Deep phylogenetic relationships in the angiosperms had long been uncertain. However, by the end of the 1990s, large-scale studies contributed to the current well resolved picture of the tree of flowering plants, in which eudicots, monocots, and magnoliids are the three largest clades. Whereas monocots and eudicots have been recognized since the very first phylogenetic analyses, the monophyly of magnoliids (Canellales, Laurales, Magnoliales, and Piperales) is a more recent result. Magnoliidae, as now circumscribed, consist of 20 families and ca. 10,000 species mostly distributed in the tropics. Before the present thesis, several parts of the magnoliid tree had been well studied, but little was known about the evolutionary history of Magnoliidae as a whole. The first chapter of this thesis is a phylogenetic study conducted to clarify the relationships among families and orders of Magnoliidae. To do so, I sampled 199 species of Magnoliidae and 12 molecular markers from the three genomes and conducted phylogenetic analyses using parsimony, maximum likelihood, and Bayesian methods. The results confirm, with a greater level of support, two clades in Magnoliidae: Canellale + Piperales, and Laurales + Magnoliales. In addition, the relationships among the 20 families are generally well supported, and Lactoridaceae and Hydnoraceae are nested within Aristolochiaceae (Piperales). In the second chapter, the ages and phylogenetic positions of 10 fossils attributed to Magnoliidae were reviewed in detail. The goal of this study was to provide new reliable calibration points in order to conduct molecular dating analyses. These fossils were selected from the rich fossil record of the group because of their previous inclusion in phylogenetic analyses with extant taxa. The resulting calibration scheme provides six solid, internal minimum age constraints. The third chapter includes molecular dating analyses using the present calibration scheme and the same molecular dataset of Chapter 1. This study tends to push back in time the ages of the crown nodes of Magnoliidae (127.1-198.9 Ma), and of the four orders, Canellales (126.3-141.0 Ma), Piperales (88.2-157.7 Ma), Laurales (111.8-165.6 Ma), and Magnoliales (115.0-164.2 Ma). In the same chapter, I investigated the mode of diversification in the group. The strongly imbalanced distribution of species appears to be best explained by models of diversification with 6 to 14 diversification rate shifts. Finally, in the last chapter, I traced the evolution of 26 floral characters to reconstruct the ancestral flowers in key nodes of Magnoliidae. I used the phylogeny of Chapter 1 and an exemplar approach. Our results show that the most recent common ancestor of all Magnoliidae was a tree bearing actinomorphic, bisexual flowers with a differentiated perianth of two alternate, trimerous whorls of free perianth parts (outer and inner tepals) and probably three free stamens. This work provides key results on the evolution of Magnoliidae and raises several new questions such as the impact of geological crises on diversification of the group or the influence of pollinators and the environment on the evolution of floral morphology.

Orientadores: João Semir, Vera Nisaka Solferini / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-10T01:49:26Z (GMT). No. of bitstreams: 1 Verola_ChristianoFranco_D.pdf: 10625038 bytes, checksum: b967e9a3a66d2136c32eb7131de9a7ef (MD5) Previous issue date: 2008 / Resumo:Um estudo biossistemático foi realizado no gênero neotropical e endêmico do Brasil, Hoffmannseggella H.G. Jones. Este gênero é caracterizado por ser exclusivamente rupícola e apresentar flores de cores variadas, vívidas e contrastantes. As espécies estão distribuídas ao longo dos complexos rupestres de altitude, principalmente na região sudeste (MG, RJ e ES) e nordeste (BA). Foram descritos os padrões de distribuição geográfica para 34 espécies de Hoffmannseggella e três espécies de Dungsia, por meio de técnicas de georeferenciamento. Os resultados indicaram a formação de quatro subconjuntos de espécies: Chapada Diamantina - BA, centro-sul e centro-norte da Cadeia do Espinhaço - MG, e Complexos Rupestres do RJ/ES. As análises de PAE (Parsimony Analysis of Endemicity) e Modelagem Ecológica indicaram 12 áreas prioritárias para conservação, além de três áreas complementares para garantir a manutenção e sobrevivência destas espécies. São apresentados os resultados da datação molecular com ênfase em Hoffmannseggella, incluindo gêneros relacionados, sob uma perspectiva histórico-evolutiva. O cenário biogeográfico e histórico mais provável em Laeliinae, indica o surgimento e confinamento das espécies basais do grupo na América Central no Mioceno, com posterior irradiação de grupos derivados para a América do Sul, através da ligação parcial entre Ilhas da ¿Proto América Central¿. Os principais eventos de cladogênese em Hoffmannseggella não estão associados a áreas específicas, mas a múltiplos eventos associados à expansão e retração de áreas campestres ocorridas entre o Plioceno e o Pleistoceno. Foram realizados estudos de biologia floral e ecologia da polinização em oito espécies de Hoffmannseggella, com atenção aos mecanismos de isolamento reprodutivo entre espécies sincronopátricas. As espécies são polinizadas por himenópteros de diferentes famílias, com sistemas de polinização não específicos e baseados no engano do polinizador, contrariando suposições anteriores que caracterizavam estas espécies como ornitófilas. O estudo dos sistemas reprodutivos de 13 espécies em 36 diferentes populações revelou que a maioria das espécies é auto-incompatível, porém uma mesma espécie pode apresentar diferentes sistemas reprodutivos dependendo da população. A quebra da autoincompatibilidade em algumas espécies está fortemente associada à ocorrência da poliploidia, situação relativamente comum em Angiospermas, mas descrita pela primeira vez em Orchidaceae. A quebra da auto-incompatibilidade parece conferir vantagens ao estabelecimento de linhagens poliplóides em Hoffmannseggella, pois estas espécies apresentam mecanismos de auto-polinização espontânea. Foi realizado um estudo cromossômico, no qual foram obtidas contagens inéditas para 12 espécies e dois híbridos naturais em 24 diferentes populações, enfatizando a importância da poliploidia para a evolução deste grupo. Algumas espécies apresentaram citótipos, que foram discutidos sob uma visão citogeográfica e evolutiva, com ênfase nos principais mecanismos associados ao estabelecimento de complexos poliplóides. A poliploidia é um fenômeno relativamente recente em Hoffmannseggella, e surgiu independentemente várias vezes ao longo da sua história evolutiva. É descrita uma nova espécie, H. viridiflora, morfologicamente relacionada com as espécies de escapos curtos, flores pequenas e amarelas, ocorrentes no Planalto de Diamantina - MG. Por fim é apresentada uma visão biossistemática geral e conservacionista que revela os principais problemas associados à manutenção de áreas naturais com grande diversidade de espécies de Hoffmannseggella / Abstract: A biosystematic study of the neotropical and Brazilian endemic genus Hoffmannseggella H. G. Jones was carried out. This genus is characterized by rupiculous habit, with varied-contrasting flowers colors. These species are distributed at high altitude rocky complexes, mainly in the Southeast (MG, RJ and ES) and Northeast (BA). The geographic distribution patterns of 34 Hoffmannseggella and three Dungsia species by GIS techniques were described. The results point to four sub-sets of species groups: Chapada Diamantina - BA, Northern and Southern part of Central area of the Espinhaço Range ¿ MG and rocky complexes of RJ/ES. Parsimony analysis of endemicity and ecological modeling indicated 12 priority areas for conservation and more three complementary areas to guarantee the species survival for a long time. The results of molecular dating are presented, with emphasis on Hoffmannseggella, including related genera, in a historical-evolutive perspective. The most probable biogeographic and historical scenario in Laeliinae points to the origin and confinement of basal species in Central America in the Miocene, with posterior irradiation of derivated groups to South America, through a partial link by islands in ¿Proto Central America¿. The main cladogenesis events in Hoffmannseggella are not associated with specific areas, but happen in multiple events associated to the expansion and retraction of open vegetation in the Plio-Pleistocene. Floral biology and pollination ecology studies were carried out in eight Hoffmannseggella species, with attention to the reproductive isolation mechanisms between sincronopatric species. Hoffmannseggella species are pollinated by small bees (Hymenoptera) of different families, with unspecific and deceit based pollination systems that discredit previous suppositions that characterized Hoffmannseggella as ornithophilous. Breeding system studies of 13 species and 36 different populations revealed that most species are self-compatible, but the same species can present different breeding systems depending on the population. The break up of self-incompatibility in some species is associated to polyploidy, and this phenomenon is relatively frequent in Angiosperms, but had been never described in orchids. Selfcompatibility in polyploid species can confer advantages in establishment of polyploid lineages. A review of chromosome numbers in Hoffmannseggella, show new counts for 12 species and two natural hybrids in 24 different populations, with emphasis in the importance of polyploidy for the evolution of this group. Some species presented different cytotypes, and this is discussed in a cytogeographic and evolutive perspective, with emphasis on the main factors related with establishment of polyploid complexes. Polyploidy is a recent phenomenon in Hoffmannseggella, but can appear independently many times in its evolutionary history. A new species, H. viridiflora, is described and morphologically related to species with short racemes, yellow and smaller flowers, occurring at the Diamantina Plateau - MG. Finally, we present a general biosystematic and conservationist view, which points the main problems associated with the maintenance of natural areas with high diversity of Hoffmannseggella species / Doutorado / Doutor em Ecologia

