The mechanisms behind the high level of plant diversity and endemism observed in the Cape Floral Region (CFR) of South Africa have been the focus of many studies. Recently developed methods that employ DNA sequence data are making major contributions in reconstructing evolutionary histories of CFR species. Concurrently, palaeoenvironmental evidence is used increasingly to explain the impact of past climates on species ranges. This paper combines these two approaches by analysing the distribution of genetic diversity of the Afro-montane liverwort Jamesoniella colorata and associating its inferred evolutionary history with major palaeoclimatic trends in South Africa. Liverworts are generally well-suited for phylogeographical studies because they often have low dispersal rates, broad geographical ranges and long evolutionary persistence. In addition, the high among-population diversity observed in J colorata is conducive to the interpretation of significant historical events. The GIS-based bioclimatic envelope shows a strong correlation between potential habitat and the known distribution of J colorata and indicates that sampling in this study was sufficient to make accurate phylogeographical inferences. A combination of phylogeographical data and population genetics evidence suggests that populations of J colorata in the Western Cape Province have experienced range contractions into upper-montane refugia and range expansions into lower altitudes in response to warming and cooling climatic trends, respectively. These range shifts have probably taken place throughout the Quaternary glacial-interglacials cycles, , which are thought to have been influential in shaping modem patterns of diversity. In lV an attempt to assign approximate dates to the two expansion events inferred for J. colorata, an average chloroplast mutation rate was applied to the trnL-F cpDNA mismatch distribution. The results roughly place the expansions within the last glacial period, demonstrating the general accordance of the phylogeographical and palaeoclimatic data. The molecular work in this study also brought into question the taxonomic status of several specimens that showed distinctly divergent DNA sequences. Preliminary morphological inspection of the specimens revealed subtle but clear differences in leaf and stem anatomy that were once associated with J. oenops, a species synonymised with J. colorata in 1971.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-03-23T19:08:09Z No. of bitstreams: 1 fernandasampaio.pdf: 1013409 bytes, checksum: a971117fc3bdd9c19272fe04cac30974 (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-03-24T12:55:01Z (GMT) No. of bitstreams: 1 fernandasampaio.pdf: 1013409 bytes, checksum: a971117fc3bdd9c19272fe04cac30974 (MD5) / Made available in DSpace on 2017-03-24T12:55:01Z (GMT). No. of bitstreams: 1 fernandasampaio.pdf: 1013409 bytes, checksum: a971117fc3bdd9c19272fe04cac30974 (MD5) Previous issue date: 2009-02-13 / O gênero Lippia é um dos principais da família Verbenaceae e em sua maior parte está concentrado no Brasil, México, Paraguai e Argentina com poucas espécies endêmicas na África. O objetivo deste trabalho foi a construção de uma hipótese filogenética para 39 espécies do gênero Lippia ocorrentes no Brasil, Argentina, Bolívia, Paraguai e Uruguai com base em dados moleculares das regiões ITS, Waxy, TrnL-F e trnQ-rps16. As sequências foram amplificadas e purificadas para posterior seqüenciamento. As análises foram feitas utilizando-se Máxima Verossimilhança e Inferência Bayesiana. O presente trabalho revelou, pela primeira vez, aspectos filogenéticos de espécies do gênero Lippia com base em caracteres moleculares. De modo geral, as árvores filogenéticas baseadas nas diferentes regiões gênicas estudadas revelaram questões importantes como é o caso do monofiletismo da seção Goniostachyum. Outro ponto importante envolve a falta de resolução das seções Dipterocalix, Rhodolippia e Zapania. Dentre elas destaca-se a seção Zapania que constitui em vários aspectos estudados, a seção mais diversa. Embora o presente trabalho tenha mostrado aspectos inéditos com relação à organização filogenética de espécies e seções do gênero Lippia, a questão da especiação no gênero permanece em aberto. É possível que para resolver este problema sejam necessários estudos populacionais e filogeográficos, embasados por uma análise filogenética com maior número de genes e principalmente, envolvendo um maior número de espécies. / Lippia is one of the most important genus of the Verbenaceae family. It is mainly concentrated in Brazil, Mexico, Paraguay and Argentina with few endemic species in Africa. The present study was done in order to construct a phylogenetic hypothesis for 39 species of the genus Lippia from Brazil, Argentina, Bolivia, Paraguay and Uruguay based on molecular data of regions ITS, Waxy, TrnL-F and rps16-trnQ. The sequences were amplified and purified for subsequent sequencing. The phylogenetic analyses were done using the Maximum Likelihood and Bayesian Inference. It was possible to show for the first time, phylogenetic aspects of the genus Lippia based on molecular data. In general, the phylogenetic trees based on different gene regions revealed important points such as the monophyly of Goniostachyum section. Another important point involves the lack of resolution of the sections Dipterocalix, Rhodolippia and mainly Zapania which is the most diverse among them. Although this work has shown new aspects about the phylogenetic organization of sections and species of the genus Lippia, the speciation process of the genus remains an open question. To resolve this problem, additional studies using phylogeographic and population genetics approaches, based on a phylogenetic analysis with greater numbers of genes and mainly involving a great number of species should be necessary.