The genus Capricornis Ogilby, 1837, is divided into three species and widely distributed in sourthern China, Tibet, Myanmar, IndoChinese peninsula, Malaysia peninsula, Sumatra, Japanese archipelagos and Taiwan. Using complete cytochrome b sequences (1140 bp) analyzes the genetic variation and phylogeny of genus Capricornis from Taiwan, Japan and Mainland China. Constructed by both distance and maximum parsimony methods, the phyloenetic tree distinguish the Capricornis to three clades: Formosan serow, Japanese serow, and Sumatran serow from mainland China. Formosan serow is more familiar with Sumatran serow than Japanese serow. Local populations of Formosan serow of Taiwan island and Japanese serow of the Japanese archipelagos are already differentiated. Serow and goral are apparently distinguishable. The results of Principal Component Analysis and Discriminant Analysis show that serows from Taiwan, Japan and mainland China and goral are apparently distinguishable at morphological characters. The variation of morphological analysis may be a good tool to identify serow and goral. From the paleogeology and fossil records of serow of Quaternary, we could infer that ancestors of serow from southwestern mountain of mainland China migrated to Taiwan island and Japanese archipelagos through the land bridge of east Asian islands to mainland China in the early Pleistocene caused by the glaciation of Quaternary, then separated from mainland of east Asia and speciation of serow occured in Taiwan island and Japanese archipelagos after the end of the glaciation of Quaternary.

This study examines the evolutionary history of Pectis L., a neotropical genus of ~90 species of xeric-adapted, herbaceous, annuals and perennials. Pectis is rare among the Asteraceae, as it uses C₄ photosynthesis, a complex suite of traits that concentrates carbon around Rubisco. Plants with C₄ photosynthesis do well in environments of high light and high heat, and the C₄ syndrome is thought to have evolved as a response to such environments. Pectis is most diverse in Mexico, the Caribbean Islands, and South America, and its distribution mirrors the disjunctions of patches of desert, thornscrub, coastal plains, savanna, and openings in seasonally-dry tropical forests and oak-pine woodlands. Vicariance and long-distance dispersal theories can explain the patchy distribution of xeric-adapted plants, as well as the origin of Caribbean species. To answer evolutionary questions about a group, one must understand how its members are related. The most comprehensive taxonomic treatment of Pectis is over 100 years old, and includes only North American species. Recent revisions still leave half the species unassigned to section. Molecular studies have found Pectis sister to, or encompassing, the genus Porophyllum. To infer evolutionary relationships between and within Pectis and Porophyllum, DNA from the nuclear and chloroplast genomes of 78 Pectis and 22 Porophyllum species were sampled, sequenced, and analyzed. The molecular phylogeny was used to suggest updated sections based on monophyletic groups. To infer the photosynthetic pathway of Pectis and Porophyllum species, carbon isotope ratios were obtained from 62 Pectis and 18 Porophyllum species. The timing and location of the evolution of Pectis and Porophyllum has implications for the evolution of C₄ photosynthesis. The carbon isotope data were combined with the phylogeny to determine the extent and direction of the evolution of C₄ photosynthesis, and the timing of its evolution was inferred from a fossil-calibrated analysis using chloroplast data from species across the Asteraceae. Distribution data was combined with the Pectis phylogeny to answer questions regarding the biogeographical history of Pectis, including questions regarding its disjuncted distribution, the timing of the evolution of desert species, and the timing and pattern of dispersal to and from the Caribbean Islands. / text

