Mesoamerica is considered a biodiversity hot spot with levels of endemism and species diversity likely underestimated. For mammals, the patterns of diversification of Mesoamerican taxa still are controversial. Reasons for this include the region's complex geologic history, and the relatively recent timing of such geological events. Previous studies, however, support the view that substantial migration between North (NA) and South America (SA) occurred prior or/and during the Great American Biotic Interchange (GABI) ~3.5 Ma. This was followed by repeated periods of isolation during Pleistocene climatic oscillations, which produced most of the diversification in the region. From a North American origin, the subfamily Sigmodontinae migrated to SA, where most of its present day diversity exists. The taxonomic history of this subfamily, and of Oryzomynii, its largest tribe, has been exceptionally complex. Recently, extensive studies have helped to clarify genealogical relationships among major clades, but have left the evolutionary histories of several groups unresolved. Such is the case for the genus Handleyomys that includes nine species; seven of which are endemic to Mesoamerica; and of its phylogenetic position among closely related genera Euryoryzomys, Hylaeamys, Oecomys, Nephelomys and Transandinomys. The results supported the monophyly of Handleyomys, and four clades with inter-generic levels of divergence within the genus, three of these clades restricted to Mesoamerica (the alfaroi, chapmani and melanotis species groups). Furthermore, the estimated time for the split of the Mesoamerican Handleyomys is on average, 2.0 Myr older than the proposed migrations to NA during the GABI. In addition, the position of Handleyomys as the sister clade to Euryoryzomys, Hylaeamys, Oecomys, Nephelomys and Transandinomys was well supported, as it was a biogeographic hypotheses that depicted a polyphyletic origin for these genera and Handleyomys 5.5-6.0 Ma. The integrative approach implemented in this dissertation allowed the development of more biologically realistic hypothesis than has previously been conducted in Mesoamerica, where half of the endemic mammals are listed under the IUCN Red list; and where mammals with small ranges, which are the most vulnerable to extinction, are found largely outside reserves. The continued decline of the ecosystems health in this region calls for a more precise account of its biodiversity for its proper conservation; and for rigorous biogeographic studies for its management, since the region also serves as a biological corridor for intercontinental connectivity.

Verrucariaceae are a family including mostly lichenized species (Verrucariales, Ascomycota). Its current generic classification, which mainly relies on three morphological characters (spore septation, thallus structure, and hymenial algae), has never been subjected to molecular data. Because these characters were suspected to be homoplastic, the monophyly of the genera as currently delimited based on morphology need to be assessed. A three-gene phylogenetic analysis was carried out using three methods (Maximum Parsimony, Maximum Likelihood, and a Bayesian approach) on 83 taxa, selected from 15 genera in Verrucariaceae. Ancestral state reconstructions were undertaken for four characters (spore septation, thallus structure, hymenial algae, and upper cortex structure). The results confirmed that most of the genera were not monophyletic, and that the most recent common ancestor of Verrucariaceae was most likely crustose, lacking hymenial algae, and with simple spores and a pseudocortex. The use of symplesiomorphic traits to define Verrucaria, the largest and type genus for the Verrucariaceae, as well as the non monophyly of the genera Polyblastia, Staurothele and Thelidium, explain most of the discrepancies between the current classification and a classification using monophyly as a grouping criterion. In order to accommodate newly inferred monophyletic groups, existing genera were re-delimited and three new genera were proposed. Recent broad-scale phylogenetic analyses have shown that Verrucariales was sister to Chaetothyriales, an order first known as including mostly saprophytes and opportunistic animal and human parasites. Investigations of fungal communities colonizing rocks in extreme environments have shown that some slow-growing melanized fungi inhabiting bare rock surfaces belonged to the Chaetothyriales. Multigene phylogenetic analyses were carried out using Maximum Likelihood and a Bayesian approach in order to confirm the affiliation of 25 of these rock isolates. Ancestral state reconstructions were then undertaken on two different datasets to look at the evolutionary history of lichenization within Pezizomycotina, and the rock-inhabiting habit within Eurotiomycetes. Results suggest that the ancestor of the lineage including Verrucariales and Chaetothyriales was likely to be an extremotolerant non-lichenized, rock-inhabiting fungus. Virulence factors of opportunistic parasites within Chaetothyriales, such as melanization and meristematic growth, might have primary been adaptations for life in extreme habitats. / Dissertation

