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.

Este projeto é um estudo taxonômico detalhado sobre o gênero de bagres lepidófagos Ochmacanthus. O táxon faz parte do conjunto de peixes neotropicais conhecidos popularmente como candirus, de especial relevância evolutiva, comportamental e ecológica, mas ainda pouco conhecidos em todos os aspectos de sua sistemática e biologia. O gênero Ochmacanthus contém atualmente cinco espécies consideradas válidas. Entretanto, a última revisão ocorreu há quase 100 anos, e é amplamente reconhecido que a taxonomia do gênero encontra-se severamente deficiente. As delimitações e diagnoses das espécies são insatisfatórias, tornando as identificações incertas ou impossíveis. Esta situação é particularmente conspícua em vista da abundância de representantes do gênero e sua aparente importância ecológica em muitos habitats neotropicais. Assim, primeiramente o trabalho realizou uma avaliação do número e da delimitação das espécies de Ochmacanthus. Das cinco espécies originalmente descritas para o gênero somente uma não foi considerada válida sendo que Ochmacanthus. reinhardtii foi sinonimizada em O. flabelliferus Essa última apresenta pelo menos quatro padrões de coloração diferentes, que, no entanto, não fornecem subsídio concreto para separação em diferentes espécies porque as características osteológicas, morfométricas e merísticas não variam. Foi realizado uma redescrição completa de O. batrachostoma. A segunda parte do trabalho é uma análise filogenética que testa o monofiletismo e determina seu posicionamento filogenético dentre os Stegophilinae, subfamília a qual pertence o gênero. Ochmacanthus é um grupo natural com diversas sinapomorfias principalmente relacionadas a região do pedúnculo caudal e dentição. Posiciona-se junto a Haemomaster e Stegophilus em um clado separado dos demais trichomicterídeos, sendo que Stegophilus é seu táxon de maior proximidade evolutiva. / This project proposes a detailed taxonomic study on the genus of catfish that eats scales Ochmacanthus. The taxon is part of the neotropical fish popularly known as candirus, of particular evolutionary relevance, behavioral and ecological, but still little known in all aspects of their systematics and biology. The Ochmacanthus genus currently contains five species considered valid. However, the latest revision occurred almost 100 years ago, and is widely recognized that the taxonomy of the genus is severely deficient. The delimitation of species and diagnoses are unsatisfactory, making identifications uncertain or impossible. This is particularly conspicuous in view of the abundance of the genus and its apparent ecological importance in many neotropical habitats. So, initially, the job conducted an assessment of the number and delimitation of species of Ochmacanthus. Of the five species originally described, only one was not consider as a valid species, Ochmacanthus reinhardti is the senior synonym of O. flabelliferus. This last species shows, at least, four different coloration patterns that, however, do not argue for species separation because the ostheological, morphometrical and meristics features do not vary. Also, is offered a redescription of O. batrachostoma. The second step is a phylogenetic analysis that tested the monophyly of Ochmacanthus and determined its phylogenetic position among Stegophilinae, subfamily which belongs to genus. Ochmacanthus is a monophyletic genus with several synapomorphies mainly focus on caudal peduncle and dentition. The group, with Haemomaster and Stegophilus, forms a distant clade from the others trichomycterids. Within this clade, is the sister-group of the genus Stegophilus.

A tribo Pyrophorini (sensu Costa, 1975) comprende 144 espécies e 19 gêneros descritos que ocorrem na região Neotropical, sul da região Neártica e na Oceania. São tradicionalmente considerados como um gupo monofilético, compartilhando como suposta sinapomorfia a presença de órgãos bioluminescentes. No presente estudo é apresentada a análise cladística para a tribo, baseada na morfologia dos adultos, que resultou em oito hipóteses filogenéticas alternativas. Os cladogramas mais parcimoniosos demonstram que Pyrophorini (sensu Costa, 1975) não é monofilética, porque inclui, entre os descendentes de seu ancestral exclusivo, seis gêneros de Heligmini: Meroplinthus Candéze, 1891, Schistogyne Costa, 1975, Agnostelater Costa, 1975, Paraphileus Candèze, 1881, Euplinthus Costa, 1975 e Compsoplinthus Costa, 1975. A presença de um par de órgãos luminescentes sobre o pronoto é confirmada como sinapomorfia para a tribo, mas esta condição foi perdida três vezes independentemente e adquirida paralelamente pelo menos uma vez no grupo interno. Os gêneros Pyrearinus Costa, 1975, Deilelater Costa, 1975, Lygelater Costa, 1975 e Ptesimopsia Costa, 1975 foram subdivididos em grupos de espécies que foram incluídos como táxons terminais na análise e resultaram merofiléticos, levando ao reconhecimento de quatro novos gêneros: Gênero B gen n., Gênero C gen n., Gênero D gen n. e Gênero E gen n.. Para uma espécie não descrita também é erigido o Gênero A gen n.. É reafirmada a hipótese de monofilia entre os gêneros da Oceania e da região