Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Habitat fragmentation through the loss and modification of natural ecosystems poses a serious threat to biodiversity globally. Mechanisms and ecological implications of fragmentation have been extensively studied, yet new and meaningful insights continue to be produced. The highly diverse and ecologically complex fynbos shrubland communities that occur in the Cape Floristic Region of South Africa are amongst the most threatened by habitat fragmentation by urban, agricultural and silvicultural land uses and to the spread of invasive alien plants. Fynbos vegetation communities are fire-adapted and exploit the post-fire regeneration niche. Natural stochasticity in the fire regime means that these communities are temporally unstable; a factor that allows for the coexistence of such extreme diversity. Few studies have attempted to assess the influence of habitat fragmentation on this stochasticity, or to investigate the response of biological communities to the conditions that result. It is unknown whether this temporal instability will lead to delayed extinctions in fragmented communities, thus generating extinction debt. South Outeniqua Sandstone Fynbos occurs as a unique landscape mosaic of both insular and extensive habitats, suited to study through an island biogeography framework. Vegetation community stability was assessed through the comparison of historic and recent data sets. The responses of local vegetation and avifaunal communities to habitat fragmentation were assessed and compared on the basis of their differing motility. The unique habitat configurations also allowed for the investigation of extinction debt in the local communities and provided an opportunity to assess the influence of the surrounding matrix on species persistence and on connectivity in the artificial fragments. Data were analysed through simple regression analyses, modified Chi-squared tests and through ordination analyses. Ultimately the value of the artificial habitat fragments for the conservation of biological communities was assessed. Stability was observed in the vegetation species-area relationship for the natural islands and the mainland sites over twenty-two years. Smaller islands were found to receive fewer fires than large islands and the mainland. This consistently over-extended fire-return interval reduces the stochasticity of the local fire regime causing stable yet depauperate vegetation communities to result. Vegetation communities in the artificial fragments were found to hold area-related extinction debt, possibly due to the relatively long-term demographic turnover that typically occurs in fynbos. Avifaunal communities varied in their response to fragmentation relative to the vegetation. Birds – being motile – were found to be unaffected by isolation distance or surrounding matrix type – their response due more to changes experienced in the vegetation community than to geographic constraints. Fynbos-typical birds responded to the post-fire age of vegetation. Frugivorous birds and the matrix-habitat edge were identified as sources of alien and non-fynbos plant species that colonise the artificial fragments, potentially reducing the quality of these habitats for avifauna. Fragmented communities of South Outeniqua Sandstone Fynbos have the potential to function as biological reserves. This potential can be realised through the implementation of a fire regime that acknowledges the stochasticity required by the vegetation, the frequency required by the vegetation and the avifauna, and the practicality required by surrounding anthropogenic land-uses. / AFRIKAANSE OPSOMMING: Habitat-fragmentering, deur die verlies en verandering van natuurlike ekosisteme, hou 'n ernstige bedreiging in vir biodiversiteit wêreldwyd. Meganismes en ekologiese implikasies van die fragmentering is al breedvoerig bestudeer, maar nuwe en betekenisvolle insigte word voortaan vervaardig. Die hoogs diverse en ekologies komplekse fynbos-struikveld gemeenskappe wat in die Kaapse Floristiese Streek van Suid-Afrika voorkom, word meeste bedreig deur habitat-fragmentering deur verstedeliking, landbou en houtteeltkundige grondgebruike en die verspreiding van indringerplante. Fynbos gemeenskappe is aangepas tot vuur en die uitbuiting van post- vuur herlewing nis. Natuurlike stogastisiteit in die vuur-bedeling beteken dat hierdie gemeenskappe tydelik onstabiel word, 'n faktor wat die mede-bestaan van uiterste diversiteit moontlik maak. Min studies het al die invloed van habitat-fragmentering op hierdie stogastisiteit ondersoek, of die reaksie van biologiese-gemeenskappe tot die voortspruitende omstandighede. Dit is onbekend of die tydelike onstabiliteit sal lei tot vertraagde uitsterwing in gefragmenteerde gemeenskappe, dus genereer uitsterwings-skuld. Suid Outeniqua Sandsteen Fynbos kom as 'n unieke landskap mosaïek van beide die eilande en uitgebreide habitatte voor, geskik om deur 'n eiland biogeografie raamwerk bestudeer te word. Plant-gemeenskappe se stabiliteit is bestudeer deur die vergelyking van historiese en onlangse data stelle. Die reaksies van die plaaslike plantegroei en voëllewe gemeenskappe tot hul habitat is bestudeer en vergelyk op grond van hul verskillende beweeglikheid. Die unieke habitat konfigurasies het ook toegelaat vir die ondersoek van uitsterwings-skuld in die plaaslike gemeenskappe en 'n geleentheid gebied om die invloed van die omliggende habitat-matriks op spesies volharding en op konneksie in die kunsmatige fragmente te bepaal. Die data is ontleed deur middel van eenvoudige regressie analises, aangepasde Chi -kwadraat toetse en deur koördinerings ontledings. Ten einde die waarde van die kunsmatige habitat fragmente vir die bewaring van biologiese gemeenskappe te bepaal. Stabiliteit in die plantspesies-area verhouding vir die natuurlike eilande en die vasteland van webwerwe oor twee en twintig jaar was waargeneem. Kleiner eilande het minder brande aangeneem as groot eilande en die vasteland. Hierdie herhaalde oor-uitbrei over-extended vuur-interval het die stogastisiteit verminder van die plaaslike vuur-bedeling wat stabiele tog spesie-arme plantegroei gemeenskappe veroorsaak het. Plantegroei gemeenskappe in die kunsmatige fragmente is bevind om spesie- area -verhouding uitsterwings-skuld te bevat, moontlik as gevolg van die relatiewe lang termyn demografiese omset wat tipies voorkom in fynbos. Voëllewe gemeenskappe het gewissel in hul reaksie tot die fragmentering relatief tot die plantegroei. Voëls – weens hul beweeglikheid – blyk om nie beinvloed te word deur isolasie afstand of omliggende habitat-matriks tipe nie - hul reaksie blyk meer asgevolg van veranderinge wat ervaar word in die plantegroei gemeenskap as geografiese beperkinge. Fynbos-tipiese voëls reageer op die post- vuur ouderdom van plantegroei. Vrugte-etende voëls en die habitat-matriks rand is geïdentifiseer as bronne van uitheemse en nie-fynbos plantspesies wat die kunsmatige fragmente koloniseer, wat potensieel die kwaliteit van hierdie habitatte vir voëls verminder. Gefragmenteerde gemeenskappe van Suid Outeniqua Sandsteen Fynbos het die potensiaal om as biologiese reserwes te funksioneer. Hierdie potensiaal kan verwesenlik word deur die implementering van 'n vuur-bedeling wat erkenning verleen aan die stogastiesiteit vereis deur die plantegroei, die frekwensie wat deur die plantegroei en die voëllewe vereis word , en die praktiese vereistes van die omliggende menslike grondgebruike.

No description available.

No description available.