Living sloths represent two distinct lineages of small-sized mammals that independently evolved arboreality from terrestrial ancestors. The six extant species are the survivors of an evolutionary radiation marked by the extinction of large terrestrial forms at the end of the Quaternary. Until now, sloth evolutionary history has mainly been reconstructed from phylogenetic analyses of morphological characters. Here, we used ancient DNA methods to successfully sequence 10 extinct sloth mitogenomes encompassing all major lineages. This includes the iconic continental ground sloths Megatherium, Megalonyx, Mylodon, and Nothrotheriops and the smaller endemic Caribbean sloths Parocnus and Acratocnus. Phylogenetic analyses identify eight distinct lineages grouped in three well-supported clades, whose interrelationships are markedly incongruent with the currently accepted morphological topology. We show that recently extinct Caribbean sloths have a single origin but comprise two highly divergent lineages that are not directly related to living two-fingered sloths, which instead group with Mylodon. Moreover, living three-fingered sloths do not represent the sister group to all other sloths but are nested within a clade of extinct ground sloths including Megatherium, Megalonyx, and Nothrotheriops. Molecular dating also reveals that the eight newly recognized sloth families all originated between 36 and 28 million years ago (mya). The early divergence of recently extinct Caribbean sloths around 35 mya is consistent with the debated GAARlandia hypothesis postulating the existence at that time of a biogeographic connection between northern South America and the Greater Antilles. This new molecular phylogeny has major implications for reinterpreting sloth morphological evolution, biogeography, and diversification history. Extant sloths are the survivors of an evolutionary radiation marked by the extinction of large terrestrial forms of the Ice Age. By sequencing ten mitogenomes from extinct sloths, Delsuc et al. present a new molecular phylogeny revealing widespread morphological convergence with major implications for reinterpreting sloth evolutionary history.

Pantosteus, a subgenus of Catostomus, includes the mountain sucker (Catostomus playthyrnchus), whose speculated older origins in the Miocene/Pliocene can provide insight into the ancient geographical events of western North America. We believe that major geologic events influencing the diversification of mountain suckers include the rise of the Colorado Plateau, the connections between the ancient Snake River system and the Lahontan system and subsequently the connection of the Snake River system to the Columbia Basin, dispersal of mountain suckers across the continental divide, as well as the Pleistocene Bonneville flood. If this is true, we should see evidence of geologic separation and timing through studying the phylogenetics of the mountain sucker. In order to clarify relationships of the mountain sucker with respect to other Pantosteus species, we examined cytochrome b (cyt b) sequences for 144 mountain suckers, 24 other Pantosteus species, and ten outgroup species. Phylogenetic relationships among haplotypes were constructed based on maximum likelihood and Bayesian criterion. In an effort to provide better resolution at some nodes, we also sequenced additional mitochondrial genes (ND1, ND2, ATPase, ND4L, ND4, ND5, ND6, and cyt b) for a subset of 44 individuals taken from the major clades obtained from the cyt b phylogentic analyses. Trees from this data set were also constructed under maximum likelihood and Bayesian criterion. All phylogenetic analysis revealed that mountain sucker are paraphyletic, with two major clades of mountain suckers separated by other members of the subgenus Pantosteus. One clade included two sub-clades, one from the upper Snake River drainage/northern Bonneville/Green River drainage Basins and the other from the southern Bonneville Basin. The other major clade included sub-clades from the Lahontan Basin, Columbia River Basin, and Upper Missouri River Basin. Molecular clock analysis revealed that Pantosteus likely split from Catostomus during the Miocene and that major speciation events within Pantosteus occurred during the Pliocene and Pleistocene. Genetic structuring and gene flow estimates for mountain sucker populations, with groupings based on major drainage basins, were calculated with AMOVA and Fst estimates in Arlequin and revealed that most of the genetic structuring was explained by variation among drainage basins with limited gene flow occurring between drainage basins. Based on this study, the role of the Colorado Plateau's geologic history in the evolution of the mountain sucker remains unclear. However, all other geologic events as discussed in this study seem to have played a significant role in the evolution of the mountain sucker.

Orientador: Ana Maria Goulart de Azevedo Tozzi / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-16T00:59:35Z (GMT). No. of bitstreams: 1 Silva_MarcosJoseda_D.pdf: 19424513 bytes, checksum: 8c7cb269238ddaf0c944b29ae376b8d3 (MD5) Previous issue date: 2010 / Resumo: Lonchocarpus Kunth (Leguminosae, Papilionoideae, Millettieae) é predominantemente neotropical e inclui cerca de 150 espécies. Estudos considerando a sistemática de Lonchocarpus são necessários, devido à sua classificação infragenérica que apresenta problemas nomenclaturais e taxonômicos, correlacionados com a alta diversidade morfológica de seus representantes. Há controvérsias referentes ao número, ao nome e à definição de suas séries, seções e subgêneros, bem como à sua própria circunscrição genérica. Entre as seções de Lonchocarpus, L. sect. Laxiflori (Benth.) Taub. e L. sect. Punctati (Benth.) Taub. são distintas morfologicamente das demais e têm distribuição geográfica quase que restrita à América do Sul, sendo a revisão taxonômica delas fundamental para a delimitação de Lonchocarpus. Ainda neste contexto, a precisa circunscrição do gênero só é possível com o entendimento das relações de Lonchocarpus com gêneros relacionados. Entre as poucas referências de estudos filogenéticos que incluem espécies de Lonchocarpus, uma apresenta Lonchocarpus s. str. como monofilético se as espécies sulamericanas da seção Punctati forem excluídas. Considerando os resultados apresentados nos estudos filogenéticos e os problemas relacionados à circunscrição e à classificação infragenérica de Lonchocarpus, esta tese teve como objetivos 1) estudar a filogenia de Lonchocarpus, com o intuito de precisar sua circunscrição, bem como sua origem, idade, diversificação geográfica, e de elucidar suas relações com alguns gêneros cotribais, e 2) revisar Lonchocarpus sect. Punctati e L. sect. Laxiflori. O estudo filogenético baseou-se em fragmentos seqüências de macromoléculas derivadas do DNA do cloroplasto (trnL-F e matK) e nuclear (ITS1+5.8S+ITS2), analisadas individualmente ou de maneira combinadas entre si e com dados morfológicos, através dos métodos de parcimônia e bayesiano, enquanto que os estudos taxonômicos revisionais fundamentaram-se nos procedimentos taxonômicos tradicionais. No capítulo 1, que trata da filogenia e biogeografia de Lonchocarpus e afins, as análises cladísticas mostraram que Lonchocarpusconforme atualmente circunscrito é parafilético e que em Lonchocarpus sensu lato três grandes clados podem ser reconhecidos: clado Laxiflori, clado Dahlstedtia e clado Lonchocarpus s. str., sendo os dois primeiros predominantemente sulamericanos e o último principalmente mesoamericano. As espécies de Lonchocarpus sect. Punctati ficaram no clado Dahlstedtia, enquanto que no clado Laxiflori também foram incluídas as espécies de Bergeronia Micheli e Margaritolobium Harms. Com estes resultados, em adição à consistência da delimitação morfológica, houve a necessidade de se propor o reestabelecimento de Muellera L.f., gênero neotropical com apenas duas espécies antes de sua sinonimização com Lonchocarpus, para incluir as espécies do clado Laxiflori, e a ampliação da circunscrição de Dahlstedtia, para incluir as espécies até então subordinadas à seção Punctati. Na recircunscrição e revisão do gênero Dahlstedtia Malme (capítulo 2) foram reconhecidas 16 espécies incluindo as duas anteriormente aceitas e as 3 novas para a ciência, e propostas 12 combinações novas e dois sinônimos novos. Dahlstedtia possui distribuição neotropical, com centro de diversidade na porção sudeste da América do Sul. O estudo visando o restabelecimento e revisão do gênero Muellera L.f. (capítulo 3) resultou na sinonimização de Lonchocarpus sect. Laxiflori e dos gêneros Bergeronia e Margaritolobium com Muellera, totalizando 26 espécies, das quais 10 novas. O gênero é sulamericano, com duas espécies atingindo a América Central. Estão sendo propostas seis lectotipificações, 10 sinonimizações e 17 combinações novas. Descrições, ilustrações, comentários taxonômicos, mapas de distribuição geográfica e chaves para identificação das espécies foram apresentadas. A análise de datação molecular revelou que Lonchocarpus s.s originou-se a cerca de 8,7±0,05Ma na América Central, diferentemente dos clados Dahlstedtia e Laxiflori que surgiram na América do Sul, em 6,3±0,05Ma e 8,0±0,09Ma, respectivamente, e que ocorreu pelo menos três eventos de migração deste gênero da América Central para a do Sul e um único para o continente africano. / Abstract: Lonchocarpus Kunth (Leguminosae, Papilionoidae, Millettiae) is predominantly neotropical and it includes around 150 species. It is necessary to make studies of the systematics of Lonchocarpus owing to its problematic nomenclatural and taxonomical infrageneric classification, which is related to the great morphological diversity of its representatives. There is a controversy over the number, the name, the definition of itsseries, sections and subgenus, as well its generic circumscription. Among the sections of Lonchocarpus, only L. sect. Laxiflori (Benth) Taub. and L. Sect. Punctati (Benth) Taub. Are morphologically distinct from the others. And their geographical distribution is mostly restricted to South America. Hence, it is extremely important to perform a taxonomical revision to delimit Lonchocarpus. Moreover, a precise circumscription of the genus is only possible if one has an understanding of the relationship between Lonchocarpus and related genera. Among the few references to phylogenetic studies which include species of Lonchocarpus, one refers to