Resumen
Desde los inicios de la biología, clasificar a los organismos ha sido un requisito para tratar de entender la diversidad. La teoría de la evolución de Darwin como en otros campos constituye un parteaguas para entender las relaciones entre los seres vivos. Sin embargo, la aplicación de la teoría evolutiva a la sistemática tardó ca. 100 años; prevaleciendo durante ese tiempo la similitud como un criterio clasificatorio. Se describen brevemente las perspectivas fenética, neodarwinista y cladista, enfatizando su importancia en sistemática, al privilegiar la ancestría común sobre criterios de similitud y divergencia adaptativa para agrupar o segregar agrupamientos taxonómicos. Adicionalmente se discuten las principales fuentes de evidencia en sistemática; como la morfología, con su reciente enfoque de fenómica y molecular desde secuenciación Sanger hasta genómica.
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Adams, M.D., S.E. Celniker, R.A Holt, C.A. Evans, J.D. Gocayne, et al. 2000. The genome sequence of Drosophila melanogaster. Science 287: 2185–2195.
Adanson, M. 1763. Families des plantes. Vincent. Paris. 640 pp.
Ané, C., B. Larget, D.A.Baum, S.D. Smith, A. Rokas. 2007. Bayesian estimation of concordance among gene trees. Mol. Biol. Evol. 24:412–26.
Arabidopsis Genome Initiative 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815.
Ashlock, P.D. 1979. An evolutionary systematist's view of classification. Syst. Zool. 28: 441-450.
Bauhin, C. 1671. Pinax theatri botanici. Arion. Basilea. 518 pp.
Benoît, D. 2003. The roots of phylogeny: how did Haeckel build his trees? Syst. Biol. 52:515–527.
Bräutigam, A. y U. Gowik 2010. What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biol. 12: 831-841.
Chun, J. y F.A. Rainey 2014. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int. J. Syst. Evol. Microbiol. 64: 316–324.
Claßen-Bockhoff, R. 2001. Plant morphology: the historic concepts of Wilhelm Troll, Walter Zimmermann and Agnes Arber. Ann. Bot. 88: 1153-1172.
Darwin, C. 1859. On the origin of species. Murray. London. 458 pp.
De Queiroz, K. 1988. Systematics and the Darwinian revolution. Philos. Sci. 55: 238-259.
Delarbre, C., Y. Kashi, P. Boursot, J.S. Beckmann, P. Kourilsky, F. Bonhomme y G. Gachelin 1988. Phylogenetic distribution in the genus Mus of t-complex-specific DNA and protein markers: inferences on the origin of t-haplotypes. Mol. Biol. Evol. 5:120–133.
Delsuc, F., H. Brinkmann y H. Philippe. 2005. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6:361–375.
Donoghue, M. J. y J.W. Kadereit 1992. Walter Zimmermann and the growth of phylogenetic theory. Syst. Biol. 141:74-85.
De Sousa, F., Y.J.K. Bertrand, S. Nylinder, B. Oxelton, J.S. Eriksson, B.E. Pfeil. 2014. Phylogenetic properties of 50 nuclear loci in Medicago (Leguminosae) generated using multiplexed sequence capture and next- generation sequencing. PloS ONE. 9(10):e109704.
El-Metwally S, Hamza T, Zakaria M, Helmy M. 2013. Next-generation sequence assembly: four stages of data processing and computational challenges. PLOS Comput. Biol. 9 (12): e1003345.
Farris, J. 1983. The logical basis of phylogenetic analysis. En: Advances in Cladistics. (Platnick, N.I., y V.A. Funk , eds.) Columbia University Press. New York. 7–36 pp.
Fisher, R.A. 1930. The genetical theory of natural selection. The Clarendon Press. Oxford. 272 pp.
Goldschmidt, R. 1940. The material basis of evolution. Yale University Press. New Haven. 436 pp.
