La remise en cause de ces différents présupposés (à part le point (2)) est le fil rouge du travail effectué durant cette thèse et sera abordé au travers de ses trois chapitres

Partie 1 : Diversité fonctionnelle des communautés végétales alpines et effets d’échelles

Le point (1) rejoint la problématique d’échelle spatiale, c’est à dire à la surface

spa-tiale sur laquelle sont définies la communauté et la surface géographique de la “région”

qui sert à définir le pool d’espèces. Et le point (3) à la problématique d’échelle

organi-sationnelle, c’est-à-dire le niveau taxonomique auquel est identifié un individu (individu,

espèce, genre...) et le niveau phylogénétique regroupant l’ensemble des individus étudiés.

Face à ces échelles, on peut se poser la question : “Les patrons de diversité sont-ils

similaires à toutes les échelles spatiales et organisationnelles ? Quelles sont les

implica-tions en termes de règles d’assemblage ?”. C’est la question que j’aborde dans la partie 1,

en interaction avec l’idée de varier les choix méthodologiques (4) en terme de modèle nul

et de pool d’espèce.

Partie 2 : Décompositionα, β, γdes nombres de Hill - extensions méthodologiques

Ce chapitre s’intéresse exclusivement au point (4), c’est-à-dire aux perspectives

qu’ap-porte la remise en cause des présupposés méthodologiques contenus dans le choix des

indices de diversité. Comme mentionné précédemment, la littérature scientifique sur les

indices de diversité est très (trop) riche, mais récemment de nombreuses unifications ont

été proposées, notamment celles qui concernent la généralisation des nombres de Hill. À

travers cela, la première partie se consacre à la remise en cause de la façon de prendre en

compte le patron d’abondance des communautés et la façon d’évaluer la similarité

éco-logique entre espèces à partir des données de traits fonctionnels et de la phylogénie. On

peut se poser la question : “Les patrons de diversité sont-ils similaires selon le choix de

l’indice de diversité ? Quelles sont les implications en termes de règles d’assemblage ?”

Partie 3 : Aspects méthodologiques de l’analyse des données de métabarcoding

Le méta-barcoding est en train de s’affirmer comme une nouvelle approche pour

étu-dier les communautés [POISOT et collab., 2013; TABERLET et collab., 2012]. Elle amène

des perspectives importantes pour l’étude de communautés qu’il est difficile

d’échan-tillonner par des techniques classiques : bactéries, champignons ou archées. C’est en

re-vanche un type de données assez différent des données de communautés traditionnelles

et qui présente de nombreux défis. Les données de méta-barcoding se caractérisent

no-tamment par une assignation taxonomique partielle, ce qui, rejoignant le point (3) amène

une perspective différente sur ce qu’est “une espèce” dans un échantillon de barcoding.

Ce dernier chapitre comprend principalement des travaux préliminaires qui explorent les

défis méthodologiques posées par le méta-barcoding dans le contexte de son utilisation

pour étudier les patrons de diversité “taxonomique” et phylogénétique.

6 Références

ADLER, P., J. HILLERISLAMBERSet J. LEVINE. 2007, «A niche for neutrality»,Ecology Letters,

vol. 10, n

o

2, p. 95–104. 11

ADLER, P. B., R. SALGUERO-GÓMEZ, A. COMPAGNONI, J. S. HSU, J. RAY-MUKHERJEE,

C. MBEAU-ACHEet M. FRANCO. 2014, «Functional traits explain variation in plant life

history strategies»,PNAS, vol. 111, n

o

2, p. 740–745. 5

AGUILÉE, R., D. CLAESSENet A. LAMBERT. 2013, «Adaptive radiation driven by the

inter-play of eco-evolutionary and landscape dynamics», Evolution, vol. 67, n

o

5, p. 1291–

1306. 2

ANGERT, A. L. 2009, «The niche, limits to species’ distributions, and spatiotemporal

varia-tion in demography across the elevavaria-tion ranges of two monkeyflowers»,PNAS, vol. 106,

p. 19 693–19 698.13

DE BELLO, F., J. N. PRICE, T. MÜNKEMÜLLER, J. LIIRA, M. ZOBEL, W. THUILLER, P. GE

-RHOLD, L. GÖTZENBERGER, S. LAVERGNE, J. LEPS, K. ZOBELet M. PÄRTEL. 2012,

«Func-tional species pool framework to test for biotic effects on community assembly»,

