Submitted by Cecília Ártico Banho null (ce_artico@hotmail.com) on 2016-03-08T19:36:05Z No. of bitstreams: 1 Dissertação Cecilia.pdf: 1070495 bytes, checksum: 573c295e487d66626d45f19a66a72a3a (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-03-09T17:56:35Z (GMT) No. of bitstreams: 1 banho_ca_me_sjrp.pdf: 1070495 bytes, checksum: 573c295e487d66626d45f19a66a72a3a (MD5) / Made available in DSpace on 2016-03-09T17:56:35Z (GMT). No. of bitstreams: 1 banho_ca_me_sjrp.pdf: 1070495 bytes, checksum: 573c295e487d66626d45f19a66a72a3a (MD5) Previous issue date: 2016-03-02 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Pentatomomorpha é composta por cerca de 14.000 espécies, distribuídas em seis superfamílias, entre as quais estão inclusas Pentatomoidea e Coreoidea. Pentatomoidea possui 7.000 espécies distribuídas em 15 famílias, das quais Pentatomidae é a maior, com 4.500 espécies e 760 gêneros, estando representados no Estado de São Paulo 163 espécies. A superfamília Coreoidea é composta por cinco famílias, contudo apenas Coreidae, Rophalidae e Alydidae estão presentes no Neotrópico. A família Coreidae possui 1.884 espécies, divididas em quatro subfamílias, das quais Coreinae tem oito tribos com representantes no Brasil. Embora as famílias Pentatomidae e Coreidae apresentem um significante papel como pragas de culturas agrícolas, são escassas análises cladísticas envolvendo esses táxons, o que resulta na ausência de uma única hipótese de classificação, tornando pesquisas com abordagens de sistemática filogenética necessárias para essas famílias. Portanto, o presente estudo buscou caracterizar as relações filogenéticas das famílias Pentatomidae e suas subfamílias por meio dos genes 16S, ND5 (mitocondriais), 18S e 28S (nucleares) e da família Coreidae e sua respectiva subfamília Coreinae por meio dos genes 18S e 28S. Objetivou-se também, confirmar a classificação atual das tribos e subfamílias das espécies de Pentatomidae e Coreidae, que é embasada em caracteres morfológicos, assim como avaliar a variabilidade genética das sequências correspondentes aos genes mitocondriais e nucleares analisados. A partir dos resultados foi observado que os genes nucleares são conservados ao passo que os mitocondriais são altamente variáveis e com tendência as bases AT. Este estudo evidenciou que os genes nucleares 18S e 28S não são ideais para resoluções filogenéticas em nível de famílias, subfamílias e tribos de Coreidae e Pentatomidae, visto que os suportes dos ramos não permitem que haja confiabilidade nas análises. Além disso, alguns grupos que são considerados monofiléticos, com base em caracteres morfológicos, como as subfamílias de Pentatomidae, não tiveram sua monofilia resgatada. Contudo ao considerar as topologias obtidas com os genes nucleares aliados aos mitocondriais, para a família Pentatomidae, obteve-se alto suporte nos ramos, e, portanto, grande confiabilidade nas análises, resgatando a monofilia da maioria das tribos estudadas. Dessa forma, estudos utilizando diferentes marcadores moleculares, em especial, genes mitocondriais, são necessários, pois podem auxiliar no esclarecimento e suporte da classificação atual das relações intrafamiliares de Pentatomidae e Coreidae que permanecem pendentes. / Pentatomomorpha consists about 14.000 species distributed in six superfamilies, to which Pentatomoidea and Coreoidea are included. Pentatomidae has 7000 species in 15 families, of which Pentatomidae is the largest, with 4500 species and 760 genera, although in the state of São Paulo only 163 species are present. The Coreoidae superfamily consists of five families, however only Coreidae, Rophalidae and Alydidae are present in the Neotropics. The Coreidae family has 1884 species, divided into four subfamilies, of which Coreinae has eight tribes with representatives in Brazil. Although Pentatomidae and Coreidae families have a significant role as pests of agricultural crops, the cladistic analysis involving these taxa are scarce, which results in the absence of a single hypothesis classification, making research on phylogenetic systematic approaches necessary for these families. Therefore, this study aimed to characterize the phylogenetic relationships of Pentatomidae families and subfamilies through the 16S, ND5, 18S and 28S genes and Coreidae family and their respective Coreinae subfamily through the 18S and 28S genes. We aimed also to confirm the current classification of tribes and subfamilies of Pentatomidae and Coreidae, which is grounded on morphological characters, as well as to evaluate the genetic variability of the sequences corresponding to the mitochondrial and nuclear genes analyzed. From the results it was observed that the nuclear genes are conserved while the mitochondrial are highly variable and tend to AT base. Our study showed that nuclear genes 18S and 28S are not ideal for phylogenetic resolution at the level of families, subfamilies and tribes of Coreidae and Pentatomidae, because the supports of the branches do not allow that there is confiability in the analysis. Furthermore, groups considered monophyletic, based on morphological characteristics, such as Pentatomidae subfamilies, have not had their monophyly rescued. But when we consider the topologies obtained with nuclear genes combined with mitochondrial genes for the Pentatomidae family, we had high support in the branches, and thus high confiability in the analysis, rescuing the monophyly of most of the studied tribes. Thus, studies using different molecular markers, in particular mitochondrial genes are needed, because they can help in understanding and support of the current classification of intra-family relations Pentatomidae and Coreidae that remain pending.

