Phylogeographic studies have relied on surveying neutral genetic variation in natural populations as a way of gaining better insights into the evolutionary processes shaping present day population demography. Recent emphasis on understanding putative adaptive variation have brought to light the role of epigenetic variation in influencing phenotypes and the mechanisms underlying local adaptation. While much is known about how methylation acts at specific loci to influence known phenotypes, there is little information on the spatial genetic structure of genome-wide patterns of methylation and the extent to which it can extend our understanding of both neutral and putatively adaptive processes. This research examines spatial genetic structure using paired nucleotide and methylation genetic markers in the Sonoran bark beetle, Araptus attenuatus, for which we have a considerable knowledge about its neutral demographic history, demography, and factors influencing ongoing genetic connectivity. Using the msAFLP approach, we attained 703 genetic markers. Of those, 297 were polymorphic in both nucleotide (SEQ) and methylation (METH) were assayed from 20 populations collected throughout the species range. Of the paired SEQ and METH locis, the METH were both more frequent (16% vs. 7%), maintained more diversity (Shannon IMeth = 0.361 vs. ISeq=0.272), and had more among-population genetic structure (ΦST; Meth = 0.035 vs. ΦST; Seq= 0.008) than their paired SEQ loci. Interpopulation genetic distance in both SEQ and METH markers were highly correlated, with 16% of the METH loci having sufficient signal to reconstruct phylogeographic history. Allele frequency variation at five loci (two SEQ and three METH) showed significant relationships with at-site bioclimatic variables suggesting the need for subsequent analysis addressing non-neutral evolution. These results suggest that methylation can be as informative as nucleotide variation when examining spatial genetic structure for phylogeography, connectivity, and, identifying putatively adaptive genetic variance.

The twisted-wing parasites (Strepsiptera) are an endoparasitic order of insects with cosmopolitan distribution, which are sister group of Coleoptera. There are about 600 known species up to date. Strepsiptera parasitize seven insect orders (Thysanura, Orthoptera, Blattodea, Mantodea, Hemiptera, Diptera, Hymenoptera). The family Xenidae is one of the most derived groups of Strepsiptera. Its representatives parasitize aculeate Hymenoptera of three families (Vespidae, Sphecidae, Crabronidae). In comparison to the basal groups, there are well-known hosts for genera of the family Xenidae. Therefore, this group is suitable object for study of the evolution of host specialization. Phylogeny of the family Xenidae was constructed on the basis of molecular analysis of three genes. Moreover, the mapping of ancestral host major groups and biogeographic areas was performed using two methods (parsimony, maximum likelihood). According to the results, the family Xenidae is monophyletic group with Old World origin. There were a several independent switches to the same host groups. This significantly changes the existing ideas about evolution of host specialization and requires a taxonomic revision. Within the family Xenidae, there were several cases of dispersal between the Old World and the New World. Furthermore,...

Climate change is one of the most important factor determining species ranges. In Europe there is now evidence for northward areal expansion in many Mediterranean insects including the praying mantis (Mantis religiosa). This species is the only representative of the order Mantodea inhabiting central Europe. The northern edge of the species distribution currently reaches latitude 53ř North. Although, the praying mantis is well known insect there is not enough evidence about its phylogeography. In this work three mitochondrial genes (COI, COII, Cyt b) were selected for phylogenetic study. Results indicate three statistically supported distinct lineages in Europe: Eastern European, Central European and Western European. Presumably these lineages are consistent with isolation during the last glacial and re-colonization from glacial refugia. Reduced haplotype diversity on the northern edge suggests currently established populations at the northern distribution border. To validate mtDNA results it was also considered four microsatellite loci. Due to different type of inheritance mtDNA and nuclear DNA it is possible to compare two independent genetic datasets. Microsatellite analysis confirmed results obtained on mitochondrial data. Three major genetic clusters were found: east, west and central. Spatial...

