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Küpfer, Philippe

Nom
Küpfer, Philippe
Affiliation principale
Fonction
Professeur honoraire
Email
philippe.kuepfer@unine.ch
Identifiants
https://libra.unine.ch/handle/123456789/301

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  • Publication
    Accès libre
    Inferring reciprocal evolutionary histories in associated species of plants and insects in two european pollination systems
    (2010)
    Espíndola, María Anahí
    ;
    Alvarez, Nadir
    ;
    Rahier, Martine 
    ;
    Carstens, Bryan C.
    ;
    Després, Laurence
    ;
    Gibernau, Marc
    ;
    Gugerli, Felix
    ;
    Küpfer, Philippe 
    Coevolution is defined as reciprocal evolutionary changes that might arise at any spatiotemporal scale. Despite every organism on Earth undergoes coevolutionary interactions, cases of one-to-one specific relationships are generally rare. However, because of the reduced number of interacting species they concern, these species-specific associations are interesting to evolutionary biologists because they allow testing hypotheses in simple frameworks. Despite the history and evolution of coevolutionary interactions have been studied in several cases in the last decade, this topic remains difficult to fully circumscribe because of the multiplicity of factors that affect one or the other species concerned. Moreover, a lot is known about coevolution at a small scale, but little has been done at larger and more integrative scales spanning wider spatiotemporal ranges. Phylogeography is a young area of biology that allows understanding the distribution of lineages in space and time. Despite that the idea of parallely studying the history of species involved in specific interactions appears simple, this has rarely been done until now probably because of the technical efforts this would represent. From a theoretical point of view, we could propose that in specific interactions, because of the dependence between the partners involved, we should observe some phylogeographic pattern associated to the type of interaction studied. In this way, while partners of mutualistic interactions should present similar postglacial histories, this should not be true for those associated by antagonistic relationships. In this thesis, we exploit different techniques and approaches to test this general hypothesis. The final aim of this study is thus to understand if it is possible to identify a pattern of comparative phylogeography in relation to the type of interaction, using as case-studies two specific and obligate European interactions: the antagonistic relationship established between Arum maculatum L. (Araceae) and its Psychodid (Diptera) pollinating flies, and the nursery pollination mutualism involving Trollius europaeus L. (Ranunculaceae) and the Chiastocheta (Diptera: Anthomyiidae) species complex. Before testing our comparative phylogeographic hypotheses and because studying the phylogeography of interactions requires a wide knowledge of the environmental, taxonomic and historical frameworks in which these ecological relationships arose, it was first needed to clearly delimitate the identity of species, their distribution and the environmental factors influencing their survival to finally understand their comparative history. We thus took advantage of the potentialities that interdisciplinary approaches provide, applying molecular taxonomy, biological and evolutionary methods, biogeographic inferences, ecological niche models and hindcasting techniques, as well as classical and recently-developed phylogeographic analyses. Our results indicate that the phylogeographic patterns of these specific and obligate antagonistic and mutualistic relationships appear to be related to the type of interaction. Antagonistic partners presented incongruent phylogeographic patterns, what can be notably explained by differences in their life-history traits. Species involved in mutualistic interactions partly showed congruent phylogeographic patterns (particularly in the cases of T. europaeus and C. dentifera). Flies interacting with T. europaeus appear moreover to present different histories, regardless of their important ecological similarities. These results demonstrate that the systems studied appear to be far more complex than initially supposed, with crossed effects of environmental and historical features on the dynamics of the interaction. Because of the high complexity and interdependency of factors affecting one or the other partner, performing investigations in an interdisciplinary framework appears indispensable to disentangle the dynamics of interactions.