Goloboff, P.A., J.S. Farris y K.C. Nixon 2008. TNT, a free program for phylogenetic analysis. Cladistics 24:774–786.
Goloboff, P.A., S.A. Catalano, M.J. Mirande, C. Szumik, S. Arias, M. Källersjö, J.S. Farris 2009. Phylogenetic analysis of 73060 taxa corroborates major eukaryotic groups. Cladistics 25: 211–230.
Hackett, S.J., y R.T. Kimball, S. Reddy, R.C.K. Bowie, E.L. Braun EL, et al. 2008. A phylogenomic study of birds reveals their evolutionary history. Science 320:1763–1768.
Haeckel, E. 1894. Systematische phylogenie. Reimer. Berlin. 400 pp.
Haldane, J.B.S. 1932. The causes of evolution. Princeton University Press. London. 235 pp.
Hamilton, J.P. y C.R. Buell 2012. Advances in plant genome sequencing. Plant J. 70:177–190.
Hawkins, J.A., C.E. Hughes, R.W. Scotland 1997. Primary homology assessment, characters and character states. Cladistics 13:275–283.
Hennig, W. 1966. Phylogenetic systematics. University of lllinois Press. Urbana. 263 pp.
Hermsen, E.J. y J.R. Hendricks 2008. W(h)ither fossils? Studying morphological character evolution in the age of molecular sequences. Ann. Missouri Bot. Gard. 95:72–110.
Heyduk, K., D.W. Trapnell, C.F. Barrett, M.J. Leebens 2016. Phylogenomic analyses of species relationships in the genus Sabal (Arecaceae) using targeted sequence capture. Biol. J. Linnean Soc. 117: 106-120.
Hillis, D.M., C. Moritz, B.K. Mable 1996. Molecular Systematics. Sinauer Associates. Sunderland. 655 pp.
Huelsenbeck, J.P., F. Ronquist, R. Nielsen y J.P. Bollback 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310–2314.
Huxley, J.S. 1940. The new systematics. Clarendon Press. Oxford. 586 pp.
Huxley, J.S. 1959. Clades and grades. En: Function and taxonomic importance, (Cain, A.J., ed.) Systematics Association. London. 21–22 pp.
Ilie, L, F. Fazayeli S. Ilie 2011. HiTEC: accurate error correction in high-throughput sequencing data. Bioinformatics 27:295–302.
Johnson, N.F. 2012. A collaborative, integrated and electronic future for taxonomy. Invertebr. Syst. 25:471–475.
Katoh, K., K. Misawa, K. Kuma y T. Miyata 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30(14): 3059–3066.
Keightley, P.D. y T. Johnson 2004. MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution. Genome Res. 14:442–450.
Kim, K.M., J.H. Park, D. Bhattacharya y H.S. Yoon 2014. Aplications of next- generation sequencing to unravelling the evolutionary history of algae. Int. J. Syst. Evol. Micr. 64: 333-345.
Kircher, M. y J. Kelso 2010. High-throughput DNA sequencing--concepts and limitations. BioEssays 32:524–536.
Kubatko, L.S., B.C. Carstens y L. Knowles 2009. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25:971–73.
Larkin, M.A. G. Blackshields, N.P. Brown, R. Chenna, P.A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948.
Lemmon, E.M., y A.R. Lemmon 2013. High-Throughput Genomic Data in Systematics and Phylogenetics. Annu. Rev. Ecol. Syst. 44:99–121.
Linneo, C. 1753. Species plantarum: exhibentes plantas rite cognitas, ad genera relatas, cum differentiis specificis, nominibus trivialibus, synonymis selectis, locis natalibus, secundum systema sexuale digestas. Holmiae-Impensis Laurentii Salvii. Estocolmo. 560 pp.
Llorente-Bouquets, J. 1990. La búsqueda del método natural. Fondo de Cultura Económica. México. 155 pp.
