Bibliografía

Bibliografía Recomendada


TEMA 1. ¿Qué es una filogenia molecular y para qué sirve?

AVISE, J.C. 1989. A Role for Molecular Genetics in the Recognition and Conservation of Endangered Species. Trends in Ecology and Evolution 4: 279-281.
AVISE, J.C. 2000. Phylogeography: the history and formation of species. Harvard University Press, Cambridge, MA.
AVISE, J.C. 2009. Phylogeography: retrospect and prospect. Journal of Biogeography 36: 3-15.
CRANDALL, K.A., BININDA-EMONDS, O.R.P., MACE, G.M. AND R.K. WAYNE. 2000. Considering evolutionary processes in conservation biology. Trends in Ecology and Evolution 15: 290-295.
HENNIG W. 1966. Phylogenetic Systematics. University of Illinois Press, Urbana. Pp.263.
KLEPPE, K., OHTSUKA, E., KLEPPE, R., MOLINEUX, I., AND H.G. KHORANA. 1971. Studies on polynucleotides: XCVI. Repair replication of short synthetic DNA's as catalyzed by DNA polymerases. Journal of Molecular Biology 56: 341-361.
MULLIS, K.B. AND F.A. FALOONA. 1987. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods in Enzymology 155: 335-350.
RICKLEFS, R.E. 2007. Estimating diversification rates from phylogenetic information. Trends Ecology and Evolution 22: 601-610.
RONQUIST, F. AND I. SANMARTÍN. 2011. Phylogenetic methods in historical biogeography. Annual Review of Ecology, Evolution and Systematics 42: 441-464.
SANGER, F. AND A.R. COULSON. 1975. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of Molecular Biology 94: 441-446.
SCHAAL, B.A., HAYWORTH, D.A., OLSEN, K.M., RAUSCHER, J.T., AND W.A.
SMITH. 1998. Phylogeographic studies in plants: Problems and prospects. Molecular Ecology 7: 465-474.
SHAW J., E. B. LICKEY, J. T. BECK, S. B. FARMER, W. LIU, J. MILLER, K. C.
SIRIPUN, C. T. WINDER, E. E. SCHILLING, AND R. L. SMALL. 2005. The tortoise and the hare II: Relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 92: 142-166.
SHAW J., E. B. LICKEY, E. E. SCHILLING, AND R. L. SMALL. 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: The Tortoise and the hare III. American Journal of Botany 94: 275-288.
SMALL R. L., J. A. RYBURN, R. C. CRONN, T. SEELANAN, AND J. F. WENDEL. 1998. The tortoise and the hare: Choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany 85: 1301-1315.
ZIMMERMANN, W. 1930. Die Phylogenie der Pflanzen. G. Fischer, Jena, Germany.
ZIMMERMANN, W. 1934. Research on phylogeny of species and of single characters. American Naturalist 68: 381-384.
ZUCKERKANDL E. and L. PAULING. 1965. Evolutionary divergence and convergence in proteins. Evolving Genes and Proteins 97-166.

TEMA 2.1. Breve introducción a las técnicas y métodos de reconstrucción filogenética

FARRIS J. S., V. A. ALBERT, M. KÄLLERSJÖ, D. LIPSCOMB, AND A. G. KLUGE. 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12: 99-124.
GAUT B. S. and P. O. LEWIS. 1995. Success of maximum likelihood phylogeny inference in the four-taxon case. Molecular Biology and Evolution 12: 152-162.
HENDY M. D. and D. PENNY. 1982. Branch and bound algorithms to determine minimal evolutionary trees. Mathematical Biosciences 59: 277-290.
HILLIS D. M., C. MORITZ, AND B. K. MABLE. 1996. Molecular Systematics. Sinauer Associates, Sunderland. Pp. 665.
HUELSENBECK J. P. 1995. Performance of phylogenetic methods in simulation. Systematic Biology 44: 17-48.
HUELSENBECK J. P. 1998. Systematic Bias in Phylogenetic Analysis: Is the Strepsiptera Problem Solved? Systematic Biology 47: 519-537.
NEI, S. AND, M. KUMAR. 2000. Molecular evolution and phylogenetics. Oxford university Press, New York.
PIONTKIVSKA H. 2004. Efficiencies of maximum likelihood methods of phylogenetic inferences when different substitution models are used. Molecular Phylogenetics and Evolution 31: 865-873.
PLATNICK N. I. 1985. Philosophy and the transformation of cladistics revisited. Cladistics 1: 87-94.
SALTER L. A. and D. K. PEARL. 2001. Stochastic search strategy for estimation of maximum likelihood phylogenetic trees. Systematic Biology 50: 7-17.
STEEL M. A., M. D. HENDY, AND D. PENNY. 1988. Loss of information in genetic distances. Nature 336: 118.
WILLIAMS D. M. 1992. DNA analysis: Theory. In Forey P. L., C. J. Humphries, I. J. Kitching, R. W. Scotland, D. J. Siebert and D. M. Williams [eds.], Cladistics: A practical course in sistematics, 89-101. Oxford Univsersity Press, Oxford.

TEMA 2.2. Puntos clave en el diseño y elaboración de una filogenia molecular.

