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

Area of Science:

• Conservation genomics
• Population genetics
• Wildlife conservation

Background:

• Genomic approaches are crucial for endangered species management.
• The impact of sequencing methods on detecting inbreeding has been overlooked.
• Long-term small populations can affect individual fitness.

Purpose of the Study:

• Compare whole-genome and reduced-representation sequencing for inbreeding detection.
• Assess the effects of inbreeding on kākāpō reproductive success.
• Evaluate how sequencing choice influences runs of homozygosity (ROH) identification.

Main Methods:

• Sequencing 148 kākāpō individuals using whole-genome and reduced-representation approaches.
• Analyzing runs of homozygosity (ROH) to estimate genome-wide inbreeding (FROH).
• Correlating inbreeding estimates with female reproductive success (egg hatching).

Main Results:

• Both sequencing methods yielded comparable FROH estimates.
• Consistent effects of inbreeding on egg hatching success were observed.
• Whole-genome sequencing allowed chromosome-level analysis, showing no strong chromosome-specific effects.

Conclusions:

• Reduced-representation sequencing can detect inbreeding depression in wild populations.
• Kākāpō inbreeding depression appears widespread across chromosomes, not localized.
• Whole-genome sequencing enhances precision of genome-wide inbreeding estimates.