Recentes análises filogenéticas, baseadas em dados moleculares, indicaram que Didiereaceae s.s. é filogeneticamente relacionada a gêneros tradicionalmente pertencentes à Portulacaceae s.l.. Sendo incluídos os gêneros Ceraria, Portulacaria e Calyptrotheca em Didiereaceae e essa dividida em três subfamílias: Didieroideae (11 espécies), Portulacarioideae (7 espécies) e Calyptrothecoideae (1espécie). Análises moleculares apresentaram alto suporte para o monofiletismo da família e circunscrição das três subfamílias, contudo, nenhuma dessas análises elucidou completamente as relações entre os gêneros. Com a expansão de sua circunscrição, a família se tornou mais heterogênea, surgindo assim, a necessidade da investigação de características para o estabelecimento de sinapomorfias ou para corroborar suas relações dentro de Portulacineae. Diante disso, o presente trabalho realizou análises de Inferência Bayesiana e Máxima Parcimônia para sete sequências diferentes do DNA do cloroplasto, trnA-trnB, trnL-trnF, trnT-trnL, trnS-trnG, trnQUUG-rps16, rps16 e rpl16, para todas as 19 espécies de Didiereaceae e investigou a ontogênese foliar e da região de sua axila para Didieroideae e Portulacarioideae. Os resultados das análises filogenéticas corroboraram o monofiletismo da família e de suas três subfamílias, além de elucidar as relações internas em Didieroideae e Portulacarioideae. Os dois gêneros de Portulacarioideae, Portulacaria e Ceraria, não são monofiléticos e as espécies de Ceraria foram transferidas para Portulacaria. Também foi caracterizado o desenvolvimento dos diferentes padrões de variações morfológicas da folha e das folhas modificadas em espinhos e profilos. A partir dos resultados do desenvolvimento e da filogenia molecular, foi feita uma análise de reconstrução da região da axila foliar para o ancestral de Didiereaceae, que indicou a presença de braquiblastos portadores de profilos na axila foliar do ancestral comum. Como consequência, foram estabelecidas homologias entre esses profilos e os profilos de Talinaceae e espinhos de Cactaceae / Recent phylogenetic analysis, based on molecular data, indicated that Didiereaceae s.s. is phylogenetic related to former Portulacaceae s.l. genera. The genera Ceraria, Portulacaria and Calyptrotheca were included in Didiereaceae and the family was divided in three subfamilies: Didieroideae (11 species), Portulacarioideae (7 species) and Calyptrothecoideae (1specie). Molecular analyses presented high statistical support to the monophyletism of the Didiereaceae and its division in three subfamilies, however, none of these analyses elucidated the relations among genera. With the expansion of its circumscription, the family became rather heterogenic, resulting in the need to investigate characteristics to the establishment of synapomorphies to the family or corroborate its relations inside Portulacineae. Therefore, we performed Bayesian Inference and Maximum Parsimony analyses for seven different chloroplast DNA regions, trnA-trnB, trnL-trnF, trnT-trnL, trnS-trnG, trnQUUG-rps16, rps16 and rpl16, for all 19 species of Didiereaceae and investigated the leaf and leaf axil region ontogenesis for Didieroideae and Portulacarioideae. Our analyses corroborated the monophyly of the Didiereaceae and of its three subfamilies and elucidated internal relationships between the Didieroideae and the Portulacarioideae. The two genera of the Portulacarioideae, Portulacaria and Ceraria, are not monophyletic and the 5 accepted species for Ceraria are transferred to Portulacaria. Also, the ontogenesis for different morphological patterns of leaf and spines and prophyll were characterized. Based on the ontogenetical results and the molecular phylogeny, was made the reconstruction to the ancestor character for the leaf axil of Didiereaceae. This analysis indicated the presence of brachyblasts bearing prophylls in the leaf axil of the common ancestor. As a consequence, homologies between these prophylls and Talinaceae prophylls and Cactaceae spines were established

