Dissertations / Theses on the topic 'Phylogeney'

The study of phylogeny, i.e. the evolutionary history of species, is a central problem in biology and a key for understanding characteristics of contemporary species. Many problems in this area can be formulated as combinatorial optimisation problems which makes it particularly interesting for computer scientists. The reconstruction of the phylogeny of species can be based on various kinds of data, e.g. morphological properties or characteristics of the genetic information of the species. Maximum parsimony is a popular and widely used method for phylogenetic reconstruction aiming for an explanation of the observed data requiring the least evolutionary changes. A certain property of the genetic information gained much interest for the reconstruction of phylogeny in recent time: the organisation of the genomes of species, i.e. the arrangement of the genes on the chromosomes. But the idea to reconstruct phylogenetic information from gene arrangements has a long history. In Dobzhansky and Sturtevant (1938) it was already pointed out that “a comparison of the different gene arrangements in the same chromosome may, in certain cases, throw light on the historical relationships of these structures, and consequently on the history of the species as a whole”. This kind of data is promising for the study of deep evolutionary relationships because gene arrangements are believed to evolve slowly (Rokas and Holland, 2000). This seems to be the case especially for mitochondrial genomes which are available for a wide range of species (Boore, 1999). The development of methods for the reconstruction of phylogeny from gene arrangement data has made considerable progress during the last years. Prominent examples are the computation of parsimonious evolutionary scenarios, i.e. a shortest sequence of rearrangements transforming one arrangement of genes into another or the length of such a minimal scenario (Hannenhalli and Pevzner, 1995b; Sankoff, 1992; Watterson et al., 1982); the reconstruction of parsimonious phylogenetic trees from gene arrangement data (Bader et al., 2008; Bernt et al., 2007b; Bourque and Pevzner, 2002; Moret et al., 2002a); or the computation of the similarities of gene arrangements (Bergeron et al., 2008a; Heber et al., 2009). 1 1 Introduction The central theme of this work is to provide efficient algorithms for modified versions of fundamental genome rearrangement problems using more plausible rearrangement models. Two types of modified rearrangement models are explored. The first type is to restrict the set of allowed rearrangements as follows. It can be observed that certain groups of genes are preserved during evolution. This may be caused by functional constraints which prevented the destruction (Lathe et al., 2000; Sémon and Duret, 2006; Xie et al., 2003), certain properties of the rearrangements which shaped the gene orders (Eisen et al., 2000; Sankoff, 2002; Tillier and Collins, 2000), or just because no destructive rearrangement happened since the speciation of the gene orders. It can be assumed that gene groups, found in all studied gene orders, are not acquired independently. Accordingly, these gene groups should be preserved in plausible reconstructions of the course of evolution, in particular the gene groups should be present in the reconstructed putative ancestral gene orders. This can be achieved by restricting the set of rearrangements, which are allowed for the reconstruction, to those which preserve the gene groups of the given gene orders. Since it is difficult to determine functionally what a gene group is, it has been proposed to consider common combinatorial structures of the gene orders as gene groups (Marcotte et al., 1999; Overbeek et al., 1999). The second considered modification of the rearrangement model is extending the set of allowed rearrangement types. Different types of rearrangement operations have shuffled the gene orders during evolution. It should be attempted to use the same set of rearrangement operations for the reconstruction otherwise distorted or even wrong phylogenetic conclusions may be obtained in the worst case. Both possibilities have been considered for certain rearrangement problems before. Restricted sets of allowed rearrangements have been used successfully for the computation of parsimonious rearrangement scenarios consisting of inversions only where the gene groups are identified as common intervals (Bérard et al., 2007; Figeac and Varré, 2004). Extending the set of allowed rearrangement operations is a delicate task. On the one hand it is unknown which rearrangements have to be regarded because this is part of the phylogeny to be discovered. On the other hand, efficient exact rearrangement methods including several operations are still rare, in particular when transpositions should be included. For example, the problem to compute shortest rearrangement scenarios including transpositions is still of unknown computational complexity. Currently, only efficient approximation algorithms are known (e.g. Bader and Ohlebusch, 2007; Elias and Hartman, 2006). Two problems have been studied with respect to one or even both of these possibilities in the scope of this work. The first one is the inversion median problem. Given the gene orders of some taxa, this problem asks for potential ancestral gene orders such that the corresponding inversion scenario is parsimonious, i.e. has a minimum length. Solving this problem is an essential component 2 of algorithms for computing phylogenetic trees from gene arrangements (Bourque and Pevzner, 2002; Moret et al., 2002a, 2001). The unconstrained inversion median problem is NP-hard (Caprara, 2003). In Chapter 3 the inversion median problem is studied under the additional constraint to preserve gene groups of the input gene orders. Common intervals, i.e. sets of genes that appear consecutively in the gene orders, are used for modelling gene groups. The problem of finding such ancestral gene orders is called the preserving inversion median problem. Already the problem of finding a shortest inversion scenario for two gene orders is NP-hard (Figeac and Varré, 2004). Mitochondrial gene orders are a rich source for phylogenetic investigations because they are known for more than 1 000 species. Four rearrangement operations are reported at least in the literature to be relevant for the study of mitochondrial gene order evolution (Boore, 1999): That is inversions, transpositions, inverse transpositions, and tandem duplication random loss (TDRL). Efficient methods for a plausible reconstruction of genome rearrangements for mitochondrial gene orders using all four operations are presented in Chapter 4. An important rearrangement operation, in particular for the study of mitochondrial gene orders, is the tandem duplication random loss operation (e.g. Boore, 2000; Mauro et al., 2006). This rearrangement duplicates a part of a gene order followed by the random loss of one of the redundant copies of each gene. The gene order is rearranged depending on which copy is lost. This rearrangement should be regarded for reconstructing phylogeny from gene order data. But the properties of this rearrangement operation have rarely been studied (Bouvel and Rossin, 2009; Chaudhuri et al., 2006). The combinatorial properties of the TDRL operation are studied in Chapter 5. The enumeration and counting of sorting TDRLs, that is TDRL operations reducing the distance, is studied in particular. Closed formulas for computing the number of sorting TDRLs and methods for the enumeration are presented. Furthermore, TDRLs are one of the operations considered in Chapter 4. An interesting property of this rearrangement, distinguishing it from other rearrangements, is its asymmetry. That is the effects of a single TDRL can (in the most cases) not be reversed with a single TDRL. The use of this property for phylogeny reconstruction is studied in Section 4.3. This thesis is structured as follows. The existing approaches obeying similar types of modified rearrangement models as well as important concepts and computational methods to related problems are reviewed in Chapter 2. The combinatorial structures of gene orders that have been proposed for identifying gene groups, in particular common intervals, as well as the computational approaches for their computation are reviewed in Section 2.2. Approaches for computing parsimonious pairwise rearrangement scenarios are outlined in Section 2.3. Methods for the computation genome rearrangement scenarios obeying biologically motivated constraints, as introduced above, are detailed in Section 2.4. The approaches for the inversion median problem are covered in Section 2.5. Methods for the reconstruction of phylogenetic trees from gene arrangement data are briefly outlined in Section 2.6.3 1 Introduction Chapter 3 introduces the new algorithms CIP, ECIP, and TCIP for solving the preserving inversion median problem. The efficiency of the algorithm is empirically studied for simulated as well as mitochondrial data. The description of algorithms CIP and ECIP is based on Bernt et al. (2006b). TCIP has been described in Bernt et al. (2007a, 2008b). But the theoretical foundation of TCIP is extended significantly within this work in order to allow for more than three input permutations. Gene order rearrangement methods that have been developed for the reconstruction of the phylogeny of mitochondrial gene orders are presented in the fourth chapter. The presented algorithm CREx computes rearrangement scenarios for pairs of gene orders. CREx regards the four types of rearrangement operations which are important for mitochondrial gene orders. Based on CREx the algorithm TreeREx for assigning rearrangement events to a given tree is developed. The quality of the CREx reconstructions is analysed in a large empirical study for simulated gene orders. The results of TreeREx are analysed for several mitochondrial data sets. Algorithms CREx and TreeREx have been published in Bernt et al. (2008a, 2007c). The analysis of the mitochondrial gene orders of Echinodermata was included in Perseke et al. (2008). Additionally, a new and simple method is presented to explore the potential of the CREx method. The new method is applied to the complete mitochondrial data set. The problem of enumerating and counting sorting TDRLs is studied in Chapter 5. The theoretical results are covered to a large extent by Bernt et al. (2009b). The missing combinatorial explanation for some of the presented formulas is given here for the first time. Therefor, a new method for the enumeration and counting of sorting TDRLs has been developed (Bernt et al., 2009a).

