No hay crisis, no estamos en extincion, ni somos ermitaños.

Ellos dicen que los taxónomos no estamos en peligro de extinción, ni somos ermitaños antisociales. Segun ellos, no hay crisis en la taxonomia! Esa es la conclusión de un estudio recientemente publicado en TREE:

Lucas N. Joppa, David L. Roberts, Stuart L. Pimm, The population ecology and social behaviour of taxonomists, Trends in Ecology & Evolution, Volume 26, Issue 11, November 2011, Pages 551-553, ISSN 0169-5347, 10.1016/j.tree.2011.07.010.
http://www.sciencedirect.com/science/article/pii/S0169534711002084

Entre varios análisis que presentan, uno me llama la atención: el numero de especies describibles e investigables por taxónomos esta decreciendo! ..... Yo ya aparte mi grupo ..... grrrrrr .... :))

-
Esta es parte de la gráfica 1:

Trends over time in species discovery rates and taxonomic effort. (a) The number of species described per 5 years, (b) the cumulative number of species, (c) the number of taxonomists involved in species descriptions and the (d) species per taxonomists.

Segun esto, el número de especies descritas ha aumentado (A) y el de taxónomos se ha incrementado ..... exponencialmente! (C).

Siendo la referencia de partida los años 1800s, no me resulta sorprendente, ni creo que sea significativo este tipo de incrementos: todo se ha incrementado! No se cuales son los datos, ni de donde vienen, pues los datos no se presentan en el articulo. Pero se esperaría que los datos fueran de algún modo estandarizados, por ejemplo, numero de taxónomos proporcional a la población? Visto asi probablemente el numero de taxónomos no se ha incrementado tanto como otras cosas desde los 1800s!

PD:
Solo como un ejemplo reciente, lean esta nota sobre el estado de la taxonomia en Canada.
Taxonomy in trouble in Canada - November 18, 2010

.... y esta otra nota sobre la Taxonomia en Latinoamerica:
Análisis cienciométrico del estado de la Sistemática en Latinoamerica

Como ven?

Filogenética bajo Verosimilitud con un enfoque para "PhDs"

A cuantos de nosotros el Profesor del curso de Filogenética nos obligó a calcular la longitud (parsimonia) y/o verosimilitud de un árbol, "a mano"? La idea de esta experiencia "pedagógica" era entender los procedimientos y cálculos básicos en los métodos filogenéticos.

Bueno, ahora los profesores de este siglo ya no hacemos eso. Pero, los estudiantes a partir de mañana tendrán que hacer P O R S E P A R A D O la selección de modelos con ModelTest, la verosimilitud con PhyML y las probabilidades Bayesianas con Mr Bayes y todas las estimaciones de estabilidad, robustez, soporte, etc con varios programas particulares. Para que sufran!

Además, es por su bien! Sin duda ese "sufrimiento" es la única manera que les permitirá entender los métodos y les hará apreciar las bondades del nuevo paquete integrado de programas: "PALM: Phylogenetic reconstruction with Automatic Likelihood Model selectors". Se ha anunciado la disponibilidad de este paquete en un articulo recién publicado en PlosONE: Shu-Hwa Chen et al. 2009. PALM: A Paralleled and Integrated Framework for Phylogenetic Inference with Automatic Likelihood Model Selectors.
Fantástico!

Esta plataforma no es para instalarse en su computadora personal. Funciona desde un servidor al que el usuario ingresa sus datos de secuencias y recibe los arboles y otros resultados de los análisis. Así de sencillo! Se evita "el sufrimiento" de esas tareas que consumen tanto tiempo de computadora personal: cálculo para seleccionar el mejor modelo, cálculo del mejor árbol, cálculo de bootstraps, y otras propiedades de los árboles, etc etc. Demasiado tedioso y complicado! Mejor aún, los autores de PALM nos garantizan que ya no necesitaremos estudiar y preocuparnos por educarnos y entender lo que hacemos:

"However, such time consuming, computationally intensive tasks rely on knowledge of substitution model theories and related expertise to run through all possible combinations of several separate programs. "

"researchers unfamiliar with phylogenetic analysis can easily use this server to submit sequences, retrieve the output, and re-submit a job based on a previous result if some sequences are to be deleted or added for phylogenetic reconstruction."

