The Domestication Makeup: Evolution, Survival, and Challenges

Domestication is an evolutionary process by which animals are artificially selected and undergo huge phenotypic behavioral and physiological ... Articles FulvioCruciani SapienzaUniversityofRome,Italy MuniyandiNagarajan CentralUniversityofKerala,India PaulGepts UniversityofCalifornia,Davis,UnitedStates Theeditorandreviewers'affiliationsarethelatestprovidedontheirLoopresearchprofilesandmaynotreflecttheirsituationatthetimeofreview. Abstract Introduction AnimalDomestication DomesticationandEvolution DomesticationStudies DomesticationGenes ChallengesandProspects Conclusion AuthorContributions Funding ConflictofInterest Acknowledgments Footnotes References SuggestaResearchTopic> DownloadArticle DownloadPDF ReadCube EPUB XML(NLM) Supplementary Material Exportcitation EndNote ReferenceManager SimpleTEXTfile BibTex totalviews ViewArticleImpact SuggestaResearchTopic> SHAREON OpenSupplementalData REVIEWarticle Front.Ecol.Evol.,08May2020 |https://doi.org/10.3389/fevo.2020.00103 TheDomesticationMakeup:Evolution,Survival,andChallenges HafizIshfaqAhmad1,2,MuhammadJamilAhmad3,FarwaJabbir4,SunnyAhmar5,NisarAhmad2,AbdelmotalebA.Elokil6andJinpingChen1* 1GuangdongKeyLaboratoryofAnimalConservationandResourceUtilization,GuangdongPublicLaboratoryofWildAnimalConservationandUtilization,GuangdongInstituteofAppliedBiologicalResources,Guangzhou,China 2DepartmentofLivestockProduction,UniversityofVeterinaryandAnimalSciences,Pattoki,Pakistan 3CollegeofAnimalScienceandTechnology,HuazhongAgriculturalUniversity,Wuhan,China 4DepartmentofBiotechnology,UniversityofSargodha,Sargodha,Pakistan 5NationalKeyLaboratoryofCropGeneticImprovement,CollegeofPlantScienceandTechnology,HuazhongAgriculturalUniversity,Wuhan,China 6AnimalProductionDepartment,FacultyofAgriculture,BenhaUniversity,Benha,Egypt Animaldomesticationisconsideredacomplexandmultistageprocessthatalteredbehaviorally,morphologically,andphysiologicallythedomesticatesrelativetotheirwildancestors.EversinceDarwin,scientistshavebeenconcernedaboutthehistoryofdomestication.Todeterminethedomesticationoriginsofthespecies,itiscrucialtodiscovertheirancestorsandidentifytheapproximatelocaldomestication.Domesticationhasbeenthefocusofseveralstudiesfromdifferentspecialties.Studyingwhen,where,andhowdomesticationhappenedisessentialtounderstandtheoriginsofcivilizationsandtheevolutionofdomesticatedspecies.Thedevelopmentofbothhumansanddomesticanimalsishardtojustify,andthegeneticvariationsthatoccurredduringtheearlyanimaldomesticationprocessremainvague.Therecentandpotentialapplicationsofevolutionarybiologymaydeliveranswersformainsocialchallenges.Itisimportanttoexaminetherelationshipamongtheenvironmentandthetraitsoforganismsthathavebeeninfluencedthroughtheadaptationtomodernenvironmentsandthepatternsofselectiontriggeredbytheirenvironmentsduringdomesticationperiod.Oncedomesticationoccurred,severaleventssuchasgeneflowandselectivepressuresoccurred,leadingtogenomicandphenotypicalterations.Inthisreview,wediscussthecurrentknowledgeaboutthespatiotemporaloutlinesofdomesticationanddebatessurroundingtheintent,speed,andevolutionarylandscapesofthisevent.Wealsofocusonthecorechallengesforfutureresearch.Inconclusion,wearguethatalthoughthecurrentgrowthindomesticationinformationhasbeenremarkable,thenexterawillproduceevenmoresignificantinsightsintonotonlyhowdomesticationoccurredbutalsowhereandwhenitdidso. Introduction Domesticationisanevolutionaryprocessbywhichanimalsareartificiallyselectedandundergohugephenotypicbehavioralandphysiologicalalterations(Trutetal.,2009).Thesetransformationsoccurredatthesametimeinseveralregionswithatremendousimpactonhumansocieties(Neolithization)(Vigne,2011).Domesticationiswellknownnotonlyforitsslowcoursebutalsoforitsextremetechno-economicalterations,fromhunting-gatheringtofoodproduction(Price,1999).Itdependsonmanyimportantfactors,suchasstrongdemographictransition,cultivation,andhusbandryofvaluabledomesticates(Bocquet-Appel,2008),alongwithprofoundsocialandspiritualchanges(Price,2002). Dogs(Canislupusfamiliaris)weretheearliestspeciesdomesticatedbyAsianandEuropeangatherersduringthelateglacialperiodapproximately17–15thousandyears(kyrs)beforethepresent(BP)(Pionnier-Capitanetal.,2011;Frantzetal.,2016)followedlaterbythedomesticationoflivestockandcrops(Mignon-Grasteauetal.,2005).Interestingly,whileinsomespecies(dogsandcattle),domesticationwasahuman-drivenprocess,forotherspecies(cat,rat,andhousesparrow),itoccurrednaturally(Driscolletal.,2009).Nowadays,severalauthorsagreethatthereareapproximately40animalspeciesdomesticatedindifferentgeographicareas(ScherfandPilling,2015;Leroyetal.,2018). Differencesinmorphologicalfeaturesandbehaviorofmostdomesticanimalsfromtheirwildcounterpartscameaboutbycontrollingbreedingandpersistentanimalhusbandry.Thesepracticesalsodesignedandshapedthediversegeneticmakeupamongdifferentbreedingpopulations.ThevariationinthephenotypesofthedomesticatedanimalledtothebasisoftheDarwinianevolutionarystudy,whichhighlightedseveralqueriesforfurtherstudies,namely:when,where,andhowdidthedomesticationoftheseanimalsstart,andwhatarethegeneticoriginsofdomesticationdevelopment(Darwin,1859).Darwin’sinitialobservationsin“OntheOriginofSpecies,”andhisvariationunderdomesticationbegananessentialdebateforfutureworks(Darwin,2010).Commonly,fordifferentdomesticanimals,therearetwoevolutionaryphases:anancientdomesticationeventwhereawildancestorbecomeadomesticatedspeciesfollowedbyamodernbreedingprocess(Driscolletal.,2009).Ancientdomesticationoccurredapproximately12,000–14,000yearsago,duringtheagriculturalsurgeoftheinitialNeolithicperiod,alongwiththedomesticationofmajorcrops(Wangetal.,2014b).Ontheotherhand,modernbreedingoccurredonlyinthepast300years(sincetheeighteenthcentury)andstartedwiththeselectionofbreedinganimalsbasedontheirdemandbyhumansocieties(CrowleyandAdelman,1998). Inthecurrentreview,wetrytosummarizetheexistinginformationondomesticationfromtheliterature.Westartbyaddressingtheevolutionofanimaldomesticationthroughanevolutionaryperspective.Weaddresstheroots,demographichistory,andimpactsondomestication,geneticarchitecture,andmethodologiestakentomonitordomesticationproceduresbyselectivepressures.Wealsoconcludepresentingthechallengestotheresearchandapreviewoffuturedirectionsforthisthematic. AnimalDomestication