Neotropical, cuja disjunção é, provavelmente, devida à tectônica da Gondwana, durante o Mesosóico. O cladograma de consenso aponta as seguintes relações filogenéticas para a tribo Pyrophorini sensu novo: ((Noxlumenes (Nyctophyxis + Cryptolampros)) + (Gênero A gen. n. (Pyrophorus (Fulgeochlizus (Meroplinthus (Ptesimopsia paralella (Ptesimopsia (Hapsodrilus (Pyroptesis Sooporanga))))) + ((Gênero B gen. n., Pyrearinus, (Phanophorus+Hypsiophthalmus )) + (Gênero C gen. n. (Gênero D gen. n. (Coctolelater (Agnostelater (Paraphileus (Euplinthus (Campsoplinthus (Hifo (Opselater, grupo melanurus, Lygelater, L. bifossulatus, Deilelater, (Photophorus + Ignelater ), (Gênero E gen. n. (V. sirius comb. n. (V gemmiferus + Vesperelater ))))))))))))))))). É proposta uma nova composição para a tribo Pyrophorini, que passa a incluir 159 espécies e 30 gêneros divididos em duas subtribos, Nyctophyxina Costa, 1975 e Pyrophorina Candèze, 1863. É apresentada uma revisão taxonômica para esses gêneros, incluindo caracteres novos do metanoto, do mesoventrito e da genitália masculina e ilustrações para grande parte dos caracteres. / The tribe Pyrophorini (sensu Costa, 1975) comprises 144 species and 19 genera that occur in Neotropical, Southern Neartic and Australian Regions. They have been traditionally recognized as a monophyletic group, sharing as a presumed synapomorphy the bioluminescent organs. I present here a cladistic analysis of the tribe, based on the adult morphology. This study resulted in eight alternative phylogenetic hypotheses. The most parsimonious cladograms show that Pyrophorini (sensu Costa, 1975) is paraphyletic, because it includes, among the descendants of its most recent ancestor, six genera of Heligmini: Meroplinthus Candèze, 1891, Schistogyne Costa, 1975, Agnostelater Costa, 1975, Paraphileus Candèze, 1881, Euplinthus Costa, 1975 and Compsoplinthus Costa, 1975. The presence of a pair of bioluminescent organs on pronotum is corroborated as synapomorphy for the tribe, but this condition was lost three times independently and it was acquired homoplastically at least once in the internal group. The genera Pyrearinus Costa, 1975, Deilelater Costa, 1975, Lygelater Costa, 1975 and Ptesimopsia Costa, 1975 were subdivided in species groups that were included as terminal taxa in the analysis; they resulted polyphyletic. Four new genera were recognized: Genus B gen n., Genus C gen n., Genus D gen n. and Genus E gen n. For an undescribed species is also proposed the Genus A gen n. The monophyly of the Oceanic and Neotropical genera is confirmed, their disjunction is, probably, due to the tectonic of Gondwana, during the Mesozoic. The consensus cladogram show the following phylogenetic relationships for the tribe Pyrophorini sensu novo: ((Noxlumenes (Nyctophyxis + Cryptolampros)) + (Gênero A the gen. n. (Pyrophorus (Fulgeochlizus (Meroplinthus (Ptesimopsia paralella (Ptesimopsia (Hapsodrilus (Pyroptesis Sooporanga))))) + ((Gênero B gen. n., Pyrearinus, (Phanophorus+Hypsiophthalmus)) + (Gênero C gen. n. (Gênero D gen. n. (Coctilelater (Agnostelater (Paraphileus (Euplinthus (Campsoplinthus (Hifo (Opselater, group melanurus, Lygelater, L. bifossulatus, Deilelater, (Photophorus + Ignelater), (Gênero E gen. n. (V. sirius comb. n. (V gemmiferus + Vesperelater))))))))))))))))). A new composition is proposed for the tribe Pyrophorini, including now 159 species and 30 genera subdivided in two subtribes, Nyctophyxina Costa, 1975 and Pyrophorina Candèze, 1863. Taxonomic revisions of all genera, including new characters mainly of the metanotum, mesoventrite, aedeagous and illustrations for most of them are also given.

As espécies do gênero Trypanosoma parasitam vertebrados de todas as classes (peixes, anfíbios, répteis, aves e mamíferos) e possuem ciclos de vida com alternância entre vertebrados e invertebrados. A maioria das espécies se desenvolve em artrópodes hematófagos, que podem pertencer a diversas ordens e famílias. A maioria das espécies não é patogênica, T. cruzi é a única espécie patogênica para o homem nas Américas. Estudos realizados com algumas espécies de tripanossomas apontam uma grande complexidade do ciclo silvestre. Ressalta-se o fato que existam poucos trabalhos realizados no estado de Minas Gerais em animais silvestres. Até o momento, poucos estudos avaliaram os pequenos mamíferos terrestres e morcegos como reservatórios silvestres destes parasitas neste estado, com ausência de estudos com outros grupos de vertebrados. O presente projeto tem por objetivo principal, o conhecimento da diversidade de parasitas do gênero Trypanosoma em animais silvestres da ilha pluvial e Estação ecológica de Pirapitinga, Minas Gerais através do isolamento, caracterização molecular e estudos filogenéticos com marcadores tradicionais. Foram realizadas duas campanhas de captura nos meses de outubro de 2013 e março de 2014 totalizando 183 pequenos mamíferos terrestres, de 12 espécies pertencentes, a três diferentes Ordens (Calomys callosus, Cerradomys subflavus, Rhipidomys sp., Akodon sp., Hylaemys megacephalus, Delomys sp., Oligoryzomys sp., Didelphis albiventris, Micoreus sp., Gracilinanus agilis, Monodelphis domestica e Cabassous unicinctus, a espécie mais