Gastrotricha are small aquatic invertebrates with approximately 770 known species. The group has a cosmopolitan distribution and is currently classified into two orders, Chaetonotida and Macrodasyida. The gastrotrich fauna of Sweden is poorly known: a couple of years ago only 29 species had been reported. In Paper I, III, and IV, 5 freshwater species new to science are described. In total 56 species have been recorded for the first time in Sweden during the course of this thesis. Common species with a cosmopolitan distribution, e. g. Chaetonotus hystrix and Lepidodermella squamata, as well as rarer species, e. g. Haltidytes crassus, Ichthydium diacanthum and Stylochaeta scirtetica, are reported. In Paper II molecular data is used to infer phylogenetic relationships within the morphologically very diverse marine family Thaumastodermatidae (Macrodasyida). Results give high support for monophyly of Thaumastodermatidae and also the subfamilies Diplodasyinae and Thaumastodermatinae. In Paper III the hypothesis of cryptic speciation is tested in widely distributed freshwater gastrotrichs. Heterolepidoderma ocellatum f. sphagnophilum is raised to species under the name H. acidophilum n. sp. The results indicate that L. squamata may be a complex of at least two species. In Paper III and V the phylogeny of Chaetonotidae (Chaetonotida), the largest family within Gastrotricha, is inferred. The group suffers from a troubled taxonomy and is hypothesized to be nonmonophyletic. Results show that members of Dasydytidae are nested within the group. Since only 3 of 17 sampled genera are monophyletic, it is hypothesized that the cuticular structures used in current classification do not reflect phylogenetic relationships. The phylogenetic hypothesis generated in Paper V indicates a marine origin of the predominantly limnic Chaetonotidae with a subsequent secondary invasion to marine environments of some taxa. / Gastrotricha of Sweden - Biodiversity and Phylogeny

Vertebrate hard tissues first appeared in the dermal skeletons of early jawless vertebrates (ostracoderms) and were further modified in the earliest jawed vertebrates. Fortunately, histological information is usually preserved in these early vertebrate fossils and has thus been studied for more than a century, done so by examining thin sections, which provide general information about the specific features of vertebrate hard tissues in their earliest forms. Recent progress in synchrotron X-ray microtomography technology has caused a revolution in imaging methods used to study the dermal skeletons of early vertebrates. Virtual thin sections obtained in this manner can be used to reconstruct the internal structures of dermal skeletons in three-dimensions (3D), such as vasculature, buried odontodes (tooth-like unites) and osteocytes. Several body scales of early vertebrates have been examined using this imaging method and in situ 3D models of internal structures are created. Andreolepis (an early osteichthyan) scale shows linear growth pattern of odontodes in early developmental stage, which is not observable in traditional thin sections. The scale of another early osteichthyan Psarolepis was studied in the same way. Comparison between Andreolepis and Psarolepis shows that cosmine, a tissue complex in dermal skeleton of early sarcopterygians, originated by a developmental change of odontode shape. Two scales of osteostracans, a group of extinct jawless vertebrates, were studied in 3D and more details have been revealed in comparison to previous results based solely on 2D thin sections. 3D data enables us to compare the vasculature and canal system in different taxa in great detail, which forms the basis of formulating primary homology hypothesis and phylogenetic characters. The new data resulting from this study suggests that vertebrate fossils have preserved much more histological information than we currently appreciate, and provide a new data source of microanatomical structures inside the fossils that can contribute new characters for phylogenetic analysis of early jawed vertebrates.