As planárias terrestres (Platyhelminthes, Geoplanidae) são vermes de vida livre, hermafroditas e predadores que habitam principalmente florestas úmidas. A subfamília Geoplaninae, restrita à região neotropical, compreende cerca de 270 espécies. Geoplana Stimpson, 1857, seu gênero-tipo, é atualmente composto por três espécies (Geoplana vaginuloides (Darwin, 1844), Geoplana chita Froehlich, 1956 e Geoplana pulchella Schultze & Müller, 1857), todas da mata Atlântica brasileira. A espécie-tipo do gênero, G. vaginuloides, foi descrita por Darwin a partir de um único espécime que coletou no Rio de Janeiro (RJ) em 1832. Darwin baseou-se apenas em caracteres de morfologia externa e o paradeiro do material tipo é desconhecido. Posteriormente, outros autores estudaram a espécie e atribuíram-na sete padrões de coloração dorsal, mas um estudo filogenético recente com dois indivíduos de coloridos dorsais distintos indicou que a espécie é polifilética, justificando a necessidade de sua circunscrição para estabilizar a taxonomia da subfamília. Este trabalho tem por objetivo fazer uma revisão taxonômica do gênero utilizando dados fenotípicos e genotípicos. Todo o material disponível das espécies de Geoplana citado na literatura foi analisado, além de outros espécimes disponíveis em coleção ou coletados para este propósito. As principais características morfológicas que permitiram distinguir as espécies são: cor do dorso, forma e desenvolvimento do bulbo peniano, região de encontro dos ductos eferentes, região do átrio masculino em que se assenta a papila peniana, comprimento relativo da papila peniana e distribuição das secreções associadas, espessura da musculatura do ducto ejaculatório, e tipo de epitélio de revestimento do átrio feminino. As análises filogenéticas moleculares foram realizadas a partir de sequências do gene mitocondrial Citocromo Oxidase I (COI) e do gene nuclear Fator de Elongação 1-alfa (EF-1-), isolados e concatenados, usando parcimônia e máxima verossimilhaça como critérios de optimalidade. Os resultados moleculares e morfológicos são congruentes e revelaram que G. pulchella é monofilética, mas G. chita e G. vaginuloides são polifiléticas. As relações entre as espécies variam em função do gene e do critério de optimalidade utilizados. 13 clados são constantes, cada um composto por indivíduos homogêneos morfologicamente. Esta congruência permite reconhecer 13 espécies, dez delas com aspecto compatível com G. vaginuloides, incluindo membros propostos por outros autores como coespecíficos: Geoplana vaginuloides (Darwin, 1844), G. apua Almeida & Carbayo, nom. nov., G. mogi Almeida & Carbayo, nom. nov., G. piratininga Almeida & Carbayo, nom. nov., G. paranapiacaba Almeida & Carbayo, sp. n., G. caraguatatuba Almeida & Carbayo sp. nov., G. ibiuna Almeida & Carbayo sp. nov., G. cananeia Almeida & Carbayo, sp. n., G. cambara Almeida & Carbayo sp. nov., G. iporanga Almeida & Carbayo sp. nov., G. pulchella Schultze & Müller, 1857, G. chita Froehlich, 1956, e G. boraceia Almeida & Carbayo, nom. nov. Estas espécies apresentam musculatura parenquimática longitudinal, característica incomum em Geoplaninae (conhecida apenas em Imbira) e ausente por definição em Geoplaninae. Propomos, então, emenda a diagnose de Geoplana e da subfamília. / Land planarians (Platyhelminthes, Geoplanidae) are hermaphroditic, free-living and predatory organisms, that inhabit humid forests. The subfamily Geoplaninae is restricted to the Neotropical region, and includes ca. 270 species. Currently, Geoplana Stimpson, 1857, the type-genus of the subfamily, comprises three species, Geoplana vaginuloides (Darwin, 1844), Geoplana chita Frohelich, 1956 e Geoplana pulchella Schultze & Müller, 1857, all of them found in the Brazilian Atlantic forest. The original description of the type-species of the genus, G. vaginuloides, was described from a single individual collected by Darwin in Rio de Janeiro (Brazil) in 1832. He