Botany 2011

The Botany 2011 conference web site is now open for registration, including field trips, banquets and other social events, and housing:http://www.2011.botanyconference.org/

Articulos básicos para filogenetica: Introducciones

Quiero poner a disposicion de la comunidad una lista de referencias muy ... muy básicas para filogenetica. Voy a ponerla aqui en el blog poco a poco por temas (Introducciones, caracteres, arboles, etc).

Aquí les va mi primera colección de lecturas recomendadas y los enlaces a los PDFs:

INTRODUCCIONES
Harrison, C. J & J. A. Langdale. 2006. A step by step guide to phylogeny reconstruction. PDF.
De Luna, E. J.A. Guerrero & T. Chew-Taracena. 2005. Sistemática biológica: avances y direcciones en la teoría y los métodos de la reconstrucción filogenética. PDF.
De Luna, E y B.D. Mishler. 1996. El concepto de homologia filogenetica. PDF.

Espero esta lista de lecturas sea útil a un numero amplio de interesados e incentive aportaciones de referencias (y PDFs) para compartir..... y eliminar sesgos por preferencias personales!

Por favor, en los comentarios ponga la referencia bibliográfica que quisiera agregar a esta lista. Si tiene el PDF, enviemelo por correo electrónico para depositarlo en el servidor de Filogenetica.org y compartirlo desde ahí.

Becas de la Red Latinoamericana de Botanica

Con el apoyo de Andrew W. Mellon Foundation, la Red Latinoamericana de Botánica ha abierto la

Nueva Convocatoria 2011

para postular a

• Becas de Perfeccionamiento para realizar estadías en temáticas adscritas a las Ciencias Vegetales, en alguno de los centros colaboradores de la RLB, y a
• Becas Parciales de Apoyo para el desarrollo de tesis de postgrado en Ciencias Vegetales.

EL PLAZO PARA RECIBIR LAS POSTULACIONES VENCE IMPOSTERGABLEMENTE EL LUNES 11 DE ABRIL DE 2011

Taller Avanzado de Morfometría Geométrica, Cuernavaca, MÉXICO

Facultad de Ciencias Biológicas

Centro de Investigación en Biodiversidad y Conservación

Cuerpo Académico de Biología Comparada

Taller Avanzado de Morfometría Geométrica

8-12 de Mayo de 2011

Universidad Autónoma del Estado de Morelos, Cuernavaca, México

PONENTE. Dr. P. David Polly, Associate Professor, Department of Geology, Indiana University

OBJETIVO. Es un curso teórico-práctico dirigido a estudiantes de posgrado y profesionales con conocimientos básicos de morfometría geométrica. El taller está enfocado en el uso de la morfometría geométrica para abordar temas como ecomorfología, integración morfológica, evolución morfológica y filogenia.

COSTO DE INSCRIPCIÓN. $1,500

INFORMES.

Dr. José Antonio Guerrero aguerrero@uaem.mx

Más información http://www.uaem.mx/cibyc/cursos.html

Reunión anual de la WHS en Brasil, 2011

La Willi Hennig Society ha anunciado la organización de la reunión

Hennig XXX

July 29 to August 2, 2011

São José do Rio Preto, State of São Paulo, BRAZIL

Co-organizadores: Dalton de Souza Amorim and Fernando Barbosa Noll
Patrocinadores: Universidade de São Paulo and UNESP-São José do Rio Preto.

Detalles: sitio web de la WHS

Postdoctoral Position -- Molecular Systematics

At the University of Vienna (15 faculties, 3 centres, about 180 fields
of study, approx. 8.600 members of staff, approx. 85.000 students) the
position of a University Assistant (post doc) at the Department of
Animal Biodiversity is vacant.

Identification number of advertisement: 1979

Molecular data are nowadays an indispensable source of information to
answer research questions in ecology and biodiversity. In our department
we study patterns of species diversity and species composition at the
community level in order to unravel mechanisms that generate and
maintain biodiversity. Emphasis is on tropical biota, but temperate-zone
communities are also studied (see www.univie.ac.at/animal_biodiversity).
We are seeking for a scientist with an organismal perspective and broad
command of molecular biology techniques, working at the interface
between biodiversity research, ecology, and evolution. The focus should
be on insects as target organisms. A fully equipped lab is available, as
is support through a technician. The successful candidate is expected to
develop an independent, internationally visible research agenda.
Teaching obligation is 4 hours per semester week.

Degree of Employment: 40 hours/week

Areas of work: Generating and using of DNA sequence data for research
questions in evolution and ecology. Teaching in the field of biology,
with emphasis on animal biodiversity, evolution and ecology.

