Noticias sobre Filogenética

Filogenética bajo Verosimilitud con un enfoque para "PhDs"

2009-12-05T14:20:00.032-06:00

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 el articulo publicado en "Molecular Phylogenetics and Evolution"!

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.

Cual cree Ud que sea el efecto?:

Beneficiará a la comunidad que hace estudios filogenéticos?

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

Que opina?

------

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) : doi:10.1371/journal.pone.0008116
web http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0008116
pdf

------

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. PLOs ONE, 4 (12): e8116. doi:10.1371/journal.pone.0008116

Conectese a las conferencias sobre filogenetica en linea

2009-12-02T15:57:00.001-06:00

Se ha iniciado un sitio web para brindar un servico de seminarios sobre filogenetica en linea. El servicio es administrado en el sitio Phyloseminar.org, organizado por Frederick Matsen, Miller Institute y la ayuda de David Bryant, Aaron Darling, Alexei Drummond, Stephane Guindon, Tracy Heath, Robin Kodner, Chris Nasrallah, y Tanja Stadler.
El próximo seminario es:

To attend this and other talks, learn how to connect ahead of time, and join the email list.

If you can't make it, don't fret-- you can always watch the recording.

How did flowering plants evolve to dominate Earth?

2009-12-02T15:49:00.000-06:00

December 1, 2009 06:10 PM
To Charles Darwin it was an 'abominable mystery' and it is a question which has continued to vex evolutionists to this day: when did flowering plants evolve and how did they come to dominate plant life on earth? Today a study in Ecology Letters reveals the evolutionary trigger which led to early flowering plants gaining a major competitive advantage over rival species, leading to their subsequent boom and abundance.

The study, by Dr Tim Brodribb and Dr Taylor Field of the University of Tasmania and University of Tennessee, used plant physiology to reveal how flowering plants, including crops, were able to dominate land by evolving more efficient hydraulics, or 'leaf plumbing', to increase rates of photosynthesis.
"Flowering plants are the most abundant and ecologically successful group of plants on earth," said Brodribb. "One reason for this dominance is the relatively high photosynthetic capacity of their leaves, but when and how this increased photosynthetic capacity evolved has been a mystery."

Read more>>>

Glosario Inglés-Español de Términos Técnicos empleados en Ecología, Evolución y Sistemática, con Énfasis en Ornitología

2009-11-26T15:03:00.001-06:00

Glosario Inglés-Español de Términos Técnicos Empleados en Ecología, Evolución y Sistemática, con Énfasis en Ornitología

Mantenido por C. Daniel Cadena, Lucio R. Malizia, Cintia Cornelius y Juan Martínez

"La literatura científica en inglés está llena de términos técnicos que en muchos casos no tienen términos equivalentes estándar en español. Encontrar términos apropiados ha sido con frecuencia difícil para nosotros al traducir textos para revistas ornitológicas (esto explica el sesgo hacia las aves), por lo que durante los últimos años hemos estado construyendo este glosario, que representa un intento de estandarizar la traducción al español de términos técnicos utilizados en la literatura biológica en inglés. Este glosario inicialmente era para nuestro uso personal para traducir textos de manera consistente, pero ahora esperamos que sea una herramienta más general y de mayor utilidad. Como consecuencia de la historia de esta página, hasta el momento hemos incluido términos de forma más o menos desordenada, pero esperamos añadir palabras de modo sistemático en el futuro, en la medida en que el tiempo lo permita.
Este glosario presenta traducciones de términos, pero no definiciones precisas. Si tiene cualquier comentario, crítica o sugerencia (en especial sobre palabras que le gustaría que agregáramos al glosario), por favor contáctenos. Si le interesa contribuir directamente al desarrollo de este sitio wiki, por favor lea las instrucciones para colaboradores, y escríbanos un correo. "

Visite el sitio web del Glosario aqui >>>

Resultados de la encuesta: Como usa este blog?

2009-11-23T13:51:00.008-06:00

Muchas gracias a todos los visitantes de este sitio y quienes participaron en la encuesta. En los últimos años hemos tenido un promedio de alrededor de 250 visitas diarias. Lo que se desprende de los datos de la encuesta es que la expectativa de la mayoría es usar el sitio como portal de información.