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Molecular and morphologic studies were used to determine the evolution, classification and differentiation of Nymphaea odorata. Molecular analyses of the nuclear internal transcribed spacer (ITS) region, the chloroplast trnL-F region, and inter-simple sequence repeat (ISSR) markers determined the variation present between and within two species of Nymphaea. The ITS region resulted in a phylogeny depicting strong separation between species (N. mexicana and N. odorata) and some separation between N. odorata's subspecies. The ITS region contained polymorphisms, which upon SAHN clustering and principle coordinate (PCOA) and minimum spanning tree (MST) analyses produced groups similar to the clades in the ITS phylogeny. Sixteen accessions were chosen for trnL-F analysis, where a subspecies-specific molecular marker was found. In most accessions the marker confirmed the original subspecies classification. Molecular analyses using ISSRs characterized among population variation in N. odorata and N. mexicana using five primers. ISSR markers among populations were highly variable within a species and were used in UPGMA, PCOA and MST analysis, which resulted in separation between the subspecies. Both univariate and multivariate analyses were performed on quantitative and qualitative morphological characters. An analysis of variance resulted in six morphological characteristics that were statistically significant (P< 0.05), the majority being leaf blade characteristics. Multivariate statistics of principle component analysis and discriminate analysis resulted in groups for each subspecies, both emphasized the importance of quantitative leaf blade characteristics. Overall, both morphology and molecular characteristics supported the classification of subspecies for ssp. odorata and ssp. tuberosa, due a lack of strong segregation of characteristics. / Master of Science

The Malacothamnus alliance consists of three genera, Iliamna, Malacothamnus, and Phymosia. The genera are considered taxonomically complex since hybridization freely occurs, polyploidy levels vary, and there is a lack of distinct morphological characters to delineate taxa. Several taxonomic treatments have been prepared for each genus, but relationships within the genera and the relationship of the Malacothamnus alliance to others in the Malvaceae remains unknown. This multifaceted study aimed to (a) examine the monophyly of the Malacothamnus alliance and its position in the Malvaceae, (b) determine the relationships between genera in the alliance, (c) compare variation of nuclear and chloroplast genes in the alliance, (d) prepare revised taxonomic treatments for Iliamna and Malacothamnus, and (e) examine the probability of successful hybridization in Iliamna. The monophyly of the Malacothamnus alliance was not confirmed using DNA sequences of both nuclear and chloroplast regions. In Iliamna, little sequence variation was detected among taxa in the Rocky Mountains; however, the nuclear and chloroplast regions conflicted with regard to the relationships of the western and eastern taxa. An ancestral copy of the chloroplast genome is shared between the two eastern U.S. Iliamna species and Phymosia (Bahamas and Mexico). The nuclear ITS sequences indicated the western U.S. Iliamna species were more closely related to Phymosia and Malacothamnus than to other species in Iliamna. Neither data set provided sufficient variation to resolve relationships of species in Malacothamnus. Genetic variation and the feasibility of hybridization in Iliamna supported the results of the broader phylogenetic studies. Iliamna corei and I. remota are recently derived from I. rivularis. Hybrid offspring of I. corei and I. remota had higher viability and fecundity than did hybrids between crosses of either species and I. rivularis. The Virginia populations of I. corei and I. remota are more genetically similar than either is to Illinois populations of I. remota. However, the species are morphologically distinct and can easily be distinguished from others in the genus. Revised taxonomic treatments for Iliamna and Malacothamnus based on surveys of herbarium material are presented. Taxonomic revisions include the new combinations of Iliamna grandiflora subsp. grandiflora and I. grandiflora supsp. crandallii and the resurrection of Malacothamnus hallii and M. orbiculatus. / Ph. D.

Eurybia et ses proches parents Oreostemma, Herrickia et Triniteurybia sont appelés le grade des eurybioïdes. Comprenant 31 espèces vivaces, ce grade appartient au clade Nord-américain de la tribu des Astereae. Les analyses moléculaires antérieures ont montré que ce groupe est à la fois paraphylétique aux Machaerantherinae et un groupe frère aux Symphyotrichinae. Les relations infragénériques partiellement résolues et faiblement supportées empêchent d’approfondir l'histoire évolutive des groupes et ce, particulièrement dans le genre principal Eurybia. Le but de cette étude est de reconstruire les relations phylogénétiques au sein des eurybioïdes autant par l'inclusion de toutes les espèces du grade que par l’utilisation de différents types de régions et de méthodes d'inférence phylogénétique. Cette étude présente des phylogénies basées sur l'ADN ribosomal nucléaire (ITS, ETS), de l'ADN chloroplastique (trnL-F, trnS-G, trnC-ycf6) et d’un locus du génome nucléaire à faible nombre de copie (CNGC4). Les données sont analysées séparément et combinées à l’aide des approches de parcimonie, bayesienne et de maximum de vraisemblance. Les données ADNnr n’ont pas permis de résoudre les relations entre les espèces polyploïdes des Eurybia. Les analyses combinées avec des loci d’ADNnr et d’ADNnr+cp ont donc été limitées à des diploïdes. Les analyses combinées ont montré une meilleure résolution et un meilleur support que les analyses séparées. La topologie de l’ADNnr+cp était la mieux résolue et supportée. La relation phylogénétique de genres appartenant au grade des eurybioïdes est comme suit : Oreostemma (Herrickia s.str. (Herrickia kingii (Eurybia (Triniteurybia - Machaerantherinae)))). Basé sur la topologie combinée de l’ADNnr+cp, nous avons effectué des analyses de biogéographie à l’aide des logiciels DIVA et LaGrange. Ces analyses ont révélé une première radiation des eurybioïdes dans l’Ouest de l’Amérique du Nord, suivi de deux migrations indépendantes dans l’Est de l’Amérique du Nord chez les Eurybia. Due au relatif manque de variabilité de l’ADNnr, l’ADNcp et CNGC4, où le triage de lignés incomplet était dominant, l'origine du grade est interprétée comme récente, possiblement du Pliocène. La diversification du groupe a été probablement favorisée par les glaciations Pléistocènes. / Eurybia and it relatives, Oreostemma, Herrickia, and Triniteurybia, are collectively called the eurybioid grade. Comprising 31 perennial species, this grade belongs to the North American clade of the tribe Astereae. Early molecular analyses had inferred that this group is paraphyletic to the Machaerantherinae and sister to the Symphyotrichinae. The partially resolved and poorly supported relationships at the infrageneric level within the group, particularly within the core genus Eurybia, is preventing further insights into the evolutionary history of the group. The aim of this study is to reconstruct the phylogenetic relationships among the eurybioids by including all species of the grade and by using both different types of regions and multiple phylogenetic inference methods. The present study provides phylogenies based on nuclear ribosomal DNA (ITS, ETS), chloroplastic DNA (trnL-F, trnS-G, trnC-ycf6), and a low-copy nuclear locus (CNGC4), in separate and combined datasets analyzed using maximum parsimony, Bayesian and maximum likelihood approaches. In a separate analysis of the nrDNA dataset, the relationships of polyploids in Eurybia proved to be impossible to resolve. The nrDNA and nr+cpDNA combined analyses therefore were restricted to diploids. The combined analyses provided greater resolution and support than separate analyses. The nr+cpDNA phylogeny was the best resolved and supported. The phylogenetic relationship of genera belonging to the eurybioid grade is as follows: Oreostemma (Herrickia s.str. (Herrickia kingii (Eurybia (Triniteurybia – Machaerantherinae)))). Based on the nr+ cpDNA combined topology, we performed biogeographical analyses using DIVA and LaGrange. These analyses revealed an initial radiation of the eurybioids in western North America, with two independent migrations to eastern North America within Eurybia. Based on the relative lack of variation in nrDNA, cpDNA and CNGC4, where incomplete lineage sorting was dominant, the origin of the grade is interpreted as recent, probably from the Pliocene. Diversification of the group was probably favored by the Pleistocene glaciations.

