Using Genotype Abundance to Improve Phylogenetic Inference. (20th February 2018)

• Record Type: Journal Article
• Authors: DeWitt, William S; Mesin, Luka; Victora, Gabriel D; Minin, Vladimir N; Matsen, Frederick A
• Editors: Takahashi, Aya
• Is Part Of: Molecular biology and evolution. Volume 35:Number 5(2018)
• Page Start: 1253
• Page End: 1265
• Publication Date: 2018-02-20
• Subjects: phylogenetics -- single-cell sequencing -- immunology; Molecular biology -- Periodicals; Molecular evolution -- Periodicals; Evolution, Molecular -- Periodicals; Molecular Biology -- Periodicals; 572.8
• DOI: 10.1093/molbev/msy020
• Languages: English
• ISSNs: 0737-4038

Abstract

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.