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18 de noviembre de 2008

Making sense of Mexican microcrustaceans

Fuente de la información:

The Barcode of Life blog Blog Archive Making sense of Mexican microcrustaceans

In Hidrobiologica March 2008 researchers from El Colegia de la Frontera Sur, Universidad Autonoma Metropolitana, Iztapalapa, Mexico, describe a new species of Cladocera from temporary pools in a semi-desert region. Cladocera, commonly known as “water fleas,” are minute crustaceans mostly limited to fresh water; Daphnia sp are the best known. Cladocera are of practical importance as water quality indicators.


Similar to that for other invertebrates, the species description for this minute (0.4 mm) crustacean Leberis chihuahuensis comprises about 4 pages of mysterious text and 2 pages of equally enigmatic illustrations. In addition, the DNA barcode of the type specimen is provided, as well as the more usual NJ tree, in this case showing 14% sequence divergence from its sister species L. davidi.

By including both kinds of characters, ie DNA barcode and morphology, Elias-Gutierrez and Valdez-Moreno provide what seems to me a model for any new species description, one that will enable specialists and non-specialists alike to make the most use of their findings.

12 de noviembre de 2008

VII International Congress of Systematic and Evolutionary Biology ICSEB VII "Extending the Darwinian Panorama"

From: victoria.sosa [mailto:victoria.sosa@inecol.edu.mx]
Sent: Wed, 12 Nov 2008 10:56:08 -0600

Invitamos a los investigadores y estudiantes a participar en el
VII International Congress of Systematic and Evolutionary Biology ICSEB VII
"Extending the Darwinian Panorama"
Veracruz
5-10 julio 2009
--
***************************************
Dr. Victoria Sosa
Instituto de Ecología, A. C.
Apartado Postal 63
91000 Xalapa, Veracruz
Mexico

(Mensajeria) (Street address)
Km. 2.5 antigua carretera a Coatepec #351
Congr. El Haya
91070 Xalapa, Veracruz
Mexico

Tel. (52) 228 8421874; 8421800 ext. 3006 (of.) 3015 (lab)
Fax (52) 228 8187809

31 de octubre de 2008

Stratocladistics: Integrating Temporal Data and Character Data in Phylogenetic Inference

Stratocladistics: Integrating Temporal Data and Character Data in Phylogenetic Inference - Annual Review of Ecology, Evolution, and Systematics, 39(1):365 -
Abstract

Annual Review of Ecology, Evolution, and Systematics
Vol. 39: 365-385 (Volume publication date December 2008)
(doi:10.1146/annurev.ecolsys.38.091206.095752)
First published online as a Review in Advance on September 3, 2008
Stratocladistics: Integrating Temporal Data and Character Data in Phylogenetic Inference
Daniel C. Fisher­
Museum of Paleontology and Department of Geological Sciences, University of Michigan, Ann Arbor, Michigan 48109; email:

Debate has long simmered over whether data on the order of appearance of taxa in the stratigraphic record should play any role in analyses of phylogenetic relationships among those taxa. Critics argue that temporal data are in principle inapplicable to questions of cladistic relationship, but specific versions of this claim all seem flawed. Stratocladistics offers a methodological context (patterned after that of cladistics itself) within which temporal data participate along with conventional character data in selecting most-parsimonious hypotheses. Stratocladistics outperforms cladistics in tests based on simulated histories, and additional testing will be facilitated by new software automating stratocladistic searches. As with any body of data, we may decide to include or exclude temporal data for specific reasons, but the explanatory power of hypotheses that use both temporal and conventional character data exceeds that of hypotheses based on character data alone.

Phylogenetic Approaches to the Study of Extinction

Phylogenetic Approaches to the Study of Extinction - Annual Review of Ecology, Evolution, and Systematics, 39(1):301 -
Abstract

Annual Review of Ecology, Evolution, and Systematics
Vol. 39: 301-319 (Volume publication date December 2008)
(doi:10.1146/annurev-ecolsys-063008-102010)
First published online as a Review in Advance on August 29, 2008
Phylogenetic Approaches to the Study of Extinction
Andy Purvis­
Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, United Kingdom;

Species extinction is both a key process throughout the history of life and a pressing concern in the conservation of present-day biodiversity. These two facets have largely been studied by separate communities using different approaches. This article illustrates with examples some of the ways that considering the evolutionary relationships among species—phylogenies—has helped the study of both past and present species extinction. The focus is on three topics: extinction rates and severities, phylogenetic nonrandomness of extinction, and the testing of hypotheses relating extinction-proneness to attributes of organisms or species. Phylogenetic and taxic approaches to extinction have not fully fused, largely because of the difficulties of relating discrete taxa to the underlying continuity of phylogeny. Phylogeny must be considered in comparative tests of hypotheses about extinction, but care must be taken to avoid overcorrecting for phylogenetic nonindependence among taxa

