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Spatial Models of Speciation 1.0Cm Modelos Espaciais De Especiação

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Spatial Models of Speciation 1.0Cm Modelos Espaciais De Especiação UNIVERSIDADE ESTADUAL DE CAMPINAS INSTITUTO DE BIOLOGIA CAROLINA LEMES NASCIMENTO COSTA SPATIAL MODELS OF SPECIATION MODELOS ESPACIAIS DE ESPECIAÇÃO CAMPINAS 2019 CAROLINA LEMES NASCIMENTO COSTA SPATIAL MODELS OF SPECIATION MODELOS ESPACIAIS DE ESPECIAÇÃO Thesis presented to the Institute of Biology of the University of Campinas in partial fulfill- ment of the requirements for the degree of Doc- tor in Ecology Tese apresentada ao Instituto de Biologia da Universidade Estadual de Campinas como parte dos requisitos exigidos para a obtenção do título de Doutora em Ecologia Orientador: Marcus Aloizio Martinez de Aguiar ESTE ARQUIVO DIGITAL CORRESPONDE À VERSÃO FINAL DA TESE DEFENDIDA PELA ALUNA CAROLINA LEMES NASCIMENTO COSTA, E ORIENTADA PELO PROF DR. MAR- CUS ALOIZIO MARTINEZ DE AGUIAR. CAMPINAS 2019 Ficha catalográfica Universidade Estadual de Campinas Biblioteca do Instituto de Biologia Mara Janaina de Oliveira - CRB 8/6972 Costa, Carolina Lemes Nascimento, 1989- C823s CosSpatial models of speciation / Carolina Lemes Nascimento Costa. – Campinas, SP : [s.n.], 2019. CosOrientador: Marcus Aloizio Martinez de Aguiar. CosTese (doutorado) – Universidade Estadual de Campinas, Instituto de Biologia. Cos1. Especiação. 2. Radiação adaptativa (Evolução). 3. Modelos biológicos. 4. Padrão espacial. 5. Macroevolução. I. Aguiar, Marcus Aloizio Martinez de, 1960-. II. Universidade Estadual de Campinas. Instituto de Biologia. III. Título. Informações para Biblioteca Digital Título em outro idioma: Modelos espaciais de especiação Palavras-chave em inglês: Speciation Adaptive radiation (Evolution) Biological models Spatial pattern Macroevolution Área de concentração: Ecologia Titulação: Doutora em Ecologia Banca examinadora: Marcus Aloizio Martinez de Aguiar [Orientador] Mathias Mistretta Pires Sabrina Borges Lino Araujo Rodrigo André Caetano Gustavo Burin Ferreira Data de defesa: 25-02-2019 Programa de Pós-Graduação: Ecologia Powered by TCPDF (www.tcpdf.org) Comissão Examinadora: Prof. Dr. Marcus Aloizio Martinez de Aguiar Prof. Dr. Mathias Mistretta Pires Profa. Dra. Sabrina Borges Lino Araujo Prof. Dr. Rodrigo André Caetano Prof. Dr. Gustavo Burin Ferreira Os membros da Comissão Examinadora acima assinaram a Ata de de- fesa, que se encontra no processo de vida acadêmica do aluno. Agradecimentos "A gratidão é o único tesouro dos humildes", disse Shakespeare. Eu acres- centaria que é o mais importante de todos os tesouros. Agradeço a todos que de al- guma maneira colaboraram para o desenvolvimento dessa tese. À minha família, sem a qual eu não poderia galgar nenhum dos caminhos que segui durante minha vida até hoje. Ao meu companheiro, que em todos os nossos anos juntos sempre foi meu amigo, me incentivando a me desenvolver. Aos meus amigos, que em momentos descontraí- dos trouxeram leveza à esses anos de árduo estudo, e em momentos de seriedade me ajudaram a conceber problemas e foram ainda grandes colaboradores nos projetos aqui desenvolvidos. Agradeço aos professores com quem tive oportunidade de estudar, seja assistindo encantada as suas aulas, seja em diálogos enriquecedores a dois, que com suas experiências me ajudaram a desenvolver concepções maduras sobre problemas diversos da Biologia. Agradeço ao meu orientador pelos anos de convivência, que me proporcionaram muito amadurecimento, como profissional e como pessoa. O presente trabalho foi realizado com apoio da Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil, CAPES/PROEX - 0487, processo no 1456640 - Código de Finan- ciamento 001. Espero que com os conhecimentos aqui adquiridos eu possa retribuir dignamente ao investimento que em mim foi feito. A todos que participaram de alguma maneira dos meus últimos quatro anos de vida, sem dúvida influenciando no meu desempenho profissional, meu muito obri- gada. Resumo A impressionante diversidade observada na natureza nos faz pensar quais processos podem ser responsáveis por tamanha variedade. Responder esta questão foi o objetivo de muito biólogos evolutivos, que tentaram descobrir os processos olhando para os padrões que eles poderiam gerar. O desenvolvimento de modelos teóricos, em particular modelos baseados em indivíduo, é indispensável para lidar com esta questão, pois apenas com modelos podemos isolar processos específicos em um am- biente controlado, o que não é completamente possível em experimentos naturais, e em um tempo realizável. Nesta tese eu investiguei quais são os padrões gerados por um modelo de especiação baseado em indivíduo no qual apenas processos neutros e o espaço estão regulando a dinâmica populacional. A população evoluiu sob as influên- cias combinadas de reprodução sexuada, mutação e dispersão. No primeiro capítulo, desenvolvemos um algoritmo que registra as relações de ancestralidade–descendência entre pares de indivíduos da comunidade final, e um algoritmo que registra os tem- pos exatos de especiação e extinção das espécies. Com ambas as informações foi pos- sível construir genealogias e filogenias, a partir das quais padrões macroevolutivos foram obtidos, servindo como um referencial de evolução neutra. O segundo capítulo foi dedicado a usar esta nova informação filogenética do modelo para investigar se diferentes contextos geográficos de especiação (parapátrica e simpátrica) deixam assi- naturas distintas nos padrões macroevolutivos de diversificação, como a simetria de árvores e a velocidade da diversificação. Os resultados das simulações foram com- parados com dados empíricos de radiações evolutivas. O terceiro capítulo, por fim, in- corporou barreiras espaciais ao modelo anterior, para buscar por possíveis assinaturas deixadas pela especiação alopátrica, com barreiras variando em tamanho e permitindo que indivíduos as cruzassem dependendo de seu tamanho. O modelo foi adaptado ao sistema particular dos macacos Platyrrhini, com o espaço modelado de modo a se ajustar à forma da América do Sul, e as barreiras representando os principais rios da região. O número de gerações foi adaptado a diferentes subfamílias e gêneros dos Platyrrhini, para examinar a "Riverine Hypothesis" com um enfoque de modelagem. Os resultados dos três capítulos mostraram que o espaço possui um papel fundamental na especiação quando processos neutros são os únicos a agir sob as populações, com o contexto geográfico da especiação deixando assinaturas nos padrões macroevolutivos emergentes. A incorporação de processos não neutros e a investigação do papel da extinção em moldar os padrões são possíveis passos seguintes para esta pesquisa. Abstract The impressive diversity observed in nature makes us wonder what pro- cesses could be responsible for so great variety. The answer to this question has been the goal of many evolutionary biologists, who have tried to discover the processes looking for the patterns they would generate. The development of theoretical models, particularly individual based models, is imperative to address this question, as only with models we can isolate specific processes in a controled environment, something not completely possible in natural experiments, and in a feasible time. In this thesis I investigated what are the patterns generated by an individual based model of spe- ciation in which only neutral processes and the space are regulating the dynamics of the population. The population evolved under the combined influences of sexual re- production, mutation and dispersal. In the first chapter, we developed an algorithm that records the ancestor-descendant relationships between each pair of individuals of the final community, and an algorithm which records the exact speciation and ex- tinction times of species. With both information was possible to construct genealogies and phylogenies, from which macroevolutionary patterns could be derived, offering a neutral referential of evolution. The second chapter was dedicated to use this new phy- logenetic information of the model to investigate if different geographical contexts of speciation (parapatric and sympatric) leave different signatures in the macroevolution- ary patterns of diversification, like tree symmetry and the speed of diversification. The simulations results were compared with empirical data about evolutionary radiations. The third chapter, lastly, incorporated spatial barriers to the previous model with the goal of looking for possible signatures left by allopatric speciation, with barriers vary- ing in sizes and allowing the crossing of individuals depending on the individual size. The model adapted to the particular system of Platyrrhini monkeys, with space mod- eled to fit the shape of South America, and spatial barriers representing the main rivers of the region. The number of generations was adapted to conform different subfamilies and genera of Platyrrhini monkeys, with the aim of examine the Riverine Hypothesis in a modeling approach. All results from the three chapters have showed that the space plays a fundamental role in speciation when neutral processes are the only act- ing upon populations, with the geographic context of speciation leaving signatures in the macroevolutionary patterns emerged. The incorporation of non neutral processes and the investigation of the role of extinction in shaping the patterns are possible next steps to this research. Summary 1 Introduction 11 2 Registering the evolutionary history in individual-based models of specia- tion 17 2.1 Introduction . 18 2.2 Registering the history of individuals and species . 20 2.2.1 Ancestor-descendant relationships among individuals - MRCAT 20 Asexual models . 21 Sexual models
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