Knowledge of phylogenetic relationships among organisms is essential for anchoring evolutionary studies. Phylogenomic studies use large amounts of genetic data in analyses, which is particularly important for highly phenotypically variable taxa that are difficult to distinguish from one another without the use of genetic data, due to the abundance of homoplasy in morphological characters typically used in morphological classification. Use of genome-scale molecular data has thus become the gold standard for identifying these phylogenetic relationships, specifically in comparison to past studies based on fewer genes. Greater quantities of genetic data, in addition to finer taxon sampling, may lead to different conclusions about phylogenetic relationships among organisms compared to previous studies, necessitating new analyses on organisms when new discoveries of populations and new sources of genetic data arise. Ranitomeya poison frogs (Amphibia: Dendrobatidae) are an Amazonian lineage of dendrobatid frogs consisting of 16 species possessing remarkable diversity in color pattern, range size, and parental care behavior. I present the first phylogeny based on genomic data for all species in Ranitomeya, using maximum likelihood and multi-species coalescent methods. I used ultraconserved elements (UCEs), a genome-scale nuclear marker, as my source of molecular data to construct the tree. I also present divergence time estimations using the MCMCTree program. My results indicate several differences from previous analyses in terms of interspecific relationships. Notably, I find R. toraro and R. defleri constitute different species groups, and recover R. uakarii as paraphyletic. I also designate former populations of R. fantastica from Isla Pongo, Peru and Tarapoto as R. summersi, and transfer the French Guianan R. amazonica populations to R. variabilis. My study clarifies both interspecific and intraspecific relationships within Ranitomeya, and provides key insights into phylogeny that pave the way for future studies testing hypotheses on color pattern evolution and historical biogeography.

Deserts are interesting places due to the large number of plants and animals that live there. Nocturnal wasps are extremely abundant in deserts, but they are difficult to identify and their life cycles are not well known especially the families of Chyphotidae, Tiphiidae (Brachycistidinae), and Mutillidae (velvet ants). In this dissertation, I determine how to correctly identify a particularly difficult group of species that all have black heads from the family Chyphotidae. This is important because these species make up a large proportion of specimens collected. Also, I expanded our knowledge on the distribution of the species of these three families of wasps by conducting a trap-transect study in Joshua Tree National Park catching 22 species of Brachyscistidinae based on the collection of 13,960 specimens, 11 species of Chyphotes based on the collection of 1,513 specimens and 35 species of velvet ants based on 8,447 specimens. From this study, three new species of velvet ants are described: Odontophotopsis dalyi Sadler and Pitts, sp. nov., O. odontoloxia Sadler and Pitts, sp. nov., and Photomorphus schoenwerthi Sadler and Pitts, sp. nov. Lastly, I used new molecular methods to determine relationships of the species of Brachyscistis, Chyphotes, and Odontophotopsis. These relationships suggest that the species are young, which is contradictory to evidence based on birds and mammals. These relationships also support dates for the inundation of southern California by the Boues Sea Embayment and confirm a hypothesized Baja Inner Peninsular Seaway.

