The Eastern Cape is regarded as the centre of diversity for Passerina, except for two species occurring in the outliers of eastern Africa. Ten species are endemic to the Cape Floristic Region and four are regarded as near endemics. A complete species-level phylogeny for Passerina utilising sequences from three plastid and one nuclear gene is presented. The loci sequences were rbcL, trnL-F, rps16 and ITS. Parsimony and Bayesian analysis yield identical relationships and two informal groupings are described. Passerina is well imbedded within the tribe Gnideae and not sister to it as previously suggested. The elevation of the subtribe Passerininae (under the tribe Gnidieae) to the monogeneric tribe Passerineae, is thus not supported. The age of the root node of Passerina was estimated to evaluate the widely held view that much of the diversification in the Cape occurred ca. 5Mya with the start of the Mediterranean climate. Contrary to this, the timing and the temporary dynamics of the radiation of Passerina indicated that the lineage is at least 18 million years old and that the diversification rate had declined slightly over the past 5 million years. In Passerina, it also appears that speciation has been largely allopatric with a high frequency of range shifts. / Dr. M. van der Bank

Graduation date: 1998

The relative role of cospeciation and host switching in the phylogenetic history of ascomycete foliar symbionts is addressed in the orders Leotiales and Rhytismatales, fungi associated predominantly with Pinaceae (Coniferales). Emphasis is placed on comparing the evolution of the sister genera Pseudotsuga and Larix (Pinaceae) with that of the pathogenic and endophytic fungi in the genus Rhabdocline. Pinaceae evolved during the Mesozoic and divergence of all extant genera and several infrageneric lineages (esp. in Pinus) occurred prior to the Tertiary, with subsequent species radiations following climatic changes of the Eocene. The youngest generic pair to evolve from Pinaceae, Larix and Pseudotsuga, diverged near the Cretaceous-Tertiary boundary in East Asia or western North America. Rhabdocline is comprised of seven species and subspecies, six known from two species of Pseudotsuga and one, the asexual species Meria laricis, from three species of Larix. Evidence from host distributions and from nuclear ribosomal DNA suggests that Rhabdocline speciated in western North America and has been involved in several host switches. The ancestor of Meria laricis appears to have switched from P. menziesii to its current western North American hosts, L. occidentalis, L. lyallii, and very recently may have extended its host range to the European species, L. decidua. The occurrence of two lineages of R. weirii ssp. weirii on both North American species of Pseudotsuga is also probably the result of a recent host switch. Evidence of hostmediated divergence is seen in R. parkeri, which has different internal transcribed spacer types in the geographically isolated coastal and interior forms of P. menziesii. The wide host ranges of fungal genera closely related to Rhabdocline indicates that host switching is a prevalent pattern in the evolution of foliar symbionts in Leotiales and Rhytismatales. The prevalence of host switching in this group relative to other endosymbiotic organisms can probably be attributed to differences in dispersal mechanisms. Spores of foliar fungi are dispersed horizontally by wind and rain, rather than vertically from parent to offspring. Over evolutionary time, this provides more opportunities to shift to new hosts, particularly when the hosts are closely related and have overlapping distributions. / Graduation date: 1998

M.Sc. / Five plastid regions as source for phylogenetic information were used to investigate the relationships among ten genera of Vitaceae. These comprised the tmL intron, trnL-F intergenic spacer, rpL16 intron, rbcL gene and accDpsa/ spacer. Congruent results were obtained between separate, combined and Bayesian analysis with all four major clades being shared among trees. All bootstrap consensus trees obtained from single sequences or combined analysis suggest that Vitaceae is a monophyletic group with Leea weakly supported as sister to Vitaceae. The results presented provide novel insights into the relationships within ten Vitaceae genera and suggest direction for further studies.

One goal central to ecology is to understand how species interactions and biophysical processes interact over vastly different scales to govern past, current, and future patterns of diversity. Today, this goal is particularly critical given the degree to which rapid environmental change is affecting species distributions and community composition. Natural environmental gradients provide excellent opportunities to uncover possible mechanistic links between species distributions and environmental conditions links that are invaluable for understanding how species may respond to environmental change. This dissertation builds on recent approaches that combine information on species' functional traits and evolutionary histories to refine our view of how contemporary and historical processes jointly govern the distribution of biodiversity. In the context of tropical tree communities of Puerto Rico, the following four chapters evaluate hypotheses about the distribution of different dimensions of diversity (i.e., species, functional, and phylogenetic) across regional abiotic gradients. In chapter 1, I develop an island-wide molecular phylogeny for the native and naturalized trees of Puerto Rico, and show preliminary evidence that dry forests comprise an evolutionarily clustered subset of the total island tree flora. In chapter 2, I examine functional and phylogenetic diversity across spatial resource gradients, and use these patterns to infer variation in community assembly processes along a gradient of water availability. In chapter 3, I use temporal shifts of functional and phylogenetic diversity during secondary succession to infer the shifts in the processes underlying successional change in wet forests of Puerto Rico. Finally, in chapter 4, I evaluate the linkages between species functional traits and their geographic distributions, and test the hypothesis that community-weighted mean trait values reflect the `optimal' strategy for a given set of abiotic conditions. A theme common to all chapters is the idea that functional and phylogenetic dimensions of diversity can shed light on the processes underlying patterns of diversity better than more traditional metrics of species diversity. I provide recommendations for future research directions at the end of each chapter and in the final conclusions.

