From here, we hope to assign particular events (duplication, loss of genes, loss/gain of regulatory relationships) to particular edges of the phylogenetic tree. In effect, this would allow us to reconstruct ancestral gene networks at the internal nodes of a phylogenetic tree. This may only be possible over relative short evolution timescales because, across deep evolutionary time, the gene networks that act to produce similar functions may have evolved independently, i.e., networks may do similar things but not be homologous.  

Now, given an alignment of gene networks on a phylogenetic tree (or a set of small phylogenetic trees), we can associate the evolution of network features with information about traits in the species of interest. 

We aim to model the evolutionary processes that act on gene networks, including duplication events, mutations in regulatory regions, and lost/deleted genes.