1

Biodiversity Research and Innovation in Antarctica and the 1

Southern Ocean 2

20203

PaulOldhamandJasmineKindness14

Abstract 5

ThisarticleexaminesbiodiversityresearchandinnovationinAntarcticaandtheSouthern6Oceanbasedonareviewof150,401scientificarticlesand29,690patentfamiliesfor7Antarcticspecies.Thepaperexploitsthegrowingavailabilityofopenaccessdatabases,8suchastheLensandMicrosoftAcademicGraph,alongwithtaxonomicdatafromtheGlobal9BiodiversityInformationFacility(GBIF)toexplorethescientificandpatentliteraturefor10theAntarcticatscale.Thepaperidentifiesthemaincontoursofscientificresearchin11Antarcticabeforeexploringcommerciallyorientedbiodiversityresearchanddevelopment12inthescientificliteratureandpatentpublications.Thepaperarguesthatbiodiversityisnot13afreegoodandmustbepaidfor.Waysforwardindebatesoncommercialresearchand14developmentinAntarcticacanbefoundthroughincreasingattentiontothevaluationof15ecosystemservices,newapproachestonaturalcapitalaccountingandpaymentfor16ecosystemservicesthatwouldbringtheAntarctic,andtheAntarcticTreatySystem,into17thewiderfoldofworkontheeconomicsofbiodiversity.Economicsbasedapproachescan18becriticisedforreducingbiodiversitytomonetaryexchangevaluesattheexpenseof19recognitionofthewidervaluesofbiodiversityanditsservices.However,approaches20groundedintheeconomicsofbiodiversityprovideatransparentframeworkfor21approachingcommercialactivityintheAntarcticandintroducingrequirementsfor22investmentsintheconservationofAntarcticbiodiversitybythosewhoseektoprofitfrom23it.24

25

1PaulOldhamholdsaPhDinanthropologyfromtheLondonSchoolofEconomicsandisanIndustrialFellowattheManchesterInstituteofInnovationResearch,AllianceManchesterBusinessSchool,ManchesterUniversity.HewasAdjunctSeniorFellowattheInstituteforAdvancedStudyofSustainability,UnitedNationsUniversityatthetimeoftheresearch.JasmineKindnessholdsanhonoursdegreeinanthropologyfromtheLondonSchoolofEconomicsandisanMScStudentintheHumanitiesandSocialSciencesDepartmentatOxfordBrookesUniversity.TheresearchwasfundedundertheBiospolarProject,ResearchCouncilofNorway(RCNprojectnumber257631/E10).TheauthorsthankDr.AndrewMarshforassistanceininterpretingindustrialchemistrybasedpatentdocumentsdiscussedinthispaper.

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Introduction 26

Thisarticleexaminesthescientificandpatentlandscapeforbiodiversitybasedresearch27andinnovationinAntarcticaandtheSouthernOcean.Thearticleisbasedonareviewof28150,401scientificarticlesand29,690patentfamiliesthatmakereferencetotheAntarctic29orSouthernOceanintheopenaccessLensdatabaseofscientificandpatentliterature.30

TheAntarcticregionisanimportantfocusofscientificresearchinthecontextofthe31biodiversityandclimatechangecrisis[1].Theimpactsofclimatechangeonterrestrialand32marinebiodiversitymaybebothpositiveandnegative,withparticularconcernemerging33overnon-nativespeciesinterrestrialAntarcticaandenvironmentalwarmingandocean34acidificationinthemarineenvironment[1].CommercialactivityinAntarcticaincludes35tourismandtheharvestingofmarinegeneticresourcessuchasAntarctickrilland36Antarctictoothfish[2–4].Theregionhasalsobeenafocusforbioprospectingorresearch37onthepotentiallyusefulpropertiesofAntarcticbiodiversityforthedevelopmentofnew38andusefulproducts[5–10].Theemergenceofcommerciallyorientedresearchand39developmenthasledtoincreaseddebatesaroundthegovernanceofresearchactivity,40ethicsandbenefit-sharing.Debatesonthegovernanceofresearchandbenefit-sharing41mirrordebatesonaccesstogeneticresourcesandbenefit-sharingundertheUnited42NationsConventiononBiologicalDiversityanditsNagoyaProtocol,andrelatedpolicy43processessuchasnegotiationsonanewtreatyonmarinebiodiversityinareasbeyond44nationaljurisdictionundertheUnitedNationsLawoftheSea.From2005onwards45bioprospectinghasappearedontheagendaoftheAntarcticTreatyConsultativeMeeting46(ATCM)ofContractingandConsultativePartiestotheAntarcticTreatySystem(ATS).The47AntarcticTreatySystemconsistsofasetofagreementsthataimtoensurethatthe48Antarcticisa“naturalreserve,devotedtopeaceandscience”forthebenefitofhumankind.49However,todate,activityundertheAntarcticTreatySystemwithrespectto50bioprospectinghasbeenlimitedtoinformationgatheringbytheScientificCommitteeon51AntarcticResearch(SCAR).52

Theaimofthisarticleistwofold.First,weimprovetheevidencebasefordebatesonthe53governanceofresearchinAntarcticaandtheSouthernOceanbymakingdatasetsof54scientificandpatentliteratureandtaxonomicdataabouttheAntarcticpubliclyavailable55throughtheOpenScienceFramework.Thedatasetsareintendedtocontributeto56methodologicaldevelopmentinareassuchscientometricsandmachinelearningbased57approachestonaturallanguageprocessing[11–13,13–16].2Wearguethatfurther58methodologicaldevelopmentisdesirable,includingbydataproviders,inordertoaddress59weaknessesindatacoverageanddataquality.60

Second,weexaminethemainfeaturesofthescientificandpatentlandscapesforAntarctica61andtheSouthernOceanwithafocusonbiodiversitybasedinnovation.Thepaperargues62thateffortstoaddresscommercialresearchanddevelopmentcouldusefullybeapproached63

2AvailablethroughtheBiospolarAntarcticLiteratureandPatentsrepositoryathttps://osf.io/py6ve/

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inthewidercontextoftheecosystemservicesprovidedbyAntarcticbiodiversity[17–19].64Thiscouldbeextendedtotheapplicationofnaturalcapitalaccounting,presentlybeing65incorporatedintoSystemsofNationalAccounting(SNAs),totheAntarctic[20].Theriseof66ecosystemservicesandnaturalcapitalaccountingisgroundedinincreasingrecognition67withintheeconomicscommunitythatbiodiversityandtheservicesitprovidesarenotfree68andmustbepaidfor.Ifweacceptthatbiodiversityisnotafreegoodandthateveryone69must,proportionatetotheirmeans,paysomethingweareabletoaskotherquestions,such70as:howmuch,bywhom,inwhatformandtowhatends?Thispaperdoesnotaimto71answerthesequestionsbutcontributestotheevidencebasefordeliberationonthe72opportunitiestoaddressissuesoffairness,equityandbenefit-sharingforbiodiversity73basedresearchanddevelopmentinAntarcticaandtheSouthernOcean.74

Methods 75

Thispaperisacontributionfromanthropologyanddatasciencethatcombinesanalysisof76thescientificandpatentliteraturewithtaxonomicdatafromtheGlobalBiodiversity77InformationFacility(GBIF)onAntarcticbiodiversity.Themethodconsistsoffivemain78steps:79

1. Capturingtherawuniverseofscientificandpatentpublicationsmakingreferenceto80AntarcticaandtheSouthernOceaninmultiplelanguagesusingtheLensopenaccess81databasehttps://www.lens.org/;82

2. Identifyingandcleaningauthor,organisation,inventorandpatentapplicantnames83andlinkingwithgeospatialdatasourcesusingMicrosoftAcademicGraph(MAG)data84tables(January2019release)fromMicrosoftAcademic[21];i85

3. Textminingthescientificliteratureandpatentliteraturefortaxonomicnameswitha86focusonspeciesnamesandalimitedsetofcommonnamesbasedondatafromthe87GlobalNamesIndex(GNI)andGBIF;88

4. Refiningthedatatofocusonscientificliteratureandpatentdatacontaininga89verifiableAntarcticspeciesusingacleanedversionofAntarcticcountrycodeAQdata90fromGBIF;91

5. TextminingtheresultsforAntarcticplacesnameswithaparticularfocusonpatent92datausingdatafromtheSCARCompositeGazetteerofAntarctica(CGA)andthe93GeonamesdatabaseofAntarctica(AQ)countrycodeplacenames.94

Thestepsaboveinvolvedanumberofelementsandissuesofinteresttothedatascience95communitythatcanbesummarisedasfollows.96

OpenaccessdatabasessuchastheLensfromCambiaandtheQueenslandUniversityof97Technologymakeitpossibletosearchfordatainmultiplelanguagesandtoamorelimited98degreetosearchthefulltextsofscientificpublicationsandpatentdocuments.Basedona99setofexperimentalteststhefollowingmulti-languagequerywasdevelopedtocapturethe100availableuniverseofpublicationsaboutAntarcticaandtheSouthernOceaninmultiple101languages.102

103

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104

Antarctic* OR “Southern Ocean” OR “South Pole” OR “alqarat alqatabiat aljanubia” OR Antarctique OR Antarktida 105OR Antarktidë OR Antarktik OR Antarktika OR Antarktikí OR antarktis OR Antarktis OR Antarktisz OR Antarktyda OR 106Antartaice OR Antártica OR antártida OR Antártida OR Antàrtida OR Antartide OR Antartika OR Antartikako OR 107Jacaylku OR “Nam Cực” OR “namgeug daelyug” OR Suðurskautslandið OR Ανταρκτική OR Антарктида OR 108Антарктик OR Антарктика OR Антарктикийн OR Антарктикот OR Антарктыда 109

TheLensScholarlydatabaseaggregatesdatafromanumberofdifferentsourcesincluding110MicrosoftAcademicGraph(MAG),Crossref(formetadata),PubMedformedicallyfocused111literatureandCORE(core.ac.uk)foropenaccessfulltexts.Theavailablefieldsofsearch112varyacrossdatasourceswithallexceptforCOREbeingconfinedtometadatafieldssuchas113title,abstract,keywords,affiliations,authorsetc.Table1summarisestherawsearch114resultsfromthedifferentsources.115

Table 1: Antarctic Paper Counts by Type

name papers

papers 150401

microsoft academic graph 135150

metadata 122886

CORE full texts only 27515

pubmed 16053

pubmed central 2754

Note:

Metadata refers to Antarctic search terms in titles, abstracts, keywords, fields of study and MeSH terms.

