Dung beetle radiations in Madagascar

Speciation on islands is affected by island size and the range of habitats and resources available and often also by limited interactions with other taxa. An ancestral population may evolve into a large number of species via an adaptive radiation. In Madagascar, most groups of animals and plants have radiated on the island, having arrived via oceanic dispersal during the long isolation of Madagascar. Characteristic features of Malagasy biota are exceptionally high level of endemism, high species richness as well as lack of many higher taxa that are dominant on the African mainland. Malagasy dung beetles are dominated by two tribes, Canthonini and Helictopleurina, with more than 250 endemic species. In this thesis I have reconstructed molecular phylogenies for the two tribes using several gene regions and different phylogenetic methods. Evolution of closely related species and among populations of the same species was examined with haplotype networks. The Malagasy Canthonini consists of three large lineages, while Helictopleurina forms a monophyletic group. The ancestors of each of the four clades colonised Madagascar at different times during Cenozoic. The subsequent radiations differ in terms of the number of extant species (from 37 to more than 100) and the level of ecological differentiation. In addition, Onthophagini (6 species) and Scarabaeini (3) have colonised Madagascar several times, but they have not radiated and the few species have not entered forests where Canthonini and Helictopleurina mostly occur. Among the three Canthonini radiations, speciation appears to have been mostly allopatric in the oldest and the youngest clades, while in the Epactoides clade sister species have diverged in their ecologies but have similar geographical distributions, indicating that speciation may have occurred in regional sympatry. The most likely isolating mechanisms have been rivers and forest refugia during dry and cool geological periods. Most species are generalists feeding on both carrion and dung, and competition among ecologically similar species may prevent their coexistence in the same communities. Some species have evolved to forage in the canopy and a few species have shifted to use cattle dung, a new resource in the open habitats following the introduction of cattle 1500 years ago. The latter shift has allowed species to expand their geographical ranges.

Multiple origins of European populations of giant liver fluke Fascioloides magna (Trematoda: Fasciolidae), an invasive liver parasite of ruminants

The giant liver fluke, Fascioloides magna, liver parasite of free-living and domestic ruminants of Europe and North America, was analysed in order to determine the origin of European populations and to reveal the biogeography of this originally North American parasite on the European continent. The previously selected variable fragments of the mitochondrial cytochrome c oxidase subunit I (cox1; 384 bp) and nicotinamid dehydrogenase subunit I (nad1; 405 bp) were applied as a tool. The phylogenetic trees and haplotype networks were constructed and the level of genetic structuring was evaluated using population genetic tools. In F. magna individuals originating from all European natural foci (Italy, Czech Republic, Danube floodplain forests) and from four of five major North American enzootic areas, 16 cox1 and 18 nad1 haplotypes were determined. The concatenated sequence set produced 22 distinct haplotypes. The European fluke populations were less diverse than those from North America in that they contained proportionately fewer haplotypes (8), while more substantial level of genetic diversity and higher number of haplotypes (15) were recorded in North America. Only one haplotype was shared between the European (Italy) and North American (USA/Oregon and Canada/Alberta) flukes supporting a western North American origin of the Italian F. magna population. Haplotypes found in Italy were distinct from those determined in the remaining European localities what indicates that introduction of F. magna onto the European continent is a result of more than one event. In Czech focus, a south-eastern US origin of giant liver fluke was revealed. Identical haplotypes, common for parasites from Czech Republic and from expanding focus of Danube floodplain forests, implies introduction of F. magna to the Danube region from an already established Czech focus.