described only the external aspect of the specimen and its location remains unknown. Subsequently, other authors studied this species and provided up to seven chromatic patterns of the dorsum, but in a recent paper, a polyphyletic condition of the species was demonstrated by means of molecular data. This situation entails the need to circumscribe the species in order to stabilize the txonomy of the subfamily. This works aims at achieving a taxonomic revision of the genus by using phenotypic and molecular data. All available material of Geoplana mentioned in literatute was studied, besides additional specimens from other collections or here collected for this purpose. Phenotypic examination enabled us to recognize up to 13 morphospecies, which differ each other mainly by means of these features: color of the dorsum, shape and relative development of the penis bulb; position of the junction of the sperm ducts with each other; region of the male atrium from which the penis papilla projects; relative length of the penis papilla; distribution of the secretions within the papilla; relative thickness of the musculatura wrapping the ejaculatory duct; and type of epithelium lining the female atrium. Molecular phylogenetic analyses were performed with sequences of the mitochondrial region of the cytochrome oxidase I gene and the nuclear region of the elongation factor 1-alpha, both separately and concatenated. Parsimony and maximum likelihood were used as optimality criteria. Morphological and molecular data are congruent with each other and revealed a monophyletic condition of G. pulchella, but a polyphyletic condition of G. chita and G. vaginuloides. Interrelationships among internal branches varied depending on the gene and the optimality criterion and have relatively low support. However, the external branches are constituted by morphologically homogeneous individuals. This congruence enabled us to recognize 13 species; the external aspect of ten species compares well with G. vaginuloides, including members considered conspecific in the literature. These results lead us to recognize the following taxonomic entities: Geoplana vaginuloides (Darwin, 1844), G. apua Almeida & Carbayo, nom. nov., G. mogi Almeida & Carbayo, nom. nov., G. piratininga Almeida & Carbayo, nom. nov., G. paranapiacaba Almeida & Carbayo, sp. n., G. caraguatatuba Almeida & Carbayo sp. nov., G. ibiuna Almeida & Carbayo sp. nov., G. cananeia Almeida & Carbayo, sp. n., G. cambara Almeida & Carbayo sp. nov., G. iporanga Almeida & Carbayo sp. nov., G. pulchella Schultze & Müller, 1857, G. chita Froehlich, 1956, and G. boraceia Almeida & Carbayo, nom. nov. All these species possess longitudinal parenchymatic musculature, an uncommon characteristic in Geoplaninae (only unknown from Imbira), which is, by definition, absent in the subfamily. Accordingly, we suggest to emend the diagnoses of the Geoplana and Geoplaninae.

Currently, the genus Thraupis Boie, 1826 is a monophyletic group with seven species, all of which have high molecular and morphological support. Nevertheless, the phylogenetic relationship of the species still unclear: T. abbas is the sister species of T. ornataT. palmarum clade, and a second group within the genus is composed by the T. episcopusT. sayaca clade. Furthermore, in the remaining species group, one of the species, T. glaucocolpa, has not been included in any of the previous molecular studies, even it was believed to be close related with T. sayaca. Moreover, the last species within the genus, T. cyanoptera, has an uncertain position in the genus phylogenetic tree. The T. episcopusT. sayacaT. galucocolpa species complex includes 18 subspecies and a high morphological variation and a wide distribution which includes overlapping zones of T. episcopus and T. sayaca, makes taxa identification almost impossible. Nonetheless, previous molecular studies had only used samples from two individuals of T. episcopus and one of T. sayaca. Furthermore, the group