Population Genomics: Wildlife

559 Pages·2020·17.483 MB·English

by  Paul A. Hohenlohe, Om P. Rajora

Population Genomics
Editor-in-Chief: Om P. Rajora
Paul A. Hohenlohe
Om P. Rajora  Editors
Population
Genomics:
Wildlife
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, inbreeding and outbreeding depression, demography, and bioge-
ography, and resolving evolutionary histories and phylogenetic relationships of
extant and extinct species. Population genomics research is also providing key
insights into the genomic basis of fitness, local adaptation, ecological and climate
acclimation and adaptation, speciation, complex ecologically and economically
importanttraits,anddiseaseandinsectresistanceinplants,animalsand/orhumans.
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, applicationofpopu-
lation genomics concepts and approaches facilitates plant and animal breeding,
forensics, delineation of conservation genetic units, understanding evolutionary
andgeneticimpactsofresourcemanagementpracticesandclimateandenvironmen-
tal change, and conservation and sustainable management of plant and animal
geneticresources.
ThevolumeeditorsinthisSerieshavebeencarefullyselectedandtopicswritten
byleadingscholarsfromaroundtheworld.
Moreinformationaboutthisseriesathttp://www.springer.com/series/13836
(cid:129)
Paul A. Hohenlohe Om P. Rajora
Editors
Population Genomics:
Wildlife
Editors
PaulA.Hohenlohe OmP.Rajora
DepartmentofBiologicalSciences, FacultyofForestryandEnvironmental
InstituteforBioinformaticsand Management
EvolutionaryStudies UniversityofNewBrunswick
UniversityofIdaho Fredericton,NB,Canada
Moscow,ID,USA
ISSN2364-6764 ISSN2364-6772 (electronic)
PopulationGenomics
ISBN978-3-030-63488-9 ISBN978-3-030-63489-6 (eBook)
https://doi.org/10.1007/978-3-030-63489-6
©SpringerNatureSwitzerlandAG2021
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Population Genomics Book Series
This Population Genomics book series is
dedicated to my (late) parents, and my wife
Malti and children Apoorva, Anu, and
Maneesha.
Om P. Rajora
Population Genomics: Wildlife
This book is dedicated to my family, and
wildlife lovers, researchers, educators, and
managers.
Om P. Rajora
Thisbookisdedicatedtomyfamily,andtoall
others who love the diversity of wildlife and
seek to conserve it for future generations.
Paul A. Hohenlohe
Preface
SpurredbyrecentadvancesinDNAsequencingtechnology,genomicshasreshaped
multiple fields within biology since the turn of this century. Population genomics
approaches can be applied far beyond traditional model organisms to reveal new
insights into natural populations around the globe, including wildlife. While tradi-
tional genetics tools have been increasingly applied to wildlife populations, geno-
mics provides not just increased power but also entirely new avenues of research.
Population genomics can reveal not only diverse aspects of population biology,
includingvariouspopulationgeneticcharacteristics,overallpatternsofdemography,
orrelationshipsamongpopulations,butalsothegeneticbasisofadaptation,partic-
ularlyinthefaceofrapidenvironmentalchanges.
Driven by advances in population genomics, and as part of the pioneering
Population Genomics book series covering all aspects of population genomics, the
currentvolumefocusesonwildlifepopulationgenomics.Here,weconsiderwildlife
to include primarily terrestrial, vertebrate animal species that are of concern for
conservation or management. We intend this volume to serve as a resource for
researchers in wildlife biology, who are using or may consider using population
genomics approaches, and also for conservation practitioners, wildlife managers,
and others outside the field to gain insights into the many ways that population
genomicscancontributetoourunderstandingandmanagementofwildlifespecies.
Despiteourfocusonwildlifepopulationgenomicshere,manyoftheapproaches
and topics covered in this book apply broadly, and wildlife biology can also learn
from applications of population genomics in all other organisms. For instance, the
genetics of adaptation to heterogeneous environments and adaptive differentiation
amongpopulationsisaddressedacrossanimals,plants,andotherorganisms.Many
population genomics approaches that are applicable in wildlife have been well-
developed in fish, particularly in species that are the target of intensive harvest or
management. Examples and illustrative case studies from these other taxa can be
foundthroughoutthisvolume.
Thisvolumealsofocusesspecificallyonchallengesandquestionsthatarecentral
topopulationgenomicsinwildlife.Forinstance,itisimportantinmanywildlifetaxa
vii
viii Preface
to make use of non-invasive samples, collected from hair, feathers, scat, or even
environmental DNA, and techniques for population genomics research using such
samplesarequicklyadvancing.Thisincludestechniques,suchassequencecapture
orampliconsequencing,thatarewell-suitedforusinglow-qualitygenetic/genomic
samples in wildlife studies. Many wildlife species are also limited to very small
populations,whichlimitspotentialsamplesizesandsequencingapproachesandalso
drives the research questions that are most important for population genomics to
