京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第22631号 / 理博第4620号 / 新制||理||1664(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 田村 実, 教授 工藤 洋, 教授 永益 英敏 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

京都大学 / 新制・課程博士 / 博士(理学) / 甲第23737号 / 理博第4827号 / 新制||理||1690(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 曽田 貞滋, 准教授 渡辺 勝敏, 教授 中川 尚史 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Verrucariaceae are a family including mostly lichenized species (Verrucariales, Ascomycota). Its current generic classification, which mainly relies on three morphological characters (spore septation, thallus structure, and hymenial algae), has never been subjected to molecular data. Because these characters were suspected to be homoplastic, the monophyly of the genera as currently delimited based on morphology need to be assessed. A three-gene phylogenetic analysis was carried out using three methods (Maximum Parsimony, Maximum Likelihood, and a Bayesian approach) on 83 taxa, selected from 15 genera in Verrucariaceae. Ancestral state reconstructions were undertaken for four characters (spore septation, thallus structure, hymenial algae, and upper cortex structure). The results confirmed that most of the genera were not monophyletic, and that the most recent common ancestor of Verrucariaceae was most likely crustose, lacking hymenial algae, and with simple spores and a pseudocortex. The use of symplesiomorphic traits to define Verrucaria, the largest and type genus for the Verrucariaceae, as well as the non monophyly of the genera Polyblastia, Staurothele and Thelidium, explain most of the discrepancies between the current classification and a classification using monophyly as a grouping criterion. In order to accommodate newly inferred monophyletic groups, existing genera were re-delimited and three new genera were proposed. Recent broad-scale phylogenetic analyses have shown that Verrucariales was sister to Chaetothyriales, an order first known as including mostly saprophytes and opportunistic animal and human parasites. Investigations of fungal communities colonizing rocks in extreme environments have shown that some slow-growing melanized fungi inhabiting bare rock surfaces belonged to the Chaetothyriales. Multigene phylogenetic analyses were carried out using Maximum Likelihood and a Bayesian approach in order to confirm the affiliation of 25 of these rock isolates. Ancestral state reconstructions were then undertaken on two different datasets to look at the evolutionary history of lichenization within Pezizomycotina, and the rock-inhabiting habit within Eurotiomycetes. Results suggest that the ancestor of the lineage including Verrucariales and Chaetothyriales was likely to be an extremotolerant non-lichenized, rock-inhabiting fungus. Virulence factors of opportunistic parasites within Chaetothyriales, such as melanization and meristematic growth, might have primary been adaptations for life in extreme habitats. / Dissertation

Thesis (Ph. D.)--University of Missouri-Columbia, 1997. / Typescript. Vita. Includes bibliographical references (leaves 280-303). Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 1997. / Typescript. Vita. Includes bibliographical references (leaves 280-303). Also available on the Internet.

Traditional evolutionary models depict evolution as a bifurcating pattern with a single ancestor diverging to form two lineages. However, reticulate species resulting from hybridization and recombination have unique histories shared with two independent lineages, not one. Accounting for the genetic histories of reticulate species increases the power and ability to recover biologically meaningful relationships. The genus Collomia (Polemoniaceae) is used to explore issues of reticulation and the importance of accounting for gene histories in a phylogenetic analysis. The issue of reticulation within species trees is discussed with a multilabeled, network approach being explored to better represent the genus's evolutionary history. Wherry's hypotheses regarding the relationships that exist within Collomia are addressed and the need for a new intrageneric section is recognized based on support from multiple, independent genes and morphology. Sections Collomiastrum and Courtoisia remain as previously circumscribed. Section Collomia is modified with removal of two species, C. grandiflora and C. biflora from the section and by erecting a new section, Calyperona. A morphological key is included for each section and their corresponding species, followed by sectional discussions. Finally, the evolution of lifecycle duration, seed morphology, and pollen morphology are discussed based on the phylogeny of the genus.

