Demographic Methods across the Tree of Life

401 Pages·2021·61.391 MB·English

by  Roberto Salguero-Gomez, Marlène Gamelon

DemographicMethodsacrosstheTreeofLife

Demographic
Methods across
the Tree of Life
EDITED BY
Roberto Salguero-Gómez
AssociateProfessorinEcology,UniversityofOxford,UK
TutorialFellowinEcology,PembrokeCollege,UK
GuestResearcher,MaxPlanckInstituteforDemographicResearch,Germany
HonoraryResearcher,UniversityofQueensland,Australia
Marlène Gamelon
ChargéedeRecherche,CentreNationaldelaRechercheScientifique(CNRS),University
ofLyon,France
Researcher,NorwegianUniversityofScienceandTechnology,Norway
3
3
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Foreword
Demography is at the heart of biology. Populations Thesechallengesshouldnotdeteryoufromstudy-
changeinsizeovertimeduetotemporalvariationin ingdemography,becausetherewardsfrommastering
demographicrates,andspatialvariationinpopulation thesubjectaremyriad.Demographyhasbecomepop-
dynamicsisduetodifferentdemographicratesbeing ular in biology in recent years. The first reason for
observedacrosspopulationsofthesamespeciesatdif- this popularity is in part because it is now widely
ferentlocations.Communitydynamicsaredetermined accepted as a powerful way to study eco-evolution,
bythedemographicratesofconstituentspecies.Evo- evolution in structured populations, life history evo-
lutionoccurswhendifferentgenotypeshavedifferent lution,populationdynamics,speciesinteractions,and
demographies.Agoodbiologistconsequentlyneedsto epidemiology. The reward from mastering the maths
haveafirmgraspofdemography. is worth it. The second reason is that the develop-
Despite the central role of demography in biology, ment of integral projection models (IPMs) that allow
it is not an easy subject to master for two reasons. the study of continuous phenotypic traits has solved
First,demographicdataareneithercheapnoreasyto achallengethatfaceddemographyformanyyears—
collect. The most detailed data come from repeated howtostudyquantitativecharacterswithoutarbitrari-
captures and observations of individuals that can be lysplittingthemintowide,discretebins.IPMsallow
individually identified. Not all species are amenable researchers to go seamlessly from the identification
tosuchstudy—trycollectingsuchdataonCaenorhabdi- of statistical patterns in data to demographic mod-
tiselegansorAnophelesgambiaeinthewild—andthose els. The third reason for the rise of demography is
speciesthataresuitableforsuchstudyareoftenlong- the technological advances that now allow increased
lived, surviving for many years. Studying evolution ease of data collection from wild populations. These
insuchlong-livedspeciesisunfeasible,asitcantake methodsincludeminiaturisedtags,ruggedisedlower-
numerousconsecutiveresearchgrants,orevencareers, power wireless sensor networks, cheaper and more
togainrobustinsight.Fortunately,thereareapproach- accuratesatellitetagsforanimals,andevenautomated
esbeingdevelopedtocollectdemographicdatawith- trapsthattargetwhichindividualstolivetrap.
outmarkingindividualsthatcanbeusedtoconstruct IimaginethatwhenIamaskedtowritetheforeword
powerfuldemographicmodels. forthesecondeditionofthisbook,Ihavenodoubtthat
The second reason that demography is a difficult thefourthreasonIwilllistwillbethistome.Itisavery
subjectisbecauseitismathematical.Allpopulations well-structuredbookthatcoversnotonlydatacollec-
are structured, be it by genotypes, phenotypic traits, tionbutalsomodelconstructionandanalysis,andthe
strategies, age, sex, life history stage, or some oth- contributorsaretheverypeoplewhohaveadvanced
er quantity. Modelling structured population usually the field of demography so substantially in the last
requiresmatrices,andtheanalysisofmatricesrequires, decade.Thebooksucceeds,wheresomanyfail,innot
atthebareminimum,anunderstandingoflinearalge- onlyprovidinganaccessibleintroductiontothefield
bra.Whenmodelsbecomefrequency-dependent,and forthosewhohavenotbeenimmersedinitforyears,
includetrait-mediatedinteractions,twosexes,ormul- butalsocontainingsomestate-of-the-artmethodsand
tiple interacting species, analytical methods become applications.Theeditors,whoareleadersoftheirgen-
evenmorechallenging. erationinthefieldofdemography,haveputtogethera
v
vi FOREWORD
verythoughtfuldocument:thebookhassomethingfor good biologists will have this book, well-thumbed,
everyone,fromthenovicetothedemographicwizard. centre-stageontheirbookcase.