  • Publication
    Accès libre
    Worldwide biogeography and systematics of Sapindaceae: a molecular and taxonomic survey combining large data sets and novel methodological approaches
    (2009)
    Bürki, Sven
    ;
    Küpfer, Philippe 
    ;
    Alvarez, Nadir
    La famille des Sapindaceae est importante d’un point de vue économique et comprend plus de 1900 espèces (distribuées dans approximativement 140 genres; par exemple Litchi, Paullinia), majoritairement distribuées en zone tropicale. Cependant, certains genres peuvent coloniser les zones tempérées. Depuis plus d’un siècle, la définition de cette famille (plus particulièrement la possible inclusion des Aceraceae et Hippocastanacae au sein des Sapindaceae) ainsi que les relations entre les sous-familles, ont été largement débattues (voir chapitre 1 pour un résumé). Dans ce travail, les relations au sein des Sapindaceae, ainsi que celles entre les Aceraceae et Hippocastanaceae, sont étudiées sur la base de huit marqueurs moléculaires (nucléaire et chloroplastiques) en utilisant une approche complémentaire de types supermatrice (chapitre 1) et supertree (chapitre 6). Les deux approches supportent la monophylie des Sapindaceae lorsque les Aceraceae et Hippocastanaceae sont incluses, et montrent un haut taux de paraphylie et polyphylie au niveau des sous-familles et tribus. De plus, les résultats contestent la monophylie de plusieurs genres (par exemple, Cupaniopsis, Haplocoelum, Matayba). Afin de maintenir le critère de monophylie, une nouvelle classification informelle des Sapindaceae est proposée sur la base de caractères moléculaire et morphologique. La famille des Sapindaceae est donc subdivisée en quatre sous-familles et dix groupes comme suit (les sous-familles sont triées par ordre phylogénétique): Xanthoceroideae (comprend uniquement Xanthoceras sorbifolium), Hippocastanoideae (deux groupes; comprend les Aceraceae et Hippocastanaceae), Dodonaeoideae (deux groupes) et Sapindoideae (dix groupes). De plus, des analyses moléculaires et morphologiques complémentaires ont permis de reconnaître un nouveau genre endémique de Madagascar, Gereaua, ségrégé d’Haplocoelum (chapitre 4). Une révision taxonomique du genre Lepsianthes à Madagascar est également présentée, dans laquelle une espèce nouvelle est décrite, L. sambiranensis (chapitre 5). Finalement, l’arbre phylogénétique ainsi que les données sur les fossiles et la distribution des taxa ont été utilisés pour investiguer l’histoire évolutive des Sapindaceae. Cela a été rendu possible par l’application et la comparaison des toutes dernières méthodes développées en biogéographie. Une contribution au développement des analyses biogéographiques est également proposée par la présentation d’un modèle biogéographique basé sur les relations paléogéographiques (chapitre 2). De plus, l’incertitude sur l’estimation de l’âge des clades a été considérée lors de l’interprétation des scénarios biogéographiques (chapitre 2). Finalement, l’impact des facteurs abiotiques (par exemple, les intenses activités tectoniques ou les forces orbitales) et biotiques (par exemple, la co-évolution plantes/animaux) sur la diversification des Sapindaceae ont été étudiés. Ces analyses supportent une origine des Sapindaceae en Asie tempérée au début du Crétacé suivie par une colonisation des zones tropicales depuis la fin du Paléocène (chapitre 3). Cette étude montre, pour la première fois, que le changement climatique abrupt ayant eu lieu entre l’Eocène et l’Oligocène, a accéléré le taux de diversification des Sapindaceae. Ce résultat, qui s’oppose à la majorité des paradigmes (voir chapitre 3 pour plus d’information), est principalement dû aux propriétés géologiques et climatiques rencontrées en Asie du Sud Est. En effet, cette région a favorisé de multiples contacts entre les lignées de Sapindaceae et de successives spéciations ont eu lieu sur les continents Laurasien et Gondwanien. Cette étude montre l’importance jouée par l’Asie du Sud Est dans l’évolution des Sapindaceae (ainsi que probablement d’autres familles d’angiospermes) et souligne l’importance de préserver cette région qui subit de fortes pressions humaines., The economically important soapberry family (Sapindaceae; Sapindales) comprises about 1900 species (distributed into ca. 140 genera; e.g., Litchi, Paullinia) mainly found in tropical regions, with only a few genera being restricted to temperate areas. For more than a century, the circumscription of the family (especially the potential inclusion of Aceraceae and Hippocastanaceae within the Sapindaceae) as well as the relationships among subfamilial entities have been widely challenged (chapter 1 for a review). In this study, infrafamilial