritter
4 | Methods in Ecology and Evolu on NATESH ET Al.
GT-Seqforconch(SM3b)andusedstandardopensourcetoolsfortigers(SM1h).Figure1aillustratesthestepsdescribedabove.
For tigers, genotyping success, genotype concordance acrossreplicates, relatedness between pairs of individuals of known andunknownrelationship,probabilityofidentityoftheSNPpanelandpopulationstructurewereassessed(SM1h).Forconch,genotypingsuccessandgenotypeconcordanceweretestedbycomparingSNPsacrossreplicateconches.Geneticdistanceandabilitytoassigntheconchsamplestothecorrectpopulationwasestimatedbycompari-sonofthe96transcriptomesamples(SM4).
3 | RESULTS
3.1 | Tiger
Onehundredand twenty-six targets (66%of192attempted)pro-ducedthemostconsistentresults(SM2b,SupportingInformation,
Figure S1, Table S4), and were then tested on noninvasive sam-ples from wild tigers across India and zoo individuals (Figure1b,SupportingInformation,TableS2).
The126SNPpanelforwildtigershadahighoverallgenotypingsuccessrate(Figure2,SM2c).Anaverageof95SNPs(75%,range:4–114)weresuccessfullytypedacrossallsamples.WhentigerDNAwas >0.01 ng/μl (all sample types), an averageof 105SNPs (83%,range:48–114)weretyped.
Samplereplicateswerehighlyconcordantwithahighproportionofgenotypematches(n=28triplicates,genotypeconcordance,M: 0.957,range:0.757–1.0).Differentsampletypesfromthesamein-dividualalsohadhighlyconcordantgenotypes(n = 5, concordance, M: 0.97; range: 0.91–0.99). Our error rates were comparable tolowmicrosatellitegenotypingerrorrates insomestudies (Thaden,Cocchiararo,Jarausch,&Jüngling,2017)orlowerthanothernonin-vasivestudies(Valièreetal.,2007;Mondoletal.,2014).Ourproba-bilityofmisidentificationwasvanishinglylow(pIDsibs = 1.6E- 22).
F IGURE 1 (Continued)
| 5Methods in Ecology and Evolu onNATESH ET Al.
Theco-occurringcarnivores, leopardanddhole,couldbedistin-guishedfromtigergenotypes.Thedholetissuesamplehadpoorampli-ficationsuccess(meanacrossreplicates<10SNPs).Leopardshadhighamplification success (M: 110 SNPs), but SNPsweremonomorphicand nearly identical across two individuals (M:0.03%mismatches).
Theknownparent–offspringandsiblingpairs(captiveindividu-als, India)hadrelatednessvaluesclose toexpected (0.5,Figure3).Observed pairwise relatedness was higher within than betweenknowngenetic clusters (seeNateshetal., 2017).As expected, re-latednessamongindividualsfromasmall,isolatedpopulation(NW,Figure3)washigh.Wildindividualsfellintothreegeneticclustersasexpected(SupportingInformation,FigureS2).
3.2 | Queen conch
We tested a 192 primer pair panel on 279 conch samples from14populations, including 48 fried conch fritters from Miami, Floridarestaurants.Our SNP successwas lower for conch than tigers (SM4).Approximatelyhalf the192 conchprimerpairs failed toprovidedata,but62targetsreachedan86%successratesimilartothe126good tiger targets (Supporting Information, Figure S3). Replicatesamples shared99%–100%of their alleles, anddifferent processed
conch samples were genetically identical, suggesting recapture.Therewerenoobviouscloserelativesamongthesamples(SupportingInformation,FiguresS4andS5).Outlyingislands(Aruba,St.Eustatius)weregeneticallydifferentiatedfromthecentralCaribbeanandFlorida(FST=0.037, 0.048 respectively, Supporting Information, Table S5).Samples from the same island group (e.g. Florida, Bahamas) or thesamecoastwerenotdifferentiated.Thesepatternsparallelarecentsurvey of queen conch with microsatellites (Truelove et al., 2017).
