Cynodontidae (sensu Lucena & Menezes, 1998) é uma família de Characiformes com 14 espécies válidas divididas em duas subfamílias (Cynodontinae e Roestinae). As espécies de Cynodontinae sempre foram classificadas em um mesmo grupo, enquanto que Roestinae já foi classificada junto com Characidae. Com o objetivo de testar o monofiletismo de Cynodontidae, realizamos uma análise de máxima parcimônia com o algoritmo TBR em 42 táxons representando 12 famílias de Characiformes. A análise foi realizada com três regiões nuclearas e três genes mitocondriais; entretanto, o íntron da RPS7 foi retirado da análise final por questões de homologia do alinhamento. A árvore consenso obtida com 9842 passos (IC = 0,351 e IR = 0,358) evidencia o não monofiletismo de Cynodontidae, com Cynodontinae relacionada a um clado composto por Serrasalmidae, Prochilodontidae, Hemiodontidae e Parodontidae, enquanto que Roestinae aparece dentro de Characidae relacionada à Heterocharacinae. Acestrorhynchidae foi recuperada na base do clado Roestinae/Heterocharacinae, o que condiz com outras filogenias moleculares e difere das filogenias morfológicas. As relações entre as espécies de Roestes e de Hydrolycus também foram recuperadas. As outras relações encontradas condizem com dados recentes da literatura, fortalecendo o conhecimento sobre a ictiofauna de água doce. A espécie Rhaphiodon vulpinus se destaca entre os Cynodontíneos por apresentar uma ampla distribuição geográfica, sendo encontrada em sistemas atualmente separados como as bacias do Paraná e do Amazonas. Por isso, uma análise da variabilidade e da estrutura populacional desta espécie foi realizada com o intuito de ampliar o conhecimento sobre a influência do passado geológico na distribuição da ictiofauna Neotropical, além de fornecer áreas prioritárias de conservação. Inicialmente, o estudo foi realizado com sequencias do gene da ATPase do mtDNA, e os resultados evidenciaram a existência de três grupos genéticos que foram considerados UES distintas (Bacia do Paraná, oeste da Amazônia e leste da Amazônia). Entretanto, a hipótese de contato secundário com mistura de fauna entre a Bacia do Paraná e o Rio Madeira foi postulada para explicar os resultados. Para testar tal hipótese, foi desenvolvida a biblioteca de microssatélites de R. vulpinus, já que este marcador é mais sensível para a detecção de estruturas populacionais. Foram obtidos 11 locos polimórficos, sendo que sete funcionaram em outros gêneros de Cynodontinae. A análise com microssatélites confirmou a conexão entre o oeste da Amazônia e a Bacia do Paraná, provavelmente devido à captura de riachos para a sub bacia do Rio Madeira. Uma grande diferença entre as análise é a subdivisão UES do leste da Amazônia (rios Araguaia e Xingu) devido à grande diferenciação do alto Xingu. Além disso, esta localidade parece ter contribuído no pool gênico do Araguaia após a estruturação, o que pode indicar outro evento de captura de cabeceiras. Estes eventos, no entanto, seriam relativamente recentes na história evolutiva de R. vulpinus, assim como é a barreira estabelecida pela Cachoeira do Teotônio no Rio Madeira, já que a mesma não foi detectada como barreira na análise do mtDNA. A história demográfica de Rhaphiodon vulpinus parece estar intimamente relacionada a eventos geológicos, já que a estruturação encontrada reflete o conhecimento atual sobre a formação das bacias hidrográficas. Além disso, R. vulpinus parece ser uma espécie bastante antiga, especialmente pela estruturação encontrada dentro da Bacia Amazônica. Por isso, tanto a diminuição do tamanho populacional (detectada no leste da Amazônia pelos microssatélites) quanto a expansão populacional (detectada no oeste da Amazônia pela ATPase) podem ter acontecido nesta espécie. R. vulpinus parece ser uma espécie com grande capacidade migratória, já que apresenta isolamento pela distância e estruturação relacionada à barreiras históricas. Em relação aos padrões de diversidade, ambos os marcadores evidenciaram uma diversidade moderadamente alta na Amazônia (com os maiores valores no oeste) e uma baixa diversidade na Bacia do Paraná, provavelmente devido à colonização da bacia aliado às alterações ambientais ocorridas na região. O conjunto de dados obtidos contribuirá para o esclarecimento das relações filogenéticas em Characiformes e também para a compreensão de aspectos da história evolutiva e da dinâmica de populações de R. vulpinus, uma espécie que parece ser mais antiga do que a formação atual dos sistemas de drenagem. / Cynodontidae (sensu Lucena & Menezes, 1998) is a Characiform family with 14 valid species which are divided in two subfamilies (Cynodontinae and Roestinae). Cynodontinae species were always classified in the same group meanwhile Roestinae has already been classified together with Characidae. In order to test the monophylestism of Cynodontidae, we have conducted a Maximum Parsimony Analysis using the algorithm TBR in 42 taxa, which represent 12 Characiform families. The analysis was performed with three nuclear regions and three mitochondrial genes; the first intron of RPS7 was removed from the final analysis due to problems related to alignment homology. The consensus tree obtained with 9842 steps (IC = 0,351 and IR = 0,358) does not support the monophylestism of Cynodontidae, which appears in a clade composed by Serrasalmidae, Prochilodontidae, Hemiodontidae, and Parodontidae; Roestinae appears within Characidae, close-related to Heterocharacinae. Acestrorhynchidae was recovered at the base of Roestinae/Heterocharacinae clade, which is in agreement with other molecular phylogenies and in disagreement with the morphological ones. The relationship between Roestes and Hydrolycus species was also recovered. Other relationships obtained are in agreement with recent data described elsewhere, which reinforces the knowledge on the freshwater fish fauna. The species Rhaphiodon vulpinus stands out from other Cynodontinae species due to its wide geographic distribution, occurring in basins that are currently separated as is the case of Paraná and Amazon. Within this context, population variability and structure analyses were conducted with the aim of expanding the knowledge related to the influence of geological history on the distribution of Neotropical fish fauna as well as to provide priority areas for conservation means. Initially, the study was carried out with ATPase gene sequences from mtDNA and the results evidenced the existence of three genetic groups which were considered as different ESUs (Evolutionary Significant Units; Paraná, Western Amazon, and Eastern Amazon). However, a secondary contact hypothesis with fauna mixture between Paraná and Madeira river basins was formulated in order to explain the results. In order to test such hypothesis, a microsatellite library was developed for R. vulpinus, once this marker is more sensitive for the detection of population structure. 11 polymorphic loci were obtained and among them, seven showed to be useful in other Cynodontinae genus. The microsatellite analysis confirmed the connection between the Western Amazon and the Paraná basin, which probably occurred as a result of headwaters capture by the Madeira river sub-basin. The major difference between the analyses comprises the ESU sub-division in Easter Amazon (Araguaia and Xingu rivers) due to the high differentiation of Upper Xingu. Moreover, this locality may have contributed on the Araguaia gene pool after its structuration process, which may be an indicative of another headwaters capture event. However, those events would be relatively recent in the R. vulpinus evolutive history, likewise the barrier formed by Teotônio Falls in Madeira river, once it was not detected as a barrier by mtDNA analysis. The demographic history of R. vulpinus seems to be tightly related to geologic events, once the structure obtained reflects the current knowledge on the formation of hydrographic basins. Furthermore, R. vulpinus seems to be a very old species, mainly due to the structure found within the Amazon basin. Thus, both the reduction of population size (detected in Eastern Amazon by microsatellite) and the population expansion (detected in Western Amazon by ATPase) may have occurred in this species. R. vulpinus seems to be a species with a high migration capacity, once it presents isolation by the distance and structuration related to historical barriers. Regarding the diversity patterns, both markers evidenced a slightly high diversity in the Amazon (high values on Western) and low diversity in the Paraná basin, possibly due to the occupation of the basin modulated by environmental changes that occurred in the region. Those data will contribute to resolve the phylogenetic relationships in Characiform and for the understanding of some aspects of the evolutive history and population dynamics of R. vulpinus, a species that seems to be older than the current drainage systems.

Na presente Tese foram usados métodos de inferência filogenética e de filogeografia buscando identificar os processos históricos de diversificação do gênero Conopophaga na América do Sul, em especial na Mata Atlântica. O monofiletismo do gênero e a estrutura filogeográfica das espécies distribuídas no sudeste da Mata Atlântica (Conopophaga lineata e C. melanops), foram testados utilizando seqüências de DNA mitocondrial. Para a filogenia foram utilizadas duas matrizes, sendo uma de 2270 pb (941 pb da subunidade 2 da NADH desidrogenase (ND2), 343 pb do ND3 e 986 pb do citocromo b) e outra de 878 pb (461 pb do ND2 e 417 pb do cit b). Nas análises de filogeografia de C. lineata e C. melanops foram utilizadas seqüências da região controladora de 472 pb e 439 pb, respectivamente. Os resultados demonstraram que o gênero Conopophaga é monofilético e que provavelmente uma rápida radiação ocorreu nesse gênero depois da especiação de C. melanogaster e de C. melanops. Dessa radiação, foram recuperados dois grupos: (1) Um grupo que se distribui somente na Amazônia e mantém a característica ancestral da coloração negra da mandíbula e (2) um grupo distribuindo-se na Amazônia e também na Mata Atlântica e que possui a mandíbula branca. Nesse último grupo, C. l. cearae não se agrupou com C. lineata, demonstrando que essa espécie não é uma espécie monofilética. A relação entre as espécies que apresentam a mandíbula branca parece indicar a ocorrência de uma conexão entre o leste da Amazônia e a Mata Atlântica no passado. O estudo filogeográfico de C. lineata revelou a existência de possíveis eventos de vicariância: (1) na região compreendida pelo Vale do Rio Paraíba do Sul e (2) à oeste de São Paulo e Paraná, separando as populações mais ao sul. Apesar de as inferências filogenéticas realizadas em C. melanops e C. lineata não serem totalmente concordantes, é possível que exista um padrão de vicariância nessa região. Concluindo, a ocorrência desses eventos vicariantes, tais como eventos geológicos e ciclos de alterações climáticas tenham influenciado na diversificação da família Conopophagidae. Além disso, eventos de dispersão e/ou seleção também podem auxiliar no entendimento da história biogeográfica do grupo, bem como de outros grupos na América do Sul. / In order to identify the historical processes of diversification of the gender textitConopophaga in South America, especially in the Atlantic forest, methods of phylogenetic and phylogeography inference were used in the present thesis. The genus phylogeny and the phylogeographic structure of two species ( textitConopophaga lineata and textitC. melanops) which occurs in the Southeast of the Atlantic forest were tested using sequences of mithocondrial DNA. Two matrixes were used to perform the phylogenetic analyses. The first one comprising 2270 bp (941 bp of ND2, 343 bp of ND3 and 986 bp of cytochrome b) and the second one comprising of 878 bp (461 bp of ND2 and 417 bp of cytochrome b). The phylogeography analyses of textitC. lineata and textitC. melanops were done using sequences from the control region consisting of 472 bp and 439 bp, respectively. The results demonstrated that the genus textitConopophaga is monophyletic and probably after textitC. melanogaster and textitC. melanops speciation, a rapid diversification had occurred in this genus. Following this event two distinct groups were recovered: (1) a group distributed in Amazonian, which maintains the ancestral characteristic of black jaw and (2) a group possessing white jaw occurring in the Amazonian and also in the Atlantic forest. In the last group, the subspecies C. l. cearae did not grouped with textitC. lineata demonstrating that this species is not monophyletic. Moreover, the distribution pattern of species presenting white jaw indicates a plausible a connection between the east of the Amazonian and the Atlantic forest in the past. The phylogeographic study of textitC. lineata revealed the existence of possible vicariant events: (1) in the area of Vale do Rio Paraíba do Sul and (2) in the west of São Paulo and Paraná, separating the southern south populations. Although the phylogeographic structure observed in textitC. melanops and in textitC. lineata are not in total agreement, the occurrence of vicariant events still remains as a possible explanation for the phylogeographic patterns in this region. Finally, the occurrence of these vicariant events like, geological events and climatic oscilations, may have influenced the diversification of the family Conopophagidae. Moreover, dispersion events and/or selection should also be considered for the understanding of biogeographic history of this group and also other ones in South America.

