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.

No description available.

<p> Three pieces of work are contained in this thesis. OGRe is a relational database that stores mitochondrial genomes of animals. The database has been operational for approximately five years and the number of genomes in the database has expanded to over 1000 in this period. However, sometimes, new genomes can not be added to the database because of small errors in the source ffies. Several improvements to the update method and the organizational structure of OGRe have been done, which are presented in the first part of this thesis. </p> <p> The second part of this thesis is a study on codon usage in mitochondrial genomes of mammals and fish. Codon usage bias can be caused by mutation and translational selection. In this study, we use some statistical tests and likelihood-based tests to determine which factors are most important in causing codon bias in mitochondrial genomes of mammals and fish. It is found that codon usage patterns seem to be determined principally by complex context-dependent mutational effects. </p> <p> The third part of this thesis is a phylogenetic study of 159 avian species obtained using mitochondrial rRNA sequences that were provided by Dr. van Tuinen. In this study, two methods are used: one considers sites of sequences as independently evolving; the other includes the secondary structure of rRNAs. Unfortunately, the amount of information in the rRNA sequences seems to be insufficient to determine the whole phylogeny of birds. However, our results make it clear that several traditionally defined orders are polyphyletic and therefore need to be redefined. </p> / Thesis / Master of Science (MSc)

Psiguria Arn. is a small genus of Neotropical vines in the Cucurbitaceae that grows in both wet and dry tropical forests from southern Mexico to Paraguay, and on Caribbean islands. The genus is estimated to be very young with natural history characteristics that have contributed to confusing species circumscriptions. The unique relationship of plants in the group with their butterfly pollinators makes Psiguria an interesting and important genus in tropical ecosystems. Both molecular and morphological approaches were used to investigate the monophyly of Psiguria, to elucidate the number of species in the genus, to discover sister relationships, and to identify characteristics for delineating species. Toward that end, an intensive screening of 141 primer combinations in search of phylogenetically informative low-copy nuclear markers was conducted along with a molecular phylogenetic analysis and a complete taxonomic revision of Psiguria. From the screening study, three potentially phylogenetically informative low-copy nuclear markers were discovered for Psiguria, 11 were found to be potentially useful in rosids, and 32 in other angiosperms. DNA sequences for eight chloroplast intergenic spacers (ndhF-rpL32, ndhC-trnV, rps16-trnQ, trnS-trnG, psbZ-trnM, psbM-trnD, rpoB-trnC, and psbE-petL), ITS, and the nuclear serine/threonine phosphatase intron were obtained for 70 samples of Psiguria plus 14 outgroups. Phylogenetic analyses support the monophyly of Psiguria and a sister relationship between P. umbrosa and P. warscewiczii. In the final chapter, two reviews on the genus are presented – one encapsulating the nomenclatural history, and one summarizing 35 years of ecological and natural history studies. In addition, morphological characters were databased, descriptions were written, and maps of geographic distribution were produced for all species. Considering both molecular and morphological data, six species of Psiguria are defined. To distinguish those species missing identifiable morphological characters, a set of DNA barcodes was developed. At least four chloroplast regions are required to differentiate species (ndhC-trnV, rps16- trnQ, rpoB-trnC, and ndhF-rpL32). Because of the absence of many morphological characters, two taxonomic keys are presented – one using male flowers, and the other using the set of DNA barcodes along with consistent leaf characteristics and geographic distribution. / text

The hawkweed subgenus Hieracium s. str. is notoriously known for its extreme morphological variability and variation in ploidy levels that is associated with differences in modes of reproduction. Extensive past hybridization is supposed for the subgenus, but recent hybridization was evidenced only in few cases. The subgenus attracts the attention of botanists already for more than a century. Therefore the species diversity is largely examined and the taxonomy of the subgenus is well elaborated, although several contradictory taxonomic concepts exist. However the relationships among the species are unknown and haven't been studied yet. The investigation of these relationships from a phylogenetic perspective using molecular approaches was the main aim of the presented thesis. Basic species (both diploid and polyploid), representing morphologically unique taxa, that are supposed to be the basic evolutionary units of the subgenus were studied. The sequences of two intergenic spacers of the cpDNA (trnT-trnL and trnV-ndhC) and the external transcribed spacer of the nuclear ribosomal DNA (nrDNA ETS) were analyzed. Moreover, three new low-copy nuclear markers with higher variability than nrDNA and cpDNA markers were developed and their suitability for phylogenetic studies in Hieracium s. str. was...

