Genomic erosion across avian lineages in the context of their evolutionary history

Loss of genetic diversity threatens species survival, yet its dynamics and impacts can vary widely across species depending on their evolutionary histories, life-history traits, and demographic trajectories. To investigate these differences, we analyzed the genomes of 3 species that experienced extreme and well-documented population bottlenecks, the Mauritius parakeet, the Mauritius kestrel, and the pink pigeon, and compared them to 36 species spanning the avian phylogeny with varied IUCN Red List statuses. For each species, we assessed nucleotide diversity, genetic load, and inbreeding coefficients based on runs of homozygosity (FROH). We found a negative correlation between nucleotide diversity and FROH, but neither metric was a good predictor of the species' Red List status. Rather, the effective population size to census size ratio (Ne/Nc) showed a strong correlation to Red List status. Species with larger historical effective population sizes showed greater heterozygosity but carried a higher heterozygous load, highlighting the importance of historical demography for contextualizing species' vulnerability to genomic erosion. We also found significant differences in genetic load between taxonomic groups (parrots, pigeons, and falcons), possibly due to differences in life-history traits and demographic histories, underscoring the importance of interpreting genomic erosion dynamics in an evolutionary context. By anchoring our study on 3 evolutionarily divergent endangered species from Mauritius, we show how multispecies comparisons can contextualize extreme bottlenecks within a broader evolutionary framework, thereby identifying both general patterns of genomic erosion and species-specific vulnerabilities.