does not have taxonomic stability, as shown by the multiple changes, which occur at different levels: moving from one genus to another or from species to subspecies level etc. To check the genus, I analyze 1171 specimens. The morphometric analysis outcomes show the weight as the most variable and important measure and T. cyanoptera as the only clearly different species within taxonomic units. Finally, I did a phylogenetic analysis based on two mitochondrial genes (Cyt- and ND2), in addition to three nuclear introns (intron 3 of MUSK gen, intron 5 of TGFB2 gen and a piece of the intron 5 of the BF5 gen). I performed the extractions from tissues collected at different localities around the natural distribution of the species, with emphasis on T. episcopus and T. sayaca. I ran independent locus RAxML analysis and haplotypes networks and used to group the samples on genetic taxonomic units. RAxML and haplotypes analysis shows a close relationship between T. episcopus and T. sayaca with high probably introgression process within. Furthermore, exposed a genetic structure within T. episcopus. I used this genetic taxonomic units to ran a multilocus species tree with a calibrated molecular clock. The species tree suggests that the origin of the genus Thraupis was between 5.5 and 7.5 million years before present, in the Messinian age. Also recovers T. glaucocolpa is the oldest linage in the genus and shows a relation between the morphological traits with the genetic structure within T. episcopus. Finally, I suggest synonymizing several subspecies and elevating to species level the subspecies T. episcopus cana, based on the morphological and molecular data. / O gênero Thraupis Boie, 1826 é um grupo monofilético composto por sete espécies. Entretanto, as relações entre estas espécies continuam obscuras. Thraupis abbas é a espécie irmã do clado T. ornataT. palmarum. Um segundo grupo é composto pelo clado T. episcopusT. sayaca. Por outro lado, T. glaucocolpa não foi incluída em nenhum dos trabalhos que utilizou dados moleculares, enquanto que a posição de T. cyanoptera continua ainda não é clara. O complexo de espécies T. episcopusT. sayacaT. glaucocolpa inclui 18 subespécies e uma grande variação morfológica, além de uma ampla distribuição de várias delas, com áreas de sintopia entre T. episcopus e T. sayaca, onde a identificação destas duas espécies é muito difícil. Estudos moleculares prévios só incluíram amostras de dois indivíduos de T. episcopus e uma de T. sayaca. Este complexo de espécies ainda apresenta uma grande instabilidade taxonômica. Na revisão deste gênero foram analisados 1.171 espécimes. As análises morfométricas mostraram que a massa é o parâmetro que apresenta a maior variação e que T. cyanoptera é a única mais claramente diferençável dentre as unidades taxonômicas. Foi também realizada uma análise filogenética com base em dois marcadores mitocondriais (Cyt- e ND2), além de três íntrons nucleares (íntron 3 do gen MUSK, íntron 5 do gen TGFB2 e uma parte do íntron 5 do gen BF5). Foi realizada uma análise RAxML e das redes de haplótipos independentemente para cada lócus, e esta informação foi utilizada para agrupar as amostras em unidades taxonômicas genéticas. O RAxML e as redes de haplótipos mostraram uma relação próxima entre T. episcopus e T. sayaca, além de uma alta probabilidade de um processo de introgressão entre as espécies. Há também uma evidente estruturação genética em T. episcopus. As unidades taxonômicas genéticas foram utilizadas em uma análise multilocus de árvore de espécies, com um relógio molecular calibrado. A árvore de espécies sugere que a origem do gênero Thraupis se deu entre 5.5 e 7.7 milhões de anos. Thraupis glaucocolpa é a linhagem mais antiga do gênero e a estrutura genética dentro de T. episcopus possui uma relação com as características morfológicas dessa espécie. Finalmente, são sinonimizadas várias subespécies e T. episcopus cana é elevada à espécie com base nos dados morfológicos e moleculares.