Profile: PhD degree in Biology, preferably with focus on ecology,
evolution, or zoology. Postdoc experience from a competitive research
laboratory. Experience with applying relevant analytical skills,
techniques and methods, including a broad range of molecular biology
techniques. Good command of up-to-date statistical and bioinformatics
methods to analyse molecular data. Strong interest in the field of
biodiversity and evolution. Good command of English language. Interest
in academic teaching in BSc and MSc curricula (e.g. molecular methods
for biologists, insect biodiversity). High motivation and commitment to
work in a team.

Expertise in conservation biology would be welcome.

Applications including a letter of motivation (German or English) should
be sent via Job Center to the University of Vienna
(http://jobcenter.univie.ac.at) no later than 31.03.2011 and be
referenced to the identification number 1979.

For further information please contact Univ.-Prof. Mag. Dr. Konrad
Fiedler (konrad.fiedler@univie.ac.at).

The University of Vienna intends to increase the number of women on its
faculty, particularly in high-level positions, and therefore
specifically invites applications by women. Among equally qualified
applicants women will receive preferential consideration.

Identification number of advertisement: 1979

E-Mail: jobcenter@univie.ac.at

--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Brigitte Gottsberger

Department of Animal Biodiversity
Faculty of Life Sciences
University of Vienna

Rennweg 14
A- 1030 Vienna

Tel: +43-1-4277-57405
Fax: +43-1-4277-9574

e-mail: brigitte.gottsberger@univie.ac.at
http://www.univie.ac.at/animal_biodiversity/

ASPT Research Grants for Graduate Students in Systematics

American Society of Plant Taxonomists
2011 Research Grants for Graduate Students

The ASPT is pleased to announce the Society’s annual competition for research grants
for graduate student investigators. Support is available for both masters and doctoral
students to conduct fieldwork, herbarium studies, and/or laboratory research in any area
of plant systematics. No award will exceed $1000, and it is unlikely that proposals from
previous recipients will be funded. Proposals will be funded on the basis of merit,
regardless of the research area within systematics.

Proposals will be reviewed by the Society’s Awards and Honors Committee and must
include the following:

1. Curriculum vitae;
2. Proposal (the text, including figures but excluding literature cited, should
not exceed two single-spaced pages) that describes the research to be conducted,
emphasizing the role the grant funds will play;
3. Itemized budget;
4. A letter of recommendation from the student’s major professor or primary
research facilitator at the time of the proposal.

Eligibility: Applicants must be members of ASPT at the time of the application
deadline. Details regarding ASPT membership can be found at the ASPT homepage
(http://www.aspt.net/index.php).

Proposal submission: Proposal materials and letters of recommendation must be
submitted electronically as pdf files. Items 1-3 above should be submitted as a single
document. Use the following formats for filenames for the proposal materials and
reference letter, respectively:

student name_proposalASPT.pdf
student name_letterASPT.pdf.

All application materials should be submitted to Chelsea Specht via e-mail to
cdspecht at berkeley.edu

A list of past awardees and research topics can be found at
http://www.aspt.net/society/funding/gradstudentgrants.php

Submission deadline for all materials: 9 March 2011.

This message was sent from the ASPT Business Office:

Ms. Linda Brown
Business Office Manager
American Society of Plant Taxonomists
University of Wyoming
Department of Botany 3165
1000 E University Avenue
Laramie, WY 82071

Telephone: (307) 766-2556
Fax: (307) 766-2851
Email: aspt at uwyo.edu
URL ASPT: http://www.aspt.net/
URL Systematic Botany: http://www.sysbot.org
Online Application: https://extranet.sheridan.com/aspt/

"Making comparative methods as easy as ABC" on Phyloseminar.org

RESCHEDULED:

Brian O'Meara speaks Wednesday, March 30th at 11am PST on "Making comparative methods as easy as ABC"

For decades, biologists have addressed evolutionary and ecological questions using measurements of species traits, phylogenies, and an assortment of comparative methods. Unfortunately, while there is a large assortment of these methods, they are still fairly limited and development of new methods is slow. It took seven years between the introduction of using a simple Brownian motion model for looking at trait evolution (Felsenstein, 1985) and the use of this same model for looking at rates of trait evolution (Garland, 1992), and an additional 14 years to more powerful tests using a small modification of the basic model (O'Meara et al., 2006). Still other promising methods are described and even tested but remain unavailable to empiricists because they are not put into software. As a result, the questions empiricists can ask about the world are limited by the research productivity of the few dozen scientists who develop and implement new methods in phylogenetics. We describe a new approach based on Approximate Bayesian Computation and implemented in R that will allow researchers to easily develop their own models for trait evolution without requiring them to have specialized mathematical or computational knowledge.

http://phyloseminar.org./

TaXmeX: Colección bibliográfica sobre taxonomía publicada en México ¡en línea!

TaXmeX: Colección bibliográfica sobre taxonomía publicada en México

¡Ya está disponible en línea!
Coleccion artículos taxonómicos publicados en México durante el siglo XX, esta base contiene cerca del 90% de la información producida sobre taxonomía en México durante el siglo XX y tiene aplicación histórica y taxonómica. Consta de 57 revistas capturadas, 28 revistas examinadas, 1079 volúmenes analizados, 1329 números analizados, 6578 artículos capturados, 6150 artículos analizados, 79,294 páginas totales, 2460 autores capturados, 2331 autores analizados pertenecientes a 44 países y 164 instituciones mexicanas, y 31 tipos de trabajo taxonómico, por mencionar los más importantes.

Ya está cargada el 100% de la información estamos en la fase de validación y normalización. En breve iniciaremos la actualización, fase en la que completaremos la bibliografía publicada a partir del año 2000.

Disponible en:

http://atenea.fciencias.unam.mx:8080/jspui/handle/123456789/37171 http://hydra.fciencias.unam.mx:8080/xmlui/handle/123456789/37171

Mas información:

Michán, L., & Llorente, J. (2003). La taxonomía en méxico durante el siglo XX. Publ. Esp. Mus. Zool , 13 , 1-250.

URL http://sistemas.fciencias.unam.mx/\~layla/2003/tesisdoctoradolayla.pdf

La Taxonomía en México durante el siglo XX

View more presentations from E-investigación bibliográfica, FCUNAM

Workshop on Molecular Evolution, North America 2011

Workshop on Molecular Evolution, North America 2011

Fort Collins, Colorado, USA

24 July - 6 August 2011

Application Deadline: 15 May was the preferred application deadline, after which time people will be admitted to the course following review of applications by the admissions committee. However, later applications are accepted.

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

Michael P. Cummings, Scott A. Handley and Kendra Nightingale, 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 BEAST, *BEAST, DataMonkey, FigTree, Genealogical Sorting Index, GARLI, HyPhy, LAMARC, MAFFT, MrBayes, and SeaView who provide demonstrations and consultations.

For more information and online application see the Workshop web site -

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

Phylogeny.fr Robust Phylogenetic Analysis For The Non-Specialist

Phylogeny.fr es un servicio en linea para la reconstrucción filogenética con datos moleculares.

Phylogeny.fr procesa y conecta varios programas para reconstruir un árbol filogenético a partir de una matriz de secuencias.

No solo hay la opción "One click", tambien uno puede decidir como hacer cada paso en el alineamiento y la reconstrucción ("Advanced"). Incluso hay una opción para generar una cadena de análisis especial sin los parametros automatizados: "A la Carte" Mode. Por ejemplo, uno puede seleccionar un alineamiento con Muscle, T-Coffee, ProbCons, o ClustalW y seleccionar una de las cuatro opciones disponibles para construccion del arbol: Maximum likelihood con PhyML, Parsimonia con TNT, Distancias con ProtDist/FastDist+BioNJ (o Neighbor) y probabilidades Bayesianas con MrBayes.

No pude resistir la tentación de correr un análisis. Entre directamente a TNT y use la matriz de ejemplo con 16 secuencias Angiospermas y grupos externos. Click, click, click... listo un arbol de consenso, ahí en la ventana de dialogo, en menos de lo que canta un gallo!. Muy sencillo!


Este servicio esta disponible en http://www.phylogeny.fr/

XX Congreso Nacional de Zoología, México

La Sociedad Mexicana de Zoología, A. C., en coordinación con la Universidad Autónoma del Estado de Morelos y la Secretaria de Turismo del Estado de Morelos convocan a la comunidad científica a participar en el

XX Congreso Nacional de Zoología,
Cuernavaca, Morelos,
del 14 al 18 de noviembre de 2011.

Objetivos:
Reunir a investigadores, profesores y estudiantes interesados en el estudio, manejo y conservación de la fauna con la finalidad de intercambiar, analizar, evaluar y difundir los avances realizados en el conocimiento sobre zoología en México.

Entre los varios temas se incluye: Sistemática y Biogeografía.

MAS INFORMACION >>>

Applications open for the WHS phylogenetics workshop in Xalapa, 2011

Announcement # 2:

Applications are now open for the WHS Twelfth International workshop in Phylogenetic Methods to be held in Xalapa (México) on May 23-27, 2011. This one week course is sponsored by the Graduate Program, INECOL and The Willi Hennig Society.