Orientador: George John Shepherd / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-10T11:39:18Z (GMT). No. of bitstreams: 1 Ribeiro_JoseEduardoLahozdaSilva_D.pdf: 15364889 bytes, checksum: aff367f6d443eb922d7c26df60d67b5c (MD5) Previous issue date: 2007 / Resumo: A família Moraceae é extremamente bem representada em número de indivíduos e espécies em florestas neotropicais de baixa altitude. Entretanto, a maior parte das informações disponíveis sobre o grupo, até o presente, refere-se apenas as espécies de Ficus. São raros os trabalhos sobre a evolução dos caracteres presentes nas diferentes inflorescências que ocorrem na família, que, em alguns casos, estão entre as mais complexas dentro das Angiospermae, e as informações sobre o relacionamento filogenético infrafamiliar, assim como as delimitações de suas tribos, precisam ser enriquecidas com mais dados para serem melhor compreendidas. Neste contexto, foi desenvolvido o presente trabalho, que teve como objetivos o estudo da filogenia de Moraceae, especialmente, as neotropicais, a partir de dados moleculares do segmento trnL-F do cloroplasto e de 50 caracteres morfológicos; o levantamento e análise da evolução de caracteres relacionados às inflorescências do grupo, e a caracterização morfológica das tribos da família. Além da árvore filogenética gerada a partir das análises realizadas para desenvolvimento do presente trabalho, cladogramas disponíveis na literatura, gerados a partir de informações moleculares de outros segmentos gênicos, também foram utilizados para avaliação da delimitação das tribos de Moraceae e estudo da evolução dos caracteres analisados. Os resultados das análises realizadas permitiram a proposição de uma nova tribo, Maclureae; uma nova delimitação para as tribos Dorstenieae e Moreae, correntemente aceitas; a elaboração de uma chave de identificação; a caracterização morfológica de todas as tribos apresentadas, e inferências sobre a evolução de alguns caracteres reprodutivos. Além disso, o sistema reprodutivo das 278 espécies neotropicais foi inferido a partir da observação em campo de 40 espécies, entre essas 28 espécies arbóreas, indicando que monoicia é o sistema reprodutivos mais comum no grupo, seguido de dioicia e androdioicia. As inflorescências de Antiarideae (Castilleae) bem como estruturas associadas a elas receberam novas interpretações após estudos morfológicos / Abstract: The Moraceae family is extremely well represented in individual and species number, in lowland neotropical forests. However, the most expressive part of the available information about this group, up to now, refers to Ficus species. There are few studies focusing on character evolution of the different types of inflorescences in this family, which are, in some cases, among the most complexes in the Angiospermae; and information on within-family phylogenetic relationship, as well as its tribes¿s delimitation, must be enhanced with more data, in order to be better understood. The present work was developed bearing in mind this context and aiming i) the study of the Moraceae phylogeny, especially the neotropical species, using molecular data from the chloroplast trnL-F region and from 50 morphological data; ii) the cataloging and evolutionary analysis of characters related to inflorescences of this group, and iii) the morphological characterization of the tribes. In addition to the phylogenetic tree generated from analysis carried out for the development of the present work; cladograms available in the literature, based on information of different DNA segments, were also used to evaluate the delimitation of Moraceae tribes and to study the evolution of the analyzed characters. The results of the performed analysis allowed the proposition of a new tribe, Maclureae; a new delimitation of Dorstenieae and Moreae, currently accepted; the elaboration of an identification key; the morphological characterization of all depicted tribes, and inferences about the evolution of some reproductive characters. Additionally, the reproductive system of the 278 neotropical species was inferred from field observation of 40 species, 28 of which were tree species, indicating that monoecy is the most common reproductive system in the group, followed by dioecy and androdioecy. After morphological studies, Antirideae (Castilleae) inflorescences, as well as related structures, have received new interpretation / Doutorado / Doutor em Biologia Vegetal

