DepartmentofPhysics,ChemistryandBiology

Introductionessay,2016

Correlatedbehaviouralselectionresponsesduringanimal

domestication

RebeccaKatajamaa

Supervisor:PerJensen,LinköpingUniversity

DepartmentofPhysics,ChemistryandBiology,LinköpingUniversity,SE-58183Linköping,Sweden

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AbstractThisessayisanoverviewofthedomesticationprocess,withfocusoncorrelatedselectionresponsesandgeneticmechanisms.Domesticatedanimalssharemanycommontraitsandcouldhaveemergedasacorrelatedresponsetoincreasedtameness,orlowerfearofhumans.Thechickenisanimportantmodelindomesticationresearchasitisavailableinitswildancestralformandisusedforcomparativestudiesaswellasselectionexperiments.QTLstudieshavebeenusedtofindgeneticregionsthatarecorrelatedtoquantitativetraits.Findinggenesthatcontrolbehaviourisinmostcasesdifficultbecauseofthenatureofbehavioursandbecausebehavioursareoftencontrolledbyseveralgenesofsmalleffects.Determiningthegeneticmechanismsbehindanimaldomesticationwillnotonlyshedlightonthisevolutionaryprocessbutcanalsobeusedtoimproveanimalwelfareinatimewhereincreasedproductionrateishighlyvalued.

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TableofContents

1. Animaldomestication.............................................................................................41.1 Thedomesticatedphenotype..................................................................................41.2 Thecaptiveenvironment..........................................................................................6

2. Geneticmechanismsindomestication..............................................................62.1 QTLmapping.................................................................................................................82.2 BehaviouralgeneticsandQTLstudiesonbehaviour......................................9

3. Thechicken..............................................................................................................104. Animalwelfareaspects........................................................................................115. Summary...................................................................................................................12References........................................................................................................................13

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1. AnimaldomesticationHumanshaveusedanimalsforfoodproductionandcompanionshipamongotherthingsforalongtime.Accordingtoarchaeologicalfindings,thedogwasthefirstspeciestobedomesticatedatleast12,000-14,000yearsago(Leonardetal.2002;Pennisi2002).Evidencefromgeneticstudiesevensuggestthatdogsmayhavebeendomesticatedalreadyabout32,000yearsago(Thalmannetal.2013;Wangetal.2013).Manyotheranimalspecies,predominantlylivestocklikechickensandsheep,havebeendomesticatedsincethen.Someofthedomesticatedanimalstodaywereinitiallyusedforotherpurposes.Chickens,whicharepredominantlyusedforfoodproductiontoday,wereinitiallyusedforceremonialpurposesandcockfighting(Keeling2002).AcommonlyciteddefinitionofdomesticationistheonebyPrice(1984).Domesticationcanbedefinedastheprocessbywhichanimalsbecomeadaptedtohumansandtheenvironmentthattheyprovide(Price1984).Hisdefinitionincludeseffectsthatarebroughtaboutbyexperience,e.g.docilebehaviourtowardshumansduetohabituation.JensenandWright(2014)writethat“Domesticationistheprocesswherebypopulationsofanimalschangegeneticallyandphenotypicallyinresponsetotheselectionpressureassociatedwithalifeunderhumansupervision.”Thisdefinitionclarifiesthatdomesticationisanevolutionaryprocessinwhichtheeffectsdevelopcontinuouslyovergenerations,justlikespeciation.Similartotheproblemofdefininganimalspecies,wehaveadifficultyindeterminingwhenananimalistrulydomesticated.Domesticatedanimalsarecharacterisedbyacoherentsetofphenotypicalcharacteristicsthatistermedthedomesticatedphenotype(Price1999).Duringdomestication,thegenomeofaspecieschangesovergenerationsleadingtoadaptationoftheanimaltothecaptiveenvironmentprovidedbyhumans.Themechanismsbehindthesechangesarenotyetcompletelyunderstood.Geneticlinkageandpleiotropyhavebeenproposedaspossiblemechanismsandtheywillbediscussedfurtherinthisessay.