A presente Dissertação apresenta dados sobre dois estudos complementares: a filogenia do gênero Paroaria (Aves: Passeriformes: Oscines; Capítulo 2) e a filogeografia de Paroaria dominicana (Capítulo 3). O estudo filogenético do gênero Paroaria utilizou como fonte de dados seqüências do ND2 (1041 pb) obtidas a partir de indivíduos das cinco espécies desse gênero (exceto P. baeri com 925 pb) e de seis espécies de diferentes tribos da subfamília Emberizinae como grupos externos. As reconstruções filogenéticas obtidas indicam que: 1) táxons da atual tribo Emberizini não formam um grupo monofilético; 2) Gubernatrix cristata pertence à tribo Thraupini; 3) dentre as espécies amostradas, G. cristata é a mais próxima ao gênero Paroaria; 4) o gênero Paroaria é monofilético; 5) o gênero Paroaria está dividido em dois clados principais: (P. coronata, P. dominicana) e (P. baeri (P. gularis, P. capitata)). Para auxiliar a interpretação dos resultados, as distribuições dos registros das espécies do gênero Paroaria foram obtidas por meio da compilação de informações de localidades de coleta de onze instituições. O clado (P. coronata, P. dominicana) sugere que as florestas abertas dos arredores do Chaco e da Caatinga estão relacionadas. Já o clado (P. baeri (P. gularis, P. capitata)) sugere relação entre as matas ciliares do Cerrado, da Amazônia, do Pantanal e dos arredores do Chaco. Estimativas de datas de divergências sugerem que as diversificações mais antigas dentro do gênero Paroaria ocorreram no período Plioceno, enquanto apenas a mais recente ocorreu no Pleistoceno inferior. Eventos paleogeográficos e paleoclimáticos poderiam estar associados às diversificações. Já o estudo filogeográfico da espécie P. dominicana utilizou como fonte de dados seqüências do ND3 (351 pb) e do primeiro domínio da região controladora (391 pb) obtidas a partir de 51 indivíduos dessa espécie. A espécie irmã P. coronata foi selecionada como grupo externo. Porém, devido a problemas laboratoriais ela foi substituída por P. capitata em algumas matrizes. Testes de neutralidade foram aplicados aos dados e sugerem que: 1) há fuga do modelo de populações em equilíbrio neutro causada por seleção positiva (fase pré ou pós-fixação) ou seleção negativa atuando concomitantemente ou não a uma expansão populacional recente; e 2) a não utilização do grupo externo mais adequado causou saturação nos dados, prejudicando a realização de inferências mais precisas sobre as forças causadoras do padrão de polimorfismos encontrado. Com isso, análises de demografia histórica e de tamanho populacional efetivo foram comprometidas. As análises de estrutura populacional indicam que: 1) a espécie P. dominicana não apresenta estruturação populacional para o DNAmt; 2) essa espécie deve ser tratada como uma única Unidade de Manejo; e 3) o rio São Francisco e os tipos de Caatinga não constituem barreiras geográfica e ecológica para essa espécie, respectivamente. / This Masters Thesis comprises two complementary studies: phylogeny of the genus Paroaria (Aves: Passeriformes; Oscines; Chapter 2) and phylogeography of Paroaria dominicana (Chapter 3). The phylogeny of the genus Paroaria is based on complete ND2 (1041 bp) sequences from all five Paroaria species (except P. baeri with 925 bp) and from six species from different tribes of the subfamily Emberizini as outgroups. The results indicate that: 1) the current tribe Emberizini is not monophyletic; 2) Gubernatrix cristata should be placed within the tribe Thraupini; 3) among the outgroups sampled, G. cristata is the closest to genus Paroaria; 4) genus Paroaria is monophyletic; and 5) genus Paroaria is comprised of two major clades: (P. dominicana, P. coronata) and (P. baeri (P. gularis, P. capitata)). To help interpreting the results, the distribution of sampling localities of the genus Paroaria was compiled from eleven institutions. The clade (P. dominicana, P. coronata) indicates an association between the open forests of Caatinga and around the Chaco. The clade (P. baeri (P. gularis, P. capitata)) suggests that the riparian forests of Cerrado, Amazon, Pantanal and around the Chaco are related. Date estimates of diversification indicate that the oldest splits within the genus occurred during the Pliocene, and only the youngest diversification occurred during the early Pleistocene. Paleogeographic and paleoclimate events could be related to these diversifications. The phylogeography of the species P. dominicana is based on sequences from of ND3 (351 bp) and first domain of the control region (391 bp) from 51 individuals. The sister species P. coronata was used as outgroup. However, due to technical problems it was replaced by P. capitata in some data matrices. Neutrality tests results suggest that: 1) there is departure from the neutral equilibrium population model due to negative or positive selection (pre or post fixation phases) acting simultaneously or not with a recent population expansion; and 2) the use of a non-sister outgroup caused saturation of the data, jeopardizing more precise inferences on the forces shaping the polymorphism pattern found. Therefore, historical demography and effective population size analyses could not be performed. The population structure analyses suggest that: 1) the species P. dominicana is not geographically structured based on mtDNA data; 2) this species can be considered as a single Management Unit; and 3) the São Francisco river and the types of Caatinga are not geographic and ecological barriers for this species, respectively.