La classification actuelle de la famille des Phytoseiidae n'est pas basée sur de réelles études phylogénétiques et par conséquent, de nombreuses questions se posent sur la validité des taxa supra-spécifiques mais également vis-à-vis des taxa spécifiques. Ce travail de thèse avait donc pour objectif de répondre à de telles questions pour deux genres : Phytoseiulus et Neoseiulella, en utilisant pour la première fois des approches phylogénétiques moléculaires et morphologiques. Ces études phylogénétiques ont été également associées à des études biogéographiques. Les résultats obtenus par ces deux approches sont congruents et semblent montrer que ces deux genres ne sont pas monophylétiques : le genre Phytoseiulus semble au mieux paraphylétique, tandis que le genre Neoseiulella serait polyphylétique. Ces résultats sont différents de ceux développés dans les diverses révisions successives de ces deux taxa. Ce travail de thèse a permis de répondre également à des questionnements sur cinq synonymies au sein du genre Neoseiulella. L'étude de pratiquement tous les types des espèces du genre Neoseiulella nous a permis de redéfinir le genre, en excluant trois espèces et en discutant certaines synonymies. Une clé d'identification des adultes femelles des espèces valides a également été proposée. Des études complémentaires, notamment des analyses moléculaires, seront nécessaires afin de conclure plus définitivement sur les relations évolutives entre les taxa étudiés
The present classification of the family Phytoseiidae is not based on solid phylogenetic studies and therefore, many taxonomic questions still arise, concerning the validity of supra-specific and specific taxa identified to-date. This thesis thus aimed to answer such questions for two genera, Phytoseiulus and Neoseiulella, using for the first time molecular and morphological phylogenetic analyses. Biogeographic analyses have been also carried out. Results obtained by both morphological and molecular approaches are congruent and seem to show that both genera are not monophyletic: Phytoseiulus seems paraphyletic whereas Neoseiulella seems polyphyletic. These results are different from those obtained with previous revisions of these two taxa. Furthermore, this study allowed to conclude on five synonymies within the genus Neoseiulella. The observation of nearly the totality of the species belonging to the genus Neoseiulella permitted to redefine this genus, excluding three species and discussing some synonymies. Lastly, an identification key of the adult females was proposed for the valid species of the genus Neoseiulella. Further experiments, including molecular investigations, are however still required in order to obtain more reliable conclusions on the evolutionary relationships of the studied taxa

Geometric morphometrics, the science about the study of shape, has developed much in the last twenty years. In this thesis I first study the reliability of the phylogenies built using geometric morphometrics. The effect of different evolutionary models, branch-length combinations, dimensionality and degrees of integration is explored using computer simulations. Unfortunately in the most common situations (presence of stabilizing selection, short distance between internal nodes and presence of integration) the reliability of the phylogenies is very low. Different empirical studies are analysed to estimate the degree of evolutionary integration usually found in nature. This gives an idea about how powerful the effect of integration is over the reliability of the phylogenies in empirical studies. Evolutionary integration is studied looking at the decrease of variance in the principal components of the tangent shape space using the independent contrasts of shape. The results suggest that empirical data usually show strong degrees of integration in most of the organisms and structures analysed. These are bad news, since strong degree of integration has devastating effects over the phylogenetic reliability, as suggested by our simulations. However, we also propose the existence of other theoretical situations in which strong integration may not translate into convergence between species, like perpendicular orientation of the integration patterns or big total variance relative to the distance between species in the shape space. Finally, geometric morphometrics is applied to the study of the evolution of shape in proteins. There are reasons to think that, because of their modular nature and huge dimensionality, proteins may show different patterns of evolutionary integration. Unfortunately, proteins also show strong functional demands, which influence their evolution and that cause strong integration patterns. Integration is then confirmed as a widespread property in the evolution of shape, which causes poor phylogenetic estimates.

This thesis focuses on phylogenetic and taxonomic studies of Catenulida (Platyhelminthes). Catenulida is a group of microscopic free-living worms mainly found in freshwater habitats. The Swedish catenulid fauna was previously virtually unknown. The taxonomy of Catenulida is difficult because of the paucity of good morphological characters, which makes species identification extremely difficult.

Molecular phylogenies are inferred from DNA sequences. Based on two molecular markers, 18S rDNA and 28S rDNA, the phylogenetic position of Catenulida has now been well established as the sister group to the rest of the flatworms, Rhabditophora. Within Catenulida there is a basal split between two major clades: Retronectidae + Catenulidae and Stenostomidae. The hypothesis of the marine Retronectidae as the sister group of the limnic Catenulida is rejected.