Is 80-year-old mistake leading to first species to be fished to extinction?

2009-11-19T15:15:00.002-06:00

Is 80-year-old mistake leading to first species to be fished to extinction?
A species of common skate is to become the first marine fish species to be driven to extinction by commercial fishing, due to an error of species classification 80 years ago, reveals research published November 17 in the journal Aquatic Conservation.
From the mid-19th century the common skate was described as two distinct species, the flapper skate, D. intermedia, and the blue skate, D. flossada. However, in an influential work in 1926 R.S Clark recognised only 'D. batis' as a valid species and this classification has largely gone unchallenged since.
This classification confusion has resulted in the depletion of the flapper skate, the more endangered species of the two, being masked in the catch record. This means the risk of extinction is far higher than previously assessed and without immediate and incisive action the species may be in an irreversible decline towards extinction.
Read more >>>

Postdoc postion in beetle morphology/taxonomy

2009-11-14T09:33:00.002-06:00

The International Institute for Species Exploration, Arizona State University (ASU), invites applications and nominations for a postdoc available January 1, 2010. Duties include dissections, descriptions, and digital illustrations of beetles for print and Web publications, participating in the Institute team working on various cybertaxonomy initiatives, and supporting the research of the director, currently including taxonomic studies of Eleodes (Coleoptera, Tenebrionidae).

ASU is an equal opportunity/affirmative action employer. Women and minorities are encouraged to apply. Submit statement of interest, CV, and names/email addresses of three references to: Quentin Wheeler, Vice President and Dean, College of Liberal Arts and Sciences, Arizona State University. Please submit electronically to tyna.chu@asu.edu with subject line Morphology Postdoc. Review of candidates will begin immediately and continue until the position is filled.

Quentin D. Wheeler, PhD, FLS
University Vice President;
Dean, College of Liberal Arts and Sciences;
Virginia M. Ullman Professor of Natural History and the Environment,
School of Life Sciences;
Arizona State University
PO Box 876505
Tempe, AZ 85287-6505
480-965-3375; Fax: 480-965-1093

College of Liberal Arts and Sciences

2008 Webby and Telly Winning Video 'Planet Bob'

ASU College of Liberal Arts and Sciences — Transforming learning, discovery and lives

Postdoctoral Fellowship, Biodiversity of Madagascar

2009-11-13T12:27:00.001-06:00

Postdoctoral Fellowship, Biodiversity of Madagascar

November 12, 2009
Postdoctoral Fellowship

SUMMARY:

This position is a two year appointment starting approximately July 1, 2010, involving both research in our molecular genetic laboratory and in situ field work focused on the biodiversity of Madagascar, including lemurs, carnivores, geckos, chameleons, boas, turtles and tortoises populations endemic to the island.

DUTIES AND RESPONSIBILITIES:

The scientist will employ molecular genetic techniques in the laboratory to generate species-specific microsatellites, multi-locus genotypes and DNA sequence files. The incumbent will also be responsible to apply advanced statistical methods, computer science skills and bioinformatics principles to highlight the dynamics of population genetics and systematics. The candidate’s ability for independent and critical thinking and excellent English writing skills will be vital in the writing of grants and publishable manuscripts. Excellent interpersonal skills will be key, especially in relation to our cross-cultural field research teams in Madagascar.

KNOWLEDGE, SKILLS, AND ABILITIES REQUIRED:

Excellent opportunity available for a motivated and experienced Ph.D. in the genetics, molecular biology, or cell biology fields, with a strong publication record and outstanding professional references. Emphasis in conservation science or informatics experience is a plus. Qualified candidates must show proficiency in molecular genetic techniques and computer skills capable to generate necessary data and to perform genotype and sequence analysis. The position will require attention to detail, good communication skills, strong skills in experimental design and troubleshooting, an ability to work independently and as part of a team, and dedication to doing the best job possible.