O clado \"Adenocalymma-Neojobertia\" representa um dos dois principais clados da tribo Bignonieae. Ele inclui lianas, arbustos e arvoretas distribuídas por todo o neotrópico, e possui como centro de diversidade a Amazônia brasileira e a Mata Atlântica. O clado é extremamente variável em termos da morfologia e distribuição geográfica, o que o torna um desafio taxonômico para a circunscrição de espécies e gêneros. A classificação atual de Bignonieae reconhece Adenocalymma de forma ampla (82 espécies), já Neojobertia (três espécies) está entre os menores gêneros. Aqui, nós utilizamos sequenciamento de última geração (plastomas completos ou quase completos) e sequenciamento Sanger (ndhF, rpl32-trnL, PepC) para inferir a filogenia do clado \"Adenocalymma-Neojobertia\" utilizando uma ampla amostragem de caracteres (>88,137 pb) e taxa (90% de todas as espécies). Nossos resultados indicam que Adenocalymma é parafilético como circunscrito atualmente, com Neojobertia e Pleonotoma albiflora incluídos. Padrões de evolução morfológica foram avaliados para todo o clado utilizando métodos comparativos. Sinal filogenético e evolução pontuada foram testados e estados ancestrais inferidos para 32 caracteres. Desses, 19 caracteres possuem sinal filogenético e quatro são sinapomorfias de clados internos. Pecíolos e peciólulos articulados emergiu como potencial sinapomorfia de todo o clado \"Adenocalymma-Neojobertia\". Entre os caracteres que não possuem sinal filogenético, quatro caracteres com importância ecológica chamam a atenção: (i) Habito, (ii) cor da corola, (iii) forma da corola e (iv) presença de tricomas cupulares na corola. Hábito emergiu como altamente homoplástico e está potencialmente relacionado com a ocupação de novos habitats. A morfologia floral também emergiu como altamente homoplástica e evoluindo de forma pontuada, sugerindo que a cor da corola, forma da corola e a presença de tricomas cupulares na corola podem ter sido os responsáveis pela diversificação em pelo menos parte do clado. A filogenia molecular e o estudo morfológico foram então utilizados como subsídio para propor uma sinopse atualizada de Adenocalymma. A nova circunscrição do gênero proposta aqui revisa os limites das espécies e incluí todas as espécies de Neojobertia e P. Albiflora agora todas em Adenocalymma. Ao todo, estão sendo propostas quatro novas combinações, três espécies novas apresentadas e 15 novos sinônimos, fazendo com que o Adenocalymma tenha agora 74 espécies reconhecidas. Para todas as espécies reconhecidas, nós apresentamos comentários taxonômicos, comparações com espécies próximas, informação sobre o habitat, distribuição e fenologia. Além disso, mapas de distribuição e gráficos de fenologia são apresentados para todas as espécies / The \"Adenocalymma-Neojobertia\" clade represents one of two main clades of tribe Bignonieae. It includes lianas, shrubs, and treelets that are distributed throughout the Neotropics, and centered in Amazonia and the Atlantic Forest of Brazil. This clade is extremely variable in terms of morphology and geography, which has led to a series of taxonomic challenges in the circumscription of species and genera. The most recent classification of tribe Bignonieae recognizes a broad Adenocalymma (82 species) and a small Neojobertia (three species). Here, we used NGS (complete and nearly-complete plastomes) and Sanger sequencing data (ndhF, rpl32-trnL, pepC) to infer a robust phylogeny of the \"Adenocalymma-Neojobertia\" clade based on a broad sampling of molecular characters (> 88,137 bp), and taxa (90% of the overall species diversity). Our findings indicate that Adenocalymma is paraphyletic as currently circumscribed, with Neojobertia and Pleonotoma albiflora nested herein. Patterns of morphological evolution were evaluated for the whole clade using comparative methods. Phylogenetic signal and punctuated evolution was tested and ancestral character states inferred for 32 selected characters. Of these, 19 characters have significant phylogenetic signal and four are synapomorphies of internal clades. Articulated petioles and petiolules emerged as a putative synapomorphy of the whole \"Adenocalymma-Neojobertia\" clade. Among the characters without phylogenetic signal, four morphological traits of ecological significance are particularly relevant: (i) plant habit, (ii) corolla color, (iii) corolla shape, and (iv) corolla cupular trichomes. Plant habit was shown to be highly homoplastic and is thought to be associated with the occupation of new environments. Flower morphology was also highly homoplastic and evolved in a punctuated manner, suggesting that corolla color, corolla shape, and corolla cupular trichomes may have been important drivers of evolution in at least portions of this clade. The molecular phylogeny and the morphological information were then used to subsidize an updated synopsis of Adenocalymma. The new circumscription of the genus proposed here revises species limits and includes all species of Neojobertia and P. albiflora within Adenocalymma. Overall, four new combinations, three new species, and 15 new synonomies are proposed, leading to 74 taxa within Adenocalymma. For each species recognized, we provided taxonomic comments, comparisons between closely related taxa, information on the habitat, distribution, and phenology. In addition, distribution maps, and phenology plots are also shown for all species