Most living eukaryotes are currently classified into one of five or six ‘supergroups’, which are in turn often divided between two assemblages: ‘unikonts’ and ‘bikonts’. This thesis explores the cytoskeletal morphology and phylogeny of three lineages that do not belong to any supergroup: ancyromonads, apusomonads, and breviates, likely relatives of supergroups Opisthokonta and Amoebozoa. It also investigates the phylogeny of malawimonads (basal members of supergroup Excavata) and collodictyonids (another unaffiliated lineage). Serial-section transmission electron microscopy was used to model the flagellar apparatus cytoskeletons of the ancyromonad Ancyromonas sigmoides, the breviate Breviata anathema, and the apusomonad Thecamonas trahens. Each has two main posterior microtubular roots and at least one anterior root (two in Ancyromonas). All three possess splitting posterior right microtubular roots and supernumerary singlets, features also characteristic of basal members of the supergroup Excavata (‘typical excavates’). One peripheral microtubule system in Ancyromonas, and the ‘right ribbon’ in Thecamonas, are likely homologous to dorsal fans in Breviata and ‘typical excavates’, and to the ‘r2’ root of myxogastrid Amoebozoa. One of the branches of the splitting root in Breviata and Thecamonas joins the right and intermediate roots, similarly to some myxogastrids. This implies that myxogastrids, and not the simpler pelobionts, represent the ancestral state for Amoebozoa. A phylogenomic analysis was performed focussing on apusomonads breviates, ancyromonads, and the problematic ‘typical excavate’ malawimonads, based on new transcriptomic data from Ancyromonas and an undescribed malawimonad. Rapid-site- removal analyses recover the ‘unikont’/‘bikont’ partition, and do not support the previously demonstrated affiliation between breviates and the ‘unikont’ supergroup Amoebozoa. Specifically, they group apusomonads with the ‘unikont’ supergroup Opisthokonta, and ancyromonads with breviates. Taxon-removal analyses group ancyromonads, breviates, and apusomonads together. Most analyses group malawimonads (perhaps with collodictyonids, another problematic group) between ‘unikonts’ and (other) ‘bikonts’, while other excavates are in a basal position amongst other ‘bikonts’. Combining these morphological and phylogenetic results suggests that splitting right roots, supernumerary intermediate singlets, and dorsal fans are found in multiple ‘basal’ lineages in both ‘unikont’ and ‘bikont’ portions of the eukaryotic tree, are likely characters of the last common ancestor of most or all living eukaryotes.

One of the most fundamental computational problems in biology is that of inferring evolutionary histories of groups of species from sequence data. Such evolutionary histories, known as phylogenies are usually represented as binary trees where leaves represent extant species, whereas internal nodes represent their shared ancestors. As the amount of sequence data available to biologists increases, very fast phylogenetic reconstruction algorithms are becoming necessary. Currently, large sequence alignments can contain up to hundreds of thousands of sequences, making traditional methods, such as Neighbor Joining, computationally prohibitive. To address this problem, we have developed three novel fast phylogenetic algorithms. The first algorithm, QTree, is a quartet-based heuristic that runs in O(n log n) time. It is based on a theoretical algorithm that reconstructs the correct tree, with high probability, assuming every quartet is inferred correctly with constant probability. The core of our algorithm is a balanced search tree structure that enables us to locate an edge in the tree in O(log n) time. Our algorithm is several times faster than all the current methods, while its accuracy approaches that of Neighbour Joining. The second algorithm, LSHTree, is the first sub-quadratic time algorithm with theoretical performance guarantees under a Markov model of sequence evolution. Our new algorithm runs in O(n^{1+γ(g)} log^2 n) time, where γ is an increasing function of an upper bound on the mutation rate along any branch in the phylogeny, and γ(g) < 1 for all g. For phylogenies with very short branches, the running time of our algorithm is close to linear. In experiments, our prototype implementation was more accurate than the current fast algorithms, while being comparably fast. In the final part of this thesis, we apply the algorithmic framework behind LSHTree to the problem of placing large numbers of short sequence reads onto a fixed phylogenetic tree. Our initial results in this area are promising, but there are still many challenges to be resolved.

