Using Genotype Abundance to Improve Phylogenetic Inference

Overview

Journal Mol Biol Evol

Publisher Oxford University Press

Specialty Biology

Date 2018 Feb 24

PMID 29474671

Citations 35

Authors

William S Dewitt 3rd

Luka Mesin

Gabriel D Victora

Vladimir N Minin

Frederick A Matsen 4th

Affiliations

Soon will be listed here.

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.

Citing Articles

Leveraging DAGs to improve context-sensitive and abundance-aware tree estimation.

Dumm W, Ralph D, DeWitt W, Vora A, Araki T, Victora G Philos Trans R Soc Lond B Biol Sci. 2025; 380(1919):20230315.

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New generalized metric based on branch length distance to compare B cell lineage trees.

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Isotype-aware inference of B cell clonal lineage trees from single-cell sequencing data.

Weber L, Reiman D, Roddur M, Qi Y, El-Kebir M, Khan A Cell Genom. 2024; 4(9):100637.

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Covalent penicillin-protein conjugates elicit anti-drug antibodies that are clonally and functionally restricted.

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Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels.

Iglhaut C, Pecerska J, Gil M, Anisimova M Mol Biol Evol. 2024; 41(7).

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