InconsideringtherawdatainTable1itisimportanttonotetwopoints.First,thatthe116analysisinthispaperislimitedtothe135,150papersfromMicrosoftAcademicGraph.The117reasonforthisisthattheLensdoesnotdirectlyprovideaccesstoaffiliationdatabutitis118possibletoretrievethisdatausingthefreelyavailableMicrosoftAcademicGraphdatabase119tables.Second,caseswheretheAntarcticsearchqueryonlyappearedinCOREfulltexts120meritmoredetailedinvestigationinfutureresearch.Exceptwheretheyappearin121MicrosoftAcademicGraphthesetextsareexcludedfromthequantitativeanalysisbelow.122

TheresultsofthesearchincludeanydocumentthatreferencesAntarctica,theSouthern123OceanortheSouthPoleanywhereinmetadata(includingauthoraffiliationsand124

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bibliographicreferences)ortheavailablefulltextsfromCORE.Thiswillinevitablyinclude125sourcesofobjectivenoise,suchasreferencestotheSouthPoleofMarsorTitanor126negationssuchas“exceptAntarctica”,andsubjectivenoisesuchastheexplorationofthe127roleAntarcticaplaysinthehumanimaginationinliteraryorculturalstudiesthatmaynot128beofinteresttosomereaders.Aconventionalapproachtodealingwithnoisein129bibliometrics/scientometricsistoattempttoexcludeitatsource.However,weadopteda130differentapproachinformedbythepossibilitiesoftheriseofmachinelearningapproaches131tonaturallanguageprocessingandtheirfutureapplicationtopolarresearch.132

MachinelearningbasedapproachestoNaturalLanguageProcessing(NLP)involvetraining133modelstoengageinprobabilisticclassificationoftextsandnamedentityrecognition134(e.g.placenames,speciesnames).Atthetimeofwritingpopularlibrariesincludekeras,135fasttext,scikit-learnandspaCy(amongothers).Thekeyconditionfortrainingmodelsisthe136availabilityofpreferablylargevolumesoflabelledtextsforuseintraining,testingand137evaluatingmodels.Viewedfromthisperspective,rawdatathatincludesnoisethatisclose138tothesubjectmatter(e.g.theSouthPoleofTitanor“everywhereexceptAntarctica”)is139valuable.Ratherthanexcludingnoiseatsourcewethereforeadoptedtheapproachof140leavingthedataasisandaddinglogicalTRUE/FALSEcolumnstotherawdatatableas141labelledfilters.Thefiltersarebasedontextminingofpublicationmetadata(titles,142abstracts,authorkeywords,fieldsofstudy,MeSH(medicalsubjectheadingterms).Table2143displaysthefilters.144

Table 2: Paper Counts by Subject (metadata only)

name papers

climate 37015

taxonomic name 25662

biodiversity 25233

southern ocean 12939

antarctic species 12768

arctic 10965

mammal 8365

planets 4579

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Table 2: Paper Counts by Subject (metadata only)

name papers

birds 3758

candida antarctica 3751

krill 3127

seal 2848

penguin 2559

whale 1688

acidification 652

innovation 195

ecosystem services 122

bioprospecting 99

Note:

Counts of terms appearing in paper metadata including titles, abstracts, keywords, fields of study and MeSH terms.

145

Theaimofthefiltersistoallowausertorestrictthedatatoareasofinterest.Forexample,146‘taxonomicname’isafilterforrecordscontainingauninomialorbinomialspeciesname147while‘antarcticspecies’referstospeciesthatoccurinAntarcticavalidatedinthe148taxonomicdatawithanAntarcticlocation.149

Inthesecondstep,datafromtheLenswasfederatedwithMicrosoftAcademicGraphfrom150MicrosoftAcademic(January2019,release).MicrosoftAcademicGraphisbasedondata151fromtheBingsearchengineandismadeavailablefreeofchargeasasetofdatatablesthat152containover200millionscientificrecords.FederationwasperformedusingaDatabricks153ApacheSparkclusteronMicrosoftAzurerunningRinRStudiowiththesparklyrand154

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tidyversepackagesonthemasternode[21–24].Datafederationfocusedontablejoins155betweentheLensdataandaffiliationsandauthorstablesofMicrosoftAcademicGraph156usingthesharedidentifier(thepaperid).Thisyieldedanaffiliationtablewith5,021157identifiedorganisations(affiliationid)andanauthorstablewith244,778authors158(authorid).OneimportantandknownlimitationofMicrosoftAcademicGraphisthatthe159affiliationsdataisincomplete[11].Thus,69,805ofthepapersinthedatasetwererecorded160withanaffiliationidcorrespondingwith52%ofthe135,150papers.However,raw161affiliationdataisavailableintheauthorstableforthefullMAGdatabase.Weusedamulti-162stepprocessdescribedintheOSFrepositorytoimprovecoverageto99,794(74%)of163MicrosoftAcademicGraphdataforAntarctica.Themajorityoftheoutstanding34,249164papersweremadeupofbookchapters,booksandotherdatatypesthatnormallylack165affiliationdata(17,886).Asaconsequence,dataonaffiliationsisincompleteandmustbe166classifiedasindicativeratherthandefinitive.Whiletheseresultsmaygivethe167scientometricscommunityreasonforpauseinusingMicrosoftAcademicGraph,wewould168observethatinterrogatingtheseissuesprovidesabasisforfutureimprovementssuchas169retrospectivereindexingtopickupmissingdata.170

Withrespecttopatentdata,atthetimeoftheresearchtheLensincluded115,915,955171patentdocumentsfrom63,366,633families(publicationsgroupedontotheearliestpatent172filinginaset)from115countriesincludingregionalandinternationalpatentoffices.To173retrievepatentdatathesamequerywasperformedusingfulltextsearch(titles,abstracts,174descriptionandclaims).Thisyieldedarawcountof52,701documentsin25,463patent175familiesfromthesearchterms.TheLensisalsoimportantasasourceofpatentdatafor176innovationresearchbecauseitindexesscientificpublicationsthatarecitedbypatent177documents.Whenthesedocumentswereaddedthetotalcountofpatentfamiliesrosetoa178raw29,690families.3179

Patentdocumentsarecommonlyrepublishedmultipletimes.Thus,asingleapplication180mayberepublishedasapatentgrantorwithanadministrativesearchreportorcorrection.181Thesameapplicationmayalsobesubmittedtomultiplecountrieswhereitwillalsobe182republished.Thisintroducesradicalmultipliereffectsintopatentcounts.Thus,the29,690183patentfamiliesinourrawsetarelinkedto163,615laterpatentpublications(family184members).Tocontrolforthis,patentanalystscommonlyreducelinkeddocumentsinaset185or‘family’totheearliestfirstfiling(knownastheprioritydocument).Thisarticleusesthis186approach.Weaddeda“filingorder”filtertotheLenspatentdatathatreducestheoriginal18729,690Lenspatentfamilydocumentstothe26,120earliestfirstfilings.Finally,itis188importanttoemphasisethatpatentdata,byvirtueofaccesstothefulltext,istypically189noisierthansearchesofthemetadataforscientificliteraturewithtermssuchas“South190Pole”havingmultipleuses.191

TextminingofthescientificandpatentliteraturewasperformedinRusingthespacyr192packagethatprovidesaccesstothePythonspaCylibraryformachinelearningandNatural193LanguageProcessingandtheRtidytextpackage[25,26].Textminingfocusedonthe194

3Publiclyaccessibleat:https://www.lens.org/lens/collection/179814

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identificationofbinomialanduninomialtaxonomicnamesintextsfollowedbythe195identificationofplacenames.Thiswasperformedbyextractingnounphrasesfromthe196titles,abstracts,keywords,fieldsofstudyandMeSHtermsforLensrecordsinthescientific197literature.Inthecaseofpatentdata,internalfulltextcollectionsfocusingontheUS,the198EuropeanPatentOfficeandtheinternationalPatentCooperationTreatywereusedtotext199minetheavailabletitles,abstracts,descriptionsandclaims.Toaddressmemoryissues200whenusingspaCywithspacyrweusedthetidytextpackagetoparsetextsintosentences,201twowordphrases(ngram2)andwords(ngram1).Itshouldbenotedthatapproaches202focusingonnounphrasesarepartlydependentonthelanguagemodel(English)usedfor203nounidentification.Wethereforeexpectroomforimprovementindatacaptureacross204multi-languagesources.205

Matchingwithtaxonomicnamesandplacenameswasperformedusingdictionarybased206approaches.Nounphraseswerematchedagainstadictionaryofjustover6million207binomialspeciesnamesoriginallyextractedfromtheGlobalNamesIndex(GNI)andits208webserviceathttp://gni.globalnames.org/[27].Thefulllistofbinomialswasderivedfrom209acopyoftheGlobalNamesIndexkindlyprovidedbyDavidRemsenandDmitryMozzherin210asleadingdevelopersofthewiderGlobalNamesArchitecture.Individualwords211(uninomials)werechosenformatchingwithentriesintheFamiliesofLivingOrganisms212(FALO)datasetfromGBIFthatconsistsofsingleoruninomialnamesforKingdoms,213(e.g.Animalia),Families(e.g.Ursidaeforthebearfamily)etc.[28,29].A2014specieslist214fromtheWorldRegisterofMarineSpecies(WoRMS)databasewasusedtoaddafilterfor215marinespeciesintheliteratureandpatentdatatables.Wewouldnotethatcareful216attentionisrequiredtoimprovementsintheclassificationofmarinespecies(e.g.to217distinguishbetweenterrestrialaquaticandmarineorganisms)inlaterupdatesofWoRMS218whenapproachingthisfilter.219

TherawresultsoftextminingwithdictionarieswerepassedtotheGBIFAPIusingthe220taxizepackagefromROpenScitoretrievethetaxonomichierarchy[30].Oneissuewhen221retrievingthetaxonomichierarchyforthousandsofspeciesisthatasinglespeciesname222maymatchtomultiplerecords(e.g.assynonymsorhomonyms).However,itisimpractical223tomanuallyreviewthousandsofresultswhenretrievingdata.Fortunately,thereturnfrom224taxizeincludesa‘multiplematches’columnthatidentifiesthesecases.Themultiple225matchesfilterisretainedinthetaxonomicdatatablestoallowtaxonomicspecialiststo226reviewand,asnecessary,refinethedata.227

Scientificandpatentpublicationsthatincludetaxonomicnamescommonlyinclude228multiplenames.Thisisparticularlytrueinpatentdocumentsandpresentsthechallenge229thataparticularorganismmayormaynotoccurorhavebeencollectedintheAntarctic.230GBIFmaintainsadatasetofoccurrencerecords(observations)withcountrycodeAQthat231inMay2019consistedof2,729,211occurrencerecords[31].However,atthattime,over1232millionoftherecordswererecordedatlatitude-91or-90revealingunlikelyandinvalid233records.Toaddressthis,thedatawasrestrictedtorecordscontainingatextentryfor234localityandaseconddatasetfor-60latitudeSouthwasgeneratedandcombined[32].To235addressnoisyrecordsamulti-stepprocedurewasadoptedinvolvingremovinginaccurate236coordinateswiththeROpenSciCoordinateCleanerpackageinR[33].Inthesecondstep,the237SCARCompositeGazetteerofAntarctica(CGA)of23,833names,wasusedtotextminethe238

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localityfieldinGBIFdataandsingleoccurrencerecordsweremanuallyreviewedin239VantagePointfromSearchTechnologyInc.Inthethirdstep,singlespeciesoccurrence240recordsthatlackedlocalityinformationwereidentified.Inthefourthstep,afilterwas241addedforoccurrencessouthof-60degreeslatitudeasthedemarcationpointforthe242SouthernOceanandAntarctica.Inthefifthstep,aspeciesoccurrencecountwasadded243basedontheobservationthatlowspeciesoccurrencerecordsthatlacklocalityinformation244areoftennoise.Inasixthstep,afilterwasaddedforfossilrecordsbasedontheexisting245GBIF“basisofrecord”field.OccurrencerecordswithavalidatedAntarcticlocationinthe246localityfieldbecamethebasisforthe‘antarcticspecies’filterappliedacrossthedataset.247Theadditionofan‘occurrencecount’fieldallowthespeciesrelateddatatobe248progressivelyrestrictedtothosewithavalidatedAntarcticlocationinanorderedway.249

Asthissummaryofmethodologicalstepsmakesclear,thefederationofscientificliterature,250patentliteratureandtaxonomicdatainvolvesanumberofmethodologicalchallenges.Itis251alsoclearthatwhiletheriseofopenaccessdatabasesrevolutionisestheopportunitiesfor252thistypeofanalysisatscale,thereareavarietyoflimitationsinthedatasources.This253meansthattheanalysispresentedinthispaperisindicativeratherthandefinitive.254Nevertheless,highlightingtheselimitationspresentsopportunitiestoidentifyways255forwardinimprovingdatacoverageanddataqualitytoinformdecision-making.256

Results 257

Figure1displaysanoverviewoftherawdatasetfortheAntarcticsearchterms.InFigure2581Awecanimmediatelyobservethatafterasteepincreaseinthepapercounttoapeakin2592014of7,468publicationsthedatadisplaysadecliningtrend.However,inourviewthis260willreflectdataavailabilityissueswithMicrosoftAcademicGraphratherthananactual261declineinpublicationsreferencingAntarctica.Thereasonforthisisthatasteepdecline262fromaroundthesamepointisobservablefornon-Antarcticdata.Anexplanationofthis263issuecouldusefullybeaddedtotheMicrosoftAcademicGraphdocumentationtoimprove264certaintyforusers.265

