Confidence and truth in phylogenomics

Robert Lanfear⁰
(0) ANU

Abstract
How do you estimate a good phylogeny? How do you know if it’s right? And how should you communicate your uncertainty? Phylogenies form the backbone of our understanding of the tree of life, and are crucial for understanding and tracking emerging diseases. But any phylogeny is just an estimate, and all estimates are associated with uncertainty. Accurately measuring and communicating uncertainty in these estimates is almost as important as building the phylogeny itself. Using the right measures of uncertainty can help avoid meaningless arguments, and in the case of emerging diseases can have important consequences for population health and national and international policy.

In this talk I’ll introduce a range of methods for measuring and communicating uncertainty in phylogenetics (bootstraps, concordance factors, and branch parsimony scores), and illustrate how and why each should be used with examples from estimating the tree of life to the genomic epidemiology of SARS-CoV-2.