Estimate of the mutation rate in the endangered Devils Hole pupfish provides support for the drift-barrier hypothesis at an outlying extreme

Mutation rates vary by three orders of magnitude across eukaryotes. The drift-barrier hypothesis proposes that drift overwhelms selection for lower mutation rates in small populations, leading to higher mutation rates over time due to gradual accumulation of mutator alleles. Here, we test this hypothesis in the smallest long-term isolated population in the world, the critically endangered Devils Hole pupfish (Cyprinodon diabolis). We estimated germline mutation rates in embryonic lethal and adult populations using autozygous segments caused by recent inbreeding events. Our estimate, 8.09 x 10-9 per base pair per generation, is significantly higher than the average rate for actinopterygian fishes of 5.97 x 10-9 (95% CI = 4.39 x 10-9 - 7.55 x 10-9) and is lower than expected but still consistent with predictions from the drift-barrier hypothesis of 1.23 x 10-8 (95% CI = 7.81 x 10-9 - 1.93 x 10-8), based on a recent meta-analysis of vertebrate mutation rates by Bergeron et al. (2023). We find that embryonic lethal individuals have a higher mutation rate than mature adults, potentially reflecting a segregating lethal mutator allele or damage to the cellular environment during embryo death. We also analyzed the mutational spectra of germline mutations and find that spectra between embryonic lethal and mature adults were similar, as is the spectra in Devils Hole pupfish and other fishes, despite differences in environmental temperature and oxygen stresses. Mutation rates in this critically endangered species provide new insights at one extreme into the mechanisms driving mutation rate variation across vertebrates.