address. In small populations, gathering the maximum amount of genetic informa-
tion,suchaswhole-genomesequencing,fromasmallnumberofindividualsmaybe
thebestwayatpresenttodrawmeaningfulconclusions.Importantquestionsinsmall
wildlife populations include loss of genetic diversity, the role of deleterious varia-
tion,andinbreedingdepression,andallofthesecanbeexaminedatafinescalefrom
populationgenomicdata.
Thechaptersofthisvolumearearrangedinfivepartscoveringmajorcomponents
of wildlife population genomics. Following an introductory overview of wildlife
populationgenomicsapplicationsandapproaches,thesectionscoversamplingand
sequencingapproachesforwildlife,wildlifepopulationbiology,specificchallenges
and threats to wildlife populations, and applications of population genomics to
management and conservation. In all cases, we attempt to balance discussion of
generalissuesandconceptswithchaptersfocusedonparticulartaxa,fromungulates
and amphibians to individual bird species. Case studies of population genomics
applied to wildlife populations illustrate the potential of the field across all these
chapters,andeachchapteralsoprovidesaprospectiveviewoffutureprogress.The
chaptersarewrittenbyleadingandemergingresearchscholarsinwildlifepopulation
genomics.
Threatenedwildlifespeciesareattheheartofanongoingbiodiversitycrisis,thus
expandingthescientifictoolkitformanagementandconservationiscritical.Awide
rangeofapproachesisneeded,fromsocialsciencetoecology,andinterdisciplinary
connectionsamongthesefieldsarecriticalforsciencetoguidesolutions.Population
genomics will play an important role in this network by providing general under-
standingofwildlifebiology,specificinformationtoguidemanagementdecisionsin
wildlifespecies,andefficientapproachesformonitoringwildlifepopulationsandthe
effects of our actions. We envision this book to be suitable for a wide readership,
includingundergraduateandgraduatestudents,researchscholarsandprofessionals,
and we hope that it will serve as a valuable resource for the field of wildlife
populationgenomics.
Moscow,ID,USA PaulA.Hohenlohe
Fredericton,NB,Canada OmP.Rajora
Contents
PartI Introduction
WildlifePopulationGenomics:ApplicationsandApproaches. . . . . . . .. 3
SoraiaBarbosa,SarahA.Hendricks,W.ChrisFunk,OmP.Rajora,
andPaulA.Hohenlohe
PartII WildlifeSamplingandGenomicsTechnologies
AdvancesinUsingNon-invasive,Archival,andEnvironmental
SamplesforPopulationGenomicStudies. . . . . . . . . . . . . . . . . . . . . . . . 63
KimberlyR.Andrews,MartaDeBarba,MichaelA.Russello,
andLisetteP.Waits
EnvironmentalPopulationGenomics:ChallengesandOpportunities. . . 101
CarenS.GoldbergandMeghanB.Parsley
SurmountingtheLarge-Genome“Problem”forGenomicData
GenerationinSalamanders. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
DavidW.Weisrock,PaulM.Hime,SchylerO.Nunziata,KaraS.Jones,
MasonO.Murphy,ScottHotaling,andJustinD.Kratovil
PartIII WildlifePopulations:Ecology,EvolutionandAdaptation
LandscapeGenomicsforWildlifeResearch. . . . . . . . . . . . . . . . . . . . . . 145
BrennaR.Forester,ErinL.Landguth,BrianK.Hand,andNikoBalkenhol
PopulationGenomicsofUngulates. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
DariaMartchenko,ErinPrewer,EmilyK.Latch,ChristopherJ.Kyle,
andAaronB.A.Shafer
AdvancingUnderstandingofAmphibianEvolution,Ecology,
Behavior,andConservationwithMassivelyParallelSequencing. . . . . . 211
W.ChrisFunk,KellyR.Zamudio,andAndrewJ.Crawford
ix
x Contents
PopulationGenomicsofBirds:EvolutionaryHistory
andConservation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
DavidP.L.Toews,JenniferWalsh,andLeonardoCampagna
PopulationGenomicsProvidesKeyInsightsintoAdmixture,
Speciation,andEvolutionofCloselyRelatedDucksoftheMallard
Complex. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295
PhilipLavretsky
PartIV ChallengesFacingWildlifePopulations
PopulationGenomicsandWildlifeAdaptationintheFace
ofClimateChange. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333
JacobHöglund,AnssiLaurila,andPatrikRödin-Mörch
ApplicationsofPopulationGenomicsforUnderstanding
andMitigatingWildlifeDisease. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 357
AndrewStorfer,ChristopherP.Kozakiewicz,MarcA.Beer,
andAnnaE.Savage
PopulationGenomicsofWildlifeCancer. . . . . . . . . . . . . . . . . . . . . . . . 385
SarahA.Hendricks,AndrewStorfer,andPaulA.Hohenlohe
PartV WildlifeConservationandManagement
PopulationGenomicsfortheManagementofWildVertebrate
Populations. . . . . . . . . .. . . . . . . . . . . .. . . . . . . . . . . .. . . . . . . . . . . .. 419
AshleyD.WaltersandMichaelK.Schwartz
GenomicsforGeneticRescue. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 437
SarahW.FitzpatrickandW.ChrisFunk
ExSituWildlifeConservationintheAgeofPopulationGenomics. . . . . 473
MichaelA.RusselloandEvelynL.Jensen
PopulationGenomicsAdvancesandOpportunitiesinConservation
ofKiwi(Apteryxspp.). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 493
KristinaM.RamstadandLukeT.Dunning
TheTransformativeImpactofGenomicsonSage-Grouse
ConservationandManagement. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 523
SaraJ.Oyler-McCance,KevinP.Oh,ShawnaJ.Zimmerman,
andCameronL.Aldridge
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 547