Two molecular phylogenetic studies were undertaken to examine relationships within Myricaceae. Analyses of DNA sequences of the plastid rbcL gene, trnL-Fregion and nuclear ITS region showed the family to be monophyletic. In all analyses Canacomyrica, a monotypic genus endemic to New Caledonian that bears several distinctive features such as staminodes in the female flowers, fell into a well- supported clade sister to the rest of Myricaceae. Phylogenetic analyses of ITS and trnL-F sequence data, representing all genera and subgeneric groups, were undertaken using maximum parsimony and Bayesian methods. The following relationships were strongly supported: (Canacomyrica (Comptonia (Myrica, Morella))). The clade containing all species formerly considered to comprise Myrica s.l. was split into two strongly supported clades corresponding to Myrica s.s. and Morella; this finding strengthens the argument for recognition of these as separate genera. Within Morella, two clades corresponded to previously recognized subgenera. Molecular dating analyses were performed using Penalized Likelihood. Close correlations between lineage-specific diversification and major orogenic or climatic events were inferred. This study suggests that much of the diversity in Morella arose during the Neogene and seed-dispersal by birds has been a significant factor in determining the modem distribution. A study of the conservation status of Canacomyrica was conducted using field observations and data from herbarium specimens. This species was found to occur in just eleven fragmented localities: six outside protected areas and three threatened by mining or bush fires. IUCN Red List status of Endangered was recommended. The morphology and ecology of Canacomyrica was studied to enhance knowledge of this poorly known species and provide comparative data for use in a study of the morphology of the entire family. A new classification scheme with keys was presented including, for the first time, Canacomyrica. New combinations in Morella were recommended.

O nosso conhecimento sobre a distribuição das espécies vem avançando desde as primeiras observações feitas séculos atrás. Recentemente uma melhoria nos métodos e na cobertura geográfica das amostragens tem melhorado significativamente nosso conhecimento sobre padrões de distribuição. O que tem permito diversos tipos de análises, revelando padrões macroecológicos com os observados aqui onde riqueza de répteis e anfíbios apresenta uma forte relação com o ambiente, sendo maiores em aras mais baixas, com temperatura e precipitação estáveis e maior estrutura no ambiente, enquanto que para endemismo e diversidade beta a relação é mais fraca. Porém este conhecimento sobre a distribuição das espécies não está homogeneamente distribuído por todas as regiões, sendo especialmente baixo na região Amazônica, que é justamente a região que abriga a maior riqueza local de espécies, estando concentrado ao longo das margens dos rios. Isto que pode indicar que os valores que temos disponíveis ainda são subestimados, e que quaisquer inferências sobre estes valores devem ser interpretados com cautela / Our knowledge on species distribution has advanced since the first observations made centuries ago. Recently the improvement on techniques and geographical coverage of samplings activities has improved significantly our knowledge on distribution patterns. This advance has allowed several analyses to be done, and macroecological patterns to emerge, such as the one observed ibn here with reptile and amphibian richness presenting a strong relationship with environmental conditions, with higher values at lower areas, with more stable precipitation and temperature, an higher environmental structure, while endemism and beta diversity have a weaker signal. However the knowledge on species distribution is not homogeneously distributed across all regions, being especially low at the Amazon, which is precisely the area that harbors the highest richness values, being concentrated at the rivers\' shores, suggesting that the values we have today may be far underestimated, and thus any inference using them should be interpreted with caution