relationships within the Sapindaceae and its relationships to the closely related Aceraceae and Hippocastanaceae are investigated based on eight nuclear and plastid markers and inferred from the complementary supermatrix (chapter 1) and supertree (chapter 6) approaches. Both approaches support the monophyly of Sapindaceae when Aceraceae and Hippocastanaceae are included and highlight a high level of paraphyly and polyphyly at the subfamilial and tribal levels. The monophyletic status of several genera is even contested (e.g., Cupaniopsis, Haplocoelum, Matayba). In order to maintain monophyly, a new informal classification is proposed based on molecular and morphological evidence. The soapberry family is thus subdivided into four subfamilies and 14 groups as follows (sorted according to phylogenetic relationships): Xanthoceroideae (only composed by Xanthoceras sorbifolium), Hippocastanoideae (two groups; including the previous Aceraceae and Hippocastanaceae), Dodonaeoideae (two groups) and Sapindoideae (ten groups). In addition, further molecular and morphological investigations allow the recognition of a new Malagasy genus, Gereaua, segregated from Haplocoelum (chapter 4). A taxonomic revision of Lepisanthes in Madagascar is also proposed with the description of a new species, L. sambiranensis (chapter 5). Phylogenetic framework, fossils data and taxa distributions are used to infer the evolutionary history of the soapberry family. This is achieved by applying and comparing state-of-the-art biogeographic methods. Moreover, additional contributions to the biogeographic framework are proposed, for instance the implementation of a biogeographic model based on paleogeographic connections (chapter 2). The influence of divergence time uncertainty on biogeographic scenario is also considered (chapter 2). Finally, the impact of abiotic (e.g., intense tectonic activities, orbital forces) and biotic (e.g., co-evolution plants/animals) factors on the diversification of the Sapindaceae is investigated based on biogeographic inference and divergence time estimations (chapter 3). Results strongly suggest an origin of Sapindaceae in temperate Asia sometime in the Early Cretaceous with a subsequent spread all over the tropics since the Late Paleocene (chapter 3). In this study, it is show, for the first time, that abrupt climatic change in the Eocene-Oligocene boundary triggered the diversification rates of the Sapindaceae. This paradigm-breaking result is mainly due to the geological and climatic properties of South East Asia that favoured multiple contacts between lineages and further speciation across Laurasian and Gondwanian continents. This study highlights the importance of South East Asia in the evolution of the soapberry family (as well as that of additional angiosperms families) and underlines the importance to preserve this highly endangered area.
  • Publication
    Accès libre
    Phylogenetics of tribe Exaceae (Gentianaceae) based on molecular, morphological and karyological data, with special emphasis on the genus Sebaea.: Taxonomic treatment of Exochaenium, Lagenias and the new genus Klackenbergia
    (2007)
    Kissling, Jonathan 
    ;
    Küpfer, Philippe 
    ;
    Linder, Peter
    In an attempt to understand the evolutionary history of the poorly studied genus Sebaea and its relationship to other genera of tribe Exaceae (Gentianaceae), intensive morphological and karyological character optimization based on robust molecular phylogeny was performed. Phylogenetic reconstructions support the monophyly of Exaceae, and further reveal a polyphyletic Sebaea, including four well-supported clades, hereafter treated as separate genera, based on non-molecular synapomorphies. The first clade contains the single species Lagenias pusillus, characterized by its medifix anthers, inserted at the base of the corolla tube and its seed testa cells (polygonal). The second clade, Sebaea s. str., contains most of the South African species having secondary stigmas and bilateral seeds, with rectangular testa cell. The third clade, Exochaenium, contains exclusively tropical African species, characterized by a stylar polymorphism and a papillose clavate stigma (versus smooth and bilobed). Finally the fourth clade, Klackenbergia, contains two species characterized by inflorescences with axillary subsessile flowers. Based on these results, the taxonomic reinstatement of Exochaenium (23 species) and Lagenias (1 species), along with the establishment of a new genus Klackenbergia (2 species), are proposed. In the light of the new phylogenetic relationships found within the Exaceae, new views on the evolution of (1) karyological and (2) morphological characters are proposed. Finally, the historical biogeography of the tribe is reevaluated (3). 