1.1 ThedomesticatedphenotypeThedomesticatedphenotypeisasetofphenotypictraitsthatarecommontoalldomesticatedspecies.Comparedtotheirwildancestors,domesticatedanimalsoftenhavepiebaldmarkings,theytolerateorevenseekhumancompanionship,havealteredbodyproportions(e.g.shortenedsnout,elongatedorshortenedlegs)andreproduceoutsideofthenormalbreedingseason.Reducedbodysizeseemstobeoneofthemostcommontraitsassociatedwithdomestication(Clutton-Brock1999).Therearehoweverexceptionstothisobservation,e.g.inanimalsthathavebeenselectedforproductiontraitssuchasincreasedgrowthofmuscleandhigheggyieldorlargesizeforotherreasons,e.g.indogsandhorses.

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Figure1.Anexampleoftwodifferentdomesticatedspecies,bothshownherewithfloppyearsandanalteredcoatcolourcomparedtotheirwildancestors.Earliersexualmaturityisacommontraitindomesticatedanimals.Comparedtowolves,dogsbecomesexuallymaturealreadyayearearlier(BoitaniandCiucci1995).Inchickens,weseethatthedomesticatedWhiteLeghornfemalestartslayingeggswhenitisaround20weeksold,whereastheredjunglefowlstartsaboutfiveweekslater(Schützetal.2002).Otherphysiologicalchangeshavealsooccurredindomesticatedanimals.Acommonchangeindomesticatedspeciesisasmallerrelativebrainsize.Thishasbeenreportedine.g.mink(Kruska1996),pigeons(Rehkämper,Frahm,andCnotka2008)andsheep(Ebinger1974),amongothers.Althoughmanystudieshavefoundthesamepattern,twodifferentstudiesinrainbowtroutfoundconflictingresults.Onepopulationoffishhadsmallerbrainsasexpected(MarchettiandNevitt2003)whereasanotherstudyfoundtheoppositewithdomesticatedfishhavingalargerbrain(Campbelletal.2015).Perhapsamoreinterestingobservationisthatseparatepartsofthebrainseemtohavechangedindifferingproportionsindomesticatedanimals,e.g.guineapigsKruska(2014)andsheepEbinger(1974).Reducedsensitivitytostressisanimportantchangeindomesticatedanimals.Oneofthemainregulatorsofthestressresponseisthehypothalamicpituitaryadrenal(HPA)axis.ArelaxationoftheHPA-axisresponsivityhasbeenreportedinrats(Albertetal.2008),guineapigs(KünzlandSachser1999)andsilverfoxes(Harrietal.2003)amongotherdomesticatedspecies.Domesticatedanimalsarealsomuchlessfearfulofhumans(Price2002).Thebehaviouralrepertoireofdomesticatedspecieshasgenerallynotchanged,butratherthefrequenciesofthebehavioursduetochangesinthethresholdsforthebehaviours(Price1999).Forexample,thedomesticatedWhiteLeghornlayershowslesscontrafreeloadingcomparedtotheancestralredjunglefowl(LindqvistandJensen2002)andthereisanoverallreducedlevelofactivity,morerelaxedsocial

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structuresaswellaslessexplorativebehaviour(SchützandJensen2001).Feraldogsformsocialgroupsthatcanchangeformonedaytothenextbothinsizeandcomposition,whereaswolvesaggregateinstablesocialgroupswithcloserelatives(BoitaniandCiucci1995).Speciesthathavebeendomesticatedalsosharesomekeytraitsthatmakethemsusceptibletodomestication.Thesetraitsareoftentermedaspreadaptationstodomesticationandtheyhelptheanimalscopewithlivinginthecaptiveenvironment.Forexample,theanimalsoftenhaveprecocialyoung,promiscuousmatingsystemsandeatanomnivorousdiet(Price1984).Oneofthemostusefulpreadaptationstodomesticationislivinginsocialgroupswithahierarchyasthismakesitpossibleforthehumantosubstituteastheleaderoftheflock.

