Rit LbhÍ nr 100

AncientDNAsamplingreport WalrusbonesfromAlþingisreitur

AlbínaHuldaPálsdóttir,SanneBoessenkool&BastiaanStar

AncientDNAsamplingreport

WalrusbonesfromAlþingisreitur

©AlbínaHuldaPálsdóttir,SanneBoessenkool,BastiaanStarogLandbúnaðarháskóliÍslands2018

AncientDNAsamplingreport:WalrusbonesfromAlþingisreitur

Útgefandi:LandbúnaðarháskóliÍslands

Útgáfustaður:Reykjavík

ISSN1670-5785

Coverphoto:PartialwalruspelvisfromtheAlþingisreiturexcavation.PhotobyAlbínaHuldaPálsdóttir.

TableofFigures

Figure1:2008-32-685Walruspelviswithchopmarksfromcontext#30482,bone#711.Thesmall loosefragmentbrokeoffduringZooMSsampling..................................................................................6

Figure2:2008-32-685Walruspelviswithchopmarksfromcontext#30482,bone#711.Thefour holesarefromZooMSsampling..............................................................................................................6

Figure3:2008-32-709Context#33690,walrusskullfragment,#1051.(PhotobyBrynja Guðmundsdóttir).....................................................................................................................................7

Figure4:2008-32-709Context#33690,walrusskullfragment,#1051.HolefromZooMSsampling.....7

Figure5:2009-32-2419,context#214775walrusvertebra,#1052.HolefromZooMSsampling...........8

Figure6:2009-32-2419,context#214775walrusvertebra,#1052.HolesfromZooMSsampling.........8

Figure7:Twoviewsofafragmentofthewalruspelvis.2008-32-685Walruspelviswithchopmarks fromcontext#30482,bone#711,labnumberWLR036afterancientDNAsampling.Onlythesmall loosefragmentwhichbrokeoffthepelvisduringZooMSsamplingwassampledforancientDNAto minimizedamagetothiswell-preservedbone.....................................................................................11

Figure8:2008-32-709Context#33690,walrusskullfragment,#1051,labnumberWLR035.Thebone aftersamplingforancientDNA.Hereachunkwascutoutfromthemiddleofthebone....................11

Figure10:2008-32-709Context#33690,walrusskullfragment,#1051,labnumberWLR035.The boneaftersamplingforancientDNA.Hereachunkwascutoutfromthemiddleofthebone...........12

Figure11:2009-32-2419,context#214775walrusvertebra,#1052,labnumberWLR037.Twoviews oftheboneafterancientDNAsampling...............................................................................................12

ListofTables

DNAlibrarysuitableforsequencing.EndogenousDNAcontentismeasuredasthepercentageofreads (withaminimumMapQvalueof25)aligningtothePacificwalrusnuclearreferencegenome...........10

AncientDNAsamplingreport:WalrusbonesfromAlþingisreitur

Thewalrusbonesweresampledaspartofthreeresearchprojects:

• NorthernJourneys:ReimaginingtheMedievalRevolution

• TheImpactofArt:InvestigatingArtifactsusingAncientDNAtoTraceHistoricTradeand ExploitationofAtlanticWalrus

• TrackingViking-assistedDispersalofBiodiversityusingAncientDNA

TheprojectsareledbyDr.JamesBarrett,UniversityofCambridge(PI:NorthernJourneys),Dr. BastiaanStar,UniversityofOslo(PI:TheImpactofArt)andDr.SanneBoessenkool,UniversityofOslo (PI:Viking-assistedDispersal).

BonessentforancientDNAsampling

ThebonesthatweresampledforancientDNAanalysisarefromthreeofthefourphases1 ofthe AlþingisreiturexcavationindowntownReykjavíkIceland(Garðarsdóttir,2010,2013;Pálsdóttir,2010, 2013).Theirdatingisasfollows:PhaseIVAD871-1226,PhaseIIIAD1226-1500,PhaseIIAD1500-1800.

TheboneswerepreviouslysampledforZooMS(Buckleyetal.,2014,2015).Thepreservationofthe bonesvariesbuttwoofthemhavebluepatches,likelythemineralvivianite(McGowan&Prangnell, 2006;“vivianite(mineral),”2013),formedduetothepartiallywaterloggedconditionsatthesitealong withthehighironcontentofthesoil.DetailedinformationabouteachboneislistedinTable1.

Explanationofnumbers

EachbagandTyveklabelshouldhavethreeseparatenumbersinthisorder:

• Thefirstnumber2009-32-4060istheNationalMuseumofIcelandnumber.Therecanbemany bonesundereachNationalMuseumnumber.(Thefirstpartistheyearexcavated,thesecond partisthenumberthemuseumgivestheexcavation,thethirdpartisauniquenumbergiven toeachfind/sample/boneintheIntrasyssystemwhichalltheexcavationinformationhasbeen recordedandstoredin).

• ThesecondnumberC#4019892thecontextnumberwherethebonewasfound.

• The#1042isthenumbergiventoallmeasuredbones/bonessentforspecialanalysis/bones withpathologyintheNABONEAccessdatabasefortheanimalbonesfromtheAlþingisreitur excavation.Thereisusuallyonlyonebonebehindanumberlikethis(itmightbeinmultiple fragmentswhichareallobviouslyfromthesamespecimenalthoughthatisrare).

