L'acarien rouge de la tomate Tetranychus evansi (Tetranychidae) est considéré comme une espèce invasive à fort impact économique sur les cultures de solanacées. Il a été découvert pour la première fois en 1954 au Brésil, d'où il est probablement originaire. Historiquement, T. evansi a d'abord été signalé en Afrique et plus récemment en Europe et en Asie. L'objectif de cette thèse était de reconstruire les routes de colonisation de T. evansi et de dégager le scénario évolutif décrivant le mieux l'histoire de l'invasion. Nous avons d'abord analysé des échantillons collectés dans son aire actuelle de distribution, à l'aide des séquences d'un fragment du gène codant pour la sous-unité I de la Cytochrome Oxydase (COI) de l'ADN mitochondrial et de la région ITS1-5,8S-ITS2 de l'ADN nucléaire ribosomique. Les données soutiennent l'hypothèse d'une origine sud américaine de cette espèce et ont révélé que des événements d'invasions multiples et cryptiques ont eu lieu lors de la colonisation de l'Europe. L'invasion résulte de deux lignées génétiquement divergentes et originaires de deux régions géographiques distantes au Brésil. Ces deux lignées semblent avoir des potentiels invasifs contrastés. Elles s'hybrident au laboratoire ainsi que dans la nature. Grâce à 16 locus microsatellites que nous avons développés et utilisés comme marqueurs, nous avons déterminé les zones géographiques de cette hybridation. Nous avons également pu estimer des paramètres historiques de l'invasion et confronter différents scénarios d'introduction, par la comparaison de la composition génétique des populations récemment introduites avec celles de l'aire d'origine de T evansi, et par l'utilisation de la méthode d'inférence bayésienne (Approximate Bayesian Computation, ABC). Les résultats ABC contredisent partiellement le scénario d'invasion basé uniquement sur des données historiques. Ils suggèrent que T. evansi serait d'abord arrivé en Europe dans le sud de l'Espagne (en Andalousie) bien avant les signalements historiques. Ainsi, l'Andalousie semble avoir servi de source de colonisation pour des nouvelles zones en Afrique, d'autres régions méditerranéennes et d'Asie. Les résultats de cette thèse ouvrent des perspectives d'étude visant à comprendre pourquoi certaines populations d'une espèce allochtone réussissent à s'établir et à envahir un nouvel écosystème / The red tomato spider mite Tetranychus evansi (Tetranychidae) is regarded as an invasive species having an important economic impact on solanaceous crops. It was first discovered in Brazil in 1954, where it probably originated. Based on historical records, T. evansi was first reported in Africa and more recently in Europe and Asia. This work aims at reconstructing the colonization routes of T. evansi and identifies the scenario that best describes the evolutionary history of the invasion. To do this, we first analyzed samples collected from most parts of the world where the mite is currently known to occur. We used sequence variation of a fragment of the mitochondrial Cytochrome Oxidase I (COI) sub-unit I gene and the ITS1-5.8S-ITS2 of the nuclear ribosomal DNA. Our results were consistent with the hypothesis of a South American origin of this species. They also suggested that the invasion of south Europe resulted from multiple cryptic introductions from two genetically divergent lineages originated from two distant geographical regions in Brazil. These two lineages seem to have a differential invasive potential. Despite the high genetic divergence, crosses between mites stemming from the two lineages do occur both in the laboratory and in nature. Second, we used 16 microsatellite loci that we developed for this study and in association with Approximate Bayesian Computation (ABC) methods; we reconstructed the historical events of the cryptic invasion of the pest. ABC results challenge the invasion scenario captured by historical data only. They suggest that T. evansi first arrived to Europe in Southern Spain (Andalusia) long before historic records. Thus, Andalusia seems to have served as a source for colonization of new areas in Africa and other Mediterranean regions. The results obtained in this thesis provide an interesting framework to further study and understand why some populations of an exotic species might become invasive.

