Supplemental Material for Walker et al., 2023
Supplemental Materials for the manuscript,
Parallel evolution of the G protein-coupled receptor GrlG and the loss of fruiting body formation in the social amoeba Dictyostelium discoideum evolved under low relatedness.
Abstract: Aggregative multicellularity relies on cooperation among formerly independent cells to form a multicellular body. Previous work with Dictyostelium discoideum showed that experimental evolution under low relatedness profoundly decreased cooperation, as indicated by the loss of fruiting body formation in many clones and an increase of cheaters that contribute proportionally more to spores than to the dead stalk. Using whole-genome sequencing and variant analysis of these lines we identified 38 single nucleotide polymorphisms (SNPs) in 29 genes. Each gene had one variant except for grlG (encoding a G protein-coupled receptor), which had ten unique SNPs and five structural variants. Variants in the 5' half of grlG — the region encoding the signal peptide and the extracellular binding domain — were significantly associated with the loss of fruiting body formation; the association was not significant in the 3' half of the gene. These results suggest that the loss of grlG was adaptive under low relatedness and that at least the 5' half of the gene is important for cooperation and multicellular development. This is surprising given some previous evidence that grlG encodes a folate receptor involved in predation, which occurs only during the single-celled stage. However, non-fruiting mutants showed little increase in a parallel evolution experiment where the multicellular stage was prevented from happening. This shows that non-fruiting mutants are not generally selected by any predation advantage, but rather by something – likely cheating – during the multicellular stage.
Contents: FileS1 contains all supporting information and supplemental figures S1 - S3. FileS2 contains supplemental tables S1 - S7. FileS3 is a compressed folder containing three VCF files, each containing all variant calls that survived hard filtration (before manual review) from each of the three variant callers (GATK, Freebayes and Delly). FileS4 is a .txt file that contains the Dictyostelium discoideum gene annotations downloaded from NCBI on 10-25-19.