Cynipid gall wasps have fascinating biology that has piqued the interest of naturalists throughout history. They induce morphologically complex, sometimes spectacular, gall structures on plants in which the larval stages develop. Gall wasps have therefore evolved an intimate association with their hosts - both metabolically, and in terms of their population histories. Gall wasps must both interact physiologically with their hosts to induce galls, and track their host plants through space and time. My thesis centres on two uses of genomic data in understanding the biology of the oak apple gall wasp Biorhiza pallida. I provide a comprehensive investigation into patterns of oak and gall wasp gene expression associated with gall induction, and a population genomic reconstruction of the population history of this species across the Western Palaearctic. While advances in sequencing technology and reduced costs have made these aims possible, analysis of the massive resulting datasets generated creates new challenges. Firstly, in reconstructing the population history of B. pallida, I describe the use of shotgun sequencing and an informatic pipeline to generate alignments of several thousand loci for three B. pallida individuals sampled from putative glacial refugia across the Western Palaearctic in Iberia, the Balkans and Iran. This dataset was analysed using a new maximum likelihood method capable of estimating population splitting and admixture among refugia across very large numbers of loci. The results showed an ancient divide between Iberia and the other two refugia, followed by very recent admixture between easternmost and westernmost regions. This suggests that gall wasps have migrated westwards along the North African coast as well as through mainland Europe. Second, I compare the gene expression profiles of gall wasp and oak tissues sampled from each of three stages of gall development, leading to new insights into potential mechanisms of gall wasp-oak interaction. A highly expressed gall wasp protein was identified that is hypothesised to stimulate somatic embryogenesis-like development of the gall through interaction with oak tissue glycoproteins. Highly expressed oak genes include those coding for nodulin-like proteins similar to those involved in legume nodule formation. Finally, analysis of the gall wasp genome has revealed potential, but as yet unconfirmed, horizontal gene transfer events into gall wasp genomes. Genes discovered in three gall wasp genomes and expressed in three transcriptomes encode plant cell wall degrading enzymes. They are not of hymenopteran origin, and are most homologous to genes of plant pathogenic bacteria. These genes could be involved in several aspects of gall wasp biology, including feeding and developmental manipulation of host plant tissue.

This thesis is a phylogeographic investigation into plant species from Patagonia, and aims to infer their past distributions from the study of genealogical lineages. These species have gone through several events such as glacial periods, volcanism and topographical change which are expected to contribute to the divergence of genetic lineages by shaping distributions, isolating populations and therefore changing their genetic structure. So understanding how these processes have affected populations is important to get information on how the biodiversity in the region has been assembled, to identify hotspots of intra-specific diversity and therefore to establish potential conservation priorities. Several multi-species phylogeographic studies have been done in the northern hemisphere, but only few are published for South America and even less for the studied area. Patagonia is an area of a great interest because is the only area in the southern hemisphere apart from Antarctica that have been covered buy a thick layer of ice within the glacial periods. It has high levels of endemism, due to its natural boundaries and environmental processes, and is a biodiversity hotspot for conservation. Its varied topography (two big mountain ranges with a north-south distribution divided by a low flat area) also makes Patagonia interesting to study, due to the likelihood of this impacting on phylogeographic patterns. This study encompass seven different Patagonian species of which one is a range restricted conifer and the rest are all angiosperms and include trees, shrubs and herbs with a broad distributions. The reason why I have chosen so many different species is to look for general phylogeographic patterns in species in this region. The thesis was constructed in five chapters. The first is an introductory chapter that provides background to the study system and concepts. Chapters 2, 3, and 4 are empirical phylogeographic studies. These are written as self-contained chapters with the intention that each will be submitted as a separate paper. This leads to some repetition between chapters, but this is intentional as each will need to ‘stand alone’ when submitted for publication. Chapter 2 is a general investigation into five different Patagonian plant species: Discaria chacaye, Donatia fascicularis, Escallonia virgata, Tepualia stipularis and Weinmannia trichosperma. Chapter 3 describes the phylogeographic structure of Gentianella magellanica an annual, cold tolerant species with a wide distribution throughout Patagonia. This species was treated separately and in more detail than the previous five species due to its marked phylogeographic structure. Chapter 4 describes the phylogeographic structure of a Chilean endemic conifer Prumnopitys andina. This has a small distribution in the Andes and only one known population in the coastal cordillera. It was treated separately due to its restricted distribution and different mode of chloroplast inheritance (paternal). Chapter 5, is a general summary, bring all of the results together and giving a wider explanation of the phylogeographic patterns for all species and an outline of future research areas.

Three subspecies of house mice of different geographic origins have reached New Zealand; M. m. domesticus (10 haplotypes), M. m. musculus (1 haplotype) both from Europe, and M. m. castaneus (3 haplotypes) from Asia. Identifying the sources of the multiple historical introductions of the house mouse is a complex issue, particularly during the peak colonisation period of 1830-1880. The early European settlers came with many bags, crates, plants, seed and livestock, which provided ample travel opportunities for stowaway rats and mice. With the assistance of volunteers, I have collected mice from various locations throughout the New Zealand region, to confirm the previously recorded haplotypes and to look for evidence of hybridisation between the colonising subspecies. Morphological characteristics traditionally used for identification of subspecies were compared with genetic characters, to establish whether the use of morphology is still a viable method of identifying subspecific distinctions between mice in New Zealand. While no M. m. musculus haplotypes were found among these samples, some mice still had the coat colouration typical of M. m. musculus. Data from mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) markers revealed some surprising results. I have found six new M. m. domesticus haplotypes, and three new M. m. castaneus haplotypes. The data have also revealed extensive hybridisation, particularly between M. m. domesticus and M. m. castaneus. The finding of the new haplotypes supports the previous assumption that there were multiple introductions of mice into New Zealand, but the finding of M. m. castaneus in inland towns and cities does not support the associated assumption that European mice were initially the only mice present in New Zealand. Rather, the wide distribution of M. m. castaneus suggests that this subspecies probably arrived during the early nineteenth century. The house mouse has long been recognised as an ideal organism for hybridisation studies, and the finding of a hybrid zone within New Zealand would provide an excellent opportunity to extend our knowledge of hybridisation and gene transfer. Previous studies found M. m. domesticus in Napier, and a M. m. musculus/M. m. castaneus hybrids in Wellington. A systematic sampling programme was undertaken between Wellington and Napier following State Highway 2 (SH2), in an attempt to locate a hybrid zone. Analysis of mtDNA and nDNA showed that, M. m. castaneus was found as far North as Dannevirke, and M. m. domesticus as far South as Featherston. There was also extensive evidence of integration of M. m. domesticus nDNA markers into mice with M. m. castaneus mtDNA. There was no clear support for a hybrid zone, but this does not mean that one has not existed in the past and that it has since been overrun by movement of mice with humans and their goods. Identification of subspecies by morphological characteristics, while used with confidence in other countries, is of little use in New Zealand. Extensive hybridisation/and or introgression between the subspecies has long since blurred any morphological distinctions the colonising mice may have had. I propose that these physical characters should be used in support of genetic analysis of the subspecies. The official classification of the New Zealand house mouse currently stands as M. m. musculus, however, data collected does not support this and it is proposed that the official classification should be changed to M. m. domesticus.

Cave organisms are classic examples of regressive evolution, as many disparate taxa have evolved similar convergent phenotypes in subterranean environments. While recent phylogeographic and population genetic analyses have greatly improved our understanding of the evolutionary and biogeographic history of cave organisms, many questions remain unanswered or poorly investigated. I investigated several evolutionary and biogeographic questions in a model system for regressive evolution and studies of ecological and evolutionary mechanisms, amblyopsid cavefishes. In chapter I, I used recently developed methods to delimit species boundaries and relationships in a widely distributed cavefish, Typhlichthys. I show that species diversity in Typhlichthys is currently underestimated and that the view of a single, widely distributed species is not valid. Rather, several morphologically cryptic lineages comprise the diversity in this clade. In chapter II, I examined regressive evolution and potential re-evolution of an eyed, surface form in amblyopsid cavefishes. Whether evolution is truly irreversible, known as Dollo’s Law, has become a question of increasing interest, as several recent studies have made claims that complex structures can be recovered after loss. Phylogenetic and ancestral character state analyses of amblyopsid cavefishes are consistent with re-evolution of eyes and pigmentation and recolonization of surface habitats in the surface-dweller Forbesichthys, providing an opportunity to rigorously discriminate between re-evolution and parallel evolution of cave phenotypes. Despite strong support for re-evolution and contradiction of Dollo’s Law, eye histological evidence and analyses of molecular evolution in the eye gene rhodopsin are consistent with Dollo’s Law supporting at least three independent subterranean colonizations and eye degeneration. Phylogenetic reconstructions of character evolution can occasionally produce strongly supported yet misleading results. In chapter III, I examined the biogeography and speciation of Typhlichthys. Phylogenetic and divergence time analyses support monophyly of Typhlichthys with the majority of cladogenic events occurring in the late Pliocene to Pleistocene, implicating climate change as the primary mechanism driving diversification. Biogeographical analyses, examination of molecular variation in rhodopsin, and structuring of genetic variation with hydrological boundaries, support multiple colonization events by a broadly distributed surface ancestor that subsequently went extinct rather than a single colonization event followed by subterranean dispersal and vicariance.

The Klamath-Siskiyou Ecoregion of northern California and southern Oregon has extremely high biodiversity, but conservation centers on the protection of habitat for the northern spotted owl. A network of late successional reserves has been established without consideration of potential for protecting overall biodiversity, including genetic diversity. Mitochondrial DNA sequences are used to examine the population structure of Acrotrichis xanthocera (Coleoptera: Ptiliidae) sampled from five late successional reserves within the Klamath-Siskiyou Ecoregion and five comparison sites from northern California. Measures of gene flow, phylogenetic analysis, and nested clade analysis are employed to infer historical demographic and phylogeographic processes. Results show that A. xanthocera populations have undergone past range expansion, but gene flow is currently limited. Individual late successional reserves do not adequately protect the genetic variation in this species. Although further research is needed, these results are likely to be congruent for other edaphic arthropod species. Improvement of the late successional reserve system is warranted for maximum protection of the genetic diversity of soil arthropod populations.