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266

Figure1:OverviewofScientificLiteratureforAntarctica267

MicrosoftAcademicGraphusesacombinationofdatafromWikipediaandmachine268learningtoidentifyandlabelpapersbysubjectscalled“FieldsofStudy”[34].Incontrast269withapproachessuchasClarivateAnalyticsWebofScience,thatcategorisejournalsrather270thanpapers,thisapproachallowsfortheuseofmultiplelabelsatdifferentlevelsofdetail271[34].272

IntheJanuary2019release,MAGFieldsofStudyconsistedof19topleveldisciplinesthat273aredisplayedinredinFigure1B.Theremainingfields,showninblue,arechildrenofthe274MAGdisciplines.Thus,inFigure1Boceanography,climatology,geomorphology,275atmosphericsciencesetc.areallchildrenofgeology.Incontrast,ecologyandbotanyare276childrenofbiology.Thesechildreninturnhavesub-childlabelsatvaryinglevelsofdetail277includinglimitedlabelsfortaxonomicclassification.Overall,thissignifiesthatpapersmay278bedividedintoverybroadfieldsandmayappearmultipletimesintherankingsatdifferent279levelsofdetail.280

Figure1Cdisplaystheavailabledataonthenumberofpapersperorganisation.Thedatais281countedbyaggregatingthepaperslinkedtoanorganisation(whichmayincludemultiple282

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authorsfromthesameentity)andthencountingthedistinctpapers.Asnotedabove,it283shouldbeemphasisedthatthisdataisindicativeratherthandefinitive.Astheresolutionof284affiliationdataimproveswewouldexpectthenumbersandrelativepositionsof285organisationsintherankingstochange.Nevertheless,thedataisindicativeofsomeofthe286mostimportantorganisationsconductingresearchinvolvingtheAntarcticinrecent287decades.288

Researchersfrom134countriesappearedintherawpublicationdatarelatingtothe289Antarctic.However,rankingsareaffectedbytheavailabilityofaffiliationdata.Wecangain290aninitialideaofthegeographicdistributionoforganisationsinvolvedbymapping291organisationsinthedatathatalsoappearinthepublicdomainGlobalResearchIdentifier292Database(GRID)https://www.grid.ac/.TheGRIDdatabaseformspartofagrowingeffort293toharmoniseinstitutionalnamesforgeographicmappingandotherpurposes.Figure2294breaksoutthefulldatafromFigure1Canddisplaysamapofavailablegeographicdatafor295organisationspublishingresearchrelatingtoAntarcticaandisaccompaniedbyarankingof296countriesbasedonthenumberofdistinctpublicationsofalltypeslinkedtoAntarctica.297

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298

Figure2:GeographicDistributionofResearchOrganisationsLinkedtoAntarctica299

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Itisworthnotingthatsomecountrieswithorganisationswithasignificantpresencein300Antarcticresearchareprobablyunder-representedintheorganisationmapbecausetheir301dataisdistributedacrossmultipleorganisationswithnoavailablegeoreferencedata,302notablyRussia(with63organisations).303

Figure1D(above)displaystherankingsofpapersbyindividualauthors.Topranking304authors,basedpurelyonthenumberofpublishedpapersordatasetsappearingin305MicrosoftAcademicGraph,includemarinegeologistGerhardKuhnattheAlfredWegener306InstituteHelmholtzCentreforPolarandMarineResearch[35],terrestrialecologistPeter307ConveyattheBritishAntarcticSurvey[3,36],andgeophysicistKarstenGohlatthe308WegenerInstitute[37,38].Leadingwomenscientistsinthedatabypublicationcount309includegeophysicistGabrieleUenzelmann-NebenattheWegenerInstitute[39,40],marine310biologistKatrinLinseattheBritishAntarcticSurvey[41,42]andclimatescientistValerie311Masson-Delmotte[43,44].Insomecasesresearchersmaybeactiveinresearchand312publicationonbothAntarcticaandtheArcticaspartofwiderpolarresearch.313

ThisglobaloverviewofresearchreferencingtheAntarcticservestodemonstratethe314potentialoftoolssuchastheLensandMicrosoftAcademicGraphtoilluminateresearch315landscapesonthegloballevel.Atthesametime,dataontrends,affiliationsand316georeferencingexposestheneedforimprovementsindataqualityandcoverage.However,317whilerecognisingtheseconstraints,thisapproachalsosignificantlyexpandsouraccessto318dataonscientificpublicationsabouttheAntarctic.Inanimportantcontributionto319bibliometricanalysisJietal.2014publishedanalysisofresearchonpublicationsinthe320Antarcticbetween1993and2012usingasearchfortheAntarcticinWebofSciencethat321yielded36,238publications(aftertheexclusionofspeciescontainingantarcticainthe322name)[45].Incontrast,forthesameperiodMicrosoftAcademicGraphproduced71,804323distinctpaperswith79,647acrosstheLens.Theincreaseinpublicationdatawillreflecta324combinationofthechoiceofsearchterms,thewiderscopeofMicrosoftAcademicGraph,325thegrowingavailabilityofdatainmultiplelanguages(with46languagesrepresentedin326thedata),thegrowingavailabilityofmillionsofopenaccessfulltextsthroughCORE327(core.ac.uk),andthegrowingemphasisonopenaccessdatainscientificpolicies.328

Theincreasingavailabilityofpublicationdataatscalebringswithitaneedtofocuson329potentialsourcesofnoisebutalsoprovidesopportunitiestodrillintothedatainspecific330areasofinterest.ExistingbibliometricresearchontheAntarctichasfocusedonthe331explorationofhighlycitedresearch[46],theroleofresearchstationsinpromoting332collaborativeresearch[47],andmappingglacierresearchwithWebofScience[48].Asthis333suggests,publicationdataonAntarcticaprovidesrichopportunitiesfortheexplorationof334specificresearchthemes.WenowturntotheanalysisofresearchonAntarcticainvolving335biodiversityatthespecieslevelasabasisforexploringcommercialinterestinAntarctic336speciesinpatentdata.337

338

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Biodiversity Research in Context 339

Asweobservedabove,theresearchprofilefortheAntarcticisdominatedbygeology,340climatologyandotherEarthSciencesubjects.Thisisreflectedinthetopcitedpublications341forAntarcticaincludingtopicssuchas:highresolutioninterpolatedclimatesurfacesfor342globallandareas[49],mixedeffectsmodellingofecologywithR[50],theIPPC4reporton343ClimateChange2007:Impacts,Adaptation,andVulnerability,globalanalysisofseasurface344temperatures[51],andtheclimateandatmospherichistoryofthepast420,000yearsfrom345theVostokicecore,Antarctica[52].346

AsweobservedinthediscussionofAntarcticfieldsofstudy,biologyisaprominentsubject347areathatisaccompaniedbyanumberoflargesubfieldssuchasecology,botanyand348biochemistry.Topcitedresearchinthefieldofbiologyincludesanewphylogeneticmethod349forcomparingmicrobialcommunitiesthatincludescomparisonofAntarcticandArctic350communities[53],theinfluenceoftemperatureonphytoplanktongrowth[54],sterol351markersformarineandterrigenousorganicmatter[55],analysisofthegenus352Nocardiopsis,includingdiscussionofNocardiopsisantarctica,asadistinctActinomycete353lineage[56],andfattyacidtrophicmarkersinthepelagicmarineenvironment[57].354

Themainfocusofthepresentresearchwasonidentifyingandextractingspecieslevel355informationfromresearchontheAntarcticusingtextmining.Asastartingpoint,research356onspeciescanbedividedintotwobroadcategories:a)directfieldresearchinvolving357Antarcticspecies,and;b)indirectorfollowonresearch,includingclassificationand358comparativeanalysis,andtheexplorationofthepropertiesoforganisms.359

Intotalweidentified1,819binomialspeciesnameswithrecordedoccurrencesinthe360scientificliteraturefortheAntarctic.Ofthese,1,666hadspecificlocalityinformation.In361thecaseofsomeanimalssuchaswhales,seals,penguins,andkrill,commonnames,362e.g.BluewhaleorAdeliepenguin,appearmorefrequentlyintheliteraturethantheirLatin363names.Toaddressthis,additionalcountswereperformedforthemajorgroupsincluding364bothcommonandtaxonomicnamesandmarkedintheaccompanyingdatatable.365InformationonapubliccollectionofbiodiversityliteratureforAntarcticaandtheSouthern366Oceanisprovidedinthesupplementarymaterial.367

Figure3displaysthedatarankedbyspeciesandthenumberofscientificpublicationsfor368the1,819species.369

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370

Figure3:TopRankingSpeciesforAntarctica371

ThedatainFigure3revealstheprominenceofCandidaantarctica(acceptedname372Moesziomycesantarcticus)andkrill(Euphausiasuperba)outsidethemajorAntarctic373mammals.ThisreflectstheeconomicimportanceofCandidaantarcticaandtheecological374andeconomicimportanceofkrill.375

Wegainamoredetailedinsightintotheprominenceofspeciesacrossthemajorkingdoms376inthescientificliteratureinFigure4.Wewillnowbrieflysummarisesomeofthehighlights377oftheliteratureandbegintofocusinonresearchwithcommercialapplications.378

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379

Figure4:TopRankingSpeciesforAntarcticabyKingdom380

ForanimalsonbothcommonandtaxonomicnamesAntarctickrillisamajorfocusofthe381literaturethatreflectssignificanteconomicinterestinoilextractionfromanabundant382speciesthatisrichinomega-3polyunsaturatedfattyacids[58–60].Muchoftheliterature383onAntarctickrilldetailsmethodsandsuccess-ratesinextractingproteins,fattyacids,384aminoacidsandlipidsfromthisspecies.Additionalworkhasfocusedonthesuitabilityof385krillspeciesasfeedinsalmonaquaculture[61,62].Thecombinationofclimatechangeand386commercialexploitationhasledtoworktomodeltheimpactsofanydeclineinAntarctic387krillbiomassonpredators[63].Antarctickrillarealsoafocusoftheecosystem-based388fisheriesmanagementapproachoftheCommissionfortheConservationofAntarctic389MarineLivingResources(CCAMLR)[64].Recentworkonkrillrevealsconcernthatwhile390ecosystemservicesintheSouthernOceanmayincreaseunderclimatechangethismay391occurattheexpenseofthedecouplingofecosystemprovisioningforendemicspecies[65].392Inotherwords,thefoodsupplyforendemicspeciesmaybedisruptedleadingtoaneedfor393specificmanagementofbiodiversity[65].394

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TheAntarcticfurseal,Arctocephalusgazella,ahistoricfocusofthesealfurtrade,hasbeen395afocusofbasicresearchonforagingbehaviouranddietwithrecentresearchexamining396theimpactofhumanassociatedEscherichiacoliinpinnipedssuchasA.gazella[66–68].397

Incontrast,theEmeraldrockcod(Trematomusbernacchii)isafocusofinterestbecauseit398haslosttheabilitytoproduceheatshockproteinsinresponsetothermalstress,acapacity399onceregardedasuniversalamongstorganisms[69,70].Intotalweidentified382articles400forAntarcticfishincludingnotothenioids,suchasNototheniacoriicepsandmembersof401Trematomus,withcoldadaptationasasignificantfocusofresearch(seebelow).402

InthecaseofFungithedataisdominatedbyCandidaantarctica.Candidaantarcticaand403PseudozymaantarcticaaresynonymsfortheacceptednameMoesziomycesantarcticus.As404theliteratureisdominatedbytheuseofthesynonymCandidaantarcticawewillcontinue405withthatpractice.ThetypespecimenforCandidaantarcticawasoriginallycollectedfrom406sedimentat9metresdepthfromLakeVandainVictoriaLand,Antarctica(mycobank407specimenrecord19800).Lipasesfromthisspecieshavebeenusedforawiderangeof408purposes.B-componentlipasederivedfromthisyeasthasbeenfoundtobeasignificantly409robustlipase.Itishighlystereospecific,andhasbeenusedasabiocatalystinawidearray410ofchemicalreactions,withusesinbiotechnology,bioengineering,biochemistryand411biofuels.[71–75]CandidaantarcticalipaseBhasalsobeenfoundtobehighlyeffectivein412aidingthedissolutionofcarbohydrates[77]andfortheproductionofaminesandamides.413AsGotorFernandezet.al.2006explain“Simplicityofuse,lowcost,commercialavailability414andrecyclingpossibilitymakethislipaseanidealtoolforthesynthesisandresolutionofa415widerangeofnitrogenatedcompoundsthatcanbeusedfortheproductionof416pharmaceuticalsandinterestingmanufacturesintheindustrialsector.”[78].417

