A computer simulation study of the accuracy of alternative maximum-likelihood methods for estimating ancestral states for discrete characters on phylogenetic treesJackson, Vanessa. Swofford, David. January 2004 (has links)
Thesis (M.S.)--Florida State University, 2004. / Advisor: Dr. David Swofford, Florida State University, College of Arts and Sciences, Dept. of Biological Science. Title and description from dissertation home page (viewed Sept. 24, 2004). Includes bibliographical references.
Akademische Festrede--Cologne (Rektoratsübergabe) 1961.
Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterionZwickl, Derrick Joel, January 1900 (has links) (PDF)
Thesis (Ph. D.)--University of Texas at Austin, 2006. / Vita. Includes bibliographical references.
Makowsky, Robert Aaron.
Thesis (Ph.D.)--University of Texas at Arlington, 2009.
Deconstructing phylogenetic reconstruction : effects of assumption violations on evolutionary inference /Kolaczkowski, Bryan, January 2006 (has links)
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.
Roshan, Usman Waheed, Warnow, Tandy,
(has links) (PDF)
Thesis (Ph. D.)--University of Texas at Austin, 2004. / Supervisor: Tandy Warnow. Vita. Includes bibliographical references.
Molecular phylogenetics of Lachnaea (Thymelaeaceae) : evidence from plastid and nuclear sequence data.Robinson, Colette 21 April 2008 (has links)
Lachnaea L. (Thymelaeaceae), a genus established in 1753, is endemic to the Cape Floristic Region (CFR) of southern Africa. It demonstrates a high level of regional endemism, with 55% of the species endemic to one of the six centres in the CFR. The first detailed taxonomic account of the genus was published by Meisner in 1840 based on the collections of Drège. Three sections were recognised, namely Sphaeroclinium Meisn., Conoclinium Meisn., and Microclinium Meisn., based mainly on the inflorescence structure. The circumscription of Lachnaea has been extended to include all five species previously placed in Cryptadenia Meisn. and at present 40 species and two subspecies are recognised. In this study a detailed species-level phylogenetic tree for Lachnaea was produced using 3 283bp of plastid DNA and 679bp of nuclear DNA for 38 accessions and various outgroups. The loci sequenced were trnL intron and trnL-F spacer, rbcL, rps16 intron and the nuclear gene ITS. Parsimony and Bayesian analyses yielded identical relationships and these are consistant with morphological data, producing the best-supported phylogenetic assesment currently available for the genus. Five informal groupings are also described in the study. The start of the diversification of Lachnaea was estimated at 7.2Mya with a major proliferation around 6Mya. Sympatric speciation in this genus appears to be plausible with patterns suggesting that altitudinal differences and pollinators have been involved in the speciation process. / Dr. M. van der Bank
Motsi, Moleboheng Cynthia
21 April 2008
Rafnia (Fabaceae, Crotalarieae) is sub endemic to the fynbos region of South Africa with one species extending to KwaZulu-Natal. Morphological analysis was unable to resolve the relationships within the genus but provided a working hypothesis for future studies. A molecular phylogeny of Rafnia (Fabaceae) is presented. Sequenced data was obtained from five regions of the chloroplast genome (rps16 intron, accD-psa1 spacer, psbA-trnH intergenic spacer, trnL intron and trnL-F intergenic spacer) and one region of the nuclear genome (ITS). Congruence between the plastid and nuclear datasets were very low and combination of datasets was difficult to justify. Several explanations for the incongruent datasets are proposed. In addition to the species-level analyses of Rafnia, a higher-level analysis was carried out with additional taxa sampled from across the ‘core genistoids’. The resulting phylogeny was used to produce an estimate for the age of Rafnia. / Dr. M. van der Bank
Phylogenetic relationships and speciation in the genus Passerina L.(Thymelaeaceae)inferred from chloroplast and nuclear sequence data.Van Niekerk, Anemari 21 April 2008 (has links)
The Eastern Cape is regarded as the centre of diversity for Passerina, except for two species occurring in the outliers of eastern Africa. Ten species are endemic to the Cape Floristic Region and four are regarded as near endemics. A complete species-level phylogeny for Passerina utilising sequences from three plastid and one nuclear gene is presented. The loci sequences were rbcL, trnL-F, rps16 and ITS. Parsimony and Bayesian analysis yield identical relationships and two informal groupings are described. Passerina is well imbedded within the tribe Gnideae and not sister to it as previously suggested. The elevation of the subtribe Passerininae (under the tribe Gnidieae) to the monogeneric tribe Passerineae, is thus not supported. The age of the root node of Passerina was estimated to evaluate the widely held view that much of the diversification in the Cape occurred ca. 5Mya with the start of the Mediterranean climate. Contrary to this, the timing and the temporary dynamics of the radiation of Passerina indicated that the lineage is at least 18 million years old and that the diversification rate had declined slightly over the past 5 million years. In Passerina, it also appears that speciation has been largely allopatric with a high frequency of range shifts. / Dr. M. van der Bank
03 October 2003
The genus Petrolisthes is the largest, the most widely distributed genus in the family Porcellanidae. It contains over 100 species distributed around the world , including over 16 species commonly found near the shore of Taiwan . We discuss the diversity and phylogeny of them, and the similarities and dissimilarites of between the molecular biology and traditional morphology. We got 15 pocerlain crabs specimen and almost 900bp and 800bp of them in the 16S rRNA and 12SrRNA of MtDNA respectively. The average pairwise distances is 0.2510 and 0.2249, and the phylogenetic relationship can be determined by observing the morphology of the Petrolisthes crabs, especially the number of spines on the anterior margin of the carpus of the chelipeds, which are an important basis for evolution and classfication. The tree is made from the morphological characters is put more weight by us to the numbers of spines on the anterior margin of the carpus of the chelipeds, and the presence or not of the spines of the outline of the chelipeds. And we can get the same resuit as the molecular phylogenetical tree. This provides an evidence to the situation that molecular phylogeny will present to the morphological character, and some of the characters are more important to the molecular evolution. The phylogeny relationship of porcelain crabs of the west and east Pacific don¡¦t be separated by the Pacific. But the primary phylogenetic relationship still present to the morphological characters. The group T is some species that evolve rapidly with the environment at the later evolution phase. The mitochondrial DNA of Petrolisthes has been sequencing two third of all and compared with the 5 previously studied species ¡]Limulus polyphemus¡BArtemia franciscana¡BDaphnia pulex¡BPenaeus mondon¡BPagurus longicarpus¡^in the class Crustacean. The results reveal that the genome of Petrolisthes is arranged most like that of the hermit crab Pagurus, suggesting they may share an ancestral phenotype. However, the start and terminal codon of Petrolisthes show a unusual similarity to that of Penaeus, the phylogenetic result of the sequence of the protein coding genes support the classification to the anomura conclude the Pagurus and Petrolisthes, and there are high bootstrap values more than 84 with the clade of Pagurus and Petrolisthes in the neighbor-joining method tree and maximum parsimony tree. These analysis showed encourage much needed research and discussion about the relationship between anomura, brachyura and macrura, of the order Decapoda.
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