Wu, Tsz Huen. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (leaves 89-106). / Abstracts in English and Chinese. / Chapter Chapter 1 --- General Introduction to thesis --- p.1 / Chapter Chapter 2 --- Literature review --- p.3 / Chapter 2.1 --- Introduction --- p.3 / Chapter 2.1.1 --- General introduction to barnacles --- p.3 / Chapter 2.1.2 --- Classification of barnacles --- p.4 / Chapter 2.1.3 --- Importance of barnacles --- p.4 / Chapter 2.2 --- Molecular phylogenetics of barnacles --- p.6 / Chapter 2.2.1 --- What is phylogenetics --- p.6 / Chapter 2.2.2 --- Phylogenetic studies on barnacles --- p.7 / Chapter 2.2.3 --- Choices on characters for barnacle phylogenetics: Morphological characters vs. molecular characters --- p.11 / Chapter 2.2.4 --- Choices of molecular markers in phylogenetic and population genetic studies on barnacles --- p.14 / Chapter 2.3 --- The use of barnacles as model organism in population genetic studies --- p.21 / Chapter 2.3.1 --- Pleistocene glaciations --- p.22 / Chapter 2.3.2 --- Oceanographic pattern and habitat availability --- p.23 / Chapter Chapter 3 --- Phylogenetic relationship of barnacles in family Chthamalidae --- p.26 / Chapter 3.1 --- Introduction --- p.26 / Chapter 3.2 --- Materials and methods --- p.31 / Chapter 3.2.1 --- "Sample collection, DNA extraction and amplification" --- p.31 / Chapter 3.2.2 --- Phylogenetic analyses --- p.34 / Chapter 3.3 --- Results --- p.35 / Chapter 3.4 --- Discussion --- p.40 / Chapter 3.4.1 --- Subfamily Notochthamalinae --- p.40 / Chapter 3.4.2 --- Subfamily Chthamalinae --- p.42 / Chapter 3.4.3 --- Subfamily Euraphiinae --- p.42 / Chapter 3.4.4 --- Phylogenetic relationship in the family Chthamalidae --- p.43 / Chapter 3.4.5 --- Suggestions on taxonomy of Chthamalidae --- p.45 / Chapter Chapter 4 --- Cryptic Diversity and Genetic Structure of the Acorn Barnacle Chthamalus moro in the Northwest Pacific --- p.47 / Chapter 4.1 --- Introduction --- p.47 / Chapter 4.2 --- Materials and methods --- p.53 / Chapter 4.2.1 --- "Sample collection, DNA extraction and amplification" --- p.53 / Chapter 4.2.2 --- Phylogenetic analysis --- p.55 / Chapter 4.2.3 --- Population genetic analysis --- p.55 / Chapter 4.3 --- Results --- p.57 / Chapter 4.3.1 --- Phylogenetic analysis --- p.57 / Chapter 4.3.2 --- "Population genetics analyses, demographic history and neutrality" --- p.61 / Chapter 4.4 --- Discussion --- p.72 / Chapter 4.4.1 --- Origin and the systematic status of the three lineages --- p.72 / Chapter 4.2.2 --- Demographic history of the three lineages --- p.81 / Chapter 4.3.3 --- Contemporary distribution and genetic connectivity of the three lineages --- p.84 / Chapter Chapter 5 --- Concluding remarks --- p.87 / References --- p.89

