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22 de mayo de 2009
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Una vez publicadas las preguntas esperamos que entre la comunidad surjan varias respuestas.
Escriba su pregunta como comentario a esta entrada.
Gracias por su participación!
20 de mayo de 2009
Secuencias “COI-like numts” inutilizan los codigos de barras de DNA
De identificadores morfológicos a identificadores moleculares
La disponibilidad de marcadores moleculares en la forma de secuencias cortas y muy especificas o restringidas a una especie permiten ahora la identificación rápida de muestras biológicas, sin claves de identificación morfológicas y sin la necesidad del taxónomo experto. Los "códigos de barras de DNA" son simplemente eso, marcadores moleculares cuya presencia permite identificar una especie.
Como sucede con cualquier atributo identificador (morfológico o molecular) los códigos de DNA fallan si la muestra pertenece a una especie que no ha sido previamente descrita y clasificada. Entonces antes de conseguir el "código genético" o DNA barcoding de la biota, los taxónomos deben explorar, descubrir, describir y clasificar las especies. Aun si el trabajo de clasificar ya esta hecho, las muestras de referencia para extraer el DNA deben estar bien identificadas, por el taxónomo experto. Ademas, el marcador molecular debe ser bien identificado tambien y exclusivo o tener poca variación intraespecífica y geográfica para asegurar un porcentaje alto de identificaciones correctas de otras muestras futuras de la especie en cuestión. Un resumen reciente y excelente de la teoría y métodos de los códigos de DNA es el de Meir (2008, cap 7, en: Wheeler, QD, ed, The new taxonomy. Syst. Assoc. vol 76. CRC press).
El ejemplo más reciente es un artículo (Buhay 2009) que revela la importancia de identificar con precisión las secuencias del marcador usado para el "codigo de DNA". El caso es el de secuencias que se obtuvieron y catalogaron como COI (cytochrome c oxidase subunit I) pero ahora un analisis cuidadoso reveló que eso fue un error muy serio, pues las secuencias realmente son de pseudogenes no codificantes (COI-like numts, nuclear copies of mitochondrial derived genes).

Comparación de dos secuencias COI fidedignas y de una secuencia mal identificada como COI. Click para ver la imagen a 1379px × 152px
Los errores de identificación ocurren donde sea: usando las clásicas claves morfológicas y también con los "codigos de barras de DNA". El problema es que ante diferentes resultados en la identificación, comúnmente se cuestiona el procedimiento morfológico pero no el resultado molecular. Este estudio minimamente debe alertar a todos pues los errores de identificación de las secuencias son mas comunes de lo que se desea aceptar. No todo lo que brilla es oro!
Referencia del articulo:
Buhay, J. (2009). “COI-like” Sequences are Becoming Problematic in Molecular Systematic and DNA Barcoding Studies Journal of Crustacean Biology, 29 (1), 96-110 DOI: 10.1651/08-3020.1
A B S T R A C T
The cytochrome c oxidase subunit I (COI) gene plays a pivotal role in a global effort to document biodiversity and continues to be a gene of choice in phylogenetic and phylogeographic studies. Due to increased attention on this gene as a species’ barcode, quality control and sequence homology issues are re-emerging. Taylor and Knouft (2006) attempted to examine gonopod morphology in light of the subgeneric classification scheme within the freshwater crayfish genus Orconectes using COI sequences. However, their erroneous analyses were not only based on supposed mitochondrial sequences but also incorporated many questionable sequences due to the possible presence of numts and manual editing or sequencing errors. In fact, 22 of the 86 sequences were flagged as ‘‘COI-like’’ by GenBank due to the presence of stop codons and indels in what should be the open reading frame of a conservative protein-coding gene. A subsequent search of ‘‘COI-like’’ accessions in GenBank turned up a multitude of taxa across Crustacea from published and unpublished studies thereby warranting this illustrated discussion about quality control, pseudogenes, and sequence composition.
