Postdoc – Plant Phylogenomics – University of Arizona

A two-year postdoctoral position is available in my lab to work on a large collaborative project on genome evolution in Oryza (rice and its wild relatives). The project’s PI is Rod Wing at the University of Arizona, and collaborators include myself (Mike Sanderson), Manyuan Long (University of Chicago), Carlos Machado (University of Maryland), Scott Jackson (Purdue University), Doreen Ware (Cold Spring Harbor), and Detlef Weigel (Max Planck Institute, Tubingen). The project’s goals focus on leveraging new genomic data sets at several scales to study diverse aspects of genome evolution, ranging from the origin of new genes, diversification of gene families, population genomic analyses, and reconstructing gene and species trees (phylogenomics). The postdoc’s responsibilities will be to spearhead the phylogenomic analyses in my lab. These promise to be a rich analytical challenge given the rampant discordance in gene trees already discovered in Oryza and the complications of gene flow, domestication, and frequent polyploidization. The candidate should have extensive experience in phylogenetic analysis of molecular sequence data, and one or more of the following interests or experience: population genetics/coalescent theory; algorithms/bioinformatics experience; experience in plant systematics, especially in taxa with closely related species. Opportunities for close collaboration with other co-PIs in the project are extensive and will be encouraged.

The position is in the Department of Ecology and Evolutionary Biology at the University of Arizona, with a starting salary of $45,000/yr, including full benefits. It is potentially renewable for up to 3 years. Computational resources in my lab include a high performance computing cluster, web servers, database storage server, a viz wall for scientific visualization, and dedicated system administration support. The Department has a strong program in evolutionary genomics, including an ongoing NSF IGERT training program, and a number of faculty working in that area: Jeremiah Hackett, Matt Sullivan, Michael Nachman, Noah Whiteman, Mike Worobey and Mike Barker (joining January 2011).

The position is open until filled and is available immediately. Please send a CV and a brief statement of research interests and experience to me at the address below, and arrange to have two letters of reference sent (e-mail is fine). A formal application will also be required through the university’s HR website (http://www.hr.arizona.edu). For further information, please contact

Mike Sanderson, Professor
Department of Ecology and Evolutionary Biology
University of Arizona
Tucson, AZ 85721
sanderm [at] email.arizona [.] edu

5th Biennial Conference of the International Biogeography Society. Greece

El registro para la 5a Conferencia de la International Biogeography Society esta abierto.
Lugar: Heraklion, Crete, Greece.
Fecha: 7-11 Enero, 2011.

Información sobre esta reunión: sitio web

Workshop on Molecular Evolution, Europe 2011

Workshop on Molecular Evolution, Europe 2011

Cesky Krumlov, Czech Republic

23 January - 4 February 2011, individual research session 4 - 11 February 2011

Application Deadline: 1 October 2009

http://www.molecularevolution.org/workshops/WME

Michael P. Cummings, Scott A. Handley and Naiara Rodriquez-Ezpeleta Co-Directors

The Workshop consists of a series of lectures, demonstrations and computer laboratories that cover various aspects of molecular evolution. Faculty are chosen exclusively for their effectiveness in teaching theory and practice in molecular evolution. Included among the faculty are developers and other experts in the use of computer programs and packages such as BLAST, BEAST, Clustal W and Clustal X, FASTA, FigTree, Genealogical Sorting Index, GARLI, LAMARC, MAFFT, Migrate-N, MrBayes, PAML, PAUP*, and SeaView who provide demonstrations and consultations.

Morfometría Geométrica y Estudios Filogenéticos, La Plata, Argentina

Primer Encuentro de

"Morfometría Geométrica y Estudios Filogenéticos"

Lugar y fecha

El primer Encuentro se realizará el día 6 de Diciembre de 2010 en el Museo de La Plata, Paseo del Bosque s/n La Plata.

Comité Organizador

Cecilia Morgan. Sección Mastozoología, División Zoología Vertebrados, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata. La Plata, Argentina.

Paula N. González. Instituto de Genética Veterinaria, Universidad Nacional de La Plata. La Plata, Argentina.