abundante foi Calomys sp, capturados com pitfalls e Shermann. Foram capturados 57 indivíduos de morcegos, com o auxilio de redes de neblina, de seis diferentes espécies (Glossophaga soricina, Artibeus sp., Platyrrhinus sp., Noctilio albiventris, Myotis sp., Choeronicus minor), a espécie mais abundante foi Glossophaga soricina. Todos os quirópteros foram negativos para tripanossomatídeos e dentre os pequenos mamíferos somente oito exemplares da espécie Monodelphis domestica foram positivas para o parasita, porém foram estabelecidas nove culturas (um dos animais estava parasitado por duas espécies de tripanossomas). Os isolados de M. domestica foram identificados como T. cruzi e uma nova espécie com morfologia distinta, mas agrupada nas filogenias com SSU rDNA e gGAPDH no Clado Lagartos/ Cobras. Esta nova espécie foi denominada T. gennarii. Os anuros e répteis foram capturados através de busca ativa e foram capturados 14 indivíduos de repteis pertencentes a 6 espécies e 88 indivíduos de anuros pertencentes a 4 espécies. Do total de anuros capturados 7 (7,95%) apresentaram hemocultura positivas e 2 (2,27%) de Leptodactylus latrans foram estabelecidas e criopreservadas com morfologia compatível a parasitas do gênero Trypanosoma. Filogenias baseadas em SSU rDNA segregou os isolados do Cerrado em um novo grupo denominado AN05 e a inclusão destes isolados evidenciaram um outro grupo, AN06 compostos de isolados obtidos de flebotomíneos. / The species of the genus Trypanosoma parasites of all vertebrate classes (Fish, amphibians, reptiles, birds and mammals) and have life cycles alternating between vertebrates and invertebrates. Most species develops in blood-sucking arthropods, which may belong to different orders and families. Most species are not pathogenic, T. cruzi is the only species pathogenic to humans in the Americas. Studies with some species of trypanosomes indicate a great complexity of the sylvatic cycle in biomes. We highlight the fact that there are few studies in the state of Minas Gerais in wild animals. To date, few studies have evaluated small terrestrial mammals and bats as wild reservoirs of these parasites in this state, with no studies with other groups of vertebrates. This project\'s main objective, knowledge of Trypanosoma parasites of the genus diversity in wild animals of the rain Island and Ecological Pirapitinga Station, Minas Gerais through isolation, molecular characterization and phylogenetic studies with traditional markers. Two arrest campaigns were conducted between October 2013 and March 2014 totaling 184 small terrestrial mammals, 12 species belonging to three different Orders (Calomys callosus, Cerradomys subflavus, Rhipidomys sp., Akodon sp., Hylaemys megacephalus, Delomys sp., Oligoryzomys sp., Didelphis albiventris, Micoreus sp., Gracilinanus agilis, Monodelphis domestica e Cabassous unicinctus, the most abundant species was Calomys callosus, captured with pitfalls and Shermann. The bats were captured with mist net and caught 57 individuals from six different species (Glossophaga soricina, Artibeus sp., Platyrrhinus sp., Noctilio albiventris, Myotis sp., Choeronicus minor), the most abundant species was Glossophaga soricina. All were negative for trypanosomatids bats and small mammals among only eight copies of Monodelphis domestica species were positive for the parasite, but nine cultures were established (one animal was infested by two species of trypanosomes). Isolates of M. domestica were identified T. cruzi and a new species with distinct morphology, but grouped in phylogenies with SSU rDNA and gGAPDH in Clade Lizards/ Snakes. This new species was named T.gennarii. Frogs and reptiles were captured through active search and were captured 14 individuals of reptiles belonging to 6 species of frogs and 88 individuals belonging to four species. Of the total of frogs captured 7 (7,95%) had positive blood culture and 2 (2.27%) of Leptodactylus latrans were established and cryopreserved with morphology compatible with the parasites of the genus Trypanosoma. Phylogenies based on SSU rDNA segregated the Cerrado isolated in a new group called AN05 and the inclusion of these isolates showed another group of compounds AN06 isolates from sand flies.

Os Charaxinae, subfamília de borboletas pertencente à família Nymphalidae, são objeto de estudo filogenético nesta tese. Com 20 gêneros válidos e cerca de 330 espécies distribuídos em 6 tribos, a subfamília tem distribuição panbiogeográfica e circuntropical. Neste estudo, foram selecionadas 70 espécies representando todos os gêneros como grupo interno incluído: Coenophlebia archidona, Consul Electra, Consul fabius, Hypna clytemnestra, Polygrapha cyanea, Polygrapha suprema, Polygrapha tyrianthina, Polygrapha xenocrates, Siderone galanthis, Zaretis callidryas, Zaretis isidora, Anaea troglodyta, Fountainea nessus, Fountainea ryphea, Memphis appias, Memphis glauce, Memphis grandis, Memphis hirta, Memphis leonida, Memphis moruus, Memphis philumena, Memphis pithyusa, Memphis polycarmes, Memphis polyxo, Memphis verticordia, Anaeomorpha splendida, Noreppa chromus, Archaeoprepona amphimacus, Archaeoprepona chalciope, Archaeoprepona demophon, Archaeoprepona demophoon, Archaeoprepona