Orientador: Orlando Necchi Junior / Banca: Valéria Cassano / Banca: Mariana Cabral de Oliveira / Resumo: Três espécies da seção Virescentia do gênero Batrachospermum foram anteriormente reconhecidas para o Brasil com base em caracteres morfológicos: B. helminthosum Bory, B. sirodotii Reis e B. vogesiacum Schultz. No entanto, em um estudo posterior da seção com base em análises morfométricas de populações da América do Norte, B. sirodotii e B. vogesiacum foram tratadas como sinônimos de B. helminthosum. O presente estudo teve como objetivo inferir as relações filogenéticas, bem como os limites de variação intra e interespecífico das espécies da seção Virescentia no Brasil com base na análise morfológica e molecular, utilizando caracteres diagnósticos atualmente aceitos e dois marcadores moleculares: gene plastidial que codifica a subunidade grande da RUBISCO (rbcL - 1.282 pares de base, pb) e região de "barcode" do gene mitocondrial que codifica a subunidade 1 da citocromo c oxidase (cox1 - 664 pb). Foram analisadas 13 amostras provenientes das regiões sul e sudeste do Brasil, além dos espécimes-tipo da seção, provenientes do Herbário PC (Paris, França). Os espécimes foram coletados em águas com baixa concentração de nutrientes e bem oxigenadas (condições oligotróficas e oligossapróbicas) sugerindo serem bioindicadores de rios/riachos de boa qualidade. Não foi possível distinguir as três espécies anteriormente reconhecidas para o Brasil com base em caracteres morfológicos. As dimensões dos carpogônios, carposporófitos e carposporângios dos espécimes brasileiros foram consideravelmente superiores às dos espécimes-tipo, indicando que o material brasileiro representa uma espécie distinta. As análises moleculares geraram os seguintes dados: rbcL - 11 sequências novas e 19 do GenBank (1 do Brasil, 13 dos E.U.A. e 5 do Japão); cox1 - 12 sequências novas e 7 do GenBank (E.U.A.). Análises... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Three species of Batrachospermum section Virescentia were previously recognized for Brazil based on morphological characters: B. helminthosum Bory, B. sirodotii Reis and B. vogesiacum Schultz. A further revisionary study of the section based on morphometric analysis for populations from North America treated B. sirodotii and B. vogesiacum as synonyms of B. helminthosum. The goals of this study were to infer the phylogenetic relationships, as well as the limits of intra and interspecific variation among the species of Virescentia section in Brazil, based on morphological and molecular analyses, using the diagnostic characters currently accepted and two molecular markers: the plastidial gene that encodes the RUBISCO large subunit (rbcL) and the "barcode" region of the mitochondrial gene cox1 that encodes the cytochrome c oxidase sub-unity 1). We analyzed 13 samples from the south and southeast regions of Brazil and six dried archival samples (type specimens) from PC Herbarium (Paris, France). The specimens were collected in well oxygenated waters with low concentration of nutrients (oligotrophic and oligosaprobic conditions), suggesting to be bioindicators of good quality environments. It was not possible to distinguish the three species previously recognized in Brazil based on morphological characters. Carpogonium, carposporophyte and carposporangium dimensions among Brazilian specimens were considerably higher in comparison to type specimens, indicating that they probably represent distinct species. Molecular analysis yielded the following data: rbcL - 11 new sequences and 19 from GenBank (1 from Brazil, 13 from USA and 5 from Japan); cox1 - 12 new sequences and 7 from GenBank (USA). Analyses based on rbcL sequences (1,282 base pairs, bp) and cox1 (664 bp) were congruent and showed section Virescentia as a clear... (Complete abstract click electronic access below) / Mestre

No description available.

A comprehensive tribal-level classification for the world's subfamilies of Hesperiidae, the skipper butterflies, is proposed for the first time. Phylogenetic relationships between tribes and subfamilies are inferred using DNA sequence data from three gene regions: 943 bp of cytochrome oxidase subunit I (COI) (in the mitochondrial genome), 739 bp of elongation factor-lα (EF-lα) and 403 bp of wingless (both in the nuclear genome). Morphological character scores were then added to the molecular matrix, for a combined simultaneous analysis. In both analyses, branch support for each clade is investigated, and conflict among data partitions is assessed using the partition congruence index. Monophyly of the family Hesperiidae is strongly supported, as are some of the traditionally recognized subfamilies, with the following relationships (from the combined molecular and morphological analysis): (Coeliadinae + (Euschemoninae + (Eudaminae + (Pyrginae + (Trapezitinae + (Heteropterinae + Hesperiinae)))))). The formerly recognized subfamily Pyrrhopyginae, while strongly supported as a monophyletic group, is downgraded to a tribe of Pyrginae. The former subfamily Megathyminae is considered to be an infra-tribal group of Hesperiinae (Erionotini), although its phylogenetic position therein remains uncertain. The Australian endemic Euschemon rafflesia is a hesperiid, given subfamily-status. Most of the traditionally recognized generic groups and subgroups currently employed to partition the subfamilies of Hesperiidae are not monophyletic. Seven subfamilies of Hesperiidae are recognized: Coeliadinae, Euschemoninae (confirmed reinstated status), Eudaminae (new status), Pyrginae, Trapezitinae, Heteropterinae (confirmed status) and Hesperiinae. Pyrrhopygini (reinstated status), Tagiadini (confirmed reinstated status), Celaenorrhinini (confirmed new status), Carcharodini (reinstated status), Achlyodini (new status), Erynnini (confirmed new status) and Pyrgini (confirmed status) are treated as tribes of Pyrginae, but the circumscription of Achlyodini and Pyrgini requires further elaboration. Tribes of Hesperiinae include Aeromachini (new status), Erionotini (new status), Baorini (new status), Taractrocerini (confirmed reinstated status), Thymelicini (confirmed reinstated status), Calpodini (reinstated status), Anthoptini (new tribe), Moncini (new tribe), and Hesperiini (confirmed reinstated status), but the circumscription of Erionotini should be considered tentative. / Graduation date: 2006

Thesis (M.S.)--Brigham Young University. Dept. of Computer Science, 2006. / Includes bibliographical references (p. 39-41).