Known as the Himalayan poppies or the blue poppies, Meconopsis is a genus with approximately 50 species distributed through the high altitude of the Himalaya and the Hengduan Mountains (SW China). This dissertation is a study of the systematics of Meconopsis primarily using molecular phylogenetic methods. DNA sequences of chloroplast matK, ndhF, trnL-trnF, rbcL, and nuclear ITS were collected to reconstruct the phylogenies of the genus. Results showed that traditional Meconopsis is a polyphyletic group and revealed extensive mismatches between the nuclear ITS tree and the chloroplast tree. Based on the phylogenies, the taxonomy of Meconopsis was revised, making Meconopsis monophyletic. Four new sections (sect. Meconopsis, sect. Aculeatae, sect. Primulinae, and sect. Grandes) were proposed as well as a species complex (M. horridula). The chloroplast phylogeny and a likelihood method (chromEvol) were applied to ancestral chromosome number estimation to reconstruct the polyploidy evolution history of the genus. The analysis recovered an ancient triploid ancestor shared by sect. Primulinae and sect. Grandes. A low-copy nuclear gene (GAPDH) network of Meconopsis was further reconstructed, which indicated that the ancient triploid ancestor was formed by hybridization. A hypothesis of reticulate history of Meconopsis was also proposed based on the GAPDH network. Using a reconstructed rbcL phylogeny of Ranunculales, the stem group of Meconopsis was estimated at ca. 22 Mya by molecular dating, which coincided with the time of Asian interior desertification and the onset of Asian monsoon. These climatic changes could possibly have been the impetus for the split between Meconopsis and its sister clade. Ancestral area reconstruction was further conducted using likelihood-based methods. The result indicated that Meconopsis originated in the Himalaya, most likely in the west Himalaya, followed by migration to the Hengduan Mountains. / text

The kingdom Fungi is taxonomically and ecologically diverse, containing an estimated 1.5 million species. Fungi include decomposers, pathogens, and plant and animal mutualists. Many fungi are microorganisms, and the processes shaping microbial diversity may be fundamentally different from those that shape plants and animals. However, ecologists do not yet fully understand how fungal species are distributed over space and time. Using fungi that inhabit the water of Sarracenia carnivorous pitchers, I describe inter and intraspecific fungal diversity and investigate the processes that shape fungal diversity. I introduce these concepts in Chapter 1. In Chapter 2, I describe changes in fungal species diversity over space and time. I enumerated fungal species in five Sarracenia populations across the United States and Canada, and show that thousands, but not hundreds of kilometers separate distinct fungal communities. I also sampled a single Sarracenia population over a Sarracenia growing season, and found that young fungal communities are significantly different from older fungal communities. Observed patterns correlate with environmental factors including temperature and pitcher pH, and with the presence or population structure of pitcher inhabiting arthropods. In Chapter 3, I describe dispersal of and competition among three common pitcher fungi. I tracked Candida glaebosa, Rhodotorula glutinis, and Pseudozyma aphidis appearances in pitchers in a single Sarracenia population, and show that different appearances reflect different dispersal times. I also describe interactions between dispersal and competition in microcosms: high numbers of propagules introduced into a microcosm give a competitive advantage to investigated fungi. In Chapter 4, I describe changes in genotype composition of a population of Candida glaebosa, which is widespread and abundant in pitchers, and disperses early in the season. I observed three C. glaebosa populations in five locations; C. glaebosa population structure does not reflect broader community structure as described in Chapter 2. Population structure instead correlates with host taxonomy, and I contrast inter and intraspecific diversity patterns and the processes that potentially cause such patterns.

No description available.

Rhadine is a Nearctic lineage of flightless ground beetles in the tribe Platynini notable for the slender and elongate habitus of the adults and, in the Southwest, the habitat preferences of many species, with several mountaintop endemics as well as microphthalmous species known from caves in central Texas. The genus is in need of a modern taxonomic revision as species identifications remain challenging, and a phylogenetic hypothesis for the overall structure of the group is needed in order to better understand the group's evolutionary history and test whether subterranean Rhadine are a monophyletic clade or not. To this end, a multigene phylogeny of Rhadine was inferred based on ~2.4-kb of aligned nucleotide sites from 3 molecular markers: cytochrome c oxidase subunit I (COI), 28S ribosomal DNA (28S), and carbamoylphosphate synthetase domain of the rudimentary gene (CAD). These gene fragments were obtained for 30 species or putative species of Rhadine as well as from members of their putative sister group, Tanystoma. Rhadine as currently circumscribed is reconstructed as paraphyletic with two species of subterranean beetles from caves in northern Mexico being resolved outside of Rhadine + Tanystoma. Rhadine sensu stricto (s. str.) is resolved with high support across analyses and is composed of two reciprocally monophyletic clades, clade I and II, the second of which is generally recovered in most analyses. Clade I includes those Rhadine with adult morphological characters defining the dissecta-, larvalis-, and subterranea-groups as well as a clade of macropthalmous subterranean perlevis-group species. Clade II, although not as robust as clade I, contains several surface-dwelling species from the western United States in the jejuna-, nivalis-, and perlevis-groups in addition to lineages of exclusively macropthalmous subterranean Rhadine. The troglobitic, cave-restricted, Rhadine classified in the subterranea-group are reconstructed in two different clades, and the clade contained within clade I also includes several species of large-eyed cavernicolous Rhadine. Those with a slender habitus (e.g., R. exilis, R. subterranea, R. austinica) evolved independently at least three times. Major biogeographic and evolutionary patterns based on these molecular results include: subterranea-group Rhadine north of the Colorado River in Texas (which all lack lateral pronotal setae) are found to comprise a monophyletic group, beetles in caves south of the Colorado River likely form another monophyletic group, and the "species pairs" of troglobitic Rhadine known to occur in the same caves that were sampled in our study are not resolved as each other's closest relatives suggesting that these caves were colonized independently by more than one lineage of Rhadine. The fine-scale attention given to populations of Rhadine isolated on mountain tops in the Madrean Sky Island region suggests that there is a great deal of genetic diversity among these lineages. In addition, these populations are resolved as reciprocally monophyletic with high support across all analyses. Haplotype networks constructed for these populations and compared with those of other described species for the same gene fragments reveal similar genetic distances between separate Sky Island Rhadine as compared to distances between described species from throughout the tree. Preliminary divergence time estimates of the Rhadine-Tanystoma lineage based on relaxed molecular clock analyses support a Miocene age for Rhadine and the Rhadine-Tanystoma lineage, with the crown ages of clade I and II being similar though not identical. All subterranean clade I Rhadine are dated to have begun diversifying within approximately the past 5 million years (Pliocene), an age that is compatible with the stratigraphy of the caves in the Balcones Escarpment. In addition, divergence estimates for the members of this clade support the climactic relict hypothesis, as they diversified during rapid temperature fluctuations during the Quaternary. However, the ages of the high altitude Sky Island Rhadine are estimated to be older than the most recent glacial maximum, suggesting that these distinct clades are considerably older than initially thought. We also performed character correlation tests using our phylogeny to test for patterns in form associated with cave habit and did not find statistical significance between subterranean habit and microphthalmy nor habit and development of the foveae of the mentum.Morphological characters that have been traditionally used to classify the genus into species groups were shown to be convergent in many cases. Despite these well-supported molecular clades, few morphological characters are consistent across all members, posing a challenge to the construction of identification tools. Nevertheless, a tentative update to the classification based on our findings is presented, and the future goals for reconstructing the phylogeny of Rhadine are discussed.

Rivers are hierarchical networks that integrate both large and small scale processes within catchments. They are highly influenced by variation in flow and are characterised by strong longitudinal movement of materials. I conducted an extensive literature review that indicated braided rivers lie at the upper end of the river complexity gradient due to the addition of strong lateral and vertical connectivity with their floodplains. The management of these rivers requires an understanding of the connective linkages that drive complexity, however in developed regions few braided river systems remain intact. The large number of relatively pristine braided rivers in New Zealand provided a unique opportunity to study physical and biotic patterns in these large dynamic systems. Initially I examined horizontal connectivity through patterns in regional and local diversity in eleven braided rivers in the North and South islands of New Zealand. Subsequently, the next component of my thesis focused on vertical connectivity through intensive investigations of energy pathways and the recipient spring stream food-webs. The eleven river survey included sampling of multiple reaches and habitats (main channels, side braids, spring sources, spring streams and ponds) and confirmed the importance of lateral habitats to invertebrate diversity. However, I found that large spatial scales made a greater contribution to diversity than small scales, such that major differences occurred between rivers rather than habitats. This result suggested either a role for catchment-scale factors, such as flow, or biogeographic patterning. Subsequent analysis of the relationships between invertebrate diversity and the physical environment indicated strong regulation by flow variability, but also biogeographic community patterns. Braided rivers are clearly disturbance dominated ecosystems, however the effects of disturbance are manifest in different ways across the riverscape. The role of vertical hydrological connectivity in linking the different components of the floodplain was investigated by tracing carbon pathways from the terrestrial floodplain to spring-fed streams and their communities. Using δ13C isotope signatures it was possible to show that inorganic carbon in groundwater was derived from terrestrial vegetation and subsequently incorporated into spring stream food-webs. However, the degree to which a stream community uses groundwater as opposed to allochthonous carbon is affected by the successional stage of riparian vegetation, a function of the shifting habitat mosaic that is regulated primarily by flow variation and sediment dynamics. In summary, the structure of braided river ecosystems is regulated primarily at the catchment scale, but connectivity at smaller scales plays an important role in determining ecological structure and function.

To test competing hypotheses about the relative roles of vicariance and dispersal in the freshwater fishes in Galaxiidae, a phylogenetic framework and a time scale for species divergence were estimated using mitochondrial and nuclear DNA sequences. Relaxed clock dating revealed that the Galaxiidae originated in Gondwana in the late Cretaceous and thus vicariance cannot be ruled out for the two basal lineages, Galaxiella and Brachygalaxias. These two lineages are ancient relicts that rafted to their present distributions or were fragmented by the separation of Australia from South America via Antarctica. The opening of the Drake passage between South America and Antarctica initiated the proto-Antarctic Circumpolar Current (pACC) and counter-clockwise circulation in the South Atlantic, on which marine stage ancestors could have dispersed to South Africa and New Zealand via Australia during the late Eocene. Thus dispersal explains the disjunct distribution of the clade comprised of G. platei, G. zebratus and Neochanna spp. in South America, South Africa, and Australasia. The narrowing of the Drake passage and collapse of the pACC from about 24-14 Mya likely prevented further contact between South America and South Africa. Tectonic events around the globe produced an anomalous warming event, which along with the uplift of New Zealand provided empty niches and promoted the radiation of Galaxias. Most of the speciation in the other clades occurred during this time. When the Antarctic Circumpolar Current was reactivated at the end of the Mid-Miocene Climatic Optimum (MMCO) about 15–14 Mya, it provided a marine conveyor belt for the dispersal of the ancestor of Galaxias maculatus from Australia to South America, and later to Australia and New Zealand. The integration of divergence times estimated on the phylogeny with ancestral area reconstruction supports an origin in Gondwana and subsequent oceanic dispersal as the explanation for the distribution of the Galaxiidae across the southern continents.