ThemostprominentbacteriaintheAntarcticliteratureistheubiquitousEscherichiacolior418E.coli.TheprominenceofE.coliintheAntarcticliteraturemainlyarisesfromitsuseasa419researchtool[79–81].ExamplesoftheuseofE.coliinAntarcticresearchincludea420dosimetertoevaluatethepenetrationofbiologicallyactiveultravioletradiationwithina421watercolumnbasedonthesensitivityofaparticularstrainofE.colitoultravioletradiation422[82].However,E.colialsoappearsinthetaxonomicrecordforAntarcticathroughrecords423fromDavisStation.Growinginterestintheimplicationsoftheincreasingpresenceof424humansinAntarcticaarereflectedinexplorationoftheimpactsofE.colistrainsinhuman425wasteupontheAntarcticenvironment[68,83].Asnotedabove,theimpactsofhuman426associatedE.colihavealsobecomeafocusofresearchinsealpopulations[68].Research427onthehealthofpenguinpopulationshasidentifiedantibioticresistantbacteriasuchasE.428coliinGentoopenguinbreedingareas[84].Thediscoveryofantibioticresistantstrainsof429E.coliinpenguinpopulationsimpliesthathumanactivitiesareresponsible[84].430

Pseudoalteromonashaloplanktis,recordedinthetaxonomicrecordatFreiMontalvaBase431onKingGeorgeIsland,appearsinover100publications.Themajorityofresearchtendsto432focusonthecapacityofthisspeciestoexistatcoldtemperatures[85–87].Beta-433galactosidasefromthisspecieshasbeenshowntooutperformothercommercialbeta-434galactosidasessuggestingthatthecold-adaptedbeta-galactosidasecouldbeusedto435hydrolyselactoseindairyproductsprocessedinrefrigeratedplants[88].Thebacterium436Oleispiraantarctica,recordedinthetaxonomicrecordatRoadBayintheRossSea,appears437

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in18publications,twoofwhichhavereceived150ormorecitationssuggestingsignificant438interest.ThisinterestappearstoarisefromO.antarctica’shydrocarbondegrading439propertieswhichmaybebeneficialinthebioremediationofoilspills[89,90].440

Inthecaseofplants,Parnikozaetal.2011highlightthatDeschampsiaantarcticaand441ColobanthusquitensisaretheonlytwofloweringplantsthathavecolonizedtheMaritime442Antarctic[91].Aswewillseebelowtheyareofsignificantcommercialinterestin443connectionwithcoldresistance[92].Deschampsiaantarcticaappearsin250papersand444dominatesthedataonplants.ExistingresearchsuggeststhatDeschampsiaantarcticamay445beusefulasabioindicatorofclimatechangeinWesternAntarctica[93]whilemorerecent446workfocusesonthemechanismsthatallowittosurviveintheAntarcticenvironment[94]447andhowthesemechanismsfareinconditionsofwarmingtemperatures[95–97].448DifficultiesintheinterpretationofthetaxonomicrecordforAntarcticaarereflectedinthe449presenceoftheAustralianseagrassAmphibolisantarcticaintherawtaxonomicdatawhich450asfaraswecanestablish,despiteitsname,doesnothavearecordeddistributionin451AntarcticaortheSouthernOcean.452

Forchromists,singleandmulticellulareukaryotesincludingsomealgaeanddiatoms,453scientificattentionhasfocusedonPhaeocystisantarcticaandDurvillaeaantarctica(New454ZealandBullKelp).ThemarinephytoplanktonPhaeocystisantarcticahasbeenafocusof455analysisinconnectionwiththeformationofalgalbloomsandcarbonsequestrationinthe456SouthernOceanandtheirroleinthecarboncycle[98].Recentworkhasfocusedonissues457suchastheroleofironincolonyformationandtheimpactsofironlimitationandocean458acidificationonP.antarctica[99,100].Thisinturnislinkedwithwiderresearchonthe459implicationsofoceanacidificationfordiatomsandothermarineorganismsinAntarctica460[101].ResearchonP.antarcticaalsoinvolvedsimulationofironfertilizationthatcanbe461linkedtomodelsforgeoengineeringexperiments[102,103].462

DurvillaeaantarcticaappearstobequitewidelydistributedintheSouthernOceanand463countriessuchasNewZealandandChile.Researchonthisspeciesincludesworkonkelp464raftsintheSouthernOceanandsubantarctic,includingtheroleofkelpmatsinthe465dispersalofmarinebivalves[104,105].Morecommerciallyorientedresearchisreflectedin466workonthenutritionalcontentoftheedibleD.Antarctica[106].Theanaerobicdigestionof467thisspeciestoproducebiogashasalsobeenevaluatedasamethodforproducing468renewableenergy[107].Researchhasalsobeenconductedtoextractsolubleβ-1,3/1,6-D-469glucanfromthisspecies,whichhasbeenindicatedtohaveimmunostimulantproperties470[108].High-Malginateextractedfromthisspecies,whichhasalsobeenshowntohave471immunostimulatoryproperties,hasbeenusedinstudiestocreateadietarysupplementfor472feedingandweaningAtlanticcod[109].473

ProtozoanshavereceivedrelativelylittlescientificattentioninAntarcticresearchtodate.474DiaphanoecagrandisisolatedfromsalineAntarcticlakesandcoastalsitesinresearch475datingtotheearly1990shasreceivedthegreatestattentionsofar[110–112].Researchon476Bicostaspiniferadatingtotheearly1980sisalsolimitedbuthasfocusedonissuessuchas477seasonalvariationinabundance[113]withmorerecentworkreportingonthePolarstern478projectintheWeddellSea[114].Inrecentwork,Cryothecomonasarmigeraisbeingusedin479

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worktodevelopabioassaytoinformwaterspecificguidelinestoaddresspollutionin480Antarctica[115–117].481

ResearchonArchaea,singlecelledmicroorganisms,inAntarcticaappearstobevery482limited(notshowninFigure4).ThemajorityofresearchhasfocusedonMethanococcoides483burtonii,withover30publications.However,anumberofthesepapershavebeen484relativelyhighlycitedsuchasworkongenomics,proteomicsandmembranelipidanalysis485inunderstandingmechanismsforcoldadaptation[118–120].Additionalworkhasalso486takenplaceonHalorubrumlacusprofundifocusingonaminoacidsubstitutionsincold487adaptedproteins[121].488

ViruseshaveverylimitedcoverageinGBIFdataandarethereforenotpickedupintext489miningwiththisdatasource.However,aswemightexpect,researchonvirusesappearsin490472publicationsforotherspeciesinthedata.ThisincludesvirusesinAntarcticlakes491[122],researchonvirusesandantibodiesinAntarcticseals[123,124],awiderreviewof492researchonvirusesincetaceans[125,126]andresearchonvirusesinpenguinpopulations493[127,128].494

Ourpurposeinthissectionhasbeentoprovideabriefoverviewofbiodiversityresearchin495AntarcticaandtheSouthernOceanandtobegintofocusonresearchactivitywithactualor496potentialcommercialvalue.Weturnnowtothegrowingbodyofliteratureon497bioprospecting,orbiologicalresearchwithacommercialfocus,intheAntarctic.498

The Bioprospecting Literature 499

Asignificantliteraturehasemergedthatmakesreferencetobioprospectingorbiological500prospectinginAntarctica,consistingofover90articles.Thesearticlesrangefromresearch501withaspecificfocusonidentifyingthepotentiallyusefulpropertiesofAntarcticorganisms502toconsiderationofthepolicyimplicationsofcommerciallyfocusedresearchand503developmentfortheAntarcticenvironmentandbenefit-sharing.504

ThemosthighlycitedarticleonbioprospectingintheAntarcticisa2013analysisoffungal505communitiesassociatedwithmacroalgaeinAntarcticawithpotentialbioactivecompounds506thathassofarreceived83citations[129,130].Otherresearchiscomparativeinnature,507suchascomparingsamplesofsoilbacteriafromaridBrazilianandAntarcticsoilsthatare508capableofdigestingcellulose[131,132].Stillotherworkfocusesonmethodological509developmentsuchasimprovedculturingfrommetagenomic(environmental)samples510fromcoldenvironments[133,134].Innovationinresearchmethodsforbioprospecting511researchalsoextendstotheuseofgenomeeditingtechniquesandsinglecellsequencing512fororganismsfromterrestrialandmarineecosystems[135,135,136].Workonmethods513andtechniquesfrequentlyreferstopolarregionsratherthannecessarilyinvolvingdirect514fieldresearch.Thisisalsoreflectedinreviewarticlesonissuessuchasfungifrom515terrestrialandmarineAntarcticenvironments[137].Recentliteratureonbioprospecting516thathasyettoattractsignificantcitationsincludesworkonenzymesfromfilamentous517fungi[138],Antarcticbacteriaasasourceofnovelantibiotics[10],andassourcesof518antimicrobial,antiparasiticandanticanceragents[139,140].Wewouldemphasisethatthe519literatureusingthetermbioprospectinghasnotincreaseddramaticallyovertheyears520

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fromthefirstrecordin2002,withapeakof8publicationsintheavailabledatafor2018521andanaverageof4publicationsayearbetween2002and2018.Inourviewtheuseofthe522termbioprospectingwillprovetobeanunreliableindicatorforwhatwewouldpreferto523callcommerciallyorientedresearchanddevelopmentfocusingonthepotential524applicationsofthepropertiesofAntarcticorganisms.525

Bioprospectingalsobecameanincreasingfocusofpolicyresearchfromtheearly2000s526onwardsinconnectionwithpotentialmeasuresundertheAntarcticTreatySystem(ATS)527andissituatedinawideremergingliteratureonthegovernanceofareasbeyondnational528jurisdiction[141,142].Thisincludespotentiallegalandpolicymeasures[6,143].Theethics529ofcommercialexploitationofAntarcticaandSouthernOceanresourceshasalsorecently530emergedasanimportanttopicnotablyina2020specialissueofEthicsinScienceand531EnvironmentalPolitics[144–147].532

DebatesaboutbioprospectinginAntarcticahavebeencloselytiedupwithpatentactivity.533Intheeconomicsliteraturepatentactivityisusedasaproxyoutputindicatorforotherwise534invisibleinvestmentsinresearchanddevelopment[6,7,148].Thatis,thefilingofapatent535applicationisanoutcomeofunderlyingfinancialinvestmentsinresearchanddevelopment536[6,7,148].Incontrast,inwiderpolicydebatesonbiodiversity,thefilingofabiodiversity537basedpatentapplicationhasbecomeassociatedwiththeconceptofbiopiracy,or538misappropriation,ofgeneticresourcesfromcountriesandcommunitiesforcommercial539gainwithoutreturningbenefitstocountries,communitiesorbiodiversityconservation.We540nowturntotheavailabledataonpatentactivityforbiodiversityfromtheAntarctic.541

Patent Activity 542

WeidentifiedpatentactivityreferencingAntarcticausingthesearchstrategydescribed543aboveacrossthefulltextsofpatentdocumentsworldwide.Therawdatawasreducedto54429,690applicationsandthenfurtherreducedto26,120earliestfirstfilingsthatformthe545basisofpatentfamilies.Wethentextminedthedocumentsforanytypeofspeciesname546andreducedtheresultstothosewithaverifiableoccurrenceinAntarcticaortheSouthern547OceanintheavailabletaxonomicrecordfromGBIF.Weidentifiedatotalof3,907patent548applicationsand2,738firstfilingsthatcontainedaverifiableAntarcticspecies.Intotalwe549identified1,212speciesinthepatentdataofwhich354wereverifiableAntarcticspecies550basedonlocalityinformationinthetaxonomicrecord.551