Eco-logy, vol. 93, n

o

10, p. 2263–2273.17

DE BELLO, F. D., S. LAVOREL, S. LAVERGNE, C. H. ALBERT, I. BOULANGEAT, F. MAZELet

W. THUILLER. 2013, «Hierarchical effects of environmental filters on the functional

structure of plant communities : a case study in the French Alps»,Ecography, vol. 36,

p. 393–402.7,11

BLOMBERG, S., T. GARLAND JRet A. IVES. 2003, «Testing for phylogenetic signal in

com-parative data : behavioral traits are more labile»,Evolution, vol. 57, n

o

4, p. 717–745.

7

CALLAWAY, R., R. BROOKER, P. CHOLER, Z. KIKVIDZE, C. LORTIE, R. MICHALET, L. PAOLINI,

F. PUGNAIRE, B. NEWINGHAM, E. ASCHEHOUG et collab.. 2002, «Positive interactions

among alpine plants increase with stress»,Nature, vol. 417, n

o

6891, p. 844–848. 12

CARLSON, B., J. RENAUD, J. DEDIEU, W. THUILLERet P. CHOLER. 2015, «Modelling snow

cover duration improves predictions of functional and taxonomic diversity for alpine

plant communities»,Annals of Botany, vol. in press, doi :10.1093/aob/mcv041. 11

CAVENDER-BARES, J., D. D. ACKERLY, D. A. BAUM et F. A. BAZZAZ. 2004, «Phylogenetic

overdispersion in Floridian oak communities»,American Naturalist, vol. 163, n

o

6, p.

823–843.7

CAVENDER-BARES, J., K. KOZAK, P. FINEet S. KEMBEL. 2009, «The merging of community

ecology and phylogenetic biology»,Ecology Letters, vol. 12, n

o

7, p. 693–715.2

CHAO, A., C.-H. CHIU et L. JOST. 2010, «Phylogenetic diversity measures based on Hill

numbers»,Philosophical Transactions of the Royal Society B : Biological Sciences, vol.

365, n

o

1558, p. 3599–3609. 17

CHESSON, P. 2000, «Mechanisms of maintenance of species diversity»,Annual review of

Ecology and Systematics, vol. 31, p. 343–366.11,12

CHOLER, P. 2005, «Consistent shifts in alpine plant traits along a mesotopographical

gra-dient»,Arctic, Antarctic, and Alpine Research, vol. 37, n

o

4, p. 444–453. 11

CHOLER, P., R. MICHALET et R. CALLAWAY. 2001, «Facilitation and competition on

gra-dients in alpine plant communities»,Ecology, vol. 82, n

o

12, p. 3295–3308.12

CLARK, J. S. 2009, «Beyond neutral science»,Trends in Ecology & Evolution, vol. 24, n

o

1,

p. 8–15. 14

CLARK, J. S., D. M. BELL, M. H. HERSH, M. C. KWIT, E. MORAN, C. SALK, A. STINE,

D. VALLE et K. ZHU. 2011, «Individual-scale variation, species-scale differences :

in-ference needed to understand diversity»,Ecology Letters, vol. 14, n

o

12, p. 1273–1287.

3

CLEMENTS, F. E. 1916,Plant succession : an analysis of the development of vegetation, 242,

Carnegie Institution of Washington.2

CONNELL, J. 1978, «Diversity in tropical rain forests and coral reefs»,Science, vol. 199, n

o

4335, p. 1302.3

CORNELL, H. V. et S. P. HARRISON. 2014, «What are species pools and when are they

im-portant ?»,Annual Review of Ecology, Evolution, and Systematics, vol. 45, p. 45–67. 8

