Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis

BIO::Phylo-phyloinformatic analysis using perl
Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen, Chase Miller.
BMC Bioinformatics 2011, 12:63
http://www.biomedcentral.com/1471-2105/12/63
open access

Abstract

Background

Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces.

Results

This paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo can interact with BioPerl, thereby giving access to the file formats that BioPerl supports. Many methods for data simulation, transformation and manipulation, the analysis of tree shape, and tree visualization are provided.

Conclusions

Bio::Phylo is composed of 59 richly documented Perl5 modules. It has been deployed successfully on a variety of computer architectures (including various Linux distributions, Mac OS X versions, Windows, Cygwin and UNIX-like systems). It is available as open source (GPL) software from http://search.cpan.org/dist/Bio-Phylo

Plazas para taxonomía vegetal, diversidad y morfología de plantas vasculares

El INECOL ha publicado una convocatoria para ocupar dos plazas de investigacion en la Red de Biodiversidad y Sistemática, en el Centro Regional del Bajío en Pátzcuaro, Michoacán.
El aspirante deberá contar con amplios conocimientos sobre la taxonomía vegetal, diversidad y morfología de plantas vasculares, además de tener experiencia en su colecta y determinación. La plaza requiere experiencia en el uso de metodologías filogenéticas y es necesario que el candidato esté familiarizado y tenga experiencia de primera mano con las técnicas de laboratorio necesarias para la recopilación de datos moleculares, así como con las técnicas para su análisis, tanto por métodos de parsimonia como de probabilidad. Se dará preferencia a los candidatos con experiencia probada en la flora mexicana, aunque no contar con la misma no cancela la candidatura.

Los detalles de la convocatoria estan en:
http://www1.inecol.edu.mx/inecol/documentos/PlazasCRB%2807abril2011%29.pdf


Transcribo el texto de la convocatoria aquí pero solo con propósitos informativos.

INSTITUTO DE ECOLOGIA A.C. (INECOL) CONVOCATORIA PARA
OCUPAR DOS PLAZAS DE INVESTIGADOR
EL INECOL es un centro público de investigación adscrito al Consejo Nacional de
Ciencia y Tecnología que lleva a cabo investigación y formación de estudiantes en los
campos de la ecología, biodiversidad y sistemática, conservación y manejo de recurso
naturales. Cuenta con instalaciones en Xalapa, Veracruz y en Pátzcuaro, Michoacán así
como con estaciones de campo en zonas templadas y desérticas de Durango y en la zona
costera de Veracruz. Actualmente se encuentran asociados al INECOL 103
investigadores de tiempo completo, 95 técnicos académicos, 88 administrativos y 134
estudiantes de posgrado. La vida académica está organizada en nueve departamentos o
redes: Biodiversidad y Sistemática, Ecología Funcional, Ambiente y Sustentabilidad,
Biología Evolutiva, Manejo Biorracional de Plagas y Vectores, Manejo Biotecnológico
de Recursos, Ecoetología, Biología y Conservación de Vertebrados e Interacciones
Multitróficas. El INECOL invita a los investigadores interesados a ocupar dos plazas,
descritas a continuación.
DOS PLAZAS DISPONIBLES
Categoría disponible: Investigador Titular A
Contratación: Tiempo completo por 12 meses. Dependiendo del desempeño académico
se renovará el contrato. Después de tres años, los candidatos podrán solicitar su
definitividad.
Descripción de la Investigación:
El candidato seleccionado formará parte de la Red de Biodiversidad y Sistemática,
estando asignado y llevando a cabo sus investigaciones en el Centro Regional del Bajío
en Pátzcuaro, Michoacán. El proyecto principal del Centro es la Flora del Bajío y de
Regiones Adyacentes, un inventario detallado de las plantas vasculares de Guanajuato,
Querétaro y la parte norte de Michoacán, y la persona elegida se incorporará a un grupo
de cuatro investigadores y cinco técnicos académicos involucrados en dicho proyecto. El
aspirante deberá contar con amplios conocimientos sobre la taxonomía vegetal,
diversidad y morfología de plantas vasculares, además de tener experiencia en su colecta
y determinación. La plaza requiere experiencia en el uso de metodologías filogenéticas y
es necesario que el candidato esté familiarizado y tenga experiencia de primera mano con
las técnicas de laboratorio necesarias para la recopilación de datos moleculares, así como
con las técnicas para su análisis, tanto por métodos de parsimonia como de probabilidad.
Se dará preferencia a los candidatos con experiencia probada en la flora mexicana,
aunque no contar con la misma no cancela la candidatura.
Responsabilidades:
• Participar en trabajo de campo para la colecta de ejemplares para el herbario IEB y su
programa de intercambio.
• Colaborar en el proyecto Flora del Bajío y de Regiones Adyacentes a través de la
preparación de fascículos y la coordinación de tratamientos taxonómicos por especialistas
externos.
• Llevar a cabo estudios a largo plazo sobre la sistemática (molecular y tradicional) de
uno o varios grupos de plantas vasculares.
• Ayudar en el equipamiento, desarrollo y manejo del laboratorio de análisis moleculares.
• Impartir cursos de posgrado y dirigir tesis en los programas de Maestría y Doctorado
del INECOL.
• Publicar artículos en revistas reconocidas internacionalmente con factor de impacto, en
revistas nacionales, de divulgación y periódicos y ocasionalmente en libros.
• Presentar proyectos de investigación ante instituciones mexicanas o internacionales
tanto gubernamentales como privadas.
Requisitos:
• Licenciatura en Biología o Ecología y contar con un Doctorado en Ciencias con
especialidad en Sistemática Vegetal.
• Contar con al menos un posdoctorado en el área de conocimiento.
• Ser autor o co-autor de 5-7 artículos en revistas científicas con factor de impacto,
habiendo publicado al menos 3 de ellos en los últimos 3 años.
• Contar con experiencia en la colecta de ejemplares botánicos.
• Haber preparado revisiones y tratamientos florísticos sobre plantas vasculares.
• Haber llevado a cabo investigación en sistemática molecular sobre un grupo de plantas
vasculares.
• Tener experiencia en el uso de metodologías filogenéticas, tanto por métodos de
parsimonia como de probabilidad
• Tener experiencia de primera mano con las técnicas de laboratorio necesarias para la
recopilación de datos moleculares
• Es deseable pero no indispensable haber vivido y trabajado en Latinoamérica.
• Hablar y escribir en español e inglés de manera correcta.
• Capacidad de trabajar en equipo, habilidad para negociar, atender con precisión y
rapidez situaciones que así lo requieran, así como llevar a cabo simultáneamente varias
tareas.
• Contar con experiencia en presentación de proyectos.
• Disposición para viajar y trabajar fuera de horario regular.
• Contar con licencia de manejo (recomendable).
Procedimiento para presentar solicitudes:
Los interesados enviarán una carta describiendo su experiencia relacionada con el perfil
de la plaza, su curriculum vitae e información de tres referencias, incluyendo sus
teléfonos y sus correos electrónicos. Se contactará únicamente a las referencias de los
candidatos finalistas. La revisión de solicitudes comenzará en la fecha de publicación de
la convocatoria y se extenderá hasta el 31 de de julio de 2011. Los candidatos
seleccionados deberán ocuparlas antes del 1 de octubre de 2011. Favor de enviar los
documentos citados en archivos PDF o Word a:
Secretaría Académica
Instituto de Ecología A. C.
Correo electrónico: secretaria.academica@inecol.edu.mx
Página web: www.inecol.edu.mx

Biennial conference of the Systematics Association, Belfast

8th Biennial Meeting: July 2011
Queen's University, Belfast

4th - 8th July 2011

Introduction

The Biennial conferences of the Systematics Association provide a forum for systematists from different disciplines to present and discuss their research. The Sixth Biennial Conference was held at Royal Botanic Garden Edinburgh in August 2007. The conference was attended by about 240 delegates from a broad international audience. The format was a mixture of open sessions and focussed thematic symposia.

MORE INFORMATION >>>

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."

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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
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http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2010.00342.x/abstract

2a. Edición del Taller Latinoamericano de Evolución Molecular, 17-28 de Enero 2011

Estimados amigos y colegas evolucionistas,

me complace anunciarles que el próximo mes de Enero se celebrará la segunda edición del "Taller Latinoamericano de Evolución Molecular". Tendrá lugar del 17 al 28 de Enero de 2011 en las instalaciones del Centro de Ciencias Genómicas y de la Licenciatura en Ciencias Genómicas del Campus Morelos (Cuernavaca, México) de la UNAM, .

Se trata de un Taller intensivo y GRATUITO dirigido a alumnos de posgrado e investigadores de cualquier institución académica, con alternancia de sesiones teóricas y prácticas (ver programa del TLEM 2011). El taller cubrirá desde aspectos bioinformáticos tales como búsqueda de secuencias homólogas en bases de datos públicas, parseo de archivos de secuencias con Perl y alineamiento múltiple de las mismas, revisando a fondo métodos de inferencia filogenética (distancias, parsimonia, máxima verosimilitud, inferencia bayesiana), de evolución molecular (fechación de clados, selección a nivel molecular) y de genética de poblaciones.

El taller estará impartido por destacados especialistas mexicanos en el área (profesores del TLEM 2011). Contaremos además con la participación de dos destacados investigadores invitados, el Dr. Sergei Kosakovsky Pond (UCSD, USA; desarrollador de HyPhy) y el Dr. Julio Rozas (Universidad de Barcelona, España; desarrollador de DNAsp).

Podrán inscribirse al curso alumnos de doctorado de cualquiera de los Programas de Posgrado de la UNAM o de otras instituciones nacionales o extranjeras, siempre y cuando puedan demostrar que tengan conocimientos básicos del área. Se expedirá un certificado de asistencia a todos los participantes. Este taller es acreditable como actividad académica semestral en los programas de posgrado de la UNAM.

El pre-registro se abrirá el día 5 de Noviembre de 2010 y se cerrará el 5 de Diciembre, efectuándose a través de la página de pre-registro del TLEM 2011.

Queremos agradecer el apoyo económico recibido por parte del Programa de Posgrado en Ciencias Biomédicas de la UNAM y del Programa de Posgrado en Ciencias Biológicas de la UNAM, para traer a los profesores invitados. Asimismo agradecemos el generoso y entusiasta apoyo al TLEM 2011 recibido por parte de los Drs. David René Romero Camarena y Rafael Palacios del Centro de Ciencias Genómicas y de la Licenciatura en Ciencias Genómicas de la UNAM, y por parte del Dr. César Domínguez del Instituto de Ecología de la UNAM.

A los lectores de "noticias en filogenetica.org" les agradezco la difusión de este mensaje entre sus colegas y estudiantes.

Reciban un cordial saludo desde Cuernavaca, México, esperando verles por aquí el próximo mes de Enero.

Para mayores informes contactar a:
Pablo Vinuesa - coordinador del
Taller Latinoamericano de Evolución Molecular

Computational Molecular Evolution, Cambridge

Computational Molecular Evolution

10-21 April 2011

Wellcome Trust Genome Campus,

Hinxton, Cambridge, UK

Deadline for applications 26 November 2010

Course summary

This joint Wellcome Trust-EMBL-EBI advanced course aims to provide researchers with the theoretical knowledge and practical skills required to carry out molecular evolutionary analysis on their own data, as well as on data drawn from sequence databases. The course will combine basic assumptions and ideas fundamental to the field with discussion of cutting-edge methodologies, and is therefore relevant to researchers with a range of different experience levels.

Topics

• interpretation of molecular phylogenetic trees and sequence alignments
• genomics resources, sequence searching and sequence alignments
• phylogeny reconstruction and models
• hypothesis testing in phylogenetics
• coalescent model and inference from population data.

Course organisers

• Nick Goldman (European Bioinformatics Institute, Hinxton, UK)
• Ziheng Yang (University College London, UK)
• Aidan Budd (European Molecular Biology Laboratory, Heidelberg, Germany)
• Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)

One-semester fellowships for graduate students at NESCent

NESCent

National Evolutionary Synthesis Center

Graduate Fellowships

The National Evolutionary Synthesis Center is now seeking to include graduate traineeship to our portfolio in facilitating broadly synthetic research to address fundamental questions in evolutionary science. We are offering one-semester fellowships for graduate students to pursue research either with a NESCent sabbatical scholar, working group, or postdoctoral fellow. The research should be in line with the goals of the sabbatical scholar and/or working group and may include integrating datasets, developing databases, performing analyses, programming and software development, etc. Support will not be provided to collect or generate new data. When relevant, graduate students are expected to be full members of working group. Ultimately we expect the graduate student to lead and author aspects of the research.

Read more >>> http://www.nescent.org/science/GraduateFellowships.php

Oportunidad de beca para estudiante de entomologia

Teaching/research assistantship for a M.S. or Ph.D. student at the University of Memphis

A teaching/research assistantship is available for a M.S. or Ph.D. student in the Department of Biological Sciences at the University of Memphis under the supervision of Dr. Duane McKenna, beginning August 2011. Students interested in insect (especially beetle) genomics, molecular phylogenetics, and/or the evolutionary ecology of insect-plant interactions are encouraged to apply. Prior laboratory and field experience preferred.

Interested students may inquire by contacting dmckenna [at] memphis [.] edu. Further information about the Department of Biological Sciences and the Graduate Program can be found at http://www.memphis.edu/biology/graduate.htm

A response to recent proposals for integrative taxonomy

Authors: PADIAL, JOSÉ M.; DE LA RIVA, IGNACIO1

Source: Biological Journal of the Linnean Society, Volume 101, Number 3, November 2010 , pp. 747-756(10)
http://www.ingentaconnect.com/content/bsc/bij/2010/00000101/00000003/art00019

Abstract:
Several proposals have been launched under the new concept `integrative taxonomy' to frame the future development of species discovery and description. We consider that some of those proposals have failed to be truly integrative, by not acknowledging the limitations of operational definitions of species, by defending some kinds of evidence as universally superior, by considering taxonomy to be irreconcilable with population genetics, or by ignoring that the heterogeneity of evolutionary processes often precludes full character congruence in species. Here we defend a taxonomy where species exist, but not in any particular way everyone might want them to exist; a taxonomy open to data and methods from population biology, phylogeography and phylogenetics, as well as any other discipline providing evidence about the origin and evolution of species. This new taxonomy embraces all the consequences of considering species as lineages of reproductive populations, encouraging the use of as many lines of evidence as possible, but without negating that a single line may also be the only one providing evidence for a particular species. Species cannot only be those reproductive populations showing broad character congruence and/or reproductive isolation, due to the different degrees of character congruence, as well as of reproductive isolation, that result from the heterogeneity of evolutionary processes causing lineage splitting and divergence. Also, any kind of character - and not only those established by tradition or fashion - is potentially relevant as evidence of lineage divergence. To conciliate the authors who only see species supported by broad character congruence as good species hypotheses, we explain how a hypothesis can gain corroboration using single or multiple lines of evidence, even in cases of discordance with other lines of evidence. Finally, we propose guidelines to identify the expected degree of stability (preliminary, unstable, and stable) of species hypotheses. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101, 747-756.

Keywords: corroboration; lineage; species concept

Document Type: Research article

DOI: 10.1111/j.1095-8312.2010.01528.x

Taxonomía: el valor del toque humano y la cooperación

Compart aquí un par de notas en Nature muy interesantes:

Taxonomy: add a human touch too
http://www.nature.com/nature/journal/v467/n7317/full/467788a.html
Antonio G. Valdecasas & Quentin D. Wheeler
Journal name: Nature Volume: 467 , Page: 788 Date published: (14 October 2010)
DOI: doi:10.1038/467788a

Norman MacLeod and colleagues' call to develop automated species-identification systems is laudable (Nature 467, 154–155; 2010), but let's not forget a core feature of taxonomic work that depends on a scholar's input — the discovery of new characters.