L'explosion des données de séquençage a permis de résoudre la plupart des relations phylogénétiques chez les archées. Néanmoins, de nombreuses questions restent à résoudre à l'échelle du domaine des archées et à l'échelle des trois domaines du vivant. Parmi elles, les relations phylogénétiques au sein du cluster II, notamment la position des archées halophiles extrêmes qui ont été placées à différentes positions dans l'arbre en fonction des marqueurs et des modèles de reconstruction utilisés, ainsi que la position de la racine des archées et la position des eucaryotes à la lumière des lignées d'archées nouvellement séquencées. Au cours de ma thèse, j'ai contribué à (i) affiner la phylogénie du domaine des Archaea en se concentrant sur les relations phylogénétiques au sein du cluster II, en particulier les positions des lignées halophiles extrêmes par rapport aux méthanogènes à travers des analyses dédiées à cette partie spécifique de l'arbre, et (ii) établir une phylogénie globale des archées afin de comprendre leur histoire évolutive ancienne et leur lien avec les eucaryotes à travers une analyse phylogénomique en deux étapes à l'échelle des trois domaines du vivant. D'abord, en utilisant des approches de génomique comparée sur 155 génomes complets appartenant aux Halobacteria, Nanohaloarchaea, méthanogènes de classe II, Archaeoglobales et Diaforarchaea, j'ai identifié 258 protéines portant un signal phylogénétique fiable pour étudier les relations de parente au sein du cluster II. En combinant différentes approches limitant l'impact du signal non phylogénétique sur l'inférence phylogénétique (comme la méthode Slow-Fast et le recodage des acides aminés), j'ai montré que les Nanohaloarchaea branchent avec les Methanocellales et les Halobacteria branchent avec les Methanomicrobiales. Ce jeu de données a ensuite été utilisé pour étudier la position d'une troisième lignée halophile extrême, les Methanonatronarchaeia, qui se positionnent entre les Archaeoglobales et les Diaforarchaea. Ces résultats suggèrent que l'adaptation à la salinité extrême serait apparue au moins trois fois de manière indépendante chez les archées et que les similitudes phénotypiques observées chez les Nanohaloarchaea, Halobacteria et Methanonatronarchaeia résulteraient d'une convergence évolutive, éventuellement accompagnée de transferts de gènes horizontaux. Enfin, ces résultats suggèrent que le groupement basal des Nanohaloarchaea avec d'autres lignées des DPANN serait la conséquence d'un artefact de reconstruction. Pour la deuxième partie de ma thèse, j'ai appliqué une stratégie consistant à analyser séparément les trois domaines du vivant considérés deux à deux, en mettant à jour 72 familles protéiques précédemment identifiées par Raymann et ses collègues (2015) pour inclure toutes les nouvelles lignées d'archées séquencées depuis la publication de cette étude comme les Asgard, les DPANN, les Stygia, les Acherontia, etc. Au total, mon échantillonnage taxonomique comprend 435 archées, 18 eucaryotes et 67 bactéries. Les résultats des analyses par la méthode Slow-Fast soutiennent une racine des Archaea située entre le superphylum basal des DPANN et le reste des archées séparées en deux groupes monophylétiques : les cluster I et cluster II, comme décrits par Raymann et ses collègues (2015), et montrent que la monophylie des Euryarchaeota est liée aux positions évoluant vite. Mes résultats placent les eucaryotes en tant que groupe frère du superphylum des TACK et montrent que leur regroupement avec les Asgard est lié aux positions évoluant vite. Ces résultats ont des implications majeures sur les inférences de la nature du dernier ancêtre commun des archées et sur l'histoire évolutive de ce domaine qui a conduit à l'apparition de la première cellule eucaryote / The burst of sequencing data has helped disentangling most of the phylogenetic relationships in Archaea. Nevertheless, many questions remain to be addressed both at the level of the archaeal domain and at the level of the three domains of life. Among them, the phylogenetic relationships inside the cluster II, in particular the position of extreme halophilic archaeal lineages relatively to the methanogens which have been placed at different positions in the tree based on the different markers and reconstruction models used, as well as the position of the root of the Archaea and the position of the eukaryotes in the light of the newly