licomedes, Prepona praeneste, Prepona laertes, Prepona pheridamas, Prepona pylene, Agrias amydon, Agrias claudina, Euxanthe eurinome, Euxanthe trajanus, Palla decius, Polyura athamas, Polyura delphis, Polyura gamma, Polyura pyrrhus, Polyura jalysus, Polyura schreiber, Charaxes varanes, Charaxes candiope, Charaxes cynthia, Charaxes lucretius, Charaxes jasius, Charaxes tiridates, Charaxes hadrianus, Charaxes nobilis, Charaxes zoolina, Charaxes eupale, Charaxes jahlusa, Charaxes pleione, Charaxes zingha, Charaxes etesipe, Charaxes etheocles, Charaxes nichetes, Charaxes laodice, Charaxes solon, Charaxes latona, Charaxes eurialus, Agatasa calydonia, Prothoe australis e Prothoe franck. Representando o grupo externo foram incluídas três espécies pertencentes a três sufamílias de Nymphalidae: Apatura iris (Apaturinae), Calinaga buddha (Calinaginae) e Amphidecta reynoldsi (Morphinae). Os objetivos deste trabalho são testar a hipótese de monofiletismo da subfamília e apresentar uma hipótese de parentesco para os níveis taxonômicos inferiores à subfamília. Os dados que geraram a matriz de caracteres são baseados em morfologia de adultos e estágios imaturos (quando disponíveis). A metodologia seguiu os princípios da parcimônia com polarização dos caracteres baseada no grupo externo. O monofiletismo da subfamília está corroborado na árvore de consenso por cinco sinapomorfias. Todas as tribos, exceto Preponini, são monofiléticas. Neste caso, Anaeomorpha splendida está mais próxima aos Anaeini, uma questão que necessitaria ainda mais investigações. O agrupamento de Prothoini com os Charaxinae neotropicais é outro resultado que emergiu da análise e muito provavelmente seu posicionamento é basal em relação ao grupo neotropical (Anaeini + Preponini) o que é indicado pela análise com pesagem sucessiva. Alguns gêneros resultaram como polifiléticos como é o caso de Charaxes, Archaeoprepona e Prepona e necessitam revisão taxonômica com base nesta filogenia. Assim, essa análise filogenética deve gerar futuramente revisões nas quais: Charaxes deve incluir as espécies do gênero Polyura, Archaeoprepona deve incluir o gênero monotípico Noreppa e Prepona deve incluir Agrias. / Charaxinae, a butterfly subfamily which belongs to the Nymphalidae, is the subject of this phylogenetic study. With 20 genera and about 330 species in 6 tribes, this subfamily is scattered all around the tropics of the world and is present in all the biogeographic regions. In this work, 70 species of all genera of the Charaxinae subfamily were chosen to represent the in-group: Coenophlebia archidona, Consul Electra, Consul fabius, Hypna clytemnestra, Polygrapha cyanea, Polygrapha suprema, Polygrapha tyrianthina, Polygrapha xenocrates,, Anaea troglodyta, Fountainea nessus, Fountainea ryphea, Memphis appias, Memphis glauce, Memphis grandis, Memphis hirta, Memphis leonida, Memphis moruus, Memphis philumena, Memphis pithyusa, Memphis polycarmes, Memphis polyxo, Memphis verticordia, Anaeomorpha splendida, Noreppa chromus, Archaeoprepona amphimacus, Archaeoprepona chalciope, Archaeoprepona demophon, Archaeoprepona demophoon, Archaeoprepona licomedes, Prepona praeneste, Prepona laertes, Prepona pheridamas, Prepona pylene, Agrias amydon, Agrias claudina, Euxanthe eurinome, Euxanthe trajanus, Palla decius, Polyura athamas, Polyura delphis, Polyura gamma, Polyura pyrrhus, Polyura jalysus, Polyura schreiber, Charaxes varanes, Charaxes candiope, Charaxes cynthia, Charaxes lucretius, Charaxes jasius, Charaxes tiridates, Charaxes hadrianus, Charaxes nobilis, Charaxes zoolina, Charaxes eupale, Charaxes jahlusa, Charaxes pleione, Charaxes zingha, Charaxes etesipe, Charaxes etheocles, Charaxes nichetes, Charaxes laodice, Charaxes solon, Charaxes latona, Charaxes eurialus, Agatasa calydonia, Prothoe australis and Prothoe franck. The out-group consisted of three species from different subfamilies of Nymphalidae: Apatura iris (Apaturinae), Calinaga buddha (Calinaginae) and Amphidecta reynoldsi (Morphinae). The main goal of this work is to test xi the monophyly hypothesis of the subfamily and to present a kinship hypothesis for the lower taxonomic levels. The matrix is composed with morphological data of adult and immature stages (when available). The methodology follows the Principles of Parsimony and the character polarization is based on out-group comparison. The monophyly of the subfamily was corroborated in the Consensus tree by four synapomorphies. All tribes are monophyletic, except for Preponini. In this case, Anaeomorpha splendida is placed with the Anaeini species, an issue that requires more scrutiny. The grouping of Prothoini and the Neotropical Charaxinae is another result derived from this analysis. It is probable that this groupings place in the cladogram is a basal one relative to the Neotropical clade (Anaeini + Preponini). This supposition is supported by successive weighting analisys. Some genera proved to be polyphyletic, and Charaxes, Archaeoprepona and Preponaneed taxonomic revision based on this phylogeny. Thus, Charaxes should include the Polyura species; Archaeoprepona should include the monotipic genus Noreppa; and Prepona should include Agrias in future taxonomic work.

Finally, the gene tree of the true crabs, Brachyura, confirms that the basal "Podotremata" is paraphyletic, with the Raninoidea and Cyclodorippoidea more closely related to Eubrachyura than to the other podotremes. Within the monophyletic Eubrachyura, the analysis supports the reciprical monophyly of the two subsections, Heterotremata and Thoracotremata. All of the Old World freshwater crabs cluster together, representing an early diverged lineage in the Heterotremata. / From the inferred phylogeny, we have obtained new insights on the evolution of decapods. First, the spiny lobster from the family Palinuridae is found to be paraphyletic with the polyphyletic Synaxidae nested within it. The Stridentes forms a monophyletic assemblage, indicating that the stridulating sound producing organ evolved only once in the spiny lobsters. Moreover, the spiny lobsters originated in the shallower water rocky reefs of the Southern Hemisphere and then invaded deep sea habitats and diversified. / In sum, I demonstrate the utility of the nuclear protein-coding gene markers in decapod phylogeny and they are informative across a wide range of taxonomic levels. I propose that nuclear protein-coding genes should constitute core markers for future phylogenetic studies of decapods, especially for higher systematics. / Second, we show that hermit crabs have a single origin, but surprisingly, that almost all other major clades and body forms within the Anomura, are derived from within the hermit crabs. The crab-like form and squat lobster form have each evolved at least twice from separate symmetrical hermit crab ancestors. These remarkable cases of multiple parallelism suggest considerable phenotypic flexibility within the hermit crab ground plan, with a general tendency towards carcinization. Rather than having a separate origin from other major clades, hermit crabs have given rise to most other major anomuran body types. / The high diversity of decapods has attracted the interest of carcinologists but there is no consensus on decapod phylogeny in spite of the endeavors using both morphological and molecular approaches. New sources of information are necessary to elucidate the phylogenetic relationships among decapods. In the present study, I attempted to develop and apply the nuclear protein-coding gene markers on decapod phylogeny. Using only two protein-coding genes, we have successfully resolved most of the infraordinal relationships with good statistical support, indicating the superior efficiency of these markers compared to nuclear ribosomal RNA and mitochondrial genes commonly used in phylogenetic reconstruction of decapods. Apparently these two types of markers suffer from the problems of alignment ambiguities and rapid saturation, respectively. Subsequently, I tried to apply the nuclear protein-coding genes in revealing interfamilial and intergeneric evolutionary history in three selected decapod groups, the spiny lobster (family Palinuridae), the infraorder Anomura and the true crabs of the infraorder Brachyura to further evaluate the utility of these markers and reconstruct the evolutionary history the groups. Trees with robust support can be obtained using sequences of three to five genes for the infraorders and families tested including the most speciose Brachyura. The genes are shown to be informative in elucidating interspecific phylogeny as well. / Tsang, Ling Ming. / Adviser: Ka Hou Chu. / Source: Dissertation Abstracts International, Volume: 73-02, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 127-153). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Pearl oysters of the genus Pinctada include some economically important species. The taxonomy of some of the species is problematic. Phylogenetic relationship of the species in the genus is also poorly studied. In the present study, phylogenetic relationships of P. chemnitzi, P. fucata, P. margaritifera, P. maxima, P. nigra, P. radiata (from China), P. fucata martensii (from Japan), P. albina and P. imbricata (from Australia) were studied with Pteria penguin as an outgroup, and genetic variation of Chinese P. fucata, Japanese P. fucata martensii and Australian P. imbricata populations were investigated (1) to address the taxonomic confusion and phylogeny of pearl oysters, (2) to understand the genetic connections between the Chinese P. fucata, Japanese P. fucata martensii and Australian P. imbricata in west Pacific and (3) to provide information for the genetic improvement program initiated in China. / Since P. fucata, P. fucata martensii and P. imbricata are synonymous, to study the genetic differentiation and genetic variation of such widely distributed populations is helpful in understanding their genetic connections. For this purpose, five populations, three from China (Daya Bay, Sanya Bay and Beibu Bay), one from Japan (Mie Prefecture) and one from Australia (Port Stephens) were studied using AFLP technique. Three primer pairs generated 184 loci among which 91.8-97.3% is polymorphic. An overall genetic among populations and an average of 0.37 within populations (ranging from 0.35 in Japanese population to 0.39 in Beibu Bay population) were observed. Genetic differentiation among the five populations is low but significant as indicated by pairwise GST (0.0079-0.0404). AMOVA further shows that differentiation is significant among the five populations but is not significant at a broader geographical scale, among the three groups of Chinese. Japanese and Australian populations or among the two groups of Australian and north Pacific populations. The low level of genetic differentiation indicated that P. fucata populations in the west Pacific are genetically linked. Among the five populations, the Australian one is more differentiated from the others, based on both pairwise AMOVA and GST analyses, and is genetically isolated by distance as indicated by Mantel test. However, genetic differences among the three Chinese populations are not correlated with the geographic distances, suggesting that Hainan Island and Leizhou Peninsula may act as barriers blocking gene flow. / The above three wild Chinese populations in southern China were compared with the three adjacent cultured populations using AFLP markers. Three pairs of primers generated 184 loci among 179 individuals in populations from Beibu Bay, Daya Bay and Sanya Bay. A high level of genetic diversity, ranging from 0.363 in a wild population in Sanya Bay to 0.388 in a wild population in Beibu Bay, was observed within both wild and cultured populations, indicating an absence of strong bottleneck effects in the history of cultured P. fucata populations. Yet cultured populations in Sanya Bay and Beibu Bay had more fixed loci than the corresponding wild populations. Genetic differentiation in most pairwise comparisons of populations was significant. AMOVA indicated that genetic variation among populations were very low (1.77%) though significant, while more than 98% variation resided among individuals within population. These findings provide no evidence to show that hatchery practice of pearl oyster in China to date has significantly affected the genetic diversity of the cultured populations, and suggest that all populations are competent for selection. Yet the significant genetic differentiation among populations implies that any translocation of individuals for genetic improvement program should be managed with caution for the preservation of genetic diversity in natural populations. / The internal transcribed spacers (ITS1 and ITS2) of nuclear ribosomal DNA were compared among the above nine taxa, based on sequences determined by the present study and those available from Genl3ank. The phylogenetic analysis indicates that the pearl oysters studied constitute three clades: clade I with the small oysters P. fucata, P. fucata martensii and P. imbricata, clade II with P. albina, P. nigra, P. chemnitzi and P. radiata, and clade III and clade III with the big pearl oysters P. margaritifera and P. maxima forming the basal clade. Clade II is made up two subclades: clade IIA consisting of P. albina and P. nigra and clade IIB consisting of P. chemnitzi and P. radiata. The topology of the phylogenetic tree and substitution pattern of ITS sequences suggest that P. margaritifera and P. maxima are primitive species and P. chemnitzi is a recent species. The genetic divergences between clades ranged from 28% to 76.5%, and between subclades, 8.7-10.2%. In clade I, the interspecific genetic divergences ranged from 0.6% to 1.4%, and overlapped with interspecific divergences (0.6-1.1%), indicating that P. fucata, P. fucata martensii and P. imbricata may be conspecific. Based on amplified fragment length polymorphism (AFLP) markers and ITS sequences from more individuals, analyses of the populations of these three taxa also support the conclusion that Chinese P. fucata, Japanese P. fucata martensii and Australian P. imbricata are the same species, with P. fucata being the correct name. The genetic divergence between P. albina and P. nigra was also very low (1.2%), suggesting that they may represent two subspecies that can only be distinguished by shell color. The genetic divergences between P. maxima and P. margaritifera, and between clade IIA and clade IIB ranged from 8.3% to 10.2%, suggesting that they are closely related, respectively. The ITS1 sequence of P. radiata from GenBank is almost identical to that of P. chemnitzi determined in the present study, suggesting that the specimen used for the P. radiata sequence was possibly misidentified. / Yu Dahui. / "August 2005." / Adviser: Ka Hou Chu. / Source: Dissertation Abstracts International, Volume: 67-11, Section: B, page: 6125. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (p. 100-124). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese. / School code: 1307.