Fast-evolving RNA viruses are a leading cause of morbidity and mortality among human and animal populations, contributing significantly to both global health and economic burden. The advent and revolution of high-throughput sequencing has empowered phylogenetic analyses with increasing amounts of temporally and spatially sampled viral data. Moreover, the parallel advancement in molecular evolution and phylogenetic methods has provided investigators with a unique opportunity to gain detailed insight into the evolutionary and epidemiological dynamics of emerging viral pathogens. Using state-of-the-art statistical approaches, this thesis addresses some of the important but controversial questions in viral emergence. Chapter 2 introduces a new framework to quantify and investigate reassortment events in influenza A viruses. By developing a computationally efficient algorithm to calculate the largest common subtree for a pair of tree sets, which are estimated from diffe rent parts of the genome for the same taxa set, the level of phylogenetic incongruency due to reassortment can be appropriately ascertained. Chapters 3, 4 and 5 investigate the evolutionary origins of three diff erent viruses: the novel emergence and cross-species transmission of SARSCoV, the genesis and dissemination of the unique HCV circulating recombinant form, and the ancient divergence of all influenza viruses, respectively. Moreover, Chapter 4 presents an improved statistical framework, which provides more precise evolutionary estimates, by utilizing the hierarchical bayes approach to investigate recombination events in emerging RNA viruses. The last empirical study, presented in Chapter 6, applies the recently developed Bayesian phylogeography models to a large viral sequence dataset sampled from southern Viet Nam to examine the fine-scale spatiotemporal dynamics of endemic dengue in Southeast Asia. The work presented here reflects both the advancements made in sequencing technology and statistical phylogenetics, along with some of the challenges that remain in studying the emergence of fast-evolving RNA viruses. This thesis proposes new and improved solutions to these evolutionary problems, such as incorporating non-vertical evolution (i.e. homologous recombination and reassortment) into the phylodynamic framework, with the aim of facilitating future investigations of emerging viral diseases.

Gymnotus, the banded electric knifefish, is a diverse genus with a range that extends from Argentina to southern Mexico and includes species distributed both east (cis-Andean) and west (trans-Andean) of the Andes. Each Gymnotus species exhibits a distinctive electric organ discharge (EOD), used for communication and navigation. Here, I present a new molecular phylogenetic hypothesis for 35 Gymnotus species based on two mitochondrial (cyt b and 16S) and two nuclear genes (RAG2 and Zic1). I found that the trans-Andean species are distributed in four distinct lineages with varying amounts of divergence from their closest cis-Andean sister taxa. I suggest that not all trans-Andean species evolved as a result of the orogeny of the Andes. I evaluate EOD phase number evolution in Gymnotus and find a trend for reduced phase numbers in both cis- and trans-Andean regions. Finally, I suggest hypotheses to account for the patterns of EOD phase number diversification.

Gymnotus, the banded electric knifefish, is a diverse genus with a range that extends from Argentina to southern Mexico and includes species distributed both east (cis-Andean) and west (trans-Andean) of the Andes. Each Gymnotus species exhibits a distinctive electric organ discharge (EOD), used for communication and navigation. Here, I present a new molecular phylogenetic hypothesis for 35 Gymnotus species based on two mitochondrial (cyt b and 16S) and two nuclear genes (RAG2 and Zic1). I found that the trans-Andean species are distributed in four distinct lineages with varying amounts of divergence from their closest cis-Andean sister taxa. I suggest that not all trans-Andean species evolved as a result of the orogeny of the Andes. I evaluate EOD phase number evolution in Gymnotus and find a trend for reduced phase numbers in both cis- and trans-Andean regions. Finally, I suggest hypotheses to account for the patterns of EOD phase number diversification.