"PALM is an integrated framework of ClustalW, PhyML, MODELTEST, ProtTest and several in-house programs to evaluate the fitness of 56 substitution models for nucleotide sequences and 112 substitution models for protein sequences with scores in various criteria. It is especially useful for biologists to perform phylogenetic analyses without prerequisite computer skills."

Esto viene en el Resumen y Discusión del articulo como una de las mejores caracteristicas del paquete! Así que todos demos gracias a PALM, pues integra ahora operaciones de ClustalW, PhyML, ModelTest y varios otros programas. La estructura del sistema de programas funcionando en paralelo en varios procesadores simétricos (symetrical multiprocesors, SMP) en varios CPUs veloces, trabajando bajo LINUX Ubuntu, garantizan un trabajo rápido y fluido, administrado por módulos (PalmDaemon, PalmMonitor, PalmTree y Palm job controller).

Desde el punto de vista del usuario, PALM inicia cuando se ingresa una matriz de secuencias o de aminoácidos pre-alineada en formato FASTA. El usuario ahora aprovecha el tiempo para otras cosas mas interesantes y productivas (como jugar a publicar en web mediante blogs como este). Mientras tanto, como parte del flujo de tareas automáticas en el servidor, PALM primero instruye a ClustalW para ejecutar un alineamiento definitivo. El alineamiento se transfiere a PhyML/ModelTest para la selección del mejor modelo. La combinación del alineamiento definitivo y el mejor modelo se somete a la tarea de cálculo del mejor árbol usando PhylML. El usuario es notificado vía correo electrónico para visitar una página web donde se despliega su arbol y su articulo publicado en "Molecular Phylogenetics and Evolution"! Un click ... un artículo!

Eso es lo que muchos quisieran, ........ pero no, .... solo se obtienen los resultados. En la versión futura?

Los autores nos prometen que en una futura versión de PALM integrarán más programas de alineamientos y también probabilidades Bayesianas:

"Other advanced algorithms for ML inference, e.g., DPRml , MrBayes and RAxML, can be integrated into PALM to provide Bayesian estimates of phylogeny and handle large phylogenetic trees in the future."

La idea de una versión PhD (Push here Dummy) para hacer filogenias no es nueva. En el afán de facilitar el uso de los programas filogenéticos, las secuencias de comandos para las operaciones y la presentación gráfica de árboles, casi todos los programas disponibles (excepto PhylLip?!) desde hace años han evolucionado hacia interfases cada vez más "user friendly". Eso ha sido bueno. Quien recuerda la supremacía de PAUP en el ambiente grafico de MAC en los 80´s cuando la competencia eran PAUP y otros programas que solo corrían con lineas de comandos en DOS o Windows 3.1? Recuerdo en esos años, eventualmente apareció TreeGardener como una interfase gráfica para facilitar el uso de Hennig86 y versiones o programas subsecuentes hasta WINCLADA y NONA.

La llegada de PALM ahora facilitará aun más la ejecución "point and click" de análisis filogenéticos bajo la epistemología de los métodos de máxima verosimilitud para las nuevas generaciones de estudiantes e investigadores.
------

Chen S-H, Su S-Y, Lo C-Z, Chen K-H, Huang T-J, et al. (2009). PALM: A Paralleled and Integrated Framework for Phylogenetic Inference with Automatic Likelihood Model Selectors plosone, 4 (12) : e8116. doi:10.1371/journal.pone.0008116
web http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0008116
pdf
------

Cual cree Ud que sea el efecto?:

• Beneficiará a la comunidad que hace estudios filogenéticos?

o

• Perjudicará la situación educativa promoviendo el uso a ciegas de los métodos de verosimilitud?

Que opina? Escriba su comentario:

Secuencias “COI-like numts” inutilizan los codigos de barras de DNA

La exploración de la biodiversidad, la clasificación filogenética y la identificación de muestras son las tres tareas fundamentales de la sistemática. Los obstáculos y dificultades en cada área son diversos, pero como biólogos todos sabemos lo difícil que es identificar taxonómicamente una colección de muestras, sean de plantas, animales, hongos, etc. Ademas de la muestra en buen estado y claves de identificación, frecuentemente se necesita el "ojo experto" del taxónomo especialista.

