Bacterial diet influences mutation rate in Pristionchus pacificus

Mutation is a major force of evolution and its accumulation is suggested to be influenced by environmental and genetic factors in both unicellular and multicellular species. While ample of evidence showed an effect of temperature on mutation rate, the influence of diet is less well characterized, especially in multicellular organisms. Here, we present mutation accumulation (MA) rate differences for the same nematode species comparing a variety of bacterial diets. MA rates were estimated from whole-genome sequencing data of MA lines of different natural isolates of the free-living nematode Pristionchus pacificus on various bacterial diets isolated from Pristionchus-associated environments. Average single-nucleotide mutation rates varied between 1.69 × 10-9 and 2.23 × 10-9 nucleotide site-1 × generation-1, whereas the average insertion rates varied between 1.53 × 10-10 and 2.90 × 10-10 nucleotide site-1 × generation-1 and the average deletion accumulation rates varied between 3.01 × 10-10 nucleotide site-1 × generation-1 and 4.51 × 10-10 nucleotide site-1 × generation-1. We observed around a 1.4-fold mutation rate difference among groups on bacterial diets. Despite mutation-rate differences, the mutation spectra are largely unchanged. These results suggest that bacterial diet influences MA rate without drastically changing other mutational features.