CORNWELL, W. K. et D. D. ACKERLY. 2009, «Community assembly and shifts in plant trait

distributions across an environmental gradient in coastal California»,Ecological

Mono-graphs, vol. 79, n

o

1, p. 109–126. 9

COSTANZA, R., R.D’ARGE, R.D. GROOT, S. FARBER, M. GRASSO, B. HANNON, K. LIMBURG,

S. NAEEM, R. V. O’NEILLet J. PARUELO. 1998, «The value of the world’s ecosystem

ser-vices and natural capital»,Ecologica Economics, vol. 25, p. 3–15. 1

DARWIN, C. 1859,The Origin of Species, John Murray, London.7

DEVICTOR, V., D. MOUILLOT, C. MEYNARD, F. JIGUET, W. THUILLERet N. MOUQUET. 2010,

«Spatial mismatch and congruence between taxonomic, phylogenetic and functional

diversity : the need for integrative conservation strategies in a changing world»,Ecology

letters, vol. 13, n

o

8, p. 1030–1040.7

DIAMOND, J. 1975, «Assembly of species communities», dans Ecology and evolution of

communities, édité par M. Cody et J. Diamond, harvard university press éd., p. 342–444.

3,8

DÍAZ, S. et M. CABIDO. 1997, «Plant functional types and ecosystem function in relation

to global change»,Journal of vegetation science, vol. 8, n

o

4, p. 463–474. 5

EHRLÉN, J. et O. ERIKSSON. 2000, «Dispersal limitation and patch occupancy in forest

herbs»,Ecology, vol. 81, n

o

6, p. 1667–1674. 6,13

FAUTH, J. E., J. BERNARDO, M. CAMARA, W. J. RESETARITS, J. VAN BUSKIRK et S. A.

MCCOLLUM. 1996, «Simplifying the jargon of community ecology : a conceptual

ap-proach»,The American Naturalist, vol. 147, n

o

2, p. 282–286.17,18

FLORES, O., E. GARNIER, I. J. WRIGHT, P. B. REICH, S. PIERCE, S. DÍAZ, R. J. PAKEMAN,

G. M. RUSCH, M. BERNARD-VERDIER, B. TESTI, J. P. BAKKER, R. M. BEKKER, B. E. L. CE

-RABOLINI, R. M. CERIANI, G. CORNU, P. CRUZ, M. DELCAMP, J. DOLEZAL, O. ERIKSSON,

A. FAYOLLE, H. FREITAS, C. GOLODETS, S. GOURLET-FLEURY, J. G. HODGSON, G. BRUSA,

M. KLEYER, D. KUNZMANN, S. LAVOREL, V. P. PAPANASTASIS, N. PÉREZ-HARGUINDEGUY,

F. VENDRAMINIet E. WEIHER. 2014, «An evolutionary perspective on leaf economics :

phylogenetics of leaf mass per area in vascular plants»,Ecol Evol, vol. 4, n

o

14, p. 2799–

2811. 5,7

GRAVEL, D., C. CANHAM, M. BEAUDETet C. MESSIER. 2006, «Reconciling niche and

neu-trality : the continuum hypothesis»,Ecology Letters, vol. 9, n

o

4, p. 399–409. 2,14

GRIME, J. P. 1977, «Evidence for the existence of three primary strategies in plants and its

relevance to ecological and evolutionary theory.»,The American Naturalist, vol. 111, n

o

982, p. 1169–1194. 5,13

GROSS, N., L. BÖRGER, S. I. SORIANO-MORALES, L. BAGOUSSE-PINGUET, J. L. QUERO,

M. GARCÍA-GÓMEZ, E. VALENCIA-GÓMEZet F. T. MAESTRE. 2013, «Uncovering

multis-cale effects of aridity and biotic interactions on the functional structure of

mediterra-nean shrublands»,Journal of Ecology, vol. 101, n

o

3, p. 637–649. 12

GROSS, N., G. KUNSTLER, P. LIANCOURT, F. DEBELLO, K. N. SUDINGet S. LAVOREL. 2009,

«Linking individual response to biotic interactions with community structure : a

trait-based framework»,Functional Ecology, vol. 23, n

o

6, p. 1167–1178. 6

HAECKEL, E. 1904,Kunstformen der Natur, prestel éd., München.1

HARDY, O. 2008, «Testing the spatial phylogenetic structure of local communities :

statis-tical performances of different null models and test statistics on a locally neutral

com-munity»,Journal of ecology, vol. 96, n

o

5, p. 914–926. 17

HILL, M. O. 1973, «Diversity and evenness : a unifying notation and its consequences»,

