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21 de febrero de 2008

Taxonomia integrativa

En el número de Enero de Systematic Entomology se ha publicado la opinión de QD Wheeler sobre la necesidad de una revaloración y redirección de la investigación en la biología sistemática. Y en el Biol. J. Linnean Society se publico la opinion de Valdecasas, Williams & Wheeler.
Me parece un llamamiento muy oportuno ante otro desfile del emperador y su nuevo traje: la fenética molecular y DNA barcoding.
Aquí transcribo el primer párrafo de la introducción de Wheeler 2008 y la conclusion de Valdecasas 2008.

"Undisciplined thinking: morphology and Hennig’s unfinished revolution"
QUENTIN D. WHEELER
Systematic Entomology (2008), 33, 2–7

There was a time, not long ago and prior to Hennig (1966), when taxonomy was widely dismissed as a mere service to ‘real’ – read experimental – sciences. Taxonomists were regarded by many to have nothing more to contribute to modern biology than the pragmatic role of identifying species and keeping track of their names. This was a legacy of the conflation of systematics with genetics by Huxley (1940), Mayr (1942) and others (see Wheeler, 1995, 2008a). Hennig re-elevated taxonomy, as phylogenetic systematics, to its rightful place as a rigorous, free-standing and central field of the biological sciences. Taxonomy is typically performed best when it is carried out for its own sake. Taxonomists are motivated to explore species, character diversity and phylogenetic relationships within monophyletic groups. The ultimate goal of taxonomists is a phylogenetic classification with associated scientific names, what Hennig described as biology’s general reference system. Oh yes, they make species identifiable, too. Current molecular initiatives, including DNA barcoding and DNA taxonomy, threaten to reduce species discovery as well as classifications to nothing more than a service. Because ‘new’ species would be ‘discovered’ on the basis of phenetic distances only, DNA barcoding might be described better as a disservice to biology (Prendini, 2005; Wheeler, 2005). After all, it offers only arbitrary averages, by contrast with explicitly testable alternatives, such as the phylogenetic species concept (Wheeler & Platnick, 2000). DNA taxonomy (in the sense
of Tautz et al., 2003) is another flawed approach that would diminish the information content of classifications (e.g. Lipscomb et al., 2003). The trend in molecular phylogenetics (‘phylogenetic biology’) has been to increasingly marginalize the evidential basis of taxonomy and to treat the creation of ‘trees’ largely as a service to those same ‘real’ sciences.

‘Integrative taxonomy’ then and now: a response to Dayrat (2005)

ANTONIO G. VALDECASAS, DAVID WILLIAMS & QUENTIN D. WHEELER

Biological Journal of the Linnean Society 93: 211-216, January 2008

The most serious problem facing our science at present is that descriptive taxonomy continues to be poorly supported, especially for inadequately known taxa, where revisions, monographs, floras, and other major descriptive activities are urgently needed. The standard should be excellence rather than the creation of sets of rules that impose particular data sources or narrow practices and ‘new paradigms’. Can we be so sure that the current molecular tools are the ultimate answer? Does our technological arrogance justify forcing compliance at the expense of other possible ways forward? Must we abandon descriptive palaeontology entirely because it is not capable of conforming to DNA standards for its species? If we tolerate palaeontology, why not morphology-based neontology since it yields vastly greater numbers of characters than fossils? Why not simply insist on excellence in terms of explicit and testable hypotheses and let scientists determine the circumstances of what they can and want to do? Peer pressure can and does shape practices; the wider community decides through publication and debate what the ‘norms’ are for current practice and these are free to change through time as theories and technologies change. Imposing strict limits or guidelines is misguided and, ultimately, unnecessary. Of course, some practitioners may very well produce bad taxonomy. Yet, this will have no permanent consequences as poorly or inaccurately described species and poor species hypotheses will in due course be falsified, rejected, and reduced to synonymy. Nevertheless, a few will actually lead to unexpected breakthroughs and insights that might have never seen the light of day should conformity of any kind be forced. The science of taxonomy works in such a way that through iterative processes of investigation a competitive enterprise can and will weed out ‘bad’ work. Using approved sources of data, sets of guidelines and unnecessary ‘paradigms’ hardly assures a more robust and ‘correct’ outcome for the taxonomic enterprise, which, although not perfect, does indeed function perfectly well.

15 de febrero de 2008

Filogenética en epidemiología

Phylogenetic Analysis as a Tool in Molecular Epidemiology of Infectious Diseases

Barry G. Hall and Miriam Barlow


Annals of Epidemiology
Volume 16, Issue 3, March 2006, Pages 157-169

"Phylogenetics is a powerful tool for microbial epidemiology, but it is a tool that is often misused and misinterpreted by the field. Microbial epidemiologists are cautioned that in order to draw any inferences about the order of descent from a common ancestor it is necessary to correctly root a phylogenetic tree. Epidemiological samples of microbial populations typically include both ancestors and their descendants. In order to illustrate the relationships of those isolates, the phylogenetic method used must be able to detect zero-length branches. Unweighted Pair-Group Method (UPGMA) is the phylogenetic method that is most widely used in microbial epidemiology. Because UPGMA cannot detect zero length branches, and because it places the root of the tree based on a usually-false assumption, UPGMA is the worst possible choice among the several phylogenetic methods available. Because microbial epidemiology deals with relationships among strains within a species, rather than with relationships among species, recombination within those species can render phylogenetic trees meaningless and positively misleading. When there is evidence of significant recombination within the species of interest phylogenetic trees should not be used at all. Instead, alternative tools such as eBURST should be used to understand relationships among isolates."

6 de febrero de 2008

Libro de filogenetica desde Colombia

Encontré la siguiente información en https://www.uis.edu.co/portal/administracion/publicaciones/libros/l81.html
sobre un nuevo libro de filogenética.
Aquí la transcribo tal cual.
Alguien local en Colombia podría ayudar a realizar la compra?
Saludos,
Efrain

SISTEMÁTICA FILOGENÉTICA


Joan Salvador ARIAS
Ivonne Janet GARZÓN ORDUÑA
Daniel Rafael MIRANDA ESQUIVEL

El libro fue pensado como soporte para las clases de sistemática de nivel básico y avanzado, además de servir de repaso para los conceptos teóricos generales pero sobre una base empírica. Consta de 12 capítulos que cubren desde manejo de caracteres y editores de datos como estrategias de búsqueda bajo parsimonia, ML o análisis bayesiano, consenso y soporte para parsimonia y ML. En todos los casos se presentan las técnicas, la metodología para el análisis, los programas de cómputo y sus comandos, además de una serie de preguntas sobre la práctica y la técnica. Cada capítulo incluye la literatura recomendada para posteriores lecturas. Se espera que el lector tenga conocimientos básicos de sistemática o este tomando un curso normal en el área; no se esperan características especiales en cuanto a dominio de computadores pero si los conocimientos básicos para un manejo apropiado de una computadora con cualquier sistema operativo; las practicas pueden realizarse en cualquier sistema operativo (Windows, MacOS o Linux). El libro surge a partir de las guías para el Laboratorio de Sistemática para el curso de Sistemática básica en el programa de pregrado en Biología de la UIS y para el curso de Sistemática en el postgrado de la Universidad de Antioquia.

ISBN: 958-8187-63-1
Fecha: 2007
Precio: 15.000



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