1.2 ThecaptiveenvironmentComparedtotheenvironmentsinwhichthewildancestorsofourdomesticatedspeciescomefrom,thecaptiveenvironmentisusuallyalotdifferent.Wetendtokeepanimalsinsmallspaceswithalotofotherindividualsbecauseofspacelimitations.Itcanbedifficultforananimaltoescapefromadominantconspecific.Animportantchangeinpracticallyalldomesticatedanimalsisthattheyarelesssensitivetoenvironmentalchange(Price1999),butthisdoesnotmeanthattheyarenotaffectedbyenvironmentalchange.Animalsintheproductionindustryareoftenmovedduringthedifferentstagesofrearing.Thiscanincludeeverythingfrommovingtoanotherpen,stableorevenacompletelydifferentfarm.Socialhierarchiesarechallengedbysuchtransitionssincetheconstellationofthesocialgroupislikelytochange.RedJunglefowlliveinsmallergroupswithaharemstructure(ColliasandCollias1996)butincommercialchickenhousingtheanimalsarecommonlyhousedingroupsofthousandsofindividuals.WhiteLeghorns(selectedforhigheggproduction)lessfrequentlyengageinsocialinteractions,aswellasotherenergydemandingbehaviours,comparedtoRedJunglefowlandSwedishBantam(SchützandJensen2001).Itisquitepossiblethatengaginglessinsocialinteractionsisbeneficialinanenvironmentwheretheamountofconspecificsislargerthanwhatanindividualiscapableofrecognising.Flocksizealsoaffectsthedegreetowhichchickensexhibitbehaviouralsynchrony,withsynchronydecreasingwithincreasingnumbersofbirdsinagroup(Keeling,Newberry,andEstevez2017).Predationpressureisgreatlyreducedoreveneliminatedinthecaptiveenvironment.Withtheremovalofpredators,traitsandbehavioursaimedatavoidingpredationbecomelessimportant.Humanscanevenfavourtraitsthatwouldbedisadvantageousinthewild.Forinstance,coatcolourvariationismoreabundantindomesticanimals(Cieslaketal.2011)andespeciallyinterestingiswhitecolourationwhichisconsidereddetrimentalforwildanimalsthatrelyoninconspicuouscoatcolourforcamouflage.

2. GeneticmechanismsindomesticationAspreviouslymentioned,thegeneticmechanismsunderlyingdomesticationarelargelyunknown.Previousresearchindicatesthatepigeneticmodificationscan