InapproachingthisdatawewouldnotethatthedataonAntarcticspeciesthatformedthe552basisforthesearchwillinevitablybeincomplete.Asdiscussedbelow,wealsonotethatthe553appearanceofanAntarcticspeciesinapatentdocumentdoesnotnecessarilymeanthatan554elementofthatspeciesisclaimedbytheapplicants.Wewillbeginwithanoverviewofthe555patentdatacontainingAntarcticspeciesandthenprogressivelynarrowthefocusbefore556concludingwithexamplesofdirectcollectionofsamplesinAntarctica.557

Figure5displaysthecountsofspeciesappearinginthefulltextsofpatentdocumentsthat558areknowntooccurinAntarctica.559

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560

Figure5:AntarcticSpeciesinPatentdocumentsRankedbyFirstFilings561

Figure5revealsthat,aswemightexpectfromthescientificliterature,thetopspeciesis562Candidaantarctica(acceptednameMoesziomycesantarcticus).Thisisfollowedbythe563ubiquitousE.coli.ThepresenceofwidespreadspeciessuchasE.coliwillinourviewreflect564theuseofthisorganismasatoolinbiotechnologyratherthanspecificstrainsfrom565Antarctica.Thiswillalsobetrueforotherwidelydistributedspeciesthathavebeen566recordedintheAntarctic.567

Oneimportantfeatureofpatentactivityisthataspeciesmaybementionedindifferent568sectionsofadocument.Asageneralrule,patentdocumentsthatmentionaspeciesinthe569title,abstractorclaimswillinsomefundamentalsenseinvolvethatspeciesinthe570invention,eitherasasourcefortheinvention,suchasalipase,orasatargetofthe571inventionsuchasapathogen.However,themaindensityofspeciesreferencesisfoundin572

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thedescriptionsection.Figure6showsthebreakdownofspeciesnamesinthepatentdata573presentedinFigure5bydocumentsectionrankedonpatentclaims.4574

575

Figure6:AntarcticSpeciesinPatentDocumentsbySectionRankedonClaims576

AsFigure6revealsthemajorityofreferencestoaspeciesappearinthedescriptionsection577withtheremainderappearingintheclaims.578

Referencestospeciesmayappearinanapplicationforanumberofdifferentreasons:579

• Aspartoftheclaimedinvention(thespeciesismaterialtotheinvention);580• Aspartofexperimentsleadingtotheclaimedinvention;581• Asanactualorpotentialcomponentoringredientintheinvention,includinginclaims582

constructedonthegenus,family,phylumorhighertaxonomiclevels;583

4BecauseaspeciesnamemayappearinmultiplepartsofthesamedocumenttheoverallcountswillbehigherthanthetotalsinFigure5.

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• Literaturecitations(seebelow);584• Passingreferences(e.g.“ineveryspeciesexcept…”,or“speciesxhasbeenusedtodo585

y”)andlonglists(notablyforviruses);586• AsDNAoraminoacidsequencesthatareeitherusedascomparativereference587

sequencesorclaimed.588

Inpractice,determiningwhetheraspeciesismaterialtoaclaimedinventionrequiresclose589attentiontoandinterpretationofthetexts.Inthediscussionbelowweprovideexamplesof590thedifferentreasonsthataspeciesmayappearinthetext.Figure7presentsanoverview591ofthe2,738firstfilings.592

593

Figure7:OverviewofPatentActivityinvolvingAntarcticOrganisms594

Figure5Arevealsarising,ifirregulartrendinfilings.Theapparentdeclineinfilingsin5952016willnormallyreflectadatalagtimeofatleasttwoyearsbetweenthefilingofapatent596applicationanditspublication.Whilearisingtrendisobservablefrom2000onwardsthe597overallnumberoffilings,peakingat220in2014,isrelativelymodest,particularlywhen598

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outstandingissuessuchasnoiseintheformofspeciesrecordedintheAntarcticthatwere599notcollectedintheAntarcticaretakenintoconsideration.600

Figure5BpresentsdataonthemaintechnologyareasbasedonInternationalPatent601Classificationsubclassesandhasbeeneditedforreadability.Figure5Bsuggeststhatthe602Antarcticdataisdominatedbybiotechnologywithpharmaceuticalormedical603preparations,detergents,foods,biocidesandcosmeticsastheothermainproduct604categories.605

IntermsofthenumberoffirstfilingsthedataisclearlyledbyNovozymeswithother606companiesandresearchorganisationssomedistancebehind.Herewewouldobservethat607Novozymeshasalongstandingpolicyofincludinginformationonthegeographicoriginof608geneticmaterialinpatentapplications.Onbalance,thenumberoffilingsoverallandby609organisationisrelativelysmallandsubjecttosignificantyearlyvariation.610

Inpractice,theemergingpatentlandscapeforAntarcticacanbedividedintosixmain611segments:a)sequencedatab)Candidaantarctica,c)Antarctickrill,d)otherspecies612recordedintheAntarctic,e)citationsoftheAntarcticscientificliterature,f)referencesto613Antarcticplacenamesascollectionsites.Wenowaddresseachoftheseinturn.614

Digital Sequence Information 615

TheprominenceofbiotechnologyrelatedactivityissuggestedbythenumberofAntarctic616relatedfilingscontainingDNAoraminoacidsequences.Sequencedata,undertheplace617holderterm‘digitalsequenceinformation’orDSI,hasbecomeanincreasingfocusof618attentionininternationalpolicydebatesonaccessandbenefit-sharingforgenetic619resourcesinrecentyearsundertheConventiononBiologicalDiversityandarangeofother620policyprocesses[149–154].Inthecontextofdebatesonanewtreatyonmarine621biodiversityundertheUnitedNationsLawoftheSea,countsofgeneticsequencesinpatent622datahavehadasignificantimpactonpolicydebatesandhaveattractedsignificantpublicity623[155–158].624

Intotal928firstfilingscontainedaverifiableAntarcticspeciesandDNAandaminoacid625sequencedata.AftertheexclusionofrecordswheretheubiquitousE.coliwastheonly626speciesrecordedinadocumentwithasequencelisting,739firstfilingscontained627sequences.628

Inpractice,considerablecautionisrequiredininterpretingthesequencedatainpatent629documents.Existingresearchhasadoptedthenovelapproachofcumulatingcountsof630sequencesinpatentdocumentsthatarelinkedtomarinespeciesinpatentsequencedata631fromtheWorldIntellectualPropertyOrganization(WIPO)[155–158].Thisservesthe632purposeofdemonstratingtheincreasingpresenceofsequencesfrommarineorganismin633patentactivityandlinkstowiderquestionsaboutbenefit-sharing.However,theuseof634cumulativecountsmayinadvertentlydisguisetherealitythatunderlyingpatentfilings,635reflectingtheoutcomesofinvestmentsinresearchanddevelopment,maybemuchweaker636andmadeupofspikesofindividualdocumentscontaininglargenumbersofsequences637[157].Figure8displaysthreedifferentapproachestocountingsequencedata.638

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639

Figure8:ApproachestoSequenceCountsforPatentActivityforAntarcticSpecies640

BeginningwithFigure8(1A)weobserveoveralltrendsinfirstfilingscontainingsequences641fordocumentsthatalsocontainanAntarcticspecies(aftertheexclusionofE.coli).Trends642infilingareclearlymodestoverthisperiodandpeakat95filingsin2014.Movingupto643Figure8(1B)wepresentcountsofthenumberofsequencesthatappearedindocumentsby644year.Thisrevealsclearspikesinactivitythatconsistofafilingin2004containing108,053645sequences,afilingin2006containing150,913sequencesandasetof7filingsin2015646containing78,771of80,602sequencesrecordedthatyear.Thesignificanceofthisbecomes647clearerwhenweconsiderFigure8(1C)whichdisplaysthecumulativesumovertime648leadingtoatotalof562,789sequences.Thismayreadilygiveanimpressionofsignificant649commercialinterestuntilwerecognisethat46%ofactivityovertheperiodismadeupof650twofilingsrisingto60%ofactivityacrossthe9filingsmentionedabove.Inshort,651cumulativetrendscanradicallyamplifyotherwiseweakunderlyingactivity.652

Itiscommonpracticeinpatentanalyticstofocusondocumentswhereasubjectofinterest653appearsinthetitles,abstractsorclaimsonthebasisthatthedocumentwillina654fundamentalwaybe‘about’thatsubject.Figure8(2)reproducestheapproachinFigure655

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8(1)butrestrictsthedata,aftertheexclusionofE.coli,tofilingswhereanAntarcticspecies656appearsinthetitles,abstractsofclaims(TAC)ofafiling.Astheirregularityofthispattern657inFigure8(2A),andtheassociatedspikeinFigure8(2B),servetohighlight,whenviewed658fromthisperspectivecommercialinterestinAntarcticspecies,asreflectedinsequence659data,canbereasonablybedescribedasemergentratherthanintense.660

Aneedforcautioninapproachingsequencedatainpatentfilingsisalsoreflectedinthefact661that,asJeffersonet.al.2013haveablydemonstrated,sequencesmayappearinpatentdata662eitherbecausetheyarecomparativereferencesequences,orbecausetheyareclaimed663[159].However,disentanglingreferencedandclaimedsequencesrequiresclose664interpretationofpatentclaimsandrepresentsaweakareainexistingmethodsinpatent665analytics.ToolssuchasPatSeqfromtheLensareopeningupthepossibilityofgreater666rigourintheinterpretationofsequencedatainpatentdocuments.667

Inourview,cumulativecountsofsequencescanserveasausefulindicatorofgrowing668commercialinterestinbiodiversityinareassuchastheAntarcticbutshouldnotbeusedin669isolationfromconventionalcounts.Cumulativecountsareparticularlyusefulfor670amplifyinganotherwiseweaksignal.However,themethodshouldlogicallyonlybeusedin671conjunctionwithothercountsinordertoavoidgivingamisleadingimpressionofintense672commercialinterestingeneticresourceswheninpracticeactivityisweakoremergent.673Furthermore,anexclusivefocusonsequencedatainthecaseofmarinegeneticresources674hasoccurredattheexpenseofrecognitionthatthemajorityofpatentactivityfor675biodiversityandmarinebiodiversitydoesnotinvolvesequences[157,160].Thus,inthe676caseoftheAntarcticdatapresentedherethe928filingscontainingsequencesconstitute67734%ofthe2,738firstfilingscontaininganAntarcticspecies.Assuch,abroaderviewthat678accommodatesthefullspectrumofpatentactivityforbiodiversityisappropriate.679

680

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Candida antarctica 681

Asnotedabove,thetypespecimenforCandidaantarctica(acceptednameMoesziomyces682antarcticus)wasoriginallycollectedfromsedimentinLakeVanda.Figure9displaysan683overviewoffilingactivityforCandidaantarctica.684

685

Figure9:OverviewofFirstFilingsforCandidaantarctica686

Candidaantarcticaisayeastspeciesthatisasourceofindustriallyimportantlipases.A687lipaseisanyenzymethatcatalysesthehydrolysisoffats.Theearliestfilingintheavailable688dataforC.antarcticacanbetracedto1986byNovozymesfortheEnzymaticSynthesisof689WaxesfocusingonMucormieheiandprovidingexamplesusingC.antarcticalinkedtoan690earlierfilinginDenmark[161].However,themosthighlycitedpatentdocumentisa1992691filingbyNovoNordisk,theoriginalparentofNovozymes,thatclaimsC.antarcticalipase692anditsvariantsincludinganumberofmodifiedaminoacidsequences[162].Fromthese693relativelyearlybeginningstheuseofCandidaantarcticalipasehasexpandedintoavariety694ofdifferentsectorsincludingmedical,detergents,fuelsandfoodstuffsforwhichwe695providebriefexamples.696

