A família Psittacidae possui 332 espécies de papagaios, periquitos e afins, e os táxons Neotropicais formam um grupo monofilético (tribo Arini), dentro desta tribo está o gênero Aratinga. A sistemática deste gênero é mal resolvida, com poucos estudos morfológicos e algumas filogenias moleculares que apontam que não seja monofilético. Porém, é preciso destacar que esses estudos não amostraram uma quantidade representativa de espécies do gênero, o que deixa essas relações incertas. Para melhor compreender a história evolutiva do gênero Aratinga, realizamos uma análise filogenética com 21 das 22 espécies do gênero, o táxon monotípico Nandayus nenday que é proximamente relacionado a algumas espécies de Aratinga e representantes de outros gêneros da tribo Arini. Foram sequenciados cinco genes mitocondriais (12S, 16S, citocromo b, NADH2, COIII) e um nuclear (RAG-1). As filogenias obtidas por máxima verossimilhança e análise Bayesiana foram congruentes e indicam a ausência de monofilia do gênero Aratinga. A maioria das espécies do gênero foi posicionada em três clados com alto suporte, mas que não se apresentam agrupados em um clado monofilético. Estes três clados são congruentes com grupos previamente propostos com base em caracteres morfológicos. Nandayus nenday está dentro de um destes clados, que é grupo irmão de um clado que contém outros quatro gêneros da tribo Arini. A única espécie que não foi incluída em nenhum destes clados é Aratinga acuticaudata, que aparentemente é mais proximamente relacionada aos gêneros Diopsittaca e Guarouba. A maioria dos eventos de divergência das espécies do gênero Aratinga nesses diferentes clados parece ter ocorrido nos últimos 5 milhões de anos (Ma.). Enquanto as estimativas de datas de divergências entre os principais clados sugerem que elas ocorreram durante o Mioceno inicial. O padrão biogeográfico da diversificação dos clados de Aratinga foi complexo, possivelmente relacionado com o soerguimento dos Andes, com múltiplas colonizações da América Central antes e depois do fechamento do Istmo do Panamá e com ciclos glaciais do Pleistoceno. Esses resultados refutam a monofilia do gênero e uma revisão taxonômica do táxon parece ser necessária. / Family Psittacidae includes 332 species of parrots and all Neotropical taxa form a monophyletic group (tribe Arini), among those, is the parakeet genus Aratinga. This genus has an unresolved systematics, with few morphological studies and some molecular phylogenies suggest that it is not monophyletic. However, these phylogenies did not include a representative sample of species of the genus. To better understand the evolutionary history of genus Aratinga, we conducted a phylogenetic analysis that included 21 of 22 species of the genus, the monospecific taxon Nadayus nenday that is closely related to some Aratinga species, plus various taxa from tribe Arini. We sequenced five mitochondrial (12S, 16S, cytochrome b, NADH2, COIII) and one nuclear (RAG-1) genes. The phylogenies were reconstructed based on maximum likelihood analysis and Bayesian inference. Relaxed molecular clock estimates were conducted under a Bayesian analysis for inferring the divergence times of the phylogeny and to study the biogeographic history of these species. The phylogenies recovered by both methods were highly congruent and support the absence of monophyly for genus Aratinga. The majority of the species from the genus Aratinga was placed in three highly supported clades that did not group in a monophyletic clade. These three clades match previously suggested groups based on morphological characters. Nandayus nenday was included in one of these clades, that is closely related to a clade that contains four other Arini genera. The only species that was not included in any of these clades was Aratinga acuticaudata, that seems to be more closely related to the genera Diopsittaca and Guarouba with high support values. Most of the speciation within the Aratinga clades may have occurred during the last 5 Mya., but the divergence times between these clades seems to have occurred during the early Miocene. The biogeograhic pattern of the diversification of the Aratinga clades was complex, possibly related to the history of the Andes, multiple colonization of Central America before and after the closure of the Panama Isthmus and also Pleistocene glacial cycles. These results further refute the monophyly of genus Aratinga and a taxonomical revision may be necessary for the taxon.

Biogeographers have long searched for common processes responsible for driving diversification in the Holarctic region. Although terrestrial flora and fauna have been well studied, much of the marine biogeographic work addresses patterns and processes occurring over a relatively recent timescale. A prerequisite to comparative biogeographic analysis requires well-resolved phylogenies of similarly distributed taxa that diverged over a similar timeframe. The overall aim of my Ph.D. thesis was to address fundamental questions in the systematics and biogeography of a family of Holarctic fish (Osmeridae) and place these results in a broad comparative biogeographic framework. With eight conflicting morphological hypotheses, the northern hemisphere smelts have long been the subjects of systematic disagreement. In addition to the uncertainty in the interrelationships within this family, the relationship of the Osmeridae to several other families remains unclear. Using DNA sequence data from three mitochondrial and three nuclear genes from multiple individuals per species, I reconstructed the phylogenetic relationships among the 6 genera and 15 osmerid species. Phylogenetic reconstruction and divergence dating yielded a well-resolved phylogeny of the osmerid genera and revealed several interesting evolutionary patterns within the family: (1) Hypomesus chishimaensis and H. nipponensis individuals are not reciprocally monophyletic, suggesting that they are conspecific and H. chishimaensis is a recently evolved freshwater ecotype that invaded the Kuril Islands following the last glaciation, (2) The trans-Pacific sister relationships in Hypomesus based on lateral line scale counts are not supported, implying that this phenotype evolved in parallel on each side of the North Pacific Ocean, (3) The Plecoglossidae are the Osmeridae sister group, (4) Over half of the characters from previous studies show evidence of parallel evolution; however, 27 traits reflect ancestral relationships, (5) Multiple divergences within the Osmeridae date to both the mid-Miocene cooling period and the Pliocene Bering Seaway opening, suggesting these events were important in the evolution of these fishes, and (6) Divergences in many marine taxa for which dated phylogenies are available are also correlated with these time periods. Future research should target additional Holarctic marine taxa for further comparative analysis. / Science, Faculty of / Zoology, Department of / Graduate

O gênero Hypostomus (Siluriformes: Loricariidae) com cerca de 130 espécies nominais, se destaca como um dos mais diversos e amplamente distribuídos gêneros de peixes de água doce neotropical. Devido a sua ampla distribuição e alta diversidade, os conhecimentos taxonômicos, filogenéticos e biogeográficos para as espécies do gênero são ainda consideravelmente incompletos. Consequentemente, pouco se sabe sobre processos naturais envolvidos em diversificação e variação morfológica para o gênero. Hypostomus ancistroides é uma espécie descrita para a bacia do Alto Paraná, uma eco-região hidrográfica tradicionalmente reconhecida por seu endemismo ictiofaunístico, ocorrendo também na bacia costeira do rio Ribeira de Iguape. Esta espécie apresenta considerável variação morfológica, cariotípica e isoenzimática em suas diferentes populações, sugerindo a existência de um complexo de espécies. Sua ampla área de distribuição, somada aos novos conhecimentos sobre padrões biogeográficos para diversas espécies de peixes do Alto Paraná, reforça essa possibilidade. Entretanto, a variação encontrada na morfologia das populações de H. ancistroides é ampla e contínua, impedindo que se defina diferentes espécies através das abordagens taxonômicas clássicas em ictiologia. Assim, este trabalho se propõe a utilizar ferramentas da sistemática molecular, genética de populações e filogeografia para responder questões fundamentais sobre a evolução desse potencial complexo de espécies. Sequências nucleotídicas completas do marcador mitocondrial ATP sintase (subunidades 6 e 8; 842 pb) foram obtidas para diversas espécies de Hypostomus, incluindo 162 exemplares de H. ancistroides provenientes de doze localidades abrangendo toda a sua área de ocorrência, além de outros gêneros da família Loricariidae, utilizados como grupos externos. Análises filogenéticas de Máxima Verossimilhança, Máxima Parcimônia e Neighbor Joining resultaram em topologias essencialmente semelhantes, sustentando a monofiletismo da espécie, e apontando como seus parentes mais próximos espécies de bacias hidrográficas adjacentes ao Alto Paraná. Esses resultados mostram ainda a existência de quatro filogrupos distintos para a espécie, com áreas de distribuição parcialmente sobrepostas. Análises populacionais e filogeográficas incluiram comparação de distância genética P, estruturação populacional baseada em distribuição de haplótipos