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Programa De Pós-Graduação Em Genética, Conservação E Biologia Evolutiva

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Programa De Pós-Graduação Em Genética, Conservação E Biologia Evolutiva Instituto Nacional de Pesquisas da Amazônia – INPA Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva Filogenia e biogeografia de três famílias de aves do Neotrópico Mateus Ferreira Manaus, Amazonas Março, 2018 Mateus Ferreira Filogenia e biogeografia de três famílias de aves do Neotrópico Orientador: Dra. Camila Cherem Ribas Tese apresentada ao Instituto Nacional de Pesquisas da Amazônia como requisito para obtenção do grau de doutor em Genética, Conservação e Biologia Evolutiva. Manaus, Amazonas Março, 2018 3 ii F383 Ferreira, Mateus Filogenia e biogeografia de três famílias de aves do Neotrópico / Mateus Ferreira. --- Manaus: [sem editor], 2018. 121 f. : il. color. Tese (Doutorado) --- INPA, Manaus, 2018. Orientadora : Camila Cherem Ribas. Programa : Genética, Conservação e Biologia Evolutiva. 1. Biogeografia. 2. Genômica. 3. Aves neotropicais. I. Título. CDD 598.7 Sinopse: Neste trabalho foram realizados estudos sobre a relação filogenética entre todas as espécies de três famílias de aves do Neotrópico. Abordamos aspectos sobre a distribuição geográfica das linhagens genéticas encontradas, conflitos entre os diferentes marcadores genéticos e a subestimação da diversidade taxonômica dos táxons estudados. Palavras-chave: Bucconidae, Galbulidae, Trogonidae, Pantropical, genômica, filogeografia, UCE iii Agradecimentos Agradeço primeiramente a minha orientadora Camila Ribas, pela paciência e confiança que depositou em mim durante esses anos de orientação. Sem sombra de dúvidas, esse trabalho não seria possível sem essa amizade e parceria. Ao meu co-orientador, Joel Cracraft, com quem tive a sorte de trabalhar durante o meu doutorado sanduíche. Pelas excelentes conversas e orientações sobre biogeografia e sobre os padrões e processos que moldaram a diversidade de aves no mundo. À Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) e ao programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, do Instituto Nacional de Pesquisas da Amazônia, pela concessão da bolsa de doutorado no país e bolsa sanduíche (# 88881.133440/2016-01), que tornaram este projeto possível. Aos curadores e responsáveis pelas coleções científicas que gentilmente cederam material para que este trabalho fosse desenvolvido: Alexandre Aleixo, Fátima Lima e Antonita Santana (MPEG); Marlene Freitas (INPA); Nate Rice (ANSP), Cristina Miyaki (LGEMA), Donna Dittman e Robb Brumfield (LSU), Paul Sweet e Tom Trombone (AMNH), Mark Robbins (KU), John Bates e Ben Marks (FMNH), Brian K. Schmidt (USNM), Sharon Birks (UWBM). E, a todas as pessoas envolvidas nas expedições de coleta dessas institutições. Ao projeto “Dimensions US-Biota: Assembly and evolution of the Amazon biota and its environment: an integrated approach”, um projeto financiado conjuntamente pela Fundação de Amparo à Pesquisa de São Paulo (FAPESP #2012/50260-6) e pelo National Science Fundation (NSF DEB 1241056). Cujo apoio e financiamento foram essenciais para a execução das várias etapas desse doutorado. A todos os colegas do EBBA, pela constante ajuda e pelas excelentes discussões e incentivos, e pelo café, especialmente pelos cafés: Robs, Fernanda, Rafael, Claudinha, Érico, Erik, Lídia, Renatinha, Jessica, Nelson, Carol, Waleskinha e todo mundo que passou por aqui. Ao pessoal que me aguentou durante esse doutorado: Mariana Tolentino, Leandro, Marina Maximiano, Ana, Marizita (Marina Carmona) Derek, Miquéias, Pedro, Cadu e Manu. Em especial à Romina, pela caminhada lado a lado durante toda a execução desse projeto, pelos puxões de orelha quando eu precisei e por ter me aguentado todo esse período. Ao pessoal do LTBM, Giselle e Paula, pela excelente companhia, pelos cafés e ajudas quando precisei. iv To everyone who received me at the AMNH during my sandwich fellowship: Lydia, Bill, Tom, Paul, Gabi, Brian, Luke, and Peter. A special thanks to Jessica and Laís for all the support and friendship during my time in NY. Também gostaria de agradecer ao Laboratório Nacional de Computação Científica (LNCC/MCTI) por fornecer recursos de computação de alto desempenho através do supercomputador SDumont, fundamentais para as análises realizadas neste estudo. Por fim, um agradecimento especial para a minha família, que me apoiou incondicionalmente em todo esse percurso, e cuja ajuda foi essencial para a finalização deste doutorado. v “Nothing in biology makes sense except in the light of evolution” Theodosius Dobzhansky “Life and Earth evolve together” Leon Croizat vi Resumo O Neotrópico é uma das regiões com os maiores índices de biodiversidade do planeta e muito tem se questionado sobre a origem de tamanha diversidade. Acredita-se que os padrões de diversidade atual dentro da região sejam um resultado da complexa história geomorfológica e climática da região. Entre os eventos geomorfológicos mais discutidos estão o soerguimento dos Andes e consequente reestruturação da drenagem continental, e o fechamento do Istmo do Panamá, que permitiu a troca intercontinental de biotas. Neste trabalho foram selecionadas três famílias de aves do Neotrópico. A família Trogonidae tem uma distribuição Pantropical, ocorrendo também nas regiões subtropicais e tropicais da África e Ásia, no entanto, a maior diversidade encontra-se justamente na região Neotropical. As famílias Bucconidae e Galbulidae são duas famílias irmãs endêmicas do Neotrópico. Foram selecionadas amostras de todas as espécies e quase todas as subespécies descritas para os três grupos. Para as espécies amplamente distribuídas foram selecionadas amostras ao longo de toda a distribuição e uma análise prévia para verificar a estrutura filogeográfica de cada grupo, com base nesses resultados, foram selecionadas amostras para o sequenciamento de milhares de loci de regiões Ultra Conservadas (Ultraconserved Elements, UCE). Dessa forma, compilamos três estudos nessa tese. No primeiro capítulo, foi estudado um complexo de aves da família Galbulidae associada aos ambientes de areia branca na região Amazônica. Através da comparação entre marcadores moleculares com diferentes métodos de herança, DNA mitocondrial e nuclear (UCE), pudemos observar um conflito entre esses dois marcadores. Através deste conflito foi possível propor um modelo de diversificação para os ambientes de areia branca na região. No segundo capítulo analisamos a diversificação global da família Trogonidae, com o auxílio dos UCEs reconstruímos a relação filogenética entre todas as espécies da família e estimamos uma árvore datada da diversificação de Trogonidae. No terceiro e último capítulo, analisamos os padrões de diversificação das famílias Galbulidae e Bucconidae através de uma abordagem filogeográfica e filogenética. Neste trabalho pudemos observar que a diversidade do grupo se encontra claramente subestimada. vii Abstract The Neotropical region has one of the highest biodiversity index in the planet and several hypotheses have been proposed to explain the origin of such diversity. Currently, landscape and climatic evolution are credited to be the two main processes responsible for shaping the patterns. Landscape evolution includes, for example, the Andean uplift and consequent continental drainage reconfiguration, and the closure of the Isthmus of Panama, which allowed the Great American Biotic Interchange. In the present study we selected three Neotropical families of birds. Trogonidae has a Pantropical distribution, members of this family inhabit tropical and subtropical regions of Africa, Asia, however, the highest diversity is currently found in the Americas. Galbulidae and Bucconidae are sister families and endemics to the Neotropics. WE sampled all species and almost all subspecies currently recognized for this three families, and for widespread species we thoroughly sampled throughout their distributions to uncover hidden phylogeographic patterns. Based on these results, we selected the samples to sequence thousands of Ultraconserved Elements (UCE). Thus, we compiled three studies for this thesis. In the first chapter, we studied one Galbulidae species complex associated with the Amazonian White-sand environments. We compared between molecular markers that have different heritage systems, the mtDNA and nuDNA (UCE), where we recovered contrasting histories between markers, and based on these results we proposed a diversification model for the White-sand environments. In the second chapter, we analyzed the global diversification of Trogonidae, employing thousands of UCE loci to propose a phylogenetic hypothesis between all species currently recognized, and we also estimated a fossil calibrated time tree for Trogonidae diversification. At last, in the third chapter, we analyzed the diversification patterns for Galbulidae and Bucconidae using a phylogeographic/phylogenetic approach. In this chapter it was clear how these groups diversity in underestimated by currently taxonomic approach. viii Sumário Agradecimentos ....................................................................................................................... iv Resumo .................................................................................................................................... vii Abstract .................................................................................................................................. viii Introdução Geral ...................................................................................................................... 1 Objetivos ...................................................................................................................................
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