“Network” is a bit more general than one would like– but there are things that are not called networks that are. Two types: * “data display” or unrooted networks. * evolutionary or rooted networks Will be talking about the second type. Hypothesis of what happened– including HGT, hybridization, and recombination. Common abstraction– have nodes of indegree 2 or more. Example of PNAS paper of a bacterial gene to an invasive coffee pest. Hybridization and recombination can be symmetric exchange of information, but HGT is directional. Can we reconstruct a hybridization network knowing the trees that are inside of it? Reticulation parsimony: input is a set of incongruent rooted gene trees, and want a phylogenetic network that has as few reticulation events as possible. Solution is not unique.
Many factors can cause incongruence. DLT reconciliations are networks– why don’t we call them such? Some folks are running tree analyses then trying to put things by hand. Paper by Paul Jenkins, Yun Song, and Rachel Brem using reticulation parsimony, but not many others. Combinatorial methods that attempt to measure distance between trees (rSPR). Statistical likelihood-based methods to determine whether incongruence is actually there. Use low-resolution parsimony to generate hypotheses, then do something statistical.