The uses of phylogenies

Inspired by a conversation today, I am wondering: What are the uses of phylogenies? I mean, as a phylogeneticist and systematist one would like to understand how species are related full stop. That is the research program. But there are many other uses beyond that, some of them in very different context. Below a potentially incomplete list, which may be updated in the future. It may also have a bit of a botanical bias.

1. Informing biological classification (Phylogenetic Systematics).

2. Understanding evolutionary and biogeographic history of individual lineages.

2.1. Simply describing the phylogenetic relationships between species.

2.2. Understanding when lineage splits or other evolutionary events happened. Example: studying whether the main lineages of mammals already existed before the K/T extinction event or only arose later.

2.3. Inferring diversification rates, in particular shifts in diversification rates correlated with trait shifts or biogeographic events, extinction rates versus speciation rates, etc. Example: higher rates of diversification after colonisation of an empty oceanic island.

2.4. Inferring rates of evolution, in particular shifts in the rate of evolution correlated with trait shifts or biogeographic events. Example: higher speed of evolution in organisms with shorter generation times.

2.5. Inferring ancestral character states. Example: was the ancestor of all eucalypts likely to have been fire-resistant?

2.6. Inferring ancestral ranges and subsequent dispersal and extinction events. Example: on what continents did the perching birds originate, and how did they colonise the rest of the world?

2.7. Studying co-evolution and host shifts. Example: where did the human AIDS virus come from?

2.8. Understanding epidemic dynamics. Example: phylogenetic analysis of virus strains, including historical samples.

3. Studying spatial patterns for biodiversity.

3.1. Inferring hotspots of phylogenetic diversity or related metrics, as opposed to merely counting species, and searching for an explanation for these patterns. Example: a climatically stable area may have accumulated many diverse lineages even as many of them were wiped out in less stable areas.

3.2. Informing conservation management (at least ideally). Example: a hotspot of phylogenetic diversity deserves protection.

3.3. Bioregionalisation, that is the definition and delineation of different biota. This can be done based on nothing but similarity in species content, but can also be done based on phylogenetic similarity metrics, thus taking into account diversity at higher levels.

4. Predicting shared traits from relatedness.

4.1. Bioprospecting. Example: related species are more likely to share similar secondary chemistry.

4.2. Informing plant breeding or gene transfer. Example: finding a wild relative of a crop plant that is very resistant against a disease, and transferring the genes conferring that resistance into the crop.

4.3. Predicting disease or pest susceptibility. Example: wild relatives of the tomato are at greater risk from introduced tomato diseases than totally unrelated species.