Lorentz Center - The Future of Phylogenetic Networks from 15 Oct 2012 through 19 Oct 2012
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    The Future of Phylogenetic Networks
    from 15 Oct 2012 through 19 Oct 2012

 

Description and Aim

Biologists continue working with phylogenetic trees, even if they realise that it is not the adequate model for the genetic phenomena they study; phylogenetic trees are less suited to capturing reticulate evolutionary phenomena such as hybridisation, recombination or lateral gene transfer.

Phylogenetic networks are a generalisation of phylogenetic trees that can display such complex evolutionary scenarios; the long-term goal of the workshop is to develop practical algorithms for these networks. This will allow the current tree model, which incorporates only vertical descent from parent to offspring, to be expanded to include horizontal (reticulate) evolution.

The first purpose of the workshop is that biologists from various sub-disciplines explain to math-ematicians and computer scientists their specific requirements for phylogenetic network models, in order to make them useful for their work. In return, the mathematicians will outline the inherent mathematical limitations of various algorithmic approaches, and highlight potentially fruitful avenues for future development. By interacting in lectures and group discussions, the key features of phylogenetic networks are identified that are important for any successful algorithm, both from the biological and computational aspects.

The ultimate goal of the workshop is that, through close collaborations, mathematical research on phylogenetic networks will lead to more practical methods, ultimately resulting in more widespread use of phylogenetic network software by biologists.

Scientific output

Although the workshop was not aimed at direct new mathematical or biological results, some subgroups of people, especially mathematicians and computer scientists, have made progress on subjects related to the workshop. The best learning moments of the workshop have been for the math/cs people to see the various ways that biologists are interested in using networks i.o.trees, which each require their own specific model. For the biologists it was to see where the mathematical developments are currently: what they may expect and what not, currently. Also they realised that they will need to make some effort to define their problems more clearly. Given the goals of the workshop, it was an enormous success, and in fact a success beyond expectation.

Organisation

The organisation of the workshop appeared to work out exceptionally well. Two aspects triggered the success. Firstly, the biologists had been selected carefully; all of them feeling the need for networks as an alternative to trees, and being interested to explain why they still were not using existing software/algorithms. Next to that David Morrison, as the biology organiser of the committee played an excellent role in moderating the discussions whenever necessary. This made the discussion sessions extremely lively and informative until the very last moment of the workshop.

Secondly, all lecturers were given very precise instructions about what was expected from them. Especially the math/cs researchers were asked to give overview lectures with a lot of empathy for the biologists in the audience. This worked out very well, maybe not in the least because we were lucky - or less moderately, some members of the organising committee appear to have enough reputation worldwide - that almost all prominent international math/cs/bioinformatics researchers in the field came to the workshop, even from the remotest places on earth like New Zealand. Thus, the knowledge on the actual state of the art on the algorithmic side of the subject was present, and they were the perfect group of people to expose the overviews.

At the end of the workshop everybody agreed that we should try to actively keep the momentum going that has been created. For sure, we will actively visit, correspond through and contribute to the blog on phylogenetic networks. We will investigate possibilities to write a EU grant proposal to help us to realise our goals: creating software ready for biologists to help them in their studies and on the way solving a lot of beautiful mathematical challenges.



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