Pesquisas envolvendo a sistemática e a taxonomia de camarões de água doce do gênero Macrobrachium Bate, 1868 ainda são pouco elucidativas para alguns de seus membros. Este é o caso de Macrobrachium olfersii (Wiegmann, 1836) que ocorre desde o sudeste dos Estados Unidos até o sul do Brasil e é comumente confundido com espécies que ocorrem preferencialmente na América Central (M. faustinum (de Saussure, 1857), M. digueti (Bouvier, 1895), M. crenulatum Holthuis, 1950, M. hancocki Holthuis, 1950 e M. acanthochirus Villalobos, 1967). Em 1969 estas espécies foram designadas por Villalobos como complexo de espécies por compartilharem características morfológicas, principalmente quanto ao segundo par de pereópodos. Outras citações afirmaram esta forte afinidade, colocando algumas espécies em sinonímia. Diante deste problema, realizou-se uma revisão taxonômica e utilizaram-se dados moleculares para verificar a validade destas espécies e explorar as relações evolutivas entre elas. As hipóteses filogenéticas foram baseadas em sequências parciais dos genes 16S rDNA, COI mtDNA, H3 e 18S nDNA por meio de análise de Máxima Verossimilhança e Inferência Bayesiana. Embora detalhada a redescrição das espécies, ressaltando as diferenças entre elas, as análises morfológicas não foram suficientes para inferir a filogenia desse grupo, devido a presença de caracteres plásticos e variáveis entre indivíduos da mesma espécie e outros conservados interespecificamente no gênero. Porém, todas as identidades foram suportadas com a análise molecular complementar baseada nos quatros marcadores, rejeitando a existência de sinonímias. Foi demonstrado através da análise baseada no gene 16S rDNA que estas espécies são evolutivamente relacionadas com M. zariqueyi Holthuis, 1949, da costa oeste da África, como compartilham características morfologicas, acredita-se que ela deva pertencer ao complexo M. olfersii, porém há a necessidade de verificar a taxonomia, analisar a morfologia e investigar outras sequências desta espécie. Os genes COI mtDNA e 16S rDNA apresentaram um amplo sinal filogenético permitindo uma boa resolução dos dendrogramas e H3 e 18S nDNA mostraram a recente divergência entre algumas espécies do grupo. / Studies on systematic and taxonomy of freshwater shrimp of the genus Macrobrachium Bate, 1868 are still unclear for some of its members, such as Macrobrachium olfersii Wiegmann, 1836). This species occurs from the southeastern United States to southern Brazil and is commonly mistaken with species that occur mainly in Central America (M. faustinum (de Saussure, 1857), M. digueti (Bouvier, 1895), M. crenulatum Holthuis, 1950, M. hancocki Holthuis, 1950 e M. acanthochirus Villalobos, 1967). In 1969 these species have been designated as a species-complex by Villalobos, because they share morphological characteristics, particularly in the second pair of pereiopod. This strong affinity and proposed some synonyms species is pointed by other authors. Faced with this problem, the validity of these species and the evolutionary relationships between them were verified by a wide taxonomic and molecular data. The phylogenetic hypotheses were based on partial sequences of 16S rDNA, COI mtDNA, 18S and H3 nDNA using analysis of Maximum Likelihood and Inference Bayesian. The diagnoses of the species were detailed, highlighting the differences between them. Nevertheless the morphological analysis were not enough to infer the phylogeny of this group because of the presence of plastic and variables characters among individuals of the same species and other preserved characters among different species of the genus. However, all identities were supported with additional molecular analysis based on four markers, rejecting the existence of synonymy. These species are evolutionarily related to M. zariqueyi Holthuis, 1949, from the west coast of Africa and share morphological character. The latter species could also belong to the M. olfersii complex because has philogenetic closeness, but before this afirmation it may be verified by morphological and molecular analysis. The mitochondrial genes (COI and 16S) showed a broad phylogenetic signal allowing a good resolution of the dendrograms. The nuclear genes (H3 and 18S) showed the recent divergence between some members of the group.