Ho Hoi Yan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2001. / Includes bibliographical references (leaves 107-118). / Abstracts in English and Chinese. / Abstract --- p.i / Abstract (Chinese) --- p.iii / Acknowledgments --- p.v / Contents --- p.vii / List of Tables --- p.x / List of Figures --- p.xi / Chapter Chapter 1 --- General Introduction --- p.1 / Chapter Chapter 2 --- Literature Review --- p.5 / Chapter 2.1 --- Introduction to phylogenetic biology --- p.5 / Chapter 2.1.1 --- Definition of phylogenetics --- p.5 / Chapter 2.1.2 --- Why employ molecular genetic markers in phylogenetics? --- p.5 / Chapter 2.2 --- DNA analysis and the contributions to phylogenetics --- p.7 / Chapter 2.2.1 --- Nuclear ribosomal DNA --- p.7 / Chapter 2.2.2 --- Animal mitochondrial DNA (mt DNA) --- p.10 / Chapter 2.3 --- Molecular phylogeny of crustaceans --- p.11 / Chapter 2.3.1 --- Phylogenetic studies of crustaceans using nuclear rRNA --- p.11 / Chapter 2.3.2 --- Population genetic and phylogenetic studies of crustaceans using mtDNA --- p.14 / Chapter 2.4 --- Taxonomy of the genus Eriocheir --- p.23 / Chapter 2.5 --- Distribution of Eriocheir s.l --- p.27 / Chapter 2.6 --- Population genetics of Eriocheir --- p.28 / Chapter 2.6.1 --- Population genetics of Eriocheir japonica --- p.28 / Chapter 2.6.2 --- Population genetics and history of invasion of Eriocheir sinensis --- p.29 / Chapter Chapter 3 --- Materials and Methods --- p.32 / Chapter 3.1 --- Specimens --- p.32 / Chapter 3.1.1 --- Specimens for phylogenetic reconstruction --- p.32 / Chapter 3.1.2 --- Specimens for population genetic study on E. sinensis --- p.33 / Chapter 3.2 --- DNA extraction --- p.33 / Chapter Chapter 3 --- Materials and Methods --- p.32 / Chapter 3.1 --- Specimens --- p.32 / Chapter 3.1.1 --- Specimens for phylogenetic reconstruction --- p.32 / Chapter 3.1.2 --- Specimens for population genetic study on E. sinensis --- p.33 / Chapter 3.2 --- DNA extraction --- p.33 / Chapter 3.3 --- Amplification of genes --- p.36 / Chapter 3.3.1 --- PCR profile --- p.38 / Chapter 3.3.1.1 --- 16S rRNA gene --- p.38 / Chapter 3.3.1.2 --- COI gene --- p.40 / Chapter 3.3.1.3 --- ITS-1 gene --- p.41 / Chapter 3.4 --- DNA sequencing --- p.41 / Chapter 3.4.1 --- Purification of extension products --- p.43 / Chapter 3.4.2 --- Electrophoresis and data collection --- p.44 / Chapter 3.4.3 --- Sequence alignment --- p.44 / Chapter 3.5 --- Phylogenetic construction --- p.45 / Chapter Chapter 4 --- Results --- p.47 / Chapter 4.1 --- Phylogenetic reconstruction of Eriocheir --- p.47 / Chapter 4.1.1 --- PCR products of mitochondrial 16S rRNA and COI gene and nuclear ribosomal ITS-1 gene --- p.47 / Chapter 4.1.2 --- Intraspecific variation --- p.49 / Chapter 4.1.3 --- Genetic variability in mitten crabs based on partial sequences of 16S rRNA gene --- p.49 / Chapter 4.1.4 --- Genetic variability in mitten crabs based on partial sequences of COI gene --- p.53 / Chapter 4.1.5 --- Genetic variability in mitten crabs based on complete sequences of ITS-1 gene --- p.62 / Chapter 4.1.6 --- Phylogenetic analysis --- p.66 / Chapter 4.1.6.1 --- Phylogenetic analysis based on 16S rDNA sequences --- p.66 / Chapter 4.1.6.2 --- Phylogenetic analysis based on COI gene sequences --- p.70 / Chapter 4.1.6.3 --- Phylogenetic analysis based on ITS-1 gene sequences --- p.73 / Chapter 4.2 --- Population genetic study of E. sinensis --- p.77 / Chapter 4.2.1 --- PCR products and intraspecific variation of mitochondrial COI gene for population genetic study of E. sinensis --- p.77 / Chapter 4.2.2 --- Genetic variability in E. sinensis based on partial sequences of COI gene --- p.79 / Chapter 4.2.3 --- Population genetic analysis based on COI gene sequences --- p.86 / Chapter Chapter 5 --- Discussion --- p.93 / Chapter 5.1 --- Phylogeny of Eriocheir --- p.93 / Chapter 5.1.1 --- Phylogenetic relationships --- p.93 / Chapter 5.1.2 --- Taxonomic implications --- p.95 / Chapter 5.1.3 --- Evolutionary history of Eriocheir --- p.97 / Chapter 5.2 --- Population study of E. sinensis --- p.101 / Chapter 5.2.1 --- Genetic variation between Chinese populations --- p.101 / Chapter 5.2.2 --- Genetic variation between native and introduced populations --- p.102 / Chapter Chapter 6 --- Conclusions --- p.104 / Literature Cited --- p.107

A diversidade de espécies e fenotípica pode variar consideravelmente entre grupos taxonômicos e ao longo do tempo em uma mesma linhagem. O estudo de tais variações tornou-se um dos principais objetivos da biologia evolutiva fornecendo informações importantes a respeito dos possíveis mecanismos que regulam a biodiversidade. Dessa forma, o objetivo geral da presente tese foi investigar os padrões da diversificação de espécies e da morfologia em um grupo cosmopolita de serpentes, a família Viperidae, e os potenciais processos subjacentes. Primeiramente, (1) reconstruímos as relações filogenéticas e estimamos os tempos de divergência entre as linhagens da família Viperidae utilizando uma abordagem Bayesiana. (2) Aplicando um método recentemente desenvolvido (BAMM), exploramos como as taxas de especiação e extinção variaram ao longo da radiação do grupo inferindo os possíveis processos