Four molecular markers, 18S rDNA, 28S rDNA, ITS-5.8S and CO1, are used as a backbone to infer phylogeny and to generate hypotheses about species delimitation in Catenulida using parsimony jackknifing and Bayesian analysis. Anokkostenostomum comes out non-monophyletic, and Suomina nested within Catenula, so two new synonymies are proposed: Stenostomum Schmidt, 1848 (Anokkostenostomum Noreña et al. 2005) and Catenula Duges, 1832 (Suomina Marcus, 1945) are proposed.

A first report on Swedish freshwater Catenulida are given. A total of 13 species are reported from Sweden. Four of them, all belonging to the taxon Stenostomum are new to science: S. gotlandense n.sp.; S. handoelense n.sp.; S. heebuktense n.sp. and S. steveoi n.sp.

Discernir as relações evolutivas entre os grandes grupos animais tem representado um formidável desafio para a Ciência. Os filos animais possuem arquiteturas corporais bastante distintas e por isso difíceis de serem comparadas. Ao mesmo tempo, seu registro fóssil converge aproximadamente para um mesmo intervalo na escala geológica, dificultando uma reconstrução filogenética com caracteres morfológicos. A disponibilidade de dados moleculares sobre os organismos abriu, contudo, novas possibilidades na filogenia animal. Esta dissertação buscou explorar essas possibilidades inferindo uma filogenia com métodos de distância e máxima verossimilhança, a partir de todos os genomas mitocondriais, completamente seqüenciados até o momento. No entanto, apenas alguns grandes agrupamentos como Diploblastica, Bilateria, Deuterostomia e Protostomia foram recuperados com forte suporte estatístico, além de pequenos agrupamentos de animais de mesma ordem ou família, indicando que os efeitos da rápida radiação no Cambriano se estenderam também ao registro molecular. Os resultados também indicam a necessidade de buscar modelos de evolução mais aderentes a este cenário. Deuterostomia, por exemplo, só foi recuperado monofileticamente assumindo-se a distribuição gama para variabilidade entre-sítios, ao custo, entretanto, da perda de definição nos ramos menores. Nematóides e Platelmintos, por sua vez, revelam um possível viés no skew (desvio) do conteúdo GC e AT de seus genes mitocondriais, que não é adequadamente mapeado por modelos de substituição reversíveis. Os indícios são de que a resolução da filogenia animal depende ainda de uma melhor compreensão da evolução molecular em escala genômica.
Inferring the evolutive relations between the animal phyla has been a formidable challenge to Science. The animal phyla represent quite distinct baupläne (body architectures) and are, therefore, difficult to compare. At the same time, their fossil record converges mostly to the same period on the geological scale. The recent availability of molecular data has, however, inaugurated a new front in animal phylogeny. The present work explores this opportunity by inferring a phylogeny with distance and maximum likelihood methods, employing all animal mitochondrial genomes ever sequenced. The results present only a few bigger groups with strong statistical support, like Diploblastica, Bilasteria, Protostomia and Deutorostomia, and many smaller groups of animals belonging to the same order or family. These results seems to confirm that the phyla radiated in such a short time interval that the phylogenetic signal did not hold out to produce a satisfactory resolution of the animal tree to date. Some limits may have yet to be tested, through models of evolution more fit to this scenario. For example was only recovered with the use of gamma distances for site-to-site substitution rate variability, at the expense of compressing the smaller branches throughout the tree. Nematodes and Platyhelminthes reveal a bias in GC and AT skew that cannot be adequately mapped by any reversible substitution pattern. Nevertheless, even if corrections are found for these issues, it is well possible that the hope of a better resolution in the animal tree will lie further on, by a better understanding of the evolutive process in a genomic scale.

Durant cette thèse je me suis intéressé à l'évolution profonde du vivant, depuis le dernier ancêtre commun universel (LUCA) jusqu'aux ancêtres des trois grands royaumes, les Archées, les Bactéries et les Eucaryotes. J'ai notamment cherché à placer quelques organismes dans l'arbre de la vie, tels que la bactérie Aquifex aeolicus et l'archée Cenarchaeum symbiosum, et j'ai également étudié l'évolution des températures de croissance il y a plusieurs milliards d'années. Pour ce faire, j'ai développé des algorithmes a n de reconstruire l'évolution de séquences géniques, puis j'ai utilisé ces séquences pour prédire les températures optimales de croissances d'organismes aujourd'hui éteints. Mes collègues et moi-même estimons que LUCA ne vivait pas à très haute température, mais que ses directs descendants les ancêtres des Bactéries et du groupe comprenant les Archées et les Eucaryotes vivaient dans des environnements plus chauds. Cela signi e que les deux lignées venant de LUCA ont subi le même type d'évolution en parallèle, qui pourrait avoir été causée par une seule et même pression de sélection. Cette pression pourrait être le résultat d'un intense bombardement météoritique il y a 3. 8 milliards d'années, et avoir été accompagnée d'un changement depuis un génome à ARN pour LUCA vers des génomes à ADN pour ses descendants. Ensuite, dans la lignée des Bactéries, les températures optimales de croissance ont chuté, ce qui pourrait correspondre à l'évolution de la température des océans au cours des 3. 5 derniers milliards d'années
During this thesis, I studied the early evolution of life, from the Last Universal Common Ancestor (LUCA) to the ancestors of the three kingdoms, Archaea, Bacteria and Eukarya. Notably, I have attempted to place a few organisms in the tree of life, namely the bacteria Aquifex aeolicus and the archaea Cenarchaeum symbiosum, and I also studied the evolution of optimal growth temperatures over the last four billion years. To this end, I developed algorithms to reconstruct ancestral gene sequences, and used these sequences to predict the optimal growth temperatures of now-extinct organisms. My colleagues and I estimate that LUCA did not live in a very hot environment, but that its descendants the ancestors of Bacteria and of the group containing Archaea and Eukarya both lived at higher temperatures. This implies that the two lineages descending from LUCA underwent the same kind of evolution in parallel, perhaps caused by the same unique selection pressure. This pressure may have resulted from an intense meteoritic bombardment 3. 8 billion years ago, and have been accompanied by the transition from an RNA genome in LUCA to DNA genomes in its descendants. Subsequently in the bacterial lineage, optimal growth temperature dropped, which may correspond to the evolution of oceanic temperatures in the last 3. 5 billion years