De identificadores morfológicos a identificadores moleculares
La disponibilidad de marcadores moleculares en la forma de secuencias cortas y muy especificas o restringidas a una especie permiten ahora la identificación rápida de muestras biológicas, sin claves de identificación morfológicas y sin la necesidad del taxónomo experto. Los "códigos de barras de DNA" son simplemente eso, marcadores moleculares cuya presencia permite identificar una especie.

Como sucede con cualquier atributo identificador (morfológico o molecular) los códigos de DNA fallan si la muestra pertenece a una especie que no ha sido previamente descrita y clasificada. Entonces antes de conseguir el "código genético" o DNA barcoding de la biota, los taxónomos deben explorar, descubrir, describir y clasificar las especies. Aun si el trabajo de clasificar ya esta hecho, las muestras de referencia para extraer el DNA deben estar bien identificadas, por el taxónomo experto. Ademas, el marcador molecular debe ser bien identificado tambien y exclusivo o tener poca variación intraespecífica y geográfica para asegurar un porcentaje alto de identificaciones correctas de otras muestras futuras de la especie en cuestión. Un resumen reciente y excelente de la teoría y métodos de los códigos de DNA es el de Meir (2008, cap 7, en: Wheeler, QD, ed, The new taxonomy. Syst. Assoc. vol 76. CRC press).

Que tan exclusiva a una especie es la presencia de cierta variante del marcador molecular? Que tanta variación y repetibilidad se conoce de esa secuencia de DNA? Realmente son buenos identificadores? Las respuestas van desde el optimismo exagerado o ingenuo hasta el escepticismo total. Los pros y cons del DNA barcoding se han debatido en la literatura (Lipscomb et al 2003, TREE 18: 65-66; Mallet & Wilmott 2003, TREE 10:57-59; Tautz et al, 2002, Nature 418: 479; 2003, TREE 18: 7074; Seberg et al 2003, TREE 18: 63-65). Lo que es un hecho es que siguen surgiendo cada vez mas los ejemplos de casos de especies que sugieren moderar las expectativas del potencial real de los identificadores moleculares (Song et al 2008).

El ejemplo más reciente es un artículo (Buhay 2009) que revela la importancia de identificar con precisión las secuencias del marcador usado para el "codigo de DNA". El caso es el de secuencias que se obtuvieron y catalogaron como COI (cytochrome c oxidase subunit I) pero ahora un analisis cuidadoso reveló que eso fue un error muy serio, pues las secuencias realmente son de pseudogenes no codificantes (COI-like numts, nuclear copies of mitochondrial derived genes).

Comparación de dos secuencias COI fidedignas y de una secuencia mal identificada como COI. Click para ver la imagen a 1379px × 152px

Los errores de identificación ocurren donde sea: usando las clásicas claves morfológicas y también con los "codigos de barras de DNA". El problema es que ante diferentes resultados en la identificación, comúnmente se cuestiona el procedimiento morfológico pero no el resultado molecular. Este estudio minimamente debe alertar a todos pues los errores de identificación de las secuencias son mas comunes de lo que se desea aceptar. No todo lo que brilla es oro!

Referencia del articulo:
Buhay, J. (2009). “COI-like” Sequences are Becoming Problematic in Molecular Systematic and DNA Barcoding Studies Journal of Crustacean Biology, 29 (1), 96-110 DOI: 10.1651/08-3020.1

A B S T R A C T
The cytochrome c oxidase subunit I (COI) gene plays a pivotal role in a global effort to document biodiversity and continues to be a gene of choice in phylogenetic and phylogeographic studies. Due to increased attention on this gene as a species’ barcode, quality control and sequence homology issues are re-emerging. Taylor and Knouft (2006) attempted to examine gonopod morphology in light of the subgeneric classification scheme within the freshwater crayfish genus Orconectes using COI sequences. However, their erroneous analyses were not only based on supposed mitochondrial sequences but also incorporated many questionable sequences due to the possible presence of numts and manual editing or sequencing errors. In fact, 22 of the 86 sequences were flagged as ‘‘COI-like’’ by GenBank due to the presence of stop codons and indels in what should be the open reading frame of a conservative protein-coding gene. A subsequent search of ‘‘COI-like’’ accessions in GenBank turned up a multitude of taxa across Crustacea from published and unpublished studies thereby warranting this illustrated discussion about quality control, pseudogenes, and sequence composition.
KEY WORDS: cytochrome c oxidase subunit I,molecular taxonomy, numt, protein-coding gene, pseudogene
DOI: 10.1651/08-3020.1