ÁLVAREZ I. and J. F. WENDEL. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434.
BALDWIN B. G., M. J. SANDERSON, J. M. PORTER, M. F. WOJCIECHOWSKI, C. S. CAMPBELL, AND M. J. DONOGHUE. 1995. The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden 82: 247-277.
BREMER K. 1990. Combinable Component Consensus. Cladistics-the International Journal of the Willi Hennig Society 6: 369-372.
BREMER K. 1994. Branch support and tree stability. Cladistics 10: 295-304.
CUMMINGS M. P., S. A. HANDLEY, D. S. MYERS, D. L. REED, A. ROKAS, AND K. WINKA. 2003. Comparing bootstrap and posterior probability values in the fourtaxon case. Systematic Biology 52: 477-487.
DOYLE J. J. 1992. Gene trees and species trees: Molecular systematics as onecharacter taxonomy. Systematic Botany 17: 144-163.
DOYLE J. J. and B. S. GAUT. 2000. Evolution of genes and taxa: A primer. Plant Molecular Biology 42: 1-23.
EDGAR, R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1979.
FELINER G. N. and J. A. ROSSELLÓ. 2007. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Molecular Phylogenetics and Evolution 44: 911-919.
FELSENSTEIN J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology 27: 401-410.
GLADSTEIN D. and W. WHEELER. 1996. POY. Software for Direct Optimization of DNA and Other Data. Available anonymously via
ftp://ftp.amnh.org/pub/molecular/POY.
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.
HILLIS D. M., C. MORITZ, AND B. K. MABLE. 1996. Molecular Systematics. Sinauer Associates, Sunderland. Pp. 665.
HILLIS D. M. 1997. Primer: phylogenetic analysis. Current Biology 7: R129-R131.
HUGHES C. E., R. J. EASTWOOD, AND C. D. BAILEY. 2006. From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction. Philosophical Transactions of the Royal Society B: Biological Sciences 361: 211-225.
JUDD W. S., C. S. CAMPBELL, E. A. KELLOGG, P. F. STEVENS, AND M. J. DONOGHUE. 2002. Plant systematics. A phylogenetic approach. Sinauer Associates, Inc., Massachusetts.
LEE M. S. Y. 2001. Unalignable sequences and molecular evolution. Trends in Ecology and Evolution 16: 681-685.
MADDISON W. P. 1997. Gene trees in species trees. Systematic Biology 46: 523-536.
MARGUSH T. and F. R. MCMORRIS. 1981. Consensus trees. Bull. Math. Biol. 43: 239-244.
MORGENSTERN B., K. FRECH, A. DRESS, AND T. WERNER. 1998. DIALIGN: Finding local similarities by multiple sequence alignment. Bioinformatics 14: 290-294.
MURPHY W. J., E. EIZIRIK, S. J. O'BRIEN, O. MADSEN, M. SCALLY, C. J. DOUADY, E. TEELING, O. A. RYDER, M. J. STANHOPE, W. W. DE JONG, AND M. S.
SPRINGER. 2001. Resolution of the early placental mammal radiation using bayesian phylogenetics. Science 294: 2348-2351.
NEE S., E. C. HOLMES, R. M. MAY, AND P. H. HARVEY. 1994. Extinction rates can be estimated from molecular phylogenies. Philosophical Transactions - Royal Society of London, B 344: 77-82.
NELSON G. 1979. Cladistic Analysis and Synthesis - Principles and Definitions, with a Historical Note on Adansons Familles Des Plantes (1763-1764). Systematic zoology 28: 1-21.
NIXON K. C. and J. M. CARPENTER. 1993. On outgroups. Cladistics 9: 413-426.
PALMER J. D. 1992. Mitochondrial DNA in plant systematics: Applications and limitations. In Soltis, Soltis and Doyle, Molecular Systematics of Plants pp. 36-49. Kluwer Academic Publisher.
PAMILO P. and M. NEI. 1988. Relationship between gene trees and species trees. Molecular Biology and Evolution 5: 568-583.
PHILIPPE H., ZHOU, Y., BRINKMANN, H., RODRIGUE, N., AND F. DELSUC. 2005. Heterotachy and long-branch attraction in phylogenetics. BMC Evolutionary Biology 5: 50.
POSADA D. 2001. The effect of branch length variation on the selection of models of molecular evolution. Journal of Molecular Evolution 52: 434-444.
POSADA D. AND T.R. 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.
SHAW J., E. B. LICKEY, J. T. BECK, S. B. FARMER, W. LIU, J. MILLER, K. C. SIRIPUN, C. T. WINDER, E. E. SCHILLING, AND R. L. SMALL. 2005. The tortoise and the hare II: Relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 92: 142-166.
SHAW J., E. B. LICKEY, E. E. SCHILLING, AND R. L. SMALL. 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: The Tortoise and the hare III. American Journal of Botany 94: 275-288.
SIMMONS M. P., H. OCHOTERENA, AND T. G. CARR. 2001. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Systematic Biology 50: 454-462.
SIMMONS M. P. and J. V. FREUDENSTEIN. 2003. The effects of increasing genetic distance on alignment of, and tree construction from, rDNA internal transcribed spacer sequences. Molecular Phylogenetics and Evolution 26: 444-451.
SMALL R. L., J. A. RYBURN, R. C. CRONN, T. SEELANAN, AND J. F. WENDEL. 1998. The tortoise and the hare: Choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany 85: 1301-1315.
SMITH A. B. 1994. Rooting molecular trees - Problems and strategies. Biological Journal of the Linnean Society51: 279-292.
SOLTIS D. E. and P. S. SOLTIS. 1998. Choosing an approach and an appropriate gene for phylogenetic analysis. Molecular Systematics of Plants II: DNA Sequencing pp.1-42. Kluwer academic Publishers, Boston.
SOLTIS D. E. and P. S. SOLTIS. 2003. The role of phylogenetics in comparative genetics. Plant Physiology 132: 1790-1800.
SULLIVAN J. and D. L. SWOFFORD. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenies. Journal of Mammal Evolution 4: 77- 86.
SUZUKI Y., G. V. GLAZKO, AND M. NEI. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proceedings of the National Academy of Sciences of the United States of America 99: 16138-16143.
TABERLET P., L. GIELLY, G. PAUTOU, AND J. BOUVET. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17: 1105-1109.
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.
WENZEL J. W. and M. E. SIDDALL. 1999. Noise. Cladistics 15: 51-64.
WHELAN S., P. LIO, AND N. GOLDMAN. 2001. Molecular phylogenetics: state-of-theart methods for looking into the past. Trends in Genetics 17: 262-272.
WHEELER W. C. 1990. Nucleic acid sequence phylogeny and random outgroups. Cladistics 6: 363-367.
WHEELER W. C. 1992. Extinction, sampling, and molecular phylogenetics. In Novacek M. J. and Q. D. Wheeler [eds.], Extinction and phylogeny, 205-215. Columbia University Press, New York.
WHEELER W. and D. GLADSTEIN. 2000. "MALIGN." Version 2.8.
YANG Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution 39: 306-314.

