Thesis (Ph. D.)--University of Hong Kong, 2001. / Includes bibliographical references (leaves 298-323).

Diss. (sammanfattning) Uppsala : Univ., 2009. / Härtill 5 uppsatser.

Thesis (Ph.D.)--Kent State University, 2008. / Title from PDF t.p. (viewed Dec. 11, 2009) Advisor: Walter R. Hoeh. Keywords: snail-kiling flies, Diptera, Sciomyzidae, freshwater mussels, feeding behavior evolution, Unionidae, Ambleminae, systematics, Bayesian phylogenetics, maximum likelihood, character optimization, DUI, diversifying selection. Includes bibliographical references.

published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

Phylogenetic tree reconstruction for a set of species is an important problem for understanding the evolutionary history of the species. Existing algorithms usually represent each species as a binary string with each bit indicating whether a particular gene/protein exists in the species. Given the topology of a phylogenetic tree with each leaf representing a species (a binary string of equal length) and each internal node representing the hypothetical ancestor, the Fitch-Hartigan algorithm and the Sankoff algorithm are two polynomial-time algorithms which assign binary strings to internal nodes such that the total Hamming distance between adjacent nodes in the tree is minimized. However, these algorithms oversimplify the evolutionary process by considering only the number of protein insertions/deletions (Hamming distance) between two species and by assuming the evolutionary history of each protein is independent. Since the function of a protein may depend on the existence of other proteins, the evolutionary history of these functionally dependent proteins should be similar, i.e. functionally dependent proteins should usually be present (or absent) in a species at the same time. Thus, in addition to the Hamming distance, the protein linkage distance for some pairs/sets of proteins: whole block linkage distance, partial block linkage distance, pairwise linkage distance is introduced. It is proved that the phylogenetic tree reconstruction problem to find the binary strings for the internal nodes of a phylogenetic tree that minimizes the sum of the Hamming distance and the linkage distance is NP-hard. In this thesis, a general algorithm to solve the phylogenetic tree reconstruction with protein linkage problem which runs in O(4^m⋅n) time for whole/partial block linkage distance and O(4^m⋅⋅ (m+n)) time for pairwise linkage distance (compared to the straight-forward O(4^m⋅ m⋅ n) or O(4^m⋅ m^2⋅⋅ n) time algorithm) is introduced where n is the number of species and m is the length of the binary string (number of proteins). It is further shown, by experiments, that our algorithm using linkage information can construct more accurate trees (better matches with the trees constructed by biologists) than the algorithms using only Hamming distance. / published_or_final_version / Computer Science / Master / Master of Philosophy

