Using genotype abundance to improve phylogenetic inference

Abstract

Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in phylogenetic inference. In this paper, we synthesize a stochastic process model with standard sequence-based phylogenetic optimality, and show that tree estimation is substantially improved by doing so. Our method is validated with extensive simulations and an experimental single-cell lineage tracing study of germinal center B cell receptor affinity maturation.

References in corpus (3)

• Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration
• Likelihood-based inference of B-cell clonal families
• The limitations of model-based experimental design and parameter estimation in sloppy systems

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