Partofdemographyisaboutprediction.Asademog-
TimCoulson
rapher,itwouldconsequentlyberemissofmetofail
ProfessorofZoology
to make a prediction. So here it is: within a year all
UniversityofOxford,UK
Acknowledgements
Thecommunityofindividualstowhomwearegrate- We warmly thank our past and present academ-
fulfortheirimpactonthisbookisasheterogeneousas ic institutions: the University of Queensland (Aus-
thediversityofquestions,methods,andapplications tralia) and the Universities of Sheffield and Oxford
ofdemographyitself. (UK) for Roberto, and the Centre d’Ecologie Fonc-
First and foremost, this attempt to bring together tionnelle et Evolutive in Montpellier, the Laboratoire
demographic methods across the Tree of Life would de Biométrie et Biologie Evolutive in Lyon (France),
havebeenimpossiblewithouttheexcellentcontribu- and the CBD in Trondheim (Norway) for Marlène.
tionsofall77authors.Theybroughtadepth,breadth, All these academic institutions, although in different
andclarityinexplanationsthatwefeelconfidentwill countries,withdifferentculturesandlanguages(and
be extremely useful to the demographic communi- versions of English!), share common denominators:
ty and beyond. The diligence and resilience of these stimulatingscientificenvironments,andopendiscus-
authors—eventhroughapandemic—keptusfocused sionsinecology,evolution,andconservationbiology,
on the delivery of their individual contributions and from which we greatly benefitted while editing and
thebook.Likewise,weareindebtedtothe44anony- writing this book. In this regard, we are extremely
mous reviewers who provided excellent, timely, and thankful for the intellectual, logistical, and emotion-
on-timesuggestionstoimprovethecontentandstylis- al support provided by Aziz Aboobaker, Mike Bon-
ticpresentationofeachchapter. sall, Stephanie Borrelle, Natalie Briscoe, Pol Capdev-
Theinceptionofthisbookstartedalmostasamat- ila,DylanChilds,TimCoulson,ShaunCoutts,Katrina
terofunconsciousintellectualdevelopmentduringour Davis, John Dwyer, Jane Elith, Rob Freckleton, Ivar
respectivepostdoctoraltimesattheMaxPlanckInsti- Herfindal,MattHolden,IrjaIdaRatikainen,AlineM.
tuteforDemographicResearch(Germany)forRober- Lee, E.J. Milner-Gulland, Maria Paniw, Henrik Pärn,
to Salguero-Gómez and at the Centre for Biodiver- Christophe Pélabon, Hugh Possingham, Mark Rees,
sity Dynamics (CBD), Norwegian University of Sci- BenC.Sheldon,JarleTufto,andPeteVesk.