O gênero Myotis é extremamente diverso, sendo atualmente reconhecidas 103 espécies, além de 94 subespécies as quais não foram avaliadas satisfatoriamente quanto seu status taxonômico. Para a América do Sul são reconhecidas 12 espécies, das quais cinco são consideradas politípicas, dentre elas Myotis nigricans, táxon considerado um complexo de espécies. Com o objetivo de caracterizar, morfologicamente e molecularmente, os táxons do gênero Myotis que ocorrem no Brasil e aqueles relacionados a Myotis nigricans, examinei 1.018 exemplares depositados em coleções científicas nacionais e internacionais. Analisei 25 caracteres de morfologia externa e craniana, e aferi 13 medidas corporais e 19 cranianas. Submeti as medidas cranianas a testes estatísticos uni e multivariados com o intuito de investigar variações inter e intraespecíficas, e verificar a existência de dimorfismo sexual em cada táxon analisado. Selecionei um gene mitocondrial, citocromo b (402pb), e um gene nuclear, RAG2 (620pb), com a finalidade de caracterizar a diversidade genética intra e interespecífica dos táxons de Myotis, dos quais obtive 78 seqüências: 58 mitocondriais e 20 nucleares. A partir deste conjunto de dados reconheci 8 espécies válidas para o gênero Myotis no Brasil (Myotis albescens, Myotis alter, Myotis levis, Myotis nigricans, Myotis riparius, Myotis ruber, Myotis simus, e Myotis sp.n.). Elevei Myotis osculati ao nível específico, táxon até então considerado uma subespécie de Myotis nigricans; e considerei Myotis punensis e Myotis chiriquensis espécies válidas, as quais eram consideradas sinonímias de Myotis nigricans nigricans. Neste contexto, reconheço 15 espécies sul-americanas do gênero Myotis, o que representa um acréscimo de 25% na diversidade anteriormente reconhecida para o grupo na região. Não encontrei dimorfismo sexual significativo nas medidas cranianas de M. albescens, M. levis, M. nigricans, M. riparius e M. ruber. Para melhor delimitar morfometricamente os táxons estudados, em especial M. nigricans de M. riparius, propus a utilização de dois índices: um craniano e outro maxilar. Os caracteres qualitativos cranianos, como a presença de crista sagital e o posicionamento dos pré-molares superiores, associados aos de morfologia externa, como a disposição de pêlos ao longo do uropatágio, o formato do pavilhão auditivo, e a angularidade da porção distal da maxila inferior, apresentaram-se como os mais robustos na delimitação dos táxons com ocorrência no Brasil. As relações filogenéticas entre as espécies de Myotis após inclusão dos táxons validados neste trabalho, ainda permanecem imprecisas. Através dos métodos de Máxima Parcimônia (MP), de distância de Neighbor-Join (NJ) e análise Bayesiana (B), houve o resgate de dois grandes clados compostos por espécies com crista sagital ausente ou discreta (clado A), e crista sagital presente (clado B). Atribuí a politomia encontrada dentro do clado A à rápida diversificação do grupo na região, com possíveis eventos simultâneos de especiação. Associo a inclusão de M. levis no clado de M nigricans com um evento de introgressão mitocondrial dado a natureza do gene, e ao número de mutações, incompatível com homoplasia do gene. O tempo de divergência estimado em 1,2Ma (±0,8), coincide com os eventos de mudanças climáticas e de retração de florestas durante o Pleistoceno, que propiciariam a hibridização destas duas linhagens. Apliquei o Teste de Mantel nas populações de M. nigricans e M. riparius presente nos domínios da Mata Atlântica, com o intuito de verificar a existência de correlação entre distância genética e distância geográfica entre as populações, testando a hipótese de isolamento por distância, a qual foi rejeitada tanto para M. nigricans (p=0,9449; r=0,23) como para M. riparius (p=0,9997; r=0,60). As populações de Myotis riparius apresentaram uma baixa divergência genética (0,8 a 1,5%) ao longo da distribuição, com compartilhamento de haplótipos entre as populações de Paraíba, São Paulo, Paraná e Paraguai. Em relação à Myotis nigricans destaco o compartilhamento de haplótipos entre as populações da Bahia, São Paulo e Paraná, e a baixa divergência (1,9 a 2,4%) entre as populações ao leste da Serra do Mar. Contudo, os níveis de divergência entre estas populações e as populações provenientes da Serra do Japi e Serra da Mantiqueira são acentuados (5,7 a 8,1%), similares aos níveis interespecíficos para o gênero. Estes dados sugerem um alto fluxo gênico no sentido Norte-Sul da Mata Atlântica ao leste da Serra do Mar, podendo esta atuar como barreira para as populações interioranas. A compreensão dos processos envolvidos na diversificação do grupo será favorecida com a inclusão a estas análises de amostras provenientes de outras populações distribuídas nas porções Leste Oeste da Mata Atlântica. / Myotis is a highly diverse genus, with 103 species recognized so far, in addition to another 94 subspecies whose taxonomical status has not