Phylogenomics: hace diez años!!

Vol. 8, Issue 3, 163-167, March 1998

INSIGHT/OUTLOOK
Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis
Jonathan A. Eisen¹
Genome Research -- Eisen 8 (3): 163

The ability to accurately predict gene function based on gene sequence is an important tool in many areas of biological research. Such predictions have become particularly important in the genomics age in which numerous gene sequences are generated with little or no accompanying experimentally determined functional information. Almost all functional prediction methods rely on the identification, characterization, and quantification of sequence similarity between the gene of interest and genes for which functional information is available. Because sequence is the prime determining factor of function, sequence similarity is taken to imply similarity of function. There is no doubt that this assumption is valid in most cases. However, sequence similarity does not ensure identical functions, and it is common for groups of genes that are similar in sequence to have diverse (although usually related) functions. Therefore, the identification of sequence similarity is frequently not enough to assign a predicted function to an uncharacterized gene; one must have a method of choosing among similar genes with different functions. In such cases, most functional prediction methods assign likely functions by quantifying the levels of similarity among genes. I suggest that functional predictions can be greatly improved by focusing on how the genes became similar in sequence (i.e., evolution) rather than on the sequence similarity itself. It is well established that many aspects of comparative biology can benefit from evolutionary studies (Felsenstein 1985), and comparative molecular biology is no exception (e.g., Altschul et al. 1989; Goldman et al. 1996). In this commentary, I discuss the use of evolutionary information in the prediction of gene function. To appreciate the potential of a phylogenomic approach to the prediction of gene function, it is necessary to first discuss how gene sequence is commonly used to predict gene function and some general features about gene evolution.

Bosque: integrated phylogenetic analysis software

Ramírez-Flandes S. & O. Ulloa (2008).
Bosque: Integrated phylogenetic analysis software.
Bioinformatics 24(21):2539-2541;
doi: 10.1093/bioinformatics/btn466

Summary:
Phylogenetic analyses today involve dealing with computer files in different formats and often several computer programs. Although some widely used applications have integrated important functionalities for such analyses, they still work with local resources only: input/output files (users have to manage them) and local computing (users have sometimes to leave their programs, on their desktop computers, running for extended periods of time). To address these problems we have developed ‘Bosque’, a multi-platform client–server software that performs standard phylogenetic tasks either locally or remotely on servers, and integrates the results on a local relational database. Bosque performs sequence alignments and graphical visualization and editing of trees, thus providing a powerful environment that integrates all the steps of phylogenetic analyses.

Availability: http://bosque.udec.cl

Contact: sram@profc.udec.cl

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!

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."

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."

Literatura reciente, 1

A Comprehensive Phylogeny of Beetles Reveals the Evolutionary Origins of a Superradiation.

Hunt, T. et al. Science 21 December 2007:Vol. 318. no. 5858, pp. 1913 - 1916

Beetles represent almost one-fourth of all described species, and knowledge about their relationships and evolution adds to our understanding of biodiversity. We performed a comprehensive phylogenetic analysis of Coleoptera inferred from three genes and nearly 1900 species, representing more than 80% of the world's recognized beetle families. We defined basal relationships in the Polyphaga supergroup, which contains over 300,000 species, and established five families as the earliest branching lineages. By dating the phylogeny, we found that the success of beetles is explained neither by exceptional net diversification rates nor by a predominant role of herbivory and the Cretaceous rise of angiosperms. Instead, the pre-Cretaceous origin of more than 100 present-day lineages suggests that beetle species richness is due to high survival of lineages and sustained diversification in a variety of niches.