In this collection of papers I have summarized my investigations into the field of evolutionary genetics and more specifically into patterns of biodiversity and evolutionary processes. The lizards (and frogs) studied here share common features in that they are largely present in unique environments, which are also regions that are biologically understudied. Most of these taxa show high degrees of endemism, interesting natural history characteristics, and each group manifests distinctive adaptations of general evolutionary interest. My work in the genus Telmatobius has been a progressive approach that began in my MS program, and it first focused on alpha taxonomy, morphological variation, and species boundaries. This work led to new studies initiated and completed at BYU involving further taxonomic revision (Formas et al., 2003; Chapter 1), and then revisiting and re-evaluating species boundaries established earlier (with allozyme markers) and this time with population level molecular (mitochondrial DNA) markers (Chapter 2). Our results indicate that the striking differences in size, coloration and general appearance in the various Lake Titicaca morphotypes are not genetically based. Further, there is evidence that these morphotypes have evolved very rapidly after demographic bottlenecks eroded present genetic variability. Telmatobius frogs of Lake Titicaca are listed by the International (IUCN) as critically endangered. We support this classification and further suggest studies to explore open questions like the possibility of adaptation along ecological resource gradients. Lizards of the genus Microlophus are interesting but for different reasons, and studies of this group constitutes the bulk of my dissertation work. The genus includes both Galapagos insular species, and continental taxa distributed in a linear gradient along > 4000 km of the western coast of South America. In studying Microlophus I first tackled the unresolved phylogenetic relationships within the genus (Chapter 3) and then pay attention to phylogeographic aspects of the most speciose lizard radiation in the Galapagos Archipelago (Chapter 4). Chapter 3 is a single manuscript provisionally accepted in the journal Systematic Biology. This paper introduces the lizard genus Microlophus (“lava lizards”) as a study system, and includes a large nuclear data set accompanied by an equally large mitochondrial data set (7877 characters in total). This paper explicitly differentiates among sequence alignments of gene regions that vary in tempo and class of mutational events. We show that this recognition is important and we suggest ways to appropriately deal with the alignment of multi-locus non-coding DNA data sets. A secondary finding in this study is that mtDNA and nDNA topologies are discordant with each other but that both are strongly supported, and that the nuclear topology is concordant with species distribution patterns along coastal South America. We hypothesize that in this particular region of the tree, the nuclear genome recovers a topology that is closer to the species tree, and conflicts occur due to likely secondary contact of distantly related taxa, suggesting that unique taxonomic relationships in the mtDNA gene tree are the result of hybridization. This last point highlights the value of dense taxonomic and character sampling for teasing apart different aspects of evolutionary processes. Chapter 4 is a manuscript to be submitted to the journal Evolution; in this study we further investigate the most speciose radiation of Microlophus in the Galapagos, based on an unparalleled sampling of most islands and small islets in the Archipelago. We use mtDNA sequences to both test hypothesized between-island colonization routes, as well as the expectation that within-island phylogeographic structure should be greater on older islands. Our mtDNA gene tree is strongly supported and allows rejection of previous alternatives, and we propose a novel sequence of between-island colonization events. Our results also reject the idea of phylogeographic structure been related solely to island age. Instead, we provide evidence to suggest that active volcanism as a major player in the generation of genetic diversity in within-island environments, and this is further compounded by the seemingly stochastic nature of within-island long-distance colonization routes mediated by ocean currents. We suggest that the direction and intensity of these currents, as currently understood, are insufficient to generate a priori hypotheses of oceanic colonization routes and their influence on gene flow. We do show that the standard stepping-stone model of migration, where genetic interchange is only possible among neighboring localities, does not explain much of the within-island population genetic structure unraveled by this study. From a biological conservation perspective the study of patterns of recent evolutionary history in the Galapagos provides with a window to evolutionary processes that have shaped and continue to impact the generation of biodiversity in the Galapagos Archipelago. Islands have long been viewed as natural laboratories of evolutionary change, and thus all island isolates are or could be distinctly important components of the larger, archipelago-wide processes. We provide working hypotheses for some of the demographic processes that might be generating within- and between-island biodiversity in this clade of lizards; confirmation of these explanations with independent data will have management implications for conserving the unique patterns observed in the Galapagos biota, but also the processes that generated these patterns.