Durvillaea, a kelp genus occurring only in the Southern Hemisphere, presents an ideal system for studies of marine connectivity and postglacial recolonisation. Durvillaea contains five currently-recognised species, four of which are non-buoyant. Whereas all non-buoyant species are restricted to the south-western Pacific, the sole buoyant species (D. antarctica) has a far wider, circumpolar distribution, strongly suggesting that long-distance dispersal in D. antarctica is achieved by rafting. This contrast in predicted dispersal ability among Durvillaea species provides an opportunity for natural phylogeographic comparisons, thereby assessing the effectiveness of rafting as a long-distance dispersal mechanism. Additionally, the inability of D. antarctica to survive in ice-affected areas, combined with its broad distribution, make it an ideal candidate for studies of postglacial recolonisation. Phylogenetic and biogeographic relationships within Durvillaea were here assessed using sequence data from mitochondrial (COI), chloroplast (rbcL) and nuclear (18S) DNA. Genetic data were obtained from more than 500 specimens, including representatives from across the geographic range of each recognised species of Durvillaea. Mitochondrial data for Durvillaea were found to be highly phylogenetically informative, with 117 variable sites observed over a 629 bp fragment of COI. Chloroplast and nuclear markers, on the other hand, showed less variation than COI, but nonetheless contributed useful phylogenetic information. Phylogenetic analyses were performed using both Maximum Likelihood and Bayesian approaches. Contrasting patterns of genetic diversity were observed across the range of D. potatorum in Australia, with genetic homogeneity throughout western sites versus relatively high levels of diversity in eastern populations. Based on these results, I hypothesise that D. potatorum recolonised much of the western part of its range postglacially, perhaps being entirely eliminated from western Tasmania during the last glacial period by altered oceanographic systems. Additionally, 'western' and 'eastern' D. potatorum haplotypes formed deeply-divergent clades, likely reflecting geographic isolation on either side of the Bassian Isthmus during Pleistocene marine regressions. Substantial genetic diversity was observed across the range of the circumpolar species D. antarctica. Within New Zealand, phylogenetic and morphological analyses of D. antarctica indicate that two morphotypes ('cape' and 'thonged' forms) likely represent reproductively isolated species, with the 'cape' lineage apparently restricted to southern New Zealand. Whereas the 'cape' lineage showed little genetic variation throughout its range, the 'thonged' lineage exhibited marked phylogeographic structure, with high genetic diversity and a clear north - south genetic disjunction delineated by the Canterbury Bight. On a broader, circumpolar scale, D. antarctica showed contrasting patterns of genetic diversity, with high levels of variation in low-latitude regions (e.g., continental coasts of New Zealand and Chile), versus near-homogeneity at high, subantarctic latitudes. These phylogeographic contrasts strongly suggest that D. antarctica recolonised much of the subantarctic region only recently, most plausibly following extirpation by ice scour at the Last Glacial Maximum (LGM). Locations of putative recolonised islands relative to 'refugial' areas indicate that Antarctic sea ice was likely more extensive at the LGM than previous studies have suggested. Latitudinal contrasts in genetic diversity were also observed among Chilean populations of D. antarctica, with a single mitochondrial haplotype detected throughout Chilean Patagonia versus high diversity in central Chile (32�-42�S). The Patagonian populations appear to have recolonised the region postglacially, following recession of the Patagonian Ice Sheet after the LGM. These populations show transoceanic ancestry, with a closer relationship to populations in the subantarctic and southern New Zealand regions than to those in central Chile. Substantial phylogeographic structure was evident across small spatial scales in central Chile, and the correspondence of major genetic disjunctions among central Chilean sites with the presence of long stretches of unsuitable substrate (beaches) strongly suggests that habitat discontinuity drives genetic isolation in this dispersive species. Broad-scale molecular phylogenetic analyses indicate that the current taxonomy of Durvillaea species requires substantial revision. Previously-recognised 'morphotypes' of Durvillaea (of D. potatorum in Australia, and D. antarctica in New Zealand), for example, were here found to be genetically distinct, likely representing reproductively-isolated species. This phylogeographic research on Durvillaea kelp sheds new light on the historical impacts of climate change on Southern Hemisphere marine environments, and on the processes driving evolution in a marine macroalga.

