A taxonomic and phylogenetic study of the tribe Habrolepidini is described. A cladistic analysis was carried out in order to establish the phylogenetic relationships of the supraspecific taxa of the tribe. An illustrated key for the identification at the level of genera is included. Based on the results of the phylogenetic analysis, the diagnosis and taxonomic descriptions of the recognized taxa are presented. A single most parsimonius parsimony tree was obtained from the cladistic analysis based on 67 morphological characters, generated by a two-step procedure using PAUP. Initially, heuristic searches considering all characters with equal weights resulted in three equally parsimonious trees. Then the method of successive approximation weighting was applied to the three trees. The values of statistic parameters of the most parsimonious tree are: length = 582 steps; consistency index = 0.4966, retention index = 0.5850. The results support the hypothesis that the tribe Habrolepidini is monophyletic. It is defined by the presence of a specialized ventral mandibular tooth that is formed through modification of a seta into a stout socketed spine and three more unambiguous characters, clava length from 2.57 to 3.28, small hexagonal sculpture of scutellum and sensilla in three circles in a straight line. The inclusion of the genera Anthemus, Arrenophagoidea, Arrenophagus, Thomsonisca and Zaomma into Habrolepidini is supported by the presence of the mandibular tooth or by sister group relationships to other taxa with the mandibular tooth. The revision of the genera Ceraptroceroideus and Homalopoda is included; the taxonomic revision of each genus includes a key, diagnosis, descriptions and illustrations for all the species.

Percomorpha is the most diverse group of Acanthomorpha, and the interrelationships among the members are unsettled. Perciformes, one order of Percomorpha, is the largest fish order with 160 families placed in 20 suborders. The relationships among the suborders of Perciformes remain conflicting between the hypotheses of phylogenetic relationships based on different characters. Presently, major studies on relationships of higher taxa are from Japanese based on the mitogenome, and the other studies were based on nuclear gene sequences. Mok recently suggest a hypothesis of the Gobioidei, it is the sister group to a clade which includes the Callionymoidei, Dactylopteriformes, and possibly Pegasidae, based on osteological characters. Following this, a phylogenetic hypothesis of the Callionymoidei based on mitochondrial and nuclear genes was conducted, and the Taiwanese and Australian specimens of G. buergeri might be treated as different species. Morphological differentiation in the sagitta in these two groups points to the same conclusion. The Pempheridae is the sister group of the Glaucosomatidae that is demonstrated by molecular evidences. It is the same with the relationship based on the morphological characters, such as otolith and swimbladder, etc. The monophyly of Callionymoidei is not recovered in this study. The Syngnathoidei may be the closest group of Callionymidae, and the Gobiesocoidei is suggested to be closest with Draconettidae. In the application of mitogenomic information, the sequcences selected by Japanese have not been decided to be unsaturated, so I made statistical inference of the variation for mitochondrial sequences and selected nuclear genes. I have found out the variation-saturated genes and discuss the application of these sequences to phylogenetic studies derived from these datasets in this study.

Nama L. is a genus of approximately 50 species of herbs and subshrubs that occurs in habitats ranging from arid deserts to mesic woodlands in the New World and the Hawaiian Islands. The group has historically been divided into five or six subgeneric groups based on habitat as well as on the morphology of the anthers, styles, leaves and seeds. At least 14 species of Nama from the Chihuahuan Desert Region are either facultatively or obligately endemic to gypsum deposits. This dissertation examines interspecies relationships within Nama from a molecular phylogenetic perspective in order to evaluate historic morphology-based subgeneric classification systems of the genus and to examine the origins of facultative and obligate gypsophily within the genus. DNA sequence data from the chloroplast regions matK and ndhF and from the nuclear ribosomal region ITS were collected from 46 species of Nama as well as from four new species and several outgroups. Data were analyzed using maximum likelihood and Bayesian methods. Phylogenetic analyses recover seven strongly supported major lineages within Nama. These lineages do not correspond to traditionally recognized subgenera, although they are largely congruent with an informal system based on ultrastructural observations of seeds. Four of the seven major lineages include gypsophilous species; these range from two lineages that include a single facultative gypsophile each, to one lineage that is almost entirely comprised of gypsophiles. Gypsum endemism in general, as well as facultative and obligate gypsophily in particular, has arisen multiple times in Nama. Parametric bootstrapping rejected the hypothetical monophyly of gypsophiles across the genus as a whole and within each of the two clades that contain multiple gypsophiles. Because approximately 20 species have been described since the last major revision of Nama nearly 80 years ago, detailed morphological observations of herbarium specimens were made in order to produce a comprehensive key to the species of Nama as well as the revision of a lineage comprising eight gypsophiles and one limestone endemic. / text