Morphological Integration and Developmental Modularity

Morphological Integration and Developmental Modularity - Annual Review of Ecology, Evolution, and Systematics, 39(1):115 - Abstract

Annual Review of Ecology, Evolution, and Systematics
Vol. 39: 115-132 (Volume publication date December 2008)
(doi:10.1146/annurev.ecolsys.37.091305.110054)
First published online as a Review in Advance on August 26, 2008
Morphological Integration and Developmental Modularity
Christian Peter Klingenberg­
Faculty of Life Sciences, The University of Manchester, Manchester M13 9PT, United Kingdom;

Biological systems, from molecular complexes to whole organisms and ecological interactions, tend to have a modular organization. Modules are sets of traits that are internally integrated by interactions among traits, but are relatively independent from other modules. The interactions within modules rely on different mechanisms, depending on the context of a study. For morphological traits, modularity occurs in developmental, genetic, functional, and evolutionary contexts. A range of methods for quantifying integration and modularity in morphological data is available, and a number of comparative and experimental designs can be used to compare the different contexts. How development produces covariation between traits can have substantial implications for understanding genetic variation and the potential for evolutionary change, but research in this area has only begun and many questions remain unanswered.

Complete mitochondrial genome of 5,000-year-old mummy yields surprise

Complete mitochondrial genome of 5,000-year-old mummy yields surprise

Researchers have revealed the complete mitochondrial genome of one of the world's most celebrated mummies, known as the Tyrolean Iceman or Ötzi. The sequence represents the oldest complete DNA sequence of modern humans' mitochondria, according to the report published online on October 30th in Current Biology, a Cell Press publication.

Mitochondria are subcellular organelles that generate all of the body's energy and house their own DNA, which is passed down from mother to child each generation. Mitochondrial DNA thus offers a window into our evolutionary past.

"Through the analysis of a complete mitochondrial genome in a particularly well-preserved human, we have obtained evidence of a significant genetic difference between present-day Europeans and a representative prehistoric human—despite the fact that the Iceman is not so old—just about 5,000 years," said Franco Rollo of the University of Camerino in Italy.

The Tyrolean Iceman witnessed the Neolithic-Copper Age transition in Central Europe more than 5,000 years ago. His mummified corpse was recovered from an Alpine glacier on the Austro-Italian border in 1991. In 2000, scientists defrosted the Iceman's body for the first time and sampled DNA from his intestines.

Earlier study of the DNA showed that he belonged to the lineage, or "subhaplogroup," known as K1. About 8% of modern Europeans belong to the K haplogroup, meaning that they share a common ancestor, and that group is divided into two "subhaplogroups," K1 and K2. The K1 haplogroup, in turn, can be divided into three clusters.

In the new study, the researchers took advantage of advanced genome-sequencing technologies to shed more light on the Iceman's genetics. They sequenced his entire mitochondrial genome and compared that sequence to other published human mitochondrial DNA sequences to construct his evolutionary (or phylogenetic) family tree.

"The surprise came when we found that the lineage of the Iceman did not fit any of the three known K1 clusters," Rollo said. His team has informally named the newly discovered branch on the human family tree "Ötzi's branch."

"This doesn't simply mean that Ötzi had some 'personal' mutations making him different from the others but that, in the past, there was a group—a branch of the phylogenetic tree—of men and women sharing the same mitochondrial DNA," Rollo said. "Apparently, this genetic group is no longer present. We don't know whether it is extinct or it has become extremely rare."

At least for the moment, he said, that means no one can claim to be "the issue of Ötzi."

Source : Cell Press

29 de octubre de 2008

Estimating Species Trees Workshop

Estimating Species Trees Workshop | Society of Systematic Biologists

Workshop at the University of Michigan, Jan 10-11, 2009
Estimating Species Trees: a Phylogenetic Paradigm for the 21st Century

Recent computational and modeling advances have produced methods for estimating species trees directly. Accurate estimates of phylogenetic relationships can be extracted from genetic data with these new approaches, sometimes with less data, by directly modeling the causes of discordance in topology and branch lengths among gene trees. Such inferences are commonly impossible under the traditional phylogenetic paradigm because of the potential for the idiosyncrasies of gene trees to obscure the actual history of species divergence.

We are offering this workshop to not only increase the visibility and use of these methods, but also address a number of significant challenges to estimating species trees, to assure that the advantages these methods offer reach a broad community of users. The goals of the workshop are to: (i) provide an understanding of the theoretical underpinnings of current methodology, (ii) present empirical examples demonstrating the utility of current methodology as well as its limitations, and (iii) offer instruction on the technical aspects involved in using current software. This will be accomplished through the combination of a series of lectures (day one) and hands-on computer training (day two).
For more information, click the "read more" link below, and see the flyer Estimating_Species_Trees.pdf.

