Inferencia Filogenetica
Lecturas
1. 5 de febrero. Presentación del curso. DG/FV
2. 12 de febrero. Introducción. FV
Hennig W (1965). Phylogenetic Systematics. Annual Reviews in Entomology 10(1), 97–116.
*Rieppel O (2008). Hypothetico-deductivism in systematics: fact or fiction? Papéis Avulsos Zoologia 48(23), 263–273.
Schuh RT (2000). Biological Systematics: Principles and Applications. Ithaca: Cornell University Press. Pp. 1-28.
Williams DM and Ebach MC (2007). Foundations of Systematics and Biogeography. Springer. Foreword & Prologue.
3. 19 de febrero. Homología. FV
*de Pinna M (1991). Concepts and tests of homology in the cladistic paradigm. Cladistics 7(4), 367–394.
Williams D and Ebach M (2006). The data matrix. Geodiversitas 28(3), 409-420.
Wagner G (2007). The developmental genetics of homology. Nature Reviews Genetics 8(6), 473–9.
4. 26 de febrero. Caracteres. FV
*Fitzhugh K (2006). The philosophical basis of character coding for the inference of phylogenetic hypotheses. Zoologica Scripta 35(3), 261–286.
Kitching IJ, Forey PL, Humphries CJ and Williams DM . 1998. Cladistics: The Theory and Practice of parsimony Analysis, 2nd edition, Oxford University Press, Oxford. Cap. 2.
5. 5 de marzo. Polarización de caracteres. FV
Lipscomb D (1992). Parsimony, homology and the analysis of multistate characters. Cladistics 8(1), 45–65.
Mickevich M and Lipscomb D (1991). Parsimony and the choice between different transformations for the same character set. Cladistics 7(2), 111–139.
Kitching IJ, Forey PL, Humphries CJ and Williams DM . 1998. Cladistics: The Theory and Practice of parsimony Analysis, 2nd edition, Oxford University Press, Oxford. Cap. 3.
*Nixon K and Carpenter J (1993). On outgroups. Cladistics 9(4), 413–426.
6. 12 de marzo. Búsquedas exactas y heurísticas. DG
Nixon KC (1999). The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15(4), 407-414.
Felsenstein J (2003). Inferring Phylogenies. Sinauer Associates, Sunderland, MA. Caps. 1-3.
Farris J (1970). Methods for computing Wagner trees. Systematic Zoology
19, 83–92.
7. 19 de marzo. Optimización de caracteres y medidas de su comportamiento. DG
Goloboff P (1993). Estimating character weights during tree search. Cladistics 9(1), 83–91.
Goloboff P (1999). Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15(4), 415-428.
Felsenstein J (2003). Inferring Phylogenies. Sinauer Associates, Sunderland, MA. Caps. 4-6.
8. 26 de marzo. Evaluación de resultados I: procesos de aleatorización.DG
Farris J (1974). Formal definitions of paraphyly and polyphyly. Systematic Zoology 23, 548–554.
Felsenstein J (2003). Inferring Phylogenies. Sinauer Associates, Sunderland, MA. Caps. 7-8, 20.
9. 2 de abril. Evaluación de resultados II: árboles de consenso. DG
Carpenter J (1988). Choosing among multiple equally parsimonious cladograms. Cladistics 4, 291–296.
Felsenstein J (2003). Inferring Phylogenies. Sinauer Associates, Sunderland, MA. Cap. 9-10, 30.
10. 16 de abril. Métodos de distancia. DG
Cavalli-Sforza LL and Edwards AWF (1965). Phylogenetic analysis: models and estimation procedures. Evolution 21: 550-70.
Saitou N and Nei M (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4, 406-25.
Felsenstein J (2003). Inferring Phylogenies. Sinauer Associates, Sunderland, MA. Cap. 11-12.
11. 23 de abril. Análisis separado y simultáneo. GS
Bull JJ, Huelsenbeck JP, Cunningham CW, Swofford DL and Waddell PJ (1993). Partitioning and combining data in phylogenetic analysis. Systematic Biology 42, 384-97.
Kitching IJ, Forey PL ,Humphries CJand Williams DM . 1998. Cladistics: The Theory and Practice of parsimony Analysis, 2nd edition, Oxford University Press, Oxford. Cap. 8.
12. 30 de abril. Modelos de evolución de caracteres. GS
Felsenstein J (2003). Inferring Phylogenies. Sinauer Associates, Sunderland, MA. Cap. 13-14.
Lewis PO (1998). Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data. Pp. 132-163 en Molecular Systematics of Plants II: DNA Sequencing (eds. DE Soltis, PS Soltis, JJ Doyle). Kluwer, Boston.
13. 7 de mayo. Máxima verosimilitud. GS
Posada D and Buckley T (2004). Model selection and model averaging in phylogenetics: advantages of Akaike Information Criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology 53(5), 793–808.
Felsenstein J (2003). Inferring Phylogenies. Sinauer Associates, Sunderland, MA. Cap. 15-16.
14. 14 de mayo. Inferencia Bayesiana. GS
Huelsenbeck JP, Larget B, Miller RE and Ronquist F (2002). Potential applications and pitfalls of Bayesian inference of phylogeny. Systematic Biology 51(15), 673-88.
Nylander, JAA, Ronquist F and Huelsenbeck JP (2004). Bayesian phylogenetic analysis of combined data. Systematic Biology 53(1), 47-67.
Felsenstein J (2003). Inferring Phylogenies. Sinauer Associates, Sunderland, MA. Cap. 17-18.
15. 21 de mayo. Probando hipótesis con parsimonia y verosimilitud. GS
Goldman N, Anderson J and Rodrigo A (2000). Likelihood-based tests of topologies in phylogenetics. Systematic Biology 49(4), 652–670.
Hipp A, Hall J and Sytsma K (2004). Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test. Systematic Biology 53(1), 81–89.
Felsenstein J (2003). Inferring Phylogenies. Sinauer Associates, Sunderland,
MA. Cap. 19, 21.
16. 28 de mayo. Examen global.