scPhyloX: Tracing the Evolution of Cells One Lineage at a Time

Researchers have introduced scPhyloX, a novel computational framework that brings phylodynamic inference into the single-cell era by modeling cellular evolution through lineage tracing. By reconstructing time-resolved phylogenetic trees from single-cell data, scPhyloX infers dynamic processes such as stem cell differentiation, tissue development, and tumor evolution. Notably, it captures time-varying biological parameters, allowing for a nuanced view of somatic selection and clonal dynamics. In real-world applications, scPhyloX uncovered stem cell population overshoot in Drosophila organs, age-related expansion of hematopoietic progenitors in humans, and Darwinian selection of tumor subclones in early colorectal cancer. This tool opens new avenues for understanding the evolutionary underpinnings of development and disease.