Lonchocarpus s. str. as monophyletic if the South American species of the section Punctati are excluded. Considering the resulted presents in the phylogenetic studies, the problems related to circumscription and the infrageneric classification of Lonchocarpus, this thesis aims at: 1) Studying the phylogeny of Lonchocarpus in order to determine its exact circumscription, its age and origin, and its geographic diversification, as well as elucidating its relationships with some cotribal genera, and 2) at revising Lonchocarpus sect Punctati and L. sect Laxiflori. The phylogenetic study was based on sequence fragments of macromolecules derived from the DNA of the chloroplast (trnL-F AND matk) AND of nuclear (ITS1 + 5.85 + ITS2), analyzed individually or combined among themselves (or with morphological data) using the parsimony and bayesian methods, while the revisional taxonomic studies were based on traditional taxonomic procedures. Chapter 1 deals with phylogeny and biogeography of Lonchocarpus and allies. In this chapter the cladistic analysis shows that according to the current circumscription Lonchocarpus is paraphyletic and that in Lonchocarpus sensu lato three great clade can be recognized: clade Laxiflori, clade Dahlstedia and clade Lochocarpus s. str., where the first two are predominantly southamerican and the last one ismainly mesoamerican. The species of Lonchocarpus sect. Punctati remained in the clade Dahlstedtia, while the species of Bergeronia Micheli and Margaritolobium Harms were also included in the clade Laxiflori. Based on these results which support the consistency of the morphological delimitation, it was necessary to propose the reestablishment of Muellera L.f., a neotropical genus with only two species before its synonymization with Lonchocarpus, in order to include the species of the clade Laxiflori. Furthermore, the circumscription of Dahlstedtia was extended to include the species which were still subordinated to the section Punctati. During the recircumscription and revision of the genus Dahlstedtia Malme (chapter 2), 16 species were recognized including the two species which were previously accepted and 3 unknown species to science. Also, 12 new combinations and 2 new synonyms were proposed. Dahlstedtia has a neotropical distribution, with its diversity center in the southern region of South America. The study intended for the reestablishment and revision of the genus Muellera L.f. (chapter 3) resulted in the synonymization of Lonchocarpus sect. Laxiflori and of the genera Bergeronia and Margaritolobium with Muellera, totalling 26 species (10 of them new). The genus is South American, with two species reaching Central America. Six lectotypifications, tem synonymizations and 17 new combinations are being proposed. Descriptions, illustrations, taxonomic commentaries, maps of the geographic distribution and species identification keys have been presented. The analysis of the molecular dating revealed that Lonchocarpus s. str. originated in Central America around 8.7± 0.05Ma. Unlike the clades Dahlstedia and Laxiflori that appeared in South America in 6.3± 0.05Ma and 8.0± 0.09Ma, respectively. The analysis also revealed that there have been at least three migrations of this genus from Central America to South America, and only one to Africa. / Doutorado / Biologia Vegetal / Doutor em Biologia Vegetal

The present thesis examines questions related to the temporal origin of the Flavivirus genus and the ecology of tick-borne pathogens. In the first study, we date the origin and divergence time of the Flavivirus genus. It has been argued that the first flaviviruses originated after the last glacial maximum. This has been contradicted by recent analyses estimating that the tick-borne flaviviruses emerged at least before 16,000 years ago. It has also been argued that the Powassan virus was introduced into North America at the time between the opening and splitting of the Beringian land bridge. Supported by tip date and biogeographical calibration, our results suggest that this genus originated circa 120,000 (156,100–322,700) years ago if the Tamana bat virus is included in the genus, or circa 85,000 (63,700–109,600) years ago excluding the Tamana bat virus. In the second study we estimate the prevalence of tick-borne encephalitis virus (TBEV) in host-seeking Ixodes ricinus from 29 localities in Sweden and compare our data with those of neighbouring countries. Nymphs and adult ticks were screened for TBEV using a real-time PCR assay. The mean TBEV prevalence for all tick stages combined was 0.26% for Sweden and 0.28% for all Scandinavian countries, excluding Iceland. The low prevalence of TBEV in nature may partly be explained by the fact that TBEV occurs in spatially small foci and that the inclusion of ticks from non-infected foci will reduce the prevalence estimate. In the third and fourth study, we conducted the first large-scale investigations to estimate the prevalence and geographical distribution of Anaplasma spp. and Rickettsia spp. in host-seeking larvae, nymphs and adults of I. ricinus ticks in Sweden. Ticks were collected from several localities in central and southern Sweden and were subsequently screened for the presence of Anaplasma spp. and Rickettsia spp. using a real-time PCR assay. For all active tick stages combined, the mean prevalence of Anaplasma spp. and Rickettsia spp. in I. ricinus in Sweden was estimated to 1.1% and 4.8%, respectively. It was also shown that A. phagocytophilum and R. helvetica are the main Anaplasma and Rickettsia species occurring in Sweden.