1. Intensive chromosome counts based on material collected and fixed in the field (157 population and c. 60 species), and exhaustive literature survey, reveal a broad set of chromosome numbers (2n = 18, 28, 32, 34, 36, 42, 52, 54, 56, 60, 62, 64, 68), and the occurrence of polyploid systems within Exacum and Sebaea. These results allow us to postulate x = 7, 8, or 9 as the possible base chromosome numbers for the Exaceae. Karyological reconstruction, based on the molecular phylogeny, suggest a basic number of x=7 for the Exaceae, followed by dysploidy event leading to secondary base number of x=8 and x=9, and several polyploidization events. 2. Optimization of morphological characters suggests that the most recent common ancestor of Exaceae (MRCA) was similar to Lagenias pusillus by having pentamerous yellow actinomorphic flowers, with anthers included in the corolla tube and dehiscing by longitudinal slits, a bilobed stigma, and the absence of secondary stigmas, and cubical seeds with polygonal testa cells. This MRCA might have then developed particular floral syndromes as indicated by long corolla tubes or presence of enantiostyly in the tribe. 3. Dating analyses and dispersal-vicariance reconstructions suggest that the Exaceae evolved c. 32 million years ago in Africa and subsequently spread to Madagascar. The colonization of Australia, New-Zealand, and Asia involved at least three long-distance dispersals. Early diversification of Exaceae in Africa might be the consequence of the development of a temperate with dry summer climate, in the Cape region (South Africa), while the Quaternary climatic variation might explain most of the species diversity of Sebaea and Exochaenium. At the generic level, molecular phylogenies of Sebaea, based on chloroplastic and nuclear DNA markers, reveals five well-supported clades. Sebaea sulphurea seems to have evolved early, and is distinct from all the remaining extant species. Each clade is supported by several characters (morphological, vegetative, phenological or geographical), and a preliminary infrageneric classification is proposed.
  • Publication
    Métadonnées seulement
    Phylogeny and biogeography of Exacum (Gentianaceae): A disjunctive distribution in the Indian Ocean Basin resulted from long distance dispersal and extensive radiation
    (2005)
    Yuan, Yong-Ming
    ;
    Wohlhauser, Sébastien
    ;
    Moller, Michael
    ;
    Klackenberg, Jens
    ;
    Callmander, Martin
    ;
    Küpfer, Philippe 
    Disjunctive distributions across paleotropical regions in the Indian Ocean Basin (IOB) often invoke dispersal/vicariance debates. Exacum (Gentianaceae, tribe Exaceae) species are spread around the IOB, in Africa, Madagascar, Socotra, the Arabian peninsula, Sri Lanka, India, the Himalayas, mainland Southeast Asia including southern China and Malaysia, and northern Australia. The distribution of this genus was suggested to be a typical example of vicariance resulting from the breakup of the Gondwanan supercontinent. The molecular phylogeny of Exacion is in principle congruent with morphological conclusions and shows a pattern that resembles a vicariance scenario with rapid divergence among lineages, but our molecular dating analysis demonstrates that the radiation is too recent to be associated with the Gondwanan continental breakup. We used our dating analysis to test the results of DIVA and found that the program predicted impossible vicariance events. Ancestral area reconstruction suggests that Exacum originated in Madagascar, and divergence dating suggests its origin was not before the Eocene. The Madagascan progenitor, the most recent common ancestor of Exacion, colonized Sri Lanka and southern India via long-distance dispersals. This colonizer underwent an extensive range expansion and spread to Socotra-Arabia, northern India, and mainland Southeast Asia in the northern IOB when it was warm and humid in these regions. This widespread common ancestor retreated subsequently from most parts of these regions and survived in isolation in Socotra-Arabia, southern India-Sri Lanka, and perhaps mainland Southeast Asia, possibly as a consequence of drastic climatic changes, particularly the spreading drought during the Neogene. Secondary diversification from these surviving centers and Madagascar resulted in the extant main lineages of the genus. The vicariance-like pattern shown by the phylogeny appears to have resulted from long-distance dispersals followed by extensive range expansion and subsequent fragmentation. The extant African species E. oldenlandioides is confirmed to be recently dispersed from Madagascar.