Genomic monitoring of the critically endangered kakapo using targeted nanopore sequencing of environmental DNA

We used environmental DNA to monitor one of the last surviving populations of the critically endangered kakapo (Strigops habroptilus). We established a metabarcoding protocol to identify the distribution of kakapo and other avian and mammalian taxa in a highly localized manner using soil samples. Harnessing targeted nanopore sequencing and the high-quality kakapo reference genