2017/08/31 by William S. DeWitt, William S. DeWitt III, Luka Mesin +4 · 1 voice
Biochemistry, Genetics and Molecular Biology · Immunology and Microbiology · #Genomics and Phylogenetic Studies #Single-cell and spatial transcriptomics #T-cell and B-cell Immunology #q-bio.PE
paper · pdf · doi:10.1093/molbev/msy020
published as William S DeWitt, Luka Mesin, Gabriel D Victora, Vladimir N Minin, Frederick A Matsen; Using Genotype Abundance to Improve Phylogenetic Inference, Molecular Biology and Evolution, msy020, 20 February 2018
openalex publication_date 2018/02/20 · arxiv created 2018/04/06 · arxiv updated 2018/04/09 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
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.