Phylogéographie comparée de la souris à pattes blanches et de la souris sylvestre, deux vecteurs de la maladie de Lyme au Québec

Mon étude vise à évaluer la propagation d’une zoonose en émergence au Québec, la maladie de Lyme, en conséquence du réchauffement climatique. Le pathogène responsable de cette infection, Borrelia burgdorferi, est transmis par l’intermédiaire d’une tique parasite, Ixodes scapularis, de plus en plus commune au Québec en raison de l’augmentation de la température moyenne du climat depuis les dernières décennies. Puisque la tique a une capacité de déplacement très restreinte, on s'attend à ce que sa dispersion soit liée à celle de son hôte primaire, soit la souris à pattes blanches (Peromyscus leucopus). Je décrirai donc d’abord les espèces impliquées, leur écologie et leur rôle dans ce système à trois niveaux (hôte/pathogène/vecteur). Puis, à l’aide de séquences d’ADN mitochondrial, je comparerai la phylogéographie des deux principales espèces de souris au Québec, la souris à pattes blanches et la souris sylvestre (P. maniculatus). Des analyses d’arbres et de réseaux d’haplotypes ont révélé des différences significatives dans la structure génétique et ainsi montré que les populations de P. leucopus seraient en expansion dans le sud du Québec. Cette étude nous a finalement permis d’émettre des hypothèses sur le patron d’établissement de la maladie de Lyme au Québec.

Filogeografia de Thoropa grupo miliaris (Anura: Cycloramphidae)

Pós-graduação em Biologia Animal - IBILCE

Filogeografia de três espécies de Passeiriformes (Suboscines) na região do Baixo Tocantins - Ilha do Marajó - Pará

A região do Baixo Tocantins - ilha do Marajó é excelente local para se realizar um estudo de integração de dados geológicos e biológicos visando-se a compreensão dos processos de diversificação de espécies. Foram estimados parâmetros de genética populacional e realizadas análises filo genéticas das populações amostradas utilizando-se o gene ND2, relacionando-os com o cenário geológico proposto para a evolução da região. Foram utilizadas inferência bayesiana e máxima verossimilhança para reconstrução de filogenias intraespecíficas, redes de haplótipos e o teste de desvio de neutralidade R2, AMOVA, F _ST e Nm para as análises populacionais, para três espécies de aves Passeriformes: Xiphorhynchus spixii e Glyphorynchs spirurus (Dendrocolaptidae) e Willisornis poecilinotus (Thamnophilidae). As populações de X spixii não apresentaram estruturação geográfica, exibindo altos níveis de fluxo gênico entre elas. A árvore filogenética de G. spirurus apresentou um grupo de haplótipos únicos da ilha do Marajó (1M) e um grupo irmão contendo haplótipos pertencentes às áreas de endemismo Xingu (XI), Belém (BE) e 1M. Essa topologia indica um aparente contato secundário recente na 1M entre uma população isolada e endêmica da própria ilha com populações do continente (XI). A árvore obtida para W poecilinotus apresentou uma topologia semelhante àquela de G. spirurus, indicando que a formação da 1M provavelmente atuou de maneira similar em diferentes espécies, com similares capacidades de dispersão, gerando padrões filogeográficos concordantes. Comparando--se as três espécies, concluímos que X spixii possui maior capacidade de dispersão respondendo de maneira distinta ao mesmo efeito vicariante. Estimativas do relógio molecular para o nó que separa o grupo de haplótipos endêmicos da ilha do Marajó mostram que tanto as populações de G. spirurus, quanto às de W. poecilinotus são muito mais antigas que os eventos que levaram à separação total da 1M em relação ao continente (aproximadamente 10.000 anos AP), com uma idade estimada aproximadamente 747.000 anos AP para G. spirurus e 798.000 anos AP para W. poecilinotus, indicando que outros processos vicariantes anteriores à separação total da Ilha do Marajó poderiam ter separado essas populações endêmicas da ilha.