The Capsalidae is a diverse family of ectoparasites of marine fish (Platyhelminthes: Monogenea). It is a large family with approximately 180 described species and many more yet to be discovered. Capsalids have a global distribution and parasitise a diversity of hosts from the Chondrichthyes to bony fishes. A morphological classification exists for the family based on a few key characters such as testes number, their arrangement and morphology of the posterior attachment organ (haptor). Phylogenetic relationships within the family and its position within the Monogenea are largely unexplored. I have used various molecular phylogenetic techniques to resolve relationships and explore the evolution and radiation of this family. Specimens from the Capsalidae and other monogenean families (outgroups) were obtained through fresh collections and generous donations by other parasitologists. Specimens were stored in 95% undenatured ethanol. Three unlinked nuclear genes (28S ribosomal RNA, Histone 3 and Elongation Factor 1 α) and two mitochondrial genes (Cytochrome Oxidase 3 and Cytochrome B) were amplified for 78 capsalid taxa in 28 genera representing all nine subfamilies and 30 outgroup taxa (eight Polyopisthocotylea and 22 Monopisthocotylea). Analyses showed the Capsalidae is monophyletic, with the sister group remaining unresolved. Some analyses supported Gyrodactylidae and Udonellidae as the sister group but in other analyses, it was unresolved with the Monocotylidae and Microbothriidae also possible sister groups. The Capsalinae, Encotyllabinae and Nitzschiinae are monophyletic, but analyses did not support monophyly for the Benedeniinae, Entobdellinae and Trochopodinae. Monophyly was supported for Capsala, Capsaloides, Encotyllabe, Entobdella, Listrocephalos, Neobenedenia, Nitzschia and Tristoma, but Metabenedeniella is paraphyletic and Benedenia and Neoentobdella are polyphyletic. Comparisons of the distribution of character states for the small number of morphological characters on a molecular phylogeny show a high frequency of apparent homoplasy. Consequently the current morphological classification for the Capsalidae shows little correspondence with the phylogenetic hypotheses I present. I also sequenced the first complete mitochondrial (mt) genome for a capsalid species, Benedenia seriolae. The mt genome of B. seriolae shows some tRNA rearrangements in comparison to three Gyrodactylus spp. (Gyrodactylidae), the only other complete monopisthocotylean mt genomes sequenced. It also lacks the duplicated, conserved non-coding regions present in Gyrodactylus spp. making the genome smaller in size. I combined this genome with other available platyhelminth mt genomes to investigate the monophyly of Monogenea and the evolution of diet across the Neodermata. Results confirm paraphyly for the Monogenea and also suggest paraphyly for the epidermal feeding Monopisthocotylea. I hypothesise that the Monopisthocotylea represent the first shift to parasitism in the Neodermata from a free living ancestor and following this, there was a dietary shift to blood feeding (Polyopisthocotylea). The Digenea and Cestoda independently evolved dietary specialisations to suit their diverse microhabitats and broad range of vertebrate final hosts. Using Elongation Factor 1 α I have estimated molecular divergence dates for the Neodermata, Monogenea and Capsalidae. Molecular clock analyses estimate the Neodermata diverged from the free living platyhelminths 513 million years ago (mya) (95% HPD [highest posterior density]: 473–605) before the appearance of vertebrates in the fossil record. The Monogenea diverged from the other neodermatan classes 441 mya (95% HPD: 420–547) coinciding with the appearance of fish in the fossil record. The most recent common ancestor of the Capsalidae arose approximately 235 million years ago (95% HPD: 200–274) following the Permian/Triassic extinction event and coinciding with the diversification of bony fishes in the marine environment. I compared the capsalid phylogeny to a phylogeny of fishes that I generated using eight nuclear and three mt genes to explore the evolution and the radiation of the Capsalidae across fishes. There is no significant global signal of coevolution with only five parasite-host associations that may be a result of coevolution. Estimated molecular divergence dates are also compared and do not reveal temporal congruence. Radiation of the family may have been driven by host switching constrained by shared host ecology, biology, behaviour and plasticity in morphological adaptations by the parasites. This study advances our understanding of the evolution of this monogenean family and provides insights into the evolution of the Neodermata and the complicated realities of reconstructing the evolutionary history of parasitic groups. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1522353 / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2010

京都大学 / 新制・課程博士 / 博士(理学) / 甲第24453号 / 理博第4952号 / 新制||理||1707(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 森 哲, 教授 中務 真人, 教授 中川 尚史 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM