Área de Concentração: 38131

Concentration area: 38131

Criação: 01/12/2021

Creation: 01/12/2021

Ativação: 03/12/2021

Activation: 03/12/2021

Nr. de Créditos: 8

Credits: 8

Carga Horária:

Workload:

Docente Responsável:

Professor:

Mario Cesar Cardoso de Pinna

Objetivos:

Fornecer as bases teóricas e metodológicas da sistemática filogenética, com um panorama geral dos métodos de reconstrução filogenética atuais e suas principais aplicações em biologia comparada.

Objectives:

To provide the theoretical and methodological bases of phylogenetic systematics, with a general overview of the methods of phylogenetic reconstruction and their main applications in comparative biology.

Justificativa:

A sistemática filogenética é uma disciplina central na biologia comparada, fornecendo os fundamentos para a elucidação de padrões evolutivos e um arcabouço geral para a ordenação do conhecimento biológico. Hipóteses filogenéticas constituem o alicerce sobre o qual grande parte das inferências em biologia evolutiva são atualmente baseadas.

Rationale:

Phylogenetic systematics is a central discipline in comparative biology, providing the foundations for the elucidatin of evolutionary patterns and a general framework for the organization of biological knowledge. Phylogenetic hypotheses are the pillars on which a major portion of evolutionary inference is based.

Conteúdo:

1. História da sistemática filogenética. 2. Bases filosóficas da sistemática biológica. 3. Dendrogramas e cladogramas: noções básicas. 4. grupos naturais e não-naturais. Relações de parentesco como hipóteses. Monofiletismo, parafiletismo e polifiletismo. 5. Dicotomias, politomias e suas interpretações evolutivas. 6. Evidências: caracteres e tipos de caracteres. 7. Apomorfias, sinapomorfias, plesiomorfias e simplesiomorfias. 8. Análise de parcimônia, homoplasias: convergências e reversões. 9. Caracteres multiestados, aditividade e não-aditividade, codificação binária aditiva. 10. Métodos de otimização, otimização em dicotomias e politomias, otimizações ambíguas. 12. Métricas de árvores: comprimento, índice de consistência, índice de retenção, índice de consistência reescalonado. 13. Ponderação de caracteres: a priori, aproximações sucessivas, pesos implicados, funções gerais de pesagem. 14. Estimativas de suporte: bootstrap, jacknife, suporte de Bremer, suporte total. 15. Diagramas não-enraizados: interpretação e aplicações, direcionalidade, métodos de enraizamento e de direcionamento. Raizes reais, raizes virtuais e localizadores de raiz. 16. Particularidades dos dados qualitativos, quantitativos e de sequências nucleotídicas, alinhamento, homologia, homologia dinâmica. 17. Homoplasia, informação filogenética e correlação hierárquica. Homoplasia e erros. O que é acurácia filogenética? 18. Inferências estatísticas de filogenias: máxima verossimilhança e análise Bayesiana, parâmetros e interpretação estatística de parcimônia. 19. Méritos e defeitos dos métodos paramétricos e não-paramétricos. 20. Modelos evolutivos. Plausibilidade ou não de mecanismos gerais em análises evolutivas: super-parametrização ou subparametrização? Atração e repulsão de ramos longos, efeitos de desigualdade de comprimento de ramos sobre inferência filogenética. 20. Análise genômica e NexGen: relevância para inferência filogenética. 21. Aplicações de hipóteses filogenéticas em outros campos: biogeografia, ecologia histórica, cenários evolutivos, filomemética, evolução cultural.

Content:

1. History of phylogenetic systematics. 2. Philosophical bases of biological systematics. 3. Dendrograms and cladograms: basic notions. 4. Natural and non-natural groupings. Kinship relationships as hypotheses. Monophyly, paraphyly and polyphyly. 5. Dichotomies, polytomies and their evolutionary interpretations. 6. Evidence: characters and types of characters. 7. Apomorphies, synapomorphies, plesiomorphies and symplesiomorphiesfias. 8. Parsimony analysis, homoplasies: convergences and reversal. 9. Multistate characters, additivity and non-additivity, additive binary coding. 10. Optimization methods, optimization in dichotomies and polytomies, ambiguous optimizations. 12. Tree metrics: tree length, consistency index, retention index, rescaled consistency index. 13. Character weighting: a priori, successive approximations, implied weights, general weighting functions. 14. Support estimation: bootstrap, jacknife, Bremer support, total support. 15. Unrooted networks: logic, mechanics, interpretations and applications, directionality, rooting and directionality methods. Real roots, virtual roots and root locators. 16. Discrete, continuous and sequence data, aligment, dynamic homology. 17. Homoplasy, hierarchical correlation; homoplasy and errors; phylogenetic accuracy? 18. Statistical inference of phylogenies: maximum likelihood and Bayesian inference; paramaters, statistical interpretation of parsimony. 19. Merits and drawbacks of parametric and non-parametric methods. 20. Evolutionary models. Plausibility and unplausibility of general mechanisms in evolutionary analyses: super-parametrization or ção ou subparametrization? Long-branch attraction and repulsion, effects of length disparity on phylogenetic accuracy. 20. Genomic analysis, multilocus and NexGen: relevance for phylogenetic inference. 21. Applications of phylogenetic hypotheses in other fields: biogeography, histprical ecology, evolutionary scenarios, phylomemetics, cultural evolution.

