Using Genotype Abundance to Improve Phylogenetic Inference

Molecular Biology and Evolution
William S DeWittFrederick A Matsen

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 article, 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.

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Citations

Jun 7, 2020·International Immunology·Keisuke TonouchiYoshimasa Takahashi
Jun 4, 2020·Molecular Biology and Evolution·Veronika Boskova, Tanja Stadler
Nov 16, 2018·Frontiers in Immunology·Kristian Davidsen, Frederick A Matsen
Oct 23, 2019·Proceedings of the National Academy of Sciences of the United States of America·Kenneth B HoehnSteven H Kleinstein
Oct 30, 2020·Nature·Carla R NowosadGabriel D Victora

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Methods Mentioned

BETA
PCR
fluorescence-activated cell sorting
genotyping

Software Mentioned

BEAST
PHYLIP
dnapars
GCtree
OncoNEM
SCITE
ETE

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