Orientador: Vinicius Castro Souza / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-19T11:20:47Z (GMT). No. of bitstreams: 1 Romao_GersonOliveira_D.pdf: 127922008 bytes, checksum: 8d69c511b2d94b53f8bea2adcc04fa1f (MD5) Previous issue date: 2011 / Resumo: O presente estudo refere-se à revisão taxonômica e estudos filogenéticos em Gaylussacia Kunth (Ericaceae). O objetivo principal foi contribuir para o conhecimento da taxonomia e das relações filogenéticas do grupo, procurando verificar se o gênero e as seções são monofiléticos. A família é cosmopolita e possui cerca de 160 gêneros e 4500 espécies. O gênero Gaylussacia é tipicamente americano e reúne 63 espécies, sendo que seis são possivelmente novos para a ciência. São levantadas 52 espécies nativas do Brasil, as quais se concentram principalmente nos campos de altitude da Floresta Atlântica e nos campos rupestres como a Cadeia do Espinhaço, além da planície litorânea e bordas de rios na Floresta Amazônica. Na região dos Andes, são encontradas três espécies, uma distribuída pela região entre Argentina e Bolívia, uma entre o Equador e Peru e outra distribuída pela Colômbia até a Venezuela. Ao leste da América do Norte são encontradas outras oitos espécies, concentradas principalmente ao longo da planície costeira até a Cadeia dos Apalaches. O trabalho está baseado no levantamento das espécies obtidas em consultas bibliográficas, atividades de campo, consultas aos acervos dos principais herbários, bem como nos resultados obtidos através da análise de seqüenciamento de DNA. Desse modo, o trabalho consta de descrições das espécies, ilustrações, chaves de identificação, mapas de distribuição geográfica, comentários, fotografias das plantas e suas estruturas, além de análise filogenética do gênero utilizando marcadores como ITS e trnL-F. A análise filogenética indica que o gênero é monofilético, mas não sustenta o reconhecimento das seções. Ao longo dos estudos, foram publicadas três novas espécies, sendo elas: Gaylussacia luizae G.O. Romão & V.C. Souza, G. paranaensis G.O. Romão & Kinoshita e G. rupestrís G.O. Romão & V.C. Souza, além de propor a elevação de três variedades a espécies: G. bocainae (Sleum.) G.O. Romão & V.C. Souza, G. hilaireana (Sleum.) G.O. Romão & V.C. Souza e G. salviifolia (Sleum.) G.O. Romão & V.C. Souza. Aqui foram designados 37 lectótipos e três neótipos. Foram identificados 12 padrões de distribuição geográfica para as espécies do gênero / Abstract: The present proposal is to support the taxonomic and philogenetic study of Gaylussaaa Kunth. The mainly objective was to accomplish a taxonomic study of the species and of the Gaylussacia section, moreover, to accomplish a phylogenetic study of Vaccinieae tribe, and to verify the relationships among Gaylussacia and other near genera. Ericaceae is a cosmopolitan family, including around 160 genera and nearly 4500 species, it includes herbs until small trees and is distributed mainly in temperate and subtropical regions worldwide. Gaylussacia is typically a American genera, are 63 recognized species and 6 taxa probably unpublished to the science, which 52 are brazilian, eight are Noth Americans and three are from Andes, one between Ecuador/Peru, one between Bolilva/Argentina and one is from Colombia to Venezuela. The elaboration of the taxonomic revision is based on the survey of the Gaylussacia species, first, through bibliographical consults, second, through analysis of the specimens deposited in the Brazilian and European herbaria, third, through field expeditions around Brazil in order to collect fresh material for the phylogenetic studies and to observe the natural habitat. The study will present a monograph of Gaylussacia species, that will consist of descriptions, illustrations, maps and geographical distribution, identification keys for the species and varieties besides taxonomical comments, photografies and phylogenetic study using ITS and trnL~F sequences. The phylogenetic analysis indicates the monophyly of the genus, but it is not the sections. During the research, three new species were published, Gaylussacia luizae G.O. Romão & V.C. Souza, G. paranaensis G.O. Romão & Kinoshita e G. rupestris G.O. Romão & V.C. Souza, besides proprosing three new status: G. bocainae (Sleum.) G.O. Romão & V.C. Souza, G. hilaireana (Sleum.) G.O. Romão & V.C. Souza e G. salviifolia (Sleum.) G.O. Romão & V.C. Souza. It were designed here 37 lectotypes and three neotypes, and identified 12 patterns of geographical distribution for the species of Gaylussacia / Doutorado / Biologia Vegetal / Doutor em Biologia Vegetal