Ecology, vol. 54, n

o

2, p. 427–432.15

HOBBIE, E. A. et P. HÖGBERG. 2012, «Nitrogen isotopes link mycorrhizal fungi and plants

to nitrogen dynamics»,New Phytologist, vol. 196, n

o

2, p. 367–382. 5,6

HUBBELL, S. P. 2001,The unified neutral theory of biodiversity and biogeography, vol. 32,

Princeton University Press.3,14

HUTCHINSON, G. E. 1957, «Concluding remarks», dansCold Spring Harbor Symposia on

Quantitative Biology, vol. 22, Cold Spring Harbor Laboratory Press, p. 415–427.3

INGER, R., R. GREGORY, J. P. DUFFY, I. STOTT, P. VORISEKet K. J. GASTON. 2014, «Common

european birds are declining rapidly while less abundant species’ numbers are rising»,

Ecology letters, vol. 18, p. 28–36. 1

JABOT, F. et J. CHAVE. 2009, «Inferring the parameters of the neutral theory of biodiversity

using phylogenetic information and implications for tropical forests»,Ecology letters,

vol. 12, n

o

3, p. 239–248. 14

JOST, L. 2006, «Entropy and diversity»,Oikos, vol. 113, n

o

2, p. 363–375. 15

KEARNEY, M. et W. P. PORTER. 2004, «Mapping the fundamental niche : physiology,

cli-mate, and the distribution of a nocturnal lizard»,Ecology, vol. 85, n

o

11, p. 3119–3131.

4

KEDDY, P. A. 1992, «Assembly and response rules : two goals for predictive community

ecology»,Journal of Vegetation Science, vol. 3, n

o

2, p. 157–164. 4,8

KÖRNER, C. 2003,Alpine Plant Life, Springer. 9,11

LALIBERTÉ, E. et P. LEGENDRE. 2010, «A distance-based framework for measuring

functio-nal diversity from multiple traits»,Ecology, vol. 91, n

o

1, p. 299–305. 15

LAVERGNE, S., E. GARNIER et M. DEBUSSCHE. 2003, «Do rock endemic and widespread

plant species differ under the leaf-height-seed plant ecology strategy scheme ?»,

Eco-logy Letters, vol. 6, n

o

5, p. 398–404. 7

LAVERGNE, S., N. MOUQUET, W. THUILLERet O. RONCE. 2010, «Biodiversity and climate

change : integrating evolutionary and ecological responses of species and

communi-ties»,Annual Review of Ecology, Evolution, and Systematics, vol. 41, p. 321–350.7,12

LAVOREL, S. et E. GARNIER. 2002, «Predicting changes in community composition and

ecosystem functioning from plant traits : revisiting the holy grail»,Functional Ecology,

vol. 16, n

o

5, p. 545–556. 4,5

LAVOREL, S., S. MCINTYRE, J. LANDSBERGet T. D. A. FORBES. 1997, «Plant functional

clas-sifications : from general groups to specific groups based on response to disturbance»,

Trends in Ecology & Evolution, vol. 12, n

o

12, p. 474–478. 4

LEIBOLD, M. A., M. HOLYOAK, N. MOUQUET, P. AMARASEKARE, J. M. CHASE, M. F.

HOOPES, R. D. HOLT, J. B. SHURIN, R. LAW, D. TILMAN, M. LOREAU et A. GONZALEZ.