Nesta Tese foram descritos padrões de diversificação de pássaros que ocorrem na Amazônia e na Mata Atlântica, os quais permitiram fazer inferências sobre os processos que podem ter influenciado a evolução das biotas residentes nestes biomas. Nós produzimos sequências de genes mitocondriais e nucleares para fazer inferências sobre a biogeografia histórica destes biomas. A Tese foi dividida em seis capítulos. Nos capítulos 1 a 4 os táxons Basileuterus leucoblepharus, Myrmotherula gularis e o complexo Synallaxis ruficapilla foram estudados para se entender a diversificação da Mata Atlântica. Estes estudos revelaram que os ciclos glaciais do fim do Pleistoceno tiveram importante papel na diversificação destes táxons. Ainda, atividades tectônicas ocorridas durante o Quaternário possivelmente contribuíram para a diversificação do complexo S. ruficapilla. No capítulo 5 o complexo Thamnomanes caesius/T. schistogynus foi analisado visando inferir a história evolutiva da Amazônia. Os resultados deste estudo mostraram que tanto a origem recente dos rios amazônicos (do Plioceno ao Pleistoceno) quanto os ciclos glaciais possivelmente foram responsáveis pela diversificação deste grupo. No capítulo 6 o grupo Suboscines foi estudado para compreender a dinâmica das conexões históricas entre as florestas Amazônica e Atlântica. Os resultados mostraram que os contatos históricos entre estes dois biomas correspondem a duas conexões espaço-temporais distintas: uma mais antiga durante o Mioceno através da porção sul da diagonal seca da América do sul, e uma mais recente durante o Plioceno e o Pleistoceno através da Caatinga e Cerrado no Nordeste do Brasil. Os dados desta Tese permitiram testar o papel de algumas hipóteses concorrentes na diversificação da Amazônia e da Mata Atlântica. A hipótese dos rios parece ter contribuído para a diversificação da Amazônia. A hipótese dos refúgios florestais possivelmente teve um papel crucial da diversificação da biota da Mata Atlântica. A hipótese dos refúgios também não pode ser rejeitada como um das forças que deu origem à biota da Amazônia que observamos atualmente. Eventos tectônicos e mudanças climáticas contribuíram para conexões históricas entre a Amazônia e Mata Atlântica / This PhD Dissertation describes patterns of diversification of species of passerines that occur in the Amazon and the Atlantic Forest and that allowed making inferences on the processes that may have influenced the evolution of the organisms that live in these forests. We generated sequences of mitochondrial and nuclear genes to study the historical biogeography of these biomes. This work includes six chapters. In chapters 1 to 4 we analyzed Basileuterus leucoblepharus, Myrmotherula gularis, and the Synallaxis ruficapilla complex in order to depict the diversification within the Atlantic Forest. These studies revealed that late Pleistocene glacial cycles played an important role on the diversification of these taxa. Furthermore, tectonic activities in the Quaternary may have contributed for the diversification of the S. ruficapilla complex. In chapter 5 we analyzed the Thamnomanes caesius/T. schistogynus complex in order to infer about the diversification in the Amazon. The results of this study showed that both the recent origin of Amazonian rivers (Pliocene to Pleistocene) as glacial cycles could be responsible for the diversification of these organisms. In chapter 6 we analyzed the New World suboscines in order to depict the historical connection dynamics between the Amazon and the Atlantic Forest. Our results pointed to two distinct spatiotemporal pathways connecting these forests in the past: (1) older connections during the Miocene through southern South America dry diagonal; (2) younger connections during the Pliocene to Pleistocene through Cerrado and Caatinga in northeastern Brazil. The results of this PhD Dissertation allowed us to test the role of concurrent hypotheses of diversification in the Amazon and the Atlantic Forest. The riverine hypothesis seems to have contributed to the evolution of the Amazonian biota. The refuge hypothesis seems to be the main force of diversification of organisms from the Atlantic Forest. Moreover, we could not reject the refuge hypothesis as a force of diversification of organisms that occur in the Amazon forest. Tectonic events and climate changes played important roles in the historical connection between the Amazon and the Atlantic Forest

A esfingofauna brasileira ainda hoje é pouco conhecida. Orecta lycidas (Sphingidae, Smerinthinae, Ambulycini) tem sido considerada uma espécie rara por conta das reduzidas séries de exemplares nas coleções entomológicas, mesmo para as localidades extensivamente amostradas. Até o momento, não se tem uma hipótese filogenética para o relacionamento de todos os gêneros de Ambulycini e, desse modo, pouco se sabe sobre o relacionamento de O. lycidas com os táxons geograficamente mais próximos. Uma das espécies neotropicais mais assemelhada a O. lycidas, que compartilha uma distribuição geográfica muito parecida e também a mesma família de planta hospedeira das larvas, é Adhemarius eurysthenes. Esta espécie está entre as mais abundantes em trabalhos recentes de levantamentos de Sphingidae para localidades de Mata Atlântica em São Paulo, podendo ser coletada em todos os meses do ano. Sendo assim, é possível conseguir, com relativamente pequeno esforço, quantidades de indivíduos satisfatórias para o estudo de suas populações. Neste trabalho, a hipótese filogenética recuperada combinou dados dos genes COI, CAD e wingless (1950 pb) com 96 caracteres da morfologia externa de adultos dos 10 gêneros de Ambulycini em uma análise de Inferencia Bayesiana. A tribo forma um grupo monofilético, bem como nove de seus gêneros. Nenhuma das sinapomorfias morfológicas de Ambulycini encontradas são