This dissertation presents the result of two separate research programs. The first elucidates the phylogeny, biogeography and systematics of the genus Menodora in the olive family. A phylogeny based on the internal transcribed spacer (ITS) of nuclear ribosomal DNA and the chloroplast rps16 and trnL introns and trnL-F intergenic spacer demonstrates that the genus is monophyletic. Within the genus, M. robusta of Patagonia is the first taxon to branch, followed by a monophyletic African clade and M. spinescens of California, though the placement of the latter does not have strong support. Most North American species are nested within the derived South Americans. A South American origin is hypothesized, with two independent dispersals to North America, and a single dispersal to Africa. The phylogeny provided new insights for the systematic treatment, where 24 species, one subspecies and six varieties are recognized, with major realignments of the intregrifolia and scabra species complexes, and a single new species described. In the second area of research, the chloroplast genome of Pelargonium × hortorum has been completely sequenced. At 217,942 base pairs (bp), it is both the largest and most rearranged land plant chloroplast genome yet sequenced. It features two copies of a greatly expanded inverted repeat (IR) of 75,741 bp each, and diminished single copy regions of 59,710 bp and 6,750 bp. Gene content is similar to other angiosperms, with the exceptions of a large number of pseudogenes, two open reading frames (ORF56 and ORF42), and the losses of accD, trnT-ggu, and possibly rpoA. The latter may be represented, however, by highly divergent set of rpoA-like ORFs. The IR expansion accounts for most of the size increase of the genome, but an additional 10% is related to the large number of repeats found. Most of these occur near rearrangement hotspots, and two different repeat associations (characterized by full or partial duplications of several genes) are localized in these regions. We propose simple models that account for the major rearrangements with a minimum of eight IR boundary changes and 12 inversions in addition to several sequence duplications. / text

Morphological characters have a long history of use in the estimation of phylogenetic trees. Datasets consisting of morphological characters are most often analyzed using the maximum parsimony criterion, which seeks to minimize the amount of character change across a phylogenetic tree. When combined with molecular data, characters are often analyzed using model-based methods, such as maximum likelihood or, more commonly, Bayesian estimation. The efficacy of likelihood and Bayesian methods using a common model for estimating topology from discrete morphological characters, the Mk model, is poorly-explored. In Chapter One, I explore the efficacy of Bayesian estimation of phylogeny, using the Mk model, under conditions that are commonly encountered in paleontological studies. Using simulated data, I describe the relative performances of parsimony and the Mk model under a range of realistic conditions that include common scenarios of missing data and rate heterogeneity. I further examine the use of the Mk model in Chapter Two. Like any model, the Mk model makes a number of assumptions. One is that transition between character states are symmetric (i.e., there is an equal probability of changing from state 0 to state 1 and from state 1 to state 0). Many characters, including alleged Dollo characters and extremely labile characters, may not fit this assumption. I tested methods for relaxing this assumption in a Bayesian context. Using empirical datasets, I performed model fitting to demonstrate cases in which modelling asymmetric transitions among characters is preferred. I used simulated datasets to demonstrate that choosing the best-fit model of transition state symmetry can improve model fit and phylogenetic estimation. In my final chapter, I looked at the use of partitions to model datasets more appropriately. Common in molecular studies, partitioning breaks up the dataset into pieces that evolve according to similar mechanisms. These pieces, called partitions, are then modeled separately. This practice has not been widely adopted in morphological studies. I extended the PartitionFinder software, which is used in molecular studies to score different possible partition schemes to find the one which best models the dataset. I used empirical datasets to demonstrate the effects of partitioning datasets on model likelihoods and on the phylogenetic trees estimated from those datasets. / text

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Species within the family Cimicidae (bed bugs) are hematophagous ectoparasites of mammals and birds. Many cimicids are of socio-economic importance. Despite the global resurgence of these pests, there is currently a paucity of information regarding the mitochondrial (mt) DNA sequences of cimicids. Therefore, I used a PCR-based primer walking strategy to amplify and sequence the near complete mitogenome of the common bed bug (Cimex lectularius), and several mitochondrial gene regions of the Eastern bat bug (Cimex adjunctus) and swallow bug (Oeciacus vicarius). I compared the mitochondrial genetic variability between C. lectularius from two populations to look for molecular markers useful for population genetic studies. Furthermore, the mt DNA sequences of these species of medical and veterinary importance were compared to those of other heteropterans to infer the evolutionary relationships of species in the family Cimicidae.

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.

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