The relative contributions of biome history and geological setting to historical assembly of species richness in biodiversity hotspots remain poorly understood. The tropical Andes is one of the world’s top biodiversity hotspots, and with its diverse biomes and the relatively recent but dramatic uplift, the Andes provides an ideal study system to address these questions. To gain insights into the historical species assembly of the tropical Andes, this study focuses on investigating patterns of plant species diversification in the Andean seasonally dry tropical forest (SDTF) biome. Three plant genera are used as study groups: Amicia (Leguminosae, Papilionoideae), Tecoma (Bignoniaceae), and Mimosa (Leguminosae, Mimosoideae). Species limits are re-evaluated to enable dense sampling of species and intraspecific diversity for phylogeny reconstruction for each group. Time-calibrated phylogenies for Amicia and Mimosa are presented and used to determine patterns of species diversification in time and space. For Tecoma, incongruence between nuclear and chloroplast gene trees precludes straightforward estimation of a species tree and this incongruence is attributed to possible reticulation caused by hybridization. Divergence time estimates and patterns of diversification for Amicia and Mimosa are compared with other Andean SDTF groups (Cyathostegia, Coursetia, Poissonia; Leguminosae) using isolation by distance and phylogenetic geographic structure analyses. Consistently deep divergences between sister species and high geographic structure across all five groups suggest that Andean SDTF lineages have persisted over the past 10 million years (My) with high endemism driven by dispersal limitation, caused by geographic isolation, following the most recent episode of rapid mountain uplift 5-10 My ago. This prolonged stasis of the Andean SDTF biome is in line with Miocene fossil and paleoclimate evidence. Finally, wider analyses of the contrasting evolutionary timescales of older SDTF and more recent high-altitude grassland diversity suggest that the exceptional plant species diversity in the Andes is the outcome of highly heterogeneous evolutionary histories reflecting the physiographical heterogeneity of the Andean biodiversity hotspot.

La phylogénie moléculaire fournit un outil complémentaire aux études paléontologiques et géologiques en permettant la construction des relations phylogénétiques entre espèces ainsi que l’estimation du temps de leur divergence. Cependant lorsqu’un arbre phylogénétique est inféré, les chercheurs se focalisent surtout sur la topologie, c'est-à-dire l’ordre de branchement relatif des différents nœuds. Les longueurs des branches de cette phylogénie sont souvent considérées comme des sous-produits, des paramètres de nuisances apportant peu d’information. Elles constituent cependant l’information primaire pour réaliser des datations moléculaires. Or la saturation, la présence de substitutions multiples à une même position, est un artefact qui conduit à une sous-estimation systématique des longueurs de branche. Nous avons décidé d’estimer l‘influence de la saturation et son impact sur l’estimation de l’âge de divergence. Nous avons choisi d’étudier le génome mitochondrial des mammifères qui est supposé avoir un niveau élevé de saturation et qui est disponible pour de nombreuses espèces. De plus, les relations phylogénétiques des mammifères sont connues, ce qui nous a permis de fixer la topologie, contrôlant ainsi un des paramètres influant la longueur des branches. Nous avons utilisé principalement deux méthodes pour améliorer la détection des substitutions multiples : (i) l’augmentation du nombre d’espèces afin de briser les plus longues branches de l’arbre et (ii) des modèles d’évolution des séquences plus ou moins réalistes. Les résultats montrèrent que la sous-estimation des longueurs de branche était très importante (jusqu'à un facteur de 3) et que l’utilisation d'un grand nombre d’espèces est un facteur qui influence beaucoup plus la détection de substitutions multiples que l’amélioration des modèles d’évolutions de séquences. Cela suggère que même les modèles d’évolution les plus complexes disponibles actuellement, (exemple: modèle CAT+Covarion, qui prend en compte l’hétérogénéité des processus de substitution entre positions et des vitesses d’évolution au cours du temps) sont encore loin de capter toute la complexité des processus biologiques. Malgré l’importance de la sous-estimation des longueurs de branche, l’impact sur les datations est apparu être relativement faible, car la sous-estimation est plus ou moins homothétique. Cela est particulièrement vrai pour les modèles d’évolution. Cependant, comme les substitutions multiples sont le plus efficacement détectées en brisant les branches en fragments les plus courts possibles via l’ajout d’espèces, se pose le problème du biais dans l’échantillonnage taxonomique, biais dû à l‘extinction pendant l’histoire de la vie sur terre. Comme ce biais entraine une sous-estimation non-homothétique, nous considérons qu’il est indispensable d’améliorer les modèles d’évolution des séquences et proposons que le protocole élaboré dans ce travail permettra d’évaluer leur efficacité vis-à-vis de la saturation. / Molecular phylogeny provides an additional tool complementary to paleontological and geological studies, allowing the reconstruction of phylogenetic relationships between species and the estimate of their divergence time. Researchers are mainly focusing on the topology of a phylogenetic tree; i.e. the relative connection between different nodes. Whereas, the branch lengths of this phylogeny are often considered as secondary, i.e. as additional parameters containing little information. However, the branch lengths are the primary information for molecular dating. Importantly, saturation, the presence of multiple substitutions at the same position, is an artifact that leads to an underestimation of the branch length. We are therefore interested in estimating the magnitude of this phenomenon and its impact on divergence time. We chose to study the mammalian mitochondrial genome, which is available for many species and displays a high level of saturation. Furthermore, the phylogenetic relationships of mammalians are known, thus allowing us to fix the topology, thus eliminating one of the parameters influencing the branch lengths. We used two main approaches to improve the detection of multiple substitutions: (i) an increase in the number of species breaks the longest branches of the tree, (ii) more realistic models of sequence evolution. The results demonstrate that there is a very pronounced underestimation of branch lengths (up to a factor of 3). Furthermore, the use of a large number of species is the factor that influences most the detection of multiple substitutions, not the improvement of the model of sequence evolution. This suggests that even the most complex evolutionary models currently available, like the CAT+ Covarion model, which takes into account the heterogeneity of the substitution process between sites and the rates of evolution over time, are still far from taking the entire complexity of biological processes into account. Despite the important underestimation of branch lengths, the impact on dating appeared to be relatively limited, because the underestimation is more or less homothetic. This is obviously true for the complex evolutionary models. Since multiple substitutions are most effectively detected when breaking the long internal branches via the addition of species. This raises the problem of bias in the taxonomic sampling, due to the impact of extinction on the history of life on earth. Because this kind of bias leads to a non-homothetic underestimation, we consider it essential to improve models of sequence evolution and suggest that the protocol developed in this work will allow to evaluate their effectiveness towards saturation.

Background. Traditional plant use was studied in Lao PDR. Research focused on medicinal plant use by the Brou, Saek and Kry ethnic groups, traditional plant repellents against parasitic arthropods and leeches, and the phylogeny and biogeography of the medicinally-important snake gourd genus (Trichosanthes, Cucurbitaceae).  Methods. The ethnobiology research used a combination of structured interviews, village surveys, botanical collecting, hydro-distillation, GC-MS analysis, literature studies, and laboratory experiments. The plant systematics research used a combination of morphological studies, molecular biology laboratory work, and phylogenetic, dating and biogeographical analysis.  Results. Informants reported the use of close to 100 species to repel arthropods and leeches, many of which have constituents with documented efficacy.  Brou, Saek and Kry informants use over 75 plant species for women’s healthcare, mainly during the postpartum period for steam sauna, steam bath, hotbed, mother roasting, medicinal decoctions and infusions, and postpartum diet.  A molecular phylogeny of Trichosanthes and Gymnopetalum using a broad sampling of ~60% of their species and 4756 nucleotides of nuclear and plastid DNA shows that Gymnopetalum is nested within Trichosanthes. Fossil-calibrated Bayesian molecular dating of the Trichosanthes phylogeny reveals an early Oligocene origin of the genus, and many of the extant sections originating and diversifying during the Miocene. Biogeographical analysis shows a likely East or South Asian origin of Trichosanthes, with lineages diversifying and spreading throughout Australasia from the early Pliocene to the Pleistocene.  Discussion. Traditional plant use in Lao PDR is common and widespread. The presence among the repellent species of economical alternatives to costly synthetic repellents is tenable, and the subject of ongoing studies.  Postpartum traditions and medicinal plant use are essential parts of childbirth and postpartum recovery in these ethnic groups, and many other groups in Lao PDR. Efforts to improve maternal healthcare and reduce maternal and infant mortality need to integrate these traditions with modern notions of healthcare to achieve wider adoption. Documenting all possible uses of commonly used medicinal plant species shows that similarity in use between these ethnic groups is relatively low considering that they share, and have shared for many generations, the same environment and resources. A lack of effective cures leads to a process of continuous innovation, where effective cures are shared between cultures, but remedies of only cultural importance, or those under evaluation are culture-specific.  The Trichosanthes phylogeny implies the merging of Gymnopetalum into Trichosanthes, and this is done using available names or new combinations. A synopsis of Trichosanthes, the new combinations, and a revision of the species in Australia, are made and presented.  Conclusions. Traditional plant use is widespread in Lao PDR, and of significance to many people as a source of primary healthcare and inexpensive repellents. The important medicinal plant genus Trichosanthes includes Gymnopetalum, and has a complex biogeographic history with multiple colonization events of Australasia.

