Population Genomics: Concepts, Approaches and Applications

824 Pages·2019·17.17 MB·English

by  Om P. Rajora

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
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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