Population Genomics: Concepts, Approaches and Applications PDF
Preview Population Genomics: Concepts, Approaches and Applications
Population Genomics Om P. Rajora Editor Population Genomics Concepts, Approaches and Applications Population Genomics Editor-in-Chief OmP.Rajora FacultyofForestryandEnvironmentalManagement UniversityofNewBrunswick Fredericton,NB,Canada ThispioneeringPopulationGenomicsSeriesdealswiththeconceptsandapproaches ofpopulationgenomicsandtheirapplicationsinaddressingfundamentalandapplied topics in a wide variety of organisms. Population genomics is a fast emerging discipline, which has created a paradigm shift in many fields of life and medical sciences, including population biology, ecology, evolution, conservation, agricul- ture,horticulture,forestry,fisheries,humanhealthandmedicine. Populationgenomicshasrevolutionizedvariousdisciplinesofbiologyincluding population, evolutionary, ecological and conservation genetics, plant and animal breeding,humanhealth,geneticmedicine,andpharmacologybyallowingtoaddress novelandlong-standingintractablequestionswithunprecedentedpowerandaccu- racy. Itemployslarge-scaleorgenome-widegeneticinformationacrossindividuals and populations and bioinformatics, and provides a comprehensive genome-wide perspectiveandnewinsightsthatwerenotpossiblebefore. Populationgenomics hasprovided novel conceptualapproaches, and is tremen- dously advancing our understanding the roles of evolutionary processes, such as mutation, genetic drift, gene flow, and natural selection, in shaping up genetic variation at individual loci and across the genome and populations, disentangling thelocus-specificeffectsfromthegenome-wideeffects,detectingandlocalizingthe functional genomic elements, improving the assessment of population genetic parametersorprocessessuchasadaptive evolution,effectivepopulationsize, gene flow,admixture,inbreedingandoutbreedingdepression,demographyandbiogeog- raphy,andresolvingevolutionaryhistoriesandphylogeneticrelationshipsofextant andextinctspecies.Populationgenomicsresearchisalsoprovidingkeyinsightsinto thegenomicbasisoffitness,localadaptation,ecologicalandclimateacclimationand adaptation,speciation,complexecologicallyandeconomicallyimportanttraits,and disease and insectresistance inplants, animals and/or humans. In fact, population genomics research has enabled the identification of genes and genetic variants associated with many disease conditions in humans, and it is facilitating genetic medicine and pharmacology. Furthermore, application of population genomics concepts and approaches can facilitate plant and animal breeding, forensics, delin- eationofconservationgeneticunits,understandingevolutionaryandgeneticimpacts of resource management practices and climate and environmental change, and conservationandsustainablemanagementofplantandanimalgeneticresources. ThevolumeeditorsinthisSerieshavebeencarefullyselectedandtopicswritten byleadingscholarsfromaroundtheworld. Om P. Rajora Editor Population Genomics Concepts, Approaches and Applications Editor OmP.Rajora FacultyofForestryandEnvironmentalManagement UniversityofNewBrunswick Fredericton,NB,Canada ISSN2364-6764 ISSN2364-6772 (electronic) PopulationGenomics ISBN978-3-030-04587-6 ISBN978-3-030-04589-0 (eBook) https://doi.org/10.1007/978-3-030-04589-0 LibraryofCongressControlNumber:2018965916 ©SpringerNatureSwitzerlandAG2019 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe materialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation, broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant protectivelawsandregulationsandthereforefreeforgeneraluse. The publisher, the authors and the editors are safe to assume that the advice and information in this bookarebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsor theeditorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinorforany errorsoromissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictional claimsinpublishedmapsandinstitutionalaffiliations. ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSwitzerlandAG Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Affectionately dedicated to my wife Malti and children Apoorva, Anu, and Maneesha. Preface Recent novel advances in sequencing technologies, bioinformatics tools, statistical methods and software, and models have created a paradigm shift in several disci- plinesofbiology(especiallypopulationbiology,ecology,evolution,andconserva- tion), agriculture, forestry, fisheries, human health, and medicine. Population genomicsisanoutcomeoftheseadvances,whichisafascinatingandfast-growing discipline. Population genomics has revolutionized various disciplines of biology includingpopulation,evolutionary,ecologicalandconservationgenetics,plantand animalbreeding,humanhealth,geneticmedicine,andpharmacologybyallowingto address novel and long-standing intractable questions with unprecedented power and accuracy. It employs large-scale or genome-wide genetic information and bioinformatics to address various fundamental and applied aspects in biology and related disciplines, and provides a comprehensive genome-wide perspective and newinsightsthatwerenotpossiblebefore. Population genomics has provided novel conceptual approaches and is tremen- dously advancing our understanding the roles of evolutionary processes, such as mutation, genetic drift, gene flow, and natural selection, in shaping up genetic variation at individual loci and across the genome, individuals and populations, disentanglingthelocus-specificeffectsfromthegenome-wideeffects,detectingand localizingthefunctionalgenomicelements,improvingtheassessmentofpopulation genetic parameters or processes such as adaptive evolution, adaptive population genetic differentiation, effective population size, gene flow, admixture, inbreeding and outbreeding depression, demography and biogeography, and resolving evolu- tionary histories and phylogenetic relationships of extant and extinct species. Pop- ulation genomics research is also providing key insights into the genomic basis of fitness,localadaptation,ecologicalandclimateacclimationandadaptation,specia- tion, colonization, complex ecologically and economically important traits, and disease and insect resistance in plants, animals and/or humans. In fact, population genomics research has enabled the identification of genes and genetic variants associated with many disease conditions in humans, and it is facilitating genetic medicine and pharmacology. Furthermore, application of population genomics vii viii Preface concepts and approaches can facilitate plant and animal breeding, forensics, delin- eationofconservationgeneticunits,understandingevolutionaryandgeneticimpacts of resource management practices and climate change, and conservation and sus- tainablemanagementofplantandanimalgeneticresources. I have been working on various aspects of molecular, population, evolutionary and conservation genetics, and genomics for about four decades. Recognizing the powerandpotentialofpopulationgenomics,Istartedorganizingapioneeringannual workshop on Population and Conservation Genomics in 2007 as a part of the premierannualInternationalPlantandAnimalGenomeConference.ThisWorkshop has provided a platform for the presentation and sharing of the latest advances in populationandconservationgenomicsattheinternationalstage.Imayhavebeenthe firsttoidentifyConservationGenomicsasaresearchareain2004whenIusedthis term in my Senior (Tier 1) Canada Research Chair title. Leading and emerging scholars have been presenting their research results at the Population and Conser- vation Genomics workshop,whichhas grownto more than one Workshop session and has given rise to several offshoot workshops. The pool of the Workshop speakersprovidedagoodresourceforrecruitingauthorsforthecurrentPopulation Genomics book. Indeed, the chapters are written by prominent pioneering, leading andemergingresearchscholarsinvariousfieldsofpopulationgenomics. This Population Genomics book discusses the concepts, approaches and appli- cations of population genomics in addressing various fundamental and applied crucial aspects outlined above in a variety of organisms from microorganisms to humans. The book provides insights into a range of emerging topics including population epigenomics, landscape genomics, paleogenomics, ecological and evo- lutionary genomics, seascape genomics, biogeography, demography, speciation, admixture, colonization and