Read more >>> http://scholarship-positions.com/postdoctoral-fellowship-biodiversity-of-madagascar/2009/11/12/

Hacia una Sociedad Argentina de Taxónomos y Sistemáticos

2009-11-11T22:10:00.001-06:00

ASOCIACIÓN PALEONTOLÓGICA ARGENTINA: Sociedad Argentina de Taxónomos y Sistemáticos

Antecedentes

La Taxonomía y la Sistemática son las ciencias que se ocupan de identificar, describir, clasificar, agrupar y nominar la biodiversidad. Esto incluye el estudio tanto de las relaciones de parentesco entre los taxones como de los principios y métodos que sustentan tales clasificaciones. Para ello, la Taxonomía y la Sistemática toman como trasfondo la teoría de la evolución, lo que les permite generar hipótesis predictivas utilizando toda la evidencia disponible de diferentes campos de la biología (morfología, comportamiento, desarrollo, distribución geográfica, fisiología, genética, genómica, etc.).

Estas ciencias, la Taxonomía y la Sistemática, se remontan al comienzo de los estudios biológicos y como consecuencia de ello poseen un cuerpo teórico y metodológico robusto, desarrollado desde la antigüedad y formalizado científicamente desde la aparición de la teoría de Darwin y principalmente a partir de la década de 1950 hasta nuestros días mediante aportes teóricos y metodológicos de variadas figuras de la biología (e.g. Mayr, Hennig, Sokal, Bremer, Rohlf, Fitch, Farris, etc.).

.........
Ante esta situación y considerando necesario nuclear a los científicos que tienen una problemática común, se propone la creación de la Sociedad Argentina de Taxónomos y Sistemáticos.
.......

Leer más >>>

FOURTH INTERNATIONAL CONFERENCE ON PHTHIRAPTERA (ICP 4), TURKEY

2009-11-11T21:56:00.002-06:00

FOURTH INTERNATIONAL CONFERENCE ON PHTHIRAPTERA (ICP 4)

JUNE 13-18, 2010
CONFERENCE HALL OF MUSTAFA HOTEL, URGUP
CAPPADOCIA, TURKEY

SYMPOSIA

• Morphology and Physiology of Lice

• Systematic, Population Genetics and Evolution

• Epidemiology of Human Lice

• Ecology and Epidemiology of Animal Lice

• Medical and Veterinary Aspects of Louse Infestations

• Microorganisms Associated with Lice

• Prophylaxis and Control of Lice

• Phthirapterists and Phthirapterology

• Techniques to study lice

More information: meeting web site

La bioinformática se consolida en la Argentina

2009-11-06T12:38:00.002-06:00

La bioinformática se consolida en la Argentina | bioinformaticos.com.ar

La bioinformática puede contribuir al diseño de drogas más eficientes o explicar cómo nuestras células toman decisiones frente a diferentes circunstancias, entre muchas otras posibilidades. En Estados Unidos y en varios países de Europa ese campo del conocimiento está en pleno auge. Se trata de una nueva ciencia que promueve el uso de la informática en el estudio de los seres vivos.
A fin de promover su desarrollo en la Argentina acaba de nacer la Asociación Argentina de Bioinformática y Biología Computacional (AABBC / http://www.a2b2c.org.ar/.). Reúne a investigadores y profesionales de distintas ramas de la biología, de la matemática, la química y la informática.
“La biología enfrenta un momento muy complejo. Actualmente somos capaces de producir una gran marea de datos, en particular con los proyectos genómicos. Pero obtener muchos datos no significa necesariamente entender mucho”, explicó Cristina Marino Buslje, presidenta de AABBC, egresada de la Universidad Autónoma de Barcelona y actualmente investigadora de la Universidad de Buenos Aires. Y agregó: “La bioinformática y la biología computacional van a ser protagonistas porque son imprescindibles para procesar esos datos y convertirlos en conocimiento”.
“La biología computacional cruza a toda la biología en forma transversal. Es posible modelar en la computadora desde ecosistemas hasta la interacción molecular de una droga con su receptor”, señaló el vicepresidente de AABBC Fernán Agüero e investigador de la Universidad de San Martín. Agüero llamó a sumar esfuerzos para divulgar la biología computacional y formar profesionales en el campo.
Asimismo, Marcelo Marti, investigador del Conicet en la Universidad de Buenos Aires y miembro de la recién inaugurada fundación afirmó que “estudiar y modelar procesos biológicos en la computadora es esencial tanto para las ciencias básicas –generando hipótesis que deben ser puestas a prueba en el laboratorio–, como para las aplicadas, ya que constituye la base de un número creciente de desarrollos.”

LEER MÁS >>>

Scientists Launch Effort To Sequence The DNA Of 10,000 Vertebrates

2009-11-05T11:28:00.006-06:00

Scientists have an ambitious new strategy for untangling the evolutionary history of humans and their biological relatives: Create a genetic menagerie made of the DNA of more than 10,000 vertebrate species. The plan, proposed by an international consortium of scientists, is to obtain, preserve, and sequence the DNA of approximately one species for each genus of living mammals, birds, reptiles, amphibians, and fish.

"Understanding the evolution of the vertebrates is one of the greatest detective stories in science," said David Haussler, a Howard Hughes Medical Institute investigator at the University of California, Santa Cruz (UCSC). "No one has ever really known how the elephant got its trunk, or how the leopard got its spots. This project will lay the foundation for work that will answer those questions and many others."
Known as the Genome 10K Project, the approximately $50 million initiative is "tremendously exciting science that will have great benefits for human and animal health," Haussler said. "Within our lifetimes, we could get a glimpse of the genetic changes that have given rise to some of the most diverse life forms on the planet."

Read more >>>

Convocatoria para el Posgrado en el INECOL, Xalapa

2009-11-02T18:49:00.000-06:00

::: INECOL ::: Maestría y Doctorado :::

Se ha publicado la Convocatoria para ingreso al Posgrado del INECOL, Xalapa (ecología, biodiversidad, sistemática, conservación y manejo de los recursos naturales)
La Secretaría de Posgrado tiene como misión la formación de recursos humanos de alto nivel (Maestria y Doctorado en Ciencias) con el objeto de:

Capacitarlos para realizar investigación científica original.
Que apliquen los conocimientos científicos y tecnológicos a la solución de los problemas concretos enfrentados por la sociedad a la cual pertenecen.

Las áreas de investigación con mayor énfasis en el programa académico del posgrado incluyen:

Biodiversidad y Sistemática
Conservación
Ecología
Manejo de Recursos

Los estudiantes latinoamericanos pueden optar a becas de CONACYT México.
La información sobre la convocatoria esta aquí >>>

Computational Biology in Colombia

2009-10-30T12:26:00.001-06:00

PLoS Computational Biology: Computational Biology in Colombia

High-throughput techniques are somewhat restricted in developing countries. However, computational resources have evolved in recent years to become available to the general public, with greater ability to solve intense computational problems at low cost. Therefore, the vast amount of information that is currently being generated and the need for finding the underpinnings of several issues in biology, have been the impetus of the computational biology area in Latin America. Colombia is no exception, as its rich genetic diversity has convened the attention of several institutions, including both governmental and academic departments, to find how, where, and when these resources could be employed to its benefit. In this review, we introduce the efforts being made throughout the country to spread the word and establish a strong network from a mid- and long-term perspective.

In Colombia, computational biology is just starting to be known as a field of research in its own right. Until now, mainly chemists and biologists have used bioinformatics as a tool to try to solve their particular research problems. We start by reviewing the work of some research groups and their projects. Next, we identify the driving forces of computational research and the problems to be faced in the future. This review is not exhaustive and we apologize for any groups that were not mentioned or acknowledged.

Restrepo S, Pinzón A, Rodríguez-R LM, Sierra R, Grajales A, et al. (2009) Computational Biology in Colombia. PLoS Comput Biol 5(10): e1000535. doi:10.1371/journal.pcbi.1000535

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000535

Postdoctoral Fellowship in Vertebrate Evolution - University of Arizona

2009-10-26T09:39:00.001-06:00

George Gaylord Simpson Postdoctoral Fellowship in Vertebrate Evolution -
University of Arizona

The Department of Ecology and Evolutionary Biology announces one
postdoctoral fellowship position for Fall 2010, named in honor of G. G.
Simpson's long tenure at the University of Arizona.