2004, «The metacommunity concept : a framework for multi-scale community

eco-logy»,Ecology Letters, vol. 7, n

o

7, p. 601–613. 13

LEINSTER, T. et C. A. COBBOLD. 2012, «Measuring diversity : the importance of species

similarity»,Ecology, vol. 93, n

o

3, p. 477–489. 17

LETTEN, A. D. et W. K. CORNWELL. 2014, «Trees, branches and (square) roots : why

evo-lutionary relatedness is not linearly related to functional distance»,Methods in Ecology

and Evolution, vol. 6, p. 439–444.7

LIU, Y., L. ZHANG, H. NIU, Y. SUNet X. XU. 2014, «Habitat-specific differences in plasticity

of foliar δ13c in temperate steppe grasses»,Ecology and Evolution, vol. 4, n

o

5, p. 648–

655.6

LOSOS, J. 2008, «Phylogenetic niche conservatism, phylogenetic signal and the

relation-ship between phylogenetic relatedness and ecological similarity among species»,

Eco-logy Letters, vol. 11, n

o

10, p. 995–1003. 7

MACARTHUR, R. H. et E. O. WILSON. 1967, «The theory of island biogeography»,Princeton

University Press, vol. 1, p. 202. 2

MAGURRAN, A. E. 2004,Measuring biological diversity, Blackwell Publishing.2,15

MAYFIELD, M. et J. LEVINE. 2010, «Opposing effects of competitive exclusion on the

phy-logenetic structure of communities»,Ecology letters, vol. 13, n

o

9, p. 1085–1093.12

MEYER, S., C. REEBet R. BOSDEVEIX. 2008, «Botanique»,Biologie et physiologie végétales.

11

MILLER, A. E. et W. D. BOWMAN. 2002, «Variation in nitrogen-15 natural abundance and

nitrogen uptake traits among co-occurring alpine species : do species partition by

ni-trogen form ?»,Oecologia, vol. 130, n

o

4, p. 609–616. 6

MOLES, A. T., D. D. ACKERLY, C. O. WEBB, J. C. TWEDDLE, J. B. DICKIE et M. WESTOBY.

2005, «A brief history of seed size»,Science, vol. 307, n

o

5709, p. 576–580.5

MOUCHET, M. A., S. VILLÉGER, N. W. MASONet D. MOUILLOT. 2010, «Functional diversity

measures : an overview of their redundancy and their ability to discriminate

commu-nity assembly rules»,Functional Ecology, vol. 24, n

o

4, p. 867–876. 15

MOUQUET, N., V. DEVICTOR, C. N. MEYNARD, F. MUNOZ, L.-F. BERSIER, J. CHAVE, P. COU

-TERON, A. DALECKY, C. FONTAINE, D. GRAVEL, O. J. HARDY, F. JABOT, S. LAVERGNE,

M. LEIBOLD, D. MOUILLOT, T. MÜNKEMÜLLER, S. PAVOINE, A. PRINZING, A. S. RO

-DRIGUES, R. P. ROHR, E. THÉBAULTet W. THUILLER. 2012, «Phylogenetic ecology :

ad-vances and perspectives»,Biological Reviews, vol. 87, n

o

4, p. 769–785. 7

MYERS, J. A., J. M. CHASE, I. JIMéNEZ, P. M. JøRGENSEN, A. ARAUJO-MURAKAMI,

N. PANIAGUA-ZAMBRANAet R. SEIDEL. 2013, «Beta-diversity in temperate and tropical

forests reflects dissimilar mechanisms of community assembly»,Ecology letters, vol. 16,

n

o

2, p. 151–157. 3

MYERS, N., R. A. MITTERMEIER, C. G. MITTERMEIER, G. A. B. DAFONSECA, J. KENTet

col-lab.. 2000, «Biodiversity hotspots for conservation priorities»,Nature, vol. 403, n

o

6772,

p. 853–858.1

MÜNKEMÜLLER, T., F.DEBELLO, C. N. MEYNARD, D. GRAVEL, S. LAVERGNE, D. MOUILLOT,

N. MOUQUETet W. THUILLER. 2012, «From diversity indices to community assembly

processes : a test with simulated data»,Ecography, vol. 35, n

o

5, p. 468–480. 14

MÜNKEMÜLLER, T., F. BOUCHER, W. THUILLERet S. LAVERGNE. 2015, «Phylogenetic niche

conservatism - common pitfalls and ways forward»,Functional Ecology, vol. in press. 7