Students, researchers, and professors interested or working with or about phylogeny and systematics are invited to submit applications for admission. The workshop is open to any student/professional based in México or Internationally.

The workshop will be limited to 25 participants. Complete applications will be evaluated competitively by an ad hoc committee.

Registration will be open only for accepted participants. Registration fee for the workshop is: Students US$300, professionals US$400. Fellowships will be offered by the WHS on a competitive basis to cover registration fee.

An application consists of

1. A completed "Application form",
2. a current CV for the applicant, and (if the case),
   
3. a letter from the student’s advisor regarding the relevance of the course to the student’s career goals.

Visit this web page for further instructions and for downloading the "Application form".

Please note that all applications for admission must be received by Friday March 4, 2011.

We look forward to receiving your application.

For more information on the course content, registration cost, fellowships, accommodations in Xalapa, travel advice, etc, please visit the web site for the workshop:

http://www.filogenetica.org/cursos/WHSworkshop/

Help us to distribute this announcement by printing and posting a one page pamphlet (PDF) in your institution.

WHS 12th International workshop in Phylogenetic Methods, Xalapa, México

The Willi Hennig Society 12th International workshop in Phylogenetic Methods

23 to 27 May, 2011.

Posgrado,
Instituto de Ecología, AC.
Xalapa, Ver (México).

---
Announcement # 1:
I am glad to announce dates for the WHS workshop in Xalapa (México).
This course will be possible thanks to the support from INECOL and WHS.
---

The Willi Hennig Society (WHS) has organized several international workshops on cladistics (Finland, Czech Republic, US). In Latin-America one has been offered in Argentina (2002) and two in Brazil (2008, 2010). This will be the first held in Mexico.

Lecturers:
The workshop will be presented by a combination of at least four or five professors, all members of WHS.

• John W. Wenzel (Carnegie Museum of Natural History, coordinator).

Syllabus:

Day 1: Introduction

• Logic and history of phylogenetics
• Optimization and tree search
• Ambiguity, Weighting, Support
• Using WinClada, Nona
• Advanced search strategy, TNT

Day 2: Morphology

• Morphological character coding
• Cladistic character coding
• More powerful searches
• Diagnosing troublesome results

Day 3: DNA sequence data

• Handling DNA sequences (GenBank, Muscle)
• Alignment

Day 4: Dynamic Homology

• Dynamic homology
• Direct Optimization and Alignment

Day 5: Likelihood and Bayesian methods

• Model-based phylogenetics
• Model-based Exercises, Garli, MrBayes

Participants:
This workshop is open to participants from Mexico, Latinamerican countries, but also to students from the US/Canada, Europe, and elsewhere. Essentially this is offered in substitution of the famous "OSU workshop on phylogenetic methods", which no longer will be offered there.
Lectures will be in English. It is expected that participating students are already familiar with basic phylogenetic methods.

Cost:
Cost for the workshop is us $300. This only includes registration fee. It does not include transportation, accommodations or food.

Fellowships:
A limited number of Fellowships will be offered by the WHS on a competitive basis. WHS Fellowships will cover registration cost only. Enrollees will be responsible for cost of transportation, accommodation and meals.

Admission:
The workshop will be limited to 25 participants.
All complete applications will be evaluated by an ad hoc committee. Registration will be open only for accepted participants. [update: link to list of admitted participants added March 18].

Further information:
Announcement of dates for the reception of an "Application form" (January 2011), notification of acceptance (March 2011), course registration (April), and additional details of the course and travel advice will be posted later in this blog and a web site for the workshop at the Filogenetica.org server.
Meanwhile, if you have any inquiry, please post a "comment" to this "Entry".

Dr. Efraín De Luna
Workshop organizer.
Biodiversidad y Sistemática, INECOL
Xalapa, Ver. México.

Aunque ud no lo crea... parsimonia es superior

La tendencia reciente señala que la popularidad de los métodos de verosimilitud y Bayesianos va en aumento, a juzgar por el número de cursos o talleres, usuarios y el de artículos publicados. A que se debe esta popularidad? Una de las ideas centrales es la preocupacion por las tasas de cambio de los caracteres. Se razona que para tomar en cuenta estas propiedades de los datos deben usarse "modelos explicitos de cambio" para los analisis de reconstrucción de la filogenia, especialmente en el caso de secuencias de DNA.

En la comparación de los atributos de los métodos de parsimonia o verosimilitud, los respectivos promotores han intentado persuadir que uno u otro enfoque es mejor bajo distintas condiciones teóricas y metodológicas. Uno de los argumentos más aludidos es el de desempeño o “consistencia” de los métodos al recuperar filogenias “correctas”.