Animaldomesticationistheprocessofaprompt,artificial,andintensiveselectionofwildanimalsthat,overthelast11,500years,hasalteredtheEarth’sbiosphere,shapedhumanevolution,andinfluencedthesizeofthehumanpopulation.ThefoundationofdomesticationislinkedtotheculturalprogressionfromhuntingtofarminginancientcivilizationsduringtheNeolithicperiod,possiblywiththeexclusionofdogs,whichweretheearliestdomesticatedanimals(Savolainenetal.,2002)anddivergefromotherspeciesregardingbothlocationandtimingofdomestication(Beja-Pereiraetal.,2006;Liuetal.,2006;Driscolletal.,2009).Theperiodswhereanimaldomesticationoccurredweredeterminedthrougharcheologicalcluesandreflectedselectionforcesgeneratedbyhumanactivitiesandbyhuman-adaptedenvironments.Duringthelastyears,severalstudies(Chenetal.,2007;Wright,2015;Hunter,2018)havefocusedonanimaldomestication,andnowadays,itispossibletoestablishatimelineforthedomesticationofseveralanimals(Figure1).Despitethis,therearestillseveralquestionsregardingthetiming,location,andtheevolutionarydomesticationprocess(LarsonandFuller,2014). FIGURE1 Figure1.Thetimelineofanimaldomestication(adaptedfromZeder,2008). SincetheNeolithicperiod,humansstruggledtodomesticatewildanimalsandusethemasfoodsources(milkandmeat),commoditymanufacturers(silkandwool),protection,andtransportation.Therearethreepathwaysdescribedfordomestication:commensal,prey,anddirectpathways(Zeder,2012;Figure2).Inthecommensalpathway,thewildanimalswereattractedtoanthropogenichabitats,mainlyforhumanfoodwasteorsmallprey,establishingacommensalrelationshipwithhumans.Dogs,cats,orchickensaresomeofthespeciesthatfollowedthispathway.Inthepreypathway,humansstarthuntingsomespecieslikepigsandcattlefortheirmeatinresponsetodepletionofthelocalstockoftheseanimals.Overtime,thesegamemanagementstrategiesdevelopedintocontrolledbreedingofthesespecies.Inthedirectpathway,humanscapturedwildanimals(horses,donkeys,andcamelids)toobtainsomeresourcesbycontrollingtheirmovements,theirnutrition,andreproduction,whichleadtoadramaticbottleneck(Zeder,2012). FIGURE2 Figure2.Differentpathwaysfromwildtodomesticanimals(adaptedfromLarsonandBurger,2013). Dogs Dogswerethefirstanimaltobedomesticatedbyhumansmorethan15,000yearsago.Theirwildancestoristheextinctgraywolf,anddespitebeingintensivelystudied,therearestillquestionsregardingtheirgeographicalandtemporaloriginsandeventsofdomestication.Intheliterature,thereareseveralplacesoforiginofdogs,includingEurope(Thalmannetal.,2013),theCentral,MiddleEast,andEastAsia(Pollingeretal.,2010;Shannonetal.,2015;Wangetal.,2016).Morerecently,astudyusingmtDNAstatesthatdogsmayhavebeendomesticatedindependentlyinEasternandWesternEurasiafromdifferentwolfpopulations.LatertheeasterndogsaccompaniedhumansthroughtheirdispersiontoWesternEurope,wheretheyreplacedtheWesternEurasianandEuropeanPaleolithicdogs(Frantzetal.,2016).ThesameeventoccurredforAmerican(Leathlobhairetal.,2018)andAfrican(Liuetal.,2018)dogsthatarrivedwithhumanexpansions.Theseexpansionsthroughtheworld,andtheevolutionarydoghistory,involvebottlenecksandgeneflow. Cattle Sinceancienttimes,wildcattleandhumansareinterconnected,andduringthelast10,500years,thenumberofdomesticatedbovinespeciesisapproximatelyfive(Helmeretal.,2005),resultedinhumanbenefitsofmeatandmilktodroughtanimals.Recentlywildcattlearethesourceofthegeneticpoolfordomesticbreeds’adaptationtochangingpressuresofclimateandinfectiousdiseases(MellettiandBurton,2014).CurrentknowledgeofcattledomesticationispredominantlybasedonmitochondrialDNAanalysis(Groeneveldetal.,2010).Taurinecattledomesticationreportedbacktothewildandnowextinctintheneareast,about8500yearsago,aftersheepandgoatdomestication(Helmeretal.,2005;Bollonginoetal.,2012). CattlewithLonghornphenotypewerethefirstonetobedomesticated;still,thisphenotypeiscommoninthenumberofBritish,French,Mediterranean,andAfricanbreedstodate(SchafbergandSwalve,2015).Firstcattlewithshorthornsreportedbackto3000yearsBC;thephenotypewasfittothesehabitatsandswitchedbynextwaveofmigrants(BradleyandMagee,2006).Britaintookthemostlong-hornformsfromAsiaandneighboringcontinentsabout1000–2000yearsBC(Epstein,1984).InEurope,themostcommontypeofcattlewasshort-hornuntilaround1000BC(Lenstraetal.,2014).Severalecosystemsinthevariousregionsoftheworldareattributedtothedomesticationanddistributionofcattletoandtheiradaptationtolocalenvironments(Lenstraetal.,2014).Moreover,several“agrotypes,”generatedbyhumanselection,letthebreedsdifferincoatcolor,developmentofhorns,anddocility(Ajmone-Marsanetal.,2010).Systematicshasacceleratedthecattlediversityinthelast200yearsandstretchedthecastlestothemainbreeds,likewithdairyproduction(Barkeretal.,1991)cattleacquiredthelargeudder.TheprocessofthedomesticationresultedinacontinuousdecreaseofsizeuntiltheMiddleAges,butitwaslesspronouncedinlong-hornedItalianformsanddraughtcattle(Lenstraetal.,2014). Sheep Primarilysheepwereraisedformeataround4000–5000yearsagobutlaterspecifiedforotherfoodstuffs.Developmentsinanimalhusbandryandapplicationofdirectmatingsystemshaveevolvedavarietyofcurrentsheepbreeds,notonlythemostadaptabletotherangeofclimatesbutalsospecifictotheproductionofmilk,meat,andwool(Chessaetal.,2009;Kijasetal.,2012).MongoliansheeporiginisthewildArgalisheepfromhighlandareasofCentralAsia.Morethan2,000yearsago,manypopulationshadmovedtothesouthoftheGreatwallforseveralreasons;hencethemostpresentChinesebreedsarelinkedtoMongoliansheep(Huangetal.,2017).However,withexposuretoachangingenvironment,andfeedingsituationstovariouseco-regionsacrossthecountrythannormalhabitat,MongolianSheepfacedextensiveartificialselectionindiverseorders(Liuetal.,2016). ThesubspeciesofMongoliansheepdisplaysubstantialchangesinseveraltraits,particularlyassociatedwithreproduction,buthowspeciesdivergenativelyrelativetothesecharactersisnotwellinterpreted(Huangetal.,2017).Thesestudiesidentifiedthegenesofsignificantimportancefordomesticationprocess(Petersenetal.,2013b;Carneiroetal.,2014),capabilitytowithstandtheharshclimates(Gouetal.,2014;Wangetal.,2014a),orconspicuouseconomiccharacters(Choietal.,2014;Yangetal.,2014;Wangetal.,2015).Tibetwildpig(Lietal.,2013)andTibetmastiffs(Gouetal.,2014;Wangetal.,2014a)havebeenasubjectforpopularstudiesfromTibetanPlate,andlinkedmanygenesforadoptiontohighaltitudeandhypoxia.Severalstudieshaveexploredthegenome-widedifferenceamongvariousindigenousbreedstofixthemolecularbasisofvariousphysicaltraitsofvitalimportanceinthelivestock,suchaschicken(FanW.