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UNIVERSITEDELAREUNION

FacultédesSciencesetTechnologies

CIRAD-UniversitédelaRéunion

THESEPourobtenirlediplômede

DOCTORAT

Discipline:Sciences

FormationDoctorale:Génétique

Implicationspourleurconservation

par

RodolpheGIGANT

Soutenancepubliquedu02Mars2012,

devantunjurycomposéde: TariqSTEVARTChercheur,MissouriBotanicalGarden, Rapporteur MichelDRONProfesseur,UniversitéParisSud, Examinateur PascaleBESSEProfesseur,UniversitédelaRéunion, DirectricedeThèse

Remerciements

REMERCIEMENTS

Toutd'abord,jesuis

l'UMRPVBMT. thèse.

FockͲBastide.

génotypagesm'ontapportéleur

Etbiensûr,je

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Table des matières

i

TABLE DES MATIERES

1. CHAPITRE 1 : Introduction................................................................................................................1

1.1. Introduction générale...............................................................................................................1

1.2. Introduction bibliographique....................................................................................................6

Chapitre d'ouvrage Biodiversity and Evolution in the Vanilla Genus.......................................6

1.3. Présentation des vanilliers aphylles........................................................................................32

1.4. Objectifs de recherche de la thèse..........................................................................................49

2. CHAPITRE 2 Stratégie d'étude et méthodes...................................................................................51

2.1. Les collaborations...................................................................................................................51

2.2. Développement des marqueurs microsatellites ....................................................................53

Article 1 Nineteen polymorphic microsatellite markers from two African Vanilla species: across-species transferability and diversity in a wild population of V. humblotii from

Mayotte. ................................................................................................................................54

3. CHAPITRE 3 Etude de V. humblotii à Mayotte...............................................................................59

3.1. Préambule.............................................................................................................................59

3.2. Article 2 Reproductive strategies and their consequences on fine-scale spatial genetic

structure and diversity of the indigenous and endangered leafless Vanilla humblotii

(Orchidaceae) from Mayotte (Comoros Archipelago, Indian Ocean)......................................61

3.2.1. Abstract.........................................................................................................................62

3.2.2. Introduction...................................................................................................................63

3.2.3. Materials and Methods.................................................................................................64

3.2.4. Results...........................................................................................................................73

3.2.5. Discussion......................................................................................................................80

3.2.6. Conclusion.....................................................................................................................87

3.3. Article 3 Impact of fragmentation on the genetic diversity of Vanilla humblotii Rchb. f.

(Orchidaceae) in Mayotte (Comoros Archipelago, Indian Ocean) and implications for

3.3.1. Abstract.........................................................................................................................96

3.3.2. Introduction..................................................................................................................97

3.3.3. Materials and Methods.................................................................................................99

3.3.4. Results.........................................................................................................................106

3.3.5. Discussion....................................................................................................................114

3.3.6. Implications for the conservation of V. humblotii in Mayotte.....................................123

4. CHAPITRE 4 Etude de V. roscheri en Afrique Du Sud...................................................................132

4.1. Préambule............................................................................................................................132

Table des matières

ii

4.2. Article 4 Active sexual reproduction but no genetic diversity in the range-edge distribution

of Vanilla roscheri Rchb. f. (Orchidaceae) in South Africa....................................................134

4.2.1. Abstract........................................................................................................................135

4.2.2. Introduction.................................................................................................................136

4.2.3. Materials and Methods................................................................................................137

4.2.4. Results..........................................................................................................................144

4.2.5. Discussion.....................................................................................................................149

4.2.6. Implications for the conservation.................................................................................156

5. CHAPITRE 5 Discussion générale, conclusions et perspectives....................................................163

5.1. Apports fondamentaux à la biologie de la reproduction des vanilliers................................163

5.2. Importance de la reproduction végétative...........................................................................169

5.3. Les phénomènes de migration et d'isolement des populations chez les vanilliers aphylles de

l'océan Indien.......................................................................................................................171

5.4. L'approche intégrative de la biologie de la reproduction et de la génétique des populations

et la complémentarité des modèles.....................................................................................176

5.5. Implications pour la conservation des espèces étudiées......................................................177

5.6. Perspectives de recherche....................................................................................................182

REFERENCES BIBLIOGRAPHIQUES.......................................................................................................185

Tableauxetfigures

iii

TABLEAUXETFIGURES

1

Listedestableaux

Tableau16

ͲTable4PairwiseF

ST 1

Tableauxetfigures

iv

Listedesfigures

thespeciesV.

Figure6Distributiondes

transfrontalièreduMaputaland

Figure

'genets'

Tableauxetfigures

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Figure24ͲFigure3Mapsoftheposterior

Figure27ͲFigure6Correlogramshowing

................139 vi

Préambule

soumission.

Chapitred'ouvrage

Article1

Resources:1Ͳ5.

Article2

BesseP(inprep)Reproductivestrategies

Article3

Article4

Rchb.f.(Orchidaceae)inSouthAfrica.

w9Cb/{.L [

Chapitre1

l'homme.

écologie

en

Chapitre1

Vanilla

Chapitre1

Vanilla,Vanillaplanifolia

Vanilla

Vanilla.Ͳ

Vanilla

V.planifoliaV.aphyllaͲ

Vanilla

Chapitre1

Vanilla,

exsitu

Chapitre1

V. lindmanianaV.palmarum

V.pompona

V.bahianaV.tahitensis

V.planifolia.

insituexsitu V. humblotiiV.roscheri Case

StudiesofEvolutionandSpatialDistribution

Vanilla.

