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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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2011
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  • Publication
    Accès libre
    Sensitivity of plant and soil ecosystems of the Alps to climate change
    (Boston: MIT Press, 1998)
    Theurillat, Jean-Paul
    ;
    Felber, François 
    ;
    Geissler, Patricia
    ;
    Gobat, Jean-Michel 
    ;
    Fierz, Marlyse
    ;
    Fischlin, Andreas
    ;
    Küpfer, Philippe 
    ;
    Schlüssel, André
    ;
    Velutti, Caterina
    ;
    Zhao, Gui-Fang
    ;
    Cebon, Peter
    ;
    Dahinden, Urs
    ;
    Davies, Huw
    ;
    Imboden, Dieter
    ;
    Jaeger, Carlo
  • 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.
  • Publication
    Métadonnées seulement
    Monophyly and relationships of the tribe Exaceae (Gentianaceae) inferred from nuclear ribosomal and chloroplast DNA sequences
    (2003)
    Yuan, Yong-Ming
    ;
    Wohlhauser, Sébastien
    ;
    Moller, Michael
    ;
    Chassot, Philippe
    ;
    Mansion, Guilhem
    ;
    Grant, Jason
    ;
    Küpfer, Philippe 
    ;
    Klackenberg, Jens
    Both chloroplast trnL (UAA) intron and nuclear ribosomal ITS sequences highly confirmed the monophyly of the tribes of the Gentianaceae defined by the recent classification, and revealed the tribe Exaceae as a basal clade just next to the basal-most lineage, the tribe Saccifolieae. Within the tribe Exaceae, Sebaea (except Sebaea madagascariensis) appeared as the most basal clade as the sister group to the rest of the tribe. The Madagascan endemic genera Gentianothamnus and Tachicrdenus were very closely related to each other, together standing as sister to a clade comprising Sebaea madagascariensis, Ornichia, and Exacum. The saprophytic genus Cotylanthera nested deeply inside Exacum. Sebaea madagascariensis was shown closer to the Madagascan endemic genus Ornichia than to any other sampled Sebaea species. Exacum appeared as the most derived taxon within this tribe. The topology of the phylogenetic trees conform with the Gondwana vicariance hypothesis regarding the biogeography of Exaceae. However, no evidence for matching the older relationships within the family to the tectonic history could be corroborated with various divergence time analyses. Divergence dating estimated a post-Gondwana diverging of the Gentianaceae about 50 million years ago (MYA), and the tribe Exaceae as about 40 MYA. The Mozambique Channel land-bridge could have played an important role in the biogeographic history of the tribe Exaceae. (C) 2003 Elsevier Science (USA). All rights reserved.
  • Publication
    Accès libre
    Cytogeography of Gentianaceae–Exaceae in Africa, with a special focus on Sebaea: the possible role of dysploidy and polyploidy in the evolution of the tribe
    (2008)
    Kissling, Jonathan 
    ;
    Zeltner, Louis
    ;
    Küpfer, Philippe 
    ;
    Mansion, Guilhem
    Unlike other tribes of Gentianaceae, Exaceae have so far received little attention regarding their karyological evolution. Indeed, only 35 chromosome number counts (19 species) have been referenced to date, representing only a negligible fraction of the tribal diversity. In this paper, we performed an intensive chromosome count on material collected in the field (South and central Africa, plus Madagascar), encompassing 155 populations and c. 60 species from four genera of Exaceae, including Exacum, Ornichia, Sebaea and Tachiadenus. Fifty nine species (14 Exacum, one Ornichia, 42 Sebaea and two Tachiadenus) were examined for the first time, revealing a broad set of chromosome numbers (2n = 18, 28, 32, 36, 42, 56) and the occurrence of polyploid systems within Exacum and Sebaea. These results allow us to postulate x = 7, 8 or 9 as possible base chromosome numbers for Exaceae and emphasize the importance of both dysploidy and polyploidy processes in the evolution of the tribe. Finally, chromosome numbers appear to be associated to some morphological or geographical traits, suggesting new systematic combinations and likely active speciation patterns in the group.
  • Publication
    Accès libre
    Phylogeny and biogeography of Balsaminaceae inferred from ITS sequences
    (2004)
    Yuan, Yong-Ming
    ;
    Song. Y.