S. Ivan Perez. División Antropología, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Argentina.


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Sagas of the Children of Time: The Importance of Phylogenetic Teaching in Biology

Sagas of the Children of Time: The Importance of Phylogenetic Teaching in Biology

Journal: Evolution: Education and Outreach
DOI 10.1007/s12052-010-0268-3
HTML

Daniel R. Brooks
Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
Abstract
Theodosius Dobznahnsky said nothing in biology makes sense except in the light of evolution. Nothing in evolution makes sense except in the light of the historical emergence of species. Species are the biological “children of time.” If we seek to understand them, historical narratives are essential elements of our causal explanations. Phylogenetic systematic analysis provides the Rosetta Stone for uncovering that narrative.

Keywords
Children of time, Phylogenetic narrative, Teaching, Evolution, Historical explanations

The Annual New Zealand Phylogenetics Meeting

Leigh 2011

The Annual New Zealand Phylogenetics Meeting

Sunday 6th - Friday 11th February, 2011

Overview:

The 15th annual New Zealand meeting on the interface of mathematics and biology in the study of phylogeny, genome analysis and molecular evolution will be held at Leigh. It will be summer in New Zealand, so expect temperatures in the mid-20s to 30s Celsius. There's heaps to do, including diving and fishing. More information on the Leigh By The Sea website.

The meeting will be held at the The Leigh Sawmill Café.

WEBSITE: http://www.math.canterbury.ac.nz/bio/events/leigh2011/

Frontiers in Biodiversity: a Phylogenetic Perspective

A two-day international symposium on frontier biodiversity research in a phylogenetic framework
Barcelona, Spain, October 1st and 2nd, 2010.
You are kindly invited to attend the international symposium “Frontiers in Biodiversity: a Phylogenetic Perspective”, which will be held in Barcelona, Spain, the 1st and 2nd of October 2010. This symposium is co-organized by the Biodiversity Research Institute of the University of Barcelona (IrBio), the Institute of Evolutionary Biology (IBE, CSIC-UPF) and the Zoological Systematics and Evolution research group on the occasion of the International year of Biodiversity.

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2010 Italian workshop on phylogenetic methods and applications

2010 Italian workshop on phylogenetic methods and applications‎ > ‎

Program
The workshop is expected to start on August 27th at 10 am, and will end in the afternoon of September 1st. Classes and tutorials will run every day from 9 am until 7 pm.
Some of the topics that will be covered in the lectures will be:

• Introduction to molecular evolution
• models of sequence evolution
• methods of sequence alignment
• methods of phylogenetic inference (distance, parsimony, maximum likelihood, bayesian inference)
• molecular clock
• supertrees
• phylogenomics
• diversification rate methods
• comparative method
• biogeography/phylogeography
  

Tutorials will be held to allow the workshop participants to become more familiar with the software packages that can be used for various kinds of analyses. Among the programs that will be used during the tutorials are:

• Mesquite (matrix manipulations, tree manipulations, comparative analyses)
• Mrbayes (bayesian phylogenetic inference)
• RAxML (manimum likelihood phylogenetic inference)
• Winclada (maximum parsimony phylogenetic inference)
• BEAST (relaxed molecular clock, coalescent studies)
• Figtree (tree graphics)
• Various applications for R (statistical package), including geiger, laser, ape, ouch (comparative analyses)
  

Students are encouraged to bring their own datasets to the workshop

To have a better idea about some of these topics, feel free to consult the page of the 2009 Workshop: http://sites.google.com/site/phylogenyworkshop/

Murio D. Hull, uno de los primeros filósofos que contribuyó al cladismo

Hoy se ha distribuido la noticia que David Hull ha muerto.
Les recomiendo dos notas en el blog Evolving thoughts, al respecto.

David Hull is dead

Posted on August 12, 2010 by John S. Wilkins

My mentor, hero and I hope friend, David Lee Hull died this morning, at the age of 74, according to Jay Odenbaugh.

If not for the fact that David marked my masters thesis and remarked that he hoped to see some of it published, I would never have considered myself competent enough to publish, and hence would never have ended up an academic (at the tender age of 48).

Read more ....

David Hull’s philosophy

Posted on August 12, 2010 by John S. Wilkins

David Hull was one of the first graduates from the University of Indiana’s HPS program. During that program he attended a seminar with Karl Popper in the course of which he wrote a paper on essentialism in biology. Popper took it upon himself to send this, without telling Hull, to the BJPS, and the first David knew of it was when the proofs arrived. He hurriedly rewrote it (in ways Popper would not have approved, but Popper never read the final version, apparently) and it became the most cited paper of its time in the philosophy of biology.

Read more ....

IAPT Research Grants in Plant Systematics

IAPT Research
Grants in
Plant Systematics
2011
The IAPT announces a competitive grants program in plant systematics, with emphasis on funding students and young investigators in developing countries, but open to applicants world-wide. The program is based on the submission of research projects, taking into consideration the following guidelines:
1. The grant application period is open until 31 December 2010.
2. The award should be preferably used for supporting field work, travel to institutions, or laboratory investigations.
3. General information should be always included on the front page (complete name of the applicant, country, institution, project title, academic degree, telephone, fax and e-mail).
4. The projects should include brief ideas of an introduction, materials, methods, objectives, literature citation and other relevant information, especially noting if any other financial support for the project exists.
5. The length of the proposals should not exceed three pages.
6. In the case of Ph.D. students, in addition to the proposal, two recommendation letters should be included.
7. The projects are to be submitted to:

Patricia Dávila-Aranda
preferably by e-mail (pdavilaa@servidor.unam.mx)

or by regular mail:

Facultad de Estudios Superiores, Iztacala, UNAM
Av. de los Barrios no. 1
Los Reyes Iztacala, Tlalnepantla
Edo. de México 54090
México

8. Applicants will be informed by e-mail of receipt of their proposals.
9. The total amount to be awarded is: US$10,000.
10. The maximum individual award is US$1,000.
11. The awarded projects will be announced on the IAPT web page and by e-mail to all the applicants on March 1, 2011.
Deadline: 31 December 2010

My-Plant.org: Phylogenetically Based Social Network for the Plant Sciences

My-Plant.org Launched!

Posted on Jul 28, 2010

The My-Plant.org Team is happy to announce that we are officially launched! My-Plant is more than just another social networking site, it provides users with a unique mechanism for finding and associating with others who share common interests in specific plant clades.

My-Plant.org is not meant to supplant other networking, web or data sites. Rather, My-Plant.org is designed to bring together the people, tools and repositories of information from across the plant science community as a whole. My-Plant.org is an evolving community and we welcome feedback from the community.

https://my-plant.org/

Profile: Douglas and Pamela Soltis: The Power of Two

Science 6 August 2010: Vol. 329. no. 5992, pp. 623 - 625 DOI: 10.1126/science.329.5992.62

News Focus

Profile: Douglas and Pamela Soltis:

The Power of Two

Elizabeth Pennisi

A University of Florida couple studying the evolution of flowering plants shows the value of doubled genomes—and joined careers.

Married, with plants. Douglas and Pamela Soltis work together in all aspects of their careers. CREDIT: E. PENNISI/SCIENCE [Larger version of this image]

PULLMAN, WASHINGTON—When Pamela Soltis first joined her husband, Douglas, on the faculty at Washington State University, Pullman, they wrote separate grants and ran separate research programs. But they worked side by side in the field and in the greenhouse and read and critiqued each other's grant proposals and papers. More often than not, they also worked together in the lab. "We knew we were interested in a lot of the same things," Pam recalls. Eventually, they gave up trying to work independently.

Today, more than 25 years later, they are known collectively as the "Solti." "We're generally viewed as one person," Pam says. True, they have separate appointments at the University of Florida, Gainesville, she at the natural history museum and he in the biology department. But students, grants, courses, publications, talks, even accolades are shared. They studied in London on the same Fulbright scholarship and were co-awardees on an international prize. "Everything they do, they do together," says Michael Donoghue, an evolutionary biologist at Yale University.

"They are the most powerful, productive couple that may have ever been in botany, certainly in my generation," says John Kress, an evolutionary biologist at the Smithsonian National Museum of Natural History in Washington, D.C. The Soltises helped bring plant systematics into the molecular age, according to peers. And their innovations have led to firsts in "approaches to questions and ultimately first answers to questions," says Vaughan Symonds, a former postdoc now at Massey University in Palmerston North, New Zealand.

