Aim: Previous studies have shown that phylogenetic divergence (i.e. the average phylogenetic displacement between species in a community) is highly sensitive to the underlying branching patterns of phylogenies, suggesting that there is a need to integrate both facets of phylogenic information to obtain a better understanding of assemblage structure. Here, we formally conceptualize the three fundamental branching patterns that can drive phylogenetic divergence, and propose a method to identify their signature in the communities based on the MPD (mean pairwise distance) metric. Location: Global. Taxa: All. Methods: Our approach consists on the joint interpretation of two MPD-derived metrics that summarize the differential contribution of individual phylogenetic branches to the observed divergence, which serves to evaluate to what extent the later emerges from contrasting branching patterns. We conduct simulation analyses to compare our two metrics with eight classical descriptors of phylogenetic structure, and use multi-strata tropical plant communities along a gradient of land-use intensity (LUI) to further illustrate our method. Results: As expected, our metrics correlated to some extent with the classical descriptors of phylogenetic structure, although the relationships were complex and varied systematically with species richness and the specific combination of metric values considered. Consequently, the information provided by our two indexes was only partially captured by their most correlated classical descriptors. We detected differential signatures of the fundamental branching patterns in our real-world dataset, either across vegetation strata and also within strata along the LUI gradient, which provided greater insight into potential assembly mechanisms. Main conclusions: While the sole use of phylogenetic divergence may lead to spurious interpretations in eco-phylogenetic studies, our approach can help to obtain a better understanding of assemblage structure by systematically analyzing phylogenetic divergence in the light of its fundamental branching patterns.