invasion, genomic selection, and plant and animal domestication. This book fills a vacuum in the field and is expected to become a primaryreferenceinPopulationGenomicsworld-wide. Thebookisorganizedintofourparts.Thefirstpartprovidesanoverviewofthe population genomics concepts, approaches, applications, challenges and future perspectives. The second part includes three chapters discussing sequencing and genotyping technologies, and bioinformatics methods as applied to population genomics.Thethirdpartfocusesonvariousconceptsandapproachesinpopulation genomics, such as population epigenomics, landscape genomics, paleogenomics, genome-wide association studies, and genomic selection. The fourth, the last part, includes nine chapters addressing population, evolutionary and ecological genetics applicationsandinferences,suchasevolutionaryandecologicalgenomics,demog- raphy,biogeography,seascapegenomics,speciation,admixture,invasionandcolo- nization, and plant and animal domestication and breed development. With such quite comprehensive and diverse topics, the book is envisioned for a wide reader- ship, including undergraduate and graduate students, research scholars, and pro- fessionalsandexpertsinthefield. Iwouldliketothankallcontributorstothisvolumeandpeerreviewers. Fredericton,NB,Canada OmP.Rajora Contents PartI Introduction PopulationGenomics:AdvancingUnderstandingofNature. . . . . . . . . . 3 GordonLuikart,MartyKardos,BrianK.Hand,OmP.Rajora, SallyN.Aitken,andPaulA.Hohenlohe PartII Methods GenotypingandSequencingTechnologiesinPopulationGenetics andGenomics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 J.A.Holliday,E.M.Hallerman,andD.C.Haak ComputationalToolsforPopulationGenomics. .. . . . .. . . .. . . .. . . .. 127 JarkkoSalojärvi PopulationandEvolutionaryGeneticInferences intheWhole-GenomeEra:SoftwareChallenges. . . . . . . . . . . . . . . . . . 161 AlexandrosStamatakis PartIII ConceptsandApproaches PopulationEpigenomics:AdvancingUnderstandingofPhenotypic Plasticity,Acclimation,AdaptationandDiseases. . . . . . . . . . . . . . . . . . 179 EhrenR.V.Moler,AbdulkadirAbakir,MariaEleftheriou, JeremyS.Johnson,KonstantinV.Krutovsky,LaraC.Lewis, AlexeyRuzov,AmyV.Whipple,andOmP.Rajora ix x Contents LandscapeGenomics:UnderstandingRelationshipsBetween EnvironmentalHeterogeneityandGenomicCharacteristics ofPopulations. . . . . . . . . .. . . . . . . . . . .. . . . . . . . . .. . . . . . . . . . .. . . 261 NikoBalkenhol,RachaelY.Dudaniec,KonstantinV.Krutovsky, JeremyS.Johnson,DavidM.Cairns,GernotSegelbacher, KimberlyA.Selkoe,SophievonderHeyden,IanJ.Wang, OliverSelmoni,andStéphaneJoost Paleogenomics:Genome-ScaleAnalysisofAncientDNA andPopulationandEvolutionaryGenomicInferences. . . . . . . . . . . . . . 323 TianyingLanandCharlotteLindqvist Genome-WideAssociationStudiesandHeritabilityEstimation intheFunctionalGenomicsEra. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361 DuniaPinoDelCarpio,RobertoLozano,MarninD.Wolfe, andJean-LucJannink GenomicSelection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 427 ElisabethJonas,FreddyFikse,LarsRönnegård, andElenaFlaviaMouresan PartIV Population,EvolutionaryandEcologicalGenetics ApplicationsandInferences PopulationGenomicsProvidesKeyInsightsinEcology andEvolution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 483 PaulA.Hohenlohe,BrianK.Hand,KimberlyR.Andrews, andGordonLuikart InferringDemographicHistoryUsingGenomicData. . . . . . . . . . . . . . . 511 JordiSalmona,RasmusHeller,MartinLascoux,andAaronShafer AdvancingBiogeographyThroughPopulationGenomics. . . . . . . . . . . . 539 JeremyS.Johnson,KonstantinV.Krutovsky,OmP.Rajora, KeithD.Gaddis,andDavidM.Cairns AdaptationWithoutBoundaries:PopulationGenomics inMarineSystems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 587 MarjorieF.Oleksiak PopulationGenomicsofSpeciationandAdmixture. . . . . . . . . . . . . . . . 613 NicolaJ.NadeauandTakeshiKawakami PopulationGenomicsofColonizationandInvasion. . . . . . . . . . . . . . . . 655 ShanaR.WellesandKatrinaM.Dlugosch PopulationGenomicsofCropDomestication:CurrentState andPerspectives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 685 PhilippeCubryandYvesVigouroux
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