e índices de diversidade, testes de neutralidade, índice de fixação FST, análise de variância molecular (AMOVA), análise espacial de variância molecular (SAMOVA), construção de rede haplotípica de parcimônia, e análise de clados hierarquizados (NCPA). Os resultados mostram 48 haplótipos repartidos em doze populações bem estruturadas, com baixo ou nenhum fluxo gênico entre si. Eventos de expansão geográfica podem ser identificados ao longo da história demográfica, sugerindo que a estruturação encontrada atualmente reflete não só as características ecológicas da espécie, como também uma história de mudanças nas condições ambientais, eventualmente favoráveis a migração e dispersão. Contatos entre populações de diferentes bacias podem ser mais frequentes através de capturas de cabeceiras do que ao longo do corpo dos rios principais. A hipótese mais plausível para a presença da espécie na bacia do Ribeira é a de uma captura de cabeceira do alto rio Tietê. Apesar de ser formado por quatro filogrupos distintos, algumas linhagens derivadas de H. ancistroides apresentam sobreposição de suas áreas de distribuição. Esse contato secundário revelado apenas por um marcador de herança matrilineal impossibilita a delimitação de diferentes espécies correspondentes aos filogrupos, sob os paradigmas clássicos de especiação em peixes neotropicais. / The genus Hypostomus (Siluriformes: Loricariidae), comprising ca. 130 nominal species, is one of the most species-rich and widely distributed genera of neotropical freshwater fish. Because of its wide distribution and vast diversity, knowledge on the taxonomy, phylogenetic relationships and biogeography of Hypostomus is still severely incomplete. Consequently, little is known about the processes involved in the diversification and morphological variation for the genus. Hypostomus ancistroides is a species described from the upper Rio Paraná drainage, a freshwater ecoregion known for its ichthyological endemism, also occurring in the coastal basin of Rio Ribeira de Iguape. This species shows considerable morphological, karyotypic and isoenzimatic variation among different populations, suggesting the existence of a species complex. Its wide distribution area, coupled with recent understanding on biogeographic patterns of several fish species from the Upper Parana, reinforces that possibility. However, morphological variation in populations of H. ancistroides is wide and continuous, and does not allow recognition of potential different species by means of traditional taxonomic approaches. Thus, this paper uses tools from molecular systematics, population genetics, and phylogeography in order to answer major questions about the evolution of this potential species complex. Complete sequences of the mitochondrial marker ATP synthase (subunits 6 and 8; 842 bp) were obtained for several species of Hypostomus, including 162 specimens of H. ancistroides from twelve localities covering its entire area of distribution, plus other loricariid genera as outgroups. Phylogenetic analysis using methods of Maximum Likelihood, Maximum Parsimony, Neighbor Joining and Bayesian Inference resulted in mostly similar topologies, supporting the monophyly of the species, and showing as its closest relatives other species from river basins bordering the Upper Parana. Results also reveal four distinct phylogroups for the species, with partially overlapping distribution areas. Population and phylogeographic analysis included comparisons of genetic distance P, population structure based on the haplotype distribution and diversity indices, neutrality tests, fixation index FST, analysis of molecular variance (AMOVA), spatial analysis of molecular variance (SAMOVA), construction of a parsimony haplotype network, and nested clade phylogeographical analysis (NCPA). Results show 48 haplotypes distributed into twelve well-structured populations with little or no gene flow. Geographic range expansion events can be identified along the demographic history of H. ancistroides, suggesting that the structure found today reflects not only the ecology of the species, but also a history of changing environmental conditions that on occasion weree favorable for migration and dispersal. Contact between populations from differente basins may be more intense through headwater stream capture than through the river channel. The most supported hypothesis for the presence of the species in the Rio Ribeira basin is a headwater capture from the upper Rio Tiete. Although H. ancistroides is split into four distinct phylogroups, some derived lineages of the species have overlapping distribution ranges. Such secondary contact is revealed only by a matrilineal inheritance marker and does not allow the recognition of separate species for the different phylogroups under the current paradigm of speciation and species limits in Neotropical fishes.

