Wednesday, October 17, 2012
The Future of Phylogenetic Networks: Day 3
There were four talks today and one discussion session. We also spent the evening on a boat cruise around the waterways north of Leiden, supping on an Indonesian buffet and consuming some distinctly non-Indonesian desserts. No-one embarrassed themselves, and so (sadly) there are no stories to be told.
Jim Whitfield started the day's talks by contemplating the varied ways in which entomologists might be interested in using a network, especially with genome-scale data. He eventually worked his way around to the topic of datasets for validating network algorithms, which would need to cover all of these possibilities.
Barbara Gravendeel continued the same theme, by presenting some datasets, mainly involving orchids, for which there is independent evidence that some of the taxa are hybrids. Such datasets could be used for algorithm validation.
The discussion session followed, which focussed on the various ways in which validation datasets could be made available. In the short term, it seems likely that a web page will be set up with this information for each dataset: (i) a link to the online dataset, (ii) a link to the relevant publication(s), and (iii) a brief description of what relevant data patterns are believed to be included in the dataset.
Mike Steel then started the very mathematical afternoon. He mainly contemplated the extent to which non-tree biological processes could create tree-like patterns in the data. There are theoretical ways to differentiate various signatures of gene tree incongruence in the context of triplets, but also sources of inconsistency in phylogeny reconstruction.
Dan Gusfield finished with a coverage of ancestral recombination graphs, including their possible use in biology, but mainly some of the potential things that create problems for reconstruction. The mathematical part of the audience looked very enthused by the end of the afternoon.