yet been completely evaluated. Twelve species are known to South America, among which five are considered polytypic, including Myotis nigricans. This taxon in considered a species complex. In order to characterize, both morphologically and molecularly, the taxa of the genus Myotis, I examined 1,018 individuals from national and foreign scientific collections. Twenty-five characters from external and cranial morphology were analyzed and 13 body and 19 cranial measures were checked. In order to investigate inter and intraspecific variations and the existence of sexual dimorphism in each taxon analyzed, I submitted the cranial measures to uni and multivariate statistic tests. To characterize intra and interspecific genetic diversity of the taxa in the genus Myotis, I selected one mitochondrial gene, cytochrome b (402pb), and a nuclear gene, RAG2 (602pb). From these two genes, I obtained 78 sequences: 58 mitochondrial and 20 nuclear. From the data obtained, I recognized as valid eight Brazilian species in the genus Myotis (Myotis albescens, Myotis alter, Myotis levis, Myotis nigricans, Myotis riparius, Myotis ruber, Myotis simus, and Myotis sp.n.). I elevated Myotis osculati, a taxon hitherto considered a subspecies of Myotis nigricans, to specific level and diagnosed Myotis punensis and Myotis chiriquensis as valid species, which were previously considered synonyms of Myotis nigricans nigricans. In this context, I recognize 15 species for the genus Myotis in South America, representing an increase of 25% in the previously known diversity for the group in the continent. I have not found significant sexual dimorphism in the cranial measures for M. albescens, M. levis, M. nigricans, M. riparius and M. ruber. To better delimitate morphometricaly the taxa herein studied, specially M. nigricans from M. riparius, I proposed the use of two indexes: one cranial and one maxillary. Qualitative characters from skull, such as presence or absence of a sagittal crest and the arrangement of upper premolars, associated to those from external morphology, such as the arrangement of the hair along the uropatagium, the shape of external ear, and the angling from the distal portion of the lower maxillae, were fundamental for diagnosing the taxa occurring in Brazil. The phylogenetic relationship among the species of genus Myotis is still imprecise, even after the inclusion of those taxa diagnosed as valid in this thesis. Through Maximum Likelihood (ML), Neighbor-Join (NJ) and Bayesian analysis methods, two clades were defined, one formed by species with absent or shallow sagittal crest (clade A), and another (clade B) with the presence of sagittal crest. I correlate the polytomy found within clade A with a fast diversification of this group in the region, possibly with simultaneous events of speciation. I correlate the inclusion of M. levis in the clade of M. nigricans with an event of mitochondrial introgression, given the nature of this gene and the number of mutations, which are not compatible with the homoplasy for this gene. The estimated divergence time of 1.2 Ma (±0.8), coincides with climatical changes and forest retraction during the Pleistocene, which allowed the hybridization of these two lineages. I ran the Test of Mantel for the populations of M. nigricans and M. riparius from the Atlantic Forest dominium, aiming at verifying the existence of a correlation between genetic distance and geographical distance in the populations, testing the hypothesis of isolation by distance, which was rejected both for M. nigricans (p=0.9449; r=0.23) and for M. riparius (p=0.9997; r=0.60). The populations of Myotis riparius showed a low genetic divergence (0.8 to 1.5%) along their distribution, with the populations from Paraíba, São Paulo, Paraná and Paraguay sharing haplotypes. Regarding Myotis nigricans, I point out that populations from Bahia, São Paulo and Paraná share haplotypes and low divergence (1.9 to 2.4%) between the populations from the western portion of Serra do Mar. Yet, the level of divergence between such populations and those from Serra do Japi and Serra da Mantiqueira is high (5.7 to 8.1%), therefore similar to the interspecific levels for the genus. These data suggest a high gene flow from the North-South direction to eastern Serra do Mar, which may be acting as a barrier to interior populations. The understanding of the processes involved in the diversification of the group will be favored by the inclusion of samples of other populations distributed in the East-West portions of the Atlantic Forest.

