A unifying goal of plant systematics is in pursuit of a natural system that means phylpgenetic relationships. We can construct it by means of various characters. There are many arguments about generic circumscription of Pteridophyta. It¡¦s worth while to reexamine some characters, such as trichome. Trichomes have long been considered one of the most important characters by pteridologists. However, The study of trichomes in Taiwan is very rare. In the present study, trichome morphology is used to assess phylogenetic relationships among genera of Dryopteridaceae (sensu Kramer et al.) . The observation of trichomes focus on hairs on the lamina and scales on the base of stipes. Lamina surface hairs are classified into unicellular hairs, club-like unicellular glands, uniseriate hairs, spine-like hairs, appressed glandular hairs, uniseriate hairs with a glandular head and verruca. Stipe base scale margins are classified into entire, serrate, unicellular branch, uniseriate branch, multicellular branch with a glandular head, and dorsi-ventral branch. Color distribution and branch dimension of scales were also good differentiation characters. The main taxonomic conclusions are as follows: (1)Trichome characters support the distinctness of Nothoperanema, Peranema, Polystichm, Dryopsis, Ctenitis, Tectaria, Athyrium, Cystopteris, Acystopteris, and Woodsia; (2) Diplazium and Dryopteris are hererogenous and show little correaltion to exist system. The latter two genera need further research.

This dissertation has two major sections. In Chapter II, complete mitochondrial (mt DNA) genome sequences were used to construct a hypothesis for affinities of most major lineages of rodents that arose quickly in the Eocene and were well established by the end of the Oligocene. Determining the relationships among extant members of such old lineages can be difficult. Two traditional schemes on subordinal classification of rodents have persisted for over a century, dividing rodents into either two or three suborders, with relationships among families or superfamilies remaining problematic. The mtDNA sequences for four new rodent taxa (Aplodontia, Cratogeomys, Erethizon, and Hystrix), along with previously published Euarchontoglires taxa, were analyzed under parsimony, likelihood, and Bayesian criteria. Likelihood and Bayesian analyses of the protein-coding genes converged on a single topology that weakly supported rodent monophyly and was significantly better than the parsimony trees. Analysis of the tRNAs failed to recover a monophyletic Rodentia and did not reach convergence on a stationary distribution after fifty million generations. Most relationships hypothesized in the likelihood topology have support from previous data. Mt tRNAs have been largely ignored with respect to molecular evolution or phylogenetic utility. In Chapter III, the mt tRNAs from 141 mammals were used to refine secondary structure models and examine their molecular evolution. Both H- and L-encoded tRNAs are AT-rich with different %G and GC-skew and a difference in skew between H- and L-strand stems. Proportion of W-C pairs is higher in the H-strand and GU/UG pairs are higher in the L-strand, suggesting increased mismatch compensation in L-strand tRNAs. Among rodents, the number of variable stem base-pairs was nearly 75% of that observed across all mammals combined. Compensatory base changes were present only at divergences of 4% or greater. Neither loop reduction nor an accumulation of deleterious mutations, both suggestive of mutational meltdown (Muller's ratchet), was observed. Mutations associated with human pathologies are correlated only with the coding strand, with H-strand tRNAs being linked to substantially more of these mutations.

Aetosaurians are a clade of pseudosuchian archosaurs that were globally dispersed during the Late Triassic Epoch. Aetosaurians are characterized by a suite of osteoderms that covered much of the body. These osteoderms are commonly recovered as fossils and possess characteristic surface ornamentation that can be diagnostic for taxa. The abundance of these osteoderms and the ease of identification have made aetosaurians ideal index taxa for Late Triassic biostratigraphy. Of special interest are specimens from South and North America and Europe that have been assigned to the genus Stagonolepis, which have been utilized for correlation of continental sedimentary units and to approximately date the timing of important biotic events. New finds have called the synonymy of these Stagonolepis-like specimens into question, jeopardizing their ability to serve as biochronological markers. Detailed examination of all of the specimens assigned to Stagonolepis robertsoni demonstrates that all of these specimens do not represent the same species. The South American material is assigned to the genera Aetosauroides, Aetobarbakinoides, and Polesinesuchus; the European material to Stagonolepis; and the North American material to Calyptosuchus, Adamanasuchus, and a newly recognized taxon, Scutarx deltatylus. Scutarx deltatylus can be differentiated from other aetosaurians by the presence of a strongly raised, triangular boss, on the posteromedial corner of the paramedian osteoderms. Scutarx deltatylus also preserves the first good skull material from a Stagonolepis-like aetosaur from North America. A dorsoventrally thickened skull roof and an anteroposteriorly short parabasisphenoid further demonstrate the distinctness of this material from that of South America and Europe. A detailed phylogenetic analysis of all known aetosaurians further demonstrates the distinctness of these taxa. This new expanded analysis of 28 taxa and 83 characters recovers Aetosauroides scagliai as the sister taxon to all other aetosaurians. Stagonolepis robertsoni from Scotland does not clade with Stagonolepis olenkae from Poland. Calyptosuchus wellesi is the sister taxon to a clade consisting of Scutarx deltatylus and Adamanasuchus eisenhardtae. However, distribution of autapomorphies across these taxa precludes them from being synonymized. As a result the Stagonolepis-like aetosaurs cannot be used for global scale correlations of Upper Triassic strata, but do appear to be of utility for regional correlations, in particular those between the Chinle Formation and Dockum Group in the American Southwest. / text

This dissertation investigates evolutionary relationships within a diverse and ancient group of arachnids, the order Opiliones, with emphasis on relationships within the suborder Laniatores. Laniatorid harvestmen encompass over two-thirds of opilionid diversity, but this suborder has received far less than commensurate phylogenetic attention. The ancient age and narrow species distributions of Laniatores, in conjunction with their representation throughout tropical and subtropical regions of the world, herald models of unparalleled utility for study of tropical diversity and biogeography. Herein I infer the phylogeny of Laniatores using a ten-gene molecular dataset, which samples for the first time every described family of the group. Based upon morphological and molecular sequence data, I describe three new families of Laniatores--two endemic to Southeast Asia and one to the Afrotropics. Focusing on the biogeography of Australasia, I contrast the evolutionary histories of two families: Sandokanidae, which are restricted to the Indo-Malay Archipelago, and Zalmoxidae, which occurs in the Neotropics and Australasia. Using molecular phylogenetic tools, I demonstrate that sandokanid distribution is largely attributable to continental vicariance in Sundaland, whereas zalmoxid distribution is attributable to a New World origin, followed by colonization of the Indo-Pacific by transoceanic dispersal.

This dissertation focuses on the systematics of the Paussinae, a lineage of approximately 775 beetle species all of which produce explosive defensive chemicals and many which are obligate associates of ants (myrmecophiles). This dissertation includes six discrete studies, which taken together span the spectrum of systematic research. It includes taxonomic projects on both larval and adult paussines. It also includes phylogenetic investigations, based on DNA sequence data and morphological data, that address the evolutionary relationships among the major lineages within Paussinae as well as the evolutionary position of the Paussinae within the beetle suborder Adephaga. The inferred trees are used to study character evolution of physiological and behavioral traits of these organisms in a phylogenetic framework. This work sets the stage for a lifetime of work on this fascinating group.

To investigate vascular-plant phylogeny at deep levels of relationship, I collected and analyzed a large set of plastid-DNA data comprising multiple protein-coding genes and associated noncoding regions. I addressed questions relating to overall tracheophyte phylogeny, including relationships among the five living lineages of seed plants, and within two of the largest living gymnosperm clades (conifers and cycads). I also examined relationships within and among the major lineages of monilophytes (ferns and relatives), including their relationship to the remaining vascular plants. Overall, I recovered three well-supported lineages of vascular plants: lycophytes, monilophytes, and seed plants. I inferred strong support for most of the phylogenetic backbones of cycads and conifers. My results suggest that the cycad family Stangeriaceae (Stangeria and Bowenia) is not monophyletic, and that Stangeria is instead more closely related to Zamia and Ceratozamia. Within the conifers, I found Pinaceae to be the sister-group of all other conifers, and I argue that two conifer genera, Cephalotaxus and Phyllocladus (often treated as monogeneric families) should be recognized under Taxaceae and Podocarpaceae, respectively. Systematic error likely affects inference of the placement of Gnetales within seed-plant phylogeny. As a result, the question of the relationships among the five living seed-plant groups still remains largely unresolved, even though removal of the most rapidly evolving characters appears to reduce systematic error. Phylogenetic analyses that included these rapidly evolving characters often led to the misinference of the “Gnetales-sister” hypothesis (Gnetales as the sister-group of all other seed plants), especially when maximum parsimony was the inference method. Filtering of rapidly evolving characters had little effect on inference of higher-order relationships within conifers and monilophytes, and generally resulted in reduced support for backbone relationships. Within the monilophytes, I found strong support for the majority of relationships along the backbone. These were generally congruent with other recent studies. Equisetaceae and Marattiaceae may be, respectively, the sister-groups of the remaining monilophytes and of the leptosporangiate ferns, but relationships among the major monilophyte lineages are sensitive to the outgroups used, and to long branches in lycophytes.

Sequencing technologies have improved significantly in the past 10 years and the staggering number of genome sequences available has led to a migration from single-gene phylogenetics to multigene phylogenetics. A protocol was developed here to compare fungal genomes through BLAST to determine which BLAST statistics may best represent phylogenetic information. The results suggested that levels of sequence identity, relative to the query length, may be useful for predicting whether a gene will yield a well-resolved and consistent tree. Moreover, it was found that about 40% of the genes in a typical filamentous fungal genome may lead to a well-resolved and concordant tree topology that also matched an 18S rDNA derived topology; but for consistent results, multigene trees with a minimum of five genes should be used. An additional script to rapidly identify regions within genes that can be easily amplified was then developed and tested on eight genes. The genes were successfully amplified and several resultant amplicon trees matched the 18S rDNA topology. / NSERC

No description available.

The thesis investigates members of the crustose and largely calcified red algal family Peyssonneliaceae through molecular analyses and anatomical and ultrastructural observations. Mitochondrial CO1 DNA barcoding was implemented, in combination with fine-scale anatomy, to recognise species boundaries and identify complexes of cryptic species. Nuclear and organellar DNA markers were employed to construct a multigene phylogeny for Vanuatu and southern Australian members of the family facilitating the recognition of two undescribed genera Annea and Incendia.

Thesis (Ph. D.)--Miami University, Dept. of Botany, 2004. / Title from second page of PDF document. Includes bibliographical references (p. 67-83).