Thesis (Ph. D.)--University of Texas at Austin, 2006. / Vita. Includes bibliographical references.

The Danthonioideae (Poaceae) has been the focus of several systematic studies. Previous studies have shown the subfamily is monophyletic, but relationships within several groups, including Danthonia, have not been examined in depth. To address the question of the monophyly in North American representatives of Danthonia, this study utilized a holistic approach, examining both molecular and morphological features. A molecular phylogeny was constructed based on the trnL-F region of the chloroplast genome, and micromorphological characters of the leaf epidermis, caryopsis, and lodicules were examined by scanning electron microscopy. This study involved a phylogenetic examination of the subfamily Danthonioideae, with emphasis on North American Danthonia. The objectives were twofold: 1) to determine whether representative species of Danthonia in North America form a monophyletic assemblage based on molecular and morphological characters, and 2) to examine relationships of the North American Danthonia species to putative related species in the Southern Hemisphere and Europe. The survey included the genera Austrodanthonia, Cortaderia, Danthonia, Merxmuellera, Notodanthonia, Rytidosperma, Tribolium, and eight North American Danthonia species. South American representatives of Danthonia were included for comparative purposes. <p> Several nicromorphological epidermal features for danthonioid grasses were examined, including macrohairs, bicellular microhairs, prickle hairs, silica bodies, and stomatal complexes. Macrohairs are large, unicellular basifixed structures. Bicellular microhairs are of three types: 1) microhairs with a long basal cell relative to the terminal cell, 2) microhairs with basal and terminal cells approximately equal in length, and 3) microhairs with a short basal cell relative to the terminal cell. Prickle hairs in the costal regions of the leaf epidermis of four species of North American Danthonia are reported for the first time. Epidermal silica bodies in danthonioid grasses are dumbbell-shaped, tall and narrow, or cross-shaped. The stomatal complexes are paracytic with two dome-shaped subsidiary cells. No distinguishing characters were found at the subfamily level. Danthonia is characterized by the absence of abaxial stomata, presence of bicellular microhairs with basal and terminal cells of equal length, as well as microhairs with long basal cells relative to terminal cells. These findings provide a new framework useful for interpretating and re-evaluating taxonomic and phylogenetic relationships in the Danthonioideae. <p>Caryopsis features were useful in reconstructing the phylogeny of the Danthonioideae. Three features associated with the caryopsis, hilum, and surface pattern of Danthonia included: 1) ovoid to obovoid caryopsis shape, 2) linear hilum, and 3) undulating or straight reticulate surface pattern. No other taxon examined in this study possesses this combination of characters. Secondly, Rytidosperma is characterized by 1) ovoid caryopses that are generally smaller than the caryopses in Danthonia, 2) punctate hila, and 3) undulating reticulate or substriate caryopsis surface patterns. Finally, Tribolium has 1) small obovoid caryopses ¡Ü1.2 mm in length, 2) punctate hila, and 3) a substriate caryopsis surface pattern. Though Cortaderia shares the linear hilum and undulating reticulate surface pattern with Danthonia, the lanceolate caryopsis differs from the ovoid to obovoid caryopsis of Danthonia. <p>The subfamily Danthonioideae is monophyletic. Within this subfamily two monophyletic clades, i.e. Danthonia and Rytidosperma, were identified. Cortaderia selloana is basal to the aforementioned clades. Although the Danthonia clade is monophyletic, this study does not support the separation of North and South American and European species, and there is poor resolution of terminal branches within the clade. Interspecific relationships within Danthonia are not clear, but evidence suggests the taxonomic separation of Danthonia from Rytidosperma, two genera that were previously considered to be closely related. The Rytidosperma clade is composed of Austrodanthonia, Notodanthonia, Rytidosperma, Tribolium, and Merxmuellera. Though taxonomic sampling of South American Rytidosperma only included one species, the trnL-F strict consensus tree shows strong support for its inclusion in the Rytidosperma clade, demonstrating that South American representatives of Rytidosperma are distinct from Danthonia. Within the Rytidosperma clade, the genus Rytidosperma may be paraphyletic.