Simpson Fellows are expected to conduct an active research program in evolutionary biology,
especially projects that are facilitated and complemented by the
Department's extensive natural history collections in ichthyology,
herpetology, ornithology, and mammalogy. The positions are part of a
renewed commitment to natural history collections on the University of
Arizona campus and an initiative in biodiversity informatics
(http://loco.biosci.arizona.edu/bdii/). Postdoctoral Fellows are
encouraged to establish research collaborations with faculty in the
Department of Ecology and Evolutionary Biology and are expected to teach
or contribute to one course per year in the Fellow's research specialty.
Salary is $37,500 plus benefits (nine-month appointment). A research
stipend of $5000 will also be included. The positions are renewable for
at least a second year contingent on satisfactory performance.

Applicants should submit application materials online at the University
of Arizona Human Resources website (https://www.uacareertrack.com; look
for job #44102), including C.V., statement of research and teaching
interests and experience, and two letters of reference. Reference
letters should be emailed directly to sand...@email.arizona.edu.
Position is open until filled, but we anticipate reviewing applications
beginning on Jan. 15, 2010.
Contact Dr. Peter Reinthal (p...@email.arizona.edu),
Dr. Renee Duckworth (r...@email.arizona.edu),or
Dr. Michael Sanderson (sand...@email.arizona.edu) for further information.

NESCent:: Call for Proposals

2009-10-22T18:22:00.004-05:00

NESCent: Science & Synthesis: Call for Proposals

Description:
We are now accepting proposals for Postdoctoral Fellowships at The National Evolutionary Synthesis Center (NESCent). We are looking to fund innovative approaches to outstanding problems in evolutionary biology.

Applications:

Proposals are due December 1.

For more information, please see our website at https://www.nescent.org/science/proposals.php.

Proposal Categories

Post-Doctoral Fellowships (December 1st deadline)

Sabbaticals (July 10th and December 1st deadlines)

Short-Term Visitors (Jan. 1st, April 1st, July 1st, Sept. 1st deadlines)

Servidor de Filogenetica.org temporalmente fuera de linea

2009-10-20T22:58:00.001-05:00

El sitio web Filogenetica.org ha estado inaccesible.

A los visitantes de Filogenetica.org les pido disculpas por esta interrupción temporal.
El sitio web debera estar en linea pronto.
--------------
Actualización: El sitio web ya esta en linea nuevamente! Oct 22.

Genomic basis of adaptation and speciation in Senecio

2009-10-18T22:32:00.003-05:00

Postdoctoral Research Assistant at University of Oxford

Applications are invited for a three-year postdoctoral position on a NERC-funded project, Genomic basis of adaptation and speciation in Senecio, led by Dr Dmitry Filatov, Department of Plant Sciences, University of Oxford. This project is devoted to a genome-wide analysis of molecular bases of speciation and adaptation in plant genus Senecio. In collaboration with Professor Hiscock’s laboratory in Bristol (UK) we will conduct functional and evolutionary genetic analyses of coding and regulatory regions in Senecio genome in order to study their evolution during adaptation to contrasting environments of high and low altitudes. The research will involve high throughput DNA pyrosequencing from three Senecio species and population genetic and evolutionary genomic analyses of these sequences.
Further particulars of the post are available at www.plants.ox.ac.uk/. It is anticipated that the successful candidate will begin on 1 February 2010 or soon thereafter and should hold a PhD or equivalent in a relevant discipline.
For more details of the Filatov laboratory see: dps.plants.ox.ac.uk/plants/staff/DmitryFilatov.aspx.
Applications, including application form, full curriculum vitae, the names and contact details of two referees, and clearly quoting reference AP09014 should be sent to the Departmental Administrator, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB or by email to recruit [at] plants.ox.ac [.] uk. The closing date for applications is noon on Thursday 19 November 2009.