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beinheritedtotheoffspring.Thismechanismofinheritancecouldberesponsiblefortheoftheobservedfastchangesintraitsseenindomesticatedanimals.Lindqvistetal.(2007)foundthatthegeneexpressionresponsetostresstreatmentwastransmittedfromparentstooffspringinWhiteLeghornchickens.Geneexpressionandmethylationpatternshavealsobeenfoundtobeconsistentinthebrainbetweenparentsandoffspringinchickens,showingthatepigeneticvariationisinheritedinthisspecies(Nättetal.2012).Onthepremisethatselectionfortamenessonlywouldbringaboutcorrelatedselectionresponsesthatresemblethedomesticatedphenotype,anexperimentwasstartedbyBelyaev(1979)in1959.Thepurposeofthestudywastomimicearlydomesticationusingsilverfoxes,aspeciesthathadnotbeendomesticatedpriortothat.Itisknownasthefarmfoxexperimentanditisaclassicexampleofcorrelatedselectionresponses.Belyaevandhisgroupselectedsilverfoxesfromafarm-bredpopulationononetraitonly,tameness.Thetestusedfortheselectionwastheglovetest,wheretheresponseofafoxtoanapproachinghumanglovedhandwasmeasured.Forbreeding,thefoxesthatshowedthehighestandlowestfearfulnesswereusedtoselecttwodifferentlinesoffoxes.Thisprocedurewasfollowedforseveralgenerations.Examplesoftraitsthatweredevelopedintheselectedfoxesarefloppyears,lossofpigmentationandfasterontogeneticdevelopment(Trut,Oskina,andKharlamova2009).Thechangesarealsocommontothedomesticdog.Itisquiteinterestingconsideringthattheonlytraitthatwasselectedforwastheleveloftameness.Similarselectionstudiesoffearfulnesstowardshumanshavebeendoneonrats(Albertetal.2009),mink(MalmkvistandHansen2002)andchickens(Agnvalletal.2012).Ratsselectedfortamebehaviourtowardshumanstoleratehandlingandtouchwhereasaggressiveratsperformbehaviourssuchasboxing,attackandscreaming(Albertetal.2008).Effectsonphysiologywerealsoseen,wheretameratshadlargerkidneys,brainsandspleens.Minkselectedforlowerfearfulnessapproachandstarttoeatnovelfoodfasterthanfearfulindividuals(MalmkvistandHansen2002).Theyarealsolessfearfulinothernovelsituationsinvolvingnovelobjectsandenvironments.Likemink,chickensselectedforlowerlevelsoffearfulnesstowardshumansarebolderinanovelobjecttest(Agnvalletal.2015).Kukekovaetal.(2011)foundanassociationbetweentameandaggressivebehaviourinfoxesatalocusontheVVU12chromosome.ThisregionisorthologoustoanotherfoundbyvonHoldtetal.(2010)indogsandwolves.Forrats,twosignificantquantitativetraitloci(QTL)fortamenesshavebeenfound(Albertetal.2009)thatarenotorthologoustothelocionfoxVVU12(Kukekovaetal.2011).Thediscoveryofnon-orthologouslocifortamenessinfoxesandratsshowsthatthereareseveralpossiblepathwaysofevolutionoftameness.Furtherresearchintothisareainotherspeciesmayrevealinterestingresults.Pleiotropyisthemainreasonforcorrelatedselectionresponses,althoughlinkagecanalsobeatransientcause(Falconer1989).Pleiotropyisdefinedasthesituationwheretwoormoreseeminglyunrelatedtraitsarecontrolledbyasinglelocus(Stearns2010).Correlatedselectionresponsesduetolinkageare

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especiallycommonincrossesbetweendivergentlinesofanimals,suchasthoseusedforQTLstudies.Genesthataresituatedclosetoeachotheronthesamechromosomehaveahigherprobabilityofbeinginheritedtogethercomparedtogenesthatarelocatedfarawayfromeachotherorevenonadifferentchromosome.Duringmeiosis,thereisrecombinationwherecrossing-overofthechromosomeshappens.Inthisrecombinationevent,geneslocatedcloselytogetherarelikelytobeinheritedtogether.WeusethistoouradvantagewhenperforminganalysesofpossibleQTLs.