This study was aimed at discovering the taxonomical identity of freshwater populations of a prevailably marine green-algal genus Ulva in the Czech Republic. Furtherly, collected samples were compared to available relevant material from European herbaria. The identity of collected specimens was successfully resolved by a combined methodology that involved classical and modern molecular techniques, and discussed in the framework of distribution and ecology of close European taxa.

Les interactions avec les pollinisateurs font partie de la niche écologique des orchidées et ont joué un rôle dans leur diversification taxonomique et florale. Au cours de cette thèse, j’ai d’abord analysé l’architecture du réseau orchidées-pollinisateurs en région Euro-Méditerranéenne et montré que la similarité de niches de pollinisation entre orchidées était fonction de leur distribution spatio-temporelle, suggérant un certain opportunisme dans les interactions orchidées-pollinisateurs. Je me suis ensuite intéressée au rôle des pollinisateurs dans l'évolution des traits floraux dans deux groupes d’orchidées. J’ai d’abord montré une différentiation dans les traits floraux des trois taxa du groupe Anacamptis coriophora, probablement causée et maintenue par un processus de sélection divergente. En cartographiant les interactions avec les pollinisateurs et les odeurs florales sur la phylogénie de la section Pseudophrys, j’ai ensuite montré que l'évolution de l'odeur florale était conditionnée par une sélection exercée par les pollinisateurs et par des contraintes phylogénétiques. Enfin, j’ai mis au point une démarche de taxonomie intégrative basée sur des données moléculaires, morphométriques et chimiques dans le genre Ophrys. Avec cette démarche, j’ai confirmé le rang taxonomique des trois espèces du groupe O. insectifera et proposé de fusionner deux paires d’espèces parmi les Pseudophrys. Une meilleure compréhension des facteurs qui façonnent la niche de pollinisation et du rôle des pollinisateurs dans l'évolution des traits floraux et la spéciation chez les orchidées Euro-Méditerranéennes devrait nous permettre d’améliorer la conservation de ces espèces emblématiques. / Interactions with pollinators are part of orchids’ ecological niches and have played a role in their taxonomic and floral diversification. During this thesis, I have analysed the architecture of the orchid-pollinator network in the Euro-Mediterranean region and shown that similarity in pollination niches between orchids primarily depends on their spatio-temporal distribution, suggesting that orchid-pollinator interactions are more opportunistic than previously thought. Then, I have been interested in the role of pollinators in floral trait evolution in two orchid groups. I have shown a differentiation in floral traits of the three taxa of the Anacamptis coriophora group, probably caused and maintained by a process of divergent selection. Then, by mapping interactions with pollinators and floral odours on the phylogeny of the section Pseudophrys, I have shown that floral odour evolution is conditioned by pollinator-mediated selection and by phylogenetic constraints. Finally, I have developed an integrative taxonomic approach based on molecular, morphometric and chemical data in the genus Ophrys. With this approach, I have confirmed the taxonomic rank of the three species of the O. insectifera group and proposed to merge two species pairs among Pseudophrys. A better understanding of the factors that have shaped pollination niches and of the role of pollinators in floral trait evolution and speciation in Euro-Mediterranean orchids should allow us to improve the conservation of these emblematic species.

