The central task in phylogenetics is to infer the evolutionary relationships among a given set of species. These relationships are usually represented by a phylogenetic tree with the species of interest at the leaves and where the internal vertices of the tree represent ancestral species. The amount of available molecular data is increasing exponentially and, given the continual advances in sequencing techniques and throughput, this explosive growth will likely continue. These vast amounts of available data mean that biologists are able to assemble large multi-gene datasets for use in phylogenetic analyses, which presents distinct computational challenges. Supertree methods comprise one approach to reconstructing large phylogenies, given estimated trees for overlapping subsets of the entire set of taxa. These source trees are combined into a single supertree on the full set of taxa using various algorithmic techniques. When the data allow, the competing approach is a combined analysis (also known as a “super-matrix” or “total evidence” approach), whereby the different sequence data matrices for each of the different subsets of taxa are put into a single super-matrix, and a tree is estimated on that super-matrix. In this dissertation, I present simulation software I designed to allow users to compare the relative performance of different supertree methods, as well as that of combined analysis, on more realistic data and on a larger scale than has been used up to this point. I present an extensive simulation study that uses this software to compare the performance of supertree methods and combined analysis, and that demonstrates a need for more topologically accurate supertree methods. I also introduce a new supertree method that I have developed that outperforms the most commonly used, and what until now has arguably been the most accurate, supertree method. / text

Human species display complex intraspecies population structure and unparalleled behavioral and cultural diversity. In order to elucidate human population history and pattern of evolutionary change of socio-cultural and ecological traits, the first composite phylogenetic tree of 574 human populations (ethno-linguistic groups) was created on the basis of 129 recently published phylogenetic hypotheses based on genomic, genetic and linguistic data, utilizing supertree method matrix representation with parsimony. Subsequently, 56 selected socio-cultural and ecological characters based on ethnographic cross-cultural data were optimized on topology of obtained supertrees in order to reconstruct patterns of evolutionary change and states present in ancestral populations. The results are discussed in the light of recent studies of human phylogeography and cultural phylogenetic studies.

Despite being found in all presently sequenced genomes, the evolution of tandemly repeated sequences has only just begun to be understood. We can represent the duplication history of tandemly repeated sequences with duplication trees. Most phylogenetic techniques need to be modified to be used on duplication trees. Due to gene loss, it is not always possible to reconstruct the duplication history of a tandemly repeated sequence. This thesis addresses this problem by providing a polynomial-time locally optimal algorithm to reconstruct the duplication history of a tandemly repeated sequence in the presence of gene loss. Supertree methods cannot be directly applied to duplication trees. A polynomial-time algorithm that takes a forest of ordered phylogenies and looks for a super duplication tree is presented. If such a super duplication tree is found then the algorithm constructs the super duplication tree. However, the algorithm does not always find a super duplication tree when one exists. The SPR topological rearrangement in its current form cannot be used on duplication trees. The necessary modifications are made to an agreement forest so that the SPR operation can be used on duplication trees. This operation is called the duplication rooted subtree prune and regraft operation (DrSPR). The size of the DrSPR neighbourhood is calculated for simple duplication trees and the tree shapes that maximize and minimize this are given.

The phylogenetic reconstruction has noted great development in recent decades. The development of computers and device for sequencing biopolymers have been an enormous amount od phylogenetic data from different sources and different types. The scientists are trying to reconstruct a comlet tree of life from these data. The phylogenetic supertree are theoretically this option because a supertree alow a combination of all information gathered so far – in contras to the phylogenetic trees. This thesis present the method of reconstruction supertrees using average konsensus method.

The Phylogenetic reconstruction has seen great development in the last 30 years. Computers have become more powerful and more generally accessible, and computer algorithms more sophisticated. It comes the effort of scientists to reconstruct the entire tree of life from a large amount of phylogenetic data. Just for this purpose are formed phylogenetic supertrees that allow the combination of all information gathered so far. The aim of this work is to find a method to construct supertree that will give correct results.