-L.etal.,2013),pig(Yangetal.,2014;Wangetal.,2015),andcattle(Choietal.,2014).However,thestudiesforChineseshortfattailsheeparelimited. Goat FertileCrescentLandhasreportedasthefirstdomesticationhabitatforgoat(Caprahircus)inNearEastalmost<10,000yearsagobyvariousgeneticandarcheologicalstudies(Pringle,1998).Thedomesticationofgoatshasasignificantroleinhumansocietybyprovidingvaluedproductssuchasmilk,meat,furs,andfiber,predominantlyinChinaandotherdevelopingcountries(Joshietal.,2004).Duringtheepoch,thesedomesticbreedsrichingeneticassetsincitedustopaymoreconsideration;consequently,keepingthedomesticanimalvarietyisimperativetoaccomplishtheforthcomingnecessities. Concerningpreciseeconomicandenvironmentalfeatures,Chinahasstartedfocusingonconservationstrategiesforthesenativebreeds,includingspecifiedconservationzone,conservationfarms,andthegenebankofthegeneticreservefordistinctivebreeds(Weietal.,2014).ThesehighlandshadallocatedWestChinaintoSouthwestandNorthwestChina,andconsequencetothediverseclimaticregionsandecologicalstructure.Chinaisanextensivesubcontinentofmergedtopographicallocations,soChinesegoatbreedsexhibitagreatrangeofvariationinproductivity,milkproduction,meat,andfiber;draughtability;heattolerance;anddiseaseresistance.Besides,severalprecedingstudiesonChinesegoatswereconductedintherestrictednumberoftrialswithinfewerbreedsandcounties(Dietal.,2011;Weietal.,2014). Cat ArecentevolutionarystudyofdomesticatedcatsusingDNAanalysissuggestedthousandyearsofinteractionbetweenthecatsandhumansbeforetheirdomestication,andthisinteractionletthecats’geneschangedpretentiouslyfromthoseofwildcatsexceptthedevelopmentofuniquestripesandspotsofthetabby(O’BrienandJohnson,2007).EvaluationoftheDNAofcatsbridgingthelast9,000years–countingtheremains,mummies,andspecimensofcatsfromancientRoman,Egypt,andmodernAfricanwildcat–suggestedthecurrentdomesticfelinehaveagreatcontributionoftwomajorcatlines(Ottonietal.,2017). Thusearly4400B.C.,earlierancestorsofourdomesticcatsspreadfromSouthwestAsiaandintoEurope(Ottonietal.,2017).Farmingcommunitiessettledthecatstocontroltherodentpatrol.Miceandratsweredrawntothecrops,andtherodentpopulationswerepossiblypursuedbycats(Montagueetal.,2014).Inturn,bothoftencameclosetothehumansettlement.Hence,thedomesticationchangedthewildcatstoadomesticatedhumancompanionwithoutchangingmuch,saysEva-MariaGeigl,theevolutionarygeneticistandarticleco-author(Ottonietal.,2017).Domesticatedcatslooklikewildcats,buttheyarenotlonelyandcapableoftoleratingbothhumansandotheranimals(O’BrienandJohnson,2007). Horses Thedateofhorsedomesticationisconceivedfromthedefinitionofdomestications(Cieslaketal.,2010).Twotheoriesofdomesticationareasfollows:first,thehumancontroloverbreedingdepictedbychangesinthesizeandvariabilityofancientskeletalsamplesfromancienthorsepopulations,andsecondincludesbroaderevidenceofskeletalanddentalactivityweapons,arts,andspiritualartifacts;andpatternsofhumanlifestyles(Ross-Ibarra,2004).Evidenceclaimhorseswerekeptasmeatanimalsbeforetrainedasworkinganimals(Hausbergeretal.,2008).Theconceptofisolatedgenotypesbetweendomesticatedandwildpopulationsleadstoexploringthedomesticationattemptsusinggeneticsorphysicaltraitsexamination(Rollin,2011).Butthesemethodscouldonlyfindthelatestfootprintsofdomesticationbutfailedtodetermineuncertainprimitivegeneflowbetweenthetwogroups(whichoccursnaturallyaslongasthedomesticatedpopulationremainswithinwildlifehabitat)(Vilàetal.,2001).Furthermore,beingdescendentofcaptive-fledgedancestors,allthedomesticatedhorses,andferalhorsesarecapableofretainingeithercharacteristic(DobbieandBraysher,1993).Timeframeschosenforthehorses’domesticationareinfluencedequally,eitherfollowingthenarrowerzoologicalconceptofdomesticationorthebroaderculturaldefinition,i.e.,thecombinationofzoologicalandarcheologicalfacts(AberleandDistl,2004).Thedateof4000BCEisbasedonevidencethatincludestheappearanceofbite-relateddentalpathologies,changesinbutcheringpractices,changesinhumans’economiesandpatternsofsettlement,thedepictionofhorsesassymbolsofpowerinartifacts,andtheappearanceofhorsebonesinhumangraves(LarsonandBurger,2013). Buffalo Thedomesticationprocessledtotheadaptationofvariousbovinespeciestoanagriculturalenvironment,andthemostimportantspeciesareindicatedandtaurinecattlefollowedbyswampandriverineandbuffalo(Barker,2014).Thesespecieshaverangedtoseveralregions,whilethedomesticformsofgaurandyakaregroupedneartheirwildancestors’sharingareas(Groves,1981).ThegenusBubalusdistributionwasinitiallystartedinthePleistocene,Europe,andSouthAsia,butwaslaterconstrainedtosoutheastAsiaandtheIndiansubcontinent(Flamandetal.,2003).Inancienttimes,thewildAsianbuffalo(ChoudhuryandBarker,2014)spreadacrosssoutheastAsiatoIndo-China.Itispresentlylistedasanendangeredspecies,withaworldpopulationlesserthan4,000,possiblyfewerthan2001.Domesticwaterbuffalo(B.bubalis)hasbeengroupedintotwotypes:riverandswampbasedonbehavioralandmorphologicalcriteria(Barker,2014).Somehavereferredtotheseasdistinctsubspecies,namingswampbuffaloB.bubaliscarabenesisandriverineB.bubalisbubalis.However,becausetheyresultedfromdifferentdomestications,heretheyaredesignateddistinctly.Thesameappliestotheswampandrivertypesofwaterbuffalo,thecross-fertilesubspeciesofthewildBubalusarnee(Groeneveldetal.,2010;Yindeeetal.,2010). Chicken