KEY WORDS: cytochrome c oxidase subunit I,molecular taxonomy, numt, protein-coding gene, pseudogene
DOI: 10.1651/08-3020.1
19 de mayo de 2009
International Phycological Congress. Japan
The IPC9 Local Organizing Committee cordially invites you to the 9th International Phycological Congress which will be held in Tokyo, Japan between 2nd and 8th August 2009.
The scientific program has been developed around the topics listed below. More details of these topics, as well as abstracts of invited and contributed papers will be available at website: http://www.ec-inc.co.jp/ipc9/.
Among several symposia, the following are of interest to the systematics community:
S-1
- Comparative evolutionary genomics, Mark Cock; Shigeyuki Kawano
- Evolution of multicellularity in the heterokont lineage: analysis of the Ectocarpus siliculosus genome sequence. J. Mark Cock*, Delphine Scornet, Akira F. Peters, Lieven Sterck, Pierre Rouzé, Yves van de Peer, Jean Weissenbach, Patrick Wincker and the Ectocarpus Genome Consortium
- The genomics of unicellular red alga Cyanidioschyzon merolae, Osami Misumi* and Tsuneyoshi Kuroiwa
- Endosymbiotic gene transfer and genome evolution in secondary plastid-containing algae: insights from cryptophytes and chlorarachniophytes. John M. Archibald
- Genome information renewing the concept of Plantae. Hisayoshi Nozaki
S-4
- Frontiers of algal speciation research. Juliet Brodie ; Mitsunobu Kamiya
- Beyond Barcoding: Understanding species' reproductive biology. Giuseppe C. Zuccarello
- Genetic separation of different entities of Mastocarpus stellatus (Stackhouse) Guiry. Kjersti Sjøtun*, M. Skage & N.T. Mikkelsen
- The genetic structure of Undaria species around Japan. Shinya Uwai*, Nozomi Emura, Teruwo Morita, Akira Kurashima, Hiroshi Kawai
- Huge diversity of microalgae; how have so many species arisen? Katherine Evans
S-11
- Phylogeny - new advances and insights. Heroen Verbruggen; Takeo Horiguchi
- Phylogenomic reconstruction of the Charophytes: a multigene approach to resolving the phylogeny of plants' closest relatives. Ruth Evangeline Timme and Charles F. Delwiche
- Insights into the diversity and evolution of green algae from biological crust habitats. Louise A. Lewis and Paul O. Lewis
- Phylogenetic trees: more than just branches and nodes. Kerstin Hoef-Emden
- Deciphering macroevolutionary patterns in the algae. Heroen Verbruggen
Web site for the meeting: http://www.ec-inc.co.jp/ipc9/topics.html
18 de mayo de 2009
Curso Introducción a la Filogeografía. Cordoba, Argentina
- Mariana Morando. CENPAT, Puerto Madryn, Chubut Argentina..
- Jack W. Sites, Jr. BYU, Provo, Utah, EEUU.
- Daniel Ruzzante. Dalhousie University, Halifax. Canadá.
- Guillermo Ortí. Nebraska University. Nebraska,EEUU.
- Arley Camargo. BYU, Provo, Utah, EEUU.
CURSO DE POSTGRADO
LUGAR: Academia Nacional de Ciencias - Córdoba.
FECHA: 18 al 22 de agosto 2009
Carga horaria: 40 horas
INSCRIPCIÒN: entre el 27 al 31 de julio 2009 Enviar CV a
Alicia Sérsic: asersic@com.
ARANCEL: general $200, alumnos del Doctorado en Ciencias
Biológicas UNC $120
Página Web: http://www.efn.