La idea de “consistencia” es que si un método esta libre de errores de estimación, este converge hacia el resultado “correcto”, sobre todo cuando los datos son abundantes. En la teoría estadística, un estimador (por ejemplo, el promedio) es “consistente” respecto a un modelo especifico ( por ejemplo, el modelo Normal) cuando la dispersión (por ejemplo, la varianza) disminuye alrededor del valor “verdadero” (por ejemplo, mu) conforme el tamaño de la muestra se incrementa.
En la teoría filogenética, un método es “consistente” si las hipótesis que produce bajo las condiciones de un modelo particular convergen hacia una filogenia "correcta" de referencia . Con este propósito, se ha intentado comparar el desempeño de los métodos de parsimonia y los probabilísticos en su habilidad de reconstruir la filogenia. Cuando se evalúa la habilidad de una balanza para estimar el peso correcto, el marco de referencia es el kilo “Patrón” y la variación permitida por una “Norma”. El problema es evidente en el caso de la estimación de la “dispersión” alrededor de la filogenia “correcta” pues los únicos marcos de referencia posibles son los escenarios evolutivos elaborados mediante simulaciones.

Uno de los primeros exámenes de la habilidad de los métodos se basó en una peculiar combinación de datos y modelos (“long branch attraction”) con lo que supuestamente se demostró que parsimonia es “inconsistente”, pues el método no recuperó la topología generada por los datos (Felsenstein, 1978; Kim, 1996). En contraposición, diferentes condiciones simuladas sugirieron que los métodos de verosimilitud también pueden ser “inconsistentes” en su desempeño al estimar la filogenia (Chang, 1996; Farris, 1999; Kolaczkowski & Thornton, 2004; Siddall, 1998). Los intentos de la calificación de métodos en estudios más elaborados solo han llegado a la conclusión de que diseñar simulaciones para medir “consistencia” es un problema muy complejo en el que interactúan tipos de tasas de cambio de los caracteres, tipos de modelos simples o complejos y tipos de topologías simétricas o asimétricas (Goloboff, 2003, Yang, 1996, 1997). Otros, han sugerido que los métodos de parsimonia bajo ciertos modelos son equivalentes a los de verosimilitud (de Queiroz & Poe, 2001, 2003; Steel & Penny, 2000; Tuffey & Steel, 1997).
Ahora desde el punto de vista empirico el artículo de Rindal y Brower (2010) examinan la pregunta logica: Hay coherencia entre las filogenias inferidas por métodos de parsimonia vs probabilísticos? Que tan frecuente es el caso que parsimonia se "equivoca"?

Do model-based phylogenetic analyses perform better than parsimony? A test with empirical data
de Cladistics Early on line de Andrew V. Z. Brower
http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2010.00342.x/abstract
Abstract

The use of model-based methods to infer a phylogenetic tree from a given data set is frequently motivated by the truism that under certain circumstances the parsimony approach (MP) may produce incorrect topologies, while explicit model-based approaches are believed to avoid this problem. In the realm of empirical data from actual taxa, it is not known (or knowable) how commonly MP, maximum-likelihood or Bayesian inference are inaccurate. To test the perceived need for “sophisticated” model-based approaches, we assessed the degree of congruence between empirical phylogenetic hypotheses generated by alternative methods applied to DNA sequence data in a sample of 1000 recently published articles. Of 504 articles that employed multiple methods, only two exhibited strongly supported incongruence among alternative methods. This result suggests that the MP approach does not produce deviant hypotheses of relationship due to convergent evolution in long branches. Our finding therefore indicates that the use of multiple analytical methods is largely superfluous. We encourage the use of analytical approaches unencumbered by ad hoc assumptions that sap the explanatory power of the evidence. © The Willi Hennig Society 2010.

Aunque Ud no lo crea las conclusiones del articulo son sencillas .... en mas del 99% de los 1000 estudios examinados los diferentes métodos no producen topologías incongruentes, como se esperaría si realmente los métodos probabilísticos fueran superiores a los de parsimonia. Los autores concluyen: "..... it is apparent that if the different methods produce the same result, then using more than one of them is redundant. Given that this appears to be the case, we think that the analytical speed, methodological clarity and interpretability of its results indicate that the MP approach is practically superior."

-----
Rindal, E., & Brower, A. (2010). Do model-based phylogenetic analyses perform better than parsimony? A test with empirical data Cladistics DOI: 10.1111/j.1096-0031.2010.00342.x
-------
http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2010.00342.x/abstract