Research

Cophylogenetic simulation

One of my research projects is developing new simulation models for producing cophylogenetic datasets. Cophylogenetic datasets are typically though of as a host phylogeny, a symbiont phylogeny, and the ecological interactions between the extant host and symbiont species. Currently, these are all found in my R package, treeducken. At present these are the possible simulation models:

• Cophylogenetic birth-death process with host-switching
• Cophylogenetic birth-death process with host-expansion
• Cophylogenetic birth-death process with both host-swtching and host-expansion (development only)
• Cophylogenetic birth-death process with anagenetic dispersal and extirpation

Using an historical biogeography model for cophylogenetics

This project uses the Bayesian Dispersal-Extinction-Cladogenesis (DEC) Model to estimate parameters of the cophylogenetic birth-death process. This is also still a work in progress...

Using machine learning for cophylogenetics

Stay tuned for more updates here!