CUPO: 25
14 de mayo de 2009
Evolution Symposium at Stony Brook: Darwin09
Darwin 2009: 150 Years of Evolutionary BiologyOn November 4-8 2009, the Department of Ecology & Evolution at Stony Brook University will celebrate the 150^th anniversary of Darwin’s “The Origin of Species” by hosting a four-day meeting where leading evolutionary biologists will lecture and help lead discussions on the
current status and future of the study evolutionary biology. We will have three stimulating days of keynote addresses, evening panels and discussion groups, and ample opportunity for communication on the important issues of the present and future of evolutionary biology. All
lectures will be in modern and pleasant facilities at Stony Brook University, with available nearby lodging and convenient transportation to the meeting site.
To register, secure lodging, and get further information on transportation, our Advisory Board, and other matters, please visit our web site
http://darwin09.org
Below is our schedule of events and speakers.
Wednesday, November 4
6:00 – 8:00 Welcoming Reception for Participants
Thursday, November 5
8:45 – 9:00 Welcome from Stony Brook University
9:00 – 9:40 Opening Keynote Address, Douglas J. Futuyma, Stony Brook University
9:40 – 10:00 Q&A
10:00 – 10:30 Coffee Break
10:30 – 11:10 History, Peter Bowler, Queens University, Belfast
11:10 – 11:30 Q&A
11:30 – 12:10 Natural Selection, Mark Kirkpatrick, University of Texas at Austin
12:10 – 12:30 Q&A
12:30 – 2:00 Lunch
2:00 – 2:40 Behavioral Ecology, Hanna Kokko, University of Helsinki
2:40 – 3:00 Q&A
3:00 – 3:40 Evolutionary Ecology, Anurag Agrawal, Cornell University
3:40 – 4:00 Q&A
4:00 – 4:30 Coffee Break
4:30 – 5:10 Organismal Adaptation, May R. Berenbaum, University of Illinois
5:10 – 5:30 Q&A
6:00 – 8:00 Dinner
8:00 – 10:00 Informal Discussions
Friday, November 6
8:45 – 9:00 Welcome and Announcements
9:00 – 9:40 Philosophy, Roberta L. Millstein, University of California, Davis
9:40 – 10:00 Q&A
10:00 – 10:30 Coffee Break
10:30 – 11:10 Evolutionary Genetics, Jianzhi George Zhang, University of Michigan
11:10 – 11:30 Q&A
11:30 – 12:10 Genetics of Population History, John Wakeley, Harvard University
12:10 – 12:30 Q&A
12:30 – 2:00 Lunch
2:00 – 2:40 Genomics, Doris Bachtrog, University of California, Berkeley
2:40 – 3:00 Q&A
3:00 – 3:40 Speciation, Richard G. Harrison, Cornell University
3:40 – 4:00 Q&A
4:00 – 4:30 Coffee Break
4:30 – 5:10 Evolvability, Günter Wagner, Yale University
5:10 – 5:30 Q&A
6:00 – 8:00 Dinner
8:00 – 10:00 Informal Discussions
Saturday, November 7
8:45 – 9:00 Welcome and Announcements
9:00 – 9:40 Ancient Origins, Antonio Lazcano, Universidad Nacional Autónoma de México
9:40 – 10:00 Q&A
10:00 – 10:30 Coffee Break
10:30 – 11:10 Tree of Life, David Hillis, University of Texas at Austin
11:10 – 11:30 Q&A
11:30 – 12:10 Evolution in the Fossil Record, to be determined
12:10 – 12:30 Q&A
12:30 – 2:00 Lunch
2:00 – 2:40 Evolutionary Developmental Biology, Gregory Wray, Duke University
2:40 – 3:00 Q&A
3:00 – 3:40 The Fossil Record of Diversity, Michael Foote, University of Chicago
3:40 – 4:00 Q&A
4:00 – 4:30 Coffee Break
4:30 – 5:10 Evolutionary Radiations, Jonathan B. Losos, Harvard University
5:10 – 5:30 Q&A
6:00 – 8:00 Dinner
8:00 – 10:00 Informal Discussions
Sunday, November 8
8:45 – 9:00 Welcome and Announcements
9:00 – 9:40 Human Origins, Tim D. White, University of California, Berkeley
9:40 – 10:00 Q&A
10:00 – 10:30 Coffee Break
10:30 – 11:10 Cultural Evolution, Peter J. Richerson, University of California, Davis
11:10 – 11:30 Q&A
11:30 – 2:30 Lunch
12:30 – 1:10 Applied Evolution, Joanne P. Webster, Imperial College London
1:10 – 1:30 Q&A
1:30 – 2:10 Closing Keynote Address, Hopi E. Hoekstra, Harvard University
Meeting web site address: http://darwin09.org
Jeffrey Levinton,
For the Organizing Committee
Lista de Colaboradores del Blog
Espero que este rearreglo sea benéfico y contribuya a facilitar la navegación en el blog.
