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, Möller, Michael, Klackenberg, Jens, Callmander, Martin W., 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 Exacum 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 Exacum, 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.
Chromosome and breeding system evolution of the genus Mercurialis (Euphorbiaceae): implications of ITS molecular phylogeny
2002, Krähenbühl, M., Yuan, Y.-M., Küpfer, Philippe
The internal transcribed spacers (ITS1 and ITS2) of nuclear ribosomal DNA were amplified and sequenced from 19 samples representing all species of the genus Mercurialis and two outgroup species, Ricinus communis and Acalypha hispida. The length of ITS1 in the ingroups ranged from 223 to 246 bp and ITS2 from 210 to 218 bp. Sequence divergence between pairs of species ranged from 1.15% to 25.88% among the ingroup species in the combined data of ITS1 and ITS2. Heuristic phylogenetic analyses using Fitch parsimony on the combined data of ITS1 and ITS2 with gaps treated as missing generated 45 equally parsimonious trees. The strict consensus tree was principally concordant with morphological classification. Within the genus, the ITS sequences recognised two main infrageneric clades: the M. perennis complex including three Eurasian stoloniferous species (M.␣leiocarpa, M. ovata and M. perennis) and the western Mediterranean group including eight both annual and perennial species. Of the western Mediterranean clade, the annual and perennial species grouped respectively into two different groups, and the annual life form is revealed as a synapomorphic character derived from perennial, whereas in the Eurasian clade ITS phylogeny suggested M. leiocarpa as basal clade sister to M.␣perennis and M. ovata. ITS phylogeny failed to resolve the relationships among the different cytotypes of M. ovata and M. perennis. ITS phylogeny also suggested rapid karyotypic evolution for the genus. The karyotypic divergence among the perennial species of western Mediterranean region did not corroborate the nucleotide sequence divergence among the species. Optimisation of chromosome numbers onto the ITS phylogeny suggested x=8 to be the ancestral basic chromosome number of the genus. ITS phylogeny confirmed that the androdioecy of M. ambigua is derived from dioecy. The nucleotide heterozygosity and additivity in ITS sequences clearly confirm the interspecific hybridisation in the genus Mercurialis.
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.
Cytotaxonomic notes on the tribe Helieae (Gentianaceae)
, Trunz, Vincent, Zeltner, Louis, Küpfer, Philippe, Grant, Jason R
A survey of all known chromosome counts of gentian tribe Helieae are presented including new reports for ten species. Amongst the novelties are four genera of the Gentianaceae that are reported for the first time, Calolisianthus and Helia (both Helieae), and Schultesia and Zygostigma (both Chironieae). In the Helieae, our results reinforce the hypothesis of Weaver 1969 that two ploidy series occur in the tribe, one polyploid based on n = 20 and one dysploid based on n = 21. The basal chromosome number for the Helieae remains to be determined.
Sensitivity of plant and soil ecosystems of the Alps to climate change
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
Chromosomal evolution of Gentiana and Jaeschkea (Gentianaceae), with further documentation of chromosome data for 35 species from western China
1998, Yuan, Yong-Ming, Küpfer, Philippe, Zeltner, Louis
Chromosome numbers were recorded for 63 populations of 34 species belonging to the genus Gentiana from the high altitude regions of western China. Counts for 22 species were reported for the first time and new numbers were found for G. heleonastes (2n = 36), G. prattii (2n = 20) and G. pseudoaquatica (2n = 40). Incorporating previous data, a complete series of gametic chromosome numbers from n = 6 to 24 and 26 was established for the genus, suggesting rapid karyotypic evolution by a combination of dysploidy and polyploidy. The cytotype 2n = 20 is proposed as the ancestral type in sect. Chondrophyllae s. l. The chromosome number 2n = 16 was found for Jaeschkea microsperma for the first time which, with previous reports of 2n = 18, 20 and 22, indicates that Jaeschkea is a typically dysploid genus.
Malagasy Dracaena Vand. ex L. (Ruscaceae): an investigation of discrepancies between morphological features and spatial genetic structure at a small evolutionary scale
2009, Buerki, Sven, Callmander, Martin W., Schüpfer, Fanny, Ravokatra, Mamy, Küpfer, Philippe, Alvarez, Nadir
Malagasy Dracaena (Ruscaceae) are divided into four species and 14 varieties, all of them showing a high level of morphological diversity and a putatively artefactual circumscription. In order to reveal relationships between those entangled entities, a span of Malagasy Dracaena were sampled and analyzed using cpDNA sequences and AFLP. The cpDNA analyses resolved three biogeographic clades that are mostly inconsistent with morphology, since similar phenotypes are found across the three clades. Bayesian inference clustering analyses based on the AFLP were not in accordance with the cpDNA analysis. This result might be explained by (1) a recent origin of the Malagasy species of Dracaena with an incomplete sorting of chloroplast lineages; (2) a high amount of hybridizations; (3) a complex migration pattern. Interestingly, when the AFLP are analyzed using the parsimony criterion, a trend towards a directional evolution of inflorescence types and ecological features was observed. This might be considered either as phenotypic plasticity and/or as the result of fast evolution in flower characters according to habitat preferences. Overall, our results point to the difficulty of defining evolutionarily significant units in Malagasy Dracaena, emphasizing the complex speciation processes taking place in tropical regions.
Conflicting phylogenies of balsaminoid families and the polytomy in Ericales: combining data in a Bayesian framework
2004, Geuten, K., Smets, E., Schols, P., Yuan, Y.-M., Janssens, S., Küpfer, Philippe, Pyck, N.
The balsaminoid Ericales, namely Balsaminaceae, Marcgraviaceae, Tetrameristaceae, and Pellicieraceae have been confidently placed at the base of Ericales, but the relations among these families have been resolved differently in recent analyses. Sister to this basal group is a large polytomy comprising all other families of Ericales, which is associated with short internodes. Because there are more than 13 kb of sequences for a large sampling of representatives, a thorough examination of the available data with novel methods seemed in place. Because of its computational speed, Bayesian phylogenetics allows for the use of parameter-rich models that can accommodate differences in the evolutionary process between partitions in a simultaneous analysis. In addition, there are recently proposed Bayesian strategies of assessing incongruence between partitions. We have applied these methods to the current problems in Ericales phylogeny, taking into account reported pitfalls in Bayesian analysis such as model selection uncertainty. Based on our results we infer several, previously unresolved relationships in the order Ericales. In balsaminoid families, we find that the closest relatives of Balsaminaceae are Marcgraviaceae. In the Ericales polytomy, we find strong support for Pentaphylacaceae sensu APG II as the sister group of Maesaceae. In addition, Symplocaceae receive a position as sister to Theaceae and these families form a monophyletic group together with Styracaceae–Diapensiaceae. At the base of this clade are Actinidiaceae and Clethraceae. The positions of Ebenaceae and Lecythidaceae remain uncertain.
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.