    ;
    Geuten, K.
    ;
    Rahelivololona, E.
    ;
    Wohlhauser, Sébastien
    ;
    Fischer, E.
    ;
    Smets, E.
    ;
    Küpfer, Philippe 
    Sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA were acquired for 112 species of Balsaminaceae worldwide and five species of its closest relatives Marcgraviaceae and Tetrameristaceae. Phylogenetic analyses applying parsimony and distance estimates confirmed the monophyly of Balsaminaceae and suggest the monophyly of Impatiens. Within Impatiens, a few clades are recognized with strong support. Two of the most important clades are the spurless Madagascan endemic group, and the one comprising species with broadly fusiform fruits and the basic chromosome number x = 8, that shows a Southeast Asia, southern India, Africa, and Madagascar connection. Despite recognition of several strongly supported small lineages, ITS data alone could not resolve relationships among most of the lineages with confident support values. ITS phylogenies are therefore of limited taxonomic value for Impatiens. However, ITS phylogenies do reveal that extant Impatiens species are of Southeast Asian origin, from where dispersals to boreal Eurasia and North America, to central Asia and eastern Europe via the Himalayas, and to India and Africa have occurred. The Madagascan Impatiens show an African origin. Molecular phylogenies suggest the ancestral basic chromosome number to be x = 10, and the spurred flowers and elongated linear fruits to be plesiomorphic states in Impatiens. A predominantly descending dysploid chromosome evolution, following dispersal of the clade with broadly fusiform fruits from Southeast Asia to India, Africa, and Madagascar, is also suggested.Sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA were acquired for 112 species of Balsaminaceae worldwide and five species of its closest relatives Marcgraviaceae and Tetrameristaceae. Phylogenetic analyses applying parsimony and distance estimates confirmed the monophyly of Balsaminaceae and suggest the monophyly of Impatiens. Within Impatiens, a few clades are recognized with strong support. Two of the most important clades are the spurless Madagascan endemic group, and the one comprising species with broadly fusiform fruits and the basic chromosome number x = 8, that shows a Southeast Asia, southern India, Africa, and Madagascar connection. Despite recognition of several strongly supported small lineages, ITS data alone could not resolve relationships among most of the lineages with confident support values. ITS phylogenies are therefore of limited taxonomic value for Impatiens. However, ITS phylogenies do reveal that extant Impatiens species are of Southeast Asian origin, from where dispersals to boreal Eurasia and North America, to central Asia and eastern Europe via the Himalayas, and to India and Africa have occurred. The Madagascan Impatiens show an African origin. Molecular phylogenies suggest the ancestral basic chromosome number to be x = 10, and the spurred flowers and elongated linear fruits to be plesiomorphic states in Impatiens. A predominantly descending dysploid chromosome evolution, following dispersal of the clade with broadly fusiform fruits from Southeast Asia to India, Africa, and Madagascar, is also suggested.
  • Publication
    Accès libre
    High paraphyly of Swertia L. (Gentianaceae) in the Gentianella -lineage as revealed by nuclear and chloroplast DNA sequence variation
    (2001)
    Chassot, P.
    ;
    Nemomissa, S.
    ;
    Yuan, Yong-Ming
    ;
    Küpfer, Philippe 
    The genus Swertia L., as currently defined, is polymorphic and mainly distributed in temperate regions of the northern hemisphere. Phylogenetic relationships between Swertia and the other genera of the Swertiinae sensu Struwe et al. (unpubl. data) are discussed based on cladistic analyses of DNA sequence data. The sequences used for this purpose include the trnL (UAA) intron, the intergenic spacers (IGS) between trnL (UAA) and trnF (GAA) exons, and between trnS (UGA) and ycf 9 exons of cpDNA, as well as the ITS region of nrDNA. Although moderately resolved, the phylogenies resulting from the separate analyses of nuclear and chloroplast data are congruent, and the incongruence length difference test (Farris et al. 1995) detected no character incongruence. The phylogeny suggested by the analysis of combined data sets defines Swertia as strongly paraphyletic in relation to the other genera. This taxon may have acted as a stem group, giving rise to diverse lineages, some of which are morphologically distinct and have been recognised at the generic level. Latouchea and Obolaria are closely related and occupy the basalmost position in the molecular tree. Swertia species are distributed in 9 different clades, three of which share a basal polytomy with Bartonia, Frasera, Gentianopsis, Halenia, Megacodon, Pterygocalyx and Veratrilla. Two lineages have an intermediate position. The remaining 4 clades occupy a more derived position. Two of the latter clades show a close relation with species of Gentianella s. str., and one is included in a large clade comprising Comastoma, Jaeschkea and Lomatogonium. Selected character states and their proposed polarity, such as number and structure of nectaries, stylar and seedcoat characteristics, pollen morphology, fusion of floral parts and chromosome number are discussed in the context of molecular data. Rugose, spinose, or winged seeds are found mainly in basal lineages, while smooth ones are typical for derived species. Chromosome numbers follow a similar pattern with x=13 restricted to basal lineages, while in more derived clades, x is always smaller than 13. With respect to the molecular phylogeny, taxonomic circumscriptions in the Swertiinae sensu Struwe et al. (unpubl. data) does not seem to reflect phyletic relationships.