2.1 QTLmappingAQuantitativeTraitLocus(QTL)isalocusthatcontainsallelesthatdifferentiallyaffecttheexpressionofacontinuouslydistributedphenotypictrait.QTL-studiesareusefulindeterminingregionsinthegenomethatarelinkedtocertainphenotypictraits.ThebasicprincipleofQTLmappinginvolvesacrossbetweentwolinesofindividualsthataredivergentinatrait.Breedingdesignsusedforthisdiffer,butacommononeisanF2-intercross.Thesegregationofgeneticmarkerscanthenbeanalysedthroughastatisticalassociationbetweenthemarkersandphenotypictraits.Traitsaffectedbyseveralgenescaninthiswaybelinkedtospecificareasonthechromosomes(Weller2009).Thisisthefirststepinfindingtheactualgenesormutationsthatareresponsibleforaproportionofthevariationinatrait.Geneticmarkers(positionsofsequencevariation)suchassinglenucleotidepolymorphisms(SNPs)andmicrosatellitesaredispersedthroughoutthegenome.TheseareusedinQTLmapping(amongothermappingtechniques)todetermineregionsofpossibleQTL.Thetraitofinterestisscoredaccordingtothefrequencyofwhichitappearsassociatedtoanyofthesemarkers.Ahighfrequencyofassociationisanindicationofthemarkerbeingclosetoageneofinterest.ThesimplestmethodofQTLmappingissinglemarkeranalysis.Whatisdonehereisacomparisonofthebehaviourofindividualswithdifferentmarkergenotypes.Statisticaltestsareusedtodetermineifthereisadifferenceinthephenotypebetweenthemarkergenotypesforeachmarkerlocationseparately.Theprincipleisthesameforintervalmapping,butinsteadofcomparingeachindividualmarkerlocationwecomparepairofadjacentmarkers.AproblemwithsinglemarkeranalysisisthattheestimationofQTLeffectswillbeaffectedbythedistancebetweentheQTLandthemarker.WewillnotbeabletodeterminewhethertheQTLhasamajoreffectandislocatedfarfromthemarkeroriftheeffectisminorwiththeQTLlocatedclosetothemarker.Forthisreason,intervalmappingispreferredoversinglemarkeranalysis.However,singlemarkeranalysisismoreflexibleasitiseasiertoaddcovariatestothemodel.Theissuewithsinglemarkeranalysisbecomessmallerwithanincreasingdensityofmarkers.Asbrieflymentionedearlier,twodivergentlinesorpopulationscanbeintercrossedtodeterminegenomicregionsthataffectatrait.Whenitcomestodomesticanimalsandthecaseswherethereisanextantancestor,thisisvery

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useful(AnderssonandGeorges2004).Thedifficultyofidentifyinggenesthataffectbehaviouraltraitsisthatbehavioursaregenerallynotcontrolledbyasinglegene.Thecontributionofeachgenecanbesmallandthereareenvironmentaleffectsthatneedtobeconsidered.Toeliminateenvironmentaleffectsonatraitinanexperimentasmuchaspossible,animalsneedtobehousedinastandardisedenvironment.Anydifferencesinphenotypeshouldthenmainlybeduetogeneticeffects.However,environmentaleffectscanbeunpredictableandacompletelystandardisedenvironmentisverydifficult,probablyevenimpossible,tocreate.Toincreasethestatisticalpowerofouranalysis,weneedtousemanyindividuals,especiallysincethegeneswearelookingforusuallyhaveasmalleffect.TheultimategoalofQTLmappingistoeventuallypinpointactualgenesandmutationsunderlyingaQTL.Therearehoweverseveraldifficultieswithdoingthat.PreviousQTL-andgenome-wideassociationstudies(GWAS)showthatsinglegenesonlyaccountforaproportionofthevariationinaquantitativetrait,whichlowerstheresolution(FlintandMackay2009).Instudieswhereactualgeneshavebeenidentified,theeffectsizeoftheQTLhasbeenveryhighcomparedtomostQTLeffectsizes(Flintetal.2005).EffectsizeistheproportionofthetraitvariationthatisattributabletoaspecificQTL.EnvironmentalfactorsaswellasotherQTLsaffectquantitativetraits.So,theprobabilityifdetectingageneormutationthatcorrespondstophenotypeinaquantitativetraitislow.Itisalsodifficulttopinpointtheexactlocationonachromosomeduetothenumberofmarkersandcrossoverevents.Difficultiesaside,thereareseveralmethodsforgoingfromaQTL-regiondowntoaspecificgene.Toincreasethemappingresolution,anadvancedintercrossline(AIL)canbemade(DarvasiandSoller1995).Insteadoftwogenerationsofintercrossingoftwodivergingstrains,severalmoregenerationsareperformedinanAIL.Thisincreasestherecombinationfrequency,whichthereforealsoincreasestheresolutionofthegeneticmapandgivesabetterestimateoftheQTL.Whenatraitiscorrelatedtoamarker,onecanassumethatageneresponsibleforthetraitislocatedclosetothemarker.Theregioncanbesequencedandcomparedtoalreadyknownsequencedgenes.Inthisway,acandidategenecanbefoundthatcorrespondstotheinvestigatedtrait.Afterthis,weneedtofurtherdeterminethefunctionofthegeneonthephenotypetobeabletodetermineifthegeneregulatesitornot.Apopularmethodinmousegeneticsisgeneknock-out.Thefunctionofageneofinterestisknockedouttodeterminewhicheffectithasonthephenotypeofthemice.Knock-outstudieshavenotbeenusedinchickenssofar,butthereissomepromisingdevelopmentintheareawiththeCRISPR/Cas9system(Wangetal.2017).