Goniothalamus is one of the largest genera in the pantropical angiosperm family Annonaceae. It includes c. 130 species of trees, distributed in tropical lowland and submontane forests in tropical Asia, Australia and Melanesia. Previous studies have indicated that Goniothalamus shows a significantly higher diversification rate in comparison to closely related taxa and that its species diversity is the result of a relatively recent radiation. The phylogenetic framework necessary for testing this hypothesis, including the investigation of potential intrinsic and environmental correlates of this putative radiation, and additional biogeographical and evolutionary studies, has not previously been available. Data from nine chloroplast DNA markers (11,214 aligned characters) and 67 ingroup accessions (c. 50% of the species diversity) of Goniothalamus are used for parsimony, maximum likelihood and Bayesian phylogenetic reconstructions. The results confirm the monophyly of Goniothalamus, indicate several strongly supported major subclades, and show that most previously described infrageneric taxa are para- or polyphyletic. Morphological character evolution in Goniothalamus is investigated using ancestral character state reconstructions and phylogenetic analysis of variance. The evolutionary patterns of 19 morphological characters for which a significant phylogenetic signal was identified are discussed in relation to function. Character correlations indicate two main fruit types: small monocarps (average diameter c. 1 cm) with glabrous seeds borne on young growth, which are hypothesized to be predominantly bird-dispersed, and larger (average diameter 1.5 cm) monocarps with hairy seeds borne on older twigs, the trunk or close to the ground, hypothesized to be predominantly mammal dispersed. Synapomorphies of several subclades of the Goniothalamus phylogeny are identified based on the ancestral character reconstructions of 11 categorical characters. Molecular dating is performed using two fossil calibrations, an uncorrelated rates relaxed molecular clock model, and the most comprehensive Annonaceae dataset to date (738 ingroup and 5 outgroup accessions, nine chloroplast markers), with the aim of investigating the historical biogeography of Goniothalamus. Mean divergence time estimates indicate a Goniothalamus crown group age of 23 Ma. Biogeographical analyses infer an ancestral area in western Southeast Asia, two dispersal events from western Southeast Asia to India, and multiple dispersal events from western Southeast Asia eastwards to the Philippines, New Guinea and Australia in the early to late Miocene. Diversification analyses corroborate previous studies which indicated that early Annonaceae diversification was characterized by a low net diversification rate and high relative extinction rate. The results of the present study, however, also indicate that the diversification rate peaked between 9.9 and 0.8 Ma, associated with a low relative extinction rate. Temporally coinciding environmental (tectonic and climatic) factors which may underlie this diversification peak are discussed. In contrast to previous studies, the results do not suggest that the species diversity in Goniothalamus is the result of a rapid, recent radiation. Significant rate shifts are not indicated when using methods that accommodate incomplete taxon sampling. Previously inferred rate shifts are probably artefacts because of inadequate taxon sampling. Significantly high diversification rates are identified in the present study in several small to medium-sized Asian genera such as Polyalthia s.str. and Monoon. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

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Not available / text

The excellent penguin fossil record is temporally long, among the oldest of modern birds, and contains fossils on every Gondwanan continent except India. However, most of fifty-nine named taxa are isolated skeletal elements, many of which are noncomparable. Fossil diversity is highest in New Zealand, with additional Antarctic and Patagonian faunas and fewer remains from Australia and South Africa. Phylogenetic hypotheses place penguins within Aves and Neornithes, but further relationships remain contentious. Recent work clarified living species' phylogeny, but none examined all fossil taxa. I describe penguin skeletal anatomy using CT scans and museum specimens, providing the first such description for all living and extinct species in an explicitly phylogenetic framework. All elements are phylogenetically variable, intergeneric variation is large, and extinct taxa are more variable than extant. I recommend that future systematic works include all elements for extinct species diagnoses, osteology for living species, and discussions of intraspecific variation. This description grounds my phylogenetic analysis, based on a 503-character matrix of osteological, myological, integumentary, and behavioral characters. This greatly expands previous datasets, and allows recovery of a highly resolved phylogeny, including monophyly of two extinct clades and the crown-group. Data partitions support different levels of relationship, whereas missing data and outgroup choice drastically affect recovered topology. Incorporating the maximum amount of data gives the highest resolution by recovering all relevant character states. I propose the first formal phylogenetic nomenclature for sphenisciforms, and define and diagnose previously used terms such as Panspheniscidae (total group), Sphenisciformes (known penguins), Spheniscidae (crown-group), Palaeeudyptidae and Paraptenodytidae (two extinct clades). I coin Spheniscoidea (Spheniscidae + Paraptenodytidae) and Australodyptinae (Aptenodytes + Pygoscelis). After calibration with geologic time, I calculate the completeness of the pencuin record and determine confidence intervals to estimate a Cretaceous origin and an Eocene crown-clade origin. These dates and the derived phylogenetic placement of penguins suggest that numerous extant bird lineages may also have Cretaceous origins. I recover a New Zealand origin for penguins and a West Antarctic origin for the crown-group and extinct clades. Correlating penguins with tectonic and climatic data indicates an Eocene adaptive radiation, probably related to latest-stage Gondwanan breakup and associated global cooling.