Une meilleure compréhension de l’origine et de l’évolution de la diversité du vivant nécessite de développer des approches biogéographiques basées sur la phylogéographie. Ce travail de thèse considère ainsi la structure phylogéographique du myrte commun (Myrtus communis L., Myrtaceae), plante caractéristique et commune des matorrals de Méditerranée, et ses liens de parenté avec le myrte de Nivelle (Myrtus nivellei Batt. & Trab.), endémique des montagnes du Sahara central. Un des objectifs consiste à examiner plus particulièrement l’influence de la paléogéographie et des changements climatiques sur la diversité génétique de ces deux taxons. La démarche choisie se veut intégrative, en combinant données génétiques (séquençage et génotypage multiloci), paléobotaniques, modélisation de l'évolution moléculaire, polymorphisme et héritabilité de la croissance en conditions contrôlées, et modélisation de la niche bioclimatique. L’analyse de 173 populations de myrte commun et de 23 populations de myrte de Nivelle a révélé un fort signal phylogéographique, dont le cadre spatio-temporel provient de la datation des divergences et de la reconstruction des aires ancestrales au sein de phylogénies moléculaires établies grâce aux méthodes bayésiennes d’analyse phylogénétique. Trois résultats principaux peuvent être présentés. (i) A partir d’une origine remontant au début du Miocène, l’histoire du myrte commun se résume à deux périodes de diversification associées aux changements environnementaux survenus à la transition Miocène / Pliocène, et au cours du Pléistocène. Si un phénomène de vicariance ancien a conduit à l’isolement d’une lignée est-méditerranéenne, des phénomènes récents de diversification ont été détectés à l’ouest avec migration en retour vers l’est de la Méditerranée, mais aussi vers la Macaronésie et vers le Sahara. (ii) Au cœur des montagnes-refuges du Sahara central, l’alternance des périodes humides et arides serait à l’origine de l’isolement des populations de myrte de Nivelle par massif et d'une forte érosion génétique. Cette forte différenciation régionale s'accompagne de flux de gènes au sein des massifs, et de multiplication végétative. (iii) Enfin, l’absence de divergence des populations insulaires méditerranéennes comme la Corse, contraste avec la persistance sur le long terme de lignées aux Açores et à Madère, et avec la spéciation au Sahara du myrte de Nivelle. La discussion de ces résultats s'ouvre sur de nouvelles perspectives en phylogéographie comparative, en génomique et en biogéographie de la conservation. / A better understanding of the origin and evolution of the diversity of life requires the development of biogeographical approaches based on the phylogeography. This PhD thesis study considers the phylogeographical structure of the Common Myrtle (Myrtus communis L., Myrtaceae), a characteristic and common plant of the Mediterranean matorral, and its relationship with the Nivelle Myrtle (Myrtus nivellei Batt. & Trab.), endemic to the central Saharan mountains. An objective is also to examine especially the influence of palaeogeography and climatic changes on the genetic diversity of these two taxa. Our approach aims at being integrative, combining palaeobotanical data, genetic data (sequencing and multilocus genotyping), modeling of molecular evolution, polymorphism and heritability of the growth in controlled conditions, and modeling of bioclimatic niche. The analysis of 173 populations of the Common Myrtle and 23 populations of the Nivelle Myrtle reveals a strong phylogeographical signal, whose spatio-temporal framework was provided by the dating of divergences and the reconstruction of ancestral areas within the molecular phylogenies using Bayesian analytical methods. Three main results can be highlighted. (i) With an origin dated to the early Miocene, the history of M. communis can be summarized by two periods of diversification associated with the environmental changes occurring in the Miocene/Pliocene transition and in the Pleistocene. A vicariance phenomenon has induced the isolation of an eastern Mediterranean lineage. Recent diversification events have also been detected in the western part of the Mediterranean Basin, with in-return migration to the eastern Mediterranean, and also dispersal to the Azores and Madeira islands, and to the Sahara. (ii) Within the refugia-mountains of the Central Sahara, the alternation of wet and dry periods seems to have induced the isolation of the populations of M. nivellei per mountain range, with a strong genetic erosion. In parallel to this high regional differentiation, gene flows within these mountain ranges and vegetative multiplication have been detected. (iii) Finally, the absence of divergence of Mediterranean insular populations of M. communis contrasts with the long-term persistence of Myrtle lineages restricted to the Azores and Madeira islands, and to the speciation of M. nivellei in the Sahara. The discussion of these results provides new perspectives on comparative phylogeography, genomics and conservation biogeography.

Phylogeography aims to understand the processes that underlie the distribution of genetic variation within and among closely related species. Although the means by which this goal might be achieved differ considerably from those that spawned the field some thirty years ago, the foundation and conceptual breakthroughs made by Avise are nonetheless the same and are as relevant today as they were two decades ago. Namely, patterns of neutral genetic variation among individuals carry the signature of a species’ demographic past, and the spatial and temporal environmental heterogeneity across a species’ geographic range can influence patterns of evolutionary change. Aquatic systems throughout Mexico provide unique opportunities to study phenotypic plasticity and evolution in relation to climatic and environmental selective forces. There are several unique, often isolated aquatic environments throughout Mexico that have a history of geographic isolation and reconnection. The first study presented herein shows significant mitochondrial sequence divergence was also discovered between L. megalotis populations on either side of the Sierra de San Marcos that bisects the valley of Cuatro Ciénegas and that the populations in the valley are genetically distinct from those found outside of the valley. The second study recovered signals of two divergence events in Cuatro Ciénegas for six codistributed taxa, and reveals that both events occured in the Pleistocene during periods of increased aridity suggesting that climatic effects might have played a role in these species’ divergence. The final study presents an Illumina-based high-resolution species phylogeny for Astyanax mexicanus providing added support that there are multiple origins to cave populations and further clarifying the uniqueness of the Sabinos and Rio Subterráneo caves.

There are a number of common distributional patterns that have provided the foundations of our current knowledge of Neotropical biogeography. A distinctive pattern is the so-called \"circum-Amazonian distribution\", which expands across the forested lowlands south and east of Amazonia, the Andean foothills, the Venezuelan Coastal Range, and the Tepuis. To date, there is no clear understanding of the processes giving rise to this distribution. To understand the evolutionary history of taxa exhibiting this pattern it is necessary to test biogeographic hypotheses offering mechanistic explanations. Comparative phylogeography allows more accurate phylogeographic hypotheses for these taxa, as well as better population genetic parameters. Comprehensive comparative studies aiming at unraveling the evolutionary and biogeographic mechanisms underlying the circum-Amazonian distribution have not been conducted yet, and only scarce descriptive information has been published. Therefore, the objective of this work was to elucidate the historical and biogeographic mechanisms underpinning circum-Amazonian distribution by performing comparative genomic analyses of a group of Suboscine passerines. Ultraconserved Elements (UCEs) were obtained for eight taxonomic groups to estimate population parameters and genealogical trees. For the Thamnophilidae species were inferred demographic histories with momi2. The best models of each taxon were analyzed in a comparative framework to relate them with previously proposed biogeographic hypotheses for the Neotropics and to propose plausible biogeographical scenarios for the circum-Amazonian pattern. The circum-Amazonian distributional pattern has two main phylogeographic units: an Andean (plus Central America region) and an eastern-forested region (Atlantic Forest ecoregion, forested areas around southeast of Amazonia), interconnected by a northern and southern corridor, allowing biotic interchanges between them (mainly from the southern) and hybridization. Species-tree analyses recovered (a) an Andean clade with two Andean subgroups in the northern Peru and central Andes, and (b) an eastern-forested clade including northern and central/southern Atlantic Forest subgroups. The demographic histories of the Thamnophilidae taxa suggest that diversification of the circum-Amazonian taxa have a strong influence of climatic fluctuations during the Pleistocene, with interconnected refugia allowing phenotypic/genetic differentiation but maintaining a considerable level of gene flow during varying dry/cool and warm/humid periods. In addition, the results of this work opened interesting taxonomic questions about some taxa that could be covered in the future (T. ruficapillus/torquatus complex, Xiphocolaptes complex). / Existe um número de padrões de distribuição comuns que forneceram os fundamentos do nosso atual conhecimento da Biogeografia Neotropical. Um padrão distintivo é o chamado padrão de distribuição circum-Amazônico, apresentado por grupos filogeneticamente relacionados habitando as florestas de baixada ao sul-leste da Amazônia, as encostas úmidas dos Andes, a área costeira da Venezuela e os Tepuis. Atualmente não existe um entendimento claro dos processos que deram surgimento a este padrão de distribuição. Para compreender a história evolutiva dos táxons exibindo este tipo de padrão é necessário testar hipóteses biogeográficas que ofereçam explicações mecanicistas. A Genômica comparativa permite hipóteses filogeográficas mais exatas para estes táxons, assim como melhores parâmetros demográficos. Estudos comparativos abrangentes visando em esclarecer os mecanismos evolutivos e biogeográficos relacionados a distribuição circum-Amazônica não tem sido elaborados ainda, e só informação descritiva escassa tem sido publicada. Portanto, os objetivo fundamental do projeto foi elucidar os mecanismos históricos e biogeográficos subjacentes à distribuição circum-Amazônica desenvolvendo analises genômicos comparativos de um grupo de Passeriformes Suboscines. Dados do gene ND2 e de Elementos Ultraconservados (UCEs) foram obtidos de oito grupos taxonômicos para estimar parâmetros populacionais e arvores genealógicas. Histórias demográficas foram inferidas só para as espécies da família Thamnophilidae usando momi2. Os melhores modelos de cada táxon foram analisados num marco comparativo para relaciona-os ás hipóteses biogeográficas propostas para o Neotrópico e propor cenários possíveis para a distribuição circum-Amazônica. O padrão de distribuição circum-Amazônico possui duas unidades filogeográficas principais: uma unidade Andina (incluindo a região de Centro América) e uma segunda unidade incluindo as regiões florestais do leste (Mata Atlântica, áreas florestais ao sudeste da Amazônia). Estas unidades estão interconectadas por corredores ao norte e sul da distribuição, permitindo intercâmbios de biota entre elas (principalmente pelo corredor sul). SNAPP identificou o clado Andino subdividido em norte do Peru e central Andes, e um segundo clado das Florestas do Leste incluindo dois subgrupos, um do norte e outro do centro-sul da Mata Atlântica. As histórias demográficas dos Thamnophilidae sugerem que a diversificação na distribuição circum-Amazônica foi altamente influenciada pelas flutuações climáticas durante o Pleistoceno, com refúgios interconectados gerando diferenciação fenotípica/genética mas mantendo certo grau de fluxo gênico nos períodos secos/frios e quentes/húmidos. Adicionalmente, algumas questões taxonômicas sobre alguns táxons estudados que poderiam ser estudadas no em futuros estudos (o complexo T. ruficapillus/torquatus e o gênero Xiphocolaptes).

Drosophila buzzatii é uma espécie cactófila associada a diferentes espécies de cactos e distribuída nos diferentes Domínios fitogeográficos da América do Sul. Baseado na diversidade de inversões cromossômicas e densidade populacional, o Chaco foi considerado por alguns autores como o centro de origem da espécie. Entretanto, trabalhos recentes, utilizando aloenzimas e DNA mitocondrial, apontaram para uma possível origem na Caatinga. Os objetivos deste trabalho foram delinear rotas de dispersão da espécie para explicar sua distribuição atual e possível distribuição durante o último período glacial, na América do Sul. Foram obtidas seqüências de 714 pb da COI do mtDNA de 132 indivíduos em 44 localidades, gerando 36 haplótipos. Foram calculados os índices de diversidade nucleotídica, o teste AMOVA, testes de neutralidade, a Mismatch Distribution, Baesyan Skyline Plot, NCPA e o sentido dos movimentos migratórios (Migrate N) a fim de determinar parte da história evolutiva da espécie. As diversidades nucleotídicas encontradas por Domínio foram de 0,0030 Caatinga; 0,0019 - Mata Atlântica; 0,0020 Cerrado; 0,0011 - Pampas e 0,0004 - Chaco. A AMOVA mostrou que 68,33% da variação é intra-populacional e que uma porção significativa da variação é devido a diferenças inter-regionais (ct = 0,07124 p = 0,00196). Os testes de Neutralidade (D de Tajima = -2,4150, p = 0,0317 e Fs de Fu = -28,6719, p = 0,00001), a forma em estrela da rede e haplótipos, e a Mismatch Distribution confirmam um evento de expansão populacional estimado em aproximadamente 494.257,3 anos atrás, segundo modelo de Rogers e Harpending (1992). Entretanto, a Baesyan Skiline Plot demonstrou que esse movimento de expansão parece ser mais antigo, cerca de 550.000 650.000 anos atrás. A NCPA demonstrou que há fluxo gênico restrito com isolamento por distância, confirmado pelo teste de Mantel e alguma dispersão a longa distância em alguns dos clados analisados. O resultado do programa Migrate N indicou um padrão complexo migratório entre os domínios, porém um padrão norte/sul pôde ser verificado. A estruturação genética pode ser explicada devido à grande área de distribuição da espécie, gerando isolamento por distância e pela presença de barreiras geográficas e climáticas (entre o Cerrado e a Caatinga) e no estado do Rio de Janeiro e Espírito Santo (ao longo da Mata Atlântica) onde há pouco ou nenhum indivíduo da espécie. Os eventos de expansão ocorreram no Quaternário durante o período glacial conhecido como Ilinioian e suas subdivisões. A partir dos resultados deste trabalho foi possível traçar diversas rotas de migração possíveis entre os domínios utilizados, sendo que o movimento mais antigo partiu da Caatinga o que vai contra a hipótese de que o Centro de Origem seja o Chaco. / The fruit-fly Drosophila buzzatii is a cactophilic species in association with cactus species distributed along the Phytogeographic Domains of Caatinga, Cerrado, Atlantic Forest, Pampas and Chaco. Based in the diversity of chromosomal inversion and populational density of the species, the Chaco Domain was considered the Center of Origin of the D. buzzatii. However, recent works, using allozymes and DNAmt, showed a possible origin of the D. buzzatii in the Caatinga. The objectives of this work were trace historical dispersion routes of D. buzzatii, current and ancient areas of distribution in the South America. We obtained DNA sequences in 132 samples in 44 localities with 714 bp length from the COI mtDNA gene, generating 36 haplotypes. The diversity indexes, AMOVA, neutrality tests, Mismatch Distribution, Baesyan Skyline Plot, NCPA and sense of migration movements was calculated, to describe part of the evolutionary history of the species. The nucleotide diversity was 0,0030 - Caatinga, 0,0019 - Mata Atlântica, 0,0020 - Cerrado, 0,0011 - Pampas and 0,0004 - Chaco. The AMOVA results, grouped by Domain showed that 68,33% of the variation is intra-population and a significant portion of the variation is due to inter-regional differences (ct = 0,07124 p = 0,00196). The Neutrality tests (Tajimas D = -2,4150, p = 0,0317 and Fus Fs = -28,6719, p = 0,00001), the star-shape of the haplotype network, and Mismatch Distribution showed population expansion signs, estimated in 494.257,3 ybp, according Rogers and Harpending model (1992). However, the BSP showed that the movement is ancient, estimated in 550.000 650.000 ybp. The NCPA showed restricted gene flow with isolation by distance, confirmed by the Mantel Test and some long distance dispersion. The results of the program Migrate N showed a complex pattern of migration between the domains, but a north/south pattern could be identified. The genetic structure can be explained to the widespread distribution of the species, that could generate isolation by distance and by the presence of geographic and climatic barriers (between Cerrado and Caatinga domains) and in the States of Rio de Janeiro and Espírito Santo (along the Atlantic Forest) when there is none or few individuals of the species D. buzzatii. The expansion movements occurred in the Quaternary Period during glaciations events in the Illinoian and their subdivisions, due to the decrease of the global moisture that generated favorable conditions to the expansion of the dry vegetation and associated species. Based on the results of this work it was possible to delineate many migration routes between the phytogeographic domains, and the more ancient movement started in the Caatinga and this result not support the hypothesis that Chaco was the Center of Origin from D. buzzatii.

Dengue virus type 1 (DENV-1) was introduced in Brazil in 1986 and caused several epidemics. The first autochthonous cases of DENV-2 and DENV-3 were detected respectively in 1990 and 2000. Since then, the viruses have spread throughout Brazil and became endemic in most areas infested with Aedes aegypti. DENV-4 was isolated for the first time in 1982 in a focal epidemic in the northwestern region of the Brazilian Amazon. Later, in 2008, this serotype emerged as an important pathogen during outbreaks. The study of the historical processes that may be responsible for the contemporary geographic distributions of viruses is critical to understand viral epidemiology. However, those processes in urban scales are not well understood. 2013 was one of the worst years for dengue in the Brazils history, with 1.4 million cases, including 6,969 severe cases and 545 deaths. This project aimed to understand the dynamics of evolutionary change, origins and distributions of different viral strains in an urban setting during 2013. We expect this study to provide new perspectives for viral control. / O vírus da dengue tipo 1 (DENV-1) foi introduzido no Brasil em 1986 e foi responsável por numerosas epidemias. Os primeiros casos autóctones do DENV-2 e DENV-3 foram detectados respectivamente em 1990 e 2000. Desde então, o vírus ter se espalhado por todo o Brasil e tornou-se endêmico na maioria das áreas infestadas com Aedes aegypti. DENV-4 foi isolado pela primeira vez em 1982, em uma epidemia focal na região noroeste da Amazônia brasileira. Porem, este sorotipo somente emergiu como um importante patógeno durante os surtos de 2008. O estudo dos processos históricos que podem ser responsáveis para as distribuições geográficas contemporâneas do vírus é fundamental para compreender a epidemiologia viral. No entanto, esses processos em escalas urbanas não são bem compreendidos. 2013 foi um dos piores anos para a dengue na história do Brasil, com 1,4 milhões de casos, incluindo 6.969 casos graves e 545 mortes. Este projeto teve como objetivo compreender a dinâmica de mudança evolutiva, origens e distribuições de diferentes cepas virais em um cenário urbano em 2013. Esperamos que este estudos contribua com novas perspectivas para o controle viral.