1 Therewereveryfewbonesretrivedfromtheyoungestphaseofthesitewhichdatestobetween1800and around1980(PhaseI).

Site

Table1:ListofthewalrusbonesselectedforancientDNAandisotopesamplingfromtheAlþingisreiturexcavationinReykjavík,Iceland

unit

Alþingisreitur, Reykjavík, Iceland

A

(1226–1500 AD)

Bone# Measurments andcomments.

Walrus Pelvis f 1 11 f 2 ch 711 Size30x13x6cm,weight313gr. Measurements:4.ca.89,645.ca55,795b. 55,166.18,087.136,888.56,729.ca. 127,4210.ca.45,8311.caca43,11.Some bluevivianitepatchesonsurface.Asmall fragmenthadpreviouslybrokeoffduring ZooMSsampling.

Alþingisreitur, Reykjavík,

Alþingisreitur, Reykjavík, Iceland

A 4 (871–1226AD)

4 (871–1226AD)

Walrus Skull f 1 11 1 1051 Size18x10x9cm,weight427gr.Some bluevivianitepatchesonsurface.

Walrus Vertebra f 1 10 u 2 1052 Size6x6x7cmweight57gr.Greatest lengthatleast63,39.BreathofProcessus articularisatleast61mm.

Photosofbonesbeforesampling

Moreviewsofeachboneavailableifneeded.AllphotosbyAlbínaHuldaPálsdóttirunlessotherwise noted.

Figure1:2008-32-685Walruspelviswithchopmarksfromcontext#30482,bone#711.Thesmallloosefragmentbrokeoff duringZooMSsampling.

Figure2:2008-32-685Walruspelviswithchopmarksfromcontext#30482,bone#711.ThefourholesarefromZooMS sampling.

Figure5:2009-32-2419,context#214775walrusvertebra,#1052.HolefromZooMSsampling.

Figure6:2009-32-2419,context#214775walrusvertebra,#1052.HolesfromZooMSsampling.

Laboratorymethods

AllDNAextractionandpre-PCRlibraryprotocolswereperformedinthededicatedancientDNA laboratoryattheDepartmentofBiosciences,UniversityofOslofollowingstrictaDNAprecautions (Allentoftetal.,2012;Cooper&Poinar,2000).Laboratoryprotocols,dataprocessingandfilteringare describedinStaretal.(2018).Inshort,afterUVexposeonallsides,samplesweremilledusingacustom designedstainless-steelmortar(Gondek,Boessenkool,&Star,2018)oraRetschMM400mixermill.

Extractionusedacombinedbleachandpre-digestionprotocol(Boessenkooletal.,2016).Specifically, bleachwasheswereperformedinduplicate(150-200mgofpowdereach)(Boessenkooletal.,2016), washedwithH2Oandpre-digested,whichwasfollowedbyanovernight,seconddigestion(Gambaet al.,2015).Thetwoeluateswereconcentrated(Amicon-30kDACentrifugalFilterUnits)afterthe overnightdigestionandcombined,extractingDNAusingMinelute(Qiagen)accordingto manufacturer’s instructions Using 60 μl pre heated (60°C) EB buffer, DNA was eluted by incubating for 15minat37°C(Staretal.,2014).Afterthis,blunt-endIlluminalibrarieswerebuilt(Meyer&Kircher, 2010;Schroederetal.,2015)andlibraryqualitywasassessedusingaBioanalyzer2100(Agilent).

Librariesthatpassedqualitycontrolweresequenced(125bppaired-end)onanIlluminaHiSeq2500 anddemultiplexedallowingzeromismatchesintheindextag.

EndogenousDNAcontentandcoverageonthemitochondrialgenomewereassessedforeachsample.

SequencingreadswereprocessedusingPALEOMIX(Schubertetal.,2014),collapsingforwardand reversereadsusingAdapterRemovalv1.5(Lindgreen,2012),andalignedtotheAtlanticwalrus mitogenome(Arnasonetal.,2002)withBWA aln v.0.7.5a-r405(Li&Durbin,2009)andthePacific walrus(O.r. divergens)nucleargenome(Footeetal.,2015).Alignmentswithaqualityscore(MapQ)of <25wereremoved.EndogenousDNAcontentismeasuredasthenumberofuniquereadsaligningto thePacificwalrusreferencegenome.

ResultsofancientDNAanalysis

Unfortunately,theDNAlibrariesfromthethreewalrusspecimensdidnotyieldsufficientendogenous DNApreservationforfurtheranalyseswithinthisstudy(Table2).Threesheepbonessampledfor ancientDNAfromtheAlþingsreiturexcavationhavealsohadeitherverylowornoendogenousDNA content(unpublishedresults).TheseresultssuggestDNApreservationatthissiteispoor.

Table2ResultsfromancientDNAanalysisofthethreewalrusbones.*n.a.;WLR035didnotyieldaDNAlibrarysuitablefor sequencing.EndogenousDNAcontentismeasuredasthepercentageofreads(withaminimumMapQvalueof25)aligningto thePacificwalrusnuclearreferencegenome.

Museumnumber Internallabnumber Sequencedreads EndogenousDNA (%) 2008 32

WLR036

WLR035

32

WLR037

0.0013

0.0006

PhotosofbonesafterancientDNAsampling

Funding

ThisworkwassupportedbytheResearchCouncilofNorwayprojects262777and230821,the NansenfondetandtheLeverhulmeTrustproject“NorthernJourneys”(MRF-2013-065).

Acknowledgements

WewouldliketothankAgataGondekandDr.JamesBarrett.WethanktheNationalMuseumof Icelandforgrantingpermissiontosamplethewalrusbones.

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