III Congreso Colombiano de Zoología. Medellin

2009-10-16T12:43:00.007-05:00

III Congreso Colombiano de Zoología,

Medellín - Antioquia,

21 al 26 de noviembre de 2010.

En nombre de las instituciones organizadoras, me es grato extenderles una invitación especial a participar en el III Congreso Colombiano de Zoología que se llevará a cabo en la ciudad de Medellín - Antioquia, del 21 al 26 de noviembre de 2010.
Motivados por el hecho de pertenecer a un país que ostenta un lugar privilegiado, al ser depositario de gran parte de la riqueza natural de nuestro planeta, este evento estará enfocado en compartir los avances en el conocimiento de los diferentes tópicos de la diversidad animal y en dimensionar la importancia de los servicios ambientales que ésta nos ofrece, especialmente sobre el impacto al que se enfrenta la humanidad con la alteración del equilibrio natural, incluyendo los efectos del cambio climático global. Siendo coherentes con este reto en el congreso hemos decidido minimizar el impacto ambiental de su desarrollo mediante la utilización de medios digitales informáticos a todo nivel y durante las diferentes fases del Evento.

José Vicente Rodríguez Mahecha

Coordinador General

III Congreso Colombiano de Zoología

Presidente Asociación Colombiana de Zoología – ACZ

X Congreso Argentino de Paleontología Y Bioestratigrafía - VII Congreso Latinoamericano de Paleontología

2009-10-11T21:59:00.003-05:00

X Congreso Argentino de Paleontología Y Bioestratigrafía - VII Congreso Latinoamericano de Paleontología

La Comisión Organizadora del X Congreso Argentino de Paleontología y Bioestratigrafía y VII Congreso Latinoamericano de Paleontología se complace en invitarlos a participar en esta reunión conjunta que se realizará en la ciudad de La Plata, Argentina, del 20 al 24 de Septiembre de 2010.

Toda la información referida a este evento se canalizará a través de nuestra página web, incluyendo la presentación de resúmenes, simposios, inscripción y fechas límite.

EDIT General Meeting (Carvoeiro, Portugal)

2009-10-01T10:27:00.008-05:00

European Distributed Institute of Taxonomy

The European Distributed Institute of Taxonomy is a network of excellence gathering 28 major institutions devoted to knowing the living world better with the support of the European Commission.

EDIT General Meeting 2009
15-17 December 2009, Hotel Tivoli Almansor, Carvoeiro

This year’s edition of EDIT’s main events will take place once again in the small town of Carvoeiro (southern Portugal). We hope to meet as many as possible of you there to discuss EDIT’s past, present and future.

EDIT Young Taxonomist Symposium
15 December 2009

Demonstrating the future of taxonomy, EDIT invites earl-career researchers to present their work. The call for applications from EDIT institutions (up to two candidates per institution) is now open.

EDIT General Meeting
15-16 December 2009

As EDIT approaches its final year, we hope to engage in a practical discussion of what taxonomy and taxonomists achieve when working together in EDIT. We will discuss the transformation of taxonomy into a global cyberscience, with speakers inside and outside EDIT defining a picture of a discipline that experiences growing relevance and capability. As in previous editions, all EDIT institutions will be able to send a number of delegates to this event.

Click here to see the event programme and speakers.

Poster and Demonstration Sessions
15-17 December 2009

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Taxonomy comes of age: Book review in Nature

2009-09-30T16:03:00.003-05:00

Taxonomy comes of age : Article : Nature

BOOK REVIEWED

Naming Nature: The Clash Between Instinct and Science
by Carol Kaesuk Yoon.
W. W. Norton: 2009.
352 pp.

Faced with the bewildering diversity of nature, humans have long attempted to classify it. In her personal and readable perspective on taxonomy, Carol Yoon argues that the basic instinct to recognize natural groups has gradually been replaced by an increased rationality.

Yoon explores the formative environment, motives and personality of the field and scientists within it, from its origins to maturity. She argues that taxonomy generates new views of the world that are counterintuitive, for example that fungi are more like animals than plants; reductionist, depending on molecular data and statistical techniques; and bewildering, such as the prolific yet invisible domains of bacteria and archaea. She is concerned that the professionalization of biology has distanced humanity from nature. But her incursions into anthropology, neuroscience and psychology to explain our empathy with nature are disappointingly superficial.