  • Publication
    Accès libre
    Genetic structure and evolution of Alpine polyploid complexes: Ranunculus kuepferi (Ranunculaceae) as a case study
    (2009)
    Burnier, Julien
    ;
    Buerki, Sven
    ;
    Arrigo, Nils
    ;
    Küpfer, Philippe 
    ;
    Alvarez, Nadir
    The alpine white-flowered buttercup, Ranunculus kuepferi Greuter & Burdet, is a polyploid complex with diploids endemic to the southwestern Alps and polyploids – which have been previously described as apomictic – widespread throughout European mountains. Due to the polymorphic status of both its ploidy level and its reproductive mode, R. kuepferi represents a key species for understanding the evolution of polyploid lineages in alpine habitats. To disentangle the phylogeography of this polyploid taxon, we used cpDNA sequences and AFLP (amplified fragment length polymorphism) markers in 33 populations of R. kuepferi representative of its ploidy level and distribution area. Polyploid individuals were shown to be the result of at least two polyploidization events that may have taken place in the southwestern Alps. From this region, one single main migration of tetraploids colonized the entire Alpine range, the Apennines and Corsica. Genetic recombination among tetraploids was also observed, revealing the facultative nature of the apomictic reproductive mode in R. kuepferi polyploids. Our study shows the contrasting role played by diploid lineages mostly restricted to persistent refugia and by tetraploids, whose dispersal abilities have permitted their range extension all over the previously glaciated Alpine area and throughout neighbouring mountain massifs.
  • Publication
    Accès libre
    History or ecology? Substrate type as a major driver of patial genetic structure in Alpine plants
    (2009)
    Alvarez, Nadir
    ;
    Thiel-Egenter, Conny
    ;
    Tribsch, Andreas
    ;
    Holderegger, Rolf
    ;
    Manel, Stéphanie
    ;
    Schönswetter, Peter
    ;
    Taberlet, Pierre
    ;
    Brodbeck, Sabine
    ;
    Gaudeul, Myriam
    ;
    Gielly, Ludovic
    ;
    Küpfer, Philippe 
    ;
    Mansion, Guilhem
    ;
    Negrini, Riccardo
    ;
    Paun, Ovidiu
    ;
    Pellecchia, Marco
    ;
    Rioux, Delphine
    ;
    Schüpfer, Fanny
    ;
    Van Loo, Marcela
    ;
    Winkler, Manuela
    ;
    Gugerli, Felix
    ;
    IntraBioDiv Consortium
    Climatic history and ecology are considered the most important factors moulding the spatial pattern of genetic diversity. With the advent of molecular markers, species' historical fates have been widely explored. However, it has remained speculative what role ecological factors have played in shaping spatial genetic structures within species. With an unprecedented, dense large-scale sampling and genome-screening, we tested how ecological factors have influenced the spatial genetic structures in Alpine plants. Here, we show that species growing on similar substrate types, largely determined by the nature of bedrock, displayed highly congruent spatial genetic structures. As the heterogeneous and disjunctive distribution of bedrock types in the Alps, decisive for refugial survival during the ice ages, is temporally stable, concerted post-glacial migration routes emerged. Our multispecies study demonstrates the relevance of particular ecological factors in shaping genetic patterns, which should be considered when modelling species projective distributions under climate change scenarios.