reguladores. Por fim, (3) analisamos se a evolução do tamanho do corpo e as taxas de especiação variam nos diferentes habitats ocupados pelos viperídeos (terrestres vs arborícola). Nesta tese geramos a filogenia molecular de viperídeos mais completa até o momento utilizando sequências para 11 genes mitocondriais e nucleares abrangendo 79% das espécies viventes (264 terminais) e todos com exceção de um gênero. De maneira geral, foi possível obter relações filogenéticas robustas para o grupo com a maioria dos gêneros sendo monofilética. Os tempos de divergência obtidos indicam que os viperídeos começaram a diversificar em meados do Paleoceno tardio/meio do Eoceno inferindo idades um pouco mais tardias que o encontrado em estudos anteriores. Durante a radiação do grupo, um aumento nas taxas de especiação parece ter ocorrido durante a diversificação dos crotalíneos (pit vipers) em decorrência não só da evolução das fossetas loreais mas também como resultado de mudanças geológicas e climáticas na Ásia e da invasão do novo mundo. Após este rápido aumento inicial, as taxas de especiação desaceleraram em direção ao presente. Por fim, os resultados aqui apresentados indicam que apesar dos habitats arborícolas limitarem a evolução morfológica nos viperídeos, a evolução da arborealidade parece não afetar as taxas de especiação que permanecem similares entre linhagens arborícolas e terrestres. Isto sugere dois cenários: (1) a especiação acontece de forma independente das mudanças morfológicas nos viperídeos; ou (2) o isolamento geográfico seria um mecanismo importante na diversificação de linhagens arborícolas contrabalançando decréscimos nas oportunidades de especiação possivelmente relacionados às pressões seletivas impostas pelo ambiente arborícola. A presente tese contribui para entendermos mais sobre como evoluíram os viperídeos ao longo dos seus ∼50 milhões de anos. Além de propor cenários e hipóteses a serem futuramente explorados com os viperídeos, elaboramos uma discussão ampla e conceitual a respeito dos possíveis mecanismos por trás da diversificação de espécies e da morfologia que poderiam também ser contemplados para outros grupos de organismos. Portanto, a presente tese contribui não só para entendermos os mecanismos que geram e mantém a diversidade de serpentes, mas também para enriquecer a discussão dos mecanismos que geram e mantém a biodiversidade como um todo / Species and phenotypic diversity may vary considerably between taxonomic groups and through time for a given lineage. The study of such variation became one of the main goals of evolutionary biology and provides important information related to the possible mechanisms regulating biodiversity. The general goal of the present thesis was to investigate the patterns of species and morphological diversification in a cosmopolitan group of snakes, the family Viperidae, and the potential underlying processes. First, (1) we estimated the phylogenetic relationships and divergence times between lineages of the family Viperidae using a Bayesian approach; then we (2) applyed a recently developed method (BAMM) to explore how speciation and extinction rates varied during the radiation of the group suggesting possible underlying processes. Finally, (3) we analyzed if body size evolution and speciation rates showed distinct patterns among vipers occurring in different habitats (terrestrial vs arboreal). Herein we generated the most complete molecular phylogeny for vipers until this moment using sequences from 11 mitochondrial and nuclear genes comprising 79% of extant species (264 terminals) and all except one genus. In general, we were able to recover well supported phylogenetic relationships with most genera being monophyletic. Divergence time estimates suggested that vipers started to diversify around the late Paleocene/middle Eocene finding older ages than previous studies. During the group radiation, an increase in speciation rates seems to have occurred during the diversification of crotalines (pit vipers) not only due to the evolution of loreal pits but also as a result of climatic and geological changes in Asia and the invasion of the New World. After this rapid initial increase, speciation rates decelerated toward the present. Lastly, the results presented here suggest that although arboreal habitats constrain morphological evolution in vipers the evolution of arboreality does not seem to affect speciation rates, which remain similar among arboreal and terrestrial lineages. Our results suggest two distinct scenarios: (1) speciation could be independent of morphological evolution in vipers; or (2) geographic isolation would be an important mechanism underlying species diversification in arboreal lineages offsetting decreases in speciation opportunities potentially related to the selective pressures imposed by the arboreal environment. The present thesis contribute to increase our understanding about how vipers evolved during their ∼50 million years. In addition to providing scenarios and hypotheses to be further explored with vipers, we elaborated a broad and conceptual discussion about the possible mechanisms underlying species and morphological diversification that might apply to other groups of organisms. Therefore, this thesis comprises a contribution that goes beyond the understanding of mechanisms generating and maintaining the diversity of snakes, but will hopefuly enrich the discussion of mechanisms that generate and maintain biodiversity as a whole

