Genomic Architecture of Inbreeding Depression Associated With Hatching Failure in an Endangered Parrot

Conservation management of endangered species increasingly relies on genomic approaches to understand how long-term small population sizes affect the fitness of extant individuals. However, despite the growing investment in genomic resources by conservation programmes, the impact that sequencing methods have on the ability to detect inbreeding-related phenomena has been largely overlooked. Here, we compare the use of whole-genome and reduced-representation sequencing approaches in 148 individuals of the critically endangered parrot, the kākāpō (Strigops habroptilus), to assess inbreeding and its effects on female reproductive success. We explore how sequencing choice influences the identification of long stretches of homozygosity across the genome (runs of homozygosity, ROH), and compare the conservation implications of the results produced by each method. Both whole-genome and reduced-representation sequencing approaches provided comparable estimates of genome-wide inbreeding (F_ROH) and revealed consistent effects on egg hatching success, suggesting that reduced-representation sequencing is capable of detecting inbreeding depression in wild populations under certain conditions. Whole-genome sequencing enabled chromosome-level inbreeding analyses, which revealed no strong evidence of chromosome-specific effects beyond the genome-wide signal. These results suggest that inbreeding depression in kākāpō reflects small effects across many chromosomes rather than strong effects on only a few, and that the primary benefit of whole-genome sequencing lies in improving the precision of genome-wide inbreeding estimates rather than identifying chromosome-specific effects. Our findings highlight the distinct benefits of each sequencing approach in conservation, particularly within the context of resource limitations.