TEMA 3.2. Obtención de matrices: búsqueda de homologías, alineamiento

DOYLE J.J. y GAUT, B.S. 2000. Evolution of genes and taxa: A primer. Plant Molecular Biology 42: 1-23.
EDGAR, R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792-1797. doi:10.1093/nar/gkh340
KELCHNER, S.A. 2000. The Evolution of Non-Coding Chloroplast DNA and Its Application in Plant Systematics. Annals of the Missouri Botanical Garden 87, 4: 482-498.
LARKIN, M.A., BLACKSHIELDS, G., BROWN, N.P., CHENNA, R., MCGETTIGAN, P.A., MCWILLIAM, H., VALENTIN, F., WALLACE, I.M., WILM, A., LOPEZ, R., THOMPSON, J.D., GIBSON, T.J. AND D.G. HIGGINS. 2007. Clustal W and Clustal X version 2.0 bioinformatics applications note 23, 21: 2947-2948.
SIMMONS, M.P. y FREUDENSTEIN, J.V. 2003. The effects of increasing genetic distance on alignment of, and tree construction from, rDNA internal transcribed spacer sequences. Molecular Phylogenetics and Evolution 26: 444-451.
SIMMONS, M.P. y OCHOTERENA, H. 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369-381.
SIMMONS M. P., H. OCHOTERENA, AND T. G. CARR. 2001. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Systematic Biology 50: 454-462.
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.

TEMA 3.4. Selección del modelo evolutivo que mejor se ajuste a nuestros datos

JUKES, T.H., AND C.R. CANTOR. 1969. Evolution of protein molecule, pp:21-132. En H.N. Munro (ed.), Mammalian Preotein Metabolism. Academic Press, New York.
KIMURA, M. 1980. A simple method for estimating evolutionaty rate of base substitutions thorugh comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111-120.
LEMMON A.R., AND E.C. MORIARTY. 2004. The importance of proper model assumption in Bayesian phylogenetics. Systematic Biology 53: 265–277.
NYLANDER, J.A.A. 2004a. MrModeltest v2. Program distributed by the author. Available from: http://www.abc.se/;nylander/. Evolutionary Biology Centre, Uppsala University.
NYLANDER, J.A.A. 2004b. MRAIC.PL. Program distributed by the author. Available from: http://www.abc.se/~nylander. Evolutionary Biology Centre, Uppsala University.
POSADA D., AND K.A. CRANDALL. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics. 14:817–818.
POSADA D. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike Information Criterion and Bayesian Information Criterion over Likelihood Ratio Tests. Systematic Biology 53: 793-808.
POSADA D. 2008. JModeltest: Phylogenetic Model Averaging. Molecular Biology and Evolution 25: 1253-1256.
SWOFFORD, D.L. 2002. PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sunderland, Massachusetts: Sinauer.

TEMA 3.5. Obtención de árboles mediante el método de inferencia bayesiana

HUELSENBECK, J.P., F. RONQUIST. 2001. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17: 754-755.
SIMMONS, M.P., AND H. OCHOTERENA. 2000. Gaps as characters in sequencebased phylogenetic analyses. Systematic Biology 49: 369-381.