características exclusivas, se incluídas espécies de outras subfamílias não investigadas. Adhemarius é um gênero polifilético com necessidade de revisão. Os quatro gêneros neotropicais estão divididos em duas linhagens e não formam um grupo monofilético. Orecta spp. Trogolegnum pseudambulyx e Adhemarius senso latu compõem a linhagem dos ademariformes, caracterizada por quatro sinapomorfias. Ainda, usando-se principalmente a região barcode do gene COI, foram analisadas filogeograficamente algumas populações de Adhemarius eurysthenes, para a obtenção de informações sobre a estrutura e a variabilidade genética, buscando padrões que possam ser transpostos para estudos de conservação dos Ambulycini na Mata Atlântica. Foram obtidos 14 haplótipos de 109 indivíduos distribuídos em 10 localidades. A localidade do Espírito Santo foi aquela com maior distância genética média para com as demais populações. Concordantemente, o teste de variança molecular que inclui o componente espacial separou as amostras em dois grupos, onde o Espírito Santo foi a localidade divergente das demais. Em contrapartida, nenhuma correlação foi obtida entre a variação genética e a distância geográfica. Sendo assim, pode ser observada uma tendência de isolamento genético da população do Espírito Santo em relação às demais. Desse modo, esta passa a ser uma localidade de particular importância para a conservação de espécies de Ambulycini endêmicas da Mata Atlântica, como A. eurysthenes e O. lycidas. Finalmente, a única sinapomorfia morfológica confiável de Ambulycini, ainda não confirmada para alguns táxons, provém do estágio de pupa, indicando a importância das formas imaturas para a sistemática da tribo. Sendo assim, foram descritos o estágio de ovo e o primeiro ínstar de O. lycidas e comparados com o que está disponível na literatura. Este é o primeiro trabalho que descreve a quetotaxia de uma larva de Ambulycini. A maioria dos trabalhos com imaturos de Sphingidae limitam-se à descrição dos padrões de coloração e formato geral do corpo das larvas. Estudos da ultraestrutura dos estágios imaturos de Ambulycini terão um papel importante na incorporação futura de novas informações em estudos sistemáticos de Ambulycini, contribuindo assim para a descoberta de sinapomorfias que dêem maior consistência para a hipótese obtida neste trabalho. / The Brazilian hawk moths are still poorly known. Orecta lycidas (Sphingidae, Smerinthinae, Ambulycini) has been considered a rare species on account of reduced series of individuals in the entomological collections, even for extensively sampled locations. So far, there is none phylogenetic hypothesis for the relationship of all genera of Ambulycini and thus little is known about the relationship of O. lycidas with the geographically closest taxa. One of the Neotropical species more closely related to O. lycidas, which shares a very similar geographic distribution, and the same family of host plant of the larvae, is Adhemarius eurysthenes. This species is among the most abundant in recent surveys of Sphingidae for Atlantic Forest localities in São Paulo, and can be collected in all months of the year. Therefore, it is possible to achieve, with relatively little effort, satisfactory amounts of individuals for the study of their populations. In this work, the recovered phylogenetic hypothesis combined data of COI genes, CAD and wingless (1950 bp) with 96 characters of adult external morphology of the 10 genera of Ambulycini in a Bayesian inference analysis. The tribe is a monophyletic group, as well as nine of their genera. No morphological synapomorphies of Ambulycini found in the present work are exclusive if other subfamilies of Sphingidae are considered. Adhemarius is a polyphyletic genus in need of revision. The four Neotropical genera are divided into two lineages and do not form a monophyletic group. Orecta spp., Trogolegnum pseudambulyx and Adhemarius sense latu comprise the lineage of ademariphorms, characterized by four synapomorphies. Still, mainly using up the COI gene barcode region, some populations of Adhemarius eurysthenes were phylogeographicaly analyzed, to obtain information on the structure and genetic variability, seeking patterns that can be transferred to the Ambulycini conservation studies in the Atlantic Forest. We obtained 14 haplotypes of 109 individuals from 10 localities. The locality of the Espírito Santo was one with the highest average genetic distance among the other populations. Accordingly, the molecular variance test that includes the spatial component separated samples into two groups, and Espírito Santo was divergent from the other localities. However, no correlation was found between genetic variation and geographic distance. Thus, it can be observed genetic isolation trend of the population of the Espírito Santo in relation to the others. Thus, it becomes a place of particular importance for the conservation of endemic species of Ambulycini, such as A. eurysthenes and O. lycidas. Finally, the only reliable morphological synapomorphy of Ambulycini, not yet confirmed for some taxa, comes from the pupal stage, indicating the importance of the immature forms for a better understanding of the tribe. Thus, we described the egg stage and the first instar of O. lycidas and compared them with what is available in the literature. This is the first report describing the chaetotaxy of an Ambulycini larva. Most work on the immature stages of Sphingidae is limited to the description of the color patterns and general shape of the body of the larvae. Ultrastructure studies of the immature stages of Ambulycini will have an important role in the future development of new information in systematic studies of Ambulycini, thus contributing to the discovery of synapomorphies that could give greater consistency to the hypothesis obtained in this work.