Forma de Avaliação:

Participação nas discussões durante a disciplina e um seminário final.

Type of Assessment:

Participation in discussions during classes and a term paper presentation.

Bibliografia:

Albert, V. A. 2006. Parsimony, Phylogeny, and Genomics. Oxford University Press. Alfaro, M. E., and M. T. Holder. 2006. The posterior and the prior in Bayesian phylogenetics. Annu. Rev. Ecol. Evol. Syst. 37: 19–42. Darlu, P. & Tassy, P. 1993. La reconstruction phylogénétique, concepts et méthodes. Masson, Paris. Farris, J. S. 1969. A successive approximations approach to character weighting. Syst. Biol. 18: 374–385. Farris, J. S. 1977. Phylogenetic analysis under Dollo’s law. Syst. Biol. 26: 77–88. Farris, J. S. 1983. The logical basis of phylogenetic analysis. In N. I. Platnick and V. A. Funk (editors), Advances in Cladistics: 277–302. New York: Columbia University Press. Farris, J. S., A. G. Kluge, and M. J. Eckardt. 1970. A numerical approach to phylogenetic systematics. Syst. Zool. 19: 172–189. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Biol. 27: 401–410. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368–376. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Sunderland. Forey, P.L., Humphries, C.J., Kitching, I.L., Scotland,R.W., Siebert, D.J. & Williams, D.M. 1992. Cladistics - A practical course in systematics. The Systematics Association, Publ. 10, Clarendon Press, Oxford. Goloboff, P. A. 1993. Estimating character weights during tree search. Cladistics 9: 83–91. Goloboff, P. A., Mattoni, C. I., and A. S. Quinteros. 2006. Continuous characters analyzed as such. Cladistics, 22: 589–601. Goloboff, P. A, M. Pittman, D. Pol, and X. Xu. 2019. Morphological data sets fit a common mechanism much more poorly than DNA sequences and call into question the Mkv model. Syst. Biol. 68: 494–504. Hall, B. 2004. Phylogenetic trees made easy: a how-to manual. Sinauer Associates, sunderland. Harvey, P. H., Leigh-Brown, A. J., Maynard-Smith, J., & Nee, S. (Eds.). 1996. New uses for new phylogenies. Oxford University Press, Oxford. Hennig, W. 1966. Phylogenetic Systematics. University of Illinois Press, Urbana. Kitching, I.L., Forey, P.L., Humphries, C.J. & Williams, D.M. 1998. Cladistics, 2nd Ed. - the theory and practice of parsimony analysis. The Systematics Association, publ. 11, Oxford University Press, Oxford. Lemey, P. Salemi, M. & Vandamme, A. M. 2009. The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. Cambridge University Press, Cambridge. Minelli, A. 1993. Biological systematics, the state of the art. Chapman & Hall, London. Nelson, G.J. & Platnick, N.I. 1981. Systematics and biogeography - cladistics and vicariance. Columbia University Press, New York. Page, R. D. M. & Holmes, E. C. 1998. Molecular evolution, a phylogenetic approach. Blackwell Science, Oxford. Parins-Fukuchi, C. 2018. Bayesian placement of fossils on phylogenies using quantitative morphometric data. Evolution 72: 1801–1814. Rieppel, O. 1988. Fundamentals of comparative biology. Birkhäuser, Basel. Salemi, M. & Vandamme, A. M. (Eds.). 2003. The phylogenetic handbook, a practical approach to DNA and protein phylogeny. Schuh, R.T. 2000. Biological systematics: principles and applications. Cornell university Press. Wägele, J. W. 2005. Foundations of phylogenetic systematics. Verlag Dr. Friedrich Pfeil, München. Wheeler, W., Aagese, L., Arango, C.P., Faivovich, J., Grant, T., D'Haese, C., Janies, D., Smith, W.L., Varón, A., & Giribet, G. 2006. Dynamic homology and phylogentic systematics: a unified approach using POY. American Museum of Natural History, New York. Wiens, J. J. (Ed.). 2000. Phylogenetic analysis of morphological data. Smithsonian Institution Press, Washington, D.C. Wiley, E.O. 1981. Phylogenetics - the theory and practice of phylogenetic systematics. wiley Interscience, New York. Wiley, E. O. , D. Siegel-Causey , D. R. Brooks , and V. A. Funk . 1991. The compleat cladist: a primer of phylogenetic procedures. Special Publication, The University of Kansas Museum of Natural History 19:1– 158. Wiley E.O.. & Lieberman. 2011. Phylogenetics: Theory and Practice of Phylogenetic Systematics, 2nd Edition. Wiley Blackwell. Wright, A. M. 2019. A Systematist’s Guide to Estimating Bayesian Phylogenies From Morphological Data. Insect Systematics and Diversity, 3(3): 2; 1–14

Bibliography:

Albert, V. A. 2006. Parsimony, Phylogeny, and Genomics. Oxford University Press. Alfaro, M. E., and M. T. Holder. 2006. The posterior and the prior in Bayesian phylogenetics. Annu. Rev. Ecol. Evol. Syst. 37: 19–42. Darlu, P. & Tassy, P. 1993. La reconstruction phylogénétique, concepts et méthodes. Masson, Paris. Farris, J. S. 1969. A successive approximations approach to character weighting. Syst. Biol. 18: 374–385. Farris, J. S. 1977. Phylogenetic analysis under Dollo’s law. Syst. Biol. 26: 77–88. Farris, J. S. 1983. The logical basis of phylogenetic analysis. In N. I. Platnick and V. A. Funk (editors), Advances in Cladistics: 277–302. New York: Columbia University Press. Farris, J. S., A. G. Kluge, and M. J. Eckardt. 1970. A numerical approach to phylogenetic systematics. Syst. Zool. 19: 172–189. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Biol. 27: 401–410. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368–376. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Sunderland. Forey, P.L., Humphries, C.J., Kitching, I.L., Scotland,R.W., Siebert, D.J. & Williams, D.M. 1992. Cladistics - A practical course in systematics. The Systematics Association, Publ. 10, Clarendon Press, Oxford. Goloboff, P. A. 1993. Estimating character weights during tree search. Cladistics 9: 83–91. Goloboff, P. A., Mattoni, C. I., and A. S. Quinteros. 2006. Continuous characters analyzed as such. Cladistics, 22: 589–601. Goloboff, P. A, M. Pittman, D. Pol, and X. Xu. 2019. Morphological data sets fit a common mechanism much more poorly than DNA sequences and call into question the Mkv model. Syst. Biol. 68: 494–504. Hall, B. 2004. Phylogenetic trees made easy: a how-to manual. Sinauer Associates, sunderland. Harvey, P. H., Leigh-Brown, A. J., Maynard-Smith, J., & Nee, S. (Eds.). 1996. New uses for new phylogenies. Oxford University Press, Oxford. Hennig, W. 1966. Phylogenetic Systematics. University of Illinois Press, Urbana. Kitching, I.L., Forey, P.L., Humphries, C.J. & Williams, D.M. 1998. Cladistics, 2nd Ed. - the theory and practice of parsimony analysis. The Systematics Association, publ. 11, Oxford University Press, Oxford. Lemey, P. Salemi, M. & Vandamme, A. M. 2009. The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. Cambridge University Press, Cambridge. Minelli, A. 1993. Biological systematics, the state of the art. Chapman & Hall, London. Nelson, G.J. & Platnick, N.I. 1981. Systematics and biogeography - cladistics and vicariance. Columbia University Press, New York. Page, R. D. M. & Holmes, E. C. 1998. Molecular evolution, a phylogenetic approach. Blackwell Science, Oxford. Parins-Fukuchi, C. 2018. Bayesian placement of fossils on phylogenies using quantitative morphometric data. Evolution 72: 1801–1814. Rieppel, O. 1988. Fundamentals of comparative biology. Birkhäuser, Basel. Salemi, M. & Vandamme, A. M. (Eds.). 2003. The phylogenetic handbook, a practical approach to DNA and protein phylogeny. Schuh, R.T. 2000. Biological systematics: principles and applications. Cornell university Press. Wägele, J. W. 2005. Foundations of phylogenetic systematics. Verlag Dr. Friedrich Pfeil, München. Wheeler, W., Aagese, L., Arango, C.P., Faivovich, J., Grant, T., D'Haese, C., Janies, D., Smith, W.L., Varón, A., & Giribet, G. 2006. Dynamic homology and phylogentic systematics: a unified approach using POY. American Museum of Natural History, New York. Wiens, J. J. (Ed.). 2000. Phylogenetic analysis of morphological data. Smithsonian Institution Press, Washington, D.C. Wiley, E.O. 1981. Phylogenetics - the theory and practice of phylogenetic systematics. wiley Interscience, New York. Wiley, E. O. , D. Siegel-Causey , D. R. Brooks , and V. A. Funk . 1991. The compleat cladist: a primer of phylogenetic procedures. Special Publication, The University of Kansas Museum of Natural History 19:1– 158. Wiley E.O.. & Lieberman. 2011. Phylogenetics: Theory and Practice of Phylogenetic Systematics, 2nd Edition. Wiley Blackwell. Wright, A. M. 2019. A Systematist’s Guide to Estimating Bayesian Phylogenies From Morphological Data. Insect Systematics and Diversity, 3(3): 2; 1–14

Tipo de oferecimento da disciplina:

Presencial

Class type:

Presencial