Servicio de información y contacto de la comunidad filogenética                              




"Teoría y Métodos Cladísticos"

Postgrado, INECOL.

Xalapa, Ver

13 de Abril a 18 de Junio, 2009.

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(Lista publicada en el articulo: De Luna, E., JA. Guerrero & T. Chew-Taracena. 2005. Sistemática Biológica: avances y direcciones en la teoría y los métodos de la reconstrucción filogenética. Hidrobiológica 15(3): 351-370.

ALBERT, V. A., M. W. CHASE & B. D. MISHLER. 1993. Character state weighting for cladistic analysis of protein-coding DNA sequences. Annals of the Missouri Botanical Garden 80: 752-766.

ALFARO, M. E., S. ZOLLER & F. LUTZONI. 2003. Bayes or Bootstrap? A simulation study comparing the performance of Bayesian Markov Chain Monte Carlo sampling and bootstraping in assessing phylogenetic confidence. Molecular Biology and Evolution 20: 255-266.

ARCHIE, J. W. 1985. Methods for coding variable morphological features for numerical taxonomic analysis. Systematic Zoology 34 (3): 326-345.

ARIAS, J. S. & D. R. MIRANDA-ESQUIVEL. 2004. Profile Parsimony (PP): an analysis under Implied Weights (IW). Cladistics 20: 56-63.

BANG, R., R. DESALLE & W. WHEELER. 2000. Transformationalism, taxism, and developmental biology in systematics. Systematic Biology 49 (1): 19-27.

BAPTESTE, E., H. BRINKMANN, J. A. LEE, D. V. MOORE, C. W. SENSEN, P. GORDON, L. DURUFLÉ, T. GAASTERLAND, P. LOPEZ, M. MÜLLER & H. PHILIPPE. 2002. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proceedings of the National Academy of Sciences 99 (3): 1414-1419.

BARRETT, M., M. J. DONOGHUE & E. SOBER. 1991. Against Consensus. Systematic Zoology 40 (4): 486-493.

BILLERA, L. J., S. P. HOLMES & K. VOGTMANN. 2001. Geometry of the space of phylogenetic trees. Advances in Applied Mathematics 27: 733-767.

BOLKER, J. A. & R. A. RAFF. 1996. Developmental genetics and traditional homology. BioEssays 18 (6): 489-494.

BROOKS, D. R. & D. A. MCLENNAN. 1991. Phylogeny, ecology, and behavior. A research program in comparative biology. The University of Chicago Press, Chicago y Londres. 434 p.

BROOKS, D. R. & D. A. MCLENNAN. 1993. Historical ecology: examining phylogenetic components of community evolution. In: R. E. Ricklefs & A. D. Schwter (Eds.). Species diversity in ecological communities. University of Chicago Press. pp. 267-296.

BRYANT, H. N. 2001. Character polarity and the rooting of cladograms. In: G. P. Wagner (Ed.). The character concept in evolutionary biology. Academic Press. pp. 321-340.

CARPENTER, J. M. 1992. Random cladistics. Cladistics 8: 147-153.

CHANG, J. T. 1996. Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters. Mathematical Biosciences 134: 189-215.

CHERNOFF, B., T. DUNCAN, T. ELIAS, M. MISHLER, E. NOVACEK, E. THERIOT, Q. D. WHEELER & D. S. WOOD. 1989. Commentary on the place of systematics. ASC Newsletter 17 (1): 1-2.

CRACRAFT, J. 2002. The seven great questions of systematic biology: An essential foundation for conservation and the sustainable use of diversity. Annals of the Missouri Botanical Garden 89: 127-144.

CRACRAFT, J. & K. HELM-BYCHOWSKI. 1991. Parsimony and phylogenetic inference using DNA sequences: some methodological strategies. In: M. M. Miyamoto & J. Cracraft (Eds.). Phylogenetic analysis of DNA sequences. Oxford University Press. pp. 184-220.

CRAWFORD, D. J. & M. E. MORT. 2003. New Trends in plant systematics. Taxon 52: 3-7.

CRISCI, J. C. 1982. Parsimony in evolutionary theory: law or methodological prescription? Journal of Theoretical Biology 97: 35-41.

CUNNINGHAM, C. W. 1997. Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods. Systematic Biology 46 (3): 464-478.

DE BEER, G. R. 1971. Homology, an unsolved problem. Oxford University Press, London. 16 p.

DE LUNA, E. 1995. Bases filosóficas de los análisis cladísticos para la investigación taxonómica. Acta Botánica Mexicana 33: 63-79.

DE LUNA, E. 1996. Epistemología de la Investigación Taxonómica: Inferencias Filogenéticas y su Evaluación. Boletín de la Sociedad Botánica de México 58: 43-53.

