Time-resolved, integrated analysis of clonally evolving genomes

Clonal genome evolution is a key aspect for parthenogenetic species and cancer. While many studies describe precise landscapes of clonal evolution in cancer, few determine the underlying evolutionary parameters from molecular data, and even fewer integrate theory with data. We derived theoretical results linking mutation rate, time, expansion dynamics, and clinical parameters. We then inferred time-resolved estimates of evolutionary parameters from mutation accumulation, mutational signatures and selection. Using this framework, we traced the speciation of the clonally evolving marbled crayfish population to a time window between 1986 and 1990, which is consistent with biological records. We also used our framework to analyze a published dataset of glioblastoma samples, which identified tumor expansion patterns, cell survival at resection, and selective forces as important factors for tumor development. In conclusion, our framework allowed a time-resolved, integrated analysis of key parameters in clonally evolving genomes, and provided novel insights into the evolutionary age of marbled crayfish and the progression of glioblastoma.