Sistemática Filogenética aplicada a la Ficología Marina

Adams E.N. 1972. “Consensus techniques and the comparison of taxonomic trees”. Systematics Zoology 37: 27–29.

Arnedo M.A. 1999. “Cladismo: la reconstrucción filogenética, basada en Parsimonia”. Boletín de la Sociedad Entomológica aragonesa 26: 57–84.

Bandelt H.J. & Dress A.W.M. 1992. “Split decomposition: A new and usefulapproach to phylogenetic analysis of distance data”. Molecular phylogenetics and evolution 1: 242–252.

Bandelt H.J. & Dress A.W.M. 1994. “An Order Theoretic Framework for Overlapping Clustering”. Discrete Mathematics 136: 21–37.

Barraclough T.G. & Vogler A.Р. 2000. “Detecting the geographical pattern of speciation from species-level phylogenies”. American Naturalist 155: 419–434.

Bollback J.P. 2006. “SIMMAP: Stochastic character mapping of discrete traits on phylogenies”. Bioinformatics 7: 88.

Bremer K. 1990. “Combinable component consensus”. Cladistics 6: 369–372.

Arnedo M.A. 1999. “Cladismo: la reconstrucción filogenética, basada en Parsimonia”. Boletín de la Sociedad Entomológica aragonesa 26: 57–84.

Bremer K. 1994. “Branch support and tree stability”. Cladistics 10: 295–304.

Bryant D. & Moulton V. 2004. “Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks”. Molecular Biology and Evolution 21: 255–265.

Castillo-Cerón J.M. & Goyenechea I. 2007. “Conceptos básicos en sistemática filogenética: los Deuterostomados como ejemplo”. In: La sistemática: base del conocimiento de la biodiversidad (Ed. by A. Contreras-Ramos, M.C. Cuevas-Cardona, I. Goyenechea & U. Iturbe), pp. 145–157. Universidad Autónoma del estado de Hidalgo. Hidalgo. México.

Camin J.H. & Sokal R.R. 1965. “A method for deducing branching sequences in phylogeny”. Evolution 19: 311–326.

Doyle J.J. 1992. “Gene trees and species trees: Molecular systematics as one character taxonomy”. Systematic Botany 17: 144–163.

Farris J.S. 1969. “A successive approximations approach to character weighting”. Systematics Zoology 18: 374–385.

Farris J.S. 1970. “Methods of computing Wagner trees”. Systematics Zoology 23: 548–554.

Farris J.S. 1989. “The retention index and homoplasy excess”. Systematics Zoology 38: 406–407

Farris, J. Abert V., Kallersjo M., Lipscomb D. & Kluge A. 1996. “Parsimony jackknifing outperforms neighbor Joining”. Cladistics 12: 99–124.

Felsenstein J. 1978. “Cases in which parsimony or compatibility methods will be positively misleading”. Systematic Zoology 27: 401–410.

Felsenstein J. 1981. “Evolutionary trees from DNA sequences: A maximum likelihood approach”. Journal of Molecular Evolution 17: 368–376.

Felsenstein J. 1986. “Confidence limits on phylogenies: An approach using bootstrap”. Evolution 39: 783–91.

Fitch W.M. 1971. “Distinguishing homólogous from analogous proteins”. Systematics Zoology 20: 406–416.

Folder O., Black M., Hoeh W., Lutz R. & Vrijenhoek R. 1994. “DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates”. Molecular Marine Biology and Biotechnology 3: 294–299.

Graur D. & Wen-Hsiung L. 2000. Fundamentals of molecular evolution, ed. 2. Sinauer Associates, Massachusetts.

Hall T.A. 1999. “BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT”. Nucleic Acids Symposium 41: 95–98.

Hendy M.D. & Penny D. 1982. “Branch and bound algorithms to determine minimal evolutionary trees”. Mathematical Biosciences 59: 277–290.

Higgins D. 2003. “Multiple alignment”. In: The phylogenetic handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing (Ed. by P. Lemey, M. Salemi & A. Vandamme), pp. 45–71. Cambridge University Press, Cambridge, UK.

Hillis D.M. 1997. “Primer: phylogenetic analysis”. Current Biology 7: R129–R131. Hillis D.M. & Bull J.J. 1993. “An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis”. Systematic Biology 42: 182-192.