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AswecanseeinFigure9Basignificantnumberofmedicalrelatedpatentapplications697involveC.antarctica.Thesedocumentstypicallytaketheformofreferencestotheactualor698potentialuseofthelipaseinmedicalcompositionsratherthanclaimstothelipaseitself.699Thus,NeosetechnologiesIncclaimaninventionthatrelatestomutantsofFibroblast700GrowthFactor(FGF),particularlyFGF-20andFGF-21,whichcontainnewlyintroducedN-701linkedorO-linkedglycosylationsite(s).Theapplicationalsodisclosespolynucleotide702codingsequencesforthemutants,expressioncassettescomprisingthecodingsequences703andcellsexpressingthemutants[163].Inasimilarway,RigelPharmaceuticalsIncdisclose7042,4-pyrimidinediaminecompoundshavingantiproliferativeactivity,compositions705comprisingthecompoundsandmethodsofusingthecompoundstoinhibitcellular706proliferationandtotreatproliferatediseasessuchastumorigeniccancers[164].Inour707viewthemajorityofmedicallyfocusedreferencesarelikelytoinvolvetheactualor708potentialuseofthelipaseratherthandirectclaimsinvolvingC.antarctica.However,more709directuseofthelipaseisreflectedinaUniversityofGeorgiaResearchFoundationIncfiling710describingnovelstructuredlipidsandtheiruseinmodulatingtotalcholesterollevels[165].711

Inthecaseofbiodiesel,WechtechBiotechCo.Ltdhaveappliedforamethodforenhancing712theactivityofanimmobilizedlipasetheyclaimisusefulinamethodofpreparingbiodiesel713bytransesterificationoftriglycerides[166].Inthecaseoffoodstuffs,AkerBiomarine714reportonnovelcompositionscontainingconjugatedlinoleicacidsthatareefficaciousas715animalfeedadditivesandhumandietarysupplementsthatuseC.antarcticalipaseinthe716esterificationprocess[167].SenomyxInchavereportedthatcertainnon-naturally717occurring,non-peptideamidecompoundsandamidederivativesareusefulflavourortaste718modifiersforfood,beverages,andothercomestibleororallyadministeredmedicinal719productsorcompositions[168].However,theC.antarcticaappearstobesimply720referencedinthisapplication.721

PatentactivityforC.antarcticaillustratesthepointthatspeciescanbesaidtoenjoycareers722insidethepatentsystem.Thesecareerstypicallystartwithfilingsonthediscoveryofa723usefulpropertyofanorganism,arefollowedbyclaimstovariantsofthatpropertyandthen724expandtotheactualorpotentialuseofthatelementinawiderrangeofclaimedinventions725andproducts.Astheusesofanelementofanorganismbecomeestablished,researchwill726alsotypicallyturntoidentifyingotherusefulpropertiesofanorganismandtheincreasing727pursuitofalternativesfromothersourcestocompetewiththoseelements.Overtime,the728bulkofactivityrelatestotheactualorpotentialuseoftheelementsofanorganismina729claimedinventionratherthandirectclaimstoelementsoftheorganism.Experience730suggeststhatthecareersofmanyspeciesinthepatentsystemfollowthistypeofpattern731andthiscanalsobeobservedinthecaseofAntarctickrill[160].732

733

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Antarctic krill 734

AntarctickrillEuphausiasuperbahasbecomeanincreasingfocusforthedevelopmentof735commercialandconsumerproductsinvolvingkrilloilandtheuseofkrillinfeedfor736commercialaquaculture.PreviousworkbyFosteret.al.2011highlightedtheproliferation737ofpatentactivityacrosssectorsforkrillanditsimplicationsforpredictingtrendsinkrill738fishery[169].739

Acrossbothscientificandcommonnamesforkrillweidentified150firstfilingslinkedtoa740totalof1,193familymembersworldwide.Wewouldnotethatthisdataisconfinedto741filingsthatmakereferencetoEuphausiasuperbaorAntarctickrillwithintheAntarctic742patentdatasetanddoesnotconsiderwiderreferencesforthesimpletermkrillinpatent743documents(supplementarymaterial).Figure10displaysanoverviewofthedataonfirst744filingsforAntarctickrill.745

746

Figure10:Antarctickrill747

Figure10revealsthatwhilefirstfilingsinrelationtokrillarerelativelysmall,thereisa748distinctriseinfilingsreflectingwiderinterestincommercialresearchanddevelopment749usingkrill.Figure10focusesontheveryfirstfilingsofpatentapplications.Incontrast,750Figure11expandsthelandscapetofocusonallknownfollowonapplicationsandgrants751aroundtheworldthatform‘familymembers’ofthefirstfilings.752

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753

Figure11:PatentFamilyMembersWorldwideforAntarcticKrill754

ComparisonbetweenFigure10andFigure11helpstoclarifythatasingleapplicationmay755leadtomultipleapplicationsandgrantsaroundtheworld.Applicantsmustpayfeesateach756stageoftheapplicationprocedureand,whererelevant,maintenancefeesforpatentgrants757ineachcountry.Followonfilingsthereforereflecttheimportanceoftheclaimedinventions758totheapplicantsinspecificmarkets.Thisdataalsodemonstratesthatarelativelysmall759numberoffilingscanhaveawiderglobalimpactasapplicantsseektoprotectand760commercialisetheirclaimedinventionsinmultiplemarkets.However,whileFigure11761showsasteeplyrisingtrendthenumbersarenotdramaticrelativetoactivityinthewider762patentsystem.763

InthecaseofAntarctickrillwearewitnessingacombinationofanincreasingnumberof764claimstoelementsofkrill,suchaskrilloil,andtheuseofkrillasanactualorpotential765ingredientinaclaimedinvention(suchasafoodstuff,animalfeedorcosmetic).Inpractice,766filingsrelatingtoAntarctickrillcanbetracedbacktothe1980sandthescientificliterature767onkrillhasplayedasignificantroleinpromotingcommercialresearchanddevelopment.768Thus,a1986articleon‘Supercriticalcarbondioxideextractionofoilsfromantarctickrill’769

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byresearchersfromJapanhasbeencitedinthepatentliteratureover55times[170].770Claimedinventionscitingthisarticleincludetheextractionofpolarlipidsand771phosopholipidsfromkrill[171],andanewkrilloilcompositionwhichwasfoundtobe772usefulasananti-inflammatory,asananti-oxidantandforimprovinginsulinresistances773andbloodlipidprofiles[172].Wealsoobserveactivityforakrillextractaimedattreating774thrombosis[173]andamethodforusingkrilloiltotreatriskfactorsforcardiovascular,775metabolicandinflammatorydisorders[174]aswellastherapeuticphospholipid776compositionsfortreatingorpreventingawiderangeofdiseasessuchascardiovascular777andneurodegenerativediseases[175].Theuseofkrillaskrillmealinaquaculturehasalso778emergedasasignificantfocusofcommercialresearchanddevelopmentsuchaskrillmeal779products[176],aswellasmethodsformakingkrillmeal[177]andusingkrillmealasa780supplement[178,179].Recentapplicationsincludeapplicationsseekingtotacklethe781harmfuleffectsofoxidisedLDLcholesterol[180],andtoprovidenutritionalsupplements782[181]andnewlipids[182].783

Antarctic literature cited in patent documents 784

TheprominenceofCandidaantarctica,Antarctickrillandthesheerdiversityofspeciesthat785appearinpatentdocumentsthatmentionAntarcticacanmakeitdifficulttoassessactivity786forotherAntarcticspecies.However,theLensdatabasehaspioneeredeffortstolinkthe787scientificliteratureandcitingpatentdocuments.Thismeansthatitispossibletoidentify788andexplorecaseswhereAntarcticresearchiscitedinapatentdocument.789

ItisimportanttonotethatascientificpublicationonAntarcticbiodiversitymayappearina790patentdocumentforanumberofreasons.Insomecountries,suchastheUnitedStates,791applicantsarerequiredtodiscloseallpotentiallyrelevantpriorart(scientificpublications792andpatents)atthetimeofapplication.Thiscantaketheformofpassingreferencesthatare793notinrealityrelevanttotheclaimedinvention.Inothercases,literatureonAntarcticamay794formpartofawiderthematicset(suchasanti-freezeproteins)thatindirectlyinformsthe795claimedinvention.Inathirdcase,anelementofanAntarcticspeciesidentifiedinthe796literaturemaydirectlyformpartofacomposition,methodorprocess.Finally,inasmall797numberofcases,Antarcticresearchersarebothpublishingandapplyingforpatent798protectionforbiodiversitycomponentsarisingfromtheirresearch.Wenowbrieflyexplore799thisdata.800

ThearticleonAntarcticbiodiversitythathasreceivedthemostpatentcitations,withover80160citations,isareviewentitled“DevelopmentswithAntarcticmicroorganisms:culture802collections,bioactivityscreening,taxonomy,PUFAproductionandcold-adaptedenzymes”803[183].Patentapplicationscitingthisarticlehavefocussedontheproductionof804polyunsaturatedfattyacids(PUFAs)frombacterialmicroorganisms[184–187],including805theproductionofthePUFAomega-3[188].AfilingbyMartekBioscienceson806polyunsaturatedfattyacid(PUFA)polyketidesynthase(PKS)systemsusingShewanella807japonicaandShewanellaolleyanaalsostatesthatS.olleyanawassourcedfromthe808AustralianCollectionofAntarcticMicroorganisms(ACAM)asstrainnumber644.However,809theaccompanyingliteraturecitationforthesamplemakesclearthatthespecificsample810wasfromanestuaryfromAustralia[189].Assuch,whiletheAntarcticliteratureinforms811theclaimedinvention,thisisanexampleofindirectinfluence.812

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AnarticleontheAntarcticnematode,Panagrolaimusdavidithatsurvivesintracellular813freezinghasreceived44literaturecitationsandiscitedin13patentfamilies[190].The814mosthighlycitedpatentfamiliesarefromZeltiqAestheticsIncandpertaintomethodsfor815coolingandtreatingsubcutaneouslipidrichcellssuchasadiposetissue[191,192],and816methodsforinterruptingorresumingtreatments[193,194].Thisisasecondexample817wheretheAntarcticliteratureindirectlyinformsorinspiresaclaimedinventionbecause818theinventionitselfisaphysicaldeviceforcoolingtissue.819

Patentclaimsinvolvingbiodiversitymaybeconstructedondifferenttaxonomiclevelssuch820asspecies,genus,familyandorder.Inthecaseoforderlevelclaims,a1974article“Four821newspeciesofthraustochytriumfromAntarcticregions…”[195]isreferencedin12patent822documentsfrom3patentfamiliesfiledbyMartekBiosciences.However,thespecific823referencetoAntarcticaislimitedtocomparisonwiththegrowthconditionsofother824Thraustochytrium.Patentdocumentswithinthethreefamiliesincludeaprocessfor825growingThraustochytriumandafoodproductwhichincludesThraustochytrium[196]and826processesforgrowingmicroorganismsoftheorderThraustochytriales[197,198].Thefirst827claimofonefilingisfor:“Aprocessforculturingamicroorganismoftheorder828Thraustochytriales…”inaculturemediumtoobtainPUFAlipids.Inthiscaseitisthe829processforobtainingthelipidsfromtheorganismsthatisthefocusoftheinventionrather830thanbiochemicalcompoundsfromtheorganismsperseasinclaimsforcompositionsof831matter[196].832

Examplesofpatentclaimsatthegenuslevelareprovidedinasetof18patentapplications833citinganarticledefiningthegenusNocardiopsis,includingNocardiopsisantarctica,[199].834ThesepatentdocumentsincludedirectclaimsrelatingtoNocardiospis,suchasafilingsby835NovozymesinrelationtoproteasesandassociatedDNAandaminoacidsequences,butuse836speciesotherthanN.antarcticasuchasN.alba[200].However,thesetypesofapplication837commonlyanticipatetheuseofthesame,orsubstantiallysimilarsequences,fromother838membersofthegenusthroughreferencetootherspecies,suchasN.antarcticaelsewhere839intheapplication.840