Die antillanische Flora ist eine der artenreichsten der Erde. Trotz jahrhundertelanger floristischer Forschung zeigen jüngere Studien, daß der Archipel noch immer weiße Flecken beherbergt. Das trifft besonders auf die Familie der Orchideen zu, deren letzte Bearbeitung für Cuba mehr als ein halbes Jahrhundert zurückliegt. Die vorliegende Arbeit basiert auf der lang ausstehenden Revision der Orchideengattung Pleurothallis R. Br. für die Flora de Cuba. Mittels weiterer morphologischer, palynologischer, molekulargenetischer, phytogeographischer und ökologischer Untersuchungen auch eines Florenteils der anderen Großen Antillen wird die Genese der großantillanischen Pleurothallis-Flora rekonstruiert. Der Archipel umfaßt mehr als 70 Arten dieser Gattung, wobei die Zahlen auf den einzelnen Inseln sehr verschieden sind: Cuba besitzt 39, Jamaica 23, Hispaniola 40 und Puerto Rico 11 Spezies. Das Zentrum der Diversität liegt im montanen Dreieck Ost-Cuba - Jamaica - Hispaniola, einer Region, die 95 % der groß-antillanischen Arten beherbergt, wovon 75% endemisch auf einer der Inseln sind. Da die meisten Arten entweder endemisch oder pankaribisch verbreitet sind, bleiben die floristischen Bezüge zwischen den Inseln und zu den kontinentalen Nachbargebieten nur schwach ausgeprägt. Immerhin lassen sich einige Verbindungen unter den Inseln der Großen Antillen und besonders zu Mittelamerika erkennen. Diese Affinitäten steigen von Ost nach West. Molekulargenetische und (mikro-)morphologische Daten zeigen ein deutliches Muster der historischen Biogeographie. Danach lassen sich die antillanischen Arten hinsichtlich ihrer Genese in drei Gruppen einteilen. 25% der Arten sind pankaribisch verbreitet, wobei der Großteil der Inselpopulationen vom mittelamerikanischen Festland stammt. Ebenfalls aus dieser Region stammen weitere 25%, die jedoch auf den Inseln neue Arten gebildet haben. Die verbleibenden 50% der groß-antillanischen Sippen sind autochthon und das Ergebnis adaptiver Radiation auf den Inseln. Diese intensive Kladogenese beschränkt sich auf drei Verwandtschaftskreise innerhalb der Gattung Pleurothallis in den Untergattungen Antilla Luer und Specklinia Lindl. (2 Linien). Es stellte sich heraus, daß der überwiegende Anteil der Artbildungsprozesse allopatrischer Natur ist. Sympatrie konnte nur in einem einzigen Fall direkt belegt werden. Das Ergebnis der allopatrischen Speziation sind zwei Typen von Vikarianz, räumlich geographischer und geologischer. In Cuba sind überraschenderweise fast 80% der endemischen Arten an einen Gesteinstyp gebunden, überwiegend an Serpentin. West-Hispaniola, wo viele Schwesternarten cubanischer Sippen beheimatet sind, besteht fast ausschließlich aus Kalkstein. Geographische Vikarianz ist daher oft geologisch unterlegt, eine Bindung die für Epiphyten kaum vermutet wurde. Hinter der Geologie verbergen sich jedoch eher Bestäuberareale und weniger physiologische Anpassung als limitierender Faktor. Eine Verfrachtung in Vegetation auf anderem petrologischen Untergrund scheint damit der Hauptauslöser für Artbildungen gewesen zu sein. Ausgangspunkt waren höchstwahrscheinlich individuenarme Gründerpopulationen die den Bedingungen eines founder events ausgesetzt waren. Neben den reichen geologischen Verhältnissen im Dreieck Ost-Cuba - Jamaica - Hispaniola wird die intensive Artbildung durch weitere spezifisch lokale Bedingungen unterstützt. Karibische Wirbelstürme dürften entlang der Hauptrouten für eine häufige Verfrachtung von Samen oder Pflanzen von Mittelamerika auf die Großen Antillen sowie zwischen den Inseln selber verantwortlich sein. Ein zweiter günstiger Umstand für erfolgreiche Migration innerhalb des Dreiecks besteht in der räumlichen Nähe der Inselgebirge und deren optimalen klimatischen Bedingungen für die Besiedlung durch mikrophytische Epiphyten. Molekulargenetische Daten lieferten weiterhin wertvolle Informationen in Bezug auf die beiden aktuell diskutierten Systeme der Pleurothallidinae, einer streng morphologischen (Luer) und einer fast ausschließlich auf DNA-Sequenzen (Pridgeon & Chase) basierenden Klassifikation. DNA-Sequenzen der cubanischen Arten stützen das neue System von Pridgeon & Chase weitestgehend, zeigen aber Widersprüche bezüglich der Monophylie in einigen der neuen oder wieder errichteten Taxa. Angesicht dessen, daß die karibische Florenregion leider nicht nur durch ihre Biodiversität zu den zehn globalen hot spots zählt, sondern auch durch die großflächige Zerstörung von Primärvegetation, war es auch ein Anliegen der vorliegenden Arbeit, ein erstes detailliertes Bild von Genese und Verbreitung antillanischer