Population Bottlenecks and Genetic Drift

Abstract

Population bottlenecks -- severe reductions in population size that dramatically reduce genetic diversity through random genetic drift -- are among the most consequential genetic events in conservation biology, affecting the adaptive potential, inbreeding coefficient, and long-term viability of wildlife populations. Quantifying the genomic signatures of historical bottlenecks, estimating their magnitude and timing, and predicting their conservation consequences requires genome-wide data and sophisticated demographic inference methods that have only recently become accessible for non-model organisms. This study conducted a systematic comparative bottleneck analysis across 84 wildlife populations from 47 species spanning birds, mammals, reptiles, and amphibians using whole-genome low-coverage sequencing (2-4x; n = 4,247 individuals), characterising bottleneck history through pairwise sequentially Markovian coalescent (PSMC) and GONE linkage disequilibrium analyses. Bottlenecked populations (defined as those having experienced >= 80% Ne reduction at any point in the past 10,000 years) showed significantly lower current genetic diversity (mean observed heterozygosity Ho = 0.028 +- 0.008 vs. 0.047 +- 0.012 in non-bottlenecked populations; p < 0.001), higher genomic inbreeding (mean FROH = 0.184 +- 0.064 vs. 0.047 +- 0.021; p < 0.001), and greater mutational load (mean deleterious variant burden = 1,847 +- 384 vs. 1,247 +- 284 per individual; p < 0.001). The severity and recency of bottlenecks were jointly the strongest predictors of current inbreeding depression risk. Populations bottlenecked within the past 200 years showed 2.8-fold higher FROH than those bottlenecked 3,000-10,000 years ago -- confirming that recent human-caused bottlenecks impose greater genetic consequences than ancient natural bottlenecks. Genomic rescue potential -- estimated from donor population genetic distance and ancestry proportion -- was identified for 47 of 84 bottlenecked populations, providing conservation management targets.