Chironius, um dos maiores gêneros da subfamília Colubrinae na América do Sul, inclui 14 espécies, diagnosticadas pela presença de 10 ou 12 fileiras de escamas dorsais no meio do corpo. O gênero apresenta uma distribuição Neotropical, que se estende desde a costa norte de Honduras até o Uruguai e o nordeste da Argentina. Neste trabalho foi realizada uma análise filogenética combinada de 75 caracteres morfológicos e 1397 caracteres moleculares (provenientes das seqüências de dois genes mitocondriais, 12S e 16S, e um gene nuclear, c-mos) pelos métodos de máxima parcimônia e inferência bayesiana. A monofilia do gênero Chironius foi corroborada e os resultados obtidos sugerem que o gênero é dividido em 10 componentes monofiléticos. Os gêneros Drymobius, Leptophis e Dendrophidion são apontados como os mais relacionados à Chironius, corroborando trabalhos anteriores. Chironius laevicollis e C. scurrulus formam o clado mais basal entre as espécies, e sua distribuição restrita a América do Sul sugere que Chironius tenha tido origem neste continente e que posteriormente tenha invadido a América Central através de eventos de dispersão. / Chironius, one of the greatest genera of the Colubrinae subfamily in South America, consists of 14 species, diagnosed by the presence of 10 or 12 rows of dorsal scales in the mid-body. The genus presents a Neotropical distribution extending from the northern coast of Honduras to Uruguay and northeastern Argentina. This study presents a combined phylogenetic analysis of 75 morphological characters and 1397 molecular characters (from the sequences of two mitochondrial genes, 12S and 16S, as well as a nuclear gene, c-mos) by means of Maximum Parsimony and Bayesian Inference. The monophylety of the genus Chironius was corroborated and the obtained results suggest that the genus is subdivided in ten monophyletic components. The genera Drymobius, Leptophis and Dendrophidion come out as the most closely related to Chironius, corroborating previous studies. Chironius laevicollis and C. scurrulus composed the most basal clade among the species. Their distribution is restricted to South America, which suggests that Chironius originated in South America and later invaded Central America through dispersion.

The aim of this dissertation is to study the systematics and evolution of Euphorbiaceae vines (tribe Plukenetieae), a diverse pantropical lineage (~365 species and 18 genera) composed of three morphologically distinct subtribes, Dalechampiinae, Plukenetiinae, and Tragiinae. Through the course of my research I largely resolved the evolutionary history of Plukenetieae and made broader contributions to the study of pollen and seed evolution, pantropical biogeography, and plant diversification. In chapter two I developed the first well-sampled molecular phylogeny for Plukenetieae (154 terminals, ~93 species, 2,207 character dataset composed of ITS and psbA-trnH with indel gap-scored data), and determined baseline species group relationships of the tribe. Molecular phylogeny largely agreed with pollen morphology hypotheses and confirmed that the large genus Tragia was para- and/or polyphyletic and should be split into smaller genera. Analysis of pollen morphology revealed a trend towards aperture reduction and loss in Tragiinae, with four origins of weakly defined apertures and up to three origins of inaperturate pollen. In chapter three, I studied the seed size evolution of Plukenetia, a pantropical genus with large edible oil-rich seeds, by developing a near-exhaustive phylogeny (83 terminals, 20 of ~24 species, 5,069 bp dataset of ETS, ITS, KEA1 introns 11 and 17, TEB exon 17, matK, ndhF) and conducting ancestral state estimation and phylogenetic regression. Seed size evolution in Plukenetia was dynamic and associated with competing selective pressures of plant size, fruit type (and inferred dispersal syndrome), and seedling ecology. In chapter four I presented a revised sectional classification of Plukenetia based on phylogeny and morphological evidence, including three new taxa from South America. Chapters three and five included biogeographical investigations on Plukenetia and Plukenetieae. Analyses revealed that pantropical disjunct distributions arose one to three times in each subtribe via periodic long-distance dispersals from the Oligocene to the Pliocene, most often from South America to Africa and then Southeast Asia. Lastly, in chapter five, I developed an improved phylogeny for Plukenetieae (289 terminals, ~109 species, 5,160 bp dataset of ETS, ITS, KEA1 intron 11, TEB exon 17, matK, ndhF) to study the influence of innovative traits (twining growth form, stinging hair defences, and pseudanthial inflorescences) on diversification in the tribe. However, increased diversification was not associated with innovative traits. Instead, diversification was associated with clades that shifted into drier open habitats, aided by habitat expansion following the Late Miocene cooling period.

