Submitted by Caroline Xavier (caroline.xavier@pucrs.br) on 2017-05-04T17:15:51Z No. of bitstreams: 1 TES_HENRIQUE_VIEIRA_FIGUEIRO_COMPLETO.pdf: 4680551 bytes, checksum: 8695b78fe6812f4690586975941c4c31 (MD5) / Made available in DSpace on 2017-05-04T17:15:51Z (GMT). No. of bitstreams: 1 TES_HENRIQUE_VIEIRA_FIGUEIRO_COMPLETO.pdf: 4680551 bytes, checksum: 8695b78fe6812f4690586975941c4c31 (MD5) Previous issue date: 2016-03-11 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior - CAPES / Conselho Nacional de Pesquisa e Desenvolvimento Cient?fico e Tecnol?gico - CNPq / In the past 10 years, high throughput sequencing has revolutionized evolutionary biology. With the technical advances that emerged with the genome sequencing of model species, it is now possible to apply these techniques to taxonomic groups without any previously available genetic resources. Complete genome sequencing and reduced representation methods have enabled us to explore deeper evolutionary questions, such as detecting ancient hybridization and signatures of selection on a genomic scale. Among the groups that could benefit from these methods is the Panthera genus. The group is composed by five species (P. onca, P. tigris, P. leo, P. pardus and P. uncia), all of which are large felids that exert important ecological role as apex predators in their habitats. Their low densities, alarming rates of habitat loss and chronic conflict with humans, all of them are threatened with extinction in the wild and thus important targets for conservation. One of the species in this group, the jaguar (P. onca), is the only member of the genus currently present in the Neotropical region, and the focus of our study. The jaguar has a color pattern similar to that of the leopard, but a much more robust constitution, with massive jaws and shorter limbs. The present study aims to characterize for the first time the jaguar genome, and to perform comparative analyses with the genomes from all other Panthera species. In addition, we seek to perform population genomic analyses with Brazilian jaguar populations and search for signatures of divergent selection in different regions. We have sequenced four genomic libraries, with an estimated coverage depth of 84x. The complete genome sequence allowed the annotation of 25,441 genes and the description of other genomic features (e.g. ncRNA, microsatellites, numts). Additionally, we have sequenced the genome of a leopard at low coverage, with an estimated depth of 25x. With the addition of these two genomes, we were able obtain a genomic data set containing all five Panthera species, which was used to perform phylogenetic discordance analyses and to detect signatures of selection using a dataset encompassing 13,143 orthologous genes. We were able to demonstrate the presence of hybridization events during the speciation process of the species, as well as signatures of selection in genes potentially involved in important characteristics of these iconic animals. Among them, the jaguar?s robust build, the social behavior of lions, cold environment adaptations in the snow leopard and the tiger?s stripes. Using an exome capture approach, we performed a population genomics study targeting jaguar populations from different Brazilian biomes. In addition to assessments of genetic diversity and population structure, we detected signals of local adaptation using multiple methods. Among the obtained results is the presence of genes under selection that are related to energetic metabolism in the Amazon, body development in the Pantanal and immunity in the Atlantic Forest. Additionally, we observed several pigmentation-related genes under selection in different biomes. Those genes affect not only pigmentation, but also have pleiotropic effects in development and immunity routes. Overall, these results help to understand the evolutionary processes that have shaped the adaptation of Panthera species, and particularly the jaguar, to the environments where they currently live. / Nos ?ltimos 10 anos, o sequenciamento gen?mico de alto desempenho revolucionou a biologia evolutiva. Com os avan?os gerados pelo sequenciamento do genoma completo de esp?cies modelo, agora ? poss?vel aplicar essas t?cnicas em animais com praticamente nenhum recurso gen?tico dispon?vel. O sequenciamento completo de genomas, bem como o uso de t?cnicas de representa??o reduzida, permitem explorar quest?es evolutivas complexas como, por exemplo, detec??o de hibrida??o e assinaturas de sele??o natural em uma escala gen?mica. Dentre os grupos taxon?micos que podem se beneficiar de tais t?cnicas est? o g?nero Panthera. O grupo ? composto por cinco esp?cies atuais (P. onca, P. tigris, P. leo, P. pardus e P. uncia), todas elas apresentando grande porte e atuando como predadores de topo nos ambientes que ocupam. Devido ?s baixas densidades, alarmante perda de habitat e constantes conflitos com humanos, o n?vel de amea?a em que essas esp?cies se encontram ? preocupante. Dentre as esp?cies do grupo, est? a on?a-pintada (P. onca), ?nica integrante do g?nero na regi?o Neotropical e o principal foco deste trabalho. Nesse sentido, o presente estudo busca caracterizar pela primeira vez o genoma da on?a-pintada, incluindo an?lises comparativas com as outras quatro esp?cies do g?nero. Al?m disso, o trabalho tem como objetivo avaliar as popula??es de on?a no Brasil e buscar assinaturas de sele??o divergente nos biomas que ela ocupa. Para o sequenciamento do genoma da esp?cie, foram utilizadas quatro bibliotecas gen?micas, com uma cobertura estimada de 84x. A sequ?ncia do genoma completo permitiu a anota??o de 25.441 genes e a descri??o de outros componentes do genoma (p.ex. ncRNA, microssat?lites, numts). Adicionalmente, foi sequenciado o genoma de um leopardo (P. pardus) com cobertura estimada de 25x. Com esses dois novos genomas, completou-se um conjunto abrangendo todas as cinco esp?cies do g?nero, permitindo a realiza??o de an?lises de discord?ncia filogen?tica para o grupo e detec??o de sele??o positiva utilizando um conjunto de 13.143 genes ort?logos. Foi poss?vel demonstrar eventos de hibrida??o durante o processo de especia??o das esp?cies do g?nero, bem como sinais de sele??o positiva em genes envolvidos em caracter?sticas que se destacam nos grandes fel?deos. Entre eles, fen?tipos potencialmente afetados por genes sob sele??o incluem o cr?nio e membros robustos da on?a-pintada, o comportamento social no le?o, adapta??o ao frio no leopardo das neves e a presen?a de listras no tigre. Com o uso de captura de exoma, que tem como objetivo o sequenciamento do conjunto de exons da esp?cie, foi poss?vel realizar uma nova avalia??o das caracter?sticas gen?ticas de popula??es de on?a-pintada, bem como a detec??o de assinaturas de adapta??o local. Entre os resultados obtidos est? a presen?a de genes sob sele??o relacionados com metabolismo energ?tico em popula??es da Amaz?nia, adapta??es relacionadas com desenvolvimento corporal no Pantanal e imunidade na Mata Atl?ntica. Adicionalmente, foram observados diversos genes de pigmenta??o com assinaturas de sele??o em diferentes biomas. Esses genes, al?m de afetarem a colora??o dos animais, possuem efeitos pleiotr?picos no desenvolvimento e imunidade da esp?cie. Esses resultados auxiliam no entendimento dos processos evolutivos que moldaram a adapta??o das esp?cies do g?nero, e em especial a on?a pintada, aos ambientes que elas ocupam atualmente.