PAVOINE, S. et M. B. BONSALL. 2011, «Measuring biodiversity to explain community

as-sembly : a unified approach»,Biological Reviews, vol. 86, n

o

4, p. 792–812. 15

PAVOINE, S., M. LOVE et M. BONSALL. 2009, «Hierarchical partitioning of evolutionary

and ecological patterns in the organization of phylogenetically-structured species

as-semblages : application to rockfish (genus : Sebastes) in the Southern California Bight»,

Ecology letters, vol. 12, n

o

9, p. 898–908.17

PIELOU, E. C. 1975,Ecological diversity, New York. 2

PIMM, S. L., G. J. RUSSELL, J. GITTLEMANet T. M. BROOKS. 1995, «The future of

biodiver-sity»,Science, vol. 269, p. 347–350. 1

POISOT, T., B. PÉQUINet D. GRAVEL. 2013, «High-Throughput Sequencing : A Roadmap

Toward Community Ecology»,Ecology and Evolution, vol. 3, n

o

4, p. 1125–1139.18

POORTER, H. et M. BERGKOTTE. 1992, «Chemical composition of 24 wild species differing

in relative growth rate»,Plant, Cell & Environment, vol. 15, n

o

2, p. 221–229. 6

PULLIAM, H. R. 2000, «On the relationship between niche and distribution»,Ecology

let-ters, vol. 3, n

o

4, p. 349–361. 3

PÉREZ-RAMOS, I. M., C. ROUMET, P. CRUZ, A. BLANCHARD, P. AUTRAN et E. GARNIER.

2012, «Evidence for a plant community economics spectrum driven by nutrient and

water limitations in a Mediterranean rangeland of southern France»,Journal of Ecology,

vol. 100, n

o

6, p. 1315–1327. 6

REICH, P. B., D. S. ELLSWORTH, M. B. WALTERS, J. M. VOSE, C. GRESHAM, J. C. VOLINet

W. D. BOWMAN. 1999, «Generality of leaf trait relationships : a test across six biomes»,

Ecology, vol. 80, n

o

6, p. 1955–1969.5,6

RICKLEFS, R. 2004, «A comprehensive framework for global patterns in biodiversity»,

Eco-logy Letters, vol. 7, n

o

1, p. 1–15. 8

RICKLEFS, R. 2008, «Disintegration of the Ecological Community»,The American

Natura-list, vol. 172, n

o

6, p. 741–750.17

RICOTTA, C. 2005, «Through the jungle of biological diversity»,Acta biotheoretica, vol. 53,

n

o

1, p. 29–38. 2

RODERICK, M. L., S. L. BERRY, A. R. SAUNDERS et I. R. NOBLE. 1999, «On the

relation-ship between the composition, morphology and function of leaves»,Functional

Eco-logy, vol. 13, n

o

5, p. 696–710. 5

SAFI, K., M. V. CIANCIARUSO, R. D. LOYOLA, D. BRITO, K. ARMOUR-MARSHALLet J. A. F.

DINIZ-FILHO. 2011, «Understanding global patterns of mammalian functional and

phylogenetic diversity», Philosophical Transactions of the Royal Society B : Biological

Sciences, vol. 366, n

o

1577, p. 2536–2544. 7

SILIM, S., R. GUY, T. PATTERSON et N. LIVINGSTON. 2001, «Plasticity in water-use

effi-ciency of Picea sitchensis, P. glauca and their natural hybrids»,Oecologia, vol. 128, n

o

3,

p. 317–325.6

SILVERTOWN, J., M. FRANCO et K. MCCONWAY. 1992, «A demographic interpretation of

Grime’s triangle»,Functional Ecology, vol. 6, p. 130–136.5

SIMONIS, J. L. et J. C. ELLIS. 2014, «Bathing birds bias beta-diversity : Frequent dispersal

by gulls homogenizes fauna in a rock-pool metacommunity»,Ecology, vol. 95, p. 1545–