Early adopters of new techniques—including molecular DNA tools—as students in the 1980s, the Soltises have shown how rapid progress can be when two minds focus on a single research program. Says Jeffrey Doyle, a systematist at Cornell University, "They are so energetic and active that seeing Doug and Pam moving into your areas is a little frightening."
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Fast, Free Phylogenies: HPC for Phylogenetics Tutorial

Topic: High Performance Computing for Phylogenetics

Meeting dates: October 13-15, 2010

Location: NIMBioS at the University of Tennessee, Knoxville

Co-sponsors: NIMBioS, iPlant, and National Institute for Computational Sciences

Tutorial leaders Eric Carr (NIMBioS); Jim Ferguson (National Institute for Computational Sciences, Univ. of Tennessee/Oak Ridge National Laboratory); Susan Holmes (Stanford Univ.); Brian O'Meara (Univ. Tennessee); Alexis Stamatakis (Technical Univ. of Munich); Dan Stanzione (Texas Advanced Computing Center/iPlant); Bob Thomson (Univ. California Davis); and James Wilgenbusch (Florida State Univ.)

Objectives: This tutorial focuses on how to use TeraGrid, the CIPRES Portal, the iPlant Discovery environment, university clusters, and other typically free HPC resources for phylogenetic analysis. The tutorial is geared primarily toward biologists (including students, postdocs and faculty) who are at least moderately experienced with phylogenetic analysis and who have datasets to run but who are typically running analyses on their own desktops, though other researchers, such as statisticians or mathematicians working in phylogenetics, are encouraged to apply. Learning can be enhanced for people applying as a team (such as a pairing of a biologist and a statistician who collaborate in their work).

MORE INFO HERE >>>

Curso Cladística - Tucumán - 16-20 Agosto

clado : Mensaje: Curso Cladística - Tucumán - 16-20 Agosto

NOMBRE DEL CURSO: CLADÍSTICA: MÉTODOS CUANTITATIVOS DE CLASIFICACIÓN

16 al 20 de Agosto de 2010
Facultad de Ciencias Naturales, Universidad Nacional de Tucumán

Docente: Pablo Goloboff (Inv. Ppal CONICET)
Ayudantes del Curso (en orden analfabético): Claudia Szumik, Marcos
Mirande, Santiago Catalano, J. Salvador Arias (todos de CONICET)

CONTENIDO Y CRONOGRAMA

DIA 1
Teórico: Parsimonia y sistemática filogenética. Optimización y mapeo de
caracteres (mapeo/reconstrucciones/cambios específicos).
Práctico: Input/output. Formatos de datasets. Archivos de instrucciones.
Opciones de output como metafiles; creación de “batch filesâ€�. Edición de árboles.
Manejo de archivos de árboles. Grupos de árboles, caracteres, y taxones.

DIA 2
Teórico: Búsquedas, parte I. Soluciones exactas, árboles de Wagner,
branch-swapping.
Optimos locales y óptimos globales; estrategias de búsqueda. Factores que
afectan la eficiencia de las búsquedas.
Práctico: Uso de secuencias múltiples de adición al azar. Constraints y
Estrategias de búsquedas heurísticas.

DIA 3
Teórico/Práctico: Reglas de colapsamiento. Consensos (incluyendo: mejoras de
consensos y superárboles). Comparaciones de topologías de árboles; distancias de SPR.
Pesado de caracteres.
Funciones de pesado definidas por el usuario.

DIA 4
Teórico/Práctico: Medidas de soporte. Soporte de Bremer; búsqueda de
árboles subóptimos. Medidas basadas en remuestreo; efectos de tipos de búsquedas y reglas de
colapsamientos.

DIA 5
Teórico/Práctico: Búsquedas, parte II: Nuevos algoritmos de búsqueda.
Análisis de datasets de gran tamaño; estrategias generales. Scripts; control de flujo, expresiones y
variables.


MODALIDAD DEL CURSO

Teórico/práctico, con fuerte énfasis en los aspectos prácticos. Las clases
teóricas se usan para introducir la problemática general en cada tema, y los prácticos se utilizan
para ilustrar y terminar de entender los temas vistos en las clases teóricas. La dinámica del
curso es bastante informal, pasando de modalidad "teórico" a modalidad "práctico" rápidamente y
a requerimiento de los participantes.
El curso se dictará en la sala de computadoras de CompuTronic, San Lorenzo 982,
San Miguel de Tucumán.
Las clases serán diarias, de 9:30 a 18:30 hs.

CUPO
El curso puede incluir hasta 30 personas; se efectuarán las inscripciones por
estricto orden de llegada.

DURACION
40 hs. aprox.

New Book: Beyond Cladistics

Systematics and Biogeography: New Book: Beyond Cladistics