The Middle East is occupied by three species of family Emballonuridae which are morfologically divided into several subspecies. Those could be defined only poorly and intraspecific diversity of these species is resolved unsatisfactorily. This is the reason why the molecular genetic analysis, which can revise the diversity on the new unused level, were used in this thesis. Based on data from sequencing of both mitochondrial and nuclear markers the phylogenetic analysis was performed. That analysis adds new information about interspecific and intraspecific relationships among populations of this family in this area. Bats (Chiroptera) of the family Emballonuridae are characterised by tail perforating the uropatagial membrane on its dorsal side in the half of its lenght and by reduction of the phalangi which makes long and narrow wing. The family is widespread circumtropically and is divided into two subfamilies. The subfamily Emballonurinae could be sometimes diveded into two tribes, new-world Diclidurini and old-world Emballonurini. The representatives of the subfamily Taphozoinae occur only in the Old World. Middle East is occupied by three species of this family. Coleura afra inhabits only southern Arabic peninsula and the populations from this area are ranked in subspecies C. a. gallarum....

Cette thèse traite de l’évolution, de l’adaptation et de la spéciation en milieu souterrain, en utilisant le genre Anthroherpon comme modèle. Ce genre appartient à la tribu des Leptodirini (Leiodidae Cholevinae), un groupe qui a connu une remarquable diversification dans le domaine souterrain. Toutes ses espèces ont développé des modifications troglomorphiques spectaculaires: anophthamie, aptérisme, élongation extrême des appendices, de la tête et du pronotum, et physogastrie. Pour comprendre l’histoire évolutive du groupe, ces adaptations troglomorphiques ont été replacées dans un cadre phylogénétique. La thèse est une analyse de la radiation évolutive des Anthroherpon, dans le cadre d’une phylogénie moléculaire datée, qui a permis de mieux comprendre les modalités de diversification du genre, de reconstruire son aire de distribution ancestrale, d’explorer la diversité des évolutions troglomorphiques en son sein et de proposer une nouvelle structure taxonomique du groupe. / The PhD research project focus on the study of evolution, adaptation, and speciation in the subterranean environment using troglobitic Coleoptera of the genus Anthroherpon as a model. Genus Anthroherpon belongs to the tribe Leptodirini (Coleoptera: Leiodidae: Cholevinae), a group that has undergone extensive diversification in the subterranean environment. All species of this genus have developed typical troglomorphic modifications: complete anophthalmy, apterism, extreme elongation of appendages, head, and pronotum, and physogastric elytra. To understand the evolutionary history of this group, the troglomorphic adaptations need to be studied in a phylogenetic framework. The thesis provide a comprehensive evolutionary analysis of the Anthroherpon radiation, using a dated molecular phylogeny as framework for understanding Anthroherpon diversification, reconstructing the ancestral range, and exploring troglomorphic diversity. In light of these findings, a new taxonomical organisation of the group has been proposed.

<p>The PhD research project focus on the study of evolution, adaptation, and speciation in<br />the subterranean environment using troglobitic Coleoptera of the genus Anthroherpon<br />as a model organism. Genus Anthroherpon belongs to the tribe Leptodirini (Coleoptera:<br />Leiodidae: Cholevinae), a group that has undergone extensive diversification in the<br />subterranean environment. All species of this genus have developed typical<br />troglomorphic modifications: complete anophthalmy, apterism, extreme elongation of<br />appendages, head, and pronotum, and physogastric elytra. To understand the<br />evolutionary history of this group, the troglomorphic adaptations need to be studied in<br />a phylogenetic framework. The thesis provide a comprehensive evolutionary analysis<br />of the Anthroherpon radiation, using a dated molecular phylogeny as a framework for<br />understanding Anthroherpon diversification, reconstructing the ancestral range, and<br />exploring troglomorphic diversity. In light of these findings, a new taxonomical<br />organisation of the group has been proposed.</p> / <p>Doktorska disertacija predstavlja studiju evolucije, adaptacije i specijacije u<br />podzemnim stani&scaron;tima troglobiontnih tvrdokrilaca roda <em>Anthroherpon</em>. Pomenuti rod<br />pripada tribusu Leptodirini (Leiodidae, Cholevinae), grupi koja je pro&scaron;la intenzivnu<br />diverzifikaciju u uslovima podzemnih stani&scaron;ta. Sve vrste pomenutog roda poseduju<br />tipične troglomorfne osobine, kao &scaron;to su: anoftalmija, apterizam, ekstremno izduženi<br />telesni nastavci, glava i pronotum, i fizogastrija. Radi razumevanja evolucione istorije<br />grupe, troglomorfne adaptacije su studirane u filogenetskom kontekstu. U analizi<br />evolutivne radijacije roda <em>Anthroherpon</em> kori&scaron;ćena je datirana molekularna filogenija<br />kao okvir za razumevanje diverzifikacije roda, evolucije troglomorfnih karaktera i<br />rekonstrukciju predačkog areala. U svetlu novih nalaza predložena je nova<br />taksonomska organizacija grupe.</p>

