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Utilizing Genealogical Phylogenetic Networks in Evolutionary Biology: Touching the Data
Description and Aim
When studying evolutionary history, biologists continue to work with phylogenetic trees, although this is not the best model for the genetic phenomena they study. Phylogenetic trees do not capture reticulate evolutionary phenomena such as hybridization, introgression, recombination or lateral gene transfer. Phylogenetic networks are a generalization of phylogenetic trees that can analyze and display such complex evolutionary scenarios.
In October 2012, we organized a Lorentz workshop on “The future of phylogenetic networks” which had as its long-term goals the development of practical algorithms for phylogenetic networks, and directing mathematical research on this topic in those directions that are most relevant for biologists. That workshop was an enormous success, and it was decided that a series of future workshops is essential.
In order to follow-up on the outcomes of that workshop, this new workshop was specifically aimed to get together both mathematicians and biologists in a specifically practical setting, in order to apply the techniques developed by the mathematicians to empirical data provided by the biologists. This was thus an applied follow-up to our previous workshop, with a limited number of presentations and ample time for discussions and data analysis.
The workshop aimed to (1) answer the specific scientific questions posed by the biologists; (2) get an insight into which tools work best on which datasets, and why; and (3) learn which tools are still needed. 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.
Although the workshop was not aimed at direct new mathematical or biological results, some subgroups of people have made progress on topics related to the workshop.
Subgroups were formed around specific empirical datasets, provided by the biologists, to evaluate their mathematical characteristics, discuss these in relation to the biological goals, and assess the extent to which current computational resources can tackle the problem. This helped the computational people to see the various ways that biologists are interested in using networks, and the biologists to see current mathematical developments, and for both groups to work out what is needed for progress in the immediate future.
Several research publications are in the pipeline, including one for the “Encyclopedia of Evolutionary Biology”. However, the main direct output is a paper in preparation for a high-profile journal setting out the basics of the biology and mathematics of phylogenetic networks.
Given the goals of the workshop, it was an enormous success.
The organization of the workshop worked very well. Two aspects triggered this success. First, many of the group participants had worked together at the previous workshop, and were very keen to repeat their successful collaborations. Both the biological participants and the computational participants were selected carefully for their demonstrated interest in networks as an alternative to trees, and for their willingness to contribute fully within the small-group setting. We also expanded our coverage of researchers who use networks to include people from the social sciences (specifically linguistics). The involvement of specialists on gene/species-tree reconciliation was also a positive point. These researchers use models that have many mathematical and conceptual similarities to phylogenetic network models, but the two communities have evolved largely isolated from each other. Their involvement was an important step towards overcoming this somewhat artificial separation.
Second, all of the lecturers were clear about what was expected from them, as were the small-group moderators. The small groups working on each empirical dataset were formed quickly and effectively; and they reported their outcomes clearly and precisely to the whole workshop. The subsequent whole-group discussions were very effective; and the participants were very pleased with the progress made. The empirical datasets will remain accessible to the general public via the website https://sites.google.com/site/touchingthedata/.
At the end of the workshop everybody agreed that we should try to actively keep the momentum going that has been created by this and the previous workshop. In particular, we will investigate possibilities for EU funding of future workshops, as well as EU grant proposals to help us to realize our goals.
Leo van Iersel (Amsterdam, Netherlands)
Steven Kelk (Maastricht, Netherlands)
David Morrison (Uppsala, Sweden)
Leen Stougie (Amsterdam, Netherlands)