A short sequence of ca. 658-bp of the mitochondrial gene COI was used to investigate its utility as a DNA barcode in the medically important Simuliidae or black flies. Sixty-five species and species complexes were tested. Results indicate that the barcoding gene discriminated among morphologically distinct species with nearly 100% of efficacy and proved useful for revealing cryptic diversity. The DNA barcoding gene was also tested for revealing phylogeographic patterns in the western cordilleran Prosimulium travisi and the Prosimulium neomacropyga species-group. Phylogeographic analyses on these species revealed areas that acted as glacial refugia, postglacial history, cryptic speciation episodes and timing of the events that lead to their present-day distribution. The results obtained concur with other phylogeographic studies on similarly-distributed cordilleran organisms. In conclusion, the barcoding gene not only resulted useful for species discrimination in black flies but also for studies at the population level, providing value-added to this molecular marker.

A short sequence of ca. 658-bp of the mitochondrial gene COI was used to investigate its utility as a DNA barcode in the medically important Simuliidae or black flies. Sixty-five species and species complexes were tested. Results indicate that the barcoding gene discriminated among morphologically distinct species with nearly 100% of efficacy and proved useful for revealing cryptic diversity. The DNA barcoding gene was also tested for revealing phylogeographic patterns in the western cordilleran Prosimulium travisi and the Prosimulium neomacropyga species-group. Phylogeographic analyses on these species revealed areas that acted as glacial refugia, postglacial history, cryptic speciation episodes and timing of the events that lead to their present-day distribution. The results obtained concur with other phylogeographic studies on similarly-distributed cordilleran organisms. In conclusion, the barcoding gene not only resulted useful for species discrimination in black flies but also for studies at the population level, providing value-added to this molecular marker.

In this study, mtDNA was used to examine the phylogenetic and molecular relationships of the freshwater shrimp family Atyidae. The phylogeographical variations of two landlocked Caridina pseudodenticulata and Neocaridina denticulata were also discussed. Four genera and 32 species of the Atyidae were identified and divided into 6 groups. In addition to 14 previously recorded species, eight of them are new records, while another 10 species remain unconfirmed. The combination of morphological and molecular characteristics can effectively differentiate species within the family Atyidae. Analysis of demographic parameters indicates a recent population expansion of C. pseudodenticulata, but not for N. denticulata. The result of Bayesian skyline plot analysis implies that the expansion of C. pseudodenticulata began about 70,000 years ago, followed by a very recent rapid expansion approximately 4,000-6,000 years ago. Four major geographical regions of N. denticulata can be identified, including: (1) Southern Taiwan group; (2) Hualian group; (3) Northern Taiwan group; and (4) Ilan group. The study on the phylogenetic relationship of Atyidae in Taiwan could provide valuable information for future study of speciation and geological variation in tropical island.

Chinese spined loach, Cobitis sinensis complex are primary benthic fishwater fishes with inhabiting on the substratum of small pebbles or coarse sand in mountain streams. In Taiwan, C. sinensis complex has been recorded from most drainages of western side of the Central Mountain Ridge including from Ilan, Taipei, even to Pingtung County. In Taiwan, all Cobitis populations have been considered as C. sinensis which types assigned from the Szechuan province, Yangtsi River basin by Sauvage and Dabry de Thiersant (1874). Due to very limited diagnostic morphological features can be detected and studied in detail, it¡¦s more important for reconstructing the molecular phylogenetic relationship by DNA sequences. We also study in the reproductive biology by the samples in Kao-ping River, and to compare the realationship by the samples in Tan-shuei River. By morphological analysis and mtDNA D-loop sequences clustering, we can recognize the C. sinensis complex of Taiwan and southern China into three group: (1) northern and middle Taiwan (NT) (as typical C. sinensis); (2) three River basins in southern Taiwan (ST) (C. sp1); (3) other samples from the Fujian provinces (ST) (C. sp2). They can be distinguished by very distinct differentiations of the scale of Canestrini. The type of NJ tree and MP tree are the overall same topology, mean that the trees of result are the stable phylogenetic tree of the whole C. sinensis complex. By the result of reproductive biological study, GSI index rise in May and drop off in September, the high peak time is close to five months. The increasing tendency of GSI is later than the temperature rising, but earlier than the rainfall begin in July. They share the similar trend among the comparison of the mature of gonad¡Bthe distribution of egg diameter and GSI index.

Title from PDF of title page (University of Missouri--Columbia, viewed on Feb 17, 2010). The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Thesis advisor: Dr. R. Lee Lyman. Includes bibliographical references.