Estudos filogeográficos para distintas espécies de Medusozoa (Cnidaria) foram conduzidos enfatizando a área nerítica central do Atlântico Sul-ocidental (ASO), entre os litorais sudeste do Brasil e o litoral da província de Buenos Aires na Argentina. Estes foram baseados em sequências de DNA dos genes mitocondriais COI e 16S e do íntron nuclear ITS1, levando em consideração tanto a heterogeneidade atual e a historia geológica das condições oceanográficas do ASO, como também as capacidades dispersivas de Liriope tetraphylla, Olindias sambaquiensis e Acharadria crocea, inferidas pelos seus ciclos de vida. Adicionalmente, a estrutura filogeográfica de Pelagia noctiluca foi avaliada em outras regiões oceânicas, considerando o Atlântico (Atl.) e o Mediterrâneo (Med.) e utilizando os marcadores COI, 16S e ITS1. Este estudo foi conduzido através de calibrações de taxas de substituição baseadas em uma divergência significativa embora filogeneticamente rasa, entre populações do Atl. e do Pacífico. Os resultados específicos indicam: 1) padrões comuns, de expansões populacionais e estruturação genética acompanhada de padrões filogenéticos sem uma correlação geográfica evidente, para as três espécies estudadas do ASO, os quais remetem a alterações de área habitável em períodos glaciais e interglaciais a partir do Pleistoceno médio ou tardio; 2) uma estrutura filogeográfica entre populações de P. noctiluca do Atl. e do Med. que remete a possíveis efeitos de isolamento entre ambas bacias durante o Gelasiano. Além disso, aspectos dos resultados que sugerem a importância de se considerar que a demografia não seria apenas afetada pela história biogeográfica são discutidos. A demografia também modularia o grau de resposta das populações aos eventos biogeográficos, podendo ser uma característica comum para populações de espécies que mostram padrões filogeográficos similares, a despeito de possuírem biologias marcadamente distaintas. É importante salientar que a prevalência na interpretação da influência da história natural nos estudos biogeográficos não se restringe a estudos microevolutivos. A origem dos metazoários é geralmente associada ao impacto biológico de mudanças ambientais que teriam desencadeando a chamada explosão cambriana. Entretanto, a atividade tectônica que propiciou estas mudanças é pouco discutida dentro de uma abordagem biogeográfica, a qual é considerada controversa. Resultados indicadores de que as principais linhagens de Cnidaria teriam surgido ao longo do Criogeniano e o Ediacarano foram obtidos, Períodos em que novos mares e áreas de plataforma rasa estavam surgindo como resultado da fragmentação da placa continental de Rodínia. A relação entre estes eventos geológicos e um possível surgimento de biotas marinhas diversificadas, as quais poderiam ser consideradas as primeiras cladogêneses em Eumetazoa relacionadas a eventos vicariantes, é uma nova hipótese a ser considerada / Phylogeographic studies for different species of Medusozoa (Cnidaria) were performed, emphasizing the central neritic area of the South-Western Atlantic (SWA), localized between the southeastern Brazilian coast and the coast of the Buenos Aires province in Argentina. These were based on DNA sequences of the mitochondrial genes COI and 16S, and the nuclear intron ITS1. They considered both the heterogeneity of the geological history and the present oceanographic conditions of the SWA, as well as the dispersal capabilities of Liriope tetraphylla, Olindias sambaquiensis and Acharadria crocea, inferred by their life cycles. Additionally, the phylogeographic structure of Pelagia noctiluca was evaluated in other oceanic regions, considering the Atlantic (Atl.) and Mediterranean (Med.) and using COI, ITS1 and 16S as molecular markers. This study was conducted through calibrations of substitution rates based on a significant but phylogenetically shallow divergence, between populations from the Atl. and the Pacific. Specific results indicate: 1) common patterns of population expansion and genetic structure associated to phylogenetic patterns without a clear geographical correlation, for the three species of the ASO, which refer to changes of the habitable area during glacial and interglacial periods since the middle or late Pleistocene; 2) genetic structure between populations of P. noctiluca from the Atl. and Med., referring to possible isolation effects between the two basins during the Gelasian. Moreover, the results also suggest the importance of considering that the demographic aspects would not be affected only by the biogeographical history. The demography would also modulate the degree of response of populations to biogeographic events, and could be a common feature for populations of species that exhibit similar phylogeographic patterns, in spite of having markedly different biological features. It is important to notice that the prevalence in the interpretation of the influence of natural history in biogeographical studies is not restricted to microevolutionary studies. The origin of metazoans is generally associated with the biological impact of environmental changes that would have triggered the Cambrian explosion. However, the tectonic activity that resulted in such changes is not discussed within a biogeographic approach, which is considered controversial. Results indicating that the main lineages of Cnidaria emerged during the Cryogenian and Ediacaran were obtained, at that Period new seas and areas of shallow platform were emerging as a result of the fragmentation of the Rodinia continental plate. The relationship between those geological events and the possible emergence of a diverse marine biota, whose could be considered as the firsts cladogenesis in Eumetazoa related to vicariant events, is a new hypothesis to be considered

