¿que hay de comer?

Algunos organismos se alimentan de las especies de un grupo monofilético en particular, mientras que otros presentan menor sesgo filogenético. Nuestra especie parece ajustarse a la segunda categoría, lo que nos ubica cerca de los generalistas. Aunque los antropólogos conocen esto desde tiempo atrás, recientemente Proches et al 2008, decidieron probar ésto utilizando filogenias de plantas. Lo que encontraron es que nuestra dependencia de algunos taxa no es muy diferente de lo esperado al azar, posiblemente la biogeografía vegetal y no sesgos filogenéticos explican mejor nuestros patrones culinarios. Les comparto este artículo >>AQUÍ>> que aborda desde un punto de vista filogenético una de las preguntas más cotidianas ¿qué hay de comer?: Pues taxa no emparentados.

North American Workshop in Cladistic Methods, 2008

The Ohio State University, with generous financial support from the Willi Hennig Society, will conduct a workshop on phylogenetic methods in Columbus, Ohio, July 21-26, 2008. The purpose is to provide further instruction and experience to students who already have some familiarity with phylogenetic analysis. The format is a series of lectures and laboratory sessions that will give students the opportunity to gain a deeper understanding of the logic of the phylogenetic method, parsimony, maximum likelihood and Bayesian approaches, tree search strategies, measures of support, DNA alignment, morphological character coding, weighting, analysis of multiple and large data sets, consensus and character hypothesis testing.

Lecturers are expected to include

• James M. Carpenter (Growth of modern systematics, Coding morphological characters),
  
• James S. Farris (Political history of phylogenetics),
  
• Pablo A. Goloboff (Optimization, Tree search, Consensus methods, Clade support, Large data sets, Weighting),
  
• Mari Källersjö (Alignment and subsequent analysis of molecular data),
  
• Laura S. Kubatko (Logic and operation of Likelihood and Bayesian approaches),
  
• John W. Wenzel (Nontraditional characters, Diagnosing problematic results), and
  
• Ward C. Wheeler (Dynamic optimization).
  

The software used for the course will include TNT, POY, RaxML, MrBayes (all distributed with the course packet) and Clustal.
Further information may be obtained at the workshop website

Algoritmos de solucion de matrices filogeneticas

¿Cuales son los algoritmos matemáticos que utilizan los software cladisticos para resolver las matrices? Mi pregunta se basa en el hecho de que mientras en la TN es perfectamente conocible que las matrices son resueltas a través de índices de similitud o de distancias y no pueden consignarse signos como ? y - para denotar que no se conoce o no es evaluable el caracter, en el caso de las matrices resueltas a traves de software filogeneticos estos signos son perfectamente admisibles y evaluables, lo cual he supuesto debe ser interpretado de alguna forma por el algoritmo empleado en la solucion. Hasta el presente no he podido encontrar los algoritmos que se utilizan en la solución de las matrices filogenéticas en los diferentes progrmas como POY,TNT, HENNIG, Mc CLADE y otos tantos.

Bibliografía Reciente sobre Filogenética

Colección de referencias desde varias Revistas que publican sus contenidos en formato RSS.

Esta "entrada" se actualizará automáticamente cada vez que alguna de las revistas monitoreadas publique contenido nuevo.

Estén pendientes!!! Se pueden suscribir aqui >>


Si encuentran útil este servicio, díganos sus sugerencias y comentarios!

Diferencias entre Sistematicas

¿Cual es la diferencia fundamental entre la Sistemática Evolutiva (SE) fundada por Huxley, Mayr y Simpson, la Taxonomia Numérica (TN) de Sneath y Sokal (Dendrogramas) y la Sistemática Filogenética (SF) de Willi Hennig (Cladística)? Conozco que la TN basa sus análisis en el parecido fenotípico de las especies actuales sin considerar a los ancestros y que la SF considera las relaciones ancestrales de esas especies actuales a través de las sinapomorfias pero además de eso se habla en algunos textos de que las diferencias radican básicamente en si se consideran, especies, individuos, poblaciones, clases o tipos. Esta parte es la que no logro contextualizar además de que nos e me hace clara la diferencia en la SF y la SE.

XXVII Reunión de la Soc. Willi Hennig

Hennig XXVII

Hotel Sol San Javier

Tucuman, Argentina

Octubre 28-31, 2008

sitio web de la reunión aquí

Curso: Sistemática y Evolución de Helechos y Bromelias

Estimada comunidad Filogenética
les anuncio para la siguiente semana del 21 al 25 de Abril 2008, se celebrará en la Universidad Autónoma del Estado de Hidalgo (UAEH) en el Centro de Investigaciones Biológicas, la semana de la "Cátedra Nacional de Biología 2008, Juan Luis Cifuentes Lemus"(México), cuya temática es la Biología de la Conservación: Sistemática y Evolución. Dicho Evento se efectuará en la Ciudad Universitaria de la UAEH.

Para dicho evento contaremos con conferencias impartidas por investigadores nacionales (de las 16 Universidades participantes) así como talleres relacionados con la Sistemática y Evolución, enfocada desde varios puntos de vista.
Dentro de los talleres se encuentra el de "Sistemática y Evolución de Helechos y Bromelias" impartidos por el Dr. Arturo Sanchez y Dra. Claudia Hornung Leoni. Dicho curso está enfocado a estudiantes de licenciatura.
Las ponencias están enfocadas a estudiantes, investigadores y público en general.

Los invitamos a participar en dicho evento!

saludos
Claudia Hornung
Profesor-Investigador, CIB, UAEH. México

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.

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."

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

Curso básico de filogenia

Curso básico de filogenia aplicada: de la secuencia al árbol

Madrid, Junio 2008. 18 horas. Precio: 775 Euros.

PROFESORADO
Dr.José M Bautista, Dra. Susana Scönhuth, María López Andreo y Rafael González Sevilla.
Dep. de Bioquímica y Biol. Mol. IV de la Fac.de Veterinaria de la Univ. Complutense de Madrid
Dra. Annie Machordom. Museo Nacional de Ciencias Naturales, CSIC, Madrid

OBJETIVO: Proporcionar los conocimientos teóricos y prácticos necesarios para iniciarse en las técnicas de análisis filogenético.
DIRIGIDO A: Este curso va dirigido a investigadores y técnicos de laboratorio de universidades y centros de investigación que estén interesados en la realización de análisis filogenéticos.

Informes >>>

Literatura reciente, 3

Ramírez, MJ (2007) Homology as a parsimony problem: a dynamic homology approach for morphological data. Cladistics 23 (6), 588–612.

"The primary data used to reconstruct phylogenies comes organized in the conceptual grid of homology correspondences, and the construction of this theory-rich grid depends in part on knowledge of relationships. This situation is not satisfactory as a conceptual system, because the evidence is not clearly delimited from the results. I explore the testing of alternative hypotheses of morphological correspondences in a quantitative cladistic context. The varying homology assessments implied by classical criteria of homology (topological equivalence, or position and connections; composition of structures, or commonality in details of construction) can be expressed as regular characters in a cladistic analysis. Doing so provides adequate transformation costs for changes in schemas of correspondences. Correspondences imply evolutionary transformations, and multiple schemas of correspondences can be compared according to the evolutionary transformations that they imply. The method is used to test the correspondences in sclerites of the male copulatory organs of spiders of the subfamily Amaurobioidinae (Arachnida, Araneae, Anyphaenidae). The correspondences of three sclerites are tested, in a data set of 93 species having one, two or three sclerites, using a simultaneous analysis of all the morphological characters. Most parsimonious trees are identified together with the correspondences they imply. Once the correspondences are integrated in the phylogenetic analysis, it is easy to evaluate the robustness of trees or decay in optimality after changes in anatomical interpretations. A Bremer support for anatomical interpretations is proposed, calculated as the increase in tree length when the specific interpretation is not used."

Literatura reciente, 2

Rensing, SA. et al. 2008.The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants. Science 4 January 2008: Vol. 319. no. 5859, pp. 64 - 69

"We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics."

TNT ahora disponible sin costo

A partir del 20 de Noviembre del 2007, el programa TNT (Tree analysis using New Technology) creado por Pablo Goloboff, James Farris y Kevin Nixon esta disponible sin costo alguno gracias a un subsidio de la sociedad Willi Hennig.

Mas información sobre el programa y la manera de obtenerlo puede ser encontrado siguiendo esta liga.

Aqui pueden leer un review >>>

Taller de métodos filogenéticos, BML

"Phylogenetic methods have revolutionized modern systematics and become indispensable tools in evolution, ecology and comparative biology, playing an increasingly important role in analyses of biological data at levels of organization ranging from molecules to ecological communities. The construction of phylogenetic trees is becoming a methodology that is well-defined, with broad agreement on the central issues and questions. A nearly standard set of topics is now taught as part of the curriculum at many colleges and universities. On the other hand, application of phylogenetic methods to interesting problems outside of systematics is an area of special excitement, innovation, and controversy, and perspectives vary widely."

"In March, 2008, for the ninth year, we will teach a workshop for graduate students interested in applying phylogenetic methods to diverse topics in biology. The one-week course will be an intensive exploration of problems to which modern phylogenetic tools are being applied. We cover a range of topics in biogeography, ecology, conservation biology, phylogenomics, functional morphology, macroevolution, speciation, and character evolution. The course starts with recent advances in phylogenetic methodology, and then focuses on methods and tools that can be brought to bear on these "applied" issues in the context of a given phylogeny."

"Application Deadline. Applications are due by January 15, 2008."