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Mastermaja305007 EH4.Pdf (573.4Kb) The history of the Polynesians inferred from high resolution HLA data. Masterthesisinhumanevolutionary genetics MajaKrzewińska Spring2007 CentreforEvolutionary andEcologicalSynthesis UniversityofOslo,Norway Table of contents Summary ................................................................................................................................ 4 1.Introduction ........................................................................................................................ 5 1.1.Background ..................................................................................................................... 5 1.2.Thehumanleukocyteantigencomplex........................................................................... 6 1.2.1.Organizationofgenesencodingclass IandIImolecules ............................................ 6 1.3.NomenclatureofHLAcomplex...................................................................................... 8 1.4.Polymorphisms................................................................................................................ 8 1.5.Inheritance....................................................................................................................... 9 1.6.Linkagedisequilibriumandrecombination..................................................................... 9 1.7.Populationgenetics ....................................................................................................... 10 2.GenesandPolynesianhistory .......................................................................................... 11 2.1.Historyandgenes .......................................................................................................... 11 2.2.ThePacific IslandsandPolynesia................................................................................. 11 2.2.1.Mangareva.................................................................................................................. 12 2.2.2.Marquesas................................................................................................................... 13 2.2.3.WesternSamoa........................................................................................................... 13 2.3.WheredidthePolynesianscomefrom?........................................................................ 14 2.3.1.Linguisticevidence .................................................................................................... 14 2.3.2.Farmingandcolonization........................................................................................... 15 2.3.3.Lapitaculture.............................................................................................................. 16 2.4.Aboutmigrations,‘slow’and‘fast boats’..................................................................... 16 2.5.Geneticevidence–mitochondrialDNAandYchromosome–2different(his)stories? .............................................................................................................................................. 18 2.5.1.Classicalmarkers........................................................................................................ 18 2.5.2.Globingene polymorphisms ...................................................................................... 18 2.5.3.MitochondrialDNA ................................................................................................... 18 2.5.4.Ychromosome ........................................................................................................... 19 3.Materialsandmethods ..................................................................................................... 21 3.1DNAsamples ................................................................................................................. 21 3.2Sample processingandconcentration ............................................................................ 21 2 3.2.1WholeDNAamplification .......................................................................................... 21 3.2.2AmplificationofHLAloci.......................................................................................... 21 3.2.3Sequencingofamplifiedproducts............................................................................... 22 3.3Statisticalanalyses.......................................................................................................... 23 3.3.1Alleleassignmentandallelefrequencies .................................................................... 23 3.3.2Populationcomparisons .............................................................................................. 24 4.Results .............................................................................................................................. 25 4.1.HLAdiversityanddistribution ..................................................................................... 25 4.1.1.Class Ialleles............................................................................................................... 26 4.1.2.Class II alleles ............................................................................................................ 28 5.Discussion ........................................................................................................................ 32 5.1.AmerindianallelesdetectedinEasternPolynesia......................................................... 32 5.2.EuropeanallelesdetectedinEasternPolynesia ............................................................ 33 6.Conclusion........................................................................................................................ 39 Appendix .............................................................................................................................. 40 Acknowledgments................................................................................................................ 43 References ............................................................................................................................ 44 3 Summary Numerousscientificinvestigationshave beenundertakentoanswerthequestionof Polynesianorigins.Mostarchaeologicalandlinguisticevidence andpreviousstudiesin populationgeneticssuggestedthatRemoteOceaniawassettledfromthe west.Thehuman colonizationofthePacific beganwiththesettlementof AustraliaandPapua NewGuinea (PNG)atleast40,000yearsago,andwasfollowedbythesettlementofRemoteOceania, startingabout3,500yearsago.Mostscholarsagreethat present-dayPolynesiansoriginatedin SoutheastAsia,andfirst enteredthe regionas Neolithicagriculturalists.Butthequestionsof thecharacterofcolonizationandtheextentoftheMelanesiancontributiontothePolynesian gene pool,aswell possibleSouthAmericancontacts,still prevail.Certainplants,suchasthe sweet potatoandbottle gourd,indicatesomecontactswithSouthAmerica.Moreover,the NorwegianexplorerThorHeyerdahlshowedthatavoyagefromSouthAmericawas physically possible,eventhoughnodirectevidenceofAmerindianancestryhas beenfound. Interestingly,recentresearchontheHLAsystem showedasignificantSouthAmerican geneticcomponentinEaster Island. Inordertoaddresstheissueof possibleancient contacts betweenPolynesiaandSouth America,andtoinvestigatethe geneticaffinities oftheEasternPolynesians,52human genomic DNAsamples fromthreelocationsinEasternPolynesia (SouthernMarquesas, MangarevaandWesternSamoa)weretestedforHLA polymorphisms.The resultsindicate thattheEasternPolynesiansare principallyderivedfromSoutheastAsia.Somerecent Europeanadmixturewasdetected,mostlikelyduetopost-Europeancontacts.Several polymorphisms pointtoa possible NorthAsianconnection(DRB1*0405andDRB1*1201) andother,rare elements(e.g.A*0212,B*3905andDRB1*1402)areclear evidenceofSouth Americanadmixture.NosignificantMelanesianancestrywas found.Phylogeneticanalysis showedthatthePolynesiansstudieddidnotdiffersignificantlyfromSoutheastAsian populationsofmixedorigins(suchasMalay,Filipino,EastTimoreseandMoluccans) but haveverylittleincommonwiththe present-dayinhabitantsofPapua NewGuinea.The results,however,couldbetheeffectofsamplingvarianceor geneticdriftinPolynesia.In general,the HLA polymorphismsobservedinthisstudy givefurthersupporttothe‘Express train’modelofthecolonizationofthePacific. 4 1. Introduction 1.1. Background Overdecades,theoriginoftheinhabitantsofRemoteOceaniahas beenthe subjectof muchscientificscrutiny.ThehumancolonizationofthewesternPacific(Australia,Papua NewGuinea(PNG) andtheSolomonIslands)has beendatedtoatleast40,000years before present(Bellwood,1978;WicklerandSpriggs,1988).Thedescendantsofthoseearlysettlers stillinhabit present-day PNGandislandMelanesia.TheyspeakPapuanlanguageswhichhave beenshowntobeof greaterantiquityintheregionthanAustronesianlanguages.Thelatter language groupissaidtohave beenintroducedintoOceania by Neolithicfarmers.The appearanceofhorticultureintheregionhas beenassociatedwiththeemergenceofthe Lapita culturecharacterizedby notchedpottery.ThelastwaveofPolynesiansettlementreachedNew Zealandabout800years ago(Anderson,1991). Numerousscientificstudiesinthefieldofmoderngeneticshave confirmedtheAsian ancestry andsignificant homogeneityof present-dayPolynesians.AlbeittheAsianoriginof thePolynesiansisundisputed,thereisevidenceof possibleSouthAmericancontacts,suchas plantsofAmericanorigin(sweet potato,bottle gourd)(Borrell,2007;Green,2000).Another puzzlingissueistheextentofcontact betweenthe protoPolynesians andtheearlier “Melanesian”settlersof Near Oceania. Differenttheorieshave beenbroughtforwardtoexplainthecolonizationofthePacific.
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