Bromeliaceae ocupa posição basal na Ordem Poales e é considerada monofilética, tendo sinapomorfias morfológicas e moleculares. Atualmente é subdividida em oito subfamílias, sendo Bromelioideae a subfamília com maiores problemas na delimitação genérica. Nesse contexto encontra-se o Complexo Nidularióide, formado pelos gêneros Nidularium Lem., Wittrockia Lindm., Neoregelia L.B.Sm., Canistropsis (Mez) Leme e Edmundoa Leme. A dificuldade na delimitação destes gêneros se dá pelo uso de um grande número de caracteres não exclusivos, que mostram o íntimo relacionamento entre estes gêneros. Embora estes gêneros não sejam monofiléticos, como indicam as filogenias recentes, o Complexo Nidularióide como um todo sempre emerge em um clado, indicando que formam uma unidade taxonômica. Neste contexto, analisamos caracteres morfológicos e anatômicos a fim de estabelecer novas sinapomorfias para o Complexo. Nossos resultados indicam que os principais caracteres morfológicos utilizados na delimitação dos gêneros do complexo Nidularióide são homoplásticos. A maior parte dos caracteres anatômicos também representam homoplasias. No entanto a anatomia foliar mostrou-se útil, provendo novas sinapomorfias para o grupo, tais como a presença de células da ala alongadas nos tricomas, e presença de células epidérmicas adaxiais com paredes levemente espessadas na lâmina foliar. No segundo capítulo, analisamos a anatomia floral de 16 espécies de Bromeliaceae, pertencente a três das oito subfamílias, a fim de estabelecer caracteres anatômicos florais úteis na sistemática do grupo, bem como discuti-los sob uma perspectiva ecológica e filogenética. Uma nova sinapomorfia é proposta para Pitcairnoideae a partir de dados sobre a vascularização do gineceu. No terceiro capítulo, analisamos o desenvolvimento foliar de três espécies de Tillandsia L. (Tillandsoideae). Neste estudo, foi possível registrar a presença de coléteres nas bainhas foliares próximas aos ápices caulinares de T. tricholepis (L.) L. Estas estruturas são responsáveis pela proteção do meristema apical caulinar (MAC) por meio de seu exsudado. Este estudo é o primeiro registro destas estruturas em Bromeliaceae / Bromeliaceae ocupies a basal position in Poales Order and is considered monophyletic by morphological and molecular sinapomorphies. The family is currently subdivided into eight subfamilies. Bromelioideae has major problems in generic delimitation. In this context is included Nidularioid Complex, formed by the genera Nidularium Lem., Wittrockia Lindm., Neoregelia L.B.Sm., Canistropsis (Mez) Leme e Edmundoa Leme. The difficulty to generic delimitation in these genera occurs by the presence of a great number of non-exclusive character, which demonstrates their intimate relashioship. Although recent phylogenies indicate these genera are not monophyletic, Nidularioid Complex always emerges as a clade, which suggests they are a true taxonomic entity. In this context, we analyzed morphological and anatomical characters to establish new sinapomorphies for the Complex. Our results indicates that the main morphological characters used in genera delimitation on Nidularioid Complex are homoplastic. The major part of anatomical characters are also homoplastic. However, leaf anatomy shows to be useful, providing new synapomorphies for this group, such as the presence of trichomes with elongated wing\'s cells and the presence of adaxial epidermal cells with lightly thickened walls on leaf blade. On the second chapter, we analyzed floral anatomy of 16 species of Bromeliaceae, belonging to three out of eight subfamilies, to establish anatomical floral characters useful in the group sistematics, as well as discuss it under an ecological and phylogenetic perspective. A new synapomorphy for Pitcairnoideae is established, by data of gynoicea vascularization. On the third chapter, we analyzed leaf development of three species of Tillandisia L. (Tillandsoideae). In this study, it was possible to describe the presence of colleters in leaf sheath, next to shoot apices of T. tricholepis (L.) L. These structures are responsible by shoot apical meristem\'s (SAM) protection by their secretion. This is the first record of colleters in Bromeliaceae