Orchideen zu vermitteln. Diese Daten können direkt für die Gestaltung und das Management von karibischen Schutzgebieten eingesetzt werden, da Orchideen in der Naturschutzpolitik einen hohen Argumentationswert besitzen. / The Antillean Flora is one of the most diverse on our globe. However, despite floristic work for centuries recent studies show that there are still blank areas. This is especially the case in the family Orchidaceae, which, in the case of the Cuban Flora, has been reviewed more than half a century ago for the last time. The work presented here is based on the long pending revision of the genus Pleurothallis R. Br. for the Flora de Cuba. Adding further morphological, palynological, molecular, and ecological data this study is aimed at the reconstruction of the Greater Antillean Pleurothallis flora. The archipelago comprises more than 70 species of this genus, with a differing diversity on the particular islands; Cuba accommodates 39 taxa, Jamaica 23, Hispaniola 40 and Puerto Rico 11. The centre of diversity lies within the triangle E Cuba - Jamaica - W Hispaniola, a region that accommodates about 95% of the Greater Antillean species. 75% of the taxa are confined to just one island. Since most of the plants are either endemic or are of pan-Caribbean distribution floristic relationships among the islands and with regard to neighbouring continental areas remain rather indistinct. The strongest affinities are with Central America. Floristic relationships with that area increase from E towards W. Molecular and (micro-)morphological data show a clear pattern of historical phytogeography. Concerning their origin there are 3 groups of species. 25% of the Greater Antillean taxa are widespread in the Pan-Caribbean area, with the majority of the island populations having their origin presumably on the Central American continent. Another 25% are derived from Central American ancestors too, however, they have evolved into new species on the islands in the course of migration. The remaining 50% of the Greater Antillean taxa are autochthonous. They are the result of adaptive radiation on the archipelago. Intense cladogenesis is confined to 3 lineages within Pleurothallis. They belong to the subgenera Antilla Luer and Specklinia Lindl. (2 lineages). The majority of speciation events shows an allopatric pattern. Sympatry during speciation could be detected in a single case only. Allopatric speciation has resulted into 2 types of vicariance, spatial geographic and geological. Indeed, 80% of the Cuban endemics are associated with a single type of rock, serpentine in most cases. In contrast, W Hispanola where many sister taxa of Cuban pleurothallids live, is formed almost exclusively by limestone. In many cases, geographic vicariance is therefore geologically defined, a surprising association in epiphytic orchids. Geological vicariance, in turn, may have been brought about by pollinator distribution rather than by physiological adaptation to the geological environment. Migration to petrologically different localities seems to be the main trigger for speciation in Cuban Pleurothallis. This process was most probably started with a small number of individuals that met conditions of a founder event. Apart from the geologically rich background in the triangle E Cuba - Jamaica - Hispaniola there are other specific local conditions that are responsible for the rich diversity. Caribbean hurricanes provide a powerful means of transport along their main routes. They should be responsible for frequent migrations from the Central American mainland to the archipelago and between the islands. Moreover, the mountains within the triangle are in close spatial neighbourhood and meet favourable climatic conditions for the colonisation of small epiphytes. Molecular data from the Cuban species of Pleurothallis yielded valuable information for the current discussion concerning the morphological (Luer) and molecular classifications (Pridgeon & Chase) of the subtribe. These data support the new molecular based system to a great extent, however, they show new inconsistencies with respect to monophyly in some of the new or resurrected taxa. Considering that the Caribbean Flora belongs to the ten global hot spots, due to its diversity on the one and the loss of primal vegetation on the other side, it was a goal of the present thesis to impart a detailed picture of the genesis and distribution of Antillean orchids. Bearing in mind the political value of orchids in conservation these data can be used directly for the organisation and management of Caribbean nature reserves.