Borya mirabilis is one of the world's most critically endangered plants. The research in this thesis has illuminated key aspects of: its reproductive biology; interspecies and intraspecies molecular relationships, mycorrhizal status, tissue culture potential and disease threats. Each of these aspects has fundamental management implications for the active management of B. mirabilis. Floral observations of B. mirabilis and related species affirmed the uniqueness of the Boryaceae amongst the Asparagales. B. mirabilis had an unusually high number of floral abnormalities compared with other species of Borya observed. B. mirabilis is fly-pollinated. Pollen of Borya species showed little difference in the characteristics of mature pollen between species, with viable pollen being prolate and unicolpate with a single colpa-style aperture and a unique patterning of the pila. The structural immaturity of B. mirabilis pollen correlated with evidence from pollen growth experiments, where B. mirabilis pollen had extremely low germination rates, with those grains that did germinate being slow to do so and with slow-growing pollen tubes compared to those of fertile Borya species. Examination of the ovules of B. mirabilis showed that morphologically they were viable compared to viable Borya species. The field population of B. mirabilis was crossed, with one seed produced (the first recorded seed for th is species). Cross-pollination using the pollen of the closely related B. constricta and B. sphaerocephala with B. mirabilis ovules proved unsuccessful. Examination of the chromosome number of B. mirabilis showed that it had approximately 66 chromosomes and is probably hexaploid, relative to the diploid number of 26 in B. constricta. This may explain its low fertility. Interspecies and intraspecies relationships of the Boryaceae and Borya mirabilis were investigated using sequences of chloroplast and nuclear DNA. The closest similarities to B. mirabilis were B. constricta and B. sphaerocephala. B. mirabilis may have emerged from alloploidy of these species in the past. Because of the consistent similarities of B. mirabilis and B. constricta chloroplast sequences, it is proposed that both shared a common ancestor with a chromosome number of 2n=22. A malfunction n meiosis may have resulted in ovules with 2n=44. The high similarity of the nuclear ribosomal ITS region DNA suggests that the nuclear DNA was derived from B. sphaerocephela. B. mirabilis may be an allopolyploid, from fertilisation of a diploid ovule of B. constricta with haploid pollen of B. sphaerocephala, resulting in a reproductively isolated polyploidy of low fertility. The wild population of B. mirabilis was determined to have a small amount of genetic variation. The genetic variation in the field population w as not fully reflected in the ex-situ population. An effective means of micro-propagation of B. nitida for use in B. mirabilis has been established, providing an effective means of mass production of the species. The research has determined: a suitable explant (shoot tips) for regeneration; an effective means of reducing contamination in tissue culture (PPM); what medium is required to micro-propagate the species (LMHM); an appropriate gelling agent (Phytagel); and a practical method for inducing roots on the shoots grown in tissue culture. B. mirabilis has been established as mycorrhizal. The predominant mycorrhizal association is a nodular arbuscular mycorrhiza, present in the form of coils in root nodules over wetter months and as spores in these nodules over dryer months. A significant increase in the health of the ex-situ population of B. mirabilis was recorded after addition of soil containing fine roots of the wild population. Of the plants associated with the wild population, Callitris rhomboidea had the most morphologically similar vesicular arbuscular mycorrhizal relationship. But molecular identification was not achieved due to recalcitrance of DNA in PCR attempts. Potential translocation sites for some of the ex-situ population of B. mirabilis were examined for Phytophthora infestation. Reid's Lookout and Mackey's Peak were infected with P. cinnamomi. Vegetation at Mackey's Peak displayed characteristic infection symptoms, resulted in isolates of P. cinnamomi from baiting and would directly receive runoff from both the walking track and the existing infested B .mirabilis site. At the Reid's Lookout site, both walking track and proposed translocation site were infested with P. cinnamomi, yet did not display the associated symptoms in the vegetation. The Pine Plantation translocation site was uninfected at the level of sampling undertaken. Its vegetation did not display any characteristic infection symptoms and was not isolated when soil samples were baited. It was therefore chosen for translocation and so far the plants are healthy and actively growing. This research has provided critical knowledge to aid the recovery team in its current and future endeavours to manage this species and bring it back from the brink of extinction.

