Dept. of Mathematics,
Lehman College, CUNY

"Detecting and Correcting Bias in Phylogenetic Tree Inference"

Mar 17, 2021 Schedule:

Virtual Tea Time

03:00 to 03:30 PM Eastern Time (US and Canada)

Virtual Colloquium

03:30 to 04:30 PM Eastern Time (US and Canada)

Click Here to Join via Zoom

Abstract:

Phylogenetic tree inference is the problem of reconstructing a phylogenetic tree, which represents the evolutionary history of a set of organisms, from some genetic data, like DNA. Tree inference methods, like maximum likelihood and Bayesian MCMC, are known to exhibit bias, meaning they can produce trees with a tendency towards certain shapes or edge lengths. We propose a comprehensive method for detecting bias in tree shape and/or edge lengths using the Billera-Holmes-Vogtmann (BHV) tree space framework. The BHV tree space is a non-positively curved (or CAT(0)) geometric space containing all possible trees for a given set of leaves. Our method employs a logarithm map to the tangent space, yielding a Euclidean space in which to perform analysis. We show that different tree inference methods have different biases and suggest methods for correcting them.