Pesquisas envolvendo a sistemática e a taxonomia de camarões de água doce do gênero Macrobrachium Bate, 1868 ainda são pouco elucidativas para alguns de seus membros. Este é o caso de Macrobrachium olfersii (Wiegmann, 1836) que ocorre desde o sudeste dos Estados Unidos até o sul do Brasil e é comumente confundido com espécies que ocorrem preferencialmente na América Central (M. faustinum (de Saussure, 1857), M. digueti (Bouvier, 1895), M. crenulatum Holthuis, 1950, M. hancocki Holthuis, 1950 e M. acanthochirus Villalobos, 1967). Em 1969 estas espécies foram designadas por Villalobos como complexo de espécies por compartilharem características morfológicas, principalmente quanto ao segundo par de pereópodos. Outras citações afirmaram esta forte afinidade, colocando algumas espécies em sinonímia. Diante deste problema, realizou-se uma revisão taxonômica e utilizaram-se dados moleculares para verificar a validade destas espécies e explorar as relações evolutivas entre elas. As hipóteses filogenéticas foram baseadas em sequências parciais dos genes 16S rDNA, COI mtDNA, H3 e 18S nDNA por meio de análise de Máxima Verossimilhança e Inferência Bayesiana. Embora detalhada a redescrição das espécies, ressaltando as diferenças entre elas, as análises morfológicas não foram suficientes para inferir a filogenia desse grupo, devido a presença de caracteres plásticos e variáveis entre indivíduos da mesma espécie e outros conservados interespecificamente no gênero. Porém, todas as identidades foram suportadas com a análise molecular complementar baseada nos quatros marcadores, rejeitando a existência de sinonímias. Foi demonstrado através da análise baseada no gene 16S rDNA que estas espécies são evolutivamente relacionadas com M. zariqueyi Holthuis, 1949, da costa oeste da África, como compartilham características morfologicas, acredita-se que ela deva pertencer ao complexo M. olfersii, porém há a necessidade de verificar a taxonomia, analisar a morfologia e investigar outras sequências desta espécie. Os genes COI mtDNA e 16S rDNA apresentaram um amplo sinal filogenético permitindo uma boa resolução dos dendrogramas e H3 e 18S nDNA mostraram a recente divergência entre algumas espécies do grupo. / Studies on systematic and taxonomy of freshwater shrimp of the genus Macrobrachium Bate, 1868 are still unclear for some of its members, such as Macrobrachium olfersii Wiegmann, 1836). This species occurs from the southeastern United States to southern Brazil and is commonly mistaken with species that occur mainly in Central America (M. faustinum (de Saussure, 1857), M. digueti (Bouvier, 1895), M. crenulatum Holthuis, 1950, M. hancocki Holthuis, 1950 e M. acanthochirus Villalobos, 1967). In 1969 these species have been designated as a species-complex by Villalobos, because they share morphological characteristics, particularly in the second pair of pereiopod. This strong affinity and proposed some synonyms species is pointed by other authors. Faced with this problem, the validity of these species and the evolutionary relationships between them were verified by a wide taxonomic and molecular data. The phylogenetic hypotheses were based on partial sequences of 16S rDNA, COI mtDNA, 18S and H3 nDNA using analysis of Maximum Likelihood and Inference Bayesian. The diagnoses of the species were detailed, highlighting the differences between them. Nevertheless the morphological analysis were not enough to infer the phylogeny of this group because of the presence of plastic and variables characters among individuals of the same species and other preserved characters among different species of the genus. However, all identities were supported with additional molecular analysis based on four markers, rejecting the existence of synonymy. These species are evolutionarily related to M. zariqueyi Holthuis, 1949, from the west coast of Africa and share morphological character. The latter species could also belong to the M. olfersii complex because has philogenetic closeness, but before this afirmation it may be verified by morphological and molecular analysis. The mitochondrial genes (COI and 16S) showed a broad phylogenetic signal allowing a good resolution of the dendrograms. The nuclear genes (H3 and 18S) showed the recent divergence between some members of the group.

Submitted by LOUISE HELENA MARTINS MARAN null (louise.maran@outlook.com) on 2016-06-28T16:37:01Z No. of bitstreams: 1 Dissertação_Definitivo.pdf: 2004003 bytes, checksum: 2157b94fbd9ba1934694a695aea03633 (MD5) / Approved for entry into archive by Juliano Benedito Ferreira (julianoferreira@reitoria.unesp.br) on 2016-06-29T18:55:46Z (GMT) No. of bitstreams: 1 maran_lhmm_me_jabo.pdf: 2004003 bytes, checksum: 2157b94fbd9ba1934694a695aea03633 (MD5) / Made available in DSpace on 2016-06-29T18:55:46Z (GMT). No. of bitstreams: 1 maran_lhmm_me_jabo.pdf: 2004003 bytes, checksum: 2157b94fbd9ba1934694a695aea03633 (MD5) Previous issue date: 2016-05-31 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Estudos recentes com a espécie Mazama americana apontam duas linhagens cromossômicas dentro deste possível complexo de espécies crípticas e entre elas verificou-se a existência de eficiente barreira reprodutiva por isolamento pós-zigótico. No entanto, o efeito das pequenas diferenças cromossômicas entre populações é ainda pouco esclarecido, não sendo claro se seriam polimorfismos intraespecíficos, diferenças subespecíficas ou específicas. Marcadores moleculares permitem investigar se ocorreu fluxo entre estas populações e se este fluxo ainda ocorre no presente, auxiliando na elucidação dos processos evolutivos que ocorreram na diferenciação cromossômica e qual o real efeito dessas variações no isolamento e especiação no táxon. Diante do exposto, o presente trabalho estudou as relações filogenéticas entre variantes cromossômicas, com alto número diplóide, de M. americana com o objetivo de compreender melhor a história evolutiva da espécie e verificar a existência de unidades evolutivamente significativas dentro deste complexo específico, contribuindo para o delineamento de programas de conservação da espécie. As relações filogenéticas da espécie foram examinadas utilizando genes mitocondriais (citocromo b, citocromo oxidade I, região controladora D-loop e NADH dehigrogenase subunit 5), com 44 indivíduos de veados-mateiro provenientes de diferentes localidades do Brasil. Os resultados encontrados não corroboram a existência de unidades evolutivamente significativas dentro do grupo amostrado. A topologia encontrada nas árvores filogenéticas não mostram agrupamentos por citótipos, mas sim uma polifilia dos clados das árvores filogenéticas. / Recent studies on the species Mazama americana point two chromosomal lineages within red brocket deer and among them there was the existence of effective reproductive barrier post-zygotic isolation. However, the effect of these small chromosomal differences between these populations is not clearly established, it is not clear whether they would be intraspecific polymorphisms, subspecific or specific diferences. The molecular markers allow to investigate if there was flows occurred between these populations and whether these flows still occur in the present, helping to unravel the evolutionary processes that have occurred on chromosome differentiation and what the actual effect of these changes in isolation and speciation in the taxon. Given the above, this research project studied the phylogenetic relationships among chromosomal variants of M. americana with the aim of elucidating the evolutionary history of the species and verify the existence of evolutionarily significant units within this particular complex, contributing to the design of programs conservation of the species. The phylogenetic relationships of the species were examined using mitochondrial genes (cytochrome-b, cytochrome oxidase I, control region D-loop and NADH dehidrogenase subunit 5), with 44 individuals of red brocket deer from different locations in Brazil. The results do not support the existence of distinct evolutionary units within the sampled groups. The topologies found in phylogenetic tree show no groupings cytotypes but a polyphyly of clades of the phylogenetic tree. / CNPq: 132063/2014-0

The Guiana Shield is a sub-region of Amazonia, one of the richest areas on earth in terms of species number. It is also one of the most pristine areas and is still largely unexplored. Species number, distribution, boundaries and their evolutionary histories remain at least unclear but most of the time largely unknown. This is the case for most Anurans, a group which is recognized as threatened globally and is disappearing even from pristine tropical forests. Given the pace of forest destruction and the growing concerns about climate change it is urgently necessary to obtain a better estimate of regional biodiversity in Amazonian frogs as well as a better understanding of the origin and distribution of Anuran diversity. Furthermore, given their sensitivity to climatic conditions, amphibians are a good model to investigate the influence of paleoclimatic events on Neotropical diversification which was supposedly the driving force on biotic evolution during Pleistocene in the Guiana Shield. I first test species boundaries in two species Scinax ruber and Rhinella margaritifera. These species are widely distributed, abundant and largely recognized as species complexes. I used an original species delineation method based on the combined use of mitochondrial and nuclear DNA in phylogenetic and phylogeographic analyses. Phylogenetic analyses demonstrated the polyphyly of Scinax ruber and Rhinella margaritifera. These species consist of multiple lineages that may all merit species status. Conflicting signals of mitochondrial and nuclear markers indicated the possibility of ongoing hybridization processes. Phylogeographic analyses added further information in support of the specific status of these lineages. Our results highlight the utility of combining phylogenetic and phylogeographic methods, as well as the use of both mitochondrial and nuclear markers within one study. This approach helped to better understand the evolutionary history of taxonomically complex groups of species. The assessment of the geographic distribution of genetic diversity in tropical amphibian communities can lead to conclusions that differ strongly from prior analyses based on the occurrence of currently recognized species alone. Such studies, therefore, hold the potential to contribute to a more objective assessment of amphibian conservation priorities in tropical areas. Subsequently, I tested if these first results on cryptic species are generalisable, questioning what would potentially be a minimum estimate of the number of cryptic frog species in Amazonia and the Guiana Shield, using mtDNA with multiple complementary approaches. I also combined isolation by distance, phylogenetic analyses, and comparison of molecular distances to evaluate threshold values for the identification of candidate species among these frogs. In most cases, geographically distant populations belong to genetically highly distinct lineages that could be considered as candidate new species. This was not universal among the taxa studied and thus widespread species of Neotropical frogs really do exist, contra to previous assumptions. Moreover, the many instances of paraphyly and the wide overlap between distributions of inter- and intra-specific distances reinforce the hypothesis that many cryptic species remain to be described. In our data set, pairwise genetic distances below 0.02 are strongly correlated with geographical distances. This correlation remains statistically significant until genetic distance is 0.05, with no such relation thereafter. This suggests that for higher genetic distances allopatric and sympatric cryptic species prevail. Based on our analyses, we propose a more inclusive pairwise genetic distance of 0.03 between taxa to target lineages that could correspond to candidate species. Using this approach, we identify 129 candidate species, two-fold greater than the 60 species included in the current study. This leads to estimates of around 170 to 460 frog taxa unrecognized in Amazonia-Guianas. As a consequence the global amphibian decline detected especially in the Neotropics may be worse than realised. The Rhinella margaritifera complex is characterisized by the presence of many cryptic species throughout its wide distribution, ranging from Panama to Bolivia and almost entire Amazonia. French Guiana has long been thought to harbor two species of this group, though molecular data analysed in previous chapters indicated as many as five lineages. I tested whether morphological measurements are correlated or not with genetic data using discriminant analysis and if diagnostic characteristics among the previously determined lineages can be used to describe these new species. This is a novel integrative method which can lead to a facilitation of the description of cryptic species that have been detected by phylogenetic and/or phylogeographic studies. These analyses, combined with published data of other Rhinella species, indicated that two of these lineages represent previously unnamed species. Two of the remaining are allocable to R. margaritifera while the status of the fifth is still unclear because so far it is morphologically indistinguishable from R. castaneotica. Determining if codistributed species responded to climate change in an independent or concerted manner is a basic objective of comparative phylogeography. Species boundaries, histories, ecologies and their geographical ranges are still to be explored in the Guiana Shield. According to the refugia hypothesis this region was supposed to host a forest refugium during climatic oscillations of the Pleistocene but the causes and timing for this have been criticized. We investigated patterns of genetic structure within 18 frog species in the eastern Guiana Shield to explore species boundaries and their evolutionary history. We used mtDNA and nuclear DNA and complementary methods to compare the genetic diversity spatially and temporally. With one exception all the species studied diversified repeatedly within the eastern Guiana Shield during the last 4 million years. Instead of one Pleistocene forest refugium the Guiana Shield has probably hosted multiple refugia during late Pliocene and Pleistocene. Most of these Pleistocene refugia were probably situated on the coast of French Guiana, Amapà, Suriname and Guyana. This diversification likely resulted from forest fragmentation. Many species deserve taxonomic revisions and their ranges to be reconsidered. The local endemism of the Anuran fauna of the Guiana Shield is likely to be much higher and some areas consequently deserve more conservation efforts. Specifically I questioned whether major intraspecific diversification started before the Pleistocene and occurred within the Guiana Shield or ex situ. According to ecological characteristics of the species involved I will test different diversification hypotheses. The consequences on the diversity and the endemism of the Guiana Shield will be explored. My results demonstrate that we have been grossly underestimating local biological diversity in the Guiana Shield but also in Amazonia in general. The order of magnitude for potential species richness means that the eastern Guiana Shield hosts one of the richest frog fauna on earth. In most of the species studied high levels of mtDNA differentiation between populations call for a reassessment of the taxonomic status of what is being recognised as single species. Most species display deep divergence between eastern Guiana Shield populations and Amazonian ones. This emphasizes that the local endemism in the Guiana Shield of these zones is higher than previously recognized and must be prioritised elements taken into account in conservation planning. Nevertheless, a few other species appear widely distributed showing that widespread species do exist. This underlines the fact that some species have efficient dispersal abilities and that the frog fauna of the eastern Guiana Shield is a mixture of old Guianan endemic lineages that diversified in situ mostly during late Pliocene and Pleistocene and more recently exchanged lineages with the rest of Amazonia. Recognizing this strong historical component is necessary and timely for local conservation as these zones are likely to be irremediably modified in the near future.

The Guiana Shield is a sub-region of Amazonia, one of the richest areas on earth in terms of species number. It is also one of the most pristine areas and is still largely unexplored. Species number, distribution, boundaries and their evolutionary histories remain at least unclear but most of the time largely unknown. This is the case for most Anurans, a group which is recognized as threatened globally and is disappearing even from pristine tropical forests. Given the pace of forest destruction and the growing concerns about climate change it is urgently necessary to obtain a better estimate of regional biodiversity in Amazonian frogs as well as a better understanding of the origin and distribution of Anuran diversity. Furthermore, given their sensitivity to climatic conditions, amphibians are a good model to investigate the influence of paleoclimatic events on Neotropical diversification which was supposedly the driving force on biotic evolution during Pleistocene in the Guiana Shield. I first test species boundaries in two species Scinax ruber and Rhinella margaritifera. These species are widely distributed, abundant and largely recognized as species complexes. I used an original species delineation method based on the combined use of mitochondrial and nuclear DNA in phylogenetic and phylogeographic analyses. Phylogenetic analyses demonstrated the polyphyly of Scinax ruber and Rhinella margaritifera. These species consist of multiple lineages that may all merit species status. Conflicting signals of mitochondrial and nuclear markers indicated the possibility of ongoing hybridization processes. Phylogeographic analyses added further information in support of the specific status of these lineages. Our results highlight the utility of combining phylogenetic and phylogeographic methods, as well as the use of both mitochondrial and nuclear markers within one study. This approach helped to better understand the evolutionary history of taxonomically complex groups of species. The assessment of the geographic distribution of genetic diversity in tropical amphibian communities can lead to conclusions that differ strongly from prior analyses based on the occurrence of currently recognized species alone. Such studies, therefore, hold the potential to contribute to a more objective assessment of amphibian conservation priorities in tropical areas. Subsequently, I tested if these first results on cryptic species are generalisable, questioning what would potentially be a minimum estimate of the number of cryptic frog species in Amazonia and the Guiana Shield, using mtDNA with multiple complementary approaches. I also combined isolation by distance, phylogenetic analyses, and comparison of molecular distances to evaluate threshold values for the identification of candidate species among these frogs. In most cases, geographically distant populations belong to genetically highly distinct lineages that could be considered as candidate new species. This was not universal among the taxa studied and thus widespread species of Neotropical frogs really do exist, contra to previous assumptions. Moreover, the many instances of paraphyly and the wide overlap between distributions of inter- and intra-specific distances reinforce the hypothesis that many cryptic species remain to be described. In our data set, pairwise genetic distances below 0.02 are strongly correlated with geographical distances. This correlation remains statistically significant until genetic distance is 0.05, with no such relation thereafter. This suggests that for higher genetic distances allopatric and sympatric cryptic species prevail. Based on our analyses, we propose a more inclusive pairwise genetic distance of 0.03 between taxa to target lineages that could correspond to candidate species. Using this approach, we identify 129 candidate species, two-fold greater than the 60 species included in the current study. This leads to estimates of around 170 to 460 frog taxa unrecognized in Amazonia-Guianas. As a consequence the global amphibian decline detected especially in the Neotropics may be worse than realised. The Rhinella margaritifera complex is characterisized by the presence of many cryptic species throughout its wide distribution, ranging from Panama to Bolivia and almost entire Amazonia. French Guiana has long been thought to harbor two species of this group, though molecular data analysed in previous chapters indicated as many as five lineages. I tested whether morphological measurements are correlated or not with genetic data using discriminant analysis and if diagnostic characteristics among the previously determined lineages can be used to describe these new species. This is a novel integrative method which can lead to a facilitation of the description of cryptic species that have been detected by phylogenetic and/or phylogeographic studies. These analyses, combined with published data of other Rhinella species, indicated that two of these lineages represent previously unnamed species. Two of the remaining are allocable to R. margaritifera while the status of the fifth is still unclear because so far it is morphologically indistinguishable from R. castaneotica. Determining if codistributed species responded to climate change in an independent or concerted manner is a basic objective of comparative phylogeography. Species boundaries, histories, ecologies and their geographical ranges are still to be explored in the Guiana Shield. According to the refugia hypothesis this region was supposed to host a forest refugium during climatic oscillations of the Pleistocene but the causes and timing for this have been criticized. We investigated patterns of genetic structure within 18 frog species in the eastern Guiana Shield to explore species boundaries and their evolutionary history. We used mtDNA and nuclear DNA and complementary methods to compare the genetic diversity spatially and temporally. With one exception all the species studied diversified repeatedly within the eastern Guiana Shield during the last 4 million years. Instead of one Pleistocene forest refugium the Guiana Shield has probably hosted multiple refugia during late Pliocene and Pleistocene. Most of these Pleistocene refugia were probably situated on the coast of French Guiana, Amapà, Suriname and Guyana. This diversification likely resulted from forest fragmentation. Many species deserve taxonomic revisions and their ranges to be reconsidered. The local endemism of the Anuran fauna of the Guiana Shield is likely to be much higher and some areas consequently deserve more conservation efforts. Specifically I questioned whether major intraspecific diversification started before the Pleistocene and occurred within the Guiana Shield or ex situ. According to ecological characteristics of the species involved I will test different diversification hypotheses. The consequences on the diversity and the endemism of the Guiana Shield will be explored. My results demonstrate that we have been grossly underestimating local biological diversity in the Guiana Shield but also in Amazonia in general. The order of magnitude for potential species richness means that the eastern Guiana Shield hosts one of the richest frog fauna on earth. In most of the species studied high levels of mtDNA differentiation between populations call for a reassessment of the taxonomic status of what is being recognised as single species. Most species display deep divergence between eastern Guiana Shield populations and Amazonian ones. This emphasizes that the local endemism in the Guiana Shield of these zones is higher than previously recognized and must be prioritised elements taken into account in conservation planning. Nevertheless, a few other species appear widely distributed showing that widespread species do exist. This underlines the fact that some species have efficient dispersal abilities and that the frog fauna of the eastern Guiana Shield is a mixture of old Guianan endemic lineages that diversified in situ mostly during late Pliocene and Pleistocene and more recently exchanged lineages with the rest of Amazonia. Recognizing this strong historical component is necessary and timely for local conservation as these zones are likely to be irremediably modified in the near future.

Made available in DSpace on 2014-06-11T19:26:07Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-10-07Bitstream added on 2014-06-13T19:53:59Z : No. of bitstreams: 1 gualberto_af_me_jabo.pdf: 464930 bytes, checksum: 799ea2a9f048c84fac80100f93c28e4f (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O veado-mateiro (Mazama americana) é a maior espécie do Gênero Mazama, e encontra distribuído geograficamente por quase toda a região neotropical. Animais originários do Estado de Rondônia têm apresentado importantes diferenças citogenéticas em relação ao padrão de outras populações, o que suscita necessidade de estudos mais aprofundados para definição da sua posição filogenética. O presente estudo objetivou identificar as diferentes populações de veado-mateiro desta região, verificando a existência de mais de uma espécie no local. Para tanto, foram obtidos 51 fragmentos de tecido de animais caçados por indígenas e pela população local em todas as regiões do Estado dos quais 33 tiveram seu DNA extraídos, amplificados (região de 480pb do citocromo b) e seqüenciados de forma satisfatória. Estas seqüências foram alinhadas e comparadas, gerando 21 haplótipos que se encontram distribuídos de forma aleatória pelas diversas regiões de coleta. Estes haplótipos serviram de base para a elaboração de redes de distância e árvores filogenéticas que quando analisadas sugeriram a existência de espécies crípticas dentro do que hoje se denomina Mazama americana no Estado de Rondônia. / The red brocket deer is the largest species of Mazama genus and it is distributed in almost all Neotropical regions. Individuals originated from Rondônia state in Brazil have been presented important cytogenetic differences when compared with populations of other regions of country; however more studies are necessary to define correct phylogenetic position of species. The objective of present study was performed the identification of different populations of red brocket deer from Rondônia state by verification of occurrence of more than one species on mentioned region. For this, 51 fragments of tissues from hunted animals were obtained with Indians and local people of all regions of Rondônia state. In 31 fragments of tissues the DNA was successful extract, amplified (480 bp region of cytochrome b) and sequenced. These sequences were aligned and compared creating 21 haplotypes, which are distributed in a randomly way thru the different regions of sampling. The haplotypes were used to elaborate distance nets and phylogenetic trees, which when analyzed suggested the existence of cryptic species on Mazama americana species that occurs in Rondônia state.

Made available in DSpace on 2014-06-11T19:26:07Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-05-27Bitstream added on 2014-06-13T19:33:20Z : No. of bitstreams: 1 carnelossi_eag_me_jabo.pdf: 5963862 bytes, checksum: c9072ade5521cd6b029cd77e62872e7a (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O veado-mateiro (Mazama americana) possui uma ampla distribuição geográfica na região neotropical. Estudos citogenéticos com a espécie revelam variações cromossômicas (citótipos) que apontam sua divisão em outras espécies. Neste trabalho, foram examinadas as relações filogenéticas desta espécie, analisando parte dos genes mitocondriais (citocromo-b e região controladora D-loop), dos genes nucleares (Beta e Kapa caseínas e do exon I do gene IRBP) e um fragmento do gene, presente no cromossomo Y, chamado SRY, para amostras de 19 indivíduos provenientes de diferentes regiões do Brasil. Os genes nucleares da kapa e beta caseína e do SRY, mostraram-se monomórficos, não sendo possível a obtenção de sequências para o gene IRBP. As inferências filogenéticas pelos genes mitocondriais revelam duas linhagens evolutivas, a dos indivíduos das populações da Bacia do Rio Paraná e a dos indivíduos do oeste da Bacia do Rio Amazonas. Também houve uma correlação entre os diferentes cariótipos e as distintas linhagens moleculares encontradas. Além disso, pode-se sugerir a ocorrência de convergência evolutiva entre estes grupos, bem como um possível caso de simpatria ou de retenção de polimorfismo ancestral nos indivíduos do leste da Amazônia. / The red brocket deer (Mazama americana) has a wide distribution in Neotropics. In this regard, cytogenetic studies in this species revealed chromosomic variations (cytotypes) which strongly suggest that red brockets can be divided into other species. In the present study, we examined phylogenetic relationships of 19 samples of individuals from different areas of Brazil through mitochondrial (cytochrome b and control region D-loop), nuclear (b-casein, k-casein, and first exon of the IRBP) and SRY gene analysis. The sequence analysis showed that b- and k-caseins as well as SRY nuclear genes were monomorphic, whereas IBRP gene sequencing was not possible. Phylogenetic inferences concerning mitochondrial gene analysis demonstrated two evolutionary lineages, one from Parana River Basin (southeast Brazil) and other from west of Amazon River Basin (northwest Brazil). Moreover, we found correlation between different karyotypes and distinct molecular lineages.

Resumo: O veado-mateiro (Mazama americana) possui uma ampla distribuição geográfica na região neotropical. Estudos citogenéticos com a espécie revelam variações cromossômicas (citótipos) que apontam sua divisão em outras espécies. Neste trabalho, foram examinadas as relações filogenéticas desta espécie, analisando parte dos genes mitocondriais (citocromo-b e região controladora D-loop), dos genes nucleares (Beta e Kapa caseínas e do exon I do gene IRBP) e um fragmento do gene, presente no cromossomo Y, chamado SRY, para amostras de 19 indivíduos provenientes de diferentes regiões do Brasil. Os genes nucleares da kapa e beta caseína e do SRY, mostraram-se monomórficos, não sendo possível a obtenção de sequências para o gene IRBP. As inferências filogenéticas pelos genes mitocondriais revelam duas linhagens evolutivas, a dos indivíduos das populações da Bacia do Rio Paraná e a dos indivíduos do oeste da Bacia do Rio Amazonas. Também houve uma correlação entre os diferentes cariótipos e as distintas linhagens moleculares encontradas. Além disso, pode-se sugerir a ocorrência de convergência evolutiva entre estes grupos, bem como um possível caso de simpatria ou de retenção de polimorfismo ancestral nos indivíduos do leste da Amazônia. / Abstract: The red brocket deer (Mazama americana) has a wide distribution in Neotropics. In this regard, cytogenetic studies in this species revealed chromosomic variations (cytotypes) which strongly suggest that red brockets can be divided into other species. In the present study, we examined phylogenetic relationships of 19 samples of individuals from different areas of Brazil through mitochondrial (cytochrome b and control region D-loop), nuclear (b-casein, k-casein, and first exon of the IRBP) and SRY gene analysis. The sequence analysis showed that b- and k-caseins as well as SRY nuclear genes were monomorphic, whereas IBRP gene sequencing was not possible. Phylogenetic inferences concerning mitochondrial gene analysis demonstrated two evolutionary lineages, one from Parana River Basin (southeast Brazil) and other from west of Amazon River Basin (northwest Brazil). Moreover, we found correlation between different karyotypes and distinct molecular lineages. / Orientador: José Maurício Barbanti Duarte / Coorientadora: Susana González / Banca: Reinaldo Otávio Alvarenga Alves de Brito / Banca: Cláudia Márcia Aparecida Carareto / Mestre

Orientador: José Maurício Barbanti Duarte / Banca: Irlan Leite de Abreu / Banca: Fernando Pacheco Rodrigues / Resumo: O veado-mateiro (Mazama americana) é a maior espécie do Gênero Mazama, e encontra distribuído geograficamente por quase toda a região neotropical. Animais originários do Estado de Rondônia têm apresentado importantes diferenças citogenéticas em relação ao padrão de outras populações, o que suscita necessidade de estudos mais aprofundados para definição da sua posição filogenética. O presente estudo objetivou identificar as diferentes populações de veado-mateiro desta região, verificando a existência de mais de uma espécie no local. Para tanto, foram obtidos 51 fragmentos de tecido de animais caçados por indígenas e pela população local em todas as regiões do Estado dos quais 33 tiveram seu DNA extraídos, amplificados (região de 480pb do citocromo b) e seqüenciados de forma satisfatória. Estas seqüências foram alinhadas e comparadas, gerando 21 haplótipos que se encontram distribuídos de forma aleatória pelas diversas regiões de coleta. Estes haplótipos serviram de base para a elaboração de redes de distância e árvores filogenéticas que quando analisadas sugeriram a existência de espécies crípticas dentro do que hoje se denomina Mazama americana no Estado de Rondônia. / Abstract: The red brocket deer is the largest species of Mazama genus and it is distributed in almost all Neotropical regions. Individuals originated from Rondônia state in Brazil have been presented important cytogenetic differences when compared with populations of other regions of country; however more studies are necessary to define correct phylogenetic position of species. The objective of present study was performed the identification of different populations of red brocket deer from Rondônia state by verification of occurrence of more than one species on mentioned region. For this, 51 fragments of tissues from hunted animals were obtained with Indians and local people of all regions of Rondônia state. In 31 fragments of tissues the DNA was successful extract, amplified (480 bp region of cytochrome b) and sequenced. These sequences were aligned and compared creating 21 haplotypes, which are distributed in a randomly way thru the different regions of sampling. The haplotypes were used to elaborate distance nets and phylogenetic trees, which when analyzed suggested the existence of cryptic species on Mazama americana species that occurs in Rondônia state. / Mestre