In biology, phylogenetic trees represent the evolutionary history and diversification of species – the “family tree” of Life. Phylogenetic trees not only describe the evolution of a group of organisms but can also be constructed from the organisms within a particular environment or ecosystem, such as the human microbiome. In this way, they can describe how this ecosystem evolved and what its functional capabilities might be.

There is remarkable biodiversity in all but the most extreme ecosystems on Earth. When many species are competing for the same finite resource, a theory called competitive exclusion suggests one species will outperform the others and drive them to extinction, limiting biodiversity. But this isn’t what we observe in nature. Theoretical models of population dynamics have not presented a fully satisfactory explanation for what has come to be known as the diversity paradox.