Eurybia et ses proches parents Oreostemma, Herrickia et Triniteurybia sont appelés le grade des eurybioïdes. Comprenant 31 espèces vivaces, ce grade appartient au clade Nord-américain de la tribu des Astereae. Les analyses moléculaires antérieures ont montré que ce groupe est à la fois paraphylétique aux Machaerantherinae et un groupe frère aux Symphyotrichinae. Les relations infragénériques partiellement résolues et faiblement supportées empêchent d’approfondir l'histoire évolutive des groupes et ce, particulièrement dans le genre principal Eurybia. Le but de cette étude est de reconstruire les relations phylogénétiques au sein des eurybioïdes autant par l'inclusion de toutes les espèces du grade que par l’utilisation de différents types de régions et de méthodes d'inférence phylogénétique. Cette étude présente des phylogénies basées sur l'ADN ribosomal nucléaire (ITS, ETS), de l'ADN chloroplastique (trnL-F, trnS-G, trnC-ycf6) et d’un locus du génome nucléaire à faible nombre de copie (CNGC4). Les données sont analysées séparément et combinées à l’aide des approches de parcimonie, bayesienne et de maximum de vraisemblance. Les données ADNnr n’ont pas permis de résoudre les relations entre les espèces polyploïdes des Eurybia. Les analyses combinées avec des loci d’ADNnr et d’ADNnr+cp ont donc été limitées à des diploïdes. Les analyses combinées ont montré une meilleure résolution et un meilleur support que les analyses séparées. La topologie de l’ADNnr+cp était la mieux résolue et supportée. La relation phylogénétique de genres appartenant au grade des eurybioïdes est comme suit : Oreostemma (Herrickia s.str. (Herrickia kingii (Eurybia (Triniteurybia - Machaerantherinae)))). Basé sur la topologie combinée de l’ADNnr+cp, nous avons effectué des analyses de biogéographie à l’aide des logiciels DIVA et LaGrange. Ces analyses ont révélé une première radiation des eurybioïdes dans l’Ouest de l’Amérique du Nord, suivi de deux migrations indépendantes dans l’Est de l’Amérique du Nord chez les Eurybia. Due au relatif manque de variabilité de l’ADNnr, l’ADNcp et CNGC4, où le triage de lignés incomplet était dominant, l'origine du grade est interprétée comme récente, possiblement du Pliocène. La diversification du groupe a été probablement favorisée par les glaciations Pléistocènes. / Eurybia and it relatives, Oreostemma, Herrickia, and Triniteurybia, are collectively called the eurybioid grade. Comprising 31 perennial species, this grade belongs to the North American clade of the tribe Astereae. Early molecular analyses had inferred that this group is paraphyletic to the Machaerantherinae and sister to the Symphyotrichinae. The partially resolved and poorly supported relationships at the infrageneric level within the group, particularly within the core genus Eurybia, is preventing further insights into the evolutionary history of the group. The aim of this study is to reconstruct the phylogenetic relationships among the eurybioids by including all species of the grade and by using both different types of regions and multiple phylogenetic inference methods. The present study provides phylogenies based on nuclear ribosomal DNA (ITS, ETS), chloroplastic DNA (trnL-F, trnS-G, trnC-ycf6), and a low-copy nuclear locus (CNGC4), in separate and combined datasets analyzed using maximum parsimony, Bayesian and maximum likelihood approaches. In a separate analysis of the nrDNA dataset, the relationships of polyploids in Eurybia proved to be impossible to resolve. The nrDNA and nr+cpDNA combined analyses therefore were restricted to diploids. The combined analyses provided greater resolution and support than separate analyses. The nr+cpDNA phylogeny was the best resolved and supported. The phylogenetic relationship of genera belonging to the eurybioid grade is as follows: Oreostemma (Herrickia s.str. (Herrickia kingii (Eurybia (Triniteurybia – Machaerantherinae)))). Based on the nr+ cpDNA combined topology, we performed biogeographical analyses using DIVA and LaGrange. These analyses revealed an initial radiation of the eurybioids in western North America, with two independent migrations to eastern North America within Eurybia. Based on the relative lack of variation in nrDNA, cpDNA and CNGC4, where incomplete lineage sorting was dominant, the origin of the grade is interpreted as recent, probably from the Pliocene. Diversification of the group was probably favored by the Pleistocene glaciations.