Lou, D.I., J.A. Hussmann, R.M. McBee, A. Acevedo, R. Andino, W.H. Press, S.L. Sawyer 2013. High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing. Proc. Natl. Acad. Sci. U.S.A. 110:19872–19877.
Mayr, E. 1969. Principles of systematic zoology. McGraw-Hill. New York. 428 pp.
Mayr, E. 2001. The philosophical foundations of Darwinism. Proc. Am. Philos. Soc. 145: 488-495.
Miklo´s, I., G.A. Lunter y I. Holmes 2004. A ‘‘long indel’’ model for evolutionary sequence alignment. Mol. Biol. Evol. 21:529–540.
Misof, B., S. Liu, K. Meusemann, R.S. Peters, A. Donath, C. Mayer, et al. 2014. Phylogenomics resolves the timing and pattern of insect evolution. Science 346:763–767.
Morgan, T.H. 1916. A Critique of the Theory of Evolution. Princeton University Press. New Jersey. 197 pp.
Morgenstern, B. 2004. DIALIGN: multiple DNA and protein sequence alignment at BiBiServ. Nucleic Acids Res. 32:W33–W36.
Morrone. J.J. 2000. El lenguaje de la cladística. UNAM-Facultad de Ciencias. México. 109 pp.
Muller, H.J. 1927. Artificial transmutation of the gene. Science 66: 84–87.
Müller, K. 2006. Incorporating information from length-mutational events into phylogenetic analysis. Mol. Phylogenet. Evol. 38:667-676.
Nater, A., R. Burri, T. Kawakami, L. Smeds, H. Ellegren 2015. Resolving evolutionary relationships in closely related species with whole-genome sequencing data. Syst. Biol. 64:1000–1017.
Nixon, C.K. y H. Ochoterena 2001. Taxonomía tradicional, cladística y construcción de hipótesis filogenéticas. En: Enfoques contemporáneos para el estudio de la biodiversidad. (Hernández, H.M., A.N. García-Aldrete, F. Álvarez y M. Ulloa. eds.) UNAM-Instituto de Biología. México. 15-37 pp.
Notredame, C., D.G. Higgins y J. Heringa 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302:205–217.
Nystedt, B., N.R. Street, A. Wetterbom, A. Zuccolo, Y.C. Lin, D.G. Scofield, et al. 2013. The Norway spruce genome sequence and conifer genome evolution. Nature 497:579–584.
O’Leary, M.A., J.I. Bloch, J.J. Flynn, T.J. Gaudin, A. Giallombardo, N.P. Giannini, et al. 2013. The Placental Mammal Ancestor and the Post–K-Pg Radiation of Placentals. Science 339:662–667.
Palmer, J.D. y D. Zamir 1982. Chloroplast DNA evolution and phylogenetic relationships in Lycopersicon. Proc. Natl. Acad. Sci. U.S.A. 79: 5006–5010.
Parks, M., R. Cronn, A. Liston 2009. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biology, 7:1–17.
Prevost, A. y M.J. Wilkinson 1999. A new system of comparing PCR primers applied to ISSR fingerprinting of potato accessions. Theor. Appl. Genet. 98:107–112.
Sanderson, M. J. y M. J. Donoghue 1989. Patterns of variation in levels of homoplasy. Evolution 43(8): 1781-1795.
Sarich, V.M. y A.C. Wilson 1967. Immunological time scale for hominid evolution. Science 158: 1200–1203.
Scornavacca, C., V. Berry, V. Lefort, E.J.P. Douzery y V. Ranwez 2008. PhySIC_IST: cleaning source trees to infer more informative supertrees. BMC Bioinformatics 9: 413.
Scotland, R.W., R.G. Olmstead, J.R. Bennett. 2003. Phylogeny reconstruction: the role of morphology. Syst. Biol. 52: 539–548.
Sibley, C.G., J.E. Ahlquist y B.L. Monroe. 1988. A classification of the living birds of the world based on DNA-DNA hybridization studies. Auk 105:409–423.