2.2 BehaviouralgeneticsandQTLstudiesonbehaviourVariationinsocialbehaviour,suchaspair-bonding,isassociatedwithmutationsinthepromoterregionoftheargininevasopressinreceptor(AVPR1a)inhumansaswellasotherspecies(Walumetal.2008;DonaldsonandYoung2008).AQTLregioncontainingtheAVPR1agene,amongothers,hasbeenfoundinthechicken(WirénandJensen2011;Wirén,Wright,andJensen2013).Theregionis

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associatedwithsocialbehaviourandislocatedonchickenchromosome1.InDrosophila,thesitterandroverphenotypesinlarvaearedeterminedbytheforgene(Osborneetal.1997).Thesearesomeexampleswheretop-downanalysishasyieldedbehaviouralgenesorregions.Usuallyitisverydifficulttogetasfarasanactualgenethatcontrolsaquantitativetrait,especiallybehaviour,sincethetraitsaremostoftencontrolledbyseveralgeneswithminoreffects.Addingtothedifficultyisthenatureofbehaviouraltraitsinthattheyareusuallynotstraightforwardtodefineandmeasurereliably.AccordingtoCrusio(2015),themosturgentissueinbehaviouralgeneticsisthatbehaviouraltestsusedforevaluatingcertainbehaviouralconstructsarenotproperlyvalidated.Inratsselectedfortameness,twoQTLwerefoundtooverlapwiththetrait(Albertetal.2009).TheseQTLadditionallyoverlapwithtwootherQTLforanxietyrelatedtraitsandadrenalglandweight.

3. ThechickenThechicken(Gallusgallus)iscommonlybelievedtohavebeendomesticatedabout8,000yearsagoinsouth-eastAsia(WestandZhou1988).OnestudyclaimsthatnorthernChinashouldalsobeaddedtoapossiblesiteofchickendomesticationbasedonanalysesonancientDNAfromsupposedchickenbones(Xiangetal.2014).Thisideahasbeenrefutedbyamorphologicalre-evaluationofsupposedchickenremainsfromcentralandnorthernChina,wherethemajorityofboneswerenotfromchickens,indicatingthatchickenswerenotwidelykeptinthoseregions(Edaetal.2016).WhileEdaetal.(2016)agreethatthetropicalregionsofsouth-eastAsiaisaprobableoriginofchickendomestication,theywritethatcandidatechickenbonesneedtobeanalysedwithancientDNAandradiocarbondatingtodetermineifthesamplesareactuallyfromthechicken.Petersetal.(2016)alsoagreethatfurtheranalysesofsupposedchickenremainsfromacrossChinaandeastAsiawillelucidatethedisagreementsconcerningthetemporalandspatialoriginsofchickendomestication.Takentogether,bothpapersreportthattheevidencethusfarindicatesthatNorthernChinaisnotaprobableoriginofchickendomesticationandthatfurtheranalysistechniquesarerequiredforcertaindetermination(Edaetal.2016;Petersetal.2016).Thereisawidevarietyofthedifferentbreedsofchickenstodaywhichareusedformeatproduction,entertainmentandcompanionshipamongotherthings.Thenaturalhabitatoftheredjunglefowlisverydifferentfromtherearingconditionsinmoderndaychickenindustry.Itconsistsofforestsandsemi-openhabitatsinsouth-eastAsiaandtheIndiansubcontinent(Al-Nasseretal.2007).Redjunglefowlsusuallyorganiseinsmallergroupsofindividuals(ColliasandCollias1996).Thegroupsaremadeupofonemalewithseveralfemales,smallergroupsofmalesorsolitarymales.AnaveragestableforlayinghensintheSwedishindustryhouses23000chickens(Svenskaägg.se).Needlesstosay,thedifferencebetweennaturalsettingandindustryhousingisclear.Thechickenprovidesaniceopportunityasananimalmodelfordomesticationresearch.Behaviourresearchersoftenstrugglewithcontrollingtheenvironment

