Dating and analysing the complete tree of life

The ongoing loss of biodiversity has negative consequences both for ecosystems themselves, and for the benefits that healthy ecosystems provide to humans. Scientists and conservation organisations aim to preserve biodiversity, but limited resources mean they must choose a limited set of species to which they devote time, money and effort. A common consideration in such prioritisation is how evolutionarily "different" a species is: the extinction of a species with no close surviving relatives may be more of a loss to the overall diversity of life than the extinction of a species with many very close relatives.

Phylogenetic diversity (PD) and evolutionary distinctiveness (ED) are metrics that attempt to quantify such intuitions by modelling which species have accumulated the most evolutionary innovation. Both take as their input a dated phylogenetic tree describing a set of species of interest. Previous work has computed PD and ED scores within certain clades of the tree of life, but the lack of a complete dated tree means that scores have never been computed for the great majority of species on Earth.

The Open Tree of Life project arranges more than two million described species into a single tree, collating information from published phylogenies and taxonomies to hypothesize a set of ancestral relationships among all known life. However, the "supertree" thus synthesized contains no information on when the hypothetical common ancestors in the tree are believed to have existed. The lack of dating information limits the scope of analyses that can be performed on the tree.

In this project, I will produce a fully dated phylogenetic tree of all life, expanding the set of common ancestors in the Open Tree of Life and estimating dates for all ancestors in the tree. I will then use the tree to perform broader analyses of phylogeny-based biodiversity metrics than have previously been possible.