The phylogenetic relationships within subfamily Ixoroideae of the coffee family are investigated by phylogenetic reconstruction of molecular data, including regions of the chloroplast DNA (matK, ndhF, rbcL, rps16, trnH-psbA, trnS-G, and trnT-F), and the nuclear ribosomal DNA (ITS). The evolution of morphological characters within the group are inferred, with focus on characters used in classification. Ixoroideae have primarily been characterized by secondary pollen presentation, contorted corolla aestivation, and fleshy fruits. Secondary pollen presentation appears synapomorhic of a clade comprising the Ixoroideae crown group together with Retiniphyllum, whereas contorted corolla aestivation has evolved earlier and is synapomorphic for the crown group, Retiniphyllum, and Steenisia. Capsules likely represent a plesiomorphy from which various dry or fleshy indehiscent fruits have evolved independently in different clades. Reductions in seed number have also occured in many clades, none of which shows a secondary increase in the number of seeds. Within Ixoroideae, the phylogeny and tribal delimitations of Alberteae and Condamineeae are studied in more detail. The former appears restricted to Alberta, Nematostylis, and Razafimandimbisonia, a new genus described here. The Condamineeae are a diverse tribe largely unresolved in previous molecular phylogenetic studies. Our results support a synonymization of both Calycophylleae and Hippotideae, because these are nested within the Condamineeae. Ancestral state reconstructions indicate that intrapetiolar stipules, poricidal anthers, and protogyny, otherwise uncommon characters in Rubiaceae, all have evolved more than once in the Condamineeae. The rare genera Jackiopsis, Glionnetia, and Trailliaedoxa previously not included in molecular phylogenetic analyses, are all found nested within the Ixoroideae, and their systematic positions are discussed. The genera Bathysa, Calycophyllum, Elaeagia, and Rustia do not appear monophyletic. Consequently, resurrections of the names Holtonia, Schizocalyx, and Semaphyllanthe, and synonymizations of Phitopis (as Schizocalyx) and Tresanthera (as Rustia) are proposed. Also proposed are five new tribal names for clades that are not associated with any previously described tribes in the phylogenetic hypotheses presented. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.

Accurate species delimitation has critical implications for ecological and conservation studies; and for understanding factors driving diversification. However, a growing body of evidence indicates that morphology-based species circumspection in lichenized ascomycetes often fails to accurately represent the number of fungal species. The use of molecular data in lichen systematics provides an important alternative to traditional morphological characters for identifying natural groups and assessing evolutionary histories in challenging lichen taxa. In this work, I examined two common lichen-forming genera in western North America, Rhizoplaca and Xanthoparmelia, as models for investigating character evolution, species delimitation in morphologically and chemically diverse species, and identification of lineages in the early stages of divergence. Phylogenetic hypotheses were reconstructed to assess character evolution using sequence data from four nuclear ribosomal markers and fragments from two nuclear loci. I applied a multifaceted approach to delimit species in Rhizoplaca and Xanthoparmelia by assembling multiple lines of evidence using DNA sequence data, and genealogical and population genetic analyses. I have found that traditionally circumscribed species are not supported by molecular data. For example, in Rhizoplaca previously unrecognized lineages were identified within what has thus far been considered a single species. In contrast, morphologically and chemically distinct species within Xanthoparmelia were not supported by molecular data. Distinct medullary chemistries, growth forms, and the production of vegetative diaspores appear to have evolved independently multiple times in Xanthoparmelia. This work clearly indicates that morphological and chemical characters do not always accurately reflect lichen species diversity within even the best known and studied genera. My study of the Rhizoplaca melanophthalma species complex demonstrates that the genus Rhizoplaca, as presently circumscribed, is more diverse in western North American than previously thought. I present these analyses as a working example of species delimitation in morphologically cryptic lichenized fungi. In Xanthoparmelia diagnostic morphological and chemical characters have evolved in a highly homoplasious manner. In contrast to other studies documenting previously undiscovered fungal lineages masked within lichen species circumscribed by traditional morphological and chemical characters, my work suggests that species diversity has been overestimated in the lichen genus Xanthoparmelia.

No description available.