Wednesday, February 5, 2014

NSF and reticulating phylogenies

In mid January, the US National Science Foundation released a new Program Solicitation, NSF 14-527. This is called the Genealogy of Life (GoLife).

The text notes:
This solicitation represents the successor program to the Assembling the Tree of Life program. The name has been changed to include projects covering the complexity of phylogenetic patterns across all of life.
So, it replaces the previous documents NSF 10-513 (the Assembling the Tree of Life program, AToL) and NSF 11-534 (the Assembling, Visualizing and Analyzing the Tree of Life program, AVAToL). The latter program has its own web page, which gives you an idea of what it has been about.

For those of us interested in phylogenetic networks, the following parts of the Introduction to the new program are of particular interest:
Understanding the tree of life has been a goal of evolutionary biologists since the time of Darwin. During the past decade, unprecedented gains in gathering and analyzing phylogenetic data have demonstrated increasingly complex genealogical patterns. 
The GoLife program builds upon the AToL program by accommodating the complexity of diversification patterns across all of life's history. Our current knowledge of processes such as hybridization, endosymbiosis and lateral gene transfer makes clear that the evolutionary history of life on Earth cannot accurately be depicted as a single, typological, bifurcating tree.
This is very good news, and a major step forward. The two Tree of Life programs were implicitly based on a rather unrealistic assumption about the shape of phylogenetic history. This new move has been a long time coming, both during prior stakeholder discussions and within the various committees. There are a number of people who will be personally pleased that this has come to fruition.

The focus of the new program is solely on biology, however:
Proposals should focus on poorly sampled clades or data layers within the Genealogy of Life where new data will have a profound impact on our understanding of the pattern of life's evolution ... Additional examples of projects that will not be considered by this program include: ... 5) projects that are solely focused on the development of new computational methods or technologies. 
This is a pity, because there needs to be method development before reticulating phylogenies can be constructed in a manner similar to what is currently used for tree building. There is likely to be a major need for practical large-scale methods for producing evolutionary networks, which unfortunately will be supported only outside of this particular program.

The project should include a plan for integration and standardization of data consistent with three AVAToL projects: Open Tree of Life, ARBOR, and Next Generation Phenomics.
This is an important requirement, as scientific data tends to disappear into a black hole unless it is prised out of the scientists' hands. The problem is that the Open Tree of Life appears to currently have no mechanism for dealing with non-tree phylogenies!

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