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oftheirmodelspecies.Chickensofferanopportunitytoenvironmentalcontrolalreadybeforetheyarehatched.Eggscanbeincubatedstraightfromlayingandaschickensareprecocial,thereisnoneedforamotherhen.Ashasalreadybeendiscussed,minimisingtheenvironmentalvariationisusefulwhenwewanttostudygenesthataffectbehaviour.Whenitcomestodomesticationgenesinchickens,someadvancementshavebeenmade.TheyellowskingeneBCDO2(beta-carotenedioxygenase2)wasidentifiedbyErikssonetal.(2008)anditrevealsthatthedomesticatedchickenmayhaveahybridoriginwithsomeinclusionofthegreyjunglefowlaswellastheredjunglefowl.AregulatorymutationinBCDO2inhibitstheexpressionoftheenzymeinonlytheskin.OnestudyinchickensfoundafewselectivesweepswithpossiblecandidategenesfordomesticationandBCDO2wasusedasareferenceasitwasalreadyaknownselectivesweepinthedomesticatedbirds(Rubinetal.2010).Selectivesweepsareregionsinthegenomewithlowdiversity(i.e.lowheterozygosity),indicativeofaselectionevent.Thyroidstimulatinghormonereceptor(TSHR)wasoneofthemostpromisingcandidategenesfoundintheselectivesweepanalysis(Rubinetal.2010).Itisinvolvedinreproductionandmetabolicregulation.AmutationintheTSHRgeneindomesticatedchickensseemstoaffectthereproductionpatterninawaywhichischaracteristicforotherdomesticatedanimalsandmaythushavebeenanimportanttargetinchickendomestication(Karlssonetal.2016).Anothergenethatwasfoundintheselectivesweepanalysiswasa-adrenergicreceptor2C(ADRA2C)thatisassociatedtostressresponseregulation.However,uponfurtherinvestigation,thegenewasnotfoundtobecorrelatedtodomesticationrelatedchangesinthestressresponseofchickens(Elfwingetal.2014).Anotherinterestinggeneisargininevasopressinreceptor1a(AVPR1a),whichisassociatedtosocialbehaviour.AmajorgrowthQTLhasbeenfoundinchickens,whichisincloselinkagewithAVPR1a,andtheregioncorrelatedwithchangesinsocialbehaviourofchickens(Wirenetal.2009).Thegeneremainsaninterestingcandidateforfutureresearchduetoitsassociationwithsocialbehaviourinotheranimals.Othercandidategeneshavebeenidentifiedaswell,e.g.PMEL17(Kerjeetal.2004)andMC1R(Kerjeetal.2003),whicharebothassociatedwithplumagecolouration.

