Time-resolved, integrated analysis of clonally evolving genomes

Abstract

Clonal genome evolution is a key aspect for parthenogenetic species and cancer. While many studies describe precise landscapes of clonal evolution in cancer, few studies determine the underlying evolutionary parameters from molecular data, and fewer integrate theory with data. We derived theoretical results linking mutation rate, time, expansion dynamics, transition to recurrence, and survival. With this, we inferred time-resolved estimates of evolutionary parameters from mutation accumulation, mutational signatures and selection. Using this framework we traced the speciation of the rapidly emerging and invasive marbled crayfish to a time window between 1947 and 1996, which is consistent with biological records. In glioblastoma samples, we determined tumor expansion patterns, and tumor cell survival ratio at resection. Interestingly, our results suggest that the expansion pattern in the primary tumor is predictive of the progress and time to recurrence. In addition, tumor cell survival was always higher after resection and was associated with the expansion pattern and time to recurrence. We further observed selection events in a subset of tumors, with longer and purifying-only selection phases in recurrent tumors. 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.

Paradigm shifts in animal epigenetics: Research on non‐model species leads to new insights into dependencies, functions and inheritance of DNA methylation

“…This apomictic parthenogenetic all‐female crayfish evolved from a single female of the Floridian slough crayfish, Procambarus fallax , by autotriploidization about 30 years ago. [ 37,38 ] It was discovered in the German aquarium trade in 1995 [ 39 ] and was distributed from there across the world. Releases in the last 20 years have led to the establishment of numerous populations in tropical to cold‐temperate biomes in more than 20 European, African and Asian countries.…”

Epigenetic ecotypes in animals: persistent environmental adaptation in the absence of genetic variation

“…The marbled crayfish, Procambarus virginalis , is another good example of environmental adaptation by epigenetic phenotypes. This apomictic parthenogenetic all-female crayfish evolved from a single female of the Floridian slough crayfish, Procambarus fallax , by autotriploidization a few decades ago (Vogt et al, 2008(Vogt et al, , 2015(Vogt et al, , 2018(Vogt et al, , 2019Martin et al, 2010Martin et al, , 2016Vogt, 2020b;Legrand et al, 2021). It first appeared in the German aquarium trade in 1995 and was distributed from there across the world.…”