sequenced archaeal lineages. During my thesis, I have contributed to (i) refine the phylogeny of the archaeal domain by focusing on the phylogenetic relationships among the cluster II Archaea, in particular the positions of the extreme halophilic lineages through dedicated analyses focusing on this specific part of the archaeal tree, and (ii) establish a global phylogeny of the Archaea to understand their early evolutionary history and their link with the eukaryotes through a large-scale two-step phylogenomic analysis at the level of the three domains of life. First, using comparative genomics approaches on 155 complete genomes belonging to the Halobacteria, Nanohaloarchaea, methanogens class II, Archaeoglobales, and Diaforarchaea, I have identified 258 proteins carrying a reliable phylogenetic signal to investigate the position of the extreme halophilic lineages in Archaea. By combining different approaches limiting the impact of non-phylogenetic signal on phylogenetic inference (like the Slow Fast method and the recoding of amino acids), I showed that the Nanohaloarchaea branch with Methanocellales, and Halobacteria branch with Methanomicrobiales. This dataset has been subsequently used to investigate the position of a third extreme halophilic lineage, the Methanonatronarchaeia, which I showed to branch in between the Archaeoglobales and Diaforarchaea. These results suggest that adaption to high salinity emerged at least three times independently in Archaea, and that the phenotypic similarities observed in Nanohaloarchaea, Halobacteria, and Methanonatronarchaeia likely result from convergent evolution, possibly accompanied by horizontal gene transfers. Finally, these results suggest that the basal grouping of Nanohaloarchaea with other DPANN lineages is likely the consequence of a tree reconstruction artefact. For the second part of my thesis, I have applied a strategy consisting in separately analyzing the three domains of life two by two, by updating 72 protein families previously identified by Raymann and colleagues (2015) to include all novel archaeal lineages that were sequenced since the publication of this study like the Asgard, the DPANN, the Stygia, the Acherontia, etc. In total, my taxonomic sampling includes 435 archaea, 18 eukaryotes, and 67 bacteria. The results of the Slow-Fast method supported a root of the Archaea lying between a basal DPANN superphylum and the rest of the Archaea separated into two monophyletic groups: the cluster I and cluster II as described by Raymann and colleagues (2015), and showed that the monophyly of the Euryarchaeota is supported only by the fast-evolving sites. My results also placed the eukaryotes as the sister group to the TACK superphylum and showed that their sister grouping with the Asgard is linked to the fast-evolving sites. These results have major implications on the inferences of the nature of the last common archaeal ancestor and the subsequent evolutionary history of this domain that led to the rise of the first eukaryotic cell

Species evolution can often be adequately described with a phylogenetic tree. Interestingly, this is the case also for the evolution of homologous genes; a gene in an ancestral species may – through gene duplication, gene loss, lateral gene transfer (LGT), and speciation events – give rise to a gene family distributed across contemporaneous species. However, molecular sequence evolution and genetic recombination make the history – the gene tree – non-trivial to reconstruct from present-day sequences. This history is of biological interest, e.g., for inferring potential functional equivalences of extant gene pairs. In this thesis, we present biologically sound probabilistic models for gene family evolution guided by species evolution – effectively yielding a gene-species tree reconciliation. Using Bayesian Markov-chain Monte Carlo (MCMC) inference techniques, we show that by taking advantage of the information provided by the species tree, our methods achieve more reliable gene tree estimates than traditional species tree-uninformed approaches. Specifically, we describe a comprehensive model that accounts for gene duplication, gene loss, a relaxed molecular clock, and sequence evolution, and we show that the method performs admirably on synthetic and biological data. Further-more, we present two expansions of the inference procedure, enabling it to pro-vide (i) refined gene tree estimates with timed duplications, and (ii) probabilistic orthology estimates – i.e., that the origin of a pair of extant genes is a speciation. Finally, we present a substantial development of the model to account also for LGT. A sophisticated algorithmic framework of dynamic programming and numerical methods for differential equations is used to resolve the computational hurdles that LGT brings about. We apply the method on two bacterial datasets where LGT is believed to be prominent, in