Titre: Histoire évolutive des symbioses entre les microsporidies et leurs hôtes amphipodes: contribution de l’étude de deux hôtes sur leurs aires de repartion géographiques.Mots clés: Symbioses, phylogénie, phylogéographie, amphipodes, hôte parasite, microsporidies.Résumé: Les microsporidies sont des endoparasites obligatoires, ils utilisent deux modes de transmission pour expoiter leurs hotes. Certaines espèces utilisent la transmission verticale et d'autres la transmission horizontale. La première favorise la co-spéciation et la spécificité hôte-parasite, tandis que la seconde favorise les échanges de parasites entre espèces hôtes. Les amphipodes d'eau douce sont des hôtes privilégiers pour de nombreuses espèces de microsporidies, mais aucun schéma général de spécificité hôte-parasite ou de co-diversification n’émerge des recherches menées depuis trente ans.Dans ce travail, la diversité des infections microsporidiennes, sur la base des données SSU rdNA, ont été évaluées dans deux complexes d'espèces de Gammarus, G. roeselii et G. balcanicus, sur l'ensemble de leur aire de répartition géographique, en s'appuyant sur des efforts d'échantillonnage importants (environ 100 sites et 2 000 individus). L’objectif de ce doctorat est (i) d’explorer la diversité microsporidienne présente dans les deux hôtes et leurs relations phylogénétiques; (ii) vérifier si la phylogéographiques de l'hôte peut expliqué l'association hôte-parasite (co-diversifications ou récents aquisition a partir de la faune locale); (iii) proposer des scénarios d'histoire évolutive hôte-parasite pour expliquer la diversité et le schéma co-bio-géographique observé chez les deux espèces hôtes chez N. granulosis.Le marqueur SSU d’ADNr a révélé un grand nombre de variants chez ces deux hôtes (c’est-à-dire 24 et 54 haplogroupes de, respectivement), regroupés en 18 taxons d’espèces, presque tous partagés entre les deux espèces hôtes. De nombreux haplogroupes de microsporidia appartenant à une espèce parasite donnée sont spécifiques à l'hôte, ce qui suggère un certain niveau de codiversification à cette échelle. Au sein de chacun des complexes d'espèces hôtes, la confrontation des phylogéographies des hôtes et des parasites suggère également un certain degré de co-diversification. Ceci reste néanmoins à confirmer, principalement parce que l'ADNr SSU atteint ses limites en termes d'informations phylogénétiques à cette échelle plus fine.Il est frappant de constater que presque tous ces taxons de microsporidia mis en évidence dans ce travail avaient déjà été détectés chez d’autres gammaridés. Certains étaient déjà des taxons parasites clairement identifiés associés aux amphipodes: Nosema granulosis, Dictyocoela roeselum, D. muelleri, D. roeselum, D. duebenum, D. berillonum, Cucumispora roeselum, C. ornata, Microsporidium sp 515 et Microsporidium sp 505). Mes résultats ont élargis les spectres taxonomiques d’hôte et les répartitions géographiques de ces parasites (souvent très étendues). Certains autres taxons étaient connus pour être extrêmement rares, et ne sont pas complètement décrits. Mon travail de doctorat a également étendu le spectre taxonomique d’hôte et / ou élargi considérablement les aires géographiques de ces taxons. Cela permet une réévaluation de ces taxons, faisant passer leur statut d'associations anecdotiques à des associations potentiellement bien établies, mais jusque là négligées, chez les amphipodes
Title: Evolutionary histories of symbioses between microsporidia and their amphipod hosts : contribution of studying two hosts over their geographic ranges.Keywords: Symbioses, Phylogeny, Phylogeography, Amphipods, Host-Parasite, MicrosporidiaAbstract: Microsporidia are obligate endoparasites, exploiting their hosts with either vertical or horizontal transmission. While the former may promote co-speciation and host-specificity, the latter may promote shifts between host species. Freshwater amphipods are hosts for many microsporidian species, but no general pattern of host specificity and co-diversification is known.In my PhD work microsporidian infections, identified with SSU rDNA, were assessed in two Gammarus species complexes, G. roeselii and G. balcanicus , over their full geographic ranges (each c. 100 sites and 2000 individuals) in aim of (i) exploring the microsporidian diversity present in both hosts and their phylogenetic relationships; (ii) testing if the host phylogeographic history might have impacted host-parasite association (co-diversifications or recent host-shifts from local fauna); (iii) proposing the host-parasite evolutionary history scenarios to explain the diversity and co-bio-geographical pattern observed in the two host species between using N. granulosis as a model.The SSU rDNA marker revealed a high number of microsporidian variants (i.e. haplogroups, 24 and 54, respectively), clustered into 18 species-level taxa, almost all being shared between the two host species. However, many microsporidian haplogroups within a given parasite species are host-specific, suggesting host-parasite co-variation. Within each host species-complex, while the confrontation between hosts and parasites phylogeography suggested some degrees of co-diversification, these patterns remain to be confirmed, mainly as SSU rDNA reached its limits in phylogenetic information content in that matter.Strikingly, almost all of these microsporidia taxa were previously detected in other gammarids, mainly within the genus Gammarus, but also in other genera of Gammaridae. Some were already clearly recognised parasite taxa associated with amphipods: Nosema granulosis, Dictyocoela roeselum, D. muelleri, D. roeselum, D. duebenum, D. berillonum, Cucumispora roeselum, C. ornata, C. dikerogammari, Microsporidium sp 515 and Microsporidium sp 505). Many times, my results increased host taxonomic spectrums and extended geographic ranges (often widely). Some other taxa were known to be extremely rare, having scarce literature records often with few or even very few geographic records and being not fully described. My PhD work either extend host taxonomic spectrum and/or deeply extend geographic ranges for these taxa. It allowed a reappraisal for such taxa, changing their status from puzzling anecdotic association to potentially overlooked established associations for amphipods

Though molecular phylogenetics has been very successful in reconstructing the evolutionary history of species, some phylogenies, particularly those involving ancient events, have proven difficult to resolve. One approach to improving the resolution of deep phylogenies is to increase the amount of data by including multiple genes assembled from public sequence databases. Using modern phylogenetic methods and abundant computing power, the vast amount of sequence data available in public databases can be brought to bear on difficult phylogenetic problems. In this thesis I outline the motivation for assembling large multigene datasets and lay out the obstacles associated with doing so. I discuss the various methods by which these obstacles can be overcome and describe a bioinformatics solution, TaxMan, that can be used to rapidly assemble very large datasets of aligned genes in a largely automated fashion. I also explain the design and features of TaxMan from a biological standpoint and present the results of benchmarking studies. I illustrate the use of TaxMan to assemble large multigene datasets for two groups of taxa – the subphylum Chelicerata and the superphylum Lophotrochozoa. Chelicerata is a diverse group of arthropods with an uncertain phylogeny. When a set of mitochondrial genes is used to analyse the relationships between the chelicerate orders, the conclusions are highly dependent upon the evolutionary model used and are affected by the presence of systematic compsitional bias in mitochondrial genomes. Lophotrochozoa is a recently-proposed group of protostome phyla. A number of distinct phylogenetic hypotheses concerning the relationships between lophotrochozoan phyla have been proposed. I compare the phylogenetic conclusions given by analysis of nuclear and mitochondrial protein-coding and rRNA genes to evaluate support for some of these hypotheses.