ence and Technology (NTNU) (Norway) for Marlène Thematurationofthecorpusofthisbookwascar-
Gamelon.Theexposuretodemographersworkingon ried over numerous internet conference calls in dif-
a wide range of systems and with an even broader ferent time zones. However, the whole thing orig-
repertoireofmethodologiesandquestionsencouraged inated from discussions between us and other col-
us to test whether those methods would be appli- leaguesatmultipleinternationalmeetings.Itisworth
cable within and beyond our specific study systems. here acknowledging the most influential venue: the
We owe a great deal of inspiration to Ruth Archer, EvolutionaryDemographySociety(EvoDemoS)annu-
OskarBurger,BrendaCasper,HalCaswell,Fernando al meetings. The intellectual exchange supported by
Colchero,DaliaConde,DavidN.Koons,SteveEllner, those meetings allowed us to fine-tune the content
SteinarEngen,Jean-MichelGaillard,OlivierGimenez, of the book as well as to recruit invaluable contribu-
Vidar Grøtan, Owen Jones, Eelke Jongejans, Hans de tionsbyexcellentjuniorandestablishedresearchersin
Kroon, Jean-Dominique Lebreton, Cory Merow, Sean thefieldofdemography.InteractionswithEvoDemoS
McMahon,JessicaMetcalf,JimOeppen,PeterPetraitis, members,aswellasmembersfromtheBritishEcolog-
Brett K. Sandercock, Ralph Schaible, Alex Scheuer- icalSocietyandtheEcologicalSocietyofAmericahave
lein, Iain Stott, Bernt-Erik Sæther, James Vaupel, and further allowed us to tailor this book for our target
Cyrille Violle for inspiring us to think beyond our audience.
particular one-species, one-population, one-method, We also acknowledge the financial support
one-questionorigins. provided by various funding agencies and schemes.
vii
viii ACKNOWLEDGEMENTS
Roberto Salguero-Gómez was supported by an Aus- This work has greatly benefitted from the time-
tralian Research Council DECRA fellowship while at ly,supportive,andencouragingadviceandguidance
theUniversityofQueensland,andaNERCIndepen- fromtheOUPteam.SpecialthanksgotoIanSherman,
dent Research Fellowship while at the University of CharlesBath,andBethanyKershaw.
Sheffield and University of Oxford. Further grants Finally,wewouldliketothankthelovedoneswho
to him and his research group by the ARC, NERC, have provided their input to this book while being
BBSRC, Royal Society, Oxford–Africa Funds, Oxford very patient for the time that this book took away
University Press John Fell Funds, and the Spanish from them. Roberto Salguero-Gómez thanks Katrina
Ministerio de Economía y Competitividad allowed Davis and Manon Salguero-Davis for their uncondi-
for interactions with key collaborators, as well as tionalsupport,love,criticalinput,andpatience.Mar-
developing and applying demographic methods to a lèneGamelon dedicates this bookto her family,who
diversityofspecies.MarlèneGamelonwassupported havealwaysbeensupportivealongtheacademicsci-
byagrantoftheFrenchNationalAgencyforWildlife entificpath.
(formerly ONCFS - now OFB), the Research Council
RobertoSalguero-Gómez
of Norway through its Centres of Excellence fund-
MarlèneGamelon
ing scheme to CBD, and the Centre National de la
RechercheScientifique(CNRS).
Contents
Foreword v
Acknowledgements vii
ListofContributors xix
Introduction:Fromlions,tolion’smanes,todandelions:howdifferent
typesofdemographicdataandmethodsareselectedandwhy 1
RobertoSalguero-GómezandMarlèneGamelon
1 Ontheoriginsofthisbook 1
2 Originsofdemographicanalyses:fromhumanstononhuman
animals,plants,fungi,andmicrobes 2
3 WhyusedemographicmethodsacrosstheTreeofLife? 2
4 Fromdataacquisitiontodemographicanalyses 3
5 Organisationofthebook 6
6 Targetaudience 11
7 Whatnext?Apleaforastronger,richer,broader,andmore
innovativedemography 12
References 12
Part1 DemographicDataCollection:FromGenestoEnvironment 15
1 Geneticdatacollection,pedigrees,andphylogenies 17
EmilyG.Simmonds,AlinaK.Niskanen,HenrikJensen,andStevenSmith
1.1 Introduction 17
1.2 Geneticpedigrees 19
1.3 Geneticphylogenies 19
1.4 Collectionofgeneticsamples 21
1.5 Processingofsamples(DNAextraction,amplification,and
sequencing) 22
1.6 Preparationofdataforanalyses 23
1.7 Usingthedatatoconstructpedigreesandphylogenies 24
1.7.1 Pedigrees 24
1.7.2 Phylogenies 25
1.8 Conclusions 29
References 29
ix