Conch DNA from deep-fried fritters had lower success ratesthanfrombiopsies.However,successwashighenoughforindivid-ual identification and initial population comparison. Twenty-threefritterswereprobablynotQueenconch (fewer than18SNPsam-plified),eightfrittersrevealedpoorSNPamplification(average41%success)and17fritterswerecomparabletofreshsamples(77%vs86%success,SupportingInformation,FigureS3).Thesesamplesre-vealed lower (average) genetic identity to Florida populations (av-erage78.6–80.5allelesshared,SupportingInformation,FigureS6)comparedtoPuertoRico,orAndros Island(81.2–82.3,SupportingInformation, Figure S6). While positive population identificationmay require greater geographic sampling and more SNPs (fromseveralwholegenomes),ourpilotdatasuggestthatthefritterswegenotypedare less likely tobe fromtheFloridaKeysandNassau.
F IGURE 2 SNPtypingsuccess(intriplicate)forvarioustigersamplesandcontrols.FilledcellsindicatesuccessfullytypedSNPs;colourindicatessampletype.DNAconcentrationsareontheright
6 | Methods in Ecology and Evolu on NATESH ET Al.
Importantly, high-resolution nuclear data were readily obtainedfrom processed commercial samples to address key conservationchallenges.
4 | DISCUSSION
OurpilotdatasetsprovideproofofconceptformultiplexSNPgeno-typingofnoninvasiveandprocessedmarketsamplesfromtwospe-cieswithvastlydifferentphysiologies,ecologiesandconservationchallenges.Theapproachissuccessfulfordegraded,cooked,mixed,orsmallandlow-concentrationsamples(downto10−3 ng DNA/μl), makingitanidealtoolformonitoringindividualsunderfieldcondi-tionsorfromcommercialmarkets.
Conservation practitioners assume that genetics is expensive.However, our method is cheap, while providing rich informationimportantforconservation.Designingasimilarprotocolforanewspecies of interest would include costs for method developmentand implementation.Developmentcosts includepolymorphicSNPascertainment, primer design and synthesis. However, note thatSNPs have already been identified for many endangered and fisher-iesspecies(e.g.Steiner,Putnam,Hoeck,&Ryder,2013).IfnoSNPshavebeenidentified,practitionerscouldascertainSNPsusingwholegenome sequencing (e.g. genome assembly of reasonable quality ~$2,000,Armstrongetal.,2018)andpooledsequencingof10indi-vidualsatapproximately50×totalcoverage,~$1,000).Theupfrontcostofprimerdesignandsynthesisisbetween$1,000and$10,000(for100to1,000primerpairs,$10perprimerpair).Oncesynthe-sized,primerscanbeusedfor38,000reactions(~400plates).The
continual advance in sequencing and oligo synthesis will drive down these initial development costs.Most important and attractive toconservationists, we estimate implementation costs (for 1,000SNPs)canbeaslowas$5persample(whenprocessingseveralhun-dredsamples).
IncreasingthenumberofSNPsbeyondafewhundredcanpro-videadditionalinformation.Forthispilot,weconstrainedthenum-beroftargetedSNPs,butitshouldbepossibletotargetmanymore.Primers chosen toamplify clustersof closely locatedSNPs shouldallow detection of very recent inbreeding using long runs of homo-zygosity (Kirinetal.,2010).LinkedSNPscouldgeneratemicrohap-lotypes, particularly useful in pedigree reconstruction (Baetscher,Clemento,Ng, Anderson, &Garza, 2018). SNP panels could allowsimultaneous species, individual and diet identification for sets ofspecies, e.g. largecarnivoresandcommonprey species in Indiaorsub- Saharan Africa.
Effective monitoring of individuals, populations and species iscritical todesigning rapid conservationactionandmanagementofendangered species like tigers. Small, isolated populationswill re-quire inbreeding management, genetics-based population assess-ment and genetically informed introduction strategies. Likewise,identificationofcommercialproductsfromillegalfishing,bushmeathunting or highly processed market samples provides importantmanagement information.Ability toassaysuchsamplescouldpro-videapowerfulincentivetoenforcelocalconservationlaws.Rapidgeneticmonitoringofendangeredspeciesfromcommonlyoccurringnoninvasivesampleswillprovideadata-pathwaytospeciesrecovery.WebelievethatmultiplexPCRpresentsanexampleofsuchrapid,ac-cessible,cheapandefficienttechnologythatwillmakethispossible.