The flora of New Zealand has evolved largely in the absence of terrestrial mammals, the predominant frugivore guilds being birds and reptiles. The evolution of divergent fruit traits in New Zealand may be a consequence of different selection pressure by these two guilds, and two contrasting putative dispersal syndromes have been proposed for New Zealand fleshy fruited plants. Coprosma (Rubiaceae: subtribe Coprosminae) is a speciose and morphologically diverse genus, which is distributed throughout the South Pacific and which also produces variably coloured drupes. It was selected as a model genus to investigate the evolution of fruit traits within this context. For this purpose, a molecular phylogeny for the subtribe Coprosminae and Coprosma was inferred using parsimony, likelihood and split decomposition analysis on sequences from the 16rps intron of cpDNA and ETS and ITS region of nrDNA. Up to 32 species were included in the subtribal analyses, whilst 53 species of Coprosma were used in subgeneric studies. The basis for the variety of fruit colours seen in New Zealand was determined using histology and pigment extractions. To test the assumption that fruit traits among species evolved in concert under selection from frugivore guilds, fruit shape, size and nutrient composition were determined in order to test predictions that these would co-vary with fruit colour. In the Coprosminae, fleshy drupes have arisen from dry fruited schizocarps and with two possible reversals to semi-dry drupes. Within Coprosma, fruit colour was found to be evolutionarily labile and varied both among and within lineages, particularly within two main groups where fruit colour had shifted from orange to blue and white, or red, pink and black colours respectively. The evolution of novel (non-orange) fruit colours was restricted to New Zealand, as was the small-leaved, divaricate growth form, the combination of which has been associated with a putative reptile dispersal syndrome. Several trans-oceanic dispersals out of New Zealand were also inferred from the phylogeny, these extending into Australia, New Guinea and Hawai�i. In these instances, fruit colour did not appear change markedly after establishment in a new country. Within New Zealand, fruit sizes were found to vary with colour as predicted, although the majority of species produced small (< 8 mm), elliptical fruits. There was no clear association between fruit colour and fruit nutrient composition. It would appear that these small, succulent, carbohydrate-rich and lipid-poor fruits cater to a wide range of generalist frugivores. The variety of fruit colours in Coprosma stemmed from qualitative and quantitative differences in carotenoid and anthocyanin composition. The genetic basis for the control of these pathways is currently unknown, but it is assumed that a few regulatory genes can control a substantial amount of phenotypic variation. Considering the evolutionary history of Coprosma, it would appear that a history of recent and rapid speciation, hybridisation and reticulate evolution may have increased the tempo of fruit colour evolution in the genus.

No description available.

Durvillaea, a kelp genus occurring only in the Southern Hemisphere, presents an ideal system for studies of marine connectivity and postglacial recolonisation. Durvillaea contains five currently-recognised species, four of which are non-buoyant. Whereas all non-buoyant species are restricted to the south-western Pacific, the sole buoyant species (D. antarctica) has a far wider, circumpolar distribution, strongly suggesting that long-distance dispersal in D. antarctica is achieved by rafting. This contrast in predicted dispersal ability among Durvillaea species provides an opportunity for natural phylogeographic comparisons, thereby assessing the effectiveness of rafting as a long-distance dispersal mechanism. Additionally, the inability of D. antarctica to survive in ice-affected areas, combined with its broad distribution, make it an ideal candidate for studies of postglacial recolonisation. Phylogenetic and biogeographic relationships within Durvillaea were here assessed using sequence data from mitochondrial (COI), chloroplast (rbcL) and nuclear (18S) DNA. Genetic data were obtained from more than 500 specimens, including representatives from across the geographic range of each recognised species of Durvillaea. Mitochondrial data for Durvillaea were found to be highly phylogenetically informative, with 117 variable sites observed over a 629 bp fragment of COI. Chloroplast and nuclear markers, on the other hand, showed less variation than COI, but nonetheless contributed useful phylogenetic information. Phylogenetic analyses were performed using both Maximum Likelihood and Bayesian approaches. Contrasting patterns of genetic diversity were observed across the range of D. potatorum in Australia, with genetic homogeneity throughout western sites versus relatively high levels of diversity in eastern populations. Based on these results, I hypothesise that D. potatorum recolonised much of the western part of its range postglacially, perhaps being entirely eliminated from western Tasmania during the last glacial period by altered oceanographic systems. Additionally, 'western' and 'eastern' D. potatorum haplotypes formed deeply-divergent clades, likely reflecting geographic isolation on either side of the Bassian Isthmus during Pleistocene marine regressions. Substantial genetic diversity was observed across the range of the circumpolar species D. antarctica. Within New Zealand, phylogenetic and morphological analyses of D. antarctica indicate that two morphotypes ('cape' and 'thonged' forms) likely represent reproductively isolated species, with the 'cape' lineage apparently restricted to southern New Zealand. Whereas the 'cape' lineage showed little genetic variation throughout its range, the 'thonged' lineage exhibited marked phylogeographic structure, with high genetic diversity and a clear north - south genetic disjunction delineated by the Canterbury Bight. On a broader, circumpolar scale, D. antarctica showed contrasting patterns of genetic diversity, with high levels of variation in low-latitude regions (e.g., continental coasts of New Zealand and Chile), versus near-homogeneity at high, subantarctic latitudes. These phylogeographic contrasts strongly suggest that D. antarctica recolonised much of the subantarctic region only recently, most plausibly following extirpation by ice scour at the Last Glacial Maximum (LGM). Locations of putative recolonised islands relative to 'refugial' areas indicate that Antarctic sea ice was likely more extensive at the LGM than previous studies have suggested. Latitudinal contrasts in genetic diversity were also observed among Chilean populations of D. antarctica, with a single mitochondrial haplotype detected throughout Chilean Patagonia versus high diversity in central Chile (32�-42�S). The Patagonian populations appear to have recolonised the region postglacially, following recession of the Patagonian Ice Sheet after the LGM. These populations show transoceanic ancestry, with a closer relationship to populations in the subantarctic and southern New Zealand regions than to those in central Chile. Substantial phylogeographic structure was evident across small spatial scales in central Chile, and the correspondence of major genetic disjunctions among central Chilean sites with the presence of long stretches of unsuitable substrate (beaches) strongly suggests that habitat discontinuity drives genetic isolation in this dispersive species. Broad-scale molecular phylogenetic analyses indicate that the current taxonomy of Durvillaea species requires substantial revision. Previously-recognised 'morphotypes' of Durvillaea (of D. potatorum in Australia, and D. antarctica in New Zealand), for example, were here found to be genetically distinct, likely representing reproductively-isolated species. This phylogeographic research on Durvillaea kelp sheds new light on the historical impacts of climate change on Southern Hemisphere marine environments, and on the processes driving evolution in a marine macroalga.

