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ECOLE NORMALE SUPERIEURE
ECOLE DOCTORALE FRONTIERES DU VIVANT
Thèse en vue d'obtenir le grade de Docteur
Sciences de la Vie et de la Santé
LA NICHE ÉCOLOGIQUE
CONCEPTS, MODÈLES, APPLICATIONS
soutenue le 15 décembre 2010 par
Arnaud Pocheville
devant le jury composé de
Pr. Régis Ferrière Directeur de thèse
Dr. Philippe Huneman Co-directeur
Dr. Sébastien Barot Rapporteur
Pr. Frédéric Bouchard Rapporteur
Dr. Minus van Baalen Examinateur
Pr. Etienne Danchin Examinateur
Dr. François Munoz Examinateur

Table des matières
Remerciements............................................................................................................................5
Résumé........................................................................................................................................7
Summary.....................................................................................................................................7
Introduction................................................................................................................................8
La niche écologique: histoire et controverses récentes
1. Histoire du concept de niche....................................................................................................9
1.1 Le concept avant la lettre...................................................................................................9
1.2 Grinnell et Elton, la nucléation du concept.....................................................................10
1.3 George Hutchinson et le principe d’exclusion compétitive............................................11
1.4 L’âge d’or : la théorie de la niche ....................................................................................14
1.5 Les années 1980 : le déclin ..............................................................................................15
1.6 Chase et Leibold, la rénovation.......................................................................................16
1.7 La théorie de la construction de niche et la niche des cellules souches.........................17
2. Le concept de niche et les théories de la coexistence............................................................18
3 La théorie neutraliste et son bouquet de controverses.............................................................21
3.1 La théorie neutre avant la lettre.......................................................................................21
3.2 Caractéristiques des modèles neutres.............................................................................22
3.3 Domaine de performance de la théorie neutre...............................................................23
3.3.1 Qualité des hypothèses...........................................................................................23
3.3.2 Qualité des prédictions...........................................................................................24
3.4 Nature de l’opposition entre théorie neutre et théorie de la niche..................................27
3.4.1 Statut de la stochasticité..........................................................................................27
3.4.2 La théorie neutre : une hypothèse nulle ? ...............................................................28
3.4.3 Dimensionnalité des modèles.................................................................................28
4 Conclusions.............................................................................................................................29
4.1 Acceptions du concept....................................................................................................29
4.2 Niche et neutralité...........................................................................................................30
Références bibliographiques......................................................................................................32
What niche construction is (not)
Introduction................................................................................................................................39
1. Our verbal formalism..............................................................................................................40
1.1 Explanation and the many scales of biology...................................................................40
1.2 The war raging between the inside and the outside........................................................42
2. The selectionist scheme(s) in biology....................................................................................43
2.1 The scheme......................................................................................................................43
2.2 Historical perspectives....................................................................................................44
The substrate of heritability............................................................................................44
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The object of selection....................................................................................................46
2.3 The selectionist scheme revisited...................................................................................49
Heredity and replication..................................................................................................49
Phenotypes of replicators (development)........................................................................50
Variations in fitness (evolution)......................................................................................51
2.4 A note on maps...............................................................................................................53
2.5 A note on spatial extension.............................................................................................54
2.6 Concluding discussion on the selectionist scheme.........................................................55
The necessary invariance................................................................................................55
Time-scale separations....................................................................................................55
Externalism and internalism ...........................................................................................56
Historical roots and leafs.................................................................................................57
3. What niche construction is.....................................................................................................57
3.1 Construction in living systems........................................................................................57
Examples..........................................................................................................................57
Definitions.......................................................................................................................57
Generalisation : niche interaction....................................................................................58
3.2 The (non-)universality of construction...........................................................................59
The thermodynamic (dis)proof.......................................................................................59
The correlation-propagation (dis)proof...........................................................................60
3.3 The many scales of niche construction: development, ecology, (micro and macro)
evolution................................................................................................................................61
3.4 The many meanings of niche construction.....................................................................61
OLF's dichotomies...........................................................................................................61
The degree of selection : mere effects vs adaptations.....................................................62
Auto vs allo-niche construction (or narrow vs broad sense)...........................................62
3.5 What the focal living system is (organisms vs genes)....................................................64
3.6 What selection pressures are: variables or invariants?...................................................66
Selection pressures as local explanans............................................................................66
Selection pressures as global explanans..........................................................................66
Selections pressures in niche construction......................................................................67
Selective environment and natural selection...................................................................68
3.7 OLF's review of past theory............................................................................................69
Coevolution......................................................................................................................69
Habitat selection..............................................................................................................71
Evolution in spatially heterogeneous environments........................................................72
Other approaches.............................................................................................................72
3.8 To build, or not to build?.................................................................................................73
Niche construction or extended phenotype?....................................................................74
3.9 Niche construction and extended phenotype..................................................................74
The relationship between genes and niche construction.................................................75
The “reciprocal causation” between construction and selection.....................................76
Conclusion on extended phenotypes...............................................................................77
3.10 Niche construction and posthumous phenotypes..........................................................77
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Niche construction and feedback.....................................................................................77
Niche construction rephrased..........................................................................................78
Examples of posthumous phenotypes.............................................................................79
Posthumous phenotypes and scale separability..............................................................80
Scale (non) separability by example................................................................................81
Rescaling: some formalism.............................................................................................83
Conclusion on posthumous phenotypes..........................................................................84
3.11 Relaxing the invariance of the phenotype-fitness map.................................................85
3.12 A note on evolutionary self and non-self......................................................................86
3.13 Concluding discussion on what niche construction is..................................................87
Niche construction revisited : definitions and invariants................................................87
Other constructionist tracks.............................................................................................88
Environment or phenotype..............................................................................................89
Space vs time...................................................................................................................89
4. Problems of niche construction : adaptation, externalism.....................................................90
4.1 Adaptation.......................................................................................................................90
Concepts of adaptation....................................................................................................91
Construction towards fit ?...............................................................................................92
4.2 Back to the basics : is selectionism an externalism ?.....................................................95
Historical perspectives....................................................................................................95
Selective laws and selective forces..................................................................................96
Back to Lewontin's equations..........................................................................................98
Constitutive vs causal construction.................................................................................99
Conclusion on externalism............................................................................................100
5. Other alternative evolutionary biologies and niche construction........................................102
5.1 The “new” explanandum...............................................................................................102
5.2 The multiple entanglements..........................................................................................102
5.3 The importance of (not so) rare events.........................................................................105
5.4 Bringing a new theory of macroevolution....................................................................106
5.5 Epistasis and the rugged fitness landscape...................................................................107
6. Conclusion............................................................................................................................107
Main point................................................................................................................................109
Glossary....................................................................................................................................110
References.................................................................................................................................113
L'écologie intra-organisme: thérapie génique et construction de niche
I. Modèle de la démographie cellulaire....................................................................................125
1. Modèle d'ordre 1.............................................................................................................125
2. Modèle d'ordre 2.............................................................................................................126
Analogie avec la physique.............................................................................................127
Différences entre les dynamiques inertielle et non inertielle: mortalité accélérée,
overshoot........................................................................................................................127
Friction, antifriction......................................................................................................128
3. Modèles à plusieurs espèces...........................................................................................129
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