F IGURE 3 Pairwiserelatedness(PI_HAT):self:threereplicatesofeachsample;sameindividualbutdifferentsample,Sibs:siblings,P-O:parent–offspringpair,W-P:withinpopulation,B-P:betweenpopulations.TruerelatednessunknownforW-PandB-P.SamplinglocationsandcorrespondingcoloursrepresentedintheIndiamap
| 7Methods in Ecology and Evolu onNATESH ET Al.
ACKNOWLEDG EMENTS
San Diego Zoo Global, CSC at Oakland Zoo, SF Zoo, Bronx Zoo,WCS Russia, El Paso Zoo, Performing Animal Welfare Society, WCS India, CWS India, WCT, Bannerghatta Zoo, Himanshu, Anubhab, Prachi,Aditya,Arun,EricaCalcagno, JackieGai for tiger samples/data, and forest departments of Rajasthan, Karnataka, MadhyaPradeshandAmericanZooAssociation,TigerSSPforpermissions,Awadhesh Pandit, NCBS- NGS facility, Steve Box, Steve Canty and NateCampbellforhelpwithconchscripts.
CONFLIC T OF INTERE S T
R.W.T. and End2End Genomics L.L.C. received NIH small business funding(R43HG009482)todeveloptoolstostudynon-modelspecies.
AUTHORS’ CONTRIBUTIONS
M.N., R.W.T., D.P., U.R., E.A.H., S.P. and N.T. designed the study.M.N., R.W.T. and N.T. conducted laboratory work and analyses.M.N.,R.W.T.,D.P.,U.R.,E.A.H.,S.P.wrotethepaper.
DATA ACCE SSIBILIT Y
Raw sequences: available from NCBI (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA516037); primer sequences: supplementaryfile;scriptsforprimerdesign,SNPcallingandfilteringavailableonDryad(tiger,https://doi.org/10.5061/dryad.q15pc00,Natesh2019)andGitHub(conch,https://doi.org/10.5281/zenodo.2580291).
R E FE R E N C E S
Armstrong,E.E.,Taylor,R.W.,Prost,S.,Blinston,P.,Meer,E.VanDer,Madzikanda, H., … Petrov, D. (2018). Cost-effective assembly ofthe African wild dog (Lycaon pictus) genome using linked reads.GigaScience, 8,1–10.https://doi.org/10.1093/gigascience/giy124
Baetscher,D.S.,Clemento,A.J.,Ng,T.C.,Anderson,C.,&Garza,J.C.(2018).Microhaplotypes provide increased power from short-read DNAsequences for relationship inference.Molecular Ecology Resources, 18(2017),296–305.https://doi.org/10.1111/1755-0998.12737
Campbell, N. R., Harmon, S., & Narum, S. R. (2014). Genotyping-in-Thousandsbysequencing(GT-seq):AcosteffectiveSNPgenotypingmethodbasedoncustomampliconsequencing.Molecular Ecology Resources, 15,855–867.https://doi.org/10.1111/1755-0998.12357
Carroll,E.L.,Bruford,M.W.,Dewoody,J.A.,Leroy,G.,Strand,A.,Waits,L., &Wang, J. (2018).Genetic and genomicmonitoringwithmini-mallyinvasivesamplingmethods.Evolutionary Applications, 11, 1–26. https://doi.org/10.1111/eva.12600
Chiou,K.L.,&Bergey,C.M.(2018).Methylation-basedenrichmentfacili-tateslow-cost,noninvasivegenomicscalesequencingofpopulationsfrom feces. Scientific Reports, January,1–10.https://doi.org/10.1038/s41598-018-20427-9
Goodrich, J.M., Lyam,A.,Miquelle,D.G.,Wibisono,H.T.,Kawanishi,K.,Pattanavibool, A., … Karanth, U. K. (2015). Panthera tigris. The IUCN redlistofthreatenedspecies2015.IUCN, e.T15955A50659951, 8235. https://doi.org/10.2305/IUCN.UK.2015-2.RLTS.T15955A50659951.en
Grabherr,M.G.,Haas,B.J.,Yassour,M.,Levin,J.Z.,Thompson,D.A.,Amit,I.,…Chen,Z.(2013).Trinity:Reconstructingafull-lengthtranscriptome
without a genome from RNA- Seq data. Nature Biotechnology, 29(7), 644–652.https://doi.org/10.1038/nbt.1883.Trinity