Astheseexamplesillustrate,patentdocumentsinvolvingbiodiversityandthebiodiversity841literaturemayinformclaimedinventionsinavarietyofwaysandrequireconsiderable842careininterpretation.WenowturntopatentfilingsthatcitetheAntarcticliteraturewhere843anAntarcticspeciesisdirectlymaterialtotheclaimedinvention.844

AnarticleexploringexopolysaccharidesproducedbymarinebacteriafoundinArcticand845Antarcticseaiceandotherextremeenvironmentshasbeencitedin10patentfamilies846[201].Theseincludetheuseofexopolysaccharidesincompositionstotreatsubterranean847formations[202]whileotherfilingsrefertotheuseofbacterialexopolysaccharidesin848cosmeticcompositions,withantioxidantproperties[203],anti-wrinkleproperties[204],849andcontrollingsebumsecretionintheskin[205].850

AnarticleidentifyingthemechanismsthroughwhichAntarcticmicroalgaChlorellavulgaris851isabletoadapttocoldconditionsandhighsalinity[206]hasbeencitedin6patentfamilies852(10documents).TheseincludetheuseofChlorellavulgarisintheproductionofnaturaloil853forthepurposeofmanufacturingtransportationfuelssuchasrenewablediesel,biodiesel,854

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andrenewablejetfuel,aswellasoleochemicalssuchasfunctionalfluids,surfactants,soaps855andlubricants[207].Thispatentapplicationhasbeencitedbyover17laterfilings.856Anotherpatentapplicationutilisingthespeciesintheproductionofrenewablefuels,which857arealsousefulasfeedstocks,alsocitesthisarticle[208].858

ResearchonalkaloidsfromtheAntarcticspongeKirkpatrickiavarialosainthemid1990s859hasbeencitedinfourpatentfamiliescontaining10documentsledbytheSpanish860pharmaceuticalandmarinebiodiscoverycompanyPharmaMarfiledfrom2000onwards861[209].Thepatentfamiliesfocusontheanti-tumourpropertiesofVariolinandits862derivatives[210–213].Threeofthepatentfamiliescontainover30familymemberswith863protectionsoughtin21countriessuggestingthattheapplicantsbelievethattheclaimed864inventionhassignificantcommercialpotential.865

Asdiscussedabove,coldtoleranceorantifreezemoleculesandproteinshavebeena866significantareaofresearchintheAntarctic.TheAntarcticgrassDeschampsiaantarcticahas867beenasignificantfocusofAntarcticresearchwith251articlesinourAntarcticliterature868datasetwithtopcitedscientificliteraturefocusingonissuessuchasheattoleranceof869photosynthesis,theevolutionofUVabsorbingcompounds,andvascularplantsas870bioindicatorsforwarminginAntarctica[214–216].871

Scientificliteraturethatiscitedbypatentapplicantsincludesworkonthreecold-872responsivegenesfromDeschampsiaantarcticabyresearchersfromChile[217].This873researchiscitedbythreepatentfamiliesincludingoneforanicerecrystallisation874inhibitionprotein,andanotherforanisolatedlowtemperatureplantpromotergene875[218,219].Otherworkofrelevanceincludesworkonthecharacterizationofantifreeze876activityinAntarcticplants[220]thatiscitedina2013patentgrantforanagentfor877cutaneousphotoprotectionagainstUVA(IandII)andUVBradiation(skinprotection878againstsundamage)containinganaqueousextractfromDeschampsiaantarcticaeither879obtainedfromitsnativeenvironmentorgrowninartificialsettings[221].Asthissuggests,880geneticelementsandcompoundsfromAntarcticspeciesmayfindapplicationsinmultiple881industrysectors.Intotal,ashighlightedinFigure5,weidentified26firstfilingsinvolving882Deschampsiaantarctica.883

Anarticleexaminingtheantifreezeproteingenefromtheantarcticmarinediatom884Chaetocerosneogracile[222]iscitedina2014patentfamilyfiledbySamsungelectronics885foran“AntifreezeMember”.Thefocusoftheclaimedinventionisthecreationofametal886substrateforsemiconductors,energyandbiosensorsthatovercomestheproblemoffrost887formationoncoolingplates.A2017USpatentgranttoSamsungclaimsthatthisproblem888canbesolvedby“arecombinantantifreezeproteininwhichametal-bindingproteinis889conjugatedtoanantifreezeproteinderivedfromChaetocerosneogracile”[223].890

Inwhatappearstobeasmallnumberofcasestheauthorsofscientificarticlesarealso891applyingforpatentprotection.OneexampleisworkbyresearchersinKoreafromthe892KoreaPolarResearchInstituteandtheKoreaOceanResearchandDevelopmentInstitutein893workontheantioxidantpropertiesoflichensfromAntarctica,notablyRamalinaterebrata894[224].Inthiscasetheresearchhasledtothefilingof5applicationsfocusingonRamalin895fromRamalinaterebrata[225,226].ThisincludestheuseofRamalinforitsantioxidant896

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properties,inpharmaceuticalproductstotreatoxidationrelateddiseases,infunctional897foodsforanti-agingpurposesandinfunctionalcosmeticsforskin-whiteningandanti-898wrinklepurposes[227].OnepatentapplicationrelatestotheuseofRamalinina899pharmaceuticalcompositiontotreatorpreventinflammatoryandimmunediseases[228].900Anotherapplicationrelatestoanti-cancertreatmentforcolorectalcancer[229].Taken901togetherthefilingssuggestastrategytocaptureabroadrangeofpotentialmedical902applicationsforRamalin.AtthetimeofwritingthescientificlandscapeforRamalin903consistsof31scientificpublicationsand21patentfamilies.Thisrepresentsasignificant904researchinvestmentandstronglysuggeststhattheapplicantsbelieveRamalinhas905commercialpotential.906

Coralsandtunicates,suchasseasquirts,havebeenamajorfocusofappliedand907commercialmarineresearch[230].InthecaseofAntarcticaSynoicumadareanumhasbeen908thesubjectofresearchonacytotoxicmacrolidethatalsoformedthebasisforapatent909applicationandgranttotheleadauthors[231,232].TheseasquirtAplidiumcyaneumhas910alsobeenafocusofresearchoncytotoxicbromoindolederivativesthatbecamethebasisof911apatentapplicationbysomeoftheauthors[233,234].912

Antarcticfishhavealsobecomeasignificantfocusofcommerciallyorientedresearchand913development.Thescientificliteraturehasfocusedonissuessuchastheroleof914NotothenioidfishinthefoodweboftheRossSeashelf[235],orneutralbuoyancyin915Notothenioid[236].CommerciallyorientedresearchforNotothenioidssuchasDissostichus916mawsonifocusesonantifreezeglycopeptidesinthetissuesandfluidsofAntarcticfish[237]917andcomparativeanalysisoftheseproteinsbetweenArcticandAntarcticfish[238].This918workhasresultedinadirectfilingin1990byatleastoneoftheresearchersatthe919UniversityofCaliforniaforthermalhysteresisproteinswithasignificantimpactonlater920patentfilingsintheformof57patentcitationsfocusingonissuessuchasice-controlling921moleculesandcryosurgery[239].Intotal7firstfilingsrelatingtoDissostichusmawsoni922wereidentifiedinthepatentdataset.923

OtherNotothenioideithatareafocusofcommercialresearchanddevelopmentincludethe924WhiteBloodedIcefish(Chaenocephalusaceratus)[240,241].Workonicefishlackingin925haemoglobinisreflectedina1999filingonmethodsfortheisolationofhemapoieticgenes926inAntarcticicefish[242].ComparativeresearchinvolvingChaenocephalusaceratus927focusingonVitaminEcontent[243]associatedwithcoldadaptationhasalsoattracteda928patentcitationbutwithaspecificfocusonakrillcomposition[244].Pagothenia929borchgrevinkiisalsoasourceforapatentfilingbyAirbusin2008foranti-freezeproteins930forapplicationtowings,rotorsandturbines[160,245].931

Astheseexamplesmakeclear,analysisofpatentdocumentsthatcitetheAntarctic932literatureprovideaclearroutetomonitoringfilingswhereanAntarcticspeciesismaterial933toaclaimedinvention.However,careisrequiredininterpretingthereasonswhyanarticle934iscitedandwhetheranAntarcticspeciesisdirectlyinvolvedormaterialtotheclaimed935invention.Weconcludethisexplorationofthepatentlandscapebybrieflyexamining936referencestoAntarcticplacenamesinpatentdata.937

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Antarctic Places 938

Oneaimoftheresearchwas,asfaraspossible,toidentifyandmapplacenamesappearing939intheliteratureandpatentdata.Twomainsourcesofdataareavailableforplacesin940Antarctica.ThefirstistheSCARCompositeGazetteer(March2018)of36,630names.The941secondsourceistheGeonamesdatabase,whichproducesafileAQforAntarctica942containing18,526placenamesand27,273variantnamesinmultiplelanguages.To943examinereferencestoAntarcticplacesinpatentdocumentswededuplicatedthenames944andthenmappedtherootsofplacenamesintothepatentdatafocusingonpatent945documentsthatalsocontainaspeciesname.Intotalweidentified267filingsthat946containedareferencetoaplacenameandaspeciesname,dominatedbytheterm947Antarctic/Antarctica.ReferencesrangefromgeneraldescriptionsofkrillasanAntarctic948speciestoAntarcticislands.Herewefocusonillustrativeexamples.949

A2010filingbyresearchersfromtheKoreaOceanResearchDevelopmentInstitute950(publishedasEP2617464A1)makesmultiplereferencestoplacesincludingKingSejon951Station,BartonPeninsulaandKingGeorgeIsland.TheapplicationfocusesonAntarctic952lichensnotablyanextractofStereocaulonalpinuminpharmaceuticalandfood953compositionstopreventortreatdiabetesorobesityandhasapatentfamilywith15954membersincludingpatentgrantsinChina,undertheEuropeanPatentConvention,Japan955andtheUnitedStates[246].Thepatentapplicationandothermembersofthepatentfamily956explainthat:957

“…the Antarctic lichen Stereocaulon alpinum (Stereocaulon alpinum (Hedw.) G.L. Sm.) used in the present 958invention was collected from the area around the King Sejong Station (S 62°13.3’, W58°47.0’) located on Barton 959Peninsula on King George Island, Antarctica, in January 2003.” 960

Animportantfeatureofthisexplicitreferenceisthatitispossibletoidentifytheprecise961pointofcollectionthroughtheuseofanamedplaceandcoordinates.Thisisalsoacase962whereatleastoneoftheauthorsofresearchonStereocaulonalpinumislistedasan963inventor[247].964

AsecondexampleofdirectcollectionofsamplesinAntarcticaalsorevealstheclose965relationshipbetweenthepublicationofscientificarticlesandpatentfilings.A2016filing966fromresearchersfromtheUniversityofSouthFloridaandtheUniversityofAlabama(UAB)967ResearchFoundationaddressesMRSABiofilmInhibition[248].Theapplicationstatesthat:968

“In the course of acquiring biodiversity to support an antibiotic screening program, the current inventors obtained 969the sponge Dendrilla membranosa from the vicinity of Palmer Station, Antarctica. The dichlorom ethane extract of 970the freeze-dried sponge was subjected to reversed-phase solid-phase extraction eluted with acetonitrile. The 971extract underwent HPLC purification to yield four major natural products, including three previously reported 972spongian diterpenes: aplysulphurin, tetrahydroaplysulphurin, and membranolide (Karuso et al., Aust. J. Chem. 9731984, 37, 1081-1093; Karuso et al., Aust. J. Chem. 1986, 39, 1643-1653; and Molinski et al., J. Org. Chem. 1989, 54, 9743902-3907). The fourth product was identified as darwinolide, a new rearranged spongian diterpene having a 975structure shown in FIG. 1. … The darwinolide skeleton is the newest of over a dozen structural motifs distinguishing 976the broad chemodiversity found in the Darwinellidae family of sponges.” [248] 977