<p>The fern family Cystopteridaceae has been a thorn in the side of fern phylogeneticists, on many levels. Until this thesis, its basic existence (as a deeply isolated clade) and composition were unrecognized, hypotheses as to the relationships of its constituents within the broader fern tree-of-life were wildly inconsistent, the relationships of its genera to each other were contested, the species limits within those genera weakly understood, and the relationships among those species unknown. This thesis first establishes the broad evolutionary context for the family, which is that it is the first-diverging branch in Eupolypods II (it is sister to the rest of the eupolypod II clade). Eupolypods II is a large clade, containing nearly a third of extant fern species, making the Cystopteridaceae's position pivotal to a full understanding of fern evolution. </p><p>The evolution of the Eupolypods II is marked by an "ancient, rapid radiation" at the base of the clade, which helps to explain the difficulty that this broad group has historically posed to evolutionary biologists. Molecular data from five plastid loci show that Eupolypods II is comprised of 10 deeply divergent lineages, each worthy of recognition at the rank of family: Cystopteridaceae, Rhachidosoraceae, Diplaziopsidaceae, Hemidictyaceae, Aspleniaceae, Thelypteridaceae, Woodsiaceae, Onocleaceae, Blechnaceae, and Athyriaceae. The ancestors of Cystopteridaceae diverged from those of the rest of the clade approximately 100 million years ago, and the family is now comprised of five extant genera: Acystopteris, Cystoathyrium (the only genus for which we lack molecular data--it may be extinct), Cystopteris, Gymnocarpium, and ×Cystocarpium.</p><p>Within the family, the relationships of Cystoathyrium are unknown. Acystopteris is sister to Cystopteris, and those two genera, together, are sister to Gymnocarpium. Gymnocarpium is the maternal parent of ×Cystocarpium, so that genus falls within Gymnocarpium in phylogenetic trees based on maternally transmitted loci (i.e., plastid or mitochondrial loci). Plastid data resolve a basal trichotomy in Gymnocarpium, among the G. disjunctum clade, the G. robertianum clade, and core Gymnocarpium. The earliest diverging branch of core Gymnocarpium is the morphologically anomalous G. oyamense, followed by a split that separates G. appalachianum and G. jessoense parvulum (on one side) from G. remotepinnatum and G. jessoense jessoense, on the other. In Acystopteris, the first division surprisingly separates A. taiwaniana (which is frequently treated as a variety of A. japonica) from A. japonica + A. tenuisecta (which are morphologically very distinct from each other).</p><p>The evolution of Cystopteris is, as expected, more complex. The first lineage to diverge from the rest of the genus is the one that gave rise to C. montana. The next division, however, is unclear; molecular data infer a trichotomy among the sudetica clade (containing C. sudetica, C. moupinensis, and C. pellucida), the bulbifera clade (containing C. bulbifera and its related allopolyploids C. tennesseensis and C. utahensis), and the C. fragilis complex. Within the C. fragilis complex relationships (and species limits) get particular messy. The diploid species of eastern North America--C. protrusa--is sister to the rest of the complex, but after that point the major named species (including C. fragilis and C. tenuis) cease to be monophyletic, being found on both sides of a major split, alongside such taxa as the Australian/New Zealand C. tasmanica, the Hawaiian C. douglasii, and the Mexican C. membranifolia and C. millefolia.</p><p>In the context of the deep divergence of Gymnocarpium from Cystopteris, and the complicated species-level patterns of relationship within each genus, it is particularly surprising that molecular data confirm that ×Cystocarpium is a hybrid between Gymnocarpium dryopteris and a European tetraploid member of the Cystopteris fragilis complex. The ancestors of Cystopteris diverged from those of Gymnocarpium approximately 58 million years ago, meaning that the ×Cystocarpium hybridization event (which happened very recently) united genomes that contain, between them, over 100 million years of independent evolution. This breadth of divergence makes ×Cystocarpium the most extreme example of wide hybridization currently documented, with important implications for the pace of evolution of reproductive isolation, and thus for species formation.</p><p>This thesis ends with a tentative synopsis of the Cystopteridaceae (Appendix E). The family, as construed here, contains five genera and approximately 36 species (three in Acystopteris, one in Cystoathyrium, ~25 in Cystopteris, seven in Gymnocarpium, and one in ×Cystocarpium), plus two named subspecies (one each in Cystopteris and Gymnocarpium), and eight named sterile hybrids (three in Cystopteris and five in Gymnocarpium). Each of these tallies is highly subjective--much further research, with an emphasis on cytological and low-copy nuclear data, is necessary before we can hope to have any confidence in the species limits and finer-scale evolutionary patterns in this family.</p> / Dissertation