No description available.

Recognizing the mechanisms of speciation and the limits of species is essential to understand the origin of biodiversity and how to conserve it. The general aims of my investigations during my doctoral studies were two-fold: to study evolutionary patterns and processes, and to provide specific and superspecific taxonomic classifications that try to reflect evolutionary history. I have focused my research on anurans in their biodiversity hotspot, the American Tropics. I have used morphological, behavioral (mating calls), and genetic (DNA sequences) characters to study species boundaries between frogs of the genus Pristimantis and the family Centrolenidae (glassfrogs). The results show that the exclusive use of single lines of evidence or the application of arbitrary thresholds impair and bias our ability to recognize new species and limit the possibility to understand evolutionary processes. Only an integrative approach combining every source of evidence provides the necessary feedback to discover all species and test their identity by comparing independent sets of data. This approach further allows identifying those species that probably represent stable comparative units (well supported species hypotheses) and to flag taxa that require further assessment. Phylogenetic reconstructions based on seven nuclear and mitochondrial genes for about 100 species of glassfrogs revealed that previous hypotheses of relationships were mislead by rampant convergent evolution at the phenotypic level. None of the previously suggested classifications fit with the reconstructed evolutionary history. Consequently, we proposed a new classification consistent with this phylogeny. I also studied the tempo and mode of diversification among glassfrogs. Based on sequences from ten genes in 87 species, I estimated species divergence times, age-range correlation between sister species, and reconstructed ancestral areas and dispersal/vicariance events. The results revealed a complex model of diversification where geographical isolation seems to be the dominant scenario for speciation and only clades of altitudinal generalists have been able to spread across the Neotropical rainforests.

