lecturas
UNIDAD 1: LOS DATOS MOLECULARES
2 DE FEBRERO
*DeSalle, R. 2006. What's in a character? Journal of Biomedical Informatics 39: 6-17.
*Metzker, M. L. 2010. Sequencing technologies - the next generation. Nature Reviews. Genetics 11: 31-46. Presentado por Guadalupe Velarde.
7 DE FEBRERO
*Eickbush, T. H., and D. G. Eickbush. 2007. Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics 175: 477-485. Presentado por Jairo Rosas.
Maddison, W. P. 1997. Gene trees in species trees. Systematic Biology 46: 523-536.
UNIDAD 2: ALINEACIÓN DE SECUENCIAS Y BASES DE DATOS
9 DE FEBRERO
*Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797. Presentado por Alejandro Kong.
*Katoh, K., K. Misawa, K. Kuma, and T. Miyata. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30: 3059-3066. Presentado por Ricardo de Santiago.
Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
Wheeler, W. C. 2003. Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search. Cladistics 19: 261-268.
UNIDAD 3: PARSIMONIA
14 DE FEBRERO
Farris, J. S. 1970. Methods for computing Wagner trees. Systematic Zoology 19: 83-92.
*Simmons, M. P., and H. Ochoterena. 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369-381. Presentado por Alejandro López.
Wiley, E. O., and B. S. Lieberman. 2011. Phylogenetics: theory and practice of phylogenetic systematics. 2nd ed. John Wiley & Sons, Hoboken. Chapter 5 pp. 107-151.
16 DE FEBRERO
UNIDAD 3: PARSIMONIA
*Goloboff, P. A. 1999. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15: 415-428. Presentado por David Ortiz.
*Nixon, K. C. 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15: 407-414. Presentado por Jesus A. Cruz.
21 DE FEBRERO
*Bergsten, J. 2005. A review of long-branch attraction. Cladistics 21: 163-193. Presentado por Catalina Juárez.
23 DE FEBRERO
*Rydin, C., and M. Källersjö. 2002. Taxon sampling and seed plant phylogeny. Cladistics 18: 485-513. Presentado por Ricardo de Santiago.
28 DE FEBRERO
*Zrzavy, J., P. Riha, L. Pialek, and J. Janouskovec. 2009. Phylogeny of Annelida (Lophotrochozoa): total-evidence analysis of morphology and six genes. BMC Evolutionary Biology 9: 189. Presentado por Carolina Piña.
UNIDAD 4: MODELOS DE SUSTITUCIÓN
6 DE MARZO
*Hayasaka, K., T. Gojobori, and S. Horai. 1988. Molecular phylogeny and evolution of primate mitochondrial DNA. Molecular Biology and Evolution 5: 626-644. Presentado por Jorge Jiménez.
*Posada, D., and T. Buckley. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike Information Criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology 53: 793-808.
8 DE MARZO
*Kelchner, S. A., and M. A. Thomas. 2007. Model use in phylogenetics: nine key questions. Trends in Ecology & Evolution 22: 87-94. Presentado por David Aquino.
UNIDAD 5: MÉTODOS DE DISTANCIA
13 DE MARZO
*Galtier, N., B. Nabholz, S. Glemin, and G. D. Hurst. 2009. Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology 18: 4541-4550. Presentado por Jairo Rosas.
Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406-425.
15 DE MARZO
*Hillis, D. M., J. P. Huelsenbeck, and C. W. Cunningham. 1994. Application and accuracy of molecular phylogenies. Science 264: 671-677. Presentado por Erika Maldonado.
UNIDAD 6: MÁXIMA VEROSIMILITUD
20 DE MARZO
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution 17: 368-376.
*Felsenstein, J. 1983. Parsimony in systematics: biological and statistical issues. Annual Review of Ecology and Systematics 14: 313-333. Presentado por Jorge Mendoza.
22 DE MARZO
*Chang, B. S. W., K. Jönsson, M. A. Kazmi, M. J. Donoghue, and T. P. Sakmar. 2002. Recreating a functional ancestral archosaur visual pigment. Molecular Biology and Evolution 19: 1483-1489. Presentado por Guadalupe Velarde.
*Sullivan, J., and D. L. Swofford. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. Journal of Mammalian Evolution 4: 77-86. Presentado por Carolina Piña.
Swofford, D. L., P. J. Waddell, J. P. Huelsenbeck, P. G. Foster, P. O. Lewis, and J. S. Rogers. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Systematic Biology 50: 525-539.
UNIDAD 7: APOYO DE RAMAS
27 DE MARZO
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
*Hillis, D. M., and J. J. Bull. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42: 182-192. Presentado por Jorge Mendoza.
29 DE MARZO
*Felsenstein, J., and H. Kishino. 1993. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Systematic Biology 42: 193-200. Presentado por Erika Maldonado.
UNIDAD 8: INFERENCIA BAYESIANA
12 DE ABRIL
*Holder, M., and P. O. Lewis. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nature Reviews Genetics 4: 275-284. Presentado por Jesus A. Cruz.
17 DE ABRIL
*Nylander, J. A. A., F. Ronquist, J. P. Huelsenbeck, and J. L. Nieves-Aldrey. 2004. Bayesian phylogenetic analysis of combined data. Systematic Biology 53: 47-67. Presentado por David Aquino.
UNIDAD 9: RELOJES MOLECULARES
19 DE ABRIL
*Nagalingum, N. S., C. R. Marshall, T. B. Quental, H. S. Rai, D. P. Little, and S. Mathews. 2011. Recent synchronous radiation of a living fossil. Science 334: 796-799. Presentado por Gerardo Contreras.
*Welch, J. J., and L. Bromham. 2005. Molecular dating when rates vary. Trends in Ecology & Evolution 20: 320-327. Presentado por Jorge Jiménez.
24 DE ABRIL
*Drummond, A. J., S. Y. W. Ho, M. J. Phillips, and A. Rambaut. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology e88: 699-717. Presentado por Catalina Juárez.
*Magallón, S. A. 2004. Dating lineages: molecular and paleontological approaches to the temporal framework of clades. International Journal of Plant Sciences 165: S7-S21. Presentado por David Ortiz.
Wertheim, J. O., M. J. Sanderson, M. Worobey, and A. Bjork. 2009. Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference. Systematic Biology 59: 1-8.
UNIDAD 10: PRUEBAS DE TOPOLOGÍAS DE ÁRBOLES
26 DE ABRIL
Farris, J. S., M. Källersjö, A. G. Kluge, and C. Bult. 1995. Testing significance of incongruence. Cladistics 10: 315-319.
*Goldman, N., J. Anderson, and A. Rodrigo. 2000. Likelihood-based tests of topologies in phylogenetics. Systematic Biology 49: 652-670.
Templeton, A. R. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37: 1-244.
8 DE MAYO
Degnan, J. H., and N. A. Rosenberg. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in Ecology & Evolution 24: 332-340.
*Hipp, A., J. Hall, and K. Sytsma. 2004. Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test. Systematic Biology 53: 81-89. Presentado por Alejandro Kong.
*Rowe, K. C., K. P. Aplin, P. R. Baverstock, and C. Moritz. 2011. Recent and rapid speciation with limited morphological disparity in the genus Rattus. Systematic Biology 60: 188-203. Presentado por Gerardo Contreras.