Echinoderms are a highly diverse phylum of marine invertebrates with a good fossil record that extends back 550 million years. The work presented here is a contribution towards documenting their long history both in terms of phylogenetic branching pattern and evolutionary biology. Taxonomy is the primary means by which evolutionary processes can be studied because it is through taxonomy that species are recognised and their relationships to one another established. Taxonomy at various levels thus forms a major part of the thesis. Species are documented and described both for specific time intervals and within monophyletic groups. Relationships above species level are derived employing cladistic methodology and used to investigate various evolutionary concepts (e.g. the molecular clock; periodicity of extinction). Much of this work deals with the phylogenetic relationships of echinoids at various taxonomic levels, but the relationships of major groups within the phylum are also investigated cladistically. Class relationships have been clarified and revised. By combining data on phylogenetic relationships with those on stratigraphical occurrence, evolutionary trees are constructed which are then used to investigate current ideas on evolutionary processes. Topics investigated include punctuated versus gradualistic evolution, periodicity of extinction, the nature of the Cambrian radiation and the 'Red Queen hypothesis'. Artefact produced by taxonomic convention is recognised as a serious problem in many palaeobiological studies. The evolving relationship between echinoderms and their environment is investigated from a functional morphological point of view. Work of Recent faunas provides the key to understanding morphological variation in the fossil record. Evolutionary changes are documented through time and interpreted in biological terms for specific topics, such as tooth ultrastructure, ambulacral arrangement and trace fossil morphology. The relationship of fossil biotas to tectonic events and their application to palaeogeographical reconstruction is investigated quantitatively, both for echinoids and other groups.

The Pterosauria is an enigmatic group of volant reptiles from the Mesozoic. Despite demonstrating conspicuous apomorphic conditions, including an enlarged humeral deltopectoral crest, elongate wing spar comprising the fourth manual digit, and unique skull bone configurations, their cladogenesis is uncertain. While the ingroup monophyly of Pterosauria is clear, their interrelationships are contentious. The earliest studies of pterosaur phylogeny were concerned with phenotypic groups. The earliest cladistic analyses of pterosaurs in the late 20th Century were simple and were superseded by more comprehensive analyses in the early 21st Century. These analyses are comparable at the genus, family, and suborder level, but the ranks between these are incongruent between authors, leading to nomenclatural disputes. This study aims to understand the differences that exist between the competing phylogenetic hypotheses, why they exist, and to establish a more robust phylogenetic hypothesis. An extensive review of pterosaur phylogeny, cladistic character coding, and data transformation is performed. A distinct cladistic analysis is developed independently of the literature, providing a reference tree for a meta-analysis of topological congruence. Furthermore, this distinct analysis is supplemented with published characters to produce a comprehensive analysis which is a robust hypothesis of pterosaur phylogeny. Taxonomic actions are taken on the wastebasket taxon Pterodactylus and the paraphyletic genus Germanodactylus, to improve the taxonomic content of the analyses. The results demonstrate that analyses sharing characters produce trees with greater levels of congruence. Although this may be due to the introduction of biases, it is far more likely that the improvement seen in the comprehensive tree at least, is due to improving the phyletic content, sampling of anatomy, and reducing the negative effects of homoplasy. This is supported by the comprehensive tree's congruence to the stratigraphic record. The comprehensive tree agrees with the common clades of other studies, but some families are found in unique positions, most notably the Anurognathidae.

Für eine umfassende Untersuchung der Phylogenie der Decapoda wurden von mir die mitochondrialen Genome von 13 Dekapoden sequenziert. Zusammen mit den in der GenBank verfügbaren Sequenzen von 31 Dekapoden und dem von der Universität Bonn zur Verfügung gestellten mitochondrialen Genom von Dromia personata deckt dieser Datensatz alle großen Teilgruppen der Decapoda ab. Maximum likelihood (ML)-Analysen und Bayesian inference (BI)-Analysen der Nucleotidsequenzen und Aminosäuresequenzen ergaben bezüglich der Verwandtschaft der hochrangigen Taxa ähnliche Topologien: (((((((Anomala, Brachyura), Thalassinida: Gebiidea) Thalassinida: Axiidea), Astacidea), Achelata), Stenopodidea), Caridea), Dendrobranchiata). Gleichwohl wurde mit den Polychelida ein problematisches Taxon mit ungewissen Verwandtschaftsbeziehungen identifiziert. Auf der Eben der Unterordnungen sind die Thalassinida paraphyletisch, was mit einigen morphologischen und einigen jüngeren molekularen Studien konsistent ist, alle anderen gebräuchlichen Taxa sind monophyletisch. Es handelt sich um eine Inversion, die sich vom S-E-F tRNA cluster bis zum I-Q-M tRNA cluster erstreckt und in Procambarus fallax f. virginalis und Homarus gammarus auftritt. Im Vergleich mit dem Genarrangement des Limulus polyphemus zeigen beide Astaciden in dieser Region exakt dieselbe Inversion wie der Priapulide Priapulus caudatus, die daher innerhalb der Ecdysozoa als konvergent angenommen werden muss. Auch neben dieser Inversion innerhalb der Astacidea zeigen die Genarrangements aller verfügbaren Dekapoden mehrere interessante Eigenschaften. Um die beobachteten einzigartigen genomischen Eigenschaften zu erklären, schlage ich mit dem „inversion triggered duplication“ Model ein neues Modell für Gen-Rearrangements vor.
For a comprehensive study of decapod phylogeny at the mitochondrial genome level, I have sequenced the mitochondrial genome of 13 decapods. Together with available sequences of 31 decapods from GenBank, and the mitochondrial genome of Dromia personata provided by the Bonn University, the dataset now cover all major decapod taxa. Maximum likelihood (ML) and Bayesian inference (BI) of the nucleotide and amino acid datasets reveal similar topologies at the higher level relationships: (((((((Anomala, Brachyura), Thalassinida: Gebiidea) Thalassinida: Axiidea), Astacidea), Achelata), Stenopodidea), Caridea), Dendrobranchiata). Nevertheless, one problematic taxon, Polychelida, with ambiguous affinities is recognized. At the lower level, most taxa are monophyletic, whereas the Thalassinida is paraphyletic, which is consistent with some morphological and molecular results. An inversion spanning from S-E-F tRNA cluster to the I-Q-M tRNA cluster occurred in Procambarus fallax f. virginalis, Homarus gammarus, and one priapulid Priapulus caudatus. Compared with the gene arrangement of the horseshoe crab Limulus polyphemus, both astacids and the priapulid exhibit the same inversion, which is therefore supposed to be a convergent event of the clade Astacidea and Priapulida among Ecdysozoa. Other than this notable feature observed in astacids, the gene arrangements in all available decapods show some interesting characters. To explain these unique genomic features observed here, a new gene rearrangement model is proposed, which is called the “inversion triggered duplication” model.