1555. 13

SPASOJEVIC, M. J., S. COPELANDet K. N. SUDING. 2014, «Using functional diversity

pat-terns to explore metacommunity dynamics : a framework for understanding local and

regional influences on community structure»,Ecography, vol. 37, n

o

10, p. 939–949. 9,

14

STOCK, W. D. et G. A. VERBOOM. 2012, «Phylogenetic ecology of foliar N and P

concen-trations and N : P ratios across mediterranean-type ecosystems»,Global Ecology and

Biogeography, vol. 21, n

o

12, p. 1147–1156. 5

SUGIHARA, G. 1982, «Comment»,Journal of the American Statistical Association, vol. 77,

n

o

379, p. 564–565.2

SVENNING, J.-C. et F. SKOV. 2007, «Could the tree diversity pattern in europe be generated

by postglacial dispersal limitation ?»,Ecology Letters, vol. 10, n

o

6, p. 453–460. 13

SWENSON, N. G., P. ANGLADA-CORDERO et J. A. BARONE. 2011, «Deterministic tropical

tree community turnover : evidence from patterns of functional beta diversity along an

elevational gradient»,Proceedings of the Royal Society B : Biological Sciences, vol. 278, n

o

1707, p. 877–884.9

TABERLET, P., E. COISSAC, F. POMPANON, C. BROCHMANN et E. WILLERSLEV. 2012,

«To-wards next-generation biodiversity assessment using DNA metabarcoding»,Molecular

ecology, vol. 21, n

o

8, p. 2045–2050. 18

THOMSON, F. J., A. T. MOLES, T. D. AULDet R. T. KINGSFORD. 2011, «Seed dispersal

dis-tance is more strongly correlated with plant height than with seed mass»,Journal of

Ecology, vol. 99, n

o

6, p. 1299–1307.13

THUILLER, W., S. LAVOREL, G. MIDGLEY, S. LAVERGNEet T. REBELO. 2004, «Relating plant

traits and species distributions along bioclimatic gradients for 88 Leucadendron taxa»,

Ecology, vol. 85, n

o

6, p. 1688–1699.5

TILMAN, D., J. KNOPS, D. WEDIN, P. REICH, M. RITCHIE et E. SIEMANN. 1997, «The

in-fluence of functional diversity and composition on ecosystem processes»,Science, vol.

277, n

o

5330, p. 1300–1302. 5

TUOMISTO, H. 2010, «A diversity of beta diversities : straightening up a concept gone awry.

Part 1. Defining beta diversity as a function of alpha and gamma diversity»,Ecography,

vol. 33, n

o

1, p. 2–22. 15

VELLEND, M., D. S. SRIVASTAVA, K. M. ANDERSON, C. D. BROWN, J. E. JANKOWSKI, E. J.

KLEYNHANS, N. J. KRAFT, A. D. LETAW, A. A. M. MACDONALD, J. E. MACLEAN, I. H.

MYERS-SMITH, A. R. NORRISet X. XUE. 2014, «Assessing the relative importance of

neu-tral stochasticity in ecological communities»,Oikos, vol. 123, n

o

12, p. 1420–1430.2,13,

14

VILLÉGER, S., N. W. H. MASONet D. MOUILLOT. 2008, «New multidimensional functional

diversity indices for a multifaceted framework in functional ecology»,Ecology, vol. 89,

n

o

8, p. 2290–2301. 15

VIOLLE, C., H. CASTRO, J. RICHARTE et M.-L. NAVAS. 2009, «Intraspecific seed trait

va-riations and competition : passive or adaptive response ?»,Functional Ecology, vol. 23,

n

o

3, p. 612–620. 6

VIOLLE, C., M. NAVAS, D. VILE, E. KAZAKOU, C. FORTUNEL, I. HUMMEL et E. GARNIER.

2007, «Let the concept of trait be functional !»,Oikos, vol. 116, n

o

5, p. 882–892. 4

VIOLLE, C., D. R. NEMERGUT, Z. PU et L. JIANG. 2011, «Phylogenetic limiting similarity

and competitive exclusion»,Ecology letters, vol. 14, n

o

8, p. 782–787. 7

VOLKOV, I., J. R. BANAVAR, S. P. HUBBELLet A. MARITAN. 2003, «Neutral theory and

rela-tive species abundance in ecology»,Nature, vol. 424, n

o

6952, p. 1035–1037. 14

WEBB, C. O., D. D. ACKERLY, M. A. MCPEEKet M. J. DONOGHUE. 2002, «Phylogenies and

community ecology»,Annual Review of Ecology and Systematics, vol. 33, n

o

1, p. 475–

505.3,4,7,9,17

WEIHER, E. et P. KEDDY. 1995, «Assembly rules, null models, and trait dispersion : new

questions from old patterns»,Oikos, vol. 74, n

o

1, p. 159–164. 9

WEIHER, E., A. WERF, K. THOMPSON, M. RODERICK, E. GARNIERet O. ERIKSSON. 1999,

«Challenging Theophrastus : a common core list of plant traits for functional ecology»,

Journal of Vegetation Science, vol. 10, n

o

5, p. 609–620.6

WEINSTEIN, B. G., B. TINOCO, J. PARRA, L. M. BROWN, J. A. MCGUIRE, F. G. STILESet

C. H. GRAHAM. 2014, «Taxonomic, phylogenetic and trait betadiversity in South

Ame-rican hummingbirds»,The American Naturalist, vol. 184, p. 211–224. 14

WESTOBY, M. 1998, «A leaf-height-seed (LHS) plant ecology strategy scheme»,Plant and

soil, vol. 199, n

o

2, p. 213–227. 5,6

WHITTAKER, R. H. 1960, «Vegetation of the siskiyou mountains, oregon and california»,

Ecological Monographs, vol. 30, n

o

3, p. 279–338. 9

WRIGHT, I., P. REICH, M. WESTOBY, D. ACKERLY, Z. BARUCH, F. BONGERS, J. CAVENDER

-BARES, T. CHAPIN, J. CORNELISSEN, M. DIEMER, J. FLEXAS, E. GARNIER, P. GROOM,

J. GULIAS, K. HIKOSAKA, B. B. LAMONT, T. LEE, W. LEE, C. LUSK, J. J. MIDGLEY,

M.-L. NAVAS, Ü. NIINEMETS, N. OLEKSYN, J. OSADA, H. POORTER, P. POOT, L. PRIOR, V. I.

PYANKOV, C. ROUMET, S. C. THOMAS, M. G. TJOELKER, V. E. J. et R. VILLA. 2004, «The

worldwide leaf economics spectrum»,Nature, vol. 428, n

o

6985, p. 821–827.5

YAWATA, Y., O. X. CORDERO, F. MENOLASCINA, J.-H. HEHEMANN, M. F. POLZ et R. STO

-CKER. 2014, «Competitionâdispersal tradeoff ecologically differentiates recently

spe-ciated marine bacterioplankton populations»,Proceedings of the National Academy of

Sciences, vol. 111, n

o

15, p. 5622–5627.2

ZANNE, A. E., D. C. TANK, W. K. CORNWELL, J. M. EASTMAN, S. A. SMITH, R. G. FITZJOHN,

D. J. MCGLINN, B. C. O’MEARA, A. T. MOLES, P. B. REICH, D. L. ROYER, D. E. SOLTIS,

P. F. STEVENS, M. WESTOBY, I. J. WRIGHT, L. AARSSEN, R. I. BERTIN, A. CALAMINUS,

R. GOVAERTS, F. HEMMINGS, M. R. LEISHMAN, J. OLEKSYN, P. S. SOLTIS, N. G. SWEN

-SON, L. WARMANet J. M. BEAULIEU. 2014, «Three keys to the radiation of angiosperms

into freezing environments»,Nature, vol. 506, n

o

7486, p. 89–92. 5

ZOBEL, M., R. OTTO, L. LAANISTO, A. NARANJO-CIGALA, M. PÄRTELet J. M. FERNÁNDEZ

-PALACIOS. 2011, «The formation of species pools : historical habitat abundance affects

current local diversity»,Global Ecology and Biogeography, vol. 20, n

o

2, p. 251–259. 17

Dans le document De la communauté à la méta-communauté, décrypter les patrons de diversité (Page 25-36)