Gene Ontology

We performed a functional analysis for genes with LoF variants identified in SNPeff and based on Jane’s annotation (Table S6). We obtained the gene IDs associated with each LoF allele identified in the SNPeff analysis from our functional annotation. We then assessed the functional classification of these LoF variants with a Gene Ontology analysis in Panther v16.0⁷⁰ using chicken as reference set. Because identifying mutational load in birds that survived the peak of the 1990s bottleneck is highly valuable to guide future conservation actions for kākāpō, we performed this analysis only on survivor birds (i.e., 35 Stewart Island birds and Richard Henry; Tables S6 and S7).