Thehistoryofdomesticchickenspeciescanbediscussedinthreedifferentperiodsoftime.Thelongestperiodistheevolutionaryhistory,sharedwithotherspeciesbeforespeciation,andalongwithvariouscoursesafterspeciation.Thecurrentlysharedancestorofbirdsandmammalsexisted300myago(Tixier-Boichardetal.,2011).Themostcommonancestorbetweenchickenandquaillived40myago(Mwacharoetal.,2013).Thesecondperiodofspeciesdomesticationstartsseveralthousandyearsagoandledtodomesticspeciesdiversification.Therecentperiodofrigorousproductiontraitselectionappliedtoasubsetofthesebreedsisshorter,withjustafewdecades(Kanginakudruetal.,2008).Therefore,onanevolutionaryscale,domesticationand,moresignificantly,agoodselectionforhigherlevelsofproductionareveryimportant(MacDonald,1992).Currentdomesticchickens’genomediversityisaresultofthefoundingeffectsatthetimeofdomestication,thelong-termdomesticationprocess,subsequentbreeddifferentiation,andrecentstrongproductionselection(Nishiborietal.,2005).Thecumulativeeffectofhuman-madedomesticationandsubsequentselectionhasgivenrisetoaremarkablephenotypicdiversificationofthechicken,bothatthemolecularlevel(MacDonald,1992). DomesticationandEvolution Domesticationhasbeenacorequestionofinterdisciplinaryscientificresearch,andthosetraitsthatenhancethesurvivalorthereproductivecompetenceoftheorganismsaresubjecttoselectionandtransferredtothenextgenerationtoincreasethepopulationprevalence(Vittietal.,2013).Since2006,thestudythedomesticationthroughcompletegenomesequencehasbecomepossible,andithasbeenassociatedwiththedetectionofselectioninalargenumberofgenomiclocithathavelikelyevolvedbyselectivepressures(Carneiroetal.,2014;Larsonetal.,2014).Carneiroetal.(2014)studiedgenesinvolvedinbrainandneuronaldevelopmentandproposedthatdomesticanimalsevolvedbyaccumulatingseveralmutationswithsmalleffectsinsteadofcriticalalterationsinafewloci.Laterin2016,Messeretal.(2016)reviewedsomelimitationstothismodelandprovidedsomeexamplesofstudiesusingfishes,bugs,andreptileswherethephenotypictraitsalteredinafewgenerations.Stronganimalhusbandrypracticesandcontrolledbreedinghaveshapedthebehavior,themorphologicalfeatures,andthegeneticdiversityofdomesticanimalswhencomparedtotheirwildancestors(Wangetal.,2014b).SeveralalterationswereobservedacrossdifferentdomesticspeciesandcaptivatedresearchersatleastsinceDarwin’findings,namelylackoffear;enhancedreproductivesystem(abletoreproduceinanyseason);disparitiesinthecoatlength,texture,andcolor;modificationsinskullform,toothcrowding,andcorporalsizes;floppyears,androlledtails(Driscolletal.,2009;Trutetal.,2009;LarsonandFuller,2014;Wilkinsetal.,2014).Thesecharacteristicsmakedomesticatedanimalsvaluedmodelsfordifferentareaswithhighlightsingeneticsandbiomedicalresearch(Andersson,2016;Wolfetal.,2018):descendantsarecommonlyknown,samplesareusuallyunlimited,manybreedsareinbred,genevariantsresponsibleforparticularphenotypiccharactersarefixed,andthegeneticdifferences(arequirementforselection)arelimited(Andersson,2001;Gentryetal.,2004;Lyonsetal.,2016).Allthesedifferencesareassociatedwithgeneticeventsasinbreeding,geneflow,andselectionpressures.Inbreedingleadstoadecreaseingeneticdiversityandisassociatedwiththeisolationofsmallpopulationsatthebeginningofthedomesticationprocess(Cieslaketal.,2011).Thereisevidenceoflong-termgeneflowbetweenwildanddomesticanimalssuchasdonkeys,horses,camelids,pigs,wolves,cats,andthereindeer(Marshalletal.,2014;Frantzetal.,2015;Bolstadetal.,2017).Oncedomesticationbecameestablished,arelaxationinthenaturalselectivepressures(bothenvironmentalandinducedbyhumans)enabledtheincreaseofnewmutations(mostlynon-synonymousmutations),leadingtoevenmoredifferentiatedspecies(Petersenetal.,2013a).Despitethis,andduetothemultitudeofselectivepressuresinvolved,itisdifficulttoisolateanycausalfactorsthatresultinspecificgeneticdifferences(Zeder,2015).Overthepast40years,severalspecies(mostlylivestock)havebeenintensivelyselected,andnotablephenotypicvariationshavebeenobserved.Sincemanyofthesegeneticmutationsleadtophenotypicalterations,identificationofthesignaturesofpositiveselectionisconsideredavaluabletooltorecognizegenesthatmightunderlieimportanttraitsallowingtolinkgeneticvariantstoaparticularphenotype(Consortium,2009). Assomeauthorssuggest,domesticationstartedunconsciously(TchernovandHorwitz,1991),andlateraconsciousselectionofhuman-definedtraitsledtoahighlevelofdiversity(Trutetal.,2009).Indeed,duringtheinitialperiodoftheirdomestication,horsesweremainlyusedformeatandmilk(Outrametal.,2009),andlatertheybecameimportantfortransportation,warfare,andsporthorseracing.Anotherexampleisthedogdomesticationprocessthatfocusednotonlyonpreferredphysicalcharacteristics,suchasbodythicknessandbodylength,texture,skullshape,tailsizeandshape(Wayne,1986),butalsoonimprovedbehavioralpatterns,withadvancedfeaturesofguarding,herding,speed,agility,andcompanionship(Ostranderetal.,2000).Indeed,alloverthedomesticationprocess,studiessuggestthathumansdidnotmaintainconstantselectivepressures.Mostlikely,theyselecteddifferenttraitsindifferentplacesatdifferenttimes.Thus,extracaremustbetakensincethediscoveryofcertaintraitsincurrentbreedsdoesnotnecessarilymeanthatthetraitwasatargetduringtheearlydomestication(MacHughetal.,2017). DomesticationStudies Domesticationhasfascinatedscientistsfromdifferentfieldsthroughitsimportanceasamodelofevolutionaryanddemographicchange(Zederetal.,2006).EversinceDarwin,scientistshavebeenconcernedaboutthehistoryofdomestication.Todeterminethedomesticationoriginsofthespecies,itiscrucialtodiscovertheirancestorsandidentifytheapproximatelocaldomestication.Forexample,dogsweredomesticatedbeforethestartofagriculturefromgraywolves(LarsonandFuller,2014).However,graywolvesweredisseminatedacrosstheNorthernhemisphere,hamperingthefindingsonhow,why,when,andwheredogsweredomesticatedandifthisprocessoccurredjustonceorindependentlyatdifferenttimes(Larson,2017).Overtheyears,differentgeneticmethodologieshavebeenusedtoexplorethesequestions(Larson,2011). Inthefirststudies,DNAswereextractedfromsamplesofagivenspecies(differentlocations,breeds,andpopulations)andusedtoamplifyandsequencecontrol-regionsofthemitochondrialgenome.Additionally,phylogenetictreesandhaplotypesnetworksweregenerated(Larson,2011).MitochondrialDNA(mtDNA)isconsideredanidealmarker,beingextremelymutablewithinspeciesandhasbeenusedtostudydemographicexpansion,geneticdiversity,andphylogeneticstructure(Brufordetal.,2003).However,thesesequencesarederivedfromthematernallyinheritedgenomeandhavealimitedpowertoidentifyandquantifyhybridizationbetweendifferentpopulations(Larson,2011).Thisapproachwasintensivelyusedforseveralspeciesasdogs(Verginellietal.,2005),pigs(Giuffraetal.,2000),horses(Jansenetal.,2002),andcattle(Loftusetal.,1994),howeverwithnodeepinsightsintotheirdomesticationprocess.SomeauthorssuggestthatrecentselectivebreedingmaycontributetounderminingthesignaturesofmtDNAbetweendomesticatesandtheirancestors(Libradoetal.,2016).Additionally,quantitativetraitloci(QTL)mappinghasbeenusedtoidentifycandidategenesassociatedwithdomesticationtraits.Withtheseanalyses,therehavebeensomeimprovementsinthedomesticationprocess,namelyforfox(Kukekovaetal.,2011),chickens(Fallahsharoudietal.,2017),pigs(Rodriguezetal.,2005),andcattle(Khatkaretal.,2004). GWAS,NGS,Microarray,andmtDNA Indomesticanimals,thegenome-wideassociationstudies(GWAS)hasbecomeanimportantmethodtostudythegenomicregionsinvolvedintraitsofconcernwiththesequencingofthepig,cow,anddoggenomes(Lindblad-Tohetal.,2005;Groenenetal.,2012;Hekmanetal.,2015).Thismethodinvestigatesthelikelihoodoftheassociationofthegeneticmarkerswithaspecifictraitindomesticanimals(Cadieuetal.,2009).Thevariationinthesetraitsisduetointensiveselectivepressureelucidatedbyasmallnumberoflociinthesespecies(Boykoetal.,2010).Consequently,inseveraldomesticatedspecies,GWAShaveeffectivelyrecognizedcontributinggenesbothforcomplextraitsandMendeliantraitscontrolledbylociwithbiginfluencesize(Hekmanetal.,2015).Theuseofgenome-widemethodsinitiatedthemicroarraygeneexpressionstudiesinthesearchforagroupofgenesorgenelinkagesinvolvedincompositephenotypesindomesticatedanimals(Evertsetal.,2005).However,theuseofmicroarraytechniquesisnarrowduetotheirdependenciesontheuseofidentifiedprobes,needingspecies-specificmarkersforthemostpreciseresults(Hekmanetal.,2015).Theintroductionofnext-generationsequencing(NGS)technologieshasrevolutionizedthegeneexpressionresearchbyremovingtheneedforpriorprobesfortranscripts.RNA-seqorRNAsequencingrequiresthehigh-throughputreadsgeneratedbyNGStocharacterizethewholetranscriptome:inotherwords,alltranscriptsgeneratedinatissuesampleplusnovelisoformsandformerlyuncharacterizedrecordedsequences(Allenetal.,2010).RNA-seqisgenerallyusedforarangeofapplications,suchastocomparethegroupofdifferentiallyexpressedgenesintissuesamplesorsamplesfromdifferentexperimentalgroupsorpopulations(Bottomlyetal.,2011;Royetal.,2013).BasedonNGSorRNA-seqdata,theindividualscanbegroupedintohealthyordiseasedbyidentifyingthegenelinkagesassociatedwithhereditarydiseasesorothergenetictraitsorbymappingvariousgeneticloci(Gautieretal.,2012;Tonomuraetal.,2015).Furthermore,mtDNAtechnologywasusedtorecognizethegenomicregionsassociatedwithimportantphenotypictraitsaswellastoidentifytheevolutionaryhistoryandtheoriginofdomesticationinanimalspeciesascomparedwithnuclearmarkers(MacHughandBradley,2001;Akeyetal.,2010).Since2000,sequencesofmtDNAfragmentssuchasD-loopandcytochromebregionshavebeenusedtostudydistributionofdifferentdomesticatedanimals,includingdogs(Savolainenetal.,2002),sheep(Hiendlederetal.,2002),pigs(Giuffraetal.,2000),cattle(Troyetal.,2001),goats(Luikartetal.,2001),horses(Jansenetal.,2002),chickens(Liuetal.,2006),donkeys(Beja-Pereiraetal.,2004),andcats(Driscolletal.,2007),aswellasthosewithmorerestricteddispersals,suchaswaterbuffalo(Kiersteinetal.,2004),andzebucattle(Chenetal.,2010).mtDNAresearchhasprovidedaviewpoint,atleastfromtheparentalside,astotheprobableancestorsandcandidatepedigreesinvolvedinthedomesticationofspecies(Wangetal.,2014b). Understandingthegeneticbasisofphenotypicvariationsisthemajoraimofgenetics.Domesticanimalsofferasubjectiveopeningformakingsignificantimprovementtowardthegoalofminimizingthegapbetweenhumanbiologyandtraditionalmodelspecies(QanbariandSimianer,2014).Thecontinuousprogressofhighthroughputsequencingtechnologiesandmodernbioinformaticsapproachesprovidethecompletegeneticvariationmapofanindividual,anditisnowlikelytotestforphenotypicvariationcausedbysinglenucleotidepolymorphisms(SNPs).Thegenome-wideassociationstudies(GWAS)andcandidategeneapproacharetwoprimarymethodsthatarecurrentlyfollowedtorecognizegenomicregionsorgenesaffectingtheparticulartrait.PopulationgenomicshaspresentedanewmodelforlinkingDNAwithaphenotypethathasbeenrevealedasaselectionsignatureanalysis.Thisisagenometophenotypemethodthatincludesthestatisticalassessmentofpopulationgenomicdatairrespectiveofphenotypetofindouttargetsofthepreviousselection.Selectionanalysiscanbeemployedinthenaturalpopulationsonumerousspecies(Akeyetal.,2010)forwhichahigh-densitygeneticrecordisavailable.Anadditionalbenefitisthatitcandetectselectionifthepreferredalleleispreviouslyfixed,whileGWASfailsinsuchacondition(QanbariandSimianer,2014). SNPChip Inmodernresearches,throughusingrecentgenomicstechnologies,ithasbecomelikelytoexplorethemicro-evolutionarydevelopmentsunderlyinganimaldomesticationatthemolecularlevel.Inthisregard,variousstudiesthathavebeendonetoproducedomesticredfox,silverfoxes(Vulpesvulpes),andrats(Rattusnorvegicus)haveprovidedvaluableunderstandingsthatwereintroducedduringthemiddleofthetwentiethcentury(Albertetal.,2009,2011;Trutetal.,2009).Furthermore,functionalgenomics,quantitativereal-timePCR,microarrayandreversetranscriptionstudiesofbraintissuesfromdomesticdogsandwolves,transcriptionalprofilingthroughRNA-sequencingofratbrainscombininggenomemappingstudieshaveidentifiednumerouscandidategenesandputativeregulatoryregionsthathaveinfluenceddocilityandviciousnessinanimals(Heyneetal.,2014).Itisnecessarytoannotatethattheacutechangesingeneexpressionlinkedtodomesticationpossiblyaffectthegrowingstagesinaspecifictissueandwillrequireextensiveworktobeconclusive(Carneiroetal.,2014).Geneenrichmentanalysisrecognizedthatneurobiologyisaffectedbythelociofthosegenesthatwereover-representedandtargetedbydirectionalselection,andprinciplefunctionalanalysesexposedthatderivedsinglenucleotidepolymorphismsindevelopmentalgenes(PAX2andSOX2)werepossibletobefixedwithin,orcloseto,regulatorysequences.Mostremarkably,itwasconcludedthatdomesticationwaspredominantlyassociatedwithselectivesweepscausinggeneticvariationsonregulatoryregionsthroughouttheanimalgenome,thereforeindicatingmicro-evolutionarydevelopmentsduringtheinitialperiodsofdomesticationofvertebratespecies(Carneiroetal.,2014).Understandingthesignificanceofsingledisease-associatedSNPallelesitselfisneithernecessarynorenoughincausalofadisease.Rather,itispossiblythecollectiveconsequenceofasetofSNPallelesenclosedbykeygenes,plusenvironmentalfactorsthatjointlyconcludewhetheranindividualexperiencesacertaindisease.Theassociationstudyprocessincludesthefrequencydeterminationoftestfactor(e.g.,anSNPallele)amongseveralpatientsandintheraceandage-matchedcontrols.Thedeterminationofthevalidityofthistestcruciallydependsonappropriatepatient-to-controlmatching(populationstratification).AnotherwayofperformingassociationstudiesmoreefficientlyisbylimitingtheSNPsthroughpre-selectionbytestingthepathogeniceffectsofSNPs.Forthebettermentofassociationstudiesdesign,onewayistoexploitpathogenicallele’slinkagedisequilibrium.WhenthereisstronglinkagedisequilibriumamongtheSNPmarkerandanunknownpathogenicallele,bothcanshowaparallelassociationwiththedisease(Pruvostetal.,2011;Corbett-Detigetal.,2015). NuclearGenesEpigenetics Morerecently(since2006),“next-generationsequencing”(NGS)technologiesallowedaccesstothewhole-genomesequencesandgainednewinformationabouttimingandlocationofdomestication(Wangetal.,2014b).Theseapproachesexpandedthescopeofcomparativegenomicsfromsinglegenestogenefamiliesandentiregenomes.MutationsinDNAcanvaryfromasinglepolymorphismtogeneduplicationorevencompletegenomeduplicationleadingtomanyconsequences,includingphenotypicalterations.Additionally,asinglegenecanbeinvolvedinmultiple,unrelatedphenotypes(Hodgkin,2002;Hartl,2009),andgenesofpolygenictraitscanactincombinationtoproduceasinglephenotype.Thevariationswithinthegenecouldbetriggeredbynucleotideexchange(non-synonymousorsynonymous)orindels,whichcangenerateadaptive,negative,orneutralalterationsinthegene.Morerecently,theseapproachesallowedtheavailabilityofgenomesforseveralspeciesandpermittedtheassociationofgenestospecifictraitsofdomesticationincattle(Yurchenkoetal.,2018),rabbits(Carneiroetal.,2014),sheep(Zamanietal.,2018),pigs(Rubinetal.,2012),horses(Zhangetal.,2018),dogs(Pendletonetal.,2018),andducks(Zhouetal.,2018).Severalotherstudiesfocusonthesearchforsignaturesofselectioninthosegenesalreadydescribedasimportantforthedomesticationprocess(Nevesetal.,2014;Ahmadetal.,2017a,b). Paleogenomics,alsoknownasgenome-wideancientDNA(aDNA)analysis,givesvaluableinformationandhasbeencrucialtoinvestigatewhen,where,andhowrapidlyadaptiveallelesspreadinthepopulations(Irving-Peaseetal.,2018;BrunsonandReich,2019).Indeed,recentstudiesusingthisapproachprovidenewinsightsintotheevolutionandhistoryofthecavebear(Barlowetal.,2018)andhorses(Gaunitzetal.,2018).Inlivestock,biotechnologyandconservativetoolshavecontributedconsiderablytoimproveproductivity,preservegeneticdiversity,andenhancetheadaptationtotheenvironment(KoandTakahashi,2006).Furthermore,functionalgenomics,quantitativereal-timePCR,microarray,andreversetranscriptionstudiesidentifiedmanycandidategenesandputativeregulatoryregionsthathaveinfluenceddocilityandviciousnessinanimals(Heyneetal.,2014). Withtheseadvancesintechnology,thegeneticarchitectureofdomesticationandthedomesticationprocessinsomespeciesbecameclearer(Caliebeetal.,2017;Kempetal.,2017;Pittetal.,2019).Forexample,itwaspossibletodiscoverthatpigpopulationsweredomesticatedinoneplaceandthenmovedtonewareassuccessivelygainedthemitochondrialsignatureofnativewildpopulations(Ottonietal.,2012).Thesameappliestoothertaxa.ThesenewapproachesalsoallowedtoverifythatAfricancattlearemixturesof“taurine”and“indicine”thatpossessbothY-chromosomesignatureandmitochondrialsignals(LarsonandFuller,2014). GenomicsandtheDomesticationProcess Thedevelopmentofgenometechnologiessuchasgenomeassemblybysequencing,whole-genomeshotgun(WGS)method(Lindblad-Tohetal.,2005),NGS(Dongetal.,2013),andthird-generationsingle-moleculesequencingtools(Korenetal.,2012)areoutstandingapproachesareadvancingourunderstandingtostudyanimaldomestication.GenomesequencingofdomesticatedspeciesnotonlyprovidesimportantresourcestoanswerthequeriesraisedbyDarwinbutalsoprovidesprospectstodiscoverthegeneticoriginofprofitabletraitsindomesticatedspecies(Hillieretal.,2014).Thecurrentinformationongenomeprojectshighlightsthedemographichistory,origins,andtheartificialselectionofdomesticatedanimalspecies(Anthonyetal.,1986).Additionally,itwasdeterminedwithapreviewoffutureguidelinesforanimaldomestication.Varioustechniqueswereestablishedtoallowthedenovoassemblyofgenomesduringthehumangenomeproject(Venteretal.,2015).ThemosteffectivetechniquewasWGSsequencing,alongwiththebuildingofphysicalmaps.By2009,fourdomesticatedanimals(horse,cat,dog,andtaurinecattle)genomesandonewildspeciesgenome(theredjunglefowl)weresequencedandassembledbasedonthismethod(Wallisetal.,2004). Thedomesticationprocessisdemonstratedthroughthedetectionofselectionataverylargenumberofgenomiclocithathavelikelyevolvedbynaturalandartificialselection(Carneiroetal.,2014;Larsonetal.,2014).Recently,ithasbecomepossibletoexplorethedomesticationprocessbycompletegenomesequencesanalysesathighresolutiontodefinehowithasformedmoderndomesticanimal.SeveralgenomiclocisuchastheDGAT1genethatisassociatedwithlactationtraitscompriseamajorquantitativetraitnucleotidehasbeenidentifiedputativelyundertheselectionthroughgenome-widecomparisonsofdatafrommoderntaurineandindicinecattle(Parketal.,2015).Furthermore,106candidategeneswerefoundunderselectionusingpopulationgenomicsapproachesthatwereparticularlyinvolvedinmuscledevelopment,growth,function,andimmunity.Thisfirstgenome-wideselectionanalysesdetectedgenesthatareconsideredasimportantcandidatesofdomestication(Ludwigetal.,2015).However,manymethodsareavailabletoretrieveandsequencegenomesroutinelyandrecognizehundredsofgenomiclociunderselectionthroughgenotyping.Itisrevealedthatpaleogenomicstechniqueswillbeusedtoinvestigatewhen,where,andhowrapidlyadaptiveallelesspreadatthepopulationindomesticanimals(MacHughetal.,2017).Severalarithmeticalmethodshavebeenestablishedbyscientiststorevealdiversefeaturesofhowtoaccomplishvariationsfromandwhatisanticipatedwithrespecttogeneticdifferencesintheneutralmodel(Voightetal.,2006).Whileallstatisticalmethodsarebasedonneutralgenomicdifferences,notallofthemarebasedonsimilarinformation.Mostofthemethodswereestablishedforcompletesequencedataandnotforgenome-widepoolsofpredeterminedSNPs,whicharepresentlyaccessibleinfewlivestockspecies(Corbett-Detigetal.,2015). EpigeneticsintheEvolutionoftheDomesticTraits Evidenceillustratesthatinadditiontogeneticfactors,epigeneticfactorscanaffectthebehavioralphenotypesaswellasothertraitswithinbreedorspecies(Jensen,2015;Béltekyetal.,2018).Forexample,thedifferenceinthebehaviorofthegreattitisstatisticallylinkedtotheDNAmethylationatdopaminereceptorgenes(Verhulstetal.,2016).Similarly,maternalbehavioraffectstheDNAmethylationofthehippocampalglucocorticoidreceptorgeneinrats(Weaveretal.,2004).Indomesticchickens,variancesinDNAmethylationarelinkedtodiseaseexposure(Tianetal.,2013),immunereactions(Berghofetal.,2013),metabolism,andgrowth(Huetal.,2013). Furthermore,epigeneticchangescanoccurjustafterindividualsareexposedtovariousrearingenvironments(Pértilleetal.,2017).AlthoughcelldivisionmaintainstheDNAmethylationpatterns,sometimesthesecouldberegulatedbyexternalstimuli(Raynaletal.,2012).TheDNAmethylationchangesthatarecontrolledbytheenvironmentcanbetransferredthroughthegermline(Guerrero-Bosagnaetal.,2010)andremainunchangedovergenerationsinsomatictissues(Franklinetal.,2010;Goerlichetal.,2012).Somaticepigeneticchangescanaffectphenotypictraits,whetherselecteddeliberatelyorinvoluntarilyorformedbytheenvironment.Therefore,mechanismsofepigeneticchangescouldbeanessentialfactorinthedevelopmentofpromptphenotypicvariationsthatariseduringdomestication.Forexample,thesemethylationchangesarecontrolledbysubstantialhyper-methylationindomesticwhiteLeghornchickensascomparedtotheredjunglefowl(Nättetal.,2012),inpedigreedogscomparedtowolves(JanowitzKochetal.,2016),andindomesticcomparedtowildworms(Xiangetal.,2013). DomesticationGenes Asdescribedabove,selectionplayedacrucialroleduringdomesticationacceleratingphenotypicvariations.Skinandcoatcolorareconsideredtheonlydomestictraitssubjecttoearlyselectionbyhumans,thusbecominganessentialgeneticmarker.Coatcolorcanhavepatterned(spotted,striped)andnon-patterned(solidcolors)phenotypesthataredefinedbytheproportionoftwopigments:eumelanin(black/brown)andpheomelanin(red/yellow)(Cieslaketal.,2011;Koseniuketal.,2018).Duringthepastyears,thishasbeenacentralquestionindomesticationstudies,andMC1R,ASIP,TYRP1,CBD103,KIT,andPMEL17geneswereassociatedwithdifferenttraitsinseveralspecies(Table1).Avarietyofmutations,includingsinglenucleotidepolymorphisms(SNPs),insertions,deletions,andduplicationsareresponsibleforcoatcolordiscrepanciesinbothdomesticandwildpopulations(Cuietal.,2018). TABLE1 Table1.Genesinvolvedindomesticationphenotypesinanimals. Withtheadvancesintechnologyandtheknowledgeondomestication,recentstudieswereabletoassociateTph1andGabra5genestotamenessandtoproducetamedanimals,namelyfoxes(Vulpesvulpes)andrats(Rattusnorvegicus)(Albertetal.,2009,2011;Trutetal.,2009).Besides,severalothergeneshavebeenassociatedwithdifferentphenotypesindifferentanimals.Indogs,genesassociatedwithwrinkledskin(HAS2),bodysize(IGF1),leglength(FGF4),andfurgrowthandtexture(FGF5,RSPO2,andKRT71)wereidentifiedandreported(Sutteretal.,2007;Cadieuetal.,2009;Parkeretal.,2009;Hellströmetal.,2010).Incattle(Grobetetal.,1997),sheep(Clopetal.,2006),pigs(Stinckensetal.,2008),goat(Zhangetal.,2012),horses(Dall’olioetal.,2010),anddogs(Mosheretal.,2007),amutationintheMSTNgeneisrelatedtoincreasedmusculardevelopment(Ahadetal.,2017).Also,incattle,theDGAT1andABCG2genesareresponsibleforvariationsinmilkproductionandcomposition,respectively(Ogorevcetal.,2009).TheHMGA2andLCORL-NCAPGgenesareassociatedwithstatureandbodysizeincattle(Pryceetal.,2011),rabbits(Carneiroetal.,2017),pigs(Rubinetal.,2012),horses(Frischknechtetal.,2015),anddogs(Jonesetal.,2008).Anothertraitthathasbeenthefocusofseveralstudiesisthemeattendernesswithgenesassociatedwithcattle(CAST2,HSP90AA1,DNAJA1,andHSPB1)(Malheirosetal.,2018)andpigs(CAST,HAL,RYR1,andRN). ChallengesandProspects Ancientinformation-richbiomoleculessuchasDNAandproteinshavelongbeenunderdiscussionandsystematicallyanalyzedbythescientists(Pääboetal.,1989).Intheearly1980s,theDNAcloningwasmadepossiblethroughacumbersomemolecularcloningapproach(Higuchietal.,1984),whicheventuallyprovedunreliable,particularlymakingfakeDNAsequencesfroma2400-year-oldEgyptianmummy(Pääbo,1985).In1980s,theamplificationofaDNAfromarcheologicalmaterialandmuseumsamplesusingpolymerasechainreaction(PCR)methodbroughtanimportantrevolution(Pääboetal.,1988).However,itwasabigchallengethatgotattentioninscientificcommunitytorecoverreliableandreproducibleDNA(Thomasetal.,1989).Therefore,theDNAfieldhasbeenaffectedwithmajortechnicalhurdlessuchasthepresenceofinhibitorsofenzymaticreactions,post-mortemloss,contaminationofpreservedsamples,andalltheinfluencesthatcanirreversiblycontainthevalidityandreproducibilityofaDNAamplifiedfromarcheologicalspecimens(Lindahl,1997;CooperandPoinar,2000).However,thefieldofarchaeo-geneticshasbeendevelopedoverthelastfourdecades,scientistshavescientificallytackledthemethodologicalchallengesrelatedtoDNArecoveryfromlong-deadmaterials,anditisnowwell-knownthatanauthenticandreproduciblegeneticsinformationcanbeproducedfromthefossilsofvertebrates.ThusaDNAresearchhashadanancientconcerninunderstandingthebiologyandevolutionofdomesticanimalsandtheirwildancestors(Troyetal.,2001;Leonardetal.,2002). DomesticationresearchhaschallengedscientistssinceDarwin,anddespitetheamountofnewliteraturepublishedeveryyear,therearestillmanyquestionsregardingthisthematic.Thisendlessprocessbeganseveralmillionyearsagoandincludeddiversepressuresthatshapedanimalsindifferentwaysanddifferentiatethemfromtheirancestors.Geneslinkedwithcoatcolorweretheonesassociatedwithearlydomestication,beingwidelystudied.Withthisexception,noothergeneswereassociatedwiththeearlystagesofanimaldomestication.Recentstudiesdescribedthatanimalswerefirstlyselectedbasedonbehavioralcharacteristics,makinghardtheresearchwhencomparedtomorphologicaltraits.Indeed,ifwelookatthecropandplantdomesticationwheretheinsightsobtainedinthepastyears,withthesameapproaches,aresignificantwhencomparingtoanimals. Withtheadvancesinsequencingandassemblytechnologies,genomesfromdifferentdomesticandwildanimalsarebecomingaccessible.Inadditiontothese,genomesfromancientpopulationsarebecomingavailable.Geneticresearchhasawiderangeoftoolkitstoexplainnotonlytherelationshipsbetweenthedomesticatedanimalsandtheirwildancestorsbutalsothedomesticationtraitsandtheirgeneticarchitecture.Theseresultsareessentialtocomparethepatternsinthemodernpopulationswiththoseofthepreviousgenerationsanddatafromphylogeographyandalsotoidentifynewgenesandassociatethemwithspecifictraits.Methylomicsandtranscriptomicanalysesareessentialtostudytheepigeneticfactorsandexpressionpresentinwildanddomesticatedanimalstosupportthevariationslinkedtodomestication. Therecentandpotentialapplicationsofevolutionarybiologymaydeliveranswersformainsocialchallenges.Itisimportanttoexaminetherelationshipamongtheenvironmentandthetraitsoforganismsthathavebeeninfluencedthroughtheadaptationtomodernenvironmentsandthepatternsofselectiontriggeredbytheirenvironmentsduringdomesticationperiod.Aconceptualperspectiveconnectingalloftheseenvironmental,genetic,anddevelopmentalmanipulationsisexpectedtoleadtobetterapplicationandcross-disciplinaryincorporationoffunctionalevolutionaryapproachestostudydomesticationofanimalsandtheirrelationshiptowildancestors.Itisimportanttohighlighttheevolutionaryplans/policiesthatmaybeusedtoaccomplishrequiredtargetsofsustainabledevelopmentforbetterhealth,useofnaturalresourceandbiodiversityconservation,includinghowdomesticationconflictshavebeenreducedtoaccomplishpreferredoutcomes.Therefore,thefactsofbuildingamoreintegratedfieldofevolutionarybiologymustbeunderscoredtoaddressglobalchallengesofdomestication.Humanimpactonthebiospherehasdeepconsequencesforbothdirectionandtherateofevolutionduringevolution.Atthesametime,animalsandotherorganismsthatareworthyforecological,aestheticoreconomicreasonsareoftennotabletoadaptrapidlyenoughtokeeppacewithchangesoftheenvironmentimpactedbyhumanactivities.Thesemoderndilemmasprogressivelythreatenanimalhealth,biologicaldiversity,anddomesticationhistory.Meanwhile,theproblemofearth’ssixthmassextinctionofspeciesbecomesimpendingasspeciesareinepttoadaptquicklytoenvironmentalvariations.Adevelopinginterestofevolutionarybiologymayhelpustoimproveourskillstocopewithchallengestosolvemostofpressingproblemsofdomesticationofanimalspeciesduringthetwenty-firstcentury. Futureworksshouldapplythesetechnologiesandobtaingenomesofalargenumberofindividualsinsidedifferentspeciesworldwideinordertobettercomprehendthegenetic,morphological,andbehavioralcharacteristicsofdifferentspecies.Withtheseachievements,wehopetofullyunderstandwhen,where,andhowanimalswheredomesticatedandconsequentlyunderstandthehumancivilizations. Conclusion Althoughthegeneticandgeographicpatternofearlyanimaldomesticationispoorlyunderstood,aclearbackgroundforunderstandingtheevolutionaryroutesofdomesticatedanimalsisprogressing.Theearlystagesofanimaldomesticationshowanextendedcoevolutionaryprogressionwithvariousphasesalongdiversetrajectoriesthatenhancedthereproductionandsurvivalofdomesticates.Naturalselectivepressuresrelaxed,andnewmutationsaroseandallowedforuniquetraits. Ourunderstandingofthegeneticbasisofanimaldomesticationfacilitatesimprovementsthroughbreedingusingnewtechniques.Definingimportanteventsofdomesticationdeliversauniqueaspectinstudyingthelinkagebetweenhumansandthenaturalworldanddeterminestheeventsthatdrivehumanculturalevolutiontointeractwiththatleadingbiologicalevolution. AuthorContributions JC,NA,AE,SA,andMA:conceptionanddesignofthework.HA:dataacquisition.HA,MA,andFJ:analysis.SA:writingofthemanuscript.HA,NA,andFJ:criticalreview. Funding ThisworkwasfundedbytheGDASprojectofScienceandTechnologyDevelopment(2019-GDASYL-0103059and2018GDASCX-0107). ConflictofInterest Theauthorsdeclarethattheresearchwasconductedintheabsenceofanycommercialorfinancialrelationshipsthatcouldbeconstruedasapotentialconflictofinterest. Acknowledgments Wethankfultoreviewersfortheircommentsandcriticalreadingofthemanuscript. 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Editedby: FulvioCruciani,SapienzaUniversityofRome,Italy Reviewedby: MuniyandiNagarajan,CentralUniversityofKerala,India PaulGepts,UniversityofCalifornia,Davis,UnitedStates Copyright©2020Ahmad,Ahmad,Jabbir,Ahmar,Ahmad,ElokilandChen.Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense(CCBY).Theuse,distributionorreproductioninotherforumsispermitted,providedtheoriginalauthor(s)andthecopyrightowner(s)arecreditedandthattheoriginalpublicationinthisjournaliscited,inaccordancewithacceptedacademicpractice.Nouse,distributionorreproductionispermittedwhichdoesnotcomplywiththeseterms. *Correspondence:JinpingChen,[email protected] COMMENTARY ORIGINALARTICLE Peoplealsolookedat SuggestaResearchTopic>