Handbook of Trait-Based Ecology: From Theory to R Tools

312 Pages·2021·16.005 MB·English

by  Francesco de Bello, Carlos P. Carmona, André T. C. Dias, Lars Götzenberger, Marco Moretti, Matty P. Berg

Handbook of Trait-Based Ecology
From Theory to R Tools
Functional ecology is the branch of ecology that focuses on various functions that
speciesplayinthecommunityorecosysteminwhichtheyoccur.Thisaccessibleguide
offers the main concepts and tools in trait-based ecology, and their tricks, covering
different trophiclevelsandorganismtypes.Itisdesignedforstudents,researchersand
practitionerswhowishtogetahandysynthesisofexistingconcepts,toolsandtrendsin
trait-based ecology, and wish to apply it to their own field of interest. Where relevant,
exercises specifically designed to be run in R are included, along with accompanying
onlineresourcesincludingsolutionsforexercisesandRfunctions,andupdatesreflect-
ing current developments in this fast-changing field. Based on more than a decade of
teaching experience, the authors developed and improved the way theoretical aspects
and analytical toolsoftrait-based ecology are introduced and explained to readers.
FrancescodeBelloisaresearcherattheSpanishNationalResearchCouncil(CSIC)and
Assistant Professor at the University of South Bohemia, Czech Republic. He has
developed and applied several widely used tools to compute indices of functional
diversity andassess communityassemblymechanisms.
Carlos P. Carmona is an Associate Professor at the University of Tartu, Estonia.
Currently he is working on the development of tools to assess functional diversity
across scales while incorporatingwithin-species trait variability.
André T. C. Dias is an Assistant Professor at the Federal University of Rio de Janeiro
(UFRJ), Brazil. His research uses trait-based approaches to understand both species
responseto environmental conditionsand theireffectson ecosystem processes.
Lars Götzenberger is a researcher at the Institute of Botany at the Czech Academy of
Sciences and the University of South Bohemia, Czech Republic. His research focuses
on how traits evolve and affect species coexistence at different spatial and
temporal scales.
Marco Moretti is a Senior Scientist at the Swiss Federal Research Institute (WSL) in
Birmensdorf, Switzerland. He uses trait-based approaches to assess the response of
communities to global stressors and the effects on ecosystem processes within and
across trophiclevels.
Matty P. Berg is an Associate Professor at the Vrije Universiteit Amsterdam,
the Netherlands and an Affiliate Professor at the Rijksuniversiteit Groningen, the
Netherlands. He uses trait-based approaches to study the assembly of soil fauna
communities, amongstother related aspects.

Handbook of Trait-Based Ecology
From Theory to R Tools
FRANCESCO DE BELLO
UniversityofSouthBohemia,CzechRepublicandSpanish
NationalResearchCouncil(CSIC)
CARLOS P. CARMONA
UniversityofTartu,Estonia
ANDRÉ T. C. DIAS
FederalUniversityofRiodeJaneiro(UFRJ),Brazil
LARS GÖTZENBERGER
InstituteofBotanyoftheCzechAcademyofSciences,CzechRepublic
andUniversityofSouthBohemia,CzechRepublic
MARCO MORETTI
SwissFederalResearchInstitute(WSL),Switzerland
MATTY P. BERG
VrijeUniversiteitAmsterdam,theNetherlandsandRijksuniversiteit
Groningen,theNetherlands
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Informationonthistitle:www.cambridge.org/9781108472913
DOI:10.1017/9781108628426
©FrancescodeBello,CarlosP.Carmona,AndréT.C.Dias,LarsGötzenberger,
MarcoMoretti,andMattyP.Berg2021
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Firstpublished2021
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LibraryofCongressCataloging–in–PublicationData
Names:Bello,Francescode,1974–author.
Title:Handbookoftrait–basedecology:fromtheorytoRtools/FrancescodeBello,UniversityofSouth
Bohemia,CzechRepublicandSpanishNationalResearchCouncil(CSIC),CarlosP.Carmona,University
ofTartu,Estonia,AndréT.C.Dias,UniversidadeFederaldoRiodeJaneiro(UFRJ),LarsGötzenberger,
InstituteofBotanyoftheCzechAcademyofSciences,MarcoMorettiMarcoMoretti,SwissFederal
ResearchInstituteWSL,MattyP.Berg,VrijeUniversiteit,AmsterdamandRijksUniversiteitGroningen.
Description:Cambridge,UK;NewYork,NY:CambridgeUniversityPress,2021.|Includesbibliographical
referencesandindex.
Identifiers:LCCN2020041965(print)|LCCN2020041966(ebook)|ISBN9781108472913(hardback)|
ISBN9781108460750(paperback)|ISBN9781108628426(epub)
Subjects:LCSH:Ecophysiology.|Ecophysiology––Statisticalmethods.|R(Computerprogramlanguage)
Classification:LCCQH541.15.E26B452021(print)|LCCQH541.15.E26(ebook)|DDC571.2––dc23
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ISBN978-1-108-46075-0Paperback
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Thetruthoftheprinciple,thatthegreatestamountoflifecanbesupportedbygreatdiversification
ofstructure,isseenundermanynaturalcircumstances.
CharlesDarwin,1859

