Lead Chief Investigator: Barbara Holland, University of Tasmania

Collaborating Chief Investigators: Christine Beveridge


Phylogenetic profiling is the long-standing idea of using presence/absence information about genes across a phylogeny to gain some information about which genes are associated with each other which could offer clues about their function. 

Our aim is to improve on current phylogenetic profiling approaches, developing a tool that could be used in a range of contexts where we want to better understand the genetic underpinning of a trait.  

The tool will also allow us to make predictions: 

  • Given a trait of interest (and usually some known set of genes that influence the trait), predict what other genes may influence the trait. 
  • Given a set of species for which a trait of interest is phenotyped, develop a predictive model based on either presence/absence data or an evolutionary rate profile that allows classification of unphenotyped species. 

We are also aiming to detect clusters and outliers. For example: 

  • Are there groups of species with similar evolutionary rate profiles? 
  • Do some genes behave very differently in one species than in other species in an otherwise similar cluster – and might that provide insight into regulation of phenotype in that species? 

Our approach

We will improve on current phylogenetic profiling approaches by: 

  • explicitly incorporating information about the phylogenetic distribution of phenotypic traits of interest to guide experimental design  
  • explicitly incorporating information about known modules of genes 
  • extending from presence/absence of genes to an evolutionary rate profile.