DE LUNA, E. & B. D. MISHLER. 1996. El concepto de Homología Filogenética y la selección de caracteres taxonómicos. Boletín de la Sociedad Botánica de México 59: 131-146.

DE PINNA, M. C. 1991. Concepts and tests of Homology in the Cladistic Paradigm. Cladistics 7: 367-394.

DE PINNA, M. C. 1996. Comparative Biology and Systematics: Some controversies in retrospective. Journal of Comparative Biology 1 (1/2): 3-16.

DE QUEIROZ, A., M. J. DONOGHUE & J. KIM. 1995. Separate versus combined analysis of phylogenetic evidence. Annual Review of Ecology and Systematics 26: 657-681.

DE QUEIROZ, K. 1997. The Linnean hierarchy and the evolutionization of taxonomy, with emphasis on the problem of nomenclature. Aliso 15(2): 125-144.

DE QUEIROZ, K. 2004. The measurement of test severity, significance tests for resolution, and a unified philosophy of phylogenetic inference. Zoologica Scripta 33 (5): 463-473.

DE QUEIROZ, K. & S. POE. 2001. Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper´s writings on corroboration. Systematic Biology 50 (3): 305-321.

DE QUEIROZ, K. & S. POE. 2003. Failed refutations: further comments on parsimony and likelihood methods and their relationship to Popper´s degree of corroboration. Systematic Biology 52 (3): 352-367.

DOUADY, C. J., F. DELSUC, Y. BOUCHER, W. F. DOOLITLE & E. J. P. DOUZERY. 2003. Comparison of Bayesian and Maximum Likelihood bootstrap measures of phylogenetic reliability. Molecular Biology and Evolution 20: 248-254.

DOYLE, J. J. 1993. DNA, Phylogeny, and the Flowering of Plant Systematics. BioScience 43 (6): 380-389.

DOYLE, J. J. & J. I. DAVIS. 1998. Homology in molecular phylogenetics: a parsimony perspective. In: D. E. Soltis & P. S. Soltis (Eds.). Molecular systematics of Plants II. DNA sequencing. Kluwer Academic Publishers. pp. 101-131.

EDWARDS, A. W. F. 1996. The origin and early development of the method of minimum evolution for the reconstruction of phylogenetic trees. Systematic Biology 45 (1): 79-91.

EDWARDS, A. W. F. & L. L. CAVALLI-SFORZA. 1964. Reconstruction of evolutionary trees. In: V. H. Heywood & J. McNeill (Eds.). Phenetic and phylogenetic classification. Systematics Association Publication 6. London. pp. 67-76.

FARRIS, J. S. 1969. A successive approximation approach to character weighting. Systematic Zoology 18: 374-385.

FARRIS, J. S. 1983. The Logical Basis of Phylogenetic Analysis. Advances in Cladistics 2: 7-35.

FARRIS, J. S. 1986. On the boundaries of phylogenetic systematics. Cladistics 2: 14-27.

FARRIS, J. S. 1999. Likelihood and inconsistency. Cladistics 15: 199-204.

FARRIS, J. S. 2000. Corroboration versus "strongest evidence". Cladistics 16: 385-393.

FARRIS, J. S. 2001. Support weighting. Cladistics 17: 389-394.

FELSENSTEIN, J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Systematic Zoology 27: 401-410.

FELSENSTEIN, J. 1981. A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biological Journal of the Linnaean Society 16: 183-196.

FELSENSTEIN, J. 1982. Numerical methods for inferring evolutionary trees. Quarterly Review of Biology 57: 127-141.

FELSENSTEIN, J. 1988. Phylogenies from molecular sequences: inference and reliability. Annual Review of Genetics 22: 521-565.

FELSENSTEIN, J. 2001. The troubled growth of statistical phylogenetics. Systematic Biology 50 (4): 465-467.

FELSENSTEIN, J. 2004. Inferring phylogenies. Sinauer Associates, Inc., Massachusetts. 664 p.

FELSENSTEIN, J. & E. SOBER. 1986. Parsimony and likelihood: an exchange. Systematic Zoology 35: 617-626.

FERRARIS, J. D. & S. R. PALUMBI. 1996. Molecular zoology. Advances strategies, and protocols. Wiley-Liss, Inc., 580 p.

FLORES-VILLELA, O., K. M. KJER, M. BENABIB & J. W. SITES. 2000. Multiple data sets, congruence, and hypothesis testing for the phylogeny of basal groups of the lizard genus Sceloporus (Squamata, Phrynosomatidae). Systematic Biology 49 (4): 713-739.

FROST, D. R. & A. G. KLUGE. 1994. A consideration of epistemology in systematic biology, with special reference to species. Cladistics 10: 259-294.

GAUCH, H. G. 1982. Multivariate analysis in community ecology. Cambridge University Press, Cambridge. 298 p.

GIFT, N. & P. F. STEVENS. 1997. Vagaries in the delimitation of character states in quantitative variation- an experimental study. Systematic Biology 46 (1): 112-125.

GIRIBET, G. 2003. Stability in phylogenetic formulations and its relationship to nodal support. Systematic Biology 52 (4): 554-564.

GOLDMAN, N. 1990. Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analysis. Systematic Zoology 39: 345-361.

GOLOBOFF, P. A. 1993. Estimating character weights during tree search. Cladistics 9: 83-91.

GOLOBOFF, P. A. 1999. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15: 415-428.

GOLOBOFF, P. A. 2003. Parsimony, likelihood and simplicity. Cladistics 19: 91-103.

GOLOBOFF, P.A., FARRIS, J.S., KÄLLERSJÖ, M., OXELMAN, B., RAMÍREZ, M.J., SZUMIK, C.A., 2003. Improvements to resampling measures of group support. Cladistics 19: 324-332.

GONZÁLEZ, D. 1996. Codificación de las inserciones-deleciones en el análisis filogenético de secuencias génicas. Boletín de la Sociedad Botánica de México 59: 115-129.

GONZÁLEZ, D. 1997. El uso de secuencias génicas para estudios taxonómicos. Boletín de la Sociedad Botánica de México 60: 137-157.

GONZÁLEZ, D. 1998. Marcadores moleculares para los estudios comparativos de la variación en Ecología y Sistemática. Revista Mexicana de Micología. 14: 1-21.

GRANT, T. & A. G. KLUGE. 2004. Transformation Series as an Ideographic Character Concept. Cladistics 20: 23-31.

GRANT, T., J. FAIVOVICH & D. POL. 2003. The perils of 'point and click' systematics. Cladistics 19 (3): 276-285.

GRAYBEAL, A. 1998. Is It Better to Add Taxa or Characters to a Difficult Phylogenetic Problem? Systematic Biology 47 (1): 9-17.

GUERRERO, J. A., E. DE LUNA & C. SANCHEZ-HERNANDEZ. 2003. Morphometrics in the quantification of character state identity for the assessment of primary homology: an analysis of character variation of the genus Artibeus (Chiroptera: Phyllostomidae). Biological Journal of the Linnaean Society 80: 45-55.

HÄRLIN, M. 2003. Taxon names as paradigms: the structure of nomenclatural revolutions. Cladistics 19: 138-143.

HARPER, C. W. J. 1979. A Bayesian probability view of phylogenetic systematics. Systematic Zoology 28: 547-553.

HARVEY, P. H. & M. D. PAGEL. 1991. The comparative method in evolutionary biology. Oxford University Press, London. p.239.

HAWKINGS, J. A. 2000. A survey of primary homology assessment: different botanists perceive and define characters in different ways. In: R. W. Scotland & R. T. Pennington (Eds.). Homology and Systematics. Taylor and Francis. pp. 22-53.

HAWKINGS, J. A., C. E. HUGES & R. W. SCOTLAND. 1997. Primary Homology Assessment, Characters and Character States. Cladistics 13: 275-283.

HENDRICKSON, J. A. 1968. Clustering in numerical cladistics: a minimum-length directed tree problem. Mathematical Biosciences 3: 371-381.

HILLIS, D. M. 1991. Discriminating between phylogenetic signal and random noise in DNA sequences. In: M. M. Miyamoto & J. Cracraft (Eds.). Phylogenetic analysis of DNA sequences. Oxford University Press. pp. 278-294.

HILLIS, D. M. 1995. Approaches for assessing phylogenetic accuracy. Systematic Biology 44 (1): 3-16.

HILLIS, D. M. 1998. Taxonomic Sampling, Phylogenetic Accuracy, and Investigator Bias. Systematic Biology 47 (1): 3-8.

HILLIS, D. M. & J. P. HUELSENBECK. 1992. Signal, noise, and reliability in molecular phylogenetic analysis. Journal of Heredity 83: 189-195.

HILLIS, D. M., C. MORITZ & B. K. MABLE (Eds.). 1996. Molecular Systematics. Sinauer Associates. Sunderland, Massachusetts, 655 p.

HOLDER, M. & P. O. LEWIS. 2003. Phylogeny estimation: Traditional and Bayesian approaches. Nature Reviews. Genetics 4: 275-284.

HUELSENBECK, J. P. & K. A. CRANDALL. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annual Review of Ecology and Systematics 28: 437-466.

HUELSENBECK, J. P. & F. RONQUIST. 2001. MrBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.

HUELSENBECK, J. P., B. LARGET, R. E. MILLER & F. RONQUIST. 2002. Potential applications and pitfalls of Bayesian inference of phylogeny. Systematic Biology 51 (5): 673-688.

HUELSENBECK, J. P., F. RONQUIST, R. NIELSEN & J. P. BOLLBACK. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310-2314.

KELLER, R. A. 1998. Bases metodológicas del uso de grupo externo en los análisis cladísticos. Tesis de Licenciatura en Biología, Facultad de Ciencias, UNAM, México. 80 p.

KELLER, R. A., R. N. BOYD & Q. D. WHEELER. 2003. The illogical basis of phylogenetic nomenclature. The Botanical Review 69 (1): 93-110.

KIM, J. 1996. General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing numbers of taxa. Systematic Biology 45 (3): 363-374.

KITCHING, I. J., P. L. FOREY, C. J. HUMPHRIES & D. M. WILLIAMS. 1998. Cladistics. The theory and practice of parsimony analysis.  The Systematics Association Publication No. 11. Oxford University Press, Oxford. 228 p.

KLUGE, A. G. 1984. The relevance of parsimony to phylogenetic inference. In: T. Duncan & Stuessy (Eds.). Cladistics: perspectives on reconstruction of evolutionary history. Columbia University Press. pp. 24-38.

KLUGE, A. G. 1997. Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13: 81-96.

KLUGE, A. G. 1999. The science of phylogenetic systematics: explanation, prediction, and test. Cladistics 15: 429-436.

KLUGE, A. G. 2001. Parsimony with and without scientific justification. Cladistics 17: 199-210.

KLUGE, A. G. 2001b. Philosophical conjectures and their refutation. Systematic Biology 50 (3): 322-330.

KLUGE, A. G. 2002. Distinguishing "or" from "and" and the case for historical identification. Cladistics 18: 585-593.

KLUGE, A. G. & A. J. WOLF. 1993. Cladistics: what’s in a word? Cladistics 9: 183-199.

KOLACZKOWSKI, B. & J. W. THORNTON. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431: 980-984.

KORNET, D. J. & H. TURNER. 1999. Coding Polymorphism for Phylogeny Reconstruction. Systematic Biology 48 (2): 365-379.

LEACHE, A. D. & T. W. REEDER. 2002. Molecular systematics of the Eastern fence lizard (Sceloporus undulatus): A comparison of parsimony, likelihood, and Bayesian approaches. Systematic Biology 51: 44-68.

LEÓN-OLEA, M. 2002. Evolución filogenética del dolor. Elementos 46: 19-23.

LEWIS, P. O. 1998. Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data. In: D. E. Soltis & P. S. Soltis (Eds.). Molecular systematics of plants II. DNA sequencing. Kluwer Academic Publishers. pp. 132-163.

LEWIS, P. O. 2001. Phylogenetic systematics turns over a new leaf. Trends in Ecology and Evolution 16: 30-37.

MABEE, P. M. 1989. Assumptions underlaying the use of ontogenetic sequences for determining character state order. Transactions of the American Fisheries Society 118: 151-158.

MISHLER, B. D. 1994. Cladistic Analysis of Molecular and Morphological Data. American Journal of Physical Anthropology 94: 143-156.

MISHLER, B. D. & E. DE LUNA. 1997. Sistemática filogenética y el concepto de especie. Boletín de la Sociedad Botánica de México 60: 45-57.

MORALES, E. 2000. El método comparativo en ecología vegetal. Boletín de la Sociedad Botánica de México 66: 37-51.

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NELSON, G. 1994. Homology and systematics. In: B. K. Hall (Eds.). Homology. The hierarchical basis of comparative biology. Academic Press. pp. 101-149.

NIELSEN, C. & P. MARTÍNEZ. 2003. Patterns of gene expression: homology or homocracy? Development, Genes and Evolution 213: 149-154.

NIXON, K. C. 1999. The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics 15: 407-414.

NIXON, K. C. & J. M. CARPENTER. 1993. On Outgroups. Cladistics 9: 413-426.

NIXON, K. C. & J. M. CARPENTER. 2000. On the other "phylogenetic systematics". Cladistics 16: 298-318.

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YANG, Z. 1996. Phylogenetic analysis using parsimony and likelihood methods. Journal of Molecular Evolution 42: 294-307.

YANG, Z. 1997. How often do wrong models produce better phylogenies?. Molecular Biology and Evolution 414: 105-108.

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

Creado:  Julio, 2006. Modificado: 17 ago 2009