AUGIST is a package for Mesquite that contains a variety of modules for explicitly dealing with uncertainty associated with various aspects of evolution.
It originally only contained modules for species tree inference, but has expanded to accommodate phylogenetic uncertainty in ancestral state estimation and discordance between gene trees and species trees.
Inferring species trees
There is inherent uncertainty when gene trees - some relationships are characterized by high confidence, while others may have little support. I developed an approach to explictly incorporation this variation in confidence by sampling genealogical relationships from a distribution that reflected the support values in differents part of the tree (Oliver 2008).
Dual trait evolution
While investigating the evolution of sexual dimorphism in butterflies, I designed an approach that estimates frequency of transition types across a distribution of trees, rather than using a single tree. Variation in the confidence of particular clades is thus incorporated into analyses of trait evolution (Oliver & Monteiro 2011).
There has been a long-held assumption that divergences in deep evolutionary history will not be characterized by discordance between gene trees and species trees. Modeling the coalescent process for such divergences, I found little support for this assumption. Discordance is indeed likely at ancient divergences, and will be more likely as the number of species sampled from a clade increase (Oliver 2013).
- Oliver, J.C. 2008. AUGIST: Inferring species trees while accommodating gene tree uncertainty. Bioinformatics 24:2932-2933. doi: 10.1093/bioinformatics/btn556
- Oliver, J.C. 2013. Microevolutionary processes generate phylogenomic discordance at ancient divergences. Evolution. doi: 10.1111/evo.12047
- Oliver, J.C. and A. Monteiro. 2011. On the origins of sexual dimorphism in butterflies. Proceedings of the Royal Society B. 278:1981-1988. doi: 10.1098/rspb.2010.2220