Copies of author's previously published articles inserted. / Includes bibliographies. / iii, 277, [81] leaves : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / The aim of this research is to investigate the phylogeny of isolates of the intestinal protozoan parasite Giardia intestinalis using molecular systematic techniques. Most of the isolates used in this study are propagated by the infection of suckling mice. Isolates are characterised allozymically and their genetic relationships are inferred using clustering methods. Seven lineages of isolates are identified, five comprising animal-derived G. intestinalis, and two comprising human-and animal-derived G. intestinalis. / Thesis (Ph.D.)--University of Adelaide, Dept. of Microbiology and Immunology, 1997?

Thysanotus R.Br. (Asparagales; Laxmanniaceae) is a genus native to Australia with c. 50 species distributed chiefly in Australia. To date, Thysanotus lacks proper and detailed systematic studies based on molecular and/or non-molecular data. Therefore, carrying out a detailed systematic study using molecular and/or non-molecular data seemed important. Furthermore, generic placement of Murchisonia Brittan has always been controversial and this placement required testing under a phylogenetic framework. The generic relationships within Laxmanniaceae/Lomandraceae are considered uncertain; therefore, a phylogenetic analysis using molecular and morphological data is necessary to properly understand the generic relationships of Laxmanniaceae. Detailed studies on stem anatomy and morphology were carried out in order to understand the systematic significance and phylogenetic signal of these characters. The cp DNA (trnL intron and trnL–F intergenic spacer) and nuclear ITS2 gene regions were amplified and the results compared and combined with a morphological analysis. Phylogenetic analyses were carried out using Arthropodium R.Br and Eustrephus R.Br as outgroup taxa. There was sufficient variation in general morphology, seed micromorphology and stem anatomy and were potentially useful in understanding phylogenetic relationships of Thysanotus. A number of synapomorphies based on general morphology and stem anatomy such as absence of pendent flowers and absence of irregular shaped epidermal cells were recognised. The molecular data and the combined data yielded highly resolved consensus trees and enabled us to recognise three main lineages within the genus, each representing life history adaptations. Murchisonia was consistently nested within Thysanotus in all analyses showing a need for the return of both species to Thysanotus. Insights to intraspecific variation were also discernable from morphological, molecular and the combined analyses in species such as T. patersonii and T. juncifolius. Two new Thysanotus species, T. unicupensis and T. racemoides are also described. Our data strongly support the current circumscription of Laxmanniaceae, but suggest that there are three main lineages within the family, rather than the two previously recognised subfamilies. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1524476 / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2010