Limnephilidae is a large family within Trichoptera, consisting of 4 subfamilies (Dicosmoecinae, Ecclisomyiinae, Limnephilinae, and Philocascinae), 98 genera, and 1178 species. It is among the most diverse families within Trichoptera. It is also ecologically diverse, occupying more habitats than any other family in the order. There are currently no published generic phylogenies of Limnephilidae based on molecular data. Here we used anchored hybrid enrichment to capture and sequence 922 loci for 57 species taken from what have been considered the full range of genera in the family. We expanded the taxon sampling by adding supplementary species with DNA barcodes, 28S sequences, or containing both from other sources. We present a favored tree from the collected data. We examine the evolutionary patterns associated with larval habitat transitions and highlight instances where our preferred evolutionary tree is incongruent with current limnephilid classification.

Si le but de la reconstruction phylogénétique est d'avoir une idée des relations de parenté réelles entre les êtres vivants, il est bon de ne pas se contenter d'un simple arbre obtenu par l'analyse combinée d'un ensemble de données. En effet, même des clades robustes apparaissant dans un tel arbre peuvent ne pas être fiables. La confiance dans une affirmation phylogénétique ne peut émerger qu'après une comparaison de résultats obtenus par des données indépendantes.<br />Dans un premier temps, la présente thèse propose de mesurer la fiabilité d'un clade à partir d'un indice de répétition prenant en compte le nombre d'occurrences obtenues pour ce clade sur un ensemble d'analyses de données indépendantes, c'est-à-dire peu susceptibles de donner lieu aux mêmes biais de reconstruction. Plus un clade est obtenu un nombre élevé de fois de cette façon, plus il peut être considéré comme fiable. Il est également tenu compte de la présence ou non de clades eux-mêmes répétés et incompatibles avec le clade d'intérêt. Plus un clade est contredit par un clade possédant un grand nombre d'occurrences, moins il doit être considéré comme fiable.<br />Dans une deuxième partie, l'indice de répétition est calculé à partir d'une série d'analyses mettant en jeu environ 200 taxons et basées sur quatre marqueurs nucléaires: Rhodopsine, MLL4, IRBP et RNF213 (ce dernier étant utilisé ici pour la première fois). Ces marqueurs sont analysés suivant des méthodes probabilistes, séparément et en combinaisons de 2, 3 ou 4, ce qui permet de bénéficier des avantages de l'analyse combinée tout en ayant des séries de résultats indépendants à comparer.<br />Les résultats de l'analyse de fiabilité sont ensuite synthétisés sous forme d'arbres incluant en priorité les clades les plus fiables, suivant des méthodes gérant de plusieurs façons les différences d'échantillonnages taxinomiques entre les jeux de données.<br />Les arbres de synthèse obtenus permettent de préciser la structure de la phylogénie des téléostéens acanthomorphes (Actinopterygii : Teleostei). De nouveaux clades fiables sont identifiés à plusieurs niveaux de résolution, et de nouveaux taxons sont placés dans la phylogénie des téléostéens acanthomorphes.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

Phylogenetics is the research of ancestor-descendant relationships among different groups of organisms, for example, species or populations of interest. The datasets involved are usually sequence alignments of various subsets of taxa for various genes. A major task of phylogenetics is often to combine estimated gene trees from many loci sampled from the genes into an overall estimate species tree topology. Eventually, one can construct the tree of life that depicts the ancestor-descendant relationships for all known species around the world. If there is missing data or incomplete sampling in the datasets, then supertree methods can be used to assemble gene trees with different subsets of taxa into an estimated overall species tree topology. In this study, we assume that gene tree discordance is solely due to incomplete lineage sorting under the multispecies coalescent model (Degnan and Rosenberg, 2009). If there is missing data or incomplete sampling in the datasets, then supertree methods can be used to assemble gene trees with different subsets of taxa into an estimated species tree topology. In addition, we examine the performance of the most commonly used supertree method (Wilkinson et al., 2009), namely matrix representation with parsimony (MRP), to explore its statistical properties in this setting. In particular, we show that MRP is not statistically consistent. That is, an estimated species tree topology other than the true species tree topology is more likely to be returned by MRP as the number of gene trees increases. For some situations, using longer branch lengths, randomly deleting taxa or even introducing mutation can improve the performance of MRP so that the matching species tree topology is recovered more often. In conclusion, MRP is a supertree method that is able to handle large amounts of conflict in the input gene trees. However, MRP is not statistically consistent, when using gene trees arise from the multispecies coalescent model to estimate species trees.