Kirin,M.,Mcquillan,R., Franklin,C. S.,Campbell,H.,Mckeigue,P.M.,& James, F. (2010). Genomic runs of homozygosity record popu-lation history and consanguinity. PLoS ONE, 5(11), 1–7. https://doi.org/10.1371/journal.pone.0013996
Kraus,R.H.S.,vonHoldt,B.,Cocchiararo,B.,Harms,V.,Bayerl,H.,Kühn,R.,…Nowak,C.(2015).Asingle-nucleotidepolymorphism-basedap-proachforrapidandcost-effectivegeneticwolfmonitoringinEuropebasedonnoninvasivelycollectedsamples.Molecular Ecology Resources, 15(2),295–305.https://doi.org/10.1111/1755-0998.12307
Mondol,S.,Kumar,N.S.,Gopalaswamy,A.,Sunagar,K.,Karanth,K.U.,&Ramakrishnan,U.(2014).Identifyingspecies,sexandindividualti-gersandleopardsintheMalenad-MysoreTigerLandscape,WesternGhats, India. Conservation Genetics Resources, 7, 353–361. https://doi.org/10.1007/s12686-014-0371-9
Natesh,M. (2019).Data from:Empoweringconservationpracticewithefficient and economical genotyping from poor quality samples.Dryad Digital Repository.https://doi.org/10.5061/dryad.q15pc00
Natesh,M.,Alta,G.,Nigam,P.,Jhala,Y.V.,Zachariah,A.,Borthakur,U.,&Ramakrishnan,U. (2017).ConservationprioritiesforendangeredIndian tigers through a genomic lens. Scientific Reports, 7(1), 1–11. https://doi.org/10.1038/s41598-017-09748-3
Ramón-Laca,A.,Soriano,L.,Gleeson,D.,&Godoy,J.A. (2015).Asim-pleandeffectivemethodforobtainingmammalDNAfromfaeces.Wildlife Biology, 21(4),195–203.https://doi.org/10.2981/wlb.00096
Snyder-Mackler,N.,Majoros,W.H.,Yuan,M.L.,Shaver,A.O.,Gordon,J.B.,Kopp,G.H.,…Tung,J.(2016).Efficientgenome-widesequenc-ingandlowcoveragepedigreeanalysisfromnon-invasivelycollectedsamples. Genetics, 203(June), 699–714. https://doi.org/10.1534/genetics.116.187492
Steiner, C. C., Putnam, A. S., Hoeck, P. E. A., & Ryder, O. A. (2013).Conservation genomics of threatened animal species. Annual Review of Animal Biosciences, 1, 261–281. https://doi.org/10.1146/annurev-animal-031412-103636
Thaden, A. V., Cocchiararo, B., Jarausch, A., & Jüngling, H. (2017).AssessingSNPgenotypingofnoninvasivelycollectedwildlife sam-ples using microfluidic arrays, (May), 1–13. Scientific Reports. 7 https://doi.org/10.1038/s41598-017-10647-w
Truelove,N.K.,Box,S.J.,Aiken,K.A.,Boman,E.M.,Booker,C.J.,Byfield,T.T.,…Allan,K.W.(2017).Isolationbyoceanicdistanceandspatialgenetic structure in an overharvested international fishery. Diversity and Distributions, 23,1292–1300.https://doi.org/10.1111/ddi.12626
Untergasser,A.,Cutcutache,I.,Koressaar,T.,Ye,J.,Faircloth,B.C.,Remm,M.,&Rozen,S.G.(2012).Primer3—newcapabilitiesandinterfaces.Nucleic Acids Research, 40(15),1–12.https://doi.org/10.1093/nar/gks596
Valière,N.,Bonenfant,C.,Toïgo,C.,Luikart,G.,Gaillard,J.M.,&Klein,F. (2007). Importance of a pilot study for non-invasive geneticsampling:Genotyping errors andpopulation size estimation in reddeer. Conservation Genetics, 8(1), 69–78. https://doi.org/10.1007/s10592-006-9149-2
SUPPORTING INFORMATION
Additional supporting information may be found online in theSupportingInformationsectionattheendofthearticle.
How to cite this article:NateshM,TaylorRW,TrueloveNK,etal.Empoweringconservationpracticewithefficientandeconomicalgenotypingfrompoorqualitysamples.Methods Ecol
Evol. 2019;00:1–7. https://doi.org/10.1111/2041-210X.13173