Using genotype abundance to improve phylogenetic inference

TL;DR

This paper introduces a new method that integrates genotype abundance data into phylogenetic inference, significantly enhancing the accuracy of evolutionary tree reconstruction through a stochastic process model validated by simulations and experimental data.

Contribution

It presents a novel approach combining genotype abundance with traditional phylogenetic methods, improving tree estimation accuracy.

Findings

Tree estimation improves substantially with abundance data.

Validated method through extensive simulations.

Confirmed effectiveness with experimental single-cell data.

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.