Ce projet vise à comprendre comment la structure génétique intra-spécifique d'espèces végétales tropicales emblématiques et de l’espèce humaine a été affectée par les variations spatio-temporelles de l’environnement actuel et passé. Nous avons développé une approche d’inférence génétique basée sur la théorie de la coalescence pour évaluer l’influence potentielle des changements climatiques passés sur l’évolution de la distribution géographique et de la diversité génétique neutre et/ou adaptative d’Amborella trichopoda Baill. en Nouvelle-Calédonie (espèce-sœur des angiospermes, données NGS et microsatellites), de Coffea canephora Pierre ex A. Froehn en Afrique tropicale (caféier Robusta, données NGS) et de populations européenne et africaine (Luhya, Kenya) d’humains anatomiquement modernes (données NGS issues du Projet 1000 Génomes). Nos travaux suggèrent que les fluctuations climatiques du Pleistocène tardif ont joué un rôle majeur sur l’évolution de la diversité génétique des espèces étudiées de milieux tropicaux et tempérés, avec une empreinte remarquable du Dernier Maximum Glaciaire (DMG, 21 000 ans avant le présent). Les contractions démographiques associées à la glaciation planétaire ont vraisemblablement conduit à la divergence entre les lignées génétiques d’Amborella et participé à l’accumulation des différences génétiques entre les lignées de C. canephora. Nos résultats suggèrent que les événements de glaciation planétaire ont probablement entraîné une différenciation génétique idiosyncratique dans les forêts tropicales humides mais l’intensité de cette réponse semble avoir varié entre espèces. Nous avons également identifié de nombreux événements passés de sélection dans les génomes de la population humaine européenne qui ont été vraisemblablement provoquées par les conditions environnementales au cours du DMG. Les adaptations phénotypiques associées ont probablement assuré le maintien de l’expansion démographique en dépit des pressions de sélection nouvelles auxquelles les populations étaient confrontées au cours du dernier âge glaciaire en Europe. / This project aims at understanding how the structure of the intra-specific genetic diversity in emblematic tropical plant species and in the human species was shaped by the spatiotemporal variation of current and past environments. We developed a genetic inference approach based on the coalescent theory to assess the potential impact of past climatic change onto the evolution of the geographic range and of the neutral and/or adaptive genetic diversity in Amborella trichopoda Baill. in New Caledonia (sister-species of all extant angiosperms, NGS and microsatellite datasets), in Coffea canephora Pierre ex A. Froehn in tropical Africa (Robusta coffee, NGS dataset) and in North-Western European and African (Luhya, Kenya) human populations (NGS dataset 1000 Genomes Project). We found that the climatic fluctuations of the Late Pleistocene influenced the evolution of genetic diversity in these species distributed in temperate and tropical environments. The environmental conditions during the Last Glacial Maximum (LGM, 21.000 years before present) appear as an important factor. The demographic contraction associated with the last global glaciation influenced the divergence between Amborella genetic lineages and contributed to the accumulation of genetic differences between C. canephora lineages. Our results suggest that global glaciation events likely drove idiosyncratic genetic differentiation in tropical rain forests but the intensity of this response varied between species. We also identified multiple events of selection in the genomes of the European human population which were likely triggered by the environmental conditions during the LGM. The associated phenotypic adaptations probably allowed the paleo-populations to maintain their demographic expansion despite the new kinds of selective pressure they faced during the last glacial age in Europe.