- David Arturo
- Carlos Sarmiento
- Alejandro
- Carlos Velázquez
- Alma Estrella
- CladoB
- Ismael
- Roberto Keller
- Camilo Mattoni
- Guillermo Suárez
- Omar Mejía
- Rodrigo Santamaría
- Julian
- David
- Lucas
- Ysbelia
- Luis Guevara
- enrique renteria arriaga
- Efrain
- Jennifer Girón
- Colaborador Invitado
- Atilano Contreras
- jackeline
- Caceres
- Susana
- David F-B
- Orthoptera
- Martín Ramírez
- Toni Guillén
- Daniel Piñero
- Luis Eguiarte
- Rodrigo Medel
- Jesús Muñoz
- José Antonio
- Claudia T. Hornung Leoni
- JLiria
- Deneb
- pvinuesa
- Rafael Miranda
- Marcelo Cardillo
- Rafael Flores Hernández
- entrophyl
- Rosario Mata-López
- Eliana Buenaventura
- Efraín De Luna
- Tania Chew
- Gerardo Salazar
- Tania Z
- RATorres
- Ramón Victor Moreno
- falv044
- Julio
- Martha
- Janet
- Gustavo A. Ballen
- Gisela Oliván
Publique su contenido.
13 de mayo de 2009
Population substructure of Mexican Mestizos : Gene Expression
Category: Genetics
Posted on: May 12, 2009 9:01 AM, by Razib
The basic issue here is that "Latino" or "Hispanic" is not a race in a genetic sense. There are Latinos of white, black and Amerindian origin, and every permutation of these three kinds. Population substructure is important for medical reasons because correlations between genetic variants & diseases might actually simply be due to the common relationship of these variants & diseases to a particular population. This is why research which shows how Ashkenazi Jews relate to other American whites is medically important; what might be typical of gentile whites might not be typical of Ashkenazi Jews (who have a history of population specific diseases).
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Lea la nota completa aqui:
http://scienceblogs.com/gnxp/2009/05/population_subscture_of_mexica.php
12 de mayo de 2009
Considerable diversidad genética entre mexicanos
Esta es la Fig 4 en el articulo, el cual esta disponible en linea (open access!).

Se ilustra la proporción de marcadores de ancestros en seis poblaciones mexicanas de los estados de Sonora, Zacatecas, Guanajuato, Yucatan, Veracruz y Guerrero.
- A. Contribución de ancestria europea.
- B. Contribución de ancestria indígena.
- C. Contribución africana.
- D. Contribución asiática.
La referencia del artículo es:
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Silva-Zolezzi, I., Hidalgo-Miranda, A., Estrada-Gil, J., Fernandez-Lopez, J., Uribe-Figueroa, L., Contreras, A., Balam-Ortiz, E., Bosque-Plata, L., Velazquez-Fernandez, D., Lara, C., Goya, R., Hernandez-Lemus, E., Davila, C., Barrientos, E., March, S., & Jimenez-Sanchez, G. (2009). Analysis of genomic diversity in Mexican Mestizo populations to develop genomic medicine in Mexico Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0903045106
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6 de mayo de 2009
Plaza de postdoctorado en entomologia
A los interesados en ocupar una plaza de postdoctorado en entomologia, por
un periodo de dos años (disponible a partir de Agosto, 2009) en el
departamento de Virologia e Inmunologia del Southwest Foundation for
Biomedical Research, favor de comunicarse con el Dr. Javier Mota Snchez al
correo electronico o al telfono (210) 290-8271 en San Antonio
Tx, USA.
Es deseable, pero no indispensable, que los interesados tengan experiencia
trabajando con Aedes aegypti y/o dengue.
3 de mayo de 2009
Bigger is better: the largest phylogenetic tree reconstructed. | Archetype
GenBank, the standard database for genetic information maintained by National Center for Biotechnology Information, has been accumulating DNA sequences for some three decades now. Since its creation in the late 1980s, it has become the de facto repository for genetic information– genetic data must now be submitted to GenBank for a paper to be accepted for publication. Most sequence data accumulated is the result of the sum of many “local” taxonomic studies, that have targeted a particular group of organism for a relatively small, but well-known collection of genes. It contents now span over hundreds of genes across all of life’s domains. So, what would happen if you were to take all the sequence information contained in GenBank and analyze it phylogenetically all together in a single, one-step study? Well, that is what Pablo A. Goloboff and coworkers just did, the results of which were published in last week’s online early edition of Cladistics, the international journal of the Willi Hennig Society.
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Lea el comentario completo en:
blog por Roberto Keller30 de abril de 2009
Cladistics: Analisis de una matriz gigante de >73000 UT
Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groupsAntes de este logro, la idea de matriz "grande" andaba en los 500-1000 unidades terminales (Uts), y los más ambiciosos se esforzaban por ensamblar y analizar matrices de 1500 a 2000 unidades. Obviamente las dificultades para realizar análisis filogenéticos crecen desmesuradamente con cada unidad agregada a la matriz. Los intentos de exploración del enorme espacio de los arboles con estrategias y software convencional (como PAUP) no permitían ni siquiera ver la posibilidad de intentar el análisis de matrices gigantes. Entonces, Goloboff et al (2009) como lo lograron?
Pablo A. Goloboff, Santiago A. Catalano, J. Marcos Mirande, Claudia A. Szumik, J. Salvador Arias, Mari Källersjö and James S. Farris.
Cladistics
http://dx.doi.org/10.1111/j.1096-0031.2009.00255.x
ABSTRACT
Obtaining a well supported schema of phylogenetic relationships among the major groups of living organisms requires considering as much taxonomic diversity as possible, but the computational cost of calculating large phylogenies has so far been a major obstacle. We show here that the parsimony algorithms implemented in TNT can successfully process the largest phylogenetic data set ever analysed, consisting of molecular sequences and morphology for 73 060 eukaryotic taxa. The trees resulting from molecules alone display a high degree of congruence with the major taxonomic groups, with a small proportion of misplaced species; the combined data set retrieves these groups with even higher congruence. This shows that tree-calculation algorithms effectively retrieve phylogenetic history for very large data sets, and at the same time provides strong corroboration for the major eukaryotic lineages long recognized by taxonomists.
Ademas del trabajo tenaz y laborioso que implica compilar una matriz con tantas unidades terminales y caracteres moleculares y morfológicos, la clave del éxito fueron las capacidades analíticas de este grupo de investigadores usando el software TNT.
Bye bye Super-Trees, bienvenidas las SUPER-MATRICES!!!
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Goloboff, P., Catalano, S., Marcos Mirande, J., Szumik, C., Salvador Arias, J., Källersjö, M., & Farris, J. (2009). Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups Cladistics DOI: 10.1111/j.1096-0031.2009.00255.x
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28 de abril de 2009
Curso Prático de Análise Filogenética. Lisboa
2º Curso Prático de Análise Filogenética
4 a 8 de Maio de 2009
Centro de Biologia Ambiental, Faculdade de Ciências da Universidade de Lisboa
Formador: Prof. Octávio Paulo
A Filogenética é uma das áreas científicas das Ciências da Vida que mais tem crescido e evoluido metodologicamente nos últimos anos. As suas aplicações vão hoje desde o estudo da evolução das espécies e populações animais até às mais inesperadas, como o averiguar da origem do vírus da Sida ou dos ciclos sazonais de Gripe.