The first major step in taxonomy was taken by Carl Linneaus some 250 years ago. In a magnificent work, Systema Naturae, he ordered the known natural world. Although the places of some organisms in his scheme have changed, his binomial system for naming organisms has stood the test of time.

A century later, in 1859, came Darwin's theory of evolution, with its seismic impact on science and society. Surprisingly, its effect on taxonomy was minimal. Taxonomists continued for another century to explore the world and discover new species as before, now drawing tree diagrams to represent the relationships between organisms and their evolution. Some of these evolutionary trees were insightful, others fanciful. Unfortunately none was testable, repeatable or objective. So taxonomy got a bad name.

Yoon rightly recognizes the role of the 1960s movement of quantitative experimentalists in being the most significant first step in transforming the field into a full science. These numerical taxonomists started a serious debate on how to articulate earlier opinions and experience, and distil them into testable conclusions. As a result, data and transparent methodology came to challenge 'expert' opinion. However, these researchers treated all data equally, without considering their relative evolutionary or biological significance.

A more rational and evolution-based approach was needed. For some this was found in DNA sequences. But this approach attracted a similar criticism, namely that a complex organism couldn't be reduced to a string of nucleotides.

Over the following period of great change in biology and computational technology, taxonomists struggled to find their way. In the 1970s, the phylogenetics movement arose with a simple message: to seek close relatives with similarities that are shared uniquely by their descendants and no other groups. With this powerful new methodological tool came fervent disciples, called 'cladists', who wanted to purge the field of non-adherents. Taxonomy again turned in on itself, ignoring the huge strides being made in areas such as developmental genetics, population genetics and population biology that could have crucially informed their interpretations of nature. Describing these ideological waves, Yoon's book comes alive with her tales of meeting influential figures, including the God-like Ernst Mayr.

Yoon leaves us with taxonomy having passed though its rebellious adolescence into maturity. But what of its future? Taxonomy has never had so many tools at its disposal and so many connections to the rest of biology. The tragedy is that there are too few taxonomists who can utilize these advances and tackle the challenging questions of our time.

Book review by
Richard Lane. Director of science at the Natural History Museum, London SW7 5BD, UK, and author of the recent report Taxonomy in Europe in the 21st Century.

La dimensión filogenética de la diversidad biológica

2009-09-23T10:25:00.002-05:00

Curso de Posgrado en la Universidad Nacional del Sur, Bahía Blanca, Buenos Aires.

"La dimensión filogenética de la diversidad biológica"

a cargo del Dr. Fernando Pérez-Miles (Sección Entomología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay)

Coordinador responsable: Dra. Adriana Ferrero

Lugar: Sala de Conferencias, Depto. De Biología, Bioquímica y Farmacia
Fecha de Inicio: lunes 19 de octubre, 17 horas.
Modalidad: Teórico – Práctico

Contacto: Lic. Nelson Ferretti, Laboratorio de Zoologia de Invertebrados II, Tel: 4595101 Int. 2425. Email

Temario Básico
Programa Teórico:

1.- Diversidad biológica y Sistemática. Bases criterios y formas de clasificación. Características de las clasificaciones científicas, jerarquía y claves. Sistemática, Taxonomía, Clasificación y Nomenclatura. El concepto de especie en sistemática.

2.- Referencias históricas de la sistemática, escuelas. Origen de la Sistemática Cladista. Filogenia y Parentesco. Principios Cladistas: parsimonia, máxima verosimilitud y distancia.

3.- Caracteres sistemáticos y variación. Tipos de caracteres. Variables cualitativas y cuantitativas. Variables discretas y contínuas. Transformación y estados de los caracteres. Homología y homoplasia. Codificación de caracteres. Ordenamiento y polarización. Criterios de optimalidad y optimización de caracteres.