The Danthonioideae (Poaceae) has been the focus of several systematic studies. Previous studies have shown the subfamily is monophyletic, but relationships within several groups, including Danthonia, have not been examined in depth. To address the question of the monophyly in North American representatives of Danthonia, this study utilized a holistic approach, examining both molecular and morphological features. A molecular phylogeny was constructed based on the trnL-F region of the chloroplast genome, and micromorphological characters of the leaf epidermis, caryopsis, and lodicules were examined by scanning electron microscopy. This study involved a phylogenetic examination of the subfamily Danthonioideae, with emphasis on North American Danthonia. The objectives were twofold: 1) to determine whether representative species of Danthonia in North America form a monophyletic assemblage based on molecular and morphological characters, and 2) to examine relationships of the North American Danthonia species to putative related species in the Southern Hemisphere and Europe. The survey included the genera Austrodanthonia, Cortaderia, Danthonia, Merxmuellera, Notodanthonia, Rytidosperma, Tribolium, and eight North American Danthonia species. South American representatives of Danthonia were included for comparative purposes. <p> Several nicromorphological epidermal features for danthonioid grasses were examined, including macrohairs, bicellular microhairs, prickle hairs, silica bodies, and stomatal complexes. Macrohairs are large, unicellular basifixed structures. Bicellular microhairs are of three types: 1) microhairs with a long basal cell relative to the terminal cell, 2) microhairs with basal and terminal cells approximately equal in length, and 3) microhairs with a short basal cell relative to the terminal cell. Prickle hairs in the costal regions of the leaf epidermis of four species of North American Danthonia are reported for the first time. Epidermal silica bodies in danthonioid grasses are dumbbell-shaped, tall and narrow, or cross-shaped. The stomatal complexes are paracytic with two dome-shaped subsidiary cells. No distinguishing characters were found at the subfamily level. Danthonia is characterized by the absence of abaxial stomata, presence of bicellular microhairs with basal and terminal cells of equal length, as well as microhairs with long basal cells relative to terminal cells. These findings provide a new framework useful for interpretating and re-evaluating taxonomic and phylogenetic relationships in the Danthonioideae. <p>Caryopsis features were useful in reconstructing the phylogeny of the Danthonioideae. Three features associated with the caryopsis, hilum, and surface pattern of Danthonia included: 1) ovoid to obovoid caryopsis shape, 2) linear hilum, and 3) undulating or straight reticulate surface pattern. No other taxon examined in this study possesses this combination of characters. Secondly, Rytidosperma is characterized by 1) ovoid caryopses that are generally smaller than the caryopses in Danthonia, 2) punctate hila, and 3) undulating reticulate or substriate caryopsis surface patterns. Finally, Tribolium has 1) small obovoid caryopses ¡Ü1.2 mm in length, 2) punctate hila, and 3) a substriate caryopsis surface pattern. Though Cortaderia shares the linear hilum and undulating reticulate surface pattern with Danthonia, the lanceolate caryopsis differs from the ovoid to obovoid caryopsis of Danthonia. <p>The subfamily Danthonioideae is monophyletic. Within this subfamily two monophyletic clades, i.e. Danthonia and Rytidosperma, were identified. Cortaderia selloana is basal to the aforementioned clades. Although the Danthonia clade is monophyletic, this study does not support the separation of North and South American and European species, and there is poor resolution of terminal branches within the clade. Interspecific relationships within Danthonia are not clear, but evidence suggests the taxonomic separation of Danthonia from Rytidosperma, two genera that were previously considered to be closely related. The Rytidosperma clade is composed of Austrodanthonia, Notodanthonia, Rytidosperma, Tribolium, and Merxmuellera. Though taxonomic sampling of South American Rytidosperma only included one species, the trnL-F strict consensus tree shows strong support for its inclusion in the Rytidosperma clade, demonstrating that South American representatives of Rytidosperma are distinct from Danthonia. Within the Rytidosperma clade, the genus Rytidosperma may be paraphyletic.

Knowledge of phylogenetic relationships among taxa is essential for comparative and evolutionary genomic research. Here, we report reconstruction of the phylogenetic tree of the genus Gossypium containing cultivated cottons of importance in agriculture by using variation of nuclear repetitive DNA sequences. Genomic DNA was isolated from 87 available accessions of 35 species representing all eight basic genome groups of the genus Gossypium and analyzed to infer phylogeny of the genus and genome origin of its polyploid species. Twenty-two interspersed repeated sequence clones derived from G. hirsutum, each representing a repeated sequence family, were hybridized to the genomic DNA of the 35 species, respectively. Southern hybridization showed that 15 of the repetitive DNA sequences could be detected in all of the eight diploid genome groups, five were A genome-specific, and two were detected in some of the non D-genome groups. A total of 642 major restriction bands of repeated sequences were used for phylogenetic analysis of the species. A phylogenetic tree of the species was constructed, based on the parsimony method and evaluated by the bootstrap approach. The tree was consistent with those previously constructed with different methods in major clades in which the genealogical lineages of species are largely congruent with genome designations and geographical distribution; but significantly different branching among some of the species was observed. These results not only further confirm the previously phylogenetic analysis of the species and the utility of repetitive DNA sequences for phylogenetic analysis of the genus Gossypium, but also provide new insights into the phylogeny of the genus.

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2009. / Härtill 4 uppsatser.