Servicio de información y contacto de la comunidad filogenética                              

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Postgrado, INECOL.

Xalapa, Ver

13 de Abril a 18 de Junio, 2009.

Semana 1: Introducción.

• C. Jill Harrison and Jane A. Langdale. 2006. A step by step guide to phylogeny reconstruction

• Efrain De Luna, José A. Guerrero y Tania Chew-Taracena. 2005. Sistemática biológica: avances y direcciones en la teoría y los métodos de la reconstrucción filogenética

• Efrain De Luna y Brent D. Mishler. 1996. El concepto de homologia filogenetica

Semana 2: Caracteres.

• N. Gift & PF Stevens. 1997.  Vagaries in the delimitation of character states

• Pablo A. Goloboff, Camilo I. Mattoni and Andrés Sebastián Quinteros. 2006.   Continuous characters analyzed as such

• David A. Morrison. 2008.  A framework for phylogenetic sequence alignment

Semana 3: Modelos.

•  David Posada. Selecting models of evolution
•  Unordered versus Ordered characters
•  Character weighting and cladistic analysis
•  Weighting against homoplasy improves phylogenetic analysis of morphological data sets

Semana 4: Selección de arboles óptimos.

•  Efficient Tree Searches with Available Algorithms
•  Techniques for Analyzing Large Data Sets
•  When are phylogeny estimates from molecular and morphological data incongruent?
•  Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups
•  Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

Semana 5: Criterios de optimalidad: parsimonia y probabilisticos.

• Phylogeny estimation .... using maximum likelihood
• Verosimilitud
• Efficiency of ML searches under different models
• Parsimony accelerated Maximum Likelihood searches
• LRT vs AIC vs BIC
• Parsimony, likelihood, and simplicity
• The Posterior and the Prior in Bayesian Phylogenetics
• PHYLOGENY ESTIMATION: TRADITIONAL AND BAYESIAN APPROACHES
• Potential Applications and Pitfalls of Bayesian Inference of Phylogeny

Semana 6: Métodos de Evaluación.

• Support versus corroboration
• Branch support and tree stability
• Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous documento
• Likelihood-Based Tests of Topologies in Phylogenetics
• Measures of Support
• Tree disagreement: Measuring and testing incongruence in phylogenies

Semana 7: Homologia dinámica.

• OPTIMIZATION ALIGNMENT: THE END OF MULTIPLE SEQUENCE ALIGNMENT IN PHYLOGENETICS?
• Homology and the Optimization of DNA Sequence Data
• Implied alignment: a synapomorphy-based multiple-sequence alignment
• The relative sensitivity of different alignment methods and character codings in sensitivity analysis
• Finding an upper limit for gap costs in direct optimization parsimony
• Phylogeny of the sea spiders (Arthropoda, Pycnogonida) based on direct optimization of six loci and morphology
• Homology as a parsimony problem: a dynamic homology approach for morphological data

Semana 8: Biogeografía cladística.

• ASSUMPTION 0 ANALYSIS: COMPARATIVE PHYLOGENETIC STUDIES IN THE AGE OF COMPLEXITY
• Introduccion .... Biogeografia Cladistica
• Computational aspects of host–parasite phylogenies
• Prospects and challenges for parametric models in historical biogeographical inference

Semana 9: Filogenomica. Filogeografia.

• A Phylogenomic Study of Birds Reveals Their Evolutionary History
• WHY DOES A METHOD THAT FAILS CONTINUE TO BE USED?
• Phylogenomics: Gene Duplication, Unrecognized Paralogy and Outgroup Choice
• Phylogenomics Reshuffles the Eukaryotic Supergroups
• The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome
• Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis
• Breakpoint graphs and ancestral genome reconstructions
• Tree of Life Based on Genome Context Networks

Semana 10: Conclusión.

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Editor: Efraín De Luna, Depto. de Biodiversidad y Sistemática, INECOL , AC.

Creado:  Julio, 2006. Modificado: 17 ago 2009