The Future of Phylogenetic Networks: Day 1

There were three talks today and two discussion sessions.

Steven Kelk and I got things rolling by introducing the topic of networks from the mathematical and biological perspectives, respectively. I thought that we both did a good job, but I learned more from Steven's talk than from my own.

Luay Nakhleh then presented some of the computational challenges of moving from a tree perspective to a network. Perhaps the most interesting of these to a biologist is the decreasing independence of reticulations as gene sampling increases (eg. due to gene linkage). Independence is a basic assumption of most computational methods in biology, and the consequences of violating this assumption are rarely addressed. However, for network construction the potential non-independence of reticulations seems to be of fundamental importance for any biological interpretation of reticulation causes.

Computationally, the obvious challenge is the complexity of scoring a network compared to a tree. Calculating the parsimony score of a network is hard enough (although trivial for a tree), and scoring the likelihood is even worse. This calls into question the practicality of using likelihood in the context of networks.

However, perhaps the most interesting challenge is how to model inter-locus incompatibility. Within-locus mutations are currently addressed using substitution/indel models in phylogenetic tree-building, but the special focus of networks is on the inter-locus patterns, about which we know much less in terms of appropriate modelling.

Axel Janke and Katharina Huber finished the day by leading discussions on why so few people currently use networks in phylogenetics, and the obvious cultural divide between mathematicians and biologists, respectively. The biologists seemed to dominate the first discussion and the mathematicians the second one.
In the former case, the main conclusion from the discussion was that the current phylogenetic "culture" is focussed so strongly on trees that the extra benefit of using a network is not obvious to practitioners. Indeed, there is still considerable focus on getting people to think in terms of trees rather than linear evolution, so that moving on to the complexity of networks simply confounds the situation. Suggestions were forthcoming about how we could be proactive in addressing this issue, including increasing the profile of networks in journals, but also the need to provide more biological information from analyses than merely the network topology.

As for the cultural divide, this is a long-standing issue that arises from the different thought processes involved in mathematics and empirical science, and the consequent differences in language. The consensus was that there are no hurdles that can't be overcome given sufficient time and patience. Moreover, trans-disciplinary people are becoming more common, which nullifies many of the potential problems.
So, a productive start to the workshop was made, which bodes well for the rest of the week. Sadly, this was the sunniest day since I arrived in the Netherlands, and I spent it indoors!