1

Biodiversity and Evolution in the

Genus

Gigant Rodolphe

1,2 , Bory Séverine 1,2 , Grisoni Michel 2 and Besse Pascale 1 1

1. Introduction

Since the publication of the first vanilla book by Bouriquet (1954c) and the more recent review on vanilla biodiversity (Bory et al., 2008b), there has been a world regain of interest for this genus, as witnessed by the recently published vanilla books (Cameron, 2011a; Havkin-Frenkel & Belanger, 2011; Odoux & Grisoni, 2010). A large amount of new data regarding the genus biodiversity and its evolut ion has also been obtained. These will be reviewed in the present paper and new data will also be presented.

2. Biogeography, taxonomy and phylogeny

2.1 Distribution and phylogeography

Plum. ex Miller is an ancient genus in the Orchidaceae family, Vanilloideae sub- family, Vanilleae tribe and Vanillinae sub-tribe (Cameron, 2004, 2005). species are distributed throughout the tropics between the 27th north and south parallels, but are absent in Australia. The genus is most diverse in tropical America (52 species), and can also be found in Africa (14 species) and the Indian ocean islands (10 species), South-East Asia and New Guinea (31 species) and Pacific islands (3 species) (Portères, 1954). From floral morphological observations, Portères (1954) suggested a primary diversification centre of the genus in Indo-Malaysia, followed by dispersion on one hand from Asia to Pacific and then America, and on the other hand from Madagascar to Africa. This hypothesis was rejected following the first phylogenetic studies of the genus (Cameron, 1999, 2000) which suggested a different scenario with an American origin of the genus (160 to 120 Mya) and a transcontinental migration of the genus before the break-up of Gondwana (Cameron, 2000, 2003, 2005; Cameron et al., 1999). The genetic differentiation between New World and Old World species observed would therefore be a consequence of the further separation of the continents. Our recent molecular phylogeny using chloroplastic B, B, bC, and L regions (Bouetard et al., 2010) supported the hypothesis of an American origin of the genus (figure 1). However, the recent discovery of a fossilized orchid pollinaria (20 Mya) (Ramirez et al., 2007) allowed the dating of Vanilloidae sub family at 72 Mya, well after the separation of Gondwana which questions the hypothesis of a vicariate evolution of the genus (Bouetard et al., 2010). Transoceanic dispersion appears more credible and would have been implied at least three times in the evolution of the genus (figure 1). This was demonstrated by dating a molecular phylogeny, testing these two extreme evolutionary scenarios (vicariate

The Dynamical Processes of Biodiversity - Case

Studies of Evolution and Spatial Distribution

2 versus

2.2 Taxonomy and phylogeny

Vanilla

Vanilla

rcb psapsbpsb

Vanilla

ǂǃDŽǂV. mexicana

Vanilla

V. angustipetalaV.

martineziiV. inodoraV. mexicanaV. parvifloraV. edwalii

Dictyophyllaria dietschianaV. dietschiana

VanillaVanilla

V. mexicana

ǂVanillaVanilla

XanataXanata

ǃTethyaDŽXanata

V. palmarumV. lindmaniana

V. bicolor

Biodiversity and Evolution in the Genus

3

Vanilla

rbcpsapsbpsbǂǃDŽ

Vanilla

Vanilla

Vanilla

Vanilla

Vanilla

LateJurassic 152 Mya

Late Cretaceous 94 Mya

Middle Eocene 50.2 Mya

Middle Miocene 14 Mya

-95 -37.4 -12.3-15.7

Group ȕ

American speciesGroup Į

Membranous species

Group Ȗ

Old World

Caribbean

species

Vanilla

V. madagascariensis

V. roscheri

V. humblotii

V. dilloniana

-129 -25.5 -10.2 -4.4-34.6 -3.6

V. palmarum

V. leprieuri

V. ensifolia

V. pompona

V. chamissonis

V. odorata

V. xtahitensis

V. planifolia

V. bahiana

V. imperialis

V. crenulata

V. africanaV. mexicana

V. albida

V. aphylla

Asia

Africa

CWI

America

subgen. subgen. sect. sect. SWIO

V. lindmaniana

Mad. India

S. Am.Asia

Eur.

N. Am.

IND. OCEANPACIFIC OCEANN. ATL.

OCEAN

S. ATL.

OCEAN

Africa

N. Am.

N. ATL.

OCEAN

S. Am.

S. ATL.

OCEAN

Africa

Mad.

IND. OCEANIndia

AsiaEur.

PACIFIC OCEAN

Mad./India

AfricaS. Am.

PACIFIC OCEAN

Eurasia

N. Am.

TETHYS OCEAN

GONDWANA

TETHYS OCEANPACIFIC OCEAN

LAURASIA

The Dynamical Processes of Biodiversity - Case

Studies of Evolution and Spatial Distribution

4 of the genus and concluded that must be considered as a TCG, a "Taxonomic

Complex Group" (Ennos et al., 2005). Indeed, it

exhibits (i) an uniparental reproduction mode (vegetative growth) (Portères, 1954) (ii) interspecific hybridization in sympatric areas (Bory et al., 2010; Bory et al., 2008c; Nielsen, 2000; Nielsen & Siegismund, 1999) and (iii) polyploidy (Bory et al., 2010; Bory et al., 2008a; Lepers-Andrzejewski et al., 2011a; Lepers-Andrzejewski et al., 2011b). These mechanisms have profound effects on the organization of the biological diversity and have been described as responsible for the difficulty to define discrete, stable and coherent taxa in such TCGs (Ennos et al., 2005). is a typical example of a genus for which the barcoding protocols (K and L) as proposed by the CBOL (M.L. Hollingsworth et al., 2009; P.M. Hollingsworth & CBOL Plant Working Group, 2009 ; Ratnasingham "esdbs_dbs9.pdfusesText_15

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