order to estimate genome-wide LGT and duplication rates. We further show that traditional methods – in which gene trees are reconstructed and reconciled with the species tree in separate stages – are prone to yield inferior gene tree estimates that will overestimate the number of LGT events. / Arters evolution kan i många fall beskrivas med ett träd, vilket redan Darwins anteckningsböcker från HMS Beagle vittnar om. Detta gäller också homologa gener; en gen i en ancestral art kan – genom genduplikationer, genförluster, lateral gentransfer (LGT) och artbildningar – ge upphov till en genfamilj spridd över samtida arter. Att från sekvenser från nu levande arter rekonstruera genfamiljens framväxt – genträdet – är icke-trivialt på grund av genetisk rekombination och sekvensevolution. Genträdet är emellertid av biologiskt intresse, i synnerhet för att det möjliggör antaganden om funktionellt släktskap mellan nutida genpar. Denna avhandling behandlar biologiskt välgrundade sannolikhetsmodeller för genfamiljsevolution. Dessa modeller tar hjälp av artevolutionens starka inverkan på genfamiljens historia, och ger väsentligen upphov till en förlikning av genträd och artträd. Genom Bayesiansk inferens baserad på Markov-chain Monte Carlo (MCMC) visar vi att våra metoder presterar bättre genträdsskattningar än traditionella ansatser som inte tar artträdet i beaktning. Mer specifikt beskriver vi en modell som omfattar genduplikationer, genförluster, en relaxerad molekylär klocka, samt sekvensevolution, och visar att metoden ger högkvalitativa skattningar på både syntetiska och biologiska data. Vidare presenterar vi två utvidgningar av detta ramverk som möjliggör (i) genträdsskattningar med tidpunkter för duplikationer, samt (ii) probabilistiska ortologiskattningar – d.v.s. att två nutida gener härstammar från en artbildning. Slutligen presenterar vi en modell som inkluderar LGT utöver ovan nämnda mekanismer. De beräkningsmässiga svårigheter som LGT ger upphov till löses med ett intrikat ramverk av dynamisk programmering och numeriska metoder för differentialekvationer. Vi tillämpar metoden för att skatta LGT- och duplikationsraten hos två bakteriella dataset där LGT förmodas ha spelat en central roll. Vi visar också att traditionella metoder – där genträd skattas och förlikas med artträdet i separata steg – tenderar att ge sämre genträdsskattningar, och därmed överskatta antalet LGT-händelser. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 5: Manuscript.</p>

The angiosperm order Malpighiales includes \(\sim 16,000\) species and constitutes up to 40% of the understory tree diversity in tropical rain forests. Despite remarkable progress in angiosperm phylogenetics during the last 20 years, relationships within Malpighiales have remained poorly resolved, possibly due to its rapid rise during the mid-Cretaceous. Using phylogenomic approaches, including analyses of 82 plastid genes from 58 species, we identified 12 new clades in Malpighiales and substantially increased resolution along the backbone (Chapter 1). This greatly improved phylogeny revealed a dynamic history of shifts in net species’ diversification rates across Malpighiales, with bursts of diversification noted in the Barbados cherries (Malpighiaceae), cocas (Erythroxylaceae), and passion flowers (Passifloraceae). We also found that commonly used a priori approaches for partitioning data in similar large-scale analyses, by gene or by codon position, performed poorly relative to the use of partitions identified a posteriori using a Bayesian mixture model. Another aspect of my thesis focused on investigating horizontal gene transfer (HGT) in Malpighiales. Recent studies have suggested that plant genomes have undergone potentially rampant HGT. Parasitic plants have provided the strongest evidence of HGT, which appears to be facilitated by the intimate physical association between the parasites and their hosts. Using phylogenomic approaches, we analyzed the nuclear transcriptome (Chapter 2) and mitochondrial genome (Chapter 3) of the holoparasite Rafflesiaceae, which represents an enigmatic subclade of Malpighiales. Our analyses show that several dozen actively transcribed nuclear genes, and as many as 34–47% of its mitochondrial gene sequences, show evidence of HGT depending on the species. Some of these HGTs appear to have maintained synteny with their donor and recipient lineages suggesting that vertically inherited genes have likely been displaced via homologous recombination, as is common in bacteria. Finally, our results establish for the first time that although the magnitude of HGT involving nuclear genes is appreciable in these parasitic plants, HGT involving mitochondrial genes is substantially higher. Moreover, the elevated rate of unidirectional host-to-parasite gene transfer raises the possibility that HGTs may provide a fitness benefit to Rafflesiaceae for maintaining these genes.