To test competing hypotheses about the relative roles of vicariance and dispersal in the freshwater fishes in Galaxiidae, a phylogenetic framework and a time scale for species divergence were estimated using mitochondrial and nuclear DNA sequences. Relaxed clock dating revealed that the Galaxiidae originated in Gondwana in the late Cretaceous and thus vicariance cannot be ruled out for the two basal lineages, Galaxiella and Brachygalaxias. These two lineages are ancient relicts that rafted to their present distributions or were fragmented by the separation of Australia from South America via Antarctica. The opening of the Drake passage between South America and Antarctica initiated the proto-Antarctic Circumpolar Current (pACC) and counter-clockwise circulation in the South Atlantic, on which marine stage ancestors could have dispersed to South Africa and New Zealand via Australia during the late Eocene. Thus dispersal explains the disjunct distribution of the clade comprised of G. platei, G. zebratus and Neochanna spp. in South America, South Africa, and Australasia. The narrowing of the Drake passage and collapse of the pACC from about 24-14 Mya likely prevented further contact between South America and South Africa. Tectonic events around the globe produced an anomalous warming event, which along with the uplift of New Zealand provided empty niches and promoted the radiation of Galaxias. Most of the speciation in the other clades occurred during this time. When the Antarctic Circumpolar Current was reactivated at the end of the Mid-Miocene Climatic Optimum (MMCO) about 15–14 Mya, it provided a marine conveyor belt for the dispersal of the ancestor of Galaxias maculatus from Australia to South America, and later to Australia and New Zealand. The integration of divergence times estimated on the phylogeny with ancestral area reconstruction supports an origin in Gondwana and subsequent oceanic dispersal as the explanation for the distribution of the Galaxiidae across the southern continents.

[Truncated abstract] The southern-temperate spider family Micropholcommatidae is a poorly-studied taxon of uncertain limits and uncertain affinities. Since the first Australian species were described in the early twentieth century, and the family was erected in 1944, the taxonomic status and phylogenetic placement of the Micropholcommatidae have been the subject of ongoing debate. Various phylogenetic hypotheses have been proposed for the family, but these hypotheses have never been tested with a robust phylogenetic analysis – a problem compounded by the inadequate state and confusing history of micropholcommatid taxonomy. To address the many gaps in our understanding of micropholcommatid interrelationships, this thesis will present a comprehensive systematic treatment of the family. Using a combination of molecular phylogenetic, morphological cladistic and taxonomic methods, micropholcommatid diversity is documented and tested at multiple systematic levels, with an alpha-taxonomic and biogeographic focus on the diverse Australian fauna. The taxonomic contribution is substantial throughout, with one new family, two new subfamilies, one new tribe, 14 new genera and 37 new species described. A combined molecular phylogenetic study is presented in Chapter 2, as a 'first pass' exploration of the monophyly, limits and phylogenetic position of the family Micropholcommatidae. The analyses incorporated 50 ingroup spider species, including 23 micropholcommatid taxa, with nucleotide sequences obtained from two nuclear ribosomal RNA genes (18S and 28S). ...The new subfamily Gigiellinae is also described for two enigmatic species in the newly-described genus Gigiella, known only from the temperate Nothofagus rainforests of south-eastern Australia and southern Chile. As a final contribution to micropholcommatid taxonomy, and as an extension to the cladistic analyses presented in Chapter 5, the new spider family Teutoniellidae is proposed in Chapter 6 for three genera from South America, South Africa and Australia. Teutoniellid monophyly is evidenced by at least two unambiguous synapomorphies, and the morphology of the family is described in relation to other symphytognathidan and EbCY spider taxa. The nominate genus Teutoniella is redescribed to include three species from South America, along with an additional new species from Tasmania. Two new teutoniellid genera are also described, each for a single new species from South Africa: Inflaticrus ansieae is described from the Langeberg Range, east of Cape Town; and Woldius hennigi is described from near Pietermaritzburg, north-west of Durban. In summary, this thesis provides a taxonomic and phylogenetic framework for all future research on micropholcommatid spiders. It presents new data on the phylogeny, phylogenetic position, composition, biogeography, molecular evolution and natural history of a previously poorly-known group of spiders, and highlights a number of remaining gaps in our knowledge of micropholcommatid and araneoid systematics. As a novel contribution to scholarship, this thesis synthesises taxonomic and phylogenetic hypotheses at multiple systematic levels, and tests those hypotheses with original, combined datasets.