4. AnimalwelfareaspectsIntensificationofselectionforproductiontraitshasbroughtaboutsomeproblemsinrespecttoanimalwelfare.Ashasbeendiscussedinthisessay,correlatedselectionresponsescansometimesleadtounpredictableresults.Forexample,intenseselectiononrapidleanmusclegrowthinfatteningpigsleadtoanincreasedfrequencyofamutationintheskeletalmuscleryanodinereceptor(ryr1),whichinturncausesmalignanthyperthermiainindividualsthatarehomozygous(Fujiietal.1991).Malignanthyperthermiacanbeinducedbystressinpigsandcanleadtosuddendeathorpoormeatquality,bothverycostlytotheindustry.Identificationoftheryr1genemutationhasmadeitpossibletogenotypefatteningpigssothatthemutatedgenecanbeavoidedinbreedingandisnolongeramajorproblem(Hocking,D’Eath,andKjaer2011).Anothergene

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thathasbeenlinkedtoanimalwelfareissuesisPMEL17inchickens(Keelingetal.2004).Individualswithawildrecessivealleleinthegene,whichcontrolsplumagemelanisation(Kerjeetal.2004),aremorelikelytobevictimsofintensefeatherpecking.Animalwelfareisaconceptthatdidnotoriginallyarisefromscience,althoughitisascientificconcepttoday(DuncanandFraser1997).Theoriginofanimalwelfarecomesfromsocietyasameanstodealwiththeethicalconcernsofhowhumanstreatanimals.Thismeansthatanimalwelfareislargelybasedonethicalvaluesandtoproperlyunderstanditonemustdelveintothemanyethicalviewsavailableforexplainingwhatis“rightandwrong”whenitcomestoourtreatmentofanimals.Tobeabletomeasureanimalwelfare,weneedaproperdefinitionsothatitisclearlystatedwhatitiswearemeasuring.Fromascientificpointofview,Broom(2008)writesthat“Thewelfareofanindividualisitsstateasregardsitsattemptstocopewithitsenvironment”.Thisdefinitionstatesanimalwelfareinthescientificviewasacharacteristicofanindividualwhereaspopularlyitmaybethoughtofsomethingthatisgivenanindividual.Intheryr1example,animalswiththeryr1mutationareclearlylesscapableofcopingwiththeirenvironmentandwecanconcludethatthoseanimalshaveapoorwelfare.Apopularviewofanimalhusbandryamongthepublicisthatanimalsthathavebeenkeptincaptivityforalongtimehavelosteithertheabilityorneedtodisplaynaturalbehaviours.Althoughwecanselectanimalsbasedontraitsthatwillhelpthemcopewiththecaptiveenvironment,careshouldbetakennottoassumethatallbehaviourscanbemodified.Behaviouralrestrictioniswhenanimalsarenotabletoperformanaturalbehaviour,beitonethatisusuallyperformedregularlyoroneforwhichthemotivationmaybetemporary.MasonandBurn(2011)comparebehaviouralrestrictioninanimalstothatofhumanswhoareplacedine.g.solitaryconfinementasapunishment.Behaviouralproblemssuchasstereotypiesoftenemergeinenvironmentswhereanimalsarenotabletoperformnaturalbehaviours.

5. SummaryMuchisyettobeknownaboutthemechanismsbehinddomestication.Throughtheuseofgenetictools,weareabletoidentifydifferencesinthegenomebetweenforexamplewildanddomesticatedspecies.Thisinformationhelpsusdeterminethemechanismsunderlyingdomestication.Differentiatingbetweenlinkageandpleiotropyisanimportantstepincompletelyunderstandingthecorrelatedselectioneffectsindomestication.Thechickenisanexcellentmodelfordomesticationresearchasthewildancestorisreadilyavailableinitsnaturalhabitataswellasincaptivity.Thisallowsforcomparativeaswellasselectionexperimentswherethedomesticationprocesscanbereplicated.Determiningthegeneticmechanismsbehindanimaldomesticationwillnotonlyshedlightonthisevolutionaryprocessbutcanalsobeusedtoimproveanimalwelfareinatimewhereincreasedproductionrateishighlyvalued.

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