The Bemisia tabaci (Gennadius) sibling species group is known to comprise several morphologically undistinguishable mitotypes which can be separated into seven major phylogeographic clades using the 3' half of the mitochondrial cytochrome oxidase I gene. B. tabaci is the only vector of begomoviruses; it transmits the complex of viruses that cause the cotton leaf curl disease, which has rapidly spread from Pakistan to the Philippines, at southeast of Asia, in the last decade. The study of B. tabaci mitotypes has been limited to variants of worldwide distribution and those associated to agroecosystems, however, the study of indigenous mitotypes has been scarce. This dissertation provides a comprehensive study of the phylogeography and population biology of mitotypes belonging to two major phylogeographic clades, the Asia II and the Americas. The Asia II major clade contains the highest number of mitotypes, in contrast, there is a large gap in knowledge about mitotypes associated to highly endemistic niches in the Americas. To study the population biology of mitotypes belonging to the Asia II major phylogeographic clade, two fragments of the mtCOI gene were amplified by polymerase chain reaction (PCR) for adult whiteflies sampled from mono and multi-cropping systems in the provinces of Punjab and Sindh in Pakistan. Phylogenetic analyses suggested that three indigenous mitotypes were distinctively distributed across ecosystems of Pakistan. The Asia II-5 and II-7 were found restricted to multi-cropping systems of Lahore, while the Asia II-1 was found widespread throughout the cotton growing region of Pakistan. Moreover, population analyses suggested the Asia II-1 is undergoing demographic expansion following a recent selective sweep or bottleneck. This event explains the predominance of Asia II-1 in Pakistan and its spread towards the southern province of Sindh. Additionally, differences in DNA polymorphism and diversity between mtCOI fragments derived in dissimilar evolutionary pairwise distances, suggestive of future implications in the “species” delimitation at a global scale when choosing one fragment over the other. The endosymbiotic bacteria assemblages associated to indigenous mitotypes Asia II-1, II-5 and II-7 were studied by analysis of 16S rRNA profiles. Besides the primary symbiont Portiera, Arsenophonus was detected almost fixed in the studied populations and several unique strains of Arsenophonus were detected in Asia II-5 and II-7, suggesting possible unique environmental adaptation capacities of these mitotypes. Hierarchical clustering of 16S rRNA profiles, proposed host-based and environmental-related differentiation. Additionally, the disruption of parallel cladogenesis between the primary symbiont and B. tabaci, disallows rejection of the hypothesis that gene flow among B. tabaci mitotypes occurs. To study the population biology of indigenous mitotypes belonging to the Americas major clade, adult whiteflies were sampled from ecosystems of nine provinces in Ecuador. Based on phylogenetic analyses, three indigenous and one invasive mitotype were detected. Among the indigenous, a previously unrecognized mitotype, named ECU3, was found. Moreover, mitotypes were found coexisting in five locations, and the invasive B is thought to have displaced endemic mitotypes to the northern and eastern coastal habitats of Ecuador.

>Magister Scientiae - MSc / Maize streak disease (MSD), caused by variants of the Maize streak virus (MSV) A strain, is the world's third and Africa’s most important maize foliar disease. Outbreaks of the disease occur frequently and in an erratic fashion across Africa and Islands in the Indian Ocean causing devastating yield losses such that the emergence, resurgence and rapid diffusion of MSV-A variants in this region presents a serious threat to maize production, farmer livelihoods and food security. To compliment current MSD management systems, a total of 689 MSV-A full genomes sampled over a 32 year period (1979-2011) from 20 countries across Africa and the adjacent Indian Ocean Islands, 286 of which were novel, were used to estimate: (i) the levels of genetic diversity using MEGA and the Sequence Demarcation Tool v1.2 (SDT); (ii) the times of occurrence and distribution of recombination using the recombination detection program (RDP v.4) and the genetic algorithm for recombination detection (GARD); (iii) selection pressure on codon positions using PARRIS and FUBAR methods implemented on the DATAMONKEY web server; (iv) reconstruct the history of spatio-temporal diffusion for MSV-A using the discrete phylogeographic models implemented in BEAST v1.8.1; (v) characterize source-sink dynamics and identify predictor variables driving MSV-A dispersal using the generalized linear models, again implemented in BEAST v1.8.1. Isolates used displayed low levels of genetic diversity (0.017 mean pairwise distance and ≥ 98% nucleotide sequence identities), and a well-structured geographical distribution where all of the 233 novel isolates clustered together with the -A1 strains. A total of 34 MSV inter-strain recombination events and 33 MSV-A intra-strain recombination events, 15 of which have not been reported in previous analyses (Owor et al., 2007, Varsani et al., 2008 and Monjane et al., 2011), were detected. The majority of intra-strain MSV-A recombination events detected were inferred to have occurred within the last six decades, the oldest and most conserved of these being events 19, 26 and 28 whereas the most recent events were 8, 16, 17, 21, 23, and 29. Intra-strain recombination events 20, 25 and 33, were widely distributed amongst East African MSV-A samples, whereas events 16, 21 and 23, occurred more frequently within West African MSV-A samples. Events 1, 4, 8, 10, 14, 17, 19, 22, 24, 25, 26, 28, and 29 were more widely distributed across East, West and Southern Africa and the adjacent Indian Ocean Islands. Whereas codon positions 12 and 19 within motif I in the coat protein transcript, and four out of the seven codon positions (147, 166, 195, 203, 242, 262, 267) in the Rep transcript (codons 195 and 203 in the Rb motif and codons 262 and 267 in site B of motif IV), evolved under strong positive selection pressure, those in the movement protein (MP) and RepA protein encoding genes evolved neutrally and under negative selection pressure respectively. Phylogeographic analyses revealed that MSV-A first emerged in Zimbabwe around 1938 (95% HPD 1904 - 1956), and its dispersal across Africa and the adjacent Indian Ocean Islands was achieved through approximately 34 migration events, 19 of which were statistically supported using Bayes factor (BF) tests. The higher than previously reported mean nucleotide substitution rate [9.922 × 10-4 (95% HPD 8.54 × 10-4 to 1.1317 × 10-3) substitutions per site per year)] for the full genome recombination-free MSV-A dataset H estimated was possibly a result of high nucleotide substitution rates being conserved among geminiviruses such as MSV as previously suggested. Persistence of MSV-A was highest in source locations that include Zimbabwe, followed by South Africa, Uganda, and Kenya. These locations were characterized by high average annual precipitation; moderately high average annual temperatures; high seasonal changes; high maize yield; high prevalence of undernourishment; low trade imports and exports; high GDP per capita; low vector control pesticide usage; high percentage forest land area; low percentage arable land; high population densities, and were in close proximity to sink locations. Dispersal of MSV-A was frequent between locations that received high average annual rainfall, had high percentage forest land area, occupied high latitudes and experienced similar climatic seasons, had high GDP per capita and had balanced maize import to export ratios, and were in close geographical proximity. / National Research Foundation (NRF), the Poliomyelitis Research Foundation (PRF), and the Thuthuka Board

Rhipicephalus microplus belongs to the Ixodidae, the largest family of ticks, which are of great economic importance due to their negative socio-economic impact on agriculture (BROUQUI 2011; PORTO NETOA et al. 2011; SONENSHINE 1991). Acaricides have been the first choice in tick control for cattle farmers, but R. microplus rapidly acquires resistance to these chemicals. Replication slippage and recombination drive genetic diversity in tick populations (BAFFI et al. 2007; GUERRERO et al. 2007; LI et al. 2007); generating point mutations and frame shifts within the genes targeted by acaricides, resulting in resistance (BAFFI et al. 2007; HERNANDEZ et al. 2002; HERNANDEZ et al. 2000; JONSSON et al. 2010; MORGAN et al. 2009). In addition, resistance can quickly accumulate in a population due to the pangamy mating structure of ticks (CHEVILLON et al. 2007b; CUTULLÉ et al. 2010) and their ability to produce multiple generations within one season (BUDELI et al. 2009; LI et al. 2007). Vaccines have become increasingly important to control ticks, as acaricide resistance can be acquired by field tick populations within two years (RODRIGUEZ-VIVAS et al. 2011). Although Bm86 has been successful against multiple-acaricide resistant ticks, recent reports indicate that the Bm86 vaccine has become ineffective, possibly due to resistance (PARIZI et al. 2009). Also, Bm86 vaccines display great variability in terms of their efficacy against ticks isolated across Argentina (GARCIA-GARCIA et al. 2000; PARIZI et al. 2009). This is hypothesised to be due to the genetic variability between R. micoplus populations. The majority of phylogenetic studies on ticks have been based on slow evolving sequences, such as 18S or 28S rRNA, which provide genus-level resolution. The COI, D3, ANT and ITS2 genes have the potential to resolve intra-specific and interspecies variation, and may assist with the identification of cryptic speciation within R. microplus of South Africa (ANSTEAD et al. 2011; BARKER 1998; CAREW et al. 2009; MURRELL et al. 2000; SONGA et al. 2011). Phylogeography is a multidisciplinary field that utilises phylogenetic (molecular evidence of speciation) and population genetic principles (coalescence theory), in combination with additional data (such as geography and population history), to determine the genetic relationships of populations within a species (AVISE 2009) and was one of the main aspects of this study. The phylogenetic and population genetic structure of R. microplus will provide valuable information to geneticists, farmers and acaricide/vaccine suppliers about the different R. microplus tick populations of South Africa. The information will facilitate more efficient and targeted tick control whether acaricide or vaccine based as opposed to the inefficient approaches generally adopted to tick control. / Dissertation (MSc)--University of Pretoria, 2014. / lk2014 / Genetics / MSc / Unrestricted

The present thesis concerns the population history, evolutionary processes and phylogenetic relationships of lineages of the redfin minnow genus Pseudobarbus. First, the population history and evolutionary processes within P. quathlambae were determined, mainly to decide the conservation value of the Mohale population. The Mohale dam threatens its survival. A divergence in mitochondrial control region and cytochrome b sequences and frequency differences in the distribution of major histocompatibility alleles were found between the Mohale population and an “Eastern” lineage. The Mohale population has therefore been historically isolated and was deemed indispensable for the conservation of P. quathlambae. Differentiation among populations of the P. afer and P. phlegethon complex were investigated, in relation to geological and climatic processes. Sea levels were about – 130 m below present levels during the last glacial maximum, about 18 000 years ago. Five historically isolated lineages were identified through analysis of mitochondrial control region sequences. The four P. afer lineages showed a strong association with proposed palaeoriver systems. A “Forest” lineage, however, reaches across two proposed palaeoriver systems. Surprisingly, this lineage is closely related to P. phlegethon. Pseudobarbus asper and P. tenuis were analysed together, because of their close phylogenetic relationship and because they occur in sympatry in the Gourits River system. Pseudobarbus tenuis showed divergence in mitochondrial control region only between the Keurbooms and Bitou River systems compared to the Gourits River system. Within P. asper, divergence was low, suggesting recent inland exchange opportunities between populations of the Gourits and Gamtoos River systems. River capture of south-eastern tributaries of the Gourits River system by the Keurbooms River would have resulted in unidirectional colonization, suggesting that speciation between P. asper and P. tenuis occurred within the Gourits River system with or without the Gamtoos River system being involved. Lower sea levels during the last glacial maximum also played an important role in the population history of P. burchelli. Differentiation in P. burchelli did not occur between two proposed palaeoriver systems, but rather within a western palaeoriver system. Divergence in mitochondrial control region and cytochrome b sequences showed that the “Breede” and “Tradou” lineages diverged within the Breede River system, before the “Heuningnes” lineage became isolated in the Heuningnes River system. Fifteen historically isolated Pseudobarbus lineages were included in a phylogenetic analysis on which biogeographic hypotheses were based. Phylogenetic relationships based on mitochondrial control region, cytochrome b and 16S and a combined dataset of all these were compared to relationships recovered from a previous morphological dataset. Conflicts between the molecular and morphological analyses, suggests that several morphological characters evolved in a complex manner. The molecular phylogenies suggest that the earliest divergence in the Pseudobarbus was between P. quathlambae in the Orange River system and the other species that occur in the Cape Foristic Region. Pseudobarbus lineages with two pairs of barbels and those with a single pair of barbels (excluding P. quathlambae) grouped together. In terms of currently described species, only the two lineages of P. quathlambae and the three lineages of P. burchelli were clearly monophyletic. Copyright / Thesis (PhD (Genetics))--University of Pretoria, 2007. / Genetics / unrestricted