Unexpected evolutionary novelties in morphology and physiology, for example, are what make taxonomic exploration rewarding. Taxonomists set out to discover and track such novelties and their evolutionary history. It is in this sense that taxonomy provides the empirical basis for understanding speciation and phylogeny.

There is a place for automated pattern detection, but it would not work with the 5,000 species of Drosophila, say, which are identified by their many different structures. Taxonomy can independently test and verify identifications without relying on patterns of single characters, as the long list of synonymies in any biological group testifies. The practice of taxonomic revision and publishing detailed monographs ensures that character distributions, species status and phylogenetic relationships are subject to repeated and critical testing.

We should beware the trend to confuse automatic identification tools with those that are useful for discovering new species. The emerging field of cybertaxonomy is an advance only if it is understood as enhancing and enabling theory-rich descriptive taxonomy, not replacing it.

As in many other modern scientific fields, including diagnostic medicine and molecular genetics, a final step involving a human expert is essential.

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Taxonomy: include social networking
http://www.nature.com/nature/journal/v467/n7317/full/467788b.html
Jonathan Silvertown
Journal name: Nature Volume: 467 , Page: 788 Date published: (14 October 2010)
DOI: doi:10.1038/467788b

Help with the shortage of professional taxonomists needed to identify organisms (Nature 467, 154–155; 2010) may also come from an unexpected source — social networking on the Internet.

Through social networking, the identification process can be made more efficient while simultaneously spreading real taxonomic knowledge. The facility is available to anyone, unlike other technologies that require specialized equipment.

In its first year of operation, the website iSpot (http://ispot.org.uk) has helped 6,000 users to identify 25,000 sightings of some 2,500 species, from lichens to birds. The website works by linking experts (including amateur experts) with beginners through a sophisticated reputation system that encourages users to help and learn from each other.

Eventually, DNA bar-code matching and image recognition might be added to the tools available. But these will be aids, not replacements, for people learning how to identify species.

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Un monumento a la filogenetica. Cuernavaca, Mexico

Rescaté del "baúl" esta foto tomada en los años 90´s en Cuernavaca, México.
Asistía a un Congreso en la Universidad Autónoma del Estado de Morelos.
La imagen digital la recuperé de una fotografía impresa muy pequeña, la cual tome durante el XIII Congreso Mexicano de Botánica, Cuernavaca, Morelos. Noviembre 5 -11, 1995.
No requiere mucha imaginación ver que es un cladograma, pero en ese entonces nadie sabia realmente en honor a que era esta escultura.
Los colegas de la UAEM o alguien saben la historia?

Why Trees Are Important

Authors

Edward O. Wiley¹

¹Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA

Abstract

Abstract

The Tree of Life is the result of the interplay of changes in information and speciation. Almost 100 years after publication of Darwin’s Origin, the inception of Phylogenetic Systematics has resulted in a revolution in data inference. I briefly trace the development of this revolution and show examples of how data are interpreted relative to phylogenetic trees. I then provide brief discussions of how to read tree diagrams and the need to access the quality of phylogenetic inference.

Keywords

Phylogenetic systematics, Phylogenetic trees, Cladistic

Tomado de: http://www.metapress.com/content/b5462355045l0h8m/

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.


MAS INFORMACION AQUI >>>

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.

READ MORE:>>>

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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

Nuevo blog de Cladistica y Biogeografia

He recibido noticia del lanzamiento en linea de un nuevo blog relacionado con Filogenia y Biogeografia:
http://cladisticaybiogeografia.blogspot.com/

Bienvenido a la blogosfera! Estaremos pendientes de este foro y le deseamos larga vida.