This paper reports a phylogeny of the African killifishes (Genus Nothobranchius, Order Cyprinodontiformes) informed by five genetic markers (three nuclear, two mitochondrial) of 80 taxa (seven undescribed and 73 of the 92 recognized species). These short-lived annual fishes occupy seasonally wet habitats in central and eastern Africa, and their distribution coincides largely with the East African Rift System (EARS). The fossil dates of sister clades used to constrain a chronometric tree of all sampled Nothobranchius recovered the origin of the genus at ~13.27 Mya. It was followed by the radiations of six principal clades through the Neogene. An ancestral area estimation tested competing biogeographical hypotheses to constrain the ancestral origin of the genus to the Nilo-Sudan Ecoregion, which seeded a mid-Miocene dispersal event into the Coastal ecoregion, followed closely (~10 Mya) by dispersals southward across the Mozambique coastal plain into the Limpopo Ecoregion. Extending westwards across the Tanzanian plateau, a pulse of radiations through the Pliocene were associated with dispersals and fragmentation of wetlands across the Kalahari and Uganda Ecoregions. We interpret this congruence of drainage rearrangements with dispersals and cladogenic events of Nothobranchius to reflect congruent responses to recurrent uplift and rifting. The coevolution of these freshwater fishes and wetlands is attributed to ultimate control by tectonics, as the EARS extended southwards during the Neogene. Geobiological consilience of the combined evidence supports a tectonic hypothesis for the evolution of Nothobranchius.

My dissertation addresses two aspects of eukaryotic evolution, 1) the organization of eukaryotic diversity and 2) genomic variation in Foraminifera. The bulk of eukaryotic diversity is microbial with plants and animals representing just two of the estimated 75 lineages of eukaryotes. Among these microbial lineages, there are many examples of dynamic genome processes. Elucidating the origin and evolution of genome features requires a robust phylogenetic framework for eukaryotes. Taxon-rich molecular analyses provide a mechanism to test hypothesized evolutionary relationships and enable placement of diverse taxa on the tree of life. These analyses result in a well-resolved eukaryotic tree of life. Relaxed molecular clock analyses of this taxon-rich dataset place the origin on eukaryotes in the Paleoproterozoic, and suggest that all of the major lineages of eukaryotes diverged before the Neoproterozoic. This robust scaffold of the tree of eukaryotes is also used to elucidate common themes in genome evolution across eukaryotes. Mapping dynamic genome features onto this tree demonstrates that they are widespread in eukaryotes, and suggests that a common mechanism underlies genome plasticity. Foraminifera, a diverse lineage of marine amoebae, provide a good model system for investigating genome dynamics because they amplify portions of their genome and go through ploidy cycles during their life cycle. Assessment of nuclear dynamics in one species of Foraminifera, Allogromia laticollaris strain CSH, reveals that genome content varies according the life cycle stage and food source, which may differentially impact organismal fitness. The inclusion of diverse microbial eukaryotes enables better resolution of eukaryotic relationships and improves our understanding the dynamic nature of eukaryotic genomes.

No description available.

O continente sul-americano é a única região biogeográfica onde podemos encontrar um grupo estenohalino de elasmobrânquios: as arraias da família Potamotrygonidae. Entre 19 e 21 espécies de potamotrigonídeos estão taxonomicamente organizadas em três gêneros, distribuídas pelas bacias dos rios Atrato, Magdalena, Maracaibo, Orinoco, Essequibo, Amazonas e do Prata, os quais desembocam no Oceano Atlântico e no Mar do Caribe. Diversos cenários biogeográficos postulados para explicar a presença de linhagens predominantemente marinhas nos sistemas fluviais da América do sul foram propostos. O mais aceito para a origem e diversificação de Potamotrygonidae é a de invasão de um ancestral caribenho no sistema fluvial sul-americano durante as ingressões marinhas do Mioceno inferior no noroeste do continente, seguido de isolamento por alteração dos padrões de drenagens do Orinoco e formação dos Andes. A fauna parasitária de Potamotrygonidae está representada predominantemente por membros de Cercomeromorpha, um clado composto por linhagens de platelmintos membros de Cestoda e Monogenoidea. Dois gêneros de monogenóideos parasitas branquiais podem ser encontrados em potamotrigonídeos: Potamotrygonocotyle (Monocotylidae), para o qual 12 espécies são conhecidas, e a monotípica Paraheteronchocotyle amazonense (Hexabothriidae). O objetivo desta tese é propor uma hipótese de relacionamento filogenético baseada em dados moleculares para as espécies de Potamotrygonocotyle, e discutir padrões de evolução da espécie P. aramasae e seu hospedeiro Paratrygon aiereba, distribuídos em diferentes rios amazônicos. Sequências nucleotídicas do gene mitocondrial cox1 e nuclear ITS1 foram utilizadas simultaneamente em uma busca de uma hipótese filogenética para todas as espécies conhecidas de Potamotrygonocotyle. Os resultados recuperaram o status monofilético de cinco espécies, sugeriram complexos de linhagens crípticas para três espécies nominais e revelaram relacionamentos de grupo-irmão não detectados na hipótese filogenética mais recente para o gênero, baseada em dados morfológicos. Adicionalmente, os resultados apresentados suportam decisões taxonômicas recentes envolvendo sinonímias entre espécie nominais de Potamotrygonocotyle. Finalmente, os relacionamentos filogenéticos de haplótipos de diferentes populações de P. aramasae e seu hospedeiro P. aiereba foram acessados pela análise cladística de múltiplos marcadores mitocondriais, com o objetivo de se detectar possíveis padrões filogeográficos e testá-los sob predições filogenéticas de três hipóteses de diversificação amazônica (Hidrogeológica, de Museu e Paleogeográfica). Sequências dos genes ribossomal 16S e citocromo oxidase 1 foram obtidas para espécimes de parasitas de seis sub-bacias amazônicas. Os hospedeiros foram amostrados em 10 sub-bacias amazônicas e na sub-bacia do rio Essequibo, para os quais foram obtidas sequências nucleotídicas dos genes mitocondriais citocromo oxidase 1, citocromo b e ATPase. Os resultados sugerem a ausência de padrões filogeográficos para o parasita, cujos resultados indicam um modelo de alta dispersão. Em contraste, P. aireba é caracterizada por populações bem estruturadas, de acordo com as sub-bacias amostradas. O padrão filogeográfico geral desta espécie é concordante com as predições da Hipótese de Museu (linhagens mais antigas em rios dos escudos pré-cambrianos; linhagens apicais na bacia sedimentar amazônica). / South America is the only biogeographical region in the world where is possible to find an exclusive stenohalin group of elasmobranchs: the Potamotrygonidae stingrays. Between 19 and 21 species of potamotrygonid stingrays are taxonomically organized in three genera, distributed in the Atrato, Magdalena, Maracaibo, Orinoco, Essequibo, Amazonas e la Plata river Basins, discharging in both Atlantic and Caribbean waters. Distinct biogeographical scenarios have been proposed to explain the presence of predominantly marine lineages in the south American fluvial systems. The most accepted theory for Potamotrygonidae is the invasion of a Caribbean ancestor in the south-American freshwater system during the marine ingression of the early Miocene in the northwest of the continent, followed by its isolation due alterations of Orinoco rivers drainage patterns, as well as formation of Andes. The parasitic fauna of potamotrygonids is predominantly represented by members of Cercomeromorpha, a clade composed by members of Cestoda and Monogenoidea. Two genera of gill parasites monogenoidean might be found in potamotrygonids: Potamotrygonocotyle (Monocotylidae), for which 12 species are currently recognized, and the monotypic Paraheteronchocotyle amazonense (Hexabothriidae). The goal of this study is to propose a phylogenetic hypothesis based in molecular data for members of Potamotrygonocotyle, as well as to discuss evolutionary patterns of the species P. aramasae and its host Paratrygon aiereba, distributed through different amazon rivers. Nucleotide sequences of the mitochondrial gene cox1, and the nuclear gene ITS1 were simultaneously used to infer phylogenetic sister-group relationships among allrecognized species of Potamotrygonocotyle. The results recovered the monophyletic status of five species, suggested cryptic lineages for three species complexes, and revealed sister-groups relationships not detected previously by the phylogenetic analysis of morphological data. Additionally, the results supports recent taxonomic decisions involving synonyms among nominal species within the genus. The phylogenetic relationships of haplotypes from distinct populations of the parasite P. aramasae, as well as from its host Paratrygon aiereba, were accessed by the cladistic analysis of mitochondrial markers, in an attempt of detecting possible phylogeographic patterns, and to test them against phylogenetic predictions of three amazonian bio-diversification hypotheses (Hydrogeology, Museum, Paleogeography). Sequences of the ribosomal 16S gene and cytochrome oxidase 1 were obtained from parasite specimens collected in six amazon sub-basins. The hosts were sampled in 10 amazon sub-basins, as well as in the Essequibo sub-basin, for which cythocrome oxidase 1, cythocrome b, and ATPase sequences were obtained. No clear phylogeographic patterns were revealed for theparasite haplotypes, and the results suggest a high dispersion model. In contrast, P. aiereb is characterized by strongly structured populations, according to the sub-basin sampled. The general phylogeographic pattern recovered for this species is in agreement with the Museum Hypothesis predictions (older lineages in rivers of the pre-cambrian shields; apical lineages inhabiting the sedimentary amazon basin).

A família Accipitridae representa uma das maiores radiações de aves atuais, ocupando habitats diversos em grande parte do planeta. Entre as divisões propostas para a família no passado, o grupo dos gaviões buteoninos figura entre um dos poucos que se aproximam em composição a uma linhagem monofilética, de acordo com análises filogenéticas recentes. Além de ocorrer tanto no Novo Mundo como no Velho Mundo, a maior parte das espécies de gaviões buteoninos está concentrada na América do Sul e na América Central, o que os torna um modelo atrativo para a análise de padrões e processos de diversificação em escalas continental e local. Outro aspecto interessante do grupo é o grande número de espécies migratórias, padrão ainda pouco explorado sob uma perspectiva filogenética. Os principais objetivos deste trabalho foram inferir as relações filogenéticas entre as espécies de gaviões buteoninos, analisar a evolução do comportamento migratório no grupo, e inferir padrões e processos de diversificação, com ênfase na região Neotropical. Foram utilizados mais de 7.000 pares de base de DNA mitocondrial e nuclear de 51 espécies de gaviões buteoninos, compreendendo o maior estudo filogenético do grupo até o momento. Do total de seqüências utilizadas, cerca de um terço foi representado por seqüências de DNA do 12S, tRNAVal e 16S, que contém uma proporção de sítios de evolução dependente resultante da existência de uma estrutura secundária. Como forma de avaliar o impacto destes sítios nas estimativas, foram também realizadas análises alternativas que incorporaram informação de estrutura secundária. Devido à indisponibilidade de um modelo de estrutura secundária de 16S para aves, este foi aqui elaborado com base em uma análise comparativa de representantes de todas as ordens de aves atuais. Os resultados sugerem que os gêneros Buteo, Leucopternis e Buteogallus como atualmente reconhecidos não são monofiléticos, o que ressalta a falta de concordância entre a classificação atual e a histórica evolutiva do grupo. Cinco linhagens principais foram encontradas, sendo a base da árvore composta por espécies predominantemente neotropicais, e a porção mais derivada principalmente por espécies neárticas e do Velho Mundo. Este resultado, associado às estimativas de tempo de divergência, sugere um longo período de diversificação na região Neotropical (com início entre o Oligoceno Superior ou o Mioceno, e se estendendo até o Pleistoceno), com colonização e diversificação recentes na região Neártica e no Velho Mundo (com início no Mioceno Superior ou no Plioceno, se estendendo até o Pleistoceno). O comportamento migratório evoluiu diversas vezes, e pode ter contribuído para a diversificação de algumas espécies, ao possibilitar a colonização de habitats antes não ocupados e promover especiação em ilhas. Na região Neotropical, disjunções de espécies de florestas de terras baixas que ocupam áreas a leste e oeste dos Andes ocorreram quatro vezes, possivelmente em dois eventos vicariantes. As disjunções mais antigas podem ter sido causadas pelo soerguimento da cordilheira, enquanto não foi possível definir claramente os processos envolvidos nas especiações mais recentes. Foram encontradas duas linhagens distribuídas em habitats alagados e ripários. Os resultados sugerem não somente um longo processo de diversificação, de forma independente das espécies de florestas não alagadas, mas também conexões históricas entre florestas de várzea da Amazônia e habitats costeiros. Espécies florestais e de áreas abertas não são reciprocamente monofiléticas. De forma similar, em alguns casos, espécies pertencentes a um mesmo bioma não são proximamente relacionadas, o que sugere uma história complexa de diversificação na região. A utilização de dados de sítios emparelhados de seqüências de RNA não trouxe mudanças significativas nas topologias e inferências de tempo de divergência, possivelmente devido à baixa variação das hastes neste grau de divergência. / The family Accipitridae represents one of the largest radiations of modern birds, with species being found in a plethora of habitats around the world. Among the divisions proposed for the family in the past, the group of the buteonine hawks is one of the few that approximate monophyletic lineages, according to recent phylogenetic analyses. Besides occurring both in the New World and Old World, most buteonine hawk species are mainly found in Central and South America, what provides an opportunity to evaluate patterns and processes of diversification in both continental and local scales. The main goals of this work were to infer phylogenetic relationships among species of buteonine hawks, analyze the evolution of migratory behaviour, and evaluate patterns and processes of diversification, especially in the Neotropical region. We obtained more than 7.000 base pairs of mitochondrial and nuclear DNA sequences from 51 species of buteonine hawks, what comprises the largest phylogenetic analysis of the group so far. Approximately one third of the total dataset was obtained from DNA sequences of 12S, tRNAVal and 16S, which are known to have paired sites that evolve in concert due to the presence of a secondary structure. Alternative analyses incorporating such information have been performed, as a way to evaluate the effects of secondary structure in the phylogenetic analyses. Since a model of secondary structure of 16S of birds was not available so far, we build one based on comparative analysis of representatives of all modern avian orders. The results suggest that the genera Buteo, Leucopternis and Buteogallus as currently accepted are not monophyletic, what stress a lack of concordance between current classification and the evolutionary history of this group. Five main lineages were found, and the most basal part of the topology is composed by mainly neotropical species, while the majority of neartic and Old World species were positioned in the most derived part of the tree. Together with divergence time estimates, those results suggest a long period of diversification in the Neotropics (possibly beginning in the Upper Miocene or Oligocene, and extending to the Pleistocene), with a latter colonization and diversification of the Neartics and Old World (possibly beginning between the Upper Oligocene or Pliocene, and extending to the Pleistocene). Migratory behaviour evolved several times, and may have contributed to diversification by means of exploitation of previously unavailable habitats as well as promotion of speciation in islands. Lowland species disjunctions between each side of the Andes occurred four times, possible due to two vicariant events. The earliest disjunctions may have been caused by Andean orogeny, but no process could be clearly attributed to the two most recent speciations. Two lineages restricted to flooded habitats were found. The results suggest not only a long process of diversification in such habitats, independently of species of non-flooded habitats, but also a historical relationship between várzea forests in Amazonia and costal habitats. Similarly, species that occupy the same biome are not the closest relatives in several cases, what suggests a complex history of diversification in the Neotropical region. Inclusion of secondary structure information did not affect significantly phylogenetic and divergence time estimates, likely due to the low variation in stems in such level of divergence.

No description available.

The group of pleurocarpous mosses comprises approximately 5000 species, which corresponds to about half of all mosses. The pleurocarpous mosses (i.e. “the Core Pleurocarps”) form a monophylum, which consists typically of perennial mosses with creeping stems and abundant lateral branches. In pleurocarpous mosses the archegonium and thus also sporophyte development is restricted to the apices of short, specialized lateral branches, in contrast to most other mosses, where archegonia and sporophytes develop terminally on the main axis (acrocarpous) or on major branches (cladocarpous). Traditionally, pleurocarpous mosses have been divided into three orders based mainly on their sporophytic characters. Brotherus described the Neckeraceae in 1925 and placed it into the Leucodontales, later the family has alternatively been divided into two or three separate families: the Thamnobryaceae, the Neckeraceae and the Leptodontaceae. These families have been placed even in different orders (Neckeraceae and Leptodontaceae among the leucodontalean mosses and Thamnobryaceae among hypnalean mosses) according to their peristome structure and the grade of peristome reduction. A growing amount of evidence indicates that a grouping based on sporophytic characters is artificial and based on convergent evolution. According to the latest phylogenetic studies of pleurocarpous mosses, based on molecular data, the Neckeraceae belong to the order Hypnales and share a sister group relationship with the Lembophyllaceae. In the most recent comprehensive classification 28 genera were included in the Neckeraceae family. This classification was based on both morphological and molecular data, but done with limited taxon sampling that did not cover all species of the family. Some previous studies based on molecular data have challenged the family concept of the Neckeraceae, indicating the need for a revision of the family. Here the family concept of the Neckeraceae is revisited, the closest relatives of the family are resolved and its position within pleurocarpous mosses is shown. In addition, new insights into the morphological evolution of the family are provided. Previous phylogenetic studies indicated that branch lengths among pleurocarpous mosses are usually extremely short. Therefore we chose to use mainly non-coding DNA sequences from rapidly evolving DNA regions. The phylogenetic reconstructions are based on extensive sequence data from all genomes: plastid trnS-trnF and rpl16, nuclear ITS1 & 2 and mitochondrial nad5. Both parsimony (PAUP and PRAP2) and Bayesian statistics (MrBayes) were employed for phylogenetic reconstructions. In order to use the information provided by length mutations indels were included in the analyses as binary data using a simple indel coding approach. No severe conflicts appeared between the different methods used, but the indel coding affected the support values of the inferred topologies. Therefore, all support values resulting from different methods are shown along the phylogenetic trees. The morphological features are studied and synapomorphies for each clade formed in the phylogenetic analyses are interpreted. A new delimitation of the family makes it necessary to reconsider the relevance of the morphological description and the morphological features characteristic of the family need to be reconsidered. Due to new groupings, some changes in the morphological circumscriptions of the genera are necessary, resulting in two new genera and several new combinations. Chapter 1 gives a broad overview of the relationships of the pleurocarpous mosses and shows the need for changes in the definition of genera, families and the corresponding nomenclature in this group. Chapter 2 is a population genetic study on the genus Thamnobryum. The main aim of this chapter is to test the species concept in Thamnobryum that are endemic to strictly restricted regions showing only minor differences in the morphological features in comparison to some more common species. In Chapter 3 the monophyly of the Neckeraceae is tested. In addition, in this chapter the ancestral character states of some morphological characters within the Neckeraceae are reconstructed. Chapters 4 and 5 resolve the genus composition and the relationships within the family in more detail. The results of this thesis show that the Neckeraceae need re-circumscription; this includes changes in the genus composition. The Lembophyllaceae is confirmed to be the sister group of the Neckeraceae. In addition to the new phylogeny, the potential evolution of several characters as a result of environmental selection pressures is analyzed. From the ancestral state reconstructions made (using BayesTraits) for both the habitat and a selection of morphological characters, character state distributions and habitat shift appear congruent, peristome reduction being a good example. However, some character states do not correlate with the habitat, suggesting very complex evolutionary patterns underlying these morphological characters. Many widely distributed genera that are composed of several species and seem to be morphologically coherent (Echinodium, Homalia, Thamnobryum, partly Neckera), are shown in this thesis to be polyphyletic. They are replaced by smaller, geographically more restricted genera that at least in some cases (e.g. Thamnomalia, Homalia s.str., Neckera s.str.) seem to form morphologically heterogeneous genera. In other words, morphology can be misleading in the family Neckeraceae even at the genus level and convergent evolution in both morphological and sequence level characters are common within the family. Special habitat conditions have been shown to result in similar morphological structures also in several other moss groups. This kind of convergent evolution occurs in aquatic mosses, and seems to have occurred among the neckeraceous species Thamnobryum alopecurum and its allies. However, similar morphological structure in similar aquatic habitats can also be due to true phylogenetic relationships as is the case within the Neckeraceae for Handeliobryum sikkimense and Hydrocryphae wardii, or the members of Touwia. The geographical grouping seems to be more strongly correlated with the phylogenetic grouping than thought before.