Phylogeography of the freshwater red alga Sirodotia (Batrachospermales, Rhodophyta) in Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Molecular phylogeography of the Woodland Ringlet (Erebia medusa [Denis and Schiffermüller] 1775) in Europe

Phylogeography is a recent field of biological research that links phylogenetics to biogeography through deciphering the imprint that evolutionary history has left on the genetic structure of extant populations. During the cold phases of the successive ice ages, which drastically shaped species’ distributions since the Pliocene, populations of numerous species were isolated in refugia where many of them evolved into different genetic lineages. My dissertation deals with the phylogeography of the Woodland Ringlet (Erebia medusa [Denis and Schiffermüller] 1775) in Central and Eastern Europe. This Palaearctic butterfly species is currently distributed from central France and south eastern Belgium over large parts of Central Europe and southern Siberia to the Pacific. It is absent from those parts of Europe with mediterranean, oceanic and boreal climates. It was supposed to be a Siberian faunal element with a rather homogeneous population structure in Central Europe due to its postglacial expansion out of a single eastern refugium. An already existing evolutionary scenario for the Woodland Ringlet in Central and Eastern Europe is based on nuclear data (allozymes). To know if this is corroborated by organelle evolutionary history, I sequenced two mitochondrial markers (part of the cytochrome oxydase subunit one and the control region) for populations sampled over the same area. Phylogeography largely relies on the construction of networks of uniparentally inherited haplotypes that are compared to geographic haplotype distribution thanks to recent developed methods such as nested clade phylogeographic analysis (NCPA). Several ring-shaped ambiguities (loops) emerged from both haplotype networks in E. medusa. They can be attributed to recombination and homoplasy. Such loops usually avert the straightforward extraction of the phylogeographic signal contained in a gene tree. I developed several new approaches to extract phylogeographic information in the presence of loops, considering either homoplasy or recombination. This allowed me to deduce a consistent evolutionary history for the species from the mitochondrial data and also adds plausibility for the occurrence of recombination in E. medusa mitochondria. Despite the fact that the control region is assumed to have a lack of resolving power in other species, I found a considerable genetic variation of this marker in E. medusa which makes it a useful tool for phylogeographic studies. In combination with the allozyme data, the mitochondrial genome supports the following phylogeographic scenario for E. medusa in Europe: (i) a first vicariance, due to the onset of the Würm glaciation, led to the formation of several major lineages, and is mirrored in the NCPA by restricted gene flow, (ii) later on further vicariances led to the formation of two sub-lineages in the Western lineage and two sub-lineages in the Eastern lineage during the Last Glacial Maximum or Older Dryas; additionally the NCPA supports a restriction of gene flow with isolation by distance, (iii) finally, vicariance resulted in two secondary sub-lineages in the area of Germany and, maybe, to two other secondary sub-lineages in the Czech Republic. The last postglacial warming was accompanied by strong range expansions in most of the genetic lineages. The scenario expected for a presumably Siberian faunal element such as E. medusa is a continuous loss of genetic diversity during postglacial westward expansion. Hence, the pattern found in this thesis contradicts a typical Siberian origin of E. medusa. In contrast, it corroboratess the importance of multiple extra-Mediterranean refugia for European fauna as it was recently assumed for other continental species.

Nuclear and plastid markers reveal the persistence of genetic identity: A new perspective on the evolutionary history of Petunia exserta

Recently divergent species that can hybridize are ideal models for investigating the genetic exchanges that can occur while preserving the species boundaries. Petunia exserta is an endemic species from a very limited and specific area that grows exclusively in rocky shelters. These shaded spots are an inhospitable habitat for all other Petunia species, including the closely related and widely distributed species P. axillaris. Individuals with intermediate morphologic characteristics have been found near the rocky shelters and were believed to be putative hybrids between P. exserta and P. axillaris, suggesting a situation where Petunia exserta is losing its genetic identity. In the current study, we analyzed the plastid intergenic spacers trnS/trnG and trnH/psbA and six nuclear CAPS markers in a large sampling design of both species to understand the evolutionary process occurring in this biological system. Bayesian clustering methods, cpDNA haplotype networks, genetic diversity statistics, and coalescence-based analyses support a scenario where hybridization occurs while two genetic clusters corresponding to two species are maintained. Our results reinforce the importance of coupling differentially inherited markers with an extensive geographic sample to assess the evolutionary dynamics of recently diverged species that can hybridize. (C) 2013 Elsevier Inc. All rights reserved.