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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
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    Alvarez, Nadir
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    Carstens, Bryan C.
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    Després, Laurence
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    Gibernau, Marc
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    Gugerli, Felix
    ;
    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
    New insights into the phylogenetics and biogeography of Arum (Araceae): unravelling its evolutionary history
    (2010)
    Espíndola, Anahí
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    Buerki, Sven
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    Bedalov, Marija
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    Alvarez, Nadir
    The heat- and odour-producing genus Arum (Araceae) has interested scientists for centuries. This long-term interest has allowed a deep knowledge of some complex processes, such as the physiology and dynamics of its characteristic lure-and-trap pollination system, to be built up. However, mainly because of its large distributional range and high degree of morphological variation, species' limits and relationships are still under discussion. Today, the genus comprises 28 species subdivided into two subgenera, two sections and six subsections. In this study, the phylogeny of the genus is inferred on the basis of four plastid regions, and the evolution of several morphological characters is investigated. Our phylogenetic hypothesis is not in agreement with the current infrageneric classification of the genus and challenges the monophyly of several species. This demonstrates the need for a new infrageneric classification based on characters reflecting the evolution of this enigmatic genus. To investigate the biogeography of Arum deeply, further spatiotemporal analyses were performed, addressing the importance of the Mediterranean basin in the diversification of Arum. Our results suggest that its centre of origin was the European–Aegean region, and that major diversification happened during the last 10 Myr.
  • Publication
    Accès libre
    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
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    Callmander, Martin W.
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    Schüpfer, Fanny
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    Ravokatra, Mamy
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    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.
  • 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
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    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
    History or ecology? Substrate type as a major driver of patial genetic structure in Alpine plants
    (2009)
    Alvarez, Nadir
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    Thiel-Egenter, Conny
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    Tribsch, Andreas
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    Holderegger, Rolf
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    Manel, Stéphanie
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    Schönswetter, Peter
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    Taberlet, Pierre
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    Brodbeck, Sabine
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    Gaudeul, Myriam
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    Gielly, Ludovic
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    Mansion, Guilhem
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    Negrini, Riccardo
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    Paun, Ovidiu
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    Pellecchia, Marco
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    Rioux, Delphine
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    Schüpfer, Fanny
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    Van Loo, Marcela
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    Winkler, Manuela
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    Gugerli, Felix
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    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.
  • Publication
    Accès libre
    Genetic structure and evolution of Alpine polyploid complexes: Ranunculus kuepferi (Ranunculaceae) as a case study
    (2009)
    Burnier, Julien
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    Buerki, Sven
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    Arrigo, Nils
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    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
    Plastid and nuclear DNA markers reveal intricate relationships at subfamilial and tribal levels in the soapberry family (Sapindaceae)
    (2009)
    Buerki, Sven
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    Forest, Félix
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    Acevedo-Rodríguez, Pedro
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    Callmander, Martin W.
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    Nylander, Johan A.A.
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    Harrington, Mark
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    Sanmartín, Isabel
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    Alvarez, Nadir
    The economically important soapberry family (Sapindaceae) comprises about 1900 species mainly found in the tropical regions of the world, with only a few genera being restricted to temperate areas. The infrafamilial classification of the Sapindaceae and its relationships to the closely related Aceraceae and Hippocastanaceae – which have now been included in an expanded definition of Sapindaceae (i.e., subfamily Hippocastanoideae) – have been debated for decades. Here we present a phylogenetic analysis of Sapindaceae based on eight DNA sequence regions from the plastid and nuclear genomes and including 85 of the 141 genera defined within the family. Our study comprises 997 new sequences of Sapindaceae from 152 specimens. Despite presenting 18.6% of missing data our complete data set produced a topology fully congruent with the one obtained from a subset without missing data, but including fewer markers. The use of additional information therefore led to a consistent result in the relative position of clades and allowed the definition of a new phylogenetic hypothesis. Our results confirm a high level of paraphyly and polyphyly at the subfamilial and tribal levels and even contest the monophyletic status of several genera. Our study confirms that the Chinese monotypic genus Xanthoceras is sister to the rest of the family, in which subfamily Hippocastanoideae is sister to a clade comprising subfamilies Dodonaeoideae and Sapindoideae. On the basis of the strong support demonstrated in Sapindoideae, Dodonaeoideae and Hippocastanoideae as well as in 14 subclades, we propose and discuss informal groupings as basis for a new classification of Sapindaceae.
  • 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) ;
    Zeltner, Louis
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    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
    Phylogeography of Pulsatilla vernalis (L.) Mill. (Ranunculaceae): chloroplast DNA reveals two evolutionary lineages across central Europe and Scandinavia
    (2008)
    Ronikier, Michał
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    Costa, Andrea
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    Fuertes Aguilar, Javier
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    Nieto Feliner, Gonzalo
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    Mirek, Zbigniew
    Aim
    The aim of this study was to test hypotheses regarding some of the main phylogeographical patterns proposed for European plants, in particular the locations of glacial refugia, the post-glacial colonization routes, and genetic affinities between southern (alpine) and northern (boreal) populations.

    Location
    The mountains of Europe (Alps, Balkans, Carpathians, Central Massif, Pyrenees, Scandinavian chain, Sudetes), and central European/southern Scandinavian lowlands.

    Methods
    As our model system we used Pulsatilla vernalis, a widely distributed European herbaceous plant occurring both in the high-mountain environments of the Alps and other European ranges and in lowlands north of these ranges up to Scandinavia. Based on a distribution-wide sampling of 61 populations, we estimated chloroplast DNA (cpDNA) variation along six regions using polymerase chain reaction–restriction fragment-length polymorphisms (PCR–RFLPs) (trnH–trnK, trnK–trnK, trnC–trnD, psbC–trnS, psaA–trnS, trnL–trnF) and further sequencing of trnL–trnF and trnH–psbA. In addition, 11 samples of other European species of Pulsatilla were sequenced to survey the genus-scale cpDNA variation.

    Results
    Eleven PCR–RFLP polymorphisms were detected in P. vernalis, revealing seven haplotypes. They formed two distinct genetic groups. Three haplotypes representing both groups dominated and were widely distributed across Europe, whereas the others were restricted to localized regions (central Alps, Tatras/Sudetes mountains) or single populations. Sequencing analysis confirmed the reliability of PCR–RFLPs and homology of haplotypes across their distribution. The chloroplast DNA variation across the section Pulsatilla was low, but P. vernalis did not share haplotypes with other species.

    Main conclusions
    The genetic distinctiveness of P. vernalis populations from the south-western Alps with respect to other Alpine populations, as well as the affinities between the former populations and those from the eastern Pyrenees, is demonstrated, thus providing support for the conclusions of previous studies. Glacial refugia in the Dolomites are also suggested. Isolation is inferred for the high-mountain populations from the Tatras and Sudetes; this is in contrast to the case for the Balkans, which harboured the common haplotype. Specific microsatellite variation indicates the occurrence of periglacial lowland refugia north of the Alps, acting as a source for the post-glacial colonization of Scandinavia. The presence of different fixed haplotypes in eastern and western Scandinavia, however, suggests independent post-glacial colonization of these two areas, with possible founder effects.