In the last week of May the idyllic mountain retreat Hameau de l'Etoile, in the Montpellier region of France, was the location for the conference Mathematical and Computational Evolutionary Biology 2013. (Well, perhaps 'mountain' is not the correct word, but for somebody based in the Netherlands the difference between a hill and a mountain is a largely academic concept...)
The main theme of the conference was the interface between phylogenetics and health. Phylogenetic networks, in all their various guises, were quite prominent at the conference. During the poster sessions themes such as maximum parsimony on networks, maximum acyclic agreement forests (used for parsimoniously merging two gene trees into a species network) and unrooted, "data display" phylogenetic networks were evident. There were also quite a few posters on parsimonious gene tree species tree reconciliation, which can, in principle, be used to build rooted phylogenetic networks.
Networks were also visible in a number of the long talks. On the first day, I closed the afternoon with an attempt to summarise in (very) broad lines the methodologies available for constructing rooted phylogenetic networks, and the extent to which these techniques have been biologically validated. This, if you remember, is a theme that has surfaced on this blog at least once or twice in the past. In the talk I argued that there is actually more work out there on validation than many people realise, particularly on horizontal gene transfer and to a lesser extent on hybridization. However, differences in the terminology and models used by different research groups means that a lot of this work is overlooked, even when the conceptual similarities are strong (e.g. DLT-reconciliation, Ancestral Recombination Graphs and networks).
On the second day, Tuesday, Bastien Boussau gave a detailed, but very clear, talk about various different flavours of reconciliation. Alongside different combinations of deletion, loss, transfer and incomplete lineage sorting he also looked at the multiple points in the traditional phylogenetic pipeline where uncertainty exists (alignment, species tree construction, gene tree construction, reconciliation) and how these can be co-estimated.
Wednesday saw Gil McVean describe his work on analysing the data harvested by the 1000-genomes project. Here, networks popped up in the form of Ancestral Recombination Graphs (ARGs). ARGs can perhaps best be summarised as "phylogenetic networks for population genetics". Rather than modelling horizontal gene transfer or hybridization, reticulations represent recombination, which requires the character data to have an explicit linear ordering (e.g. SNPs), Gil, wisely, did not try and construct an explicit ARG for the data from the 1000 genome project (think: SNP matrix with 1000 rows and several million columns/SNPs...) although he did describe a number of statistics summarising key properties of it, e.g. the average distance that has to be travelled back in time before two UK citizens reach a common ancestor.
The final talk that explicitly addressed network themes was by Darren Martin. He motivated why one should try and detect recombination, and went into detail about techniques for detecting (and interpreting) recombination in viruses. He explained how his software RDP4 for detecting recombination breakpoints works. As with many other speakers, he devoted part of his talk to HIV.
The full program, and slides for most of the long talks, are available at the following URL. Needless to say, there were also plenty of very interesting talks that had no direct connection with networks.
There are also detailed abstracts available for all the short talks and posters: