TiDeTree: a Bayesian phylogenetic framework to estimate single-cell trees and population dynamic parameters from genetic lineage tracing data

Abstract

The development of organisms and tissues is dictated by an elaborate balance between cell division, apoptosis and differentiation: the cell population dynamics. To quantify these dynamics, we propose a phylodynamic inference approach based on single-cell lineage recorder data. We developed a Bayesian phylogenetic framework—time-scaled developmental trees (TiDeTree)—that uses lineage recorder data to estimate time-scaled single-cell trees. By implementing TiDeTree within BEAST 2, we enable joint inference of the time-scaled trees and the cell population dynamics. We validated TiDeTree using simulations and showed that performance further improves when including multiple independent sources of information into the inference, such as frequencies of editing outcomes or experimental replicates. We benchmarked TiDeTree against state-of-the-art methods and show comparable performance in terms of tree topology, plus direct assessment of uncertainty and co-estimation of additional parameters. To demonstrate TiDeTree’s use in practice, we analysed a public dataset containing lineage data from approximately 100 stem cell colonies. We estimated a time-scaled phylogeny for each colony; as well as the cell division and apoptosis rates underlying the growth dynamics of all colonies. We envision that TiDeTree will find broad application in the analysis of single-cell lineage tracing data, which will improve our understanding of cellular processes during development.