Huelsenbeck J.P. & Ronquist F. 2001. “MRBAYES: Bayesian inference of phylogenetic trees. NY”. Bioinformatics 17: 754–75. Department of Biology, University of Rochester, Rochester, Huelsenbeck J.P., Ronquist F., Nielsen R. & Bollback J.P. 2001. “Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology”. Science 294: 2310–2314.

Huson D.H. & Bryant D. 2006. “Application of phylogenetic networks in evolutionary studies”. Molecular Biology and Evolution 23: 254–267.

Jukes T. & Cantor C.R. 1969. Evolution of protein molecules. In: Mamalian protein metabolism (Ed. by H.N. Munro), pp. 21−132. Academic press, New York, USA.

Kimura M. 1980. “A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences.” Journal of Molecular Evolution 16: 111–120.

Kimura M. 1981. “Estimation of evolutionary distances between homologous nucleotide sequences”. Proceedings of the National Academy of Sciences USA 78: 454–458.

Kluge A.G. 1998. “Total evidence or taxonomic congruence: cladistics or consensus classification”. Cladistics 14: 151–158.

Kumar S., Stecher G., Li M., Knyaz C. & Tamura K. 2018. “MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms”. Molecular Biology and Evolution 35: 1547–1549.

Lanyon S.M. 1985. “Detecting internal inconsistencies in distance data”. Systematics Zoology 34: 397–403.

Lee M.S.Y. 2001. “Unalignable sequences and molecular evolution”. Trends in Ecology and Evolution 16: 681–685.

Leliaert F., Verbruggen H., Vanormelingen P., Steen F., López-Bautista J.M., Zuccarello G.C. & De Clerck O. 2014. “DNA-based species delimitation in algae”. European Journal Phycology 49: 179–196.

Librado P. & Rozas J. 2009. “DnaSP v5: a software for comprehensive analysis of DNA polymorphism data”. Bioinformatics 25: 1451–1452.

Maddison W.P. 1997. “Gene trees in species trees”. Systematic Biology 46: 523–536.

Maddison W.P. & Maddison D.R. 1992. “MacClade: Analysis of Phylogeny and Character Evolution”. Sinauer Associates Massachusetts.

Morgenstern B., Frech K., Dress A. & Werner T. 1998. “DIALIGN: Finding local similarities by multiple sequence alignment”. Bioinformatics 14: 290–294.

Morrone J.J. 2005. Sistemática, Biogeografía, Evolución los patrones de la biodiversidad en tiempo-espacio. Las prensas de ciencias, Facultad de Ciencias UNAM, Ciudad de México.

Morrone J.J. 2013. Sistemática. Fundamentos, métodos, aplicaciones. Las prensas de ciencias, Facultad de Ciencias UNAM, Ciudad de México.

National Centre for Biotechnology Information, U.S. National Library of Medicine 8600 Rockville Pike, Bethesda MD, 20894 USA https://www.ncbi.nlm.nih.gov/nuccore/U04176.1?report=fasta

Nei M. & Li W.H. 1979. “Mathematical model for studying genetic variation in terms of restriction endonucleases.” Proceedings of the National Academy of Sciences USA 76: 5269–5273.

Nelson G. 1979. “Cladistic analysis and synthesis: Principles and definitions with a historical note on Adamson´s Familles des Plantes” (1763–1764). Systematics Zoology 28: 1–29.

Nixon K.C. 1999. “The parsimony ratchet, a new method for rapid parsimony analysis”. Cladistics 15: 407–415.

Nixon K.C. & Carpenter J.M. 1993. “On outgroups”. Cladistics 9: 413–426.

Page R.D.M. & Holmes E.C. 1998. Molecular evolution: A Phylogenetic Approach. Blackwell Science, Cambridge.

Piganeau G., Eyre-Walker A., Grimsley N. & Moreau H. 2011. “How and why DNA barcodes underestimate the diversity of microbial eukaryotes”. PLoS One 6: e16342.

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. & Crandall K.A. 1998. “MODELTEST: testing the model of DNA substitution”. Bioinformatics 14: 817–818.

Rambaut A. 2016. FigTree v1.4.3. Institute of Evolutionary Biology, University of Edinburgh. http://tree.bio.ed.ac.uk/software/ figtree/

Rannala B. & Yang Z.H. 1996. “Probability distribution of molecular evolutionary trees: a. new method of phylogenetic inference”. Journal of Molecular Evolution 43: 304–311.

Reid N. & Carstens B. 2012. “Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model”. BMC Evolutionary Biology 12: 196.

Ronquist F. 2004. “Bayesian inference of character evolution”. Trends in Ecology and Evolution 19: 475–481.

Ronquist F. & Huelsenbeck J.P. 2003. “MrBayes 3: Bayesian phylogenetic inference under mixed models”. Bioinformatics 19: 1572–1574.

Ronquist F., Teslenko M., van der Mark P., Ayres D.L., Darling A., Hohna S., Larget B., Liu L., Suchard M.A. & Huelsenbeck J.P. 2012. “MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space”. Systematic Biology 61: 539–542.

Simmons M.Р. & 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.

Smith A.B. 1994. “Rooting molecular trees Problems and strategies”. Biological Journal of the Linnean Society 51: 279–292.

Stamatakis A. 2006. “RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models”. Bioinformatics 22: 2688–2690. Stamatakis A., Hoover P. & Rougemont J. 2008. “A Rapid Bootstrap Algorithm for the RAxML Web-Servers”. Systematic Biology 75: 758−771.

Swofford D.L. 2003. PAUP*. Phylogenetic analysis using parsimony (*and other methods), Versión 4.0b10. Sinauer Associates, Massachusetts.

Swofford D.L & Olsen G.J. 1990. “Phylogeny reconstruction”. In: Molecular Systematic (Ed. by D.M. Hillis & C. Moritz), pp. 411–501. Sinauer Associates, Massachusetts, USA.

Swofford D.L., Olsen G.J., Waddle P.J. & Hillis D.M. 1996. “Phylogenetic inference”. In: Molecular Systematics (Ed. by D.M. Hillis & C. Moritz), pp. 407–514. Sinauer Associates, Massachusetts, USA.

Tajima F.M.N. 1984. “Estimation of evolutionary distance between nucleotide sequences”. Molecular Biology and Evolution 1: 269–285.

Tamura K. & Nei M. 1993. “Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees”. Molecular Biology and Evolution 10: 512–526.

Tamura K., Peterson D., Peterson N., Stecher G., Nei M. & Kumar S. 2011. “MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance and Maximum Parsimony Methods”. Molecular Biology and Evolution 28: 2731–2739.

Templeton A.R. 2001. “Using phylogeographic analyses of gene trees to test species status and processes”. Molecular Ecology 10: 779–791.

Upholt W.B. 1977. “Estimation of DNA sequence divergence from comparison of restriction endonuclease digests”. Nucleic Acids Research 4: 1257–1265.

Verbruggen H. 2014. “Morphological complexity, plasticity, andspecies diagnosability in the application of old species names in DNA-based taxonomies”. Journal of Phycology 50: 26–31.

Wheeler W. 1990. “Nucleic acid sequence phylogeny and random outgroups”. Cladistics 6: 363–367.

Wiens J.J. 2007. “Species delimitation: new approaches for discovering diversity”. Systematic Biology 56: 875–878.

Wiley E.O. 1981. Phylogenetics. Theory and practice of phylogenetic systematic. John Wiley and sons. New York. Wiley E.O., Siegel-Causey D., Brooks D.R. & Funk V.A. 1991. The compleat cladist: a primer of Phylogenetic procedures, vol. 19. University of Kansas Museum of Natural History, Kansas, USA.

Wilkinson M. 1995. “A comparison of two methods of character construction”. Cladistics 11: 297–308.

Williams D.M. 1992. “DNA analysis: Theory”. In: Cladistics: A practical course in Systematics (Ed. by P.L. Forey, C.J. Humphries, I.J. Kitching, R.W. Scotland, D.J. Siebert & D.M. Williams), pp. 89–101. Oxford University Press, Oxford, UK.

Jukes T. & Cantor C.R. 1969. Evolution of protein molecules. In: Mamalian protein metabolism (Ed. by H.N. Munro), pp. 21−132. Academic press, New York, USA.

Yang Z. 1994. “Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods”. Journal of Molecular Evolution 39: 306–314

Yang Z. & Rannala B. 2010. “Bayesian species delimitation using multilocus sequence data”. Proceedings of the National Academy of Sciences USA 107: 9264–9269.

Zimmermann J., Jahn R. & Gemeinholzer B. 2011. “Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols”. Organisms Diversity and Evolution 11: 173–192.