Thesis (Ph. D.)--University of Oregon, 2006.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 137-144). Also available for download via the World Wide Web; free to University of Oregon users.

This thesis deals with combinatorial problems taken frombioinformatics. In particular, we study the problem ofinferring distances between bacterial species by looking attheir respective gene orders. We regard one of the gene ordersas a permutation of the other. Given a set of valid operations,we seek the most parsimonious way to sort this permutation. Wealso look at the more complex problem of combining a set ofspecies into a phylogenetic tree, which shows the relationshipsbetween all species.The computer program Derange II by Blanchette andSanko® uses a greedy algorithm to estimate theevolutionary distance between two species. The success dependson a set of weights, which may be specified by the user. Wehave examined which weights are optimal, and also the qualityof this program using optimal weights.Derange II has been extended to solve the medianproblem, that is finding the permutation that is closest tothree other permutations. We then use this new version to buildphylogenetic trees directly from gene order permutations. Insome situations, this new method works much better thanprevious methods.There is an analytical expression for the evolutionarydistance between two species if the set of allowed operationsincludes only inversions (reversing a segment of genes).Allowing transpositions (swapping two adjacent segments) aswell, we have found a (1+")-approximation for this distance,where we have weighted the di®erent operations accordingto our results on the Derange II weights.

Abstract Mitochondrial DNA sequences were used to study the phylogeny, population structure and colonisation history of Parus species. The phylogenetic relationships of seven European and three American species were examined by sequencing a part of the cytochrome b gene. Phylogenetically the closest species were the great tit (Parus major) and the blue tit (P. caeruleus). Subgenus Poecile was divided into two clades, one consisting of the Siberian tit (P. cinctus), the Carolina chickadee (P. carolinensis) and the Black-capped chickadee (P. atricapillus) and the other consisting of the marsh tit (P. palustris) and the willow tit (P. montanus). The coal tit (P. ater) and the crested tit (P. cristatus) did not group with any of the species studied. The population structure and the colonisation history of the willow tit, the great tit and the blue tit were examined by using control region sequences. The results suggest that the historical effective population size in the willow tit has been large and not contracted by the last ice age. Current gene flow must also be extensive as no population structuring was detected. No population structuring was evident either in the great tit and the populations showed distinctive signs of a recent population expansion. The patterns of genetic variation probably reflect a population bottleneck during the ice age, and a recolonisation of the European continent thereafter, presumably from a refugium situated in the Balkans. Two maternal lineages were found in the blue tit. The southern lineage was restricted to the Iberian peninsula whereas the northern lineage was detected from all the populations. The colonisation history has been similar to the one suggested for the great tit. The southern lineage, however, may have survived the ice age in a different refugium in the Iberian peninsula and was not as successful as the northern lineage in colonising available regions when the ice retreated. Both, the blue tit and the great tit have continued to expand their distribution northwards during this century and gene flow plays an important role in homogenising the populations.

Gastrotricha are small aquatic invertebrates with approximately 770 known species. The group has a cosmopolitan distribution and is currently classified into two orders, Chaetonotida and Macrodasyida. The gastrotrich fauna of Sweden is poorly known: a couple of years ago only 29 species had been reported. In Paper I, III, and IV, 5 freshwater species new to science are described. In total 56 species have been recorded for the first time in Sweden during the course of this thesis. Common species with a cosmopolitan distribution, e. g. Chaetonotus hystrix and Lepidodermella squamata, as well as rarer species, e. g. Haltidytes crassus, Ichthydium diacanthum and Stylochaeta scirtetica, are reported. In Paper II molecular data is used to infer phylogenetic relationships within the morphologically very diverse marine family Thaumastodermatidae (Macrodasyida). Results give high support for monophyly of Thaumastodermatidae and also the subfamilies Diplodasyinae and Thaumastodermatinae. In Paper III the hypothesis of cryptic speciation is tested in widely distributed freshwater gastrotrichs. Heterolepidoderma ocellatum f. sphagnophilum is raised to species under the name H. acidophilum n. sp. The results indicate that L. squamata may be a complex of at least two species. In Paper III and V the phylogeny of Chaetonotidae (Chaetonotida), the largest family within Gastrotricha, is inferred. The group suffers from a troubled taxonomy and is hypothesized to be nonmonophyletic. Results show that members of Dasydytidae are nested within the group. Since only 3 of 17 sampled genera are monophyletic, it is hypothesized that the cuticular structures used in current classification do not reflect phylogenetic relationships. The phylogenetic hypothesis generated in Paper V indicates a marine origin of the predominantly limnic Chaetonotidae with a subsequent secondary invasion to marine environments of some taxa.
Gastrotricha of Sweden - Biodiversity and Phylogeny

CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO
Uma filogenia é uma árvore que relaciona unidades taxonômicas, baseada na similaridade de seus conjuntos de características. O problema da filogenia consiste em encontrar uma filogenia com o número mínimo de passos evolutivos. O principal objetivo deste trabalho é desenvolver heurísticas híbridas para este problema. Duas estratégias são propostas. A primeira combina a metaheurística GRASP baseada em uma nova estrutura de vizinhança (k-SPR) proposta neste trabalho com um procedimento VND de busca local. A segunda estratégia híbrida combina algoritmos genéticos com uma estratégia de cruzamento inovadora, a qual é uma extensão da técnica de intensificação denominada reconexão por caminhos que foi originalmente aplicada no contexto de outras metaheurísticas, tais como busca tabu e GRASP. Os experimentos computacionais realizados sobre instâncias geradas aleatoriamente e instâncias da literatura científica mostram que os novos algoritmos são bastante robustos e que superaram os outros algoritmos existentes na literatura em termos de qualidade de solução e tempos computacionais obtidos.
A phylogeny is a tree that relates taxonomic units, based on their similarities over a set of characters. The phylogeny problem consists in finding a phylogeny with the minimum number of evolutionary steps. The main goal of this work is to develop hybrid heuristics for this problem. Two strategies are proposed. The first combines the GRASP metaheuristic using a new neighborhood structure (k-SPR) proposed in this work with a VND local search procedure. The second hybrid strategy combines genetic algorithms with an innovative optimized crossover strategy which is an extension of the path-relinking intensification technique originally applied in the context of other metaheuristics such as tabu search and GRASP. Computational results on randomly generated and benchmark instances are reported, showing that the new heuristics are quite robust and outperform the others algorithms in the literature in terms of solution quality and computational time.

Doutoramento em Biologia
Os dinoflagelados são um grupo muito diverso de protistas que possuem um conjunto de características pouco comuns. Os peridinióides são dinoflagelados com teca que é formada por seis séries latitudinais de placas, incluindo a série cingular e um anel incompleto de placas intercalares anteriores, embora as últimas estejam ausentes em algumas espécies de Peridiniopsis. São dinoflagelados com simetria bilateral em relação ao plano apical que contem o eixo dorso-ventral. Na série sulcal há apenas uma placa posterior que contacta com o limite ventral de duas grandes placas antapicais. Entre os peridinióides, a presença ou ausência de um poro apical e o número de placas no cíngulo são geralmente consideradas marcas filogenéticas importantes ao nível de género ou família. Actualmente, a definição de Peridinium Ehrenberg, o dinoflagelado mais comum de água doce, inclui organismos com combinações diferentes destas duas características. Trabalhos anteriores sobre a ultrastrutura e afinidade filogenética das espécies tipo de Peridinium, P. cinctum, e Peridiniopsis Lemmermann, P. borgei também sugerem a necessidade de reexaminar as relações taxonómicas dos peridinióides. Esta tese combina o estudo ultrastrutural de uma selecção de espécies com hipóteses filogenéticas baseadas nas sequências de LSU rDNA, para aumentar o nosso conhecimento das diferenças e afinidades dentro dos peridinióides. Tem como objectivo aumentar o nosso conhecimento das características individuais das células que possam levar a reconhecer sinapomorfias que possam ser usadas como marcadores dos peridinióides como um todo e dos seus subgrupos. As espécies escolhidas para exame pormenorizado foram: Peridinium palatinum Lauterborn, de um grupo com duas placas intercalares anteriores, seis placas cingulares e sem poro apical; Peridinium lomnickii Wo!oszy"ska, de um grupo com poro apical, três placas intercalares e seis cingulares; Peridiniopsis berolinensis (Lemmermann) Bourrelly, uma espécie heterotrófica com poro apical, sem placas intercalares e com seis placas cingulares; e Sphaerodinium cracoviense Wo!oszy"ska, um membro de um género de formas com teca com um tipo de tabulação marginalmente peridinióide, com um suposto poro apical e quatro placas intercalares anteriores. Peridinium palatinum difere de Peridinium e Peridiniopsis típicos, quer em características da teca, quer internas. As diferenças estimadas entre as sequências parciais de LSU rDNA de P. palatinum e a espécie próxima P. pseudolaeve, relativamente a P. cinctum são comparativamente grandes e, juntamente com a topologia da árvore filogenética, apoiam a separação de P. palatinum e formas próximas ao nível de género. Palatinus nov. gen. foi, então, descrito com as novas combinações Palatinus apiculatus nov. comb. (espécie tipo; sin. Peridinium palatinum), P. apiculatus var. laevis nov. comb. e P. pseudolaevis nov. comb.. As características distintivas de Palatinus incluem uma superfície das placas lisa ou um tanto granulosa, mas não areolada, um grande pirenóide central penetrado por canais citoplasmáticos e de onde radiam lobos plastidiais, e a presença de uma fiada microtubular homóloga à de um pedúnculo. As células de Palatinus saem da teca pela zona antapicalpos- cingular. Peridinium lomnickii apresenta tabulação semelhante às formas marinhas, produtoras de quistos calcários, do género Scrippsiella A.R. Loeblich. Para comparação, adicionámos novas observações ultrastruturais de S. trochoidea. Peridinium lomnickii tem uma combinação de características diferente de Peridinium, Peridiniopsis e Scrippsiella. As hipóteses filogenéticas baseadas em DNA colocam P. lomnickii no mesmo ramo que Pfiesteria Steidinger et Burkholder, Tyrannodinium e outras Pfiesteriaceae, com as quais partilha um "microtubular basket" e uma ligação peculiar entre duas placas do sulco. As características distintivas do novo género proposto Chimonodinium gen. ined. incluem, além da tabulação, a ausência de pirenóides, a presença de um "microtubular basket" com quatro ou cinco fiadas sobrepostas de microtúbulos associados a um pequeno pedúnculo, um sistema pusular com tubos pusulares bem definidos ligados aos canais flagelares, e a produção de quistos não calcários. Peridiniopsis berolinensis partilha várias características significativas com Pfiesteria e afins, como um "microtubular basket" com a capacidade de suportar um tubo de alimentação, quimiossensibilidade para encontrar presas apropriadas, o modo de natação junto às presas e a organização geral da célula. Hipóteses filogenéticas com base em LSU rDNA confirmam a afinidade entre P. berolinensis e Pfiesteria bem como a relação mais remota com a espécie tipo de Peridiniopsis, P. borgei. Estas razões justificam a proposta de Tyrannodinium gen. nov., uma nova Pfiesteriaceae que difere de outros membros do grupo por viver em água doce e nos pormenores da tabulação. Sphaerodinium cracoviense revelou a tabulação típica do género Sphaerodinium, que apresenta um número de placas intercalares superiores e pos-cingulares maior que o que é típico em peridinióides: 4 e 6, respectivamente. Observações em SEM mostraram uma estrutura apical diferente da dos peridinióides, e um sulco apical numa das placas fazendo lembrar a área apical de alguns woloszynskióides. Os pormenores do aparelho flagelar e do sistema pusular ligam o Sphaerodinium aos woloszynskióides em geral e ao género Baldinia em particular, mas não aos peridinióides. O volumoso estigma de S. cracoviense revelou ser extraplastidial e de um modelo único, composto por elementos que se encontram em woloszynskióides, mas nunca encontrados anteriormente juntos. A análise filogenética baseada nas sequências parciais de LSU rDNA também sugerem uma maior proximidade de S. cracoviense com os woloszynskióides do que com os peridinióides. Futuras análises pormenorizadas de dinoflagelados peridinióides, em especial entre os do numeroso grupo de espécies com poro apical, serão necessárias para clarificar as suas relações taxonómicas; e a produção de descrições melhoradas das características finas particulares das células serão um requisito para perceber a evolução dos caracteres dos peridinióides por forma a podermos identificar marcadores filogenéticos.
Dinoflagellates are a diverse and widespread group of protists that combine a number of unusual features. Peridinioids are thecate dinoflagellates with six latitudinal series of plates, including the cingular series and the incomplete ring of anterior intercalary plates, although the latter is absent in some species currently classified as Peridiniopsis. They tend to be bilaterally symmetrical in relation to the apical plane containing the dorsiventral axis. In the sulcal series there is only one posterior plate, which contacts with the ventral edge of two large subequal antapical plates. Among peridinioids, the presence or absence of an apical thecal pore and the number of plates in the cingulum are often considered important phylogenetic markers at genus or family level. As currently delimited, Peridinium Ehrenberg, the most widely represented dinoflagellate genus in freshwater, includes organisms with different combinations of these features. Previous studies on the fine-structure and phylogenetic affinites of the type species of Peridinium, P. cinctum, and of Peridiniopsis Lemmermann, P. borgei, likewise suggested the need for reexamination of the taxonomical relationships of peridinioids. This thesis combines the ultrastructural examination of selected species with phylogenetic hypothesis based on partial LSU rDNA sequences to extend our knowledge of variation and affinities within the peridinioid group. It aims to advance our understanding of individual cell features that may lead to the recognition of synapomorphies that may be used as markers for the peridinioid group as a whole and for its subgroups. The species targetted for detailed examination were: Peridinium palatinum Lauterborn, representative of a group with two anterior intercalary plates, six cingular plates and no apical pore complex; Peridinium lomnickii Wo!oszy"ska, of a group with apical pore complex, three anterior intercalary and six cingular plates; Peridiniopsis berolinensis (Lemmermann) Bourrelly, an heterotrophic species with apical pore complex, zero anterior intercalary and six cingular plates; and Sphaerodinium cracoviense Wo!oszy"ska, a member of a genus of thecate forms with a marginally peridinioid type of tabulation, with a putative apical pore complex and four anterior intercalary plates. Peridinium palatinum was found to differ from typical Peridinium and Peridiniopsis in both thecal and internal features. The relatively large estimated differences in the partial LSU rDNA sequences of P. palatinum and its close relative P. pseudolaeve compared to P. cinctum, together with the topology of the molecular tree, supported the separation of P. palatinum and related forms at the generic level. Palatinus nov. gen. was therefore described with the new combinations Palatinus apiculatus nov. comb. (type species; syn. Peridinium palatinum), P. apiculatus var. laevis nov. comb. and P. pseudolaevis nov. comb.. Distinctive characters for Palatinus include a smooth or slighty granulate, but not areolate, plate surface, a large central pyrenoid penetrated by cytoplasmic channels and radiating into chloroplast lobes, and the presence of a peduncle-homologous microtubular strand. Palatinus cells exit the theca through the antapical-postcingular area. Peridinium lomnickii has a similar tabulation to the mostly marine, calcareous cyst producers of the genus Scrippsiella A.R. Loeblich and fine-structural observations on S. trochoidea were added for comparison. Peridinium lomnickii showed a different combination of features from Peridinium, Peridiniopsis and Scrippsiella. Interestingly, the DNA-base phylogenetic hypothesis placed P. lomnickii in the same clade as Pfiesteria Steidinger et Burkholder, Tyrannodinium and other pfiesteriaceans, with which it shares a microtubular basket and a peculiar connection between two plates in the sulcus. Distinctive characters of the proposed new genus Chimonodinium gen. ined., include, in addition to the tabulation, the absence of pyrenoids, the presence of a microtubular basket with four or five overlapping rows of microtubules associated with a small peduncle, a pusular system with well-defined pusular tubes connected to the flagellar canals, and the production of non-calcareous cysts. Peridiniopsis berolinensis shares a number of important features with Pfiesteria and its allies, including a microtubular basket with the capacity of driving and supporting a feeding tube, the ability to follow chemical clues to find suitable prey, the swimming behaviour near the prey and the general organization of the cell. Partial LSU rDNA-based phylogenetic hypotheses strongly confirm the close affinity between P. berolinensis and Pfiesteria and the more remote relationship with the type species of Peridiniopsis, P. borgei. These reasons justify the proposal of Tyrannodinium gen. nov., a new pfiesteriacean that differs from other genera in the group in being a freshwater form and in details of the plate arrangement. Sphaerodinium cravoviense showed the tabulation typical of its genus, which extends beyond normal peridinioid tabulation numbers in the anterior intercalary and in the postcingular series, with 4 and 6 plates, respectively. SEM observations revealed that the apical structure differed from the typical arrangement seen in peridinioids and included a furrow with knob-like protuberances reminiscent of the apical area of the thinly thecate woloszynskioids, which usually possess larger numbers of amphiesmal vesicles. Details of the flagellar apparatus and associated pusular system link Sphaerodinium to the woloszynskioids in general and to Baldinia anauniensis in partidular, rather than to peridinioids. The prominent eyespot found in S. cracoviense was shown by TEM to be extraplastidial and of a unique type, made of two components, each known from some eyespot types found in woloszynskioids, but not previously found together. A closer relationship of S. cracoviense with woloszynskioids than with peridinioids was also suggested by a phylogenetic analysis based on LSU rDNA. Further analyses of peridinioids, particularly within the sizeable group of species with an apical pore complex, is needed before general taxonomic relationships become clear; and improved descriptions of fine-structural features of cells are required to unravel the evolution of particular characters, allowing phenotypic phylogenetic markers to be identified.

