Wednesday, October 17, 2012

The Future of Phylogenetic Networks: Day 2

There were five talks today and one discussion session. We were rained upon for much of the day, although it was better in the afternoon.

Scot Kelchner started by explaining how networks are currently used in botany. Plants have long been accepted as having a complex history, and so there is great potential for using networks to explore this complexity, from detecting unexpected hybrids to assessing lineage sorting. He emphasized the valuable role of networks as a paradigm for both exploratory data analysis and hypothesis generation.

Teun Boekhout addressed the enormous network complexity of fungi, although it seems that very few practitioners are using the available mathematical methods.

James McInerney, somewhat the worse for wear, then discussed microbiology, where much attention has been given recently to horizontal evolutionary processes. He explained the continued dominance of the tree paradigm within prokaryote studies as resulting from interest in the transmission tree of the pathogens and its obvious connection to a phylogenetic tree. He then turned to the Tree of Life, which bacteriologists seem to see as their special preserve, pointing out its inadequacy as a model, before turning to the range of microbiological questions that exist only in the context of a network paradigm.

Eric Bapteste then further explored the concept of network thinking as opposed to tree thinking, emphasizing how limited the tree paradigm is when studying the known diversity of biological phenomena. Most interestingly, however, he also noted that even the network paradigm has limitations for studying biodiversity, as they need to be linked to other types of biological networks.

Vincent Moulton produced the only mathematical talk of the day, covering the mathematical quantification of branch support within networks, which is clearly of interest for both data exploration and hypothesis generation. To date, bootstraps are the only method implemented in the software, although they are rarely used in practice. Delta plots have also been proposed, and are quick to calculate, but there are other theoretical possibilities to be explored.

The topic for the discussion was not pre-determined, and turned out to be just how much automation would be useful in network analyses. The consensus is that an attempt at complete automation would be counter-productive. However, the most thorny issue of debate was exactly which types of network are likely to be most useful to biologists. The problem here is that the mathematicians need an explicit description of such networks in order to produce them, while the biologists do not yet have such a description. The issue remained unresolved when we adjourned to the coffee room.

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