Sicheritz-Pontén, T., S.G.E. Andersson 2001. A phylogenomic approach to microbial evolution. Nucleic Acids Res. 29:545–552.
Simmons, M.P. y H. Ochoterena 2000. Gaps as characters in sequence-based phylogenetic analysis. Syst. Biol. 49:369–381.
Sokal, R.R. y P.H.A. Sneath 1963. Principles of numerical taxonomy. WH Freeman and Company. San Francisco. 359 pp.
Stamatakis, A., T. Ludwig y H. Meier 2005. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21:456–63.
Steele, R.P. y C.J. Pires 2011. Biodiversity assessment: state of the art techniques in phylogenomics and species identification. Am. J. Bot. 98:415-425.
Stevens, P.F. 1984. Metaphors and typology in the development of botanical systematics 1690-1960, or the art of putting new wine in old bottles. Taxon 33:169- 211.
Straub, S.C., M. Fishbein, T. Livshultz, Z. Foster, M. Parks, R. Weitemier, R.C. Cron y A. Liston 2011. Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing. BMC Genomics 2:211-232.
Strickler, S.R., A. Bombarely, L.A. Mueller 2012. Designing a transcriptome next- generation sequencing project for a nonmodel plant species. Am. J. Bot. 99: 257-266.
Swofford, D.L., G.J. Olsen, P.J. Waddell y D.M. Hillis 1996. Phylogenetic inference. P. 407–514. En: Molecular systematics, (Hillis D.M., C. Moritz y B.K. Mable, eds.) Sinauer Associates. Sunderland.
Türktaş. M., K. YüCebilgili-KurtoğLu, G. Dorado, B. Zhang, P. Hernandez y T. Ünver 2015. Sequencing of plant genomes – a review. Turk. J. Agric. For. 39:361–376.
Varki, A., y T.K. Altheide 2005. Comparing the human and chimpanzee genomes: Searching for needles in a haystack. Genome Res.15:1746–1758.
Venter, J.C., M.D. Adams, E.W. Myers, et al. 2001. The sequence of the human genome. Science 291:1304–1351.
Vos, P., R. Hogers, M. Bleeker, M. Reijans, T. Van-de-Lee, M. Hornes, A. Frijters, J. Pot, J. Peleman, M. Kuiper y M. Zabeau. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23:4407-4414.
Wiens, J.J. 2004. The role of morphological data in phylogeny reconstruction. Syst. Biol. 53(4): 653-661.
Woese, C.R. y G.E. Fox 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA 74: 5088-5090.
Woese, C.R. 1987. Bacterial evolution. Microbiol. Rev. 51:221–271.
Woese, C.R., O. Kandler, M.L. Wheelis 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87: 4576-4579.
Wright, S. 1930 The Genetical Theory of Natural Selection: a review. J. Hered. 21:340-356.
Young, N.D. y J. Healy 2003. GapCoder automates the use of indel characters in phylogenetic analysis. BMC Bioinformatics. 4:1-6.
Zhong, B., O. Deusch, V.V. Goremykin, D. Penny, P.J. Biggs, R.A. Atherton, et al. 2011. Systematic error in seed plant phylogenomics. Genome Biol. Evol. 3:1340–1348.
Zietkiewicz, E., A. Rafalski y D. Labuda 1994. Genome fingerprinting by simple sequence repeat (SRR)-anchored polymerase chain reaction. Genomics 20: 176-183.
Zimmermann, W. 1931. Arbeitsweise der botanischen Phylogenetik und anderer Gruppierungswissenschaften. P. 941-1053. En: Abderhalden E, ed. Handbuch der biologischen Arbeilsmethoden. Urban & Schwarzenberg. Berlin.
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Derechos de autor 2017 Juan Carlos Montero Castro, Deneb García-Ávila, Edgar Ismael Olvera Mendoza, Sabina Irene Lara Cabrera