Kavli Affiliate: Erich Jarvis
| Authors: Christopher C. Kyriazis, Stefanie Grosser, Yasmin Foster, Bryce Masuda, Alison M. Flanagan, Jennifer Balacco, Erin Datlof, Olivier Fedrigo, Giulio Formenti, Catherine E. Grueber, Jacqueline A. Robinson, Jolene T. Sutton, Alan Tracey, Jonathan M.D. Wood, Erich D. Jarvis, Oliver A. Ryder, Bruce C. Robertson and Aryn P. Wilder
| Summary:
Near-extinction events impose severe genomic bottlenecks that can have lasting fitness consequences, yet the specific mechanisms involved remain poorly understood. ‘Alalā, the endemic Hawaiian crow, narrowly avoided extinction when a conservation breeding program was founded from just nine individuals. Although the breeding program has since recovered to ∼120 birds, it remains plagued by egg hatching failure rates >50%. To investigate the impacts of this bottleneck on hatching failure and other fitness components, we generated a chromosome-level reference genome and resequenced 175 individuals, including 78 deceased embryos. Although long runs of homozygosity (ROH) >1Mb are abundant in ‘Alalā (mean FROH=0.32), associations between FROH and measures of survival and reproduction, including egg failure, were weak or nonexistent. Instead, we identify two recessive lethal haplotypes that together account for ∼20% of all hatching failures and have persisted in the population at high frequency (15-25%), hinting at impaired purifying selection. Eco-evolutionary simulation models demonstrate that these limited impacts of ROH and elevated recessive lethal allele frequencies are expected for a species that has endured a severe population bottleneck and exhibits modest levels of non-ROH heterozygosity. Our findings suggest that elevated recessive allele frequencies may be a broadly important consequence of population bottlenecks.