A total of 782 sea slug species (opisthobranch molluscs) within 161 genera, 56 families, and 7 orders are authentically recorded from Taiwan¡¦s Exclusive Economic Zone. Among these species, 459 species (58.7 %) are identified to species level and the other 323 species (41.3 %) are undescribed species. In terms of the whole Opisthobranchia fauna of the tropical western Pacific Ocean, approximately 1000 species are expected from Taiwan¡¦s EEZ. As most of the previous surveys on within-area species diversity were carried out in daytime, diel variation (i.e., day and night) in the species composition of sea slugs has been neglected. In order to assess whether such estimations for community diversity based only on daytime surveys are accurate, I undertook replicated diel surveys for 12 consecutive months (from December 2009 to November 2010) at Shilang Marine Reserve, Green Island (Lyudao), Taiwan. Phyllidiella pustulosa was observed most often during the daytime surveys, while Tritonia sp. 1 (an undescribed species) was the most abundant species at night. The results showed the species composition was clear different. During the field surveys, I found the difficult to identify the phyllidiid nudibranchs. Hence, I search for the additional taxonomic characters for phyllidiid nudibranchs base on integumentary spicules and gene sequences (COI and 16S genes). The results showed the spicules characters might provide the character to distinguish the Phyllidiella from other phyllidiid genera, but they were not informative at the species level. The results on molecular phylogeny showed that taxonomic status (both at the species and generic levels) of most phyllidiid genera, except Phyllidiella, received strong supports from COI gene and 16S gene. In contrast, each Phyllidiella species did not form a clade (suggesting the possibility of over estimating the species number in this genus). Finally, I described and illustrated three distinctive new species of Tambja (Nudibranchia: Polyceridae) from Taiwan and Australia. Among these three species, two of them were collected from Australia the other was collected from Taiwan. Tambja dracomus sp. nov. which is only distribution in cool temperate coastal waters in southeastern Australia and northern New Zealand; T. caeruleocirrus sp. nov. which is distributed in warm temperate coastal waters in eastern Australia, southeast Pacific Ocean. Tambja pulcherrima sp. nov. is widely distributed throughout the tropical, subtropical and warm temperate waters in western Pacific Ocean from Japan to northern New Zealand.

Cladistic analyses of the interclass relationships of the phylum Echinodermata have not provided a phylogeny that is separately supported by both larval and adult characters. Similar to the reported incongruence with cladistic analyses, molecular analyses of ribosomal RNA (rRNA) genes have also given ambiguous results, which could be due to a number of factors. The use of short sequences, systematic errors such as long branch attraction, and mis-alignments of the data that are introduced by programs which are unsuitable for non-protein coding genes, have resulted in a controversy as to the true nature of echinoderm relationships. Historically, it is the position of the ophiuroids among the five extant classes of echinoderms that has been the most poorly understood, and the most recently published proposal is that there are three plausible relationships, albeit none of these are sufficiently supported. Re-analysis of 28S and 18S rRNA gene sequence data, with the addition of more phylogenetically informative sites as well as new taxa, the use of an alignment procedure that is based on rRNA secondary structure, and the testing of a myriad of evolutionary models have resulted in some new findings of ancestry. Interestingly, it is the phylogenetic position of the ophiuroids that proves to be among the more solid results from this analysis, while the historically supported sister group relationship between the echinoid and holothuroid classes are not greatly corroborated.

China harbors 10% of the world's salamander species. Studying their evolutionary history provides critical insights into the evolution of the fauna of the Far East. The stout newts (Pachytriton, also known as paddle-tailed newts) are a genus of aquatic montane salamanders that are widely distributed in southeastern China. Despite their longstanding popularity among the global pet trade, little is known of their biology beyond external morphology. My thesis presents the first systematic study to elucidate phylogenetic relationships, character evolution, biogeographic patterns, species delimitation, and speciation mechanisms in this genus.