978

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Theygoontoexplainthat:979

“Sponge samples were collected from various sites around Palmer Station, Antarctica in the austral summer of 9802011. The collection sites chosen were Norsel Point (64°45.674’ S, 64°05.467’W), Bonaparte Point (64°46.748’ S, 98164°02.542’W), Gamage Point (64°46.345’ S 64°02.915’W), and Laggard Island (64°48.568’ S, 64 00.984’W) at 982depths between 5-35 m below sea level. Samples were frozen and transported back to the University of South 983Florida at -70°C where tissues were lyophilized and stored at - 80°C until further processing.” 984

TheapplicantsclaimamethodfortreatingbacterialinfectionsincludingMRSAbiofilms985withadarwinolidecompound.However,thisisalsoacasewhereresearcherstimethe986submissionofascientificarticleandapatentfilinginsuchawaythattheresearcharticle,987whichwouldbecomepriorart,doesnotdestroythenoveltyoftheclaimedinvention.Thus,988theearliestfilingdateofthepatentapplicationisinApril2016shortlybeforethe989publicationofthescientificarticleinMay2016andisfollowedinOctober2017by990publicationofthePatentCooperationTreatypatentapplication[249].991

AthirdexamplehighlightsthatapplicantsmayobtainsamplesthroughAntarcticresearch992centresoperatingasintermediaries.A2009firstfilingfromIndiabecamethebasisfora9932010internationalPatentCooperationTreatyapplication[250]formethodsofpreparinga994plantextractusingliquidchromatographyandmassspectrometrywheretheplantextract995isfromDeschampsiaantarctica.Thisapplicationdescribeshow:996

“The frozen plant material was procured from Coppermine Peninsula on Robert Island, South Shetland Island, 997Antarctica and was exported to us by Instituto Antarctico Chileno…” 998

ThisapplicationalsomakesextensivereferencetothewiderliteratureonD.antarcticathat999mentionplacessuchasSignyIslandandKingGeorgeIslandsignifyingthattheintensityof1000occurrencesofreferencestoAntarcticplacesmaybeagoodindicatorofcollectionof1001samplesintheAntarctic.However,themaininsightfromthisexampleisthatinsomecases1002anAntarcticresearchinstitutemayserveasanintermediaryprovidingAntarcticmaterial1003forcommerciallyorientedresearch.Itisunclearwhethertheinstitutewasawareofthis1004purposewhenprovidingthematerialorwhetheramaterialtransferagreement(MTA)was1005establishedbetweentheinstituteandtheapplicants.1006

Afourthexampleillustratesthepointraisedabovethatasamplemaycomefrommultiple1007sources.A2006filingbytheMontereyBayAquariumResearchInstitutefor“Alight-driven1008energygenerationsystemusingproteorhodopsin”explainsthat:1009

Using the same proteorhodopsin-specific PCR primers, as for instance shown in FIGS. 2 and 3, proteorhodopsin 1010genes were also amplified from bacterioplankton extracts. As mentioned above, any proteorhodopsin-specific PCR 1011primer can be used. These bacterioplankton extracts include those from the Monterey Bay (referred to as MB 1012clones), the Southern Ocean (Palmer Station, referred to as PAL clones), and waters of the central North Pacific 1013Ocean (Hawaii Ocean Time series station, referred to as HOT clones). 1014

Asimilarmulti-sourcecaseisprovidedbyafilingfromWoodsHoleOceanographic1015InstituteformetagenomicsamplescollectedbydrillingthroughseaiceintheRossSea1016combinedwithanalysisofotherdiatomstocreatearecombinantorganismforthe1017expressionofCobalamin(vitaminB12)[251].Anadditionalexampleisafillingfora1018cryoprotectiveagentfromanovelPseudoalteromonassp.strainCY01(KCTC12867BP)1019collectedfromtheAntarcticOceanaswellasArcticstrains[252].Whiletheseapplications1020

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explicitlyinvolvesamplesfromtheAntarctic,itcanbechallengingtodeterminewhether1021theorganismsarematerialto(partof)theclaimedinvention.1022

ReferencestoAntarcticplacenamesoccurinthecontextofwiderinternationaldebateson1023disclosureoftheoriginofgeneticmaterialinpatentapplicationsandtheconsequencesof1024suchdisclosure[253].Increasingly,countriesthatarepartytotheConventiononBiological1025DiversityanditsNagoyaProtocolarerequiringdisclosureoforigininsupportofthe1026implementationoftheseagreements.However,theconsequencesofdisclosure,andfailure1027todisclose,mayvaryconsiderably.Thepresentresearchrevealsthatapplicantswilloften1028mentionAntarcticoriginandmay,aswehavejustseen,beexplicitabouttheplacesand1029coordinatesofcollection.IninternationalpolicydebatesatWIPO,agreementon1030internationalrequirementsfordisclosureoforiginhasbecomestuckondisagreements1031abouttheconsequencesofdisclosure,suchasrevocationofagrantedpatentintheabsence1032ofevidenceofpriorinformedconsentandabenefit-sharingagreementwiththecountryof1033origin[253,254].However,inthecaseoftheAntarctic,asformarinebiodiversityinAreas1034BeyondNationalJurisdiction,thefunctionofdisclosurecouldperhapsbetterbeseenas1035makingthecontributionofAntarcticbiodiversitytoinnovation(aspartlyreflectedinthe1036patentsystem)visibletothewiderworld[157,160].Thatis,disclosurecanassistwith1037supportinggreaterawarenessoftheecosystemservicesprovidedbyAntarcticbiodiversity1038andthusofAntarcticatowiderhumanwelfare.However,debatesondisclosureoforigin1039alsoraiseharderquestionsaboutthecontributionthatthosewhoseektocommercially1040developanduseAntarcticbiodiversityshouldmaketoitsconservation.Weturntohow1041thisissuemightbeaddressedinclosing.1042

Conclusion 1043

Thispaperhassoughttocontributetomappingthescientificandpatentlandscapefor1044biodiversityandinnovationinAntarcticaandtheSouthernOcean.Thegrowingavailability1045ofopenaccessdatabasesofscientific,patentandtaxonomicdatameansthatitispossible1046tobegintomaptheselandscapesatscaleusingmethodsthatareopen,transparentand1047accessibletoarangeofdisciplines.However,aswehavealsosoughttodemonstrate,1048exploitingopportunitiesforanalysisatscalerevealsissuesarounddatacompletenessand1049dataquality.Inthecaseofpatentdata,thesechallengesextendtorequirementsfor1050considerablecareininterpretationoftheAntarcticoriginofgeneticresourceswithin1051patentdocumentsandwhethertheyareactuallymaterialtoorpartoftheclaimed1052invention.1053

Issuesarounddatacompletenessanddataqualitycanbeaddressedthroughapproaches1054suchasre-indexingtoaddressgaps,inthecaseofMicrosoftAcademicGraph,andcloser1055attentiontodatacleaningusinglocalityinformationfortaxonomicdatafromGBIF.The1056growingavailabilityofthefulltextsofbothscientificandpatentpublicationspresents1057importantopportunitiestoimproveaccesstothefullresultsofscientificresearchbutalso1058presentschallengesinmovingbeyondpuremetadatabasedapproaches.Openaccess1059databasessuchastheLenshavemadeimportantbreakthroughsbylinkingtogether1060scientificandpatentdatathroughcitations.Thisinturnmakesiteasiertomonitorpatent1061activityarisingfromresearchinvolvingAntarcticbiodiversity.Developmentsinmachine1062learning,intheformofNaturalLanguageProcessinglibrariessuchasspaCy,meanthatitis1063

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nowpossibletoimagineapipelineapproachtomonitoringAntarcticresearchbystreaming1064newscientificpublicationsandpatentdatafromdatabaseapplicationprogramming1065interfaces(APIs),suchastheLens,throughamachinelearningmodelforclassification,1066nameentityrecognition,analysisanddistributiontothescientificandpolicycommunity.1067Thegrowingpopularityofpipelineapproachestodealingwithdataatscalereflectsthe1068widespreadavailabilityofopensourcelibrariesforanalyticsatscale.Implementingsucha1069pipelinewouldrequirefocusedinvestmentbyoneormoremembersoftheAntarctic1070TreatySystemandwouldlogicallybecoordinatedwiththeSCAR.Asthispaperhelpsto1071demonstrate,thisisanachievablegoal.1072

Thepresentresearchalsopointstopotentialwaysforwardinaddressingharderquestions1073aroundbenefit-sharingfromcommercialresearchanddevelopmentinvolvingAntarctic1074biodiversity.BioprospectinghasbeenontheagendaoftheAntarcticTreatySystemfora1075numberofyears.However,asfarasweareaware,beyondagreementtokeepdiscussing1076theissue,noconsensushasemergedonaneedforpracticalactionotherthancollecting1077moreinformationtoinformdeliberations.Thishasacertainlogicinlightofuncertainties1078aboutlevelsofactivityandtheactualorpotentialoverlapbetweengeneticresourcesinside1079theAntarcticTreatySystem,thosewithinnationaljurisdictionsandthosebeingconsidered1080bydebatesonthenewtreatyonmarinebiodiversityinareasbeyondnationaljurisdiction1081undertheLawoftheSea.1082

Onechallengewiththetreatmentofbioprospecting,orcommercialresearchand1083developmentasweprefer,isthatitislargelyseeninisolationfromotheractivitiesin1084Antarctica.Awayforwardcouldpotentiallybefoundbyviewingcommercialresearchand1085developmentfromanecosystemservicesandnaturalcapitalaccountingperspective.Many,1086ifnotallmembersoftheATS,haveembracedtheecosystemservicesapproachanda1087growingnumberaremovingtowardstestingorimplementingnaturalcapitalaccountingin1088accordancewiththeframeworkoftheSystemofEnvironmentalEconomicAccounting1089(SEEA)linkedtotheUnitedNationsSystemsofNationalAccounts(SEA)[19,20,255,256].1090Thesedevelopmentshavebeenaccompaniedbytheincreasingpromotionoftheconceptof1091PaymentsforEcosystemServices(PES)withintheenvironmentaleconomicsliteratureand1092policy,asproposedbyVerbitsky2018fortourisminAntarctica[19,257].Thistypeof1093approachwouldallowcountriestodrawonexistingexperiencewithecosystemservices1094andnaturalcapitalaccountingwhenaddressingcommercialactivityintheAntarctic.It1095shouldbeemphasisedthatthevaluationofecosystemservicesischallenginganditis1096increasinglyrecognisedthatthereisariskthatsuchapproachesmayseektoreduce1097biodiversitytoanequivalentmonetaryvalueattheexpenseofrecognitionofthemultiple1098valuesofbiodiversityanditsservices.Nevertheless,despitethesereservations,overthe1099shortandmediumtermthisapproachwouldplacetheassessmentofactivitiessuchas1100commercialresearchanddevelopmentortourismwithinaclearandtransparent1101frameworkthatwouldbringAntarcticaintothefoldofwiderworkontheeconomicsof1102biodiversity.1103

Theyear2020hasbeendescribedasasuperyearforbiodiversity.Ascountriesscrambleto1104addresstheformidabledamagecausedbyCovid-19itremainstobeseenwhetherthiswill1105becomeareality.However,oneimportantlessonfromtheenvironmentalandecological1106economicsliteratureisthatbiodiversitycannotbetreatedasafreegood.Thejoint1107

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biodiversityandclimatecrisishasitsoriginsinthetreatmentoftheenvironmentasafree1108goodwheninfactthecostsaredeferredelsewhereincludingtofuturegenerations.When1109viewedfromthisperspective,biodiversityisnotfreebuthastobepaidfor.Atpresent,as1110farasweareaware,therevenuegeneratedbybiodiversitybasedinnovationfromresearch1111intheAntarcticdoesnotcontributetotheconservationofbiodiversityintheAntarctic.11122020providesanopportunitytorethinkthelogicthatproducesthissituationby1113recognisingthatbiodiversitymustbepaidfor.Byacceptingthatbiodiversityisnotfreewe1114arethenabletoaskotherquestionsfocusingonreturningtangiblebenefitstoAntarctic1115biodiversitysuchas:howmuch,bywhom,inwhatform,andtowhatends?Thispaper1116seekstocontributetothedevelopmentoftheevidencebaseforaddressingthesequestions.1117

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