The evolution of biological species depends on changes in genes. Among these changes are the gradual accumulation of DNA mutations, insertions and deletions, duplication of genes, movements of genes within and between chromosomes, gene losses and gene transfer. As two populations of the same species evolve independently, they will eventually become reproductively isolated and become two distinct species. The evolutionary history of a set of related species through the repeated occurrence of this speciation process can be represented as a tree-like structure, called a phylogenetic tree or a species tree. Since duplicated genes in a single species also independently accumulate point mutations, insertions and deletions, they drift apart in composition in the same way as genes in two related species. The divergence of all the genes descended from a single gene in an ancestral species can also be represented as a tree, a gene tree that takes into account both speciation and duplication events. In order to reconstruct the evolutionary history from the study of extant species, we use sets of similar genes, with relatively high degree of DNA similarity and usually with some functional resemblance, that appear to have been derived from a common ancestor. The degree of similarity among different instances of the “same gene” in different species can be used to explore their evolutionary history via the reconstruction of gene family histories, namely gene trees. Orthology refers specifically to the relationship between two genes that arose by a speciation event, recent or remote, rather than duplication. Comparing orthologous genes is essential to the correct reconstruction of species trees, so that detecting and identifying orthologous genes is an important problem, and a longstanding challenge, in comparative and evolutionary genomics as well as phylogenetics. A variety of orthology detection methods have been devised in recent years. Although many of these methods are dependent on generating gene and/or species trees, it has been shown that orthology can be estimated at acceptable levels of accuracy without having to infer gene trees and/or reconciling gene trees with species trees. Therefore, there is good reason to look at the connection of trees and orthology from a different angle: How much information about the gene tree, the species tree, and their reconciliation is already contained in the orthology relation among genes? Intriguingly, a solution to the first part of this question has already been given by Boecker and Dress [Boecker and Dress, 1998] in a different context. In particular, they completely characterized certain maps which they called symbolic ultrametrics. Semple and Steel [Semple and Steel, 2003] then presented an algorithm that can be used to reconstruct a phylogenetic tree from any given symbolic ultrametric. In this thesis we investigate a new characterization of orthology relations, based on symbolic ultramterics for recovering the gene tree. According to Fitch’s definition [Fitch, 2000], two genes are (co-)orthologous if their last common ancestor in the gene tree represents a speciation event. On the other hand, when their last common ancestor is a duplication event, the genes are paralogs. The orthology relation on a set of genes is therefore determined by the gene tree and an “event labeling” that identifies each interior vertex of that tree as either a duplication or a speciation event. In the context of analyzing orthology data, the problem of reconciling event-labeled gene trees with a species tree appears as a variant of the reconciliation problem where genes trees have no labels in their internal vertices. When reconciling a gene tree with a species tree, it can be assumed that the species tree is correct or, in the case of a unknown species tree, it can be inferred. Therefore it is crucial to know for a given gene tree whether there even exists a species tree. In this thesis we characterize event-labelled gene trees for which a species tree exists and species trees to which event-labelled gene trees can be mapped. Reconciliation methods are not always the best options for detecting orthology. A fundamental problem is that, aside from multicellular eukaryotes, evolution does not seem to have conformed to the descent-with-modification model that gives rise to tree-like phylogenies. Examples include many cases of prokaryotes and viruses whose evolution involved horizontal gene transfer. To treat the problem of distinguishing orthology and paralogy within a more general framework, graph-based methods have been proposed to detect and differentiate among evolutionary relationships of genes in those organisms. In this work we introduce a measure of orthology that can be used to test graph-based methods and reconciliation methods that detect orthology. Using these results a new algorithm BOTTOM-UP to determine whether a map from the set of vertices of a tree to a set of events is a symbolic ultrametric or not is devised. Additioanlly, a simulation environment designed to generate large gene families with complex duplication histories on which reconstruction algorithms can be tested and software tools can be benchmarked is presented.

Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Here I outline these scenarios and consider the fit of the available data, including two recently sequenced genomes from members of the Aquificae, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the ?-Proteobacteria have the strongest affinities with the three Aquificae analyzed. However, this phylogenetic signal is by no means the dominant one, with the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class ?-Proteobacteria also showing strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: as observed previously, most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, while a wide range of metabolic systems strongly supported the Aquificae - ?-Proteobacteria link. Given the breadth of support for this latter relationship, a scenario of ?-proteobacterial ancestry coupled with frequent exchange among thermophilic lineages is a plausible explanation for the emergence of the Aquificae.