Participation in the workshop requires registration (go to http://www.ummz.lsa.umich.edu/sptree.html) and is free for those attending the lectures (on Jan 10) and is $25 for those attending the computer training (on Jan 11; see website for programs that will be covered). To facilitate broad and diverse participation in this important workshop, funding is available to offset transportation and lodging costs (i.e., $500 for those from the US and $1000 for international participants – see website for details on how to apply).

Co-organizers: L. Lacey Knowles, University of Michigan, and Laura S. Kubatko, Ohio State University

Location of the workshop: University of Michigan, January 10-11, 2009.

Invited speakers for workshop:
Liang Liu, Harvard University
Laura Kubatko, Ohio State University
Dennis Pearl, Ohio State University
Célcile Ané, University of Wisconsin
James Degnan, University of Canterbury
L. Lacey Knowles, University of Michigan
Luay Nakhleh, Rice University
Karen Cranston, University of Arizona
Bret Larget, University of Wisconsin
Robb Brumsfield, Louisiana State Univ.
Lisle Gibbs, Ohio State University
Scott Edwards, Harvard University
Catherine Linnen, Harvard University
Natalia Belfiore, University of California, Berkeley

For more information please contact: Dr. L. Lacey Knowles, knowlesl@umich.edu

This workshop has been made possible by funds generously provided by the Museum of Zoology, University of Michigan.

TreeTapper

TreeTapper.org: "TreeTapper
Tools to better understand biology by tapping information in phylogenies"

This is a site for finding tools to better understand biology using trees, and to identify areas where tools are missing. It's not yet fully operational, but poke around the menus for more info; you should also go to the development blog to see how the site is being created and its current status. I would really appreciate any suggestions you have, too: email me at bcomeara@nescent.org

Phylogenomics: hace diez años!!

Vol. 8, Issue 3, 163-167, March 1998

INSIGHT/OUTLOOK
Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis
Jonathan A. Eisen1

Genome Research -- Eisen 8 (3): 163

The ability to accurately predict gene function based on gene sequence is an important tool in many areas of biological research. Such predictions have become particularly important in the genomics age in which numerous gene sequences are generated with little or no accompanying experimentally determined functional information. Almost all functional prediction methods rely on the identification, characterization, and quantification of sequence similarity between the gene of interest and genes for which functional information is available. Because sequence is the prime determining factor of function, sequence similarity is taken to imply similarity of function. There is no doubt that this assumption is valid in most cases. However, sequence similarity does not ensure identical functions, and it is common for groups of genes that are similar in sequence to have diverse (although usually related) functions. Therefore, the identification of sequence similarity is frequently not enough to assign a predicted function to an uncharacterized gene; one must have a method of choosing among similar genes with different functions. In such cases, most functional prediction methods assign likely functions by quantifying the levels of similarity among genes. I suggest that functional predictions can be greatly improved by focusing on how the genes became similar in sequence (i.e., evolution) rather than on the sequence similarity itself. It is well established that many aspects of comparative biology can benefit from evolutionary studies (Felsenstein 1985), and comparative molecular biology is no exception (e.g., Altschul et al. 1989; Goldman et al. 1996). In this commentary, I discuss the use of evolutionary information in the prediction of gene function. To appreciate the potential of a phylogenomic approach to the prediction of gene function, it is necessary to first discuss how gene sequence is commonly used to predict gene function and some general features about gene evolution.

22 de octubre de 2008

Botany: Growing flowers

T . Barkman , M . Bendiksby , S . Lim , K . Salleh , J . Nais , D . Madulid , T . Schumacher. 2008. Accelerated Rates of Floral Evolution at the Upper Size Limit for Flowers. Current Biology 18: 1508 - 1513.


The world's largest flowers, of the Southeast Asian Rafflesia genus, which mimic the smell and appearance of rotting flesh, evolved much more quickly and more often than botanists expected.

Todd Barkman of Western Michigan University in Kalamazoo and his team hypothesized that it would have taken a long time for the Rafflesia flowers to evolve from their smaller ancestors to their current maximum size of one metre in diameter because of the many structural and physiological changes required to support such large flowers. To their surprise, they found that the flowers of some Rafflesia species have more or less doubled in size during the past one million to two million years. As Barkman points out, it is hard to imagine a giraffe doubling the length of its neck in the same time frame. The scientists suggest that even bigger flowers could evolve in future.

Fuente de la información: Research Highlights, Nature 455, 1010 (23 October 2008) | doi:10.1038/4551010a; Published online 22 October 2008.