La phylogénie moléculaire fournit un outil complémentaire aux études paléontologiques et géologiques en permettant la construction des relations phylogénétiques entre espèces ainsi que l’estimation du temps de leur divergence. Cependant lorsqu’un arbre phylogénétique est inféré, les chercheurs se focalisent surtout sur la topologie, c'est-à-dire l’ordre de branchement relatif des différents nœuds. Les longueurs des branches de cette phylogénie sont souvent considérées comme des sous-produits, des paramètres de nuisances apportant peu d’information. Elles constituent cependant l’information primaire pour réaliser des datations moléculaires. Or la saturation, la présence de substitutions multiples à une même position, est un artefact qui conduit à une sous-estimation systématique des longueurs de branche. Nous avons décidé d’estimer l‘influence de la saturation et son impact sur l’estimation de l’âge de divergence. Nous avons choisi d’étudier le génome mitochondrial des mammifères qui est supposé avoir un niveau élevé de saturation et qui est disponible pour de nombreuses espèces. De plus, les relations phylogénétiques des mammifères sont connues, ce qui nous a permis de fixer la topologie, contrôlant ainsi un des paramètres influant la longueur des branches. Nous avons utilisé principalement deux méthodes pour améliorer la détection des substitutions multiples : (i) l’augmentation du nombre d’espèces afin de briser les plus longues branches de l’arbre et (ii) des modèles d’évolution des séquences plus ou moins réalistes. Les résultats montrèrent que la sous-estimation des longueurs de branche était très importante (jusqu'à un facteur de 3) et que l’utilisation d'un grand nombre d’espèces est un facteur qui influence beaucoup plus la détection de substitutions multiples que l’amélioration des modèles d’évolutions de séquences. Cela suggère que même les modèles d’évolution les plus complexes disponibles actuellement, (exemple: modèle CAT+Covarion, qui prend en compte l’hétérogénéité des processus de substitution entre positions et des vitesses d’évolution au cours du temps) sont encore loin de capter toute la complexité des processus biologiques. Malgré l’importance de la sous-estimation des longueurs de branche, l’impact sur les datations est apparu être relativement faible, car la sous-estimation est plus ou moins homothétique. Cela est particulièrement vrai pour les modèles d’évolution. Cependant, comme les substitutions multiples sont le plus efficacement détectées en brisant les branches en fragments les plus courts possibles via l’ajout d’espèces, se pose le problème du biais dans l’échantillonnage taxonomique, biais dû à l‘extinction pendant l’histoire de la vie sur terre. Comme ce biais entraine une sous-estimation non-homothétique, nous considérons qu’il est indispensable d’améliorer les modèles d’évolution des séquences et proposons que le protocole élaboré dans ce travail permettra d’évaluer leur efficacité vis-à-vis de la saturation. / Molecular phylogeny provides an additional tool complementary to paleontological and geological studies, allowing the reconstruction of phylogenetic relationships between species and the estimate of their divergence time. Researchers are mainly focusing on the topology of a phylogenetic tree; i.e. the relative connection between different nodes. Whereas, the branch lengths of this phylogeny are often considered as secondary, i.e. as additional parameters containing little information. However, the branch lengths are the primary information for molecular dating. Importantly, saturation, the presence of multiple substitutions at the same position, is an artifact that leads to an underestimation of the branch length. We are therefore interested in estimating the magnitude of this phenomenon and its impact on divergence time. We chose to study the mammalian mitochondrial genome, which is available for many species and displays a high level of saturation. Furthermore, the phylogenetic relationships of mammalians are known, thus allowing us to fix the topology, thus eliminating one of the parameters influencing the branch lengths. We used two main approaches to improve the detection of multiple substitutions: (i) an increase in the number of species breaks the longest branches of the tree, (ii) more realistic models of sequence evolution. The results demonstrate that there is a very pronounced underestimation of branch lengths (up to a factor of 3). Furthermore, the use of a large number of species is the factor that influences most the detection of multiple substitutions, not the improvement of the model of sequence evolution. This suggests that even the most complex evolutionary models currently available, like the CAT+ Covarion model, which takes into account the heterogeneity of the substitution process between sites and the rates of evolution over time, are still far from taking the entire complexity of biological processes into account. Despite the important underestimation of branch lengths, the impact on dating appeared to be relatively limited, because the underestimation is more or less homothetic. This is obviously true for the complex evolutionary models. Since multiple substitutions are most effectively detected when breaking the long internal branches via the addition of species. This raises the problem of bias in the taxonomic sampling, due to the impact of extinction on the history of life on earth. Because this kind of bias leads to a non-homothetic underestimation, we consider it essential to improve models of sequence evolution and suggest that the protocol developed in this work will allow to evaluate their effectiveness towards saturation.