With rapid advances in sequencing technologies and precipitous decreases in cost, public sequence databases have increased in size apace. However, experimental characterization of novel genes and their products remains prohibitively expensive and time consuming. For these reasons, bioinformatics approaches have become increasingly necessary to generate hypotheses of biological function. Phylogenomic approaches use phylogenetic methods to place genes, chromosomes, or whole genomes within the context of their evolutionary history and can be used to predict the function of encoded proteins. In this thesis, two new phylogenomic methods and software implementations are presented that address the problems of subcellular localization prediction and functional divergence prediction within protein families respectively. Most of the widely used programs for subcellular localization prediction have been trained on model organisms and ignore phylogenetic information. As a result, their predictions are not always reliable when applied to phylogenetically divergent eukaryotes, such as unicellular protists. To address this problem, PhyloPred-HMM, a novel phylogenomic method was developed to predict sequences that are targeted to mitochondria or mitochondrion-related organelles (hydrogenosomes and mitosomes). This method was compared to existing prediction methods using an existing test dataset of mitochondrion-targeted sequences from well-studied groups, sequences from a variety of protists, and the whole proteomes of two protists: Tetrahymena thermophila and Trichomonas vaginalis. PhyloPred-HMM performed comparably to existing classifiers on mitochondrial sequences from well-studied groups such as animals, plants, and Fungi and better than existing classifiers on diverse protistan lineages. FunDi, a novel approach to the prediction of functional divergence was developed and tested on 11 biological datasets and two large simulated datasets. On the 11 biological datasets, FunDi appeared to perform comparably to existing programs, although performance measures were compromised by a lack of experimental information. On the simulated datasets, FunDi was clearly superior to existing methods. FunDi, and two other prediction programs, was then used to characterize the functional divergence in two groups of plastid-targeted glyceraldehyde-3-phosphate dehydrogenases (GAPDH) adapted to roles in the Calvin cycle. FunDi successfully identified functionally divergent residues supported by experimental data, and identified cases of potential convergent evolution between the two groups of GAPDH sequences.

Most living eukaryotes are currently classified into one of five or six ‘supergroups’, which are in turn often divided between two assemblages: ‘unikonts’ and ‘bikonts’. This thesis explores the cytoskeletal morphology and phylogeny of three lineages that do not belong to any supergroup: ancyromonads, apusomonads, and breviates, likely relatives of supergroups Opisthokonta and Amoebozoa. It also investigates the phylogeny of malawimonads (basal members of supergroup Excavata) and collodictyonids (another unaffiliated lineage). Serial-section transmission electron microscopy was used to model the flagellar apparatus cytoskeletons of the ancyromonad Ancyromonas sigmoides, the breviate Breviata anathema, and the apusomonad Thecamonas trahens. Each has two main posterior microtubular roots and at least one anterior root (two in Ancyromonas). All three possess splitting posterior right microtubular roots and supernumerary singlets, features also characteristic of basal members of the supergroup Excavata (‘typical excavates’). One peripheral microtubule system in Ancyromonas, and the ‘right ribbon’ in Thecamonas, are likely homologous to dorsal fans in Breviata and ‘typical excavates’, and to the ‘r2’ root of myxogastrid Amoebozoa. One of the branches of the splitting root in Breviata and Thecamonas joins the right and intermediate roots, similarly to some myxogastrids. This implies that myxogastrids, and not the simpler pelobionts, represent the ancestral state for Amoebozoa. A phylogenomic analysis was performed focussing on apusomonads breviates, ancyromonads, and the problematic ‘typical excavate’ malawimonads, based on new transcriptomic data from Ancyromonas and an undescribed malawimonad. Rapid-site- removal analyses recover the ‘unikont’/‘bikont’ partition, and do not support the previously demonstrated affiliation between breviates and the ‘unikont’ supergroup Amoebozoa. Specifically, they group apusomonads with the ‘unikont’ supergroup Opisthokonta, and ancyromonads with breviates. Taxon-removal analyses group ancyromonads, breviates, and apusomonads together. Most analyses group malawimonads (perhaps with collodictyonids, another problematic group) between ‘unikonts’ and (other) ‘bikonts’, while other excavates are in a basal position amongst other ‘bikonts’. Combining these morphological and phylogenetic results suggests that splitting right roots, supernumerary intermediate singlets, and dorsal fans are found in multiple ‘basal’ lineages in both ‘unikont’ and ‘bikont’ portions of the eukaryotic tree, are likely characters of the last common ancestor of most or all living eukaryotes.