Annotate nodes in gene trees as to whether each is a gene duplication event or a speciation event. Include these annotations in the trees that are exported via issue
In the future these annotations should be probabilistic, but the first priority should be able to support simple boolean assertions. In the future these annotations may be derived from simultaneous gene tree/ species tree inference, but for now they can be made be reconciling the gene trees to the species tree.
August compared multiple options for our first pass, and suggested the following: