We can observe the complex biogeographic histories that give rise to phylogenomic discordance in real time, by studying groups of closely related organisms in early stages of the diversification process. Studying these "tips of the tree" can reveal the processes shaping global phylogenetic patterns.

Although we will never be able to reconstruct the geography of divergence at difficult nodes deep in the tree of life (at least without a time machine)...

Overall, this implies that the presence of unresolvable nodes in the tree of life may be largely attributable to real biological messiness, like cases of rapid colonization with gene flow across an island archipelago, not just a lack of sequence data or appropriate models.

Ultimately, the best demographic model was a polytomy, yet a model of rapid divergence with gene flow provided a nearly identical fit to the empirical data. Even though we think true "hard polytomies" are rare in nature, rapid divergence with gene flow is becoming recognized as relatively common.

The main conclusion is in the title "Rapid divergence with gene flow creates intractable nodes in the tree of life". One favorite result was that random downsampling of the tips resulted in conflicting species trees, at times with high support! Concerning implications for higher-level phylogenetics!