Groombridge, J. | bioRxiv Science

bioRxiv2025

Genomic erosion through the lens of comparative genomics

Loss of genetic diversity threatens species survival, yet the dynamics of such loss and species responses thereof can vary widely depending on their evolutionary histories, life-history traits and demographic trajectories. Comparative genomics offers a powerful framework to explore the dynamics of genomic erosion across species. Here, we analysed the genomes of three species -- the Mauritius parakeet, the Mauritius kestrel, and the pink pigeon -- that experienced extreme and well-documented population bottlenecks. We compared them to 36 species spanning the avian phylogeny, with varied IUCN Red List statuses to investigate the genomic consequences of their demographic collapses. For each species, we assessed nucleotide diversity, genetic load, and runs of homozygosity (ROH), alongside genome synteny and transposable elements. We found a negative correlation between nucleotide diversity and ROH, but neither metric was a good predictor of the species Red List status. Rather, the population effective to census size ratio showed a strong correlation to Red List status. Moreover, species with larger historical effective population sizes showed greater heterozygosity but carried a higher heterozygous load, highlighting the importance of historical demography to assess species vulnerability to genomic erosion. We found significant differences in homozygous load between taxonomic groups of our target species, possibly due to differences in life-history traits and demographic histories. Genome structure analyses revealed differences in transposable elements and genomic rearrangements between groups, suggesting their potential role in shaping genome architecture and adaptive potential across species. Our findings underscore the value of multispecies comparisons in understanding the evolutionary dynamics of genomic erosion and its relevance for biodiversity conservation.

genomics↗

bioRxiv2022

Genetic load and adaptive potential of a recovered avian species that narrowly avoided extinction

High genetic diversity is often a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the IUCN Red List in 2020. By comparing historical, pre-bottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after the demographic recovery. We show that the proportion of severely deleterious mutations has reduced in modern individuals, but mildly deleterious mutations have remained unchanged. Computer simulations suggest that the Seychelles paradise flycatcher avoided extinction and recovered due to its long-term small Ne. This reduced the masked load and made the species more resilient to inbreeding. However, we also show that the chronically small Ne and the severe bottleneck resulted in very low genetic diversity in the modern population. Our simulations show this is likely to reduce the species adaptive potential when faced with environmental change, thereby compromising its long-term population viability. In light of rapid global rates of population decline, our work highlights the importance of considering genomic erosion and computer modelling in conservation assessments

evolutionary biology↗