Thought of as "ancient" fishes, 25 broadly recognized extant sturgeon species are classified in four genera (Acipenser, Huso, Pseudoscaphirhynchus, and Scaphirhynchus). Molecular and morphological analyses have led to broad but conflicting changes to sturgeon phylogeny. For example, the position of Scaphirhynchus among other sturgeons had been contentious, and various sets of sturgeon species have been proposed to make up the subfamily Husinae. Here, a molecular phylogeny of sturgeons, based on the full mitogenome, is presented. In this phylogeny, Scaphirhynchus is recovered with strong support as basal to the other sturgeons. Huso huso is recovered as basal within a clade containing P. kaufmanni and several species of Acipenser, and is proposed as a new, monotypic subfamily Husinae. This phylogeny is used to examine phylogenetic signal in individual genes and in gene families. The protein coding genes as a unit, and individually, along with 16s rRNA, show phylogenetic signal most similar to that of the full mitogenome. The phylogeny, along with evolutionary relationships of pinnipeds and lampreys, provides the basis for the exploration of sturgeon biogeography. Relationships among geographic areas inhabited by sturgeons are found, finding two sets of related areas- a Pacific area group and an Atlantic group. Relationships of areas within and between these groups reflect area relationships proposed by previous biogeographic and geologic studies. Phylogenetic signal is tested amongst ontogenetic characters, and is recovered in the timing at which larval sturgeon teeth are completely resorbed, indicating that the timing of ontogenetic milestones can carry signal. The phylogeny is used to remove confounding signal from, and investigate correlations among, behavioral and morphological ontogenetic characters. Correlation is found between one pair of characters.