O presente curso é destinado a estudantes ou profissionais que pretendam iniciar-se na análise filogenética e também a investigadores já com alguma experiência mas que queiram aprofundar e actualizar os seus conhecimentos. O curso consistirá em aulas teóricas alternadas com aulas práticas de utilização de software. Encorajam-se os participantes que tenham dados de sequências a trazê-los para análise.
O programa detalhado poderá ser obtido em http://cobig2.fc.ul.pt/Phylogenetics.htm
27 de abril de 2009
Wiki de ayuda para usar TNT

Se ha anunciado la disponibilidad del wiki TNT como un recurso de ayuda para los usuarios de este programa.
El término WikiWiki es de origen hawaiano que significa: rápido. "Un wiki, o una wiki, es un sitio web cuyas páginas web pueden ser editadas por múltiples voluntarios a través del navegador web. Los usuarios pueden crear, modificar o borrar un mismo texto que comparten." (http://es.wikipedia.org/wiki/Wiki)
Después de un tiempo de estructuración y edición, el WIKI TNT ya esta listo para los usuarios en general. Siga el enlace abajo para mas información sobre como participar editando contenido o contribuyendo a las discusiones.
http://tnt.insectmuseum.org/index.php/Main_Page
25 de abril de 2009
Phylogeology – A New Revolution in Phylogenetics
Systematics and Biogeography: Phylogeology – A New Revolution in Phylogenetics
Evolutionary biologists were stunned this week by the news of Geological Phylogenetics. "Genetics is dead" says geologist Prof. Trevor Bruce of the University of Ulladulla, Australia. For 20 years molecular DNA has changed the way biologists do phylogenetics. Geological Phylogenetics, or Phylogeology, proposes to dispense with biological data all together. Prof. Bruce explains, "Molecular systematics has removed any notion of morphology, anatomy and taxonomy. We intend to get rid of molecules, making phylogenetics essentially free of any biological data".
The benefits of phylogeology are that only atoms will be analyzed. "All you need is a very large industrial-strength food processor and a mass spectrometer". Prof Bruce's team has successfully pureed an array of organisms including two pot plants, a goldfish and Dr. Hall's cat. "She wasn't too happy about it, so we made her first author" says Prof. Bruce. "So far we have analyzed percentages of 30 common elements including carbon, calcium iron and copper". And success! Already Prof. Bruce's team has the data for most common household pets and their relationships. "It's simple" explains Dr. Hall, "a dog and a cat will have a similar atomic make-up, just like two similar rocks. As genetics has brought its methods and theory into phylogenetics, we bring geological techniques. Pureeing and 'mass-specing' critters are one of them".
LEA LA NOTA COMPLETA AQUI:
http://urhomology.blogspot.com/2009/04/phylogeology-new-revolution-in.html
22 de abril de 2009
Cladistics wars 2.0 | Archetype

Cladistics wars 2.0 | Archetype
Autor: Roberto Keller
There is a skirmish going on at Dechronization blog right now. This is a coauthored blog about phylogenetics. I like this blog (its right there on my blogroll —->). There are surprisingly very few blogs about phylogenetic methods these days, despite the wide use that phylogenies currently have in evolutionary biology and beyond (e.g., linguistics). I will complain that, for nine authors, they post little, sometimes not a single post during a month.
The hot post in question is a mocking of an announcement about a (to be honest, very successful) workshop in phylogenetic methods cosponsored by the Willi Hennig Society and so far held in different continents.
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Lea el comentario completo en:
"Archetype, Ant reconstruction one homology at a time"