Contents
Preface page xi
1 General Introduction 1
1.1 General Definitions 2
1.2 From Species to Functions 4
1.3 What Isa Functional Trait? 7
1.4 Responseand Effect Traits 12
1.5 Open Challenges 15
2 Trait Selectionand Standardization 17
2.1 Which Traits toSelect? 18
2.2 How Many Traits? 21
2.3 Where toGet Trait Values From? 22
2.3.1 Traits from theLiterature and Databases 22
2.3.2 Measuring Traits 28
2.4 How toExpress Trait Values? 29
2.5 Missing Trait Data 31
2.6 Trait Standards 32
2.6.1 Whyand How toStandardize Trait Measurements? 32
2.6.2 How to Work withTrait Protocols? 34
3 The Ecology ofDifferences:Groups vsContinuum 36
3.1 Historical and ConceptualOverview 37
3.1.1 Functional Groups 37
3.1.2 Trait Trade-offsand r/K Selection 39
3.1.3 C-S-R, L-H-S and ‘Spectra’ofDifferentiation 41
3.2 From Theory toNumbers 44
3.2.1 The Species (cid:1) Trait Matrix 44
3.2.2 Computing theDissimilaritybetween Species 46
3.2.3 Overlooked Issues with the Gower Distance 50
3.2.4 Grouping Species 53
vii
viii Contents
4 Response Traits and the Filtering Metaphor 57
4.1 From Early Biogeographyto Trait–Environment Relationships 57
4.1.1 Trait Variation within Species 58
4.1.2 Trait Variation across Species 60
4.2 EnvironmentalGradients 62
4.3 The EnvironmentalFiltering Metaphor 64
4.4 From Species to Communities and Back 67
4.5 Relating Functional Traits toFitness 70
4.6 TraitsandSpecies-Distribution Models 72
5 Community Metrics 75
5.1 CommunityFunctional Trait Structure 76
5.2 CommunityWeighted Mean (CWM) 78
5.2.1 Computing CWM 78
5.2.2 Considerationson Species Abundance 81
5.3 Functional Diversity Indices 86
5.3.1 Range and Convex Hull 86
5.3.2 Sumof Distances 88
5.3.3 Variance 89
5.3.4 Mean Dissimilarity 91
5.3.5 Regularity 94
5.4 Functional Diversity Components 96
5.5 Partitioning Functional Diversity 98
5.6 RToolstoCompute Functional Diversity 103
6 IntraspecificTraitVariability 105
6.1 The Sourceof Intraspecific Trait Variability 106
6.2 The Importanceof Intraspecific Trait Variability 110
6.2.1 Speciation 111
6.2.2 Population Sizeand Genetic Diversity 112
6.2.3 Adaptation 112
6.2.4 Distribution 113
6.2.5 Invasion Predictability 114
6.2.6 Community Assembly 115
6.2.7 Trait-Mediated Species Interactions 115
6.2.8 Ecosystem Processes 117
6.3 Assessing Intraspecific Trait Variability 119
6.3.1 Quantifying Intra- vs Interspecific Trait Variability 119
6.3.2 Intraspecific Trait Adjustments vsSpecies Turnover 121
6.3.3 Trait Variability across EcologicalScales 124
6.3.4 Including Intraspecific Variabilityinto Functional Diversity 124