L'acquisition des données moléculaires a été bouleversée par le développement des techniques de séquençage haut-débit. Celles-ci ont augmenté la quantité des données et ont fait diminuer le coût de manière considérable. Ces nouvelles approches ont également redonné accès à des sources de matériel biologique qui étaient auparavant inutilisables en raison de la faible quantité et la forte dégradation de l'ADN qu'elles fournissent, notamment des tissus anciens, des échantillons de musée voire du matériel fossile. Un avantage supplémentaire c'est la possibilité de multiplexer les échantillons, c'est-à-dire, les mélanger et les séquencer simultanément grâce à l'utilisation de « tags » ou étiquettes permettant de les séparer après avec des outils bioinformatiques. Un marqueur qui a grandement bénéficié de ces technologies est le génome mitochondrial. En effet, nous montrons que grâce au ratio élevé entre l'ADN mitochondrial et l'ADN nucléaire par cellule, il est possible l'obtention de mitogénomes entiers, avec de couvertures adéquates, sans qu'un enrichissement préalable de l'échantillon soit nécessaire. Ceci permet d'envisager la réalisation de projets de mitogénomique comparative pour de groupes riches en espèces, requérant un échantillonnage taxonomique exhaustif et dont les divergences génétiques rendrait difficile l'usage du séquençage classique. C'est dans ce contexte que cette thèse aborde la systématique, la phylogénie et l'évolution moléculaires d'une famille de chauves-souris néotropicales : les Phyllostomidae. Cette famille est riche en espèces, avec plus de 160 taxons mais aussi en traits d'histoire de vie contrastés notamment le régime alimentaire. Cette diversité résulte en des morphologies convergentes dont les caractères sont en conséquence peu appropriés pour reconstruire l'histoire évolutive de ce groupe. La mitogénomique a prouvé être un outil efficace dans ce dessein, mais à présent aucune étude de ce type a été conduite pour cette famille. Nous avons d'abord réussi à séquencer les mitogénomes de représentants de toutes les lignées majeures couvrant également la diversité de traits d'histoire de vie. Nous montrons ensuite que l'utilisation de ces mitogénomes permet de résoudre les relations de parenté au niveau intrafamilial avec une résolution similaire à celle d'une concaténation de marqueurs mitochondriaux et nucléaires avec un soutien statistique robuste pour la plupart des nœuds de la phylogénie. Ceci nous a permis de clarifier plusieurs relations qui restaient controversées dans des études précédentes et confirmer plusieurs des clades proposés par celles-ci. Ensuite, nous abordons l'évolution du mitogénome en relation avec les traits d'histoire de vie en utilisant comme exemple le clade des vampires, les seules Mammifères hématophages, dont le génome mitochondrial semble avoir été touché par une accélération du taux d'évolution comme conséquence de l'action combinée de forces neutres et sélectives pour répondre aux contraintes imposées par ce régime alimentaire. Finalement, le cadre phylogénétique robuste proportionné par les 100 mitogénomes que nous avons séquencés pourra être utilisé comme référence pour étudier la diversification des Phyllostomidae. / New sequencing technologies have revolutionized the acquisition of molecular data by increasing the amount of sequences at a considerably lower cost. These new technologies have also given access to samples previously neglected because they resulted in low-quantity and degraded DNA yields, as for example, old tissues, museum specimens and even fossil rests. An additional advantage comes from the possibility of multiplexing; this is, mixing several taxa in a single sample thanks to the use of tags or labels allowing late separating the sequences using bioinformatic tools. A molecular marker that has greatly benefited from these technologies is the mitochondrial genome. Indeed, we show that, thanks to the high per-cell ratio of mitochondrial to nuclear DNA, it's possible to obtain whole well-covered mitochondrial genomes without previous sample enrichment. This allows the accomplishment of projects of comparative mitogenomics for species-rich groups needing exhaustive taxon sampling and for which strong genetic divergences would difficult the use of classical sequencing.It is in this context that this thesis tackles the molecular systematics, phylogenetics and evolution of a Neotropical family of bats: the Phyllostomidae. This species-rich family, accounting for more than 160 species, is also the family of Mammals with the highest diversity of life history traits, for example, feeding on almost every possible source of food. This diversity results in convergent morphologies that make this kind of characters inadequate for reconstructing the evolutionary history of this group. Mitogenomics has proven useful in similar cases but no study of this kind has been conducted for this family. We got to sequence whole mitogenomes for representatives of all major lineages and covering the diversity of life history traits. We then show that using these mitogenomes allows solving intrafamilial relationships with a resolution similar to that resulting from a concatenation of mitochondrial and nuclear markers and with solid statistical support for most of the nodes of the phylogeny. This allowed clarifying several controversial relationships and confirming several clades proposed in previous studies. Next, we illustrate the evolution of mitogenomes and the influence of life history traits using the clade of vampire bats, the only hematophagous Mammals, whose mitogenome seem to have undergone an acceleration of evolutionary rate as a consequence of the combined action of neutral and selective forces in order to counter the constraints imposed by this feeding habit. Finally, the robust phylogenetic frame provided by the 100 mitogenomes that we sequenced, will be used for future studies about, for exemple, the diversification process of Phyllostomids.