A Amazônia abriga uma grande parcela da biodiversidade mundial, no entanto, existem grandes incertezas sobre os processos de geração e manutenção dessa enorme diversidade, com várias hipóteses propostas até o momento. Diversas características como tamanho pequeno, baixa capacidade de dispersão e fidelidade ao ambiente estritamente florestal fazem de lagartos do gênero Loxopholis (Squamata: Gymnophthalmidae) candidatos ideais para rastrear a história de modificações da paisagem no norte da América do Sul durante o Neogeno. Nesta tese, revisamos a variação morfológica, taxonomia e a distribuição geográfica das espécies do gênero Loxopholis, assim como estimamos as relações filogenéticas e o tempo de divergência entre as espécies com base em sequências de DNA provenientes do genoma mitocondrial e nuclear. Com essa base de dados, construímos um modelo de como ocorreu a história evolutiva de Loxopholis, discutindo os resultados a partir de reconstruções geológicas provenientes da literatura, e fornecendo uma datação independente para eventos geológicos que potencialmente influenciaram a história evolutiva do gênero. Neste estudo, também revelamos que a atual diversidade descrita para Loxopholis está severamente subestimada. Encontramos que a espécie L. osvaldoi representa um complexo de espécies crípticas, contendo de 8 a 14 potenciais espécies novas, com profundas divergências genéticas tanto nos genomas mitocondrial e nuclear, praticamente dobrando a diversidade conhecida no gênero. No entanto, a morfologia em Loxopholis é extremamente conservada, dificultando a diagnose das espécies novas. Finalmente, descrevemos a primeira população bissexual da espécie partenogenética L. percarinatum, discutindo as implicações deste achado para o entendimento relativo a aparição da partenogênese em Loxopholis / The Amazon rainforest houses a significant portion of the world biodiversity, however, there is still a lot of uncertainty about the processes involved in its generation and maintenance, with several hypotheses proposed so far. Loxopholis lizards (Squamata: Gymnophthalmidae) are small-sized; show low vagility, and high fidelity to the humid forest environment, making them ideal to test hypotheses on the history of landscape modifications in Northern South America, during the Neogene. In this thesis, we revise the morphological variation, the taxonomy, and the geographic distribution of Loxopholis species, as well as estimated a phylogenetic hypothesis and divergence times for these species based on sequences from mitochondrial and nuclear DNA. With this dataset, we build a model for the evolutionary history of Loxopholis and compared the results with geologic reconstructions of the Amazon available in the literature, which provided independent time estimates for geological events that potentially affected the evolutionary history of genus. In this study, we also showed that the actual diversity described for Loxopholis was severely underestimated. We found that L. osvaldoi represents a complex of cryptic species with 8-14 potential new species, and strong divergences in both the mitochondrial and the nuclear genomes, virtually doubling the actual diversity in the genus. Finally, we describe the first bisexual population for the parthenogenetic species L. percarinatum, discussing its implications to the origin of parthenogenesis in the genus

Orientador: Ricardo Cardoso Benine / Coorientador: Claudio de Oliveira / Banca: Flávio César Thadeo de Lima / Banca: Cristiano Rangel Moreira / Resumo: Não disponível / Abstract: The subfamily Aphyocharacinae comprises the genera Aphyocharax, Prionobrama, Paragoniates, Phenagoniates, Leptagoniates, Xenagoniates, Rachoviscus, and Inpaichthys. This current arrangement based on a morphological analysis is congruent with most proposed morphological phylogenetic analyses, except for the inclusion of Rachoviscus and Inpaichthys which is tenuous and not always supported by data. In this current work the goal was to investigate the monophyly of the subfamily Aphyocharacinae and to recover relationships within it using molecular and morphological analyses. Using separate parsimony and Bayesian analyses of morphological, nuclear and mitochondrial genes, I recover new relationships within Aphyocharacinae. Independent analyses recovered similar topologies for molecular and morphologic datasets. Molecular based topologies showed common generic relationships: Aphyocharacinae, excluding the genus Rachoviscus and Inpaichthys, constitutes a monophyletic group. Moreover, Aphyocharacinae has two well-marked major branches. One composed by (Paragoniates (Phenagoniates (Leptagoniates+Xenagoniates))), while the other includes Aphyocharax and Prionobrama. Also, relationships among the genera were completely resolved and supported by strong statistical indexes. Based on molecular hypotheses, I had a specific monophyletic framework to conduct morphological analysis. This approach suggests that Aphyocharacidium sp. and Microschemobrycon cf. casiquiare are most probably the sister group of Aphyocharacinae. The morphological analysis conducted with 25 unweighted and unordered characters recovers one tree, resolved at generic-species level. A similar hypothesis found using molecular data is recovered with three well-marked... (Complete abstract click electronic access below) / Mestre