M.Sc. / The tribe Podalyrieae is a group of Papilionoid legumes that are largely endemic to the Cape Floristic Region of southern Africa. A phylogenetic study of the tribe was undertaken using gene sequences obtained from the internal transcribed spacer (ITS) as well as the plastid gene rbcL. Although the resolution was poor in the resulting trees, several groupings were noted within the tribe. The subtribe Xiphothecinae remains relatively unchanged and consists of the genera Amphithalea and Xiphotheca. The subtribe Podalyriinae was found to be paraphyletic. A close relationship was observed between the genera Liparia and Podalyria with Stirtonanthus as sister. Additional chloroplast genes (trnL-F and trnS-trnG) were sequenced to obtain better resolution within this group. While Podalyria and Stirtonanthus are monophyletic, the monophyly of Liparia is still uncertain. Virgilia and Calpurnia are closely related and Cyclopia retains its isolated, monophyletic position sister to the tribe. The species of Cadia included in the phylogenetic analysis formed a sister grouping to the tribe Podalyrieae and the inclusion of this genus in Podalyrieae is discussed. A date for the root node of the tribe was estimated at 28.55 MYA, using non-parametric rate smoothing (NPRS), indicating a major radiation to have taken place during the Pliocene. By means of independent contrasts it was determined that the rate of molecular evolution is higher in reseeders than resprouters, perhaps due to more reproductive cycles in these individuals, that would in turn affect the rate of DNA substitution.

Ph.D. / Genetic variation estimates and phylogenetic studies (based on genetic differentiation) of the Podalyrieae and related tribes (family Fabaceae) are presented. The tribe is endemic to the Cape fynbos region of South Africa, except for Calpurnia. Although Podalyrieae have been the focus of many taxonomic studies no genetic variation studies have been done on this group of plants. Genetic variation in selected populations, species and genera was studied to evaluate the use of enzyme electrophoresis in systematic studies on these three levels. Eight case studies are presented. Allelic data proved to be extremely useful at the population and congeneric species level. However, at a higher level, it showed some potential when treated with caution. It is not possible to predict beforehand if meaningful results can be obtained at this higher (i.e. confamilial genus) level of divergence. A large number of plant genetic data sets from the literature was analysed to determine typical levels and ranges of genetic differentiation within families, genera and species. A graph of probability against taxonomic rank was constructed and compared with results published by Thorpe (1982, 1983). The results indicate that plant taxa have a reduced biochemical evolution (less diverse than animals at comparable taxonomic ranks) in contrast to Thorpe's (1982, 1983) reports (which were based on less data for plant taxa). Genetic identity values between 3041 pairs of taxa were used in the present study. The phylogenetic relationships among genera of the tribe Podalyrieae were estimated from sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA as well as morphological and chemical data. Morphological and. ITS sequence data produced cladograms with similar topologies, both supporting the exclusion of Hypocalyptus from Podalyrieae. A broadening of Podalyrieae, which includes Xiphothecinae, Podalyriinae and Cyclopia, is suggested. The multidisciplinary approach followed in this study provided a better understanding of taxonomic and evolutionary relationships in the Podalyrieae and some other Cape legumes.

Patterns in the distribution of homoplasy are investigated from theoretical and empirical perspectives. The history of the term "homoplasy" as used by morphologists, evolutionary systematists, cladists, and others is reviewed, especially in relation to its complement, "homology." Homoplasy is defined relative to homology, which is viewed as any similarity shared through an unbroken line of common ancestry. An investigation of levels of homoplasy based on a statistical analysis of 60 published phylogenies reveals a strong dependence of homoplasy on the number of taxa included. This relation is independent of number of characters, type of data, taxonomic rank, or organism, and suggests that large taxa should be the focus of empirical studies of homoplasy. Hence, a phylogenetic analysis of the large genus Astragalus was undertaken using 113 representative species (and varieties) found in North America. Fifty-seven binary and multistate characters were scored and the resulting matrix was subjected to numerical cladistic analysis. Two large sets of equally parsimonious trees were found at 595 and 596 steps. The sets were analyzed using consensus methods, robust clades were discussed in detail, and the phylogenies were compared to previous classifications. Character evolution of a large set of taxonomically important and morphologically varied traits was investigated. Statistical tests were developed to detect patterns of topological clustering of homoplastic character changes in cladograms. The tests use Monte-Carlo computer simulations of four null models of character evolution in an attempt to reject the hypothesis of random homoplastic distributions. For the Astragalus data set only two of 17 characters were significantly clustered, and this is close to random expectation. Another data set from the literature was also tested, and in it no characters were clustered at the 5 percent level. The explanation for these negative findings regarding homoplastic "tendencies" is explored with respect to "scope", "scale", and character "resolution," factors believed to play an important role in the analysis of character evolution.