A few thoughts on cancer molecular evolution

A random walk column has been published on JME on Cancer molecular evolution. These are a few lines with some pointers about potential uses of evolutionary approaches in cancer.

   
http://link.springer.com/article/10.1007%2Fs00239-015-9695-7

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Plenarly talk at the barcoding meeting

I talked today about species trees a the barcoding meeting in Guelph, Canada

   

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Farewell to Leo Martins!

Leo Martins has recently left our lab to start a new adventure at Molly Stevens Lab at Imperial College London. There he will work on statistical analysis of Raman spectra for different applications, and probably on other things.

 

It has been a real pleasure to work with Leo all these years. Best wishes to you and Reiko. Take care.. and have fun!

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Sampling trip to Cabo Verde (Boavista island)

We just arrive from our third sampling trip to Cape Verde.  We went to the Boa Vista Island, where we sampled several populations of Trovaoconus (and Africonus) snails with our colleages Rafa Zardoya (MNCN), Julio Rozas (UB), Manolo Tenorio (UCA) and Carlos Afonso (“Camané”, UAlgarve). The wind was a little rough so we could not dive for nudibranchs, tough.

Boavista_45 Boavista_66 DSC00932 DSC00981

 

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Two new PhD fellowships!

Congratulations to Nuria and Tamara for being awarded a competitive doctoral fellowship from the Galician Government! 2 out of 2… not bad..

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Joao Alves just joined the lab!

Joao Alves has joined our lab to do a postdoc on NGS cancer evolution. Joao comes from IPATIMUP and has worked before on human population genomics. Welcome!

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Welcome to Andrés Pérez-Figueroa

Andrés Pérez-Figueroa has joined our lab as a postdoctoral researcher to work on Conus phylotranscriptomics. Andrés is a Spanish population geneticist that comes from a neighboring lab in our department. Welcome to our lab Andrés!

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ModelTest paper among the top 100 in history!

Our old paper
 
Posada D and Crandall KA 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (9): 817-818.
 
has been ranked by Nature 76th among the top 100 all-time papers.
 
Not bad for such a simple tool. D
 

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Postdoctoral position in NGS cancer evolution (POSITION FILLED)

Postdoctoral position in NGS cancer evolution
University of Vigo, Spain – October, 2014
 
DESCRIPTION: A postdoctoral position is available within the European Research Council project PHYLOCANCER to work on cancer evolution in David Posada’s lab at the University of Vigo, Spain (http://darwin.uvigo.es).
 
JOB CONDITIONS: Initial appointments will be made for one year, with a possible extension to up to four years. Gross annual salary including benefits will be around 25,000-30,000 Euros, commensurate with experience. Starting date is negotiable.
 
MINIMUM REQUIREMENTS: Candidates should have a PhD degree and ample, demonstrable experience with NGS data analysis, in particular variant calling. Candidates without a strong NGS background will not be evaluated.
 
DESIRABLE REQUIREMENTS: Background in evolutionary/cancer genomics, programming abilities and/or statistical skills.
 
APPLICATION: Please send a letter of interest, C.V., and the names and contact details of two referees to David Posada at xb5lab@gmail.com, indicating “postdoctoral position phylocancer” in the subject of the email. Questions and requests for more information should be directed at the same address. Review of applications will begin immediately, and continue until the positions are filled.

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Unsorted Homology within Locus and Species Trees

It is now the turn for printed versions! You can find our penultimate paper in the current version of Systematic Biology (November 2014) . Here we show how classical homology categories can fail to describe homology relationships when we consider the effect of incomplete lineage sorting (ILS). In order to comprehensively describe these situations we had to rely in a three-tree representation (gene, locus and species trees), which points out the importance of considering the different phylogenetic layers to fully understand how evolution works.
 
From a pragmatic point of view, we also demonstrate how these situations can easily mislead commonly used parsimony reconciliation approaches, pointing out the need of quickly adopting the newest methodologies.
 
Last but not least, we consequently proposed a revised terminology describing the different homology categories (and subcategories).
 
Unsorted Paralogy
Reference:

Diego Mallo, Leonardo De Oliveira Martins and David Posada (2014). Unsorted Homology within Locus and Species Trees. Systematic Biology, 63: 988-992, doi: 10.1093/sysbio/syu050

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