4.- Construcción de cladogramas. Búsquedas: métodos exactos, métodos heurísticos. Permutación de ramas: podado y reinserción de sub-árboles (SPR), corte y reconección (TBR). Polaridad y enraizamiento. 9.- Pesado de caracteres y medidas de ajuste. Longitud del cladograma. Indices de consistencia, de retención y ajuste. Pesado a priori y a posteriori. Pesajes sucesivos y pesajes implicados.

5.- Soporte y medidas de confiabilidad de cladogramas y grupos. Decisividad, distribución de longitudes de árboles, “Bremer support”. Métodos probabilísticos: Bootstrap, Jacknife. Consensos: estricto, de mayoría, de Nelson, de Adams. Análisis separados versus evidencia total. Comentarios sobre nuevos métodos de búsqueda para matrices muy grandes o “sucias”.

Programa Práctico:
1.- Polarización y codificación de caracteres, matrices básicas de datos, manejo básico del programa NEXUS

2.- Análisis filogenético, búsquedas de árboles por parsimonia, manejo básico del programa TNT.

3.- Pensando en árboles, ejercicios (domiciliarios) de interpretación de árboles.

Bibliografía:

Libros

Goloboff, P.A. 1998. Principios basicos de cladística. Sociedad Argentina de Botánica, Buenos Aires, 81 pp.

Kitching, I.J., P.L. Forey, C.J. Humphries & D. M. Williams. 1998. Cladistics. The theory and practice of parsimony analysis. 2nd. Ed. Oxford Univ. Press, Oxford, 228 pp.

Lanteri, A.A. & M.M. Cigliano. Sistemática biológica fundamentos teóricos y ejercitaciones. Edlup, La Plata, 241 pp.

Diniz, J.A.F. 2000. Métodos filogenéticos comparativos. Holos, Riberao Preto, 162 pp.

Trabajos científicos

Bremer, K.1994. Branch support and tree stability. Cladistics 10:295-304.

Gobloboff, P.A. 1993. Estimating character weights during search. Cladistics 9:83-91.

Goloboff, P.A., J.Farris & K. Nixon. 2003. Tree Analisis using new technology, ver 1.1. Program and documentation at http:// www.zmuc.dk/public/phylogeny/tnt.

Platnick, N.I. 1979. Phylosophy and the transformation of cladistics. Syst. Zool. 28:537-544.

BOTANY 2010, Rhode Island

2009-09-22T20:28:00.003-05:00

Botany 2010
Call for Symposia, Colloquia, and Workshops
Overview
BOTANY 2010 will be held at Providence, Rhode Island, July 31 – August 4, 2010.

Societies participating in BOTANY 2010 will include:

the American Bryological and Lichenological Society (ABLS),
the American Fern Society (AFS),
the American Society of Plant Taxonomists (ASPT), and
the Botanical Society of America (BSA).

In preparation for Botany 2010 we are now soliciting proposals for symposia, colloquia, workshops, discussion sessions, and field trips. Symposia are organized around a topic of potential broad interest, are timely because of recent advances or synthesis in the field, or are particularly relevant to the conference venue. Colloquia are organized around more specialized topics with all presentations adhering to the standard 15 minute timeframe. The number of presentations in a colloquium is variable. Discussion sessions (“roundtable discussion”) are organized around a particular topic of interest with the bulk of the time devoted to discussion that engages the audience. Workshops are distinguished from symposia and colloquia by the inclusion of time devoted to hands-on activities (e.g., software demonstrations, data analysis tutorials, etc.).

websites
Call for Symposium - http://www.2010.botanyconference.org/2010Calls/2010ls_Symposia.php
Call for Workshops - http://www.2010.botanyconference.org/2010Calls/2010ls_Workshops.php

Escarabajo nombrado en honor a Darwin

2009-09-22T14:16:00.000-05:00

"A dung beetle from Costa Rica has been named after Charles Darwin and the Darwin Initiative (DEFRA) by scientists at the National Biodiversity Institute of Costa Rica (INBio) and the EARTH University, Costa Rica.

The beetle, named Canthidium (Eucanthidium) darwini, was discovered in a remote and unexplored UNESCO World Heritage Site in the Talamanca Mountains as part of a Natural History Museum led project."

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