Mechanisms for the generation of biodiversity in species-rich biomes such as rain forests remain unclear. Molecular phylogenies using DNA sequence data, calibrated with a temporal dimension offer a means of addressing this question, enabling the testing of different hypotheses on biogeographic histories and causes of diversification. Manilkara is a genus of trees in the Sapotaceae consisting of ~79 species distributed throughout the tropics (30 South and Central American, 35 African and 14 Southeast Asian). This species diversity in all major tropical regions of the globe makes it an ideal candidate for in-depth biogeographic studies. Maximum parsimony and Bayesian analyses of nuclear (ITS) and chloroplast (rpl32-trnL, rps16-trnK and trnS-trnFM) sequences were used to reconstruct a species level phylogeny of Manilkara and related genera in the tribe Mimusopeae. Manilkara, as currently defined, is not monophyletic due to the placement of three Asian taxa (M. fasciculata, M. dissecta and M. udoido), which are more closely related to the Madagascan genera Labourdonnaisia and Faucherea than to Manilkara s.s. and need to be re-circumscribed in a new genus. Letestua is nested in Manilkara and the genera Faucherea and Labourdonnaisia are not monophyletic. Nuclear and chloroplast datasets were mostly congruent, however, three instances of hard incongruence were demonstrated, suggesting chloroplast capture events. Bayesian analyses of ITS sequences using a relaxed molecular clock calibrated with fossils, focused on testing biogeographical hypotheses on the origin of Manilkara’s pantropical disjunct distribution and spatio-temporal diversification patterns on each continent. Mimusopeae, originated during the Eocene ~46-57 Ma and fossil evidence supports its existence in the boreotopical region of the northern hemisphere during this time. This suggests that the tribe may have evolved there and found refuge in Africa when Oligocene climatic cooling made higher latitudes uninhabitable for megathermal taxa. The subtribe Manilkarinae was resolved as ~42-36 Myo. These ages fall on the Eocene-Oligocene boundary and the crown node age coincides with the onset of Oligocene cooling and the closing of the boreotropical route. The genus Manilkara is estimated to have evolved ~36-33 Ma. The current distribution of the genus could not, therefore, have been the result of Gondwanan vicariance or migration through the boreotropics, but results instead support long distance dispersal as an important factor influencing the distribution of the group. Resolution along the backbone of the phylogeny is weak and the area of origin is, therefore, difficult to determine. However, all sister taxa to Manilkara are African and this suggests that the most likely explanation is an African origin for the genus with subsequent inter-continental dispersal during the Miocene. Manilkara spread from Africa to the Neotropics and Asia via at least three separate long distance dispersal events. A single lineage dispersed to the Neotropics ~27-21 Ma and spread across the Isthmus of Panama before its closure. Another lineage dispersed to Southeast Asia ~30-25 Ma from mainland Africa and subsequently diversified throughout the region. A third dispersal from Madagascar to the Sahul Shelf, occurred ~31-16 Ma in the M. fasciculata/dissecta/udoido lineage. In South America, diversification is consistent with both aridification and the rearrangement of drainage patterns in the Amazon basin as a result of Andean orogeny. The Atlantic coastal forest clade and the Amazonian clade of Manilkara split from one another ~14 Ma, at approximately the same time as the dry biomes of the Cerrado and Caatinga were forming between them. In Africa diversification coincides with Tertiary cycles of aridification and uplift of the east African plateaux. In Southeast Asia Wallace’s Line did not affect the dispersal of Manilkara. Instead, the limiting factor was the appearance of land in New Guinea ~10 Ma, which coincides with the dispersal and establishment of new taxa east of Wallace’s Line. Spatio-temporal patterns of diversification in Manilkara were compared to those of 34 other wet tropical genera which have intercontinental disjunctions. Ages of disjunctions ranged from the Eocene to the Pliocene, indicating that compilation of the tropical rain forest biome is a dynamic process which has been occurring throughout the Tertiary. Recent migration via long distance dispersal is a significant phenomenon in biome construction. Geo-climatic events have also been shown to be important drivers of diversification in all continental regions.

A Amazônia abriga uma grande parcela da biodiversidade mundial, no entanto, existem grandes incertezas sobre os processos de geração e manutenção dessa enorme diversidade, com várias hipóteses propostas até o momento. Diversas características como tamanho pequeno, baixa capacidade de dispersão e fidelidade ao ambiente estritamente florestal fazem de lagartos do gênero Loxopholis (Squamata: Gymnophthalmidae) candidatos ideais para rastrear a história de modificações da paisagem no norte da América do Sul durante o Neogeno. Nesta tese, revisamos a variação morfológica, taxonomia e a distribuição geográfica das espécies do gênero Loxopholis, assim como estimamos as relações filogenéticas e o tempo de divergência entre as espécies com base em sequências de DNA provenientes do genoma mitocondrial e nuclear. Com essa base de dados, construímos um modelo de como ocorreu a história evolutiva de Loxopholis, discutindo os resultados a partir de reconstruções geológicas provenientes da literatura, e fornecendo uma datação independente para eventos geológicos que potencialmente influenciaram a história evolutiva do gênero. Neste estudo, também revelamos que a atual diversidade descrita para Loxopholis está severamente subestimada. Encontramos que a espécie L. osvaldoi representa um complexo de espécies crípticas, contendo de 8 a 14 potenciais espécies novas, com profundas divergências genéticas tanto nos genomas mitocondrial e nuclear, praticamente dobrando a diversidade conhecida no gênero. No entanto, a morfologia em Loxopholis é extremamente conservada, dificultando a diagnose das espécies novas. Finalmente, descrevemos a primeira população bissexual da espécie partenogenética L. percarinatum, discutindo as implicações deste achado para o entendimento relativo a aparição da partenogênese em Loxopholis / The Amazon rainforest houses a significant portion of the world biodiversity, however, there is still a lot of uncertainty about the processes involved in its generation and maintenance, with several hypotheses proposed so far. Loxopholis lizards (Squamata: Gymnophthalmidae) are small-sized; show low vagility, and high fidelity to the humid forest environment, making them ideal to test hypotheses on the history of landscape modifications in Northern South America, during the Neogene. In this thesis, we revise the morphological variation, the taxonomy, and the geographic distribution of Loxopholis species, as well as estimated a phylogenetic hypothesis and divergence times for these species based on sequences from mitochondrial and nuclear DNA. With this dataset, we build a model for the evolutionary history of Loxopholis and compared the results with geologic reconstructions of the Amazon available in the literature, which provided independent time estimates for geological events that potentially affected the evolutionary history of genus. In this study, we also showed that the actual diversity described for Loxopholis was severely underestimated. We found that L. osvaldoi represents a complex of cryptic species with 8-14 potential new species, and strong divergences in both the mitochondrial and the nuclear genomes, virtually doubling the actual diversity in the genus. Finally, we describe the first bisexual population for the parthenogenetic species L. percarinatum, discussing its implications to the origin of parthenogenesis in the genus