20 de octubre de 2008

Bosque: integrated phylogenetic analysis software



Ramírez-Flandes S. & O. Ulloa (2008).
Bosque: Integrated phylogenetic analysis software.
Bioinformatics 24(21):2539-2541;

doi: 10.1093/bioinformatics/btn466

Summary:
Phylogenetic analyses today involve dealing with computer files in different formats and often several computer programs. Although some widely used applications have integrated important functionalities for such analyses, they still work with local resources only: input/output files (users have to manage them) and local computing (users have sometimes to leave their programs, on their desktop computers, running for extended periods of time). To address these problems we have developed ‘Bosque’, a multi-platform client–server software that performs standard phylogenetic tasks either locally or remotely on servers, and integrates the results on a local relational database. Bosque performs sequence alignments and graphical visualization and editing of trees, thus providing a powerful environment that integrates all the steps of phylogenetic analyses.

Availability: http://bosque.udec.cl

Contact: sram@profc.udec.cl

15 de octubre de 2008

Filogenética en la lingüistica

The Austronesian Basic Vocabulary Database: from bioinformatics to lexomics
Simon J. Greenhill, Robert Blust and Russell D. Gray
Publication Date: 15 Oct 2008
Evolutionary Bioinformatics 2008:4

Abstract

Phylogenetic methods have revolutionised evolutionary biology and have recently been applied to studies of linguistic and cultural evolution. However, the basic comparative data on the languages of the world required for these analyses is often widely dispersed in hard to obtain sources. Here we outline how our Austronesian Basic Vocabulary Database (ABVD) helps remedy this situation by collating wordlists from over 500 languages into one web-accessible database. We describe the technology underlying the ABVD and discuss the benefits that an evolutionary bioinformatic approach can provide. These include facilitating computational comparative linguistic research, answering questions about human prehistory, enabling syntheses with genetic data, and safe-guarding fragile linguistic information.

7 de octubre de 2008

Estudios de posgrado en Sistemática, INECOL, México

CONVOCATORIA 2009
ASPIRANTES A ESTUDIOS DE MAESTRÍA O DOCTORADO EN CIENCIAS

El Instituto de Ecología A.C. (INECOL), convoca a todos los profesionistas interesados en biodiversidad y sistemática a cursar la Maestría o el Doctorado en Ciencias. Estos programas están dirigidos principalmente a los egresados de Biología, Agronomía, Química, Ecología, Veterinaria y otras carreras afines, aunque cualquier profesionista titulado puede concursar para lograr su ingreso.

El plan de estudios enfatiza la asesoría en el trabajo de tesis, con un mayor seguimiento y control del avance de cada estudiante. Los estudiantes deberán obtener su grado en un tiempo de 2 años en el caso de la maestría y de 4 años en el caso del doctorado.

La Maestría en Ciencias se enfoca a la investigación y a la práctica profesional, mientras que el Doctorado en Ciencias esta orientado a la investigación.

La Maestría y el Doctorado en Ciencias pertenecen al Programa Nacional de Posgrados (PNPC) lo que facilita que los estudiantes mexicanos y extranjeros puedan obtener una beca del CONACYT.

Más información sobre la investigación en Biodiversidad y Sistemática en el INECOL aquí>>

Más información sobre la Convocatoria aquí>>

18 de septiembre de 2008

XXVII International Meeting of the Willi Hennig Society

The meeting is getting closer!

Some people asked about flights to Tucumán… and yes, it is a pain in the neck, as we the locals verify every time we have to attend a meeting anywhere else. This time it's your turn! One of the good offers to fly to Tucumán is with a new company, Andes Líneas Aereas, whose web page is at www.andesonline.com.

We still don't have the final program (the deadline for reception of abstracts was extended, at the request of many people, and we are still receiving abstracts), but we do know some details…

The meeting will be starting in the morning of the 28th, at the Hotel Sol (http://www.hotelsolsanjavier.com.ar). All the talks, and the banquet (night of the 30th) will be held at the Hotel Sol. The Hotel Sol is up in the hill, west of the city of San Miguel de Tucumán. We will try to be at the airport for incoming flights, but just in case you're on your own, you can tell the taxi driver to go to the "Hotel Sol, Cerro San Javier". See map below.

The only other venue is going to be the Instituto Lillo (adress: Miguel Lillo 205, it's near the "Abasto" –the neighborhood is known by that name because the "Abasto" market used to be there). We will have a reception there the day before the meeting (as usual for Hennig meetings), that is, the evening of the 27th, and begin with registrations. At the Instituto Lillo, registration will start from 5pm, the reception will start after 6:30pm, of Monday October 27th.

If you have not yet registered for the Hotel, you should. The hotel is a lovely place, and it is not expensive. It is not very big, so we may run out of rooms. They have been holding some rooms for us, but they won't hold them for much longer. Don't risk missing it! If no more rooms are available when you try to book, and you have to get a room down town (and the "down" here is quite literal), we will be providing transportation to the Hotel everyday, with a bus which will fit about 40 people. Otherwise, you can just take a taxi (from the center, it's about 20 dollars, so that splitting among three people should be rather cheap).

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