Libellulidae compreende a maior família de Anisoptera com mais de mil espécies, sendo uma das mais abundantes de Odonata. As investigações do padrão de relacionamento filogenético entre os gêneros dessa família têm sido demonstradas complexas, com hipóteses largamente divergentes, sendo as análises consideradas complicadas. Nesse trabalho é apresentada pela primeira vez uma análise cladística de uma de suas maiores subfamílias \'Sympetrinae\' baseada em 171 caracteres morfológicos de adultos com ênfase no grupo com a armadura femoral especializada (Erythemismorpha) que contém os gêneros Acisoma, Carajathemis, Cyanothemis, Erythemis, Porpax, Rhodopygia, Rhodothemis e Viridithemis. Representantes de quase todas as subfamílias de Libellulidae, assim como de todos os gêneros de \'Sympetrinae\' foram incluídos, totalizando 69 táxons terminais. Essa ampla amostragem objetivou testar de modo robusto o monofiletismo de Erythemismorpha e identificar grupos monofiléticos em \'Sympetrinae\'. Duas análises diferentes foram executadas uma com a parcimônia de Fitch e outra a de Sankoff, ambas com diferentes esquemas de ponderação de caracteres. A parcimônia de Sankoff foi utilizada para minimizar a influência dos \"gaps\" e demonstrou ser inapropriada para cálculos de índices de estabilidade com técnicas de reamostragem devido às exigências computacionais. Erythemismorpha foi demonstrado monofilético e além dos gêneros previamente citados inclui pelo menos Erythrodiplax castanea. Os gêneros Rhodothemis, Rhodopygia e Acisoma também tiveram suas hipóteses de monofiletismo suportas, enquanto Erythemis demonstrou ser parafilético em quase todas as árvores contrariando resultados anteriores. A maior parte dos nós internos de Eyrthemismorpha é inconclusiva, no entanto Cyanothemis + Porpax, assim como Carajathemis + Rhodopygia apresentaram suporte alto. A composição completa de Erythemismorpha permanece em aberto e dados de outras fontes devem ser incorporados. Também são discutidos extensivamente alguns conceitos equivocados sobre homoplasia e suas implicações em relação aos caracteres da venação alar em Anisoptera, advogando em favor da prevalência do padrão sobre o processo no paradigma da cladística. Defende-se homoplasia como um erro, um erro no estabelecimento da homologia primária, portanto, convergência reversão e conceitos similares, ligados ao processo e fortemente dependes de hipótese ad hoc não são concretos e tampouco observados no mudo real / Libellulidae comprises the largest family of Anisoptera with more than a thousand of species and one of the most abundant among dragonflies\' families. The investigations of its phylogenetic pattern of relationships, especially among their genera have been shown complex, with widely divergent hypotheses, and considered tricky. A first cladistic analysis of \'Sympetrinae\' based on 171 characters from adults morphology, with an emphasis on the \'armed leg group\' (Erythemismorpha) including the genera Acisoma, Carajathemis, Cyanothemis, Erythemis, Porpax, Rhodopygia, Rhodothemis and Viridithemis is presented here. Representatives of almost all Libellulidae subfamilies, as well as all genera of \'Sympetrinae\' were also included, summing up a total of 69 terminal taxa. This broad sampling aimed to provide a strong test to hypothesis of monophyly of Erythemismorpha and identify monophyletic groups in \'Sympetrinae\'. Two different analyzes were performed, each Fitch and Sankoff parsimony, both with distinct weighting schemes. The Sankoff parsimony was adopted to minimize the influence of \'gaps\' on the results, but proved be inappropriate for to obtain stability indexes with resampling techniques, due to the high cost of computational requirements. Erythemismorpha was shown be monophyletic and further than to those genera previously cited, also includes, at least Erythrodiplax castanea. The genera Acisoma, Rhodothemis, and Rhodopygia were has each their hypotheses of monophyly also supported by the analyses performed here, however Erythemis showed be paraphyletic in almost all trees contradicting previous results. Almost all of the internal nodes of Erythemismorpha are inconclusive, however Cyanothemis + Porpax, as well as Carajathemis + Rhodopygia presents both high support. The entire composition of Erythemismorpha still open, pending the inclusion of other data sources. Also was discussed the misconceptions about homoplasy and its implications on venational characters of Anisoptera dragonflies. Is advocated the already discussed prevalence of pattern over process in cladistics paradigm. Homoplasy in cladistics is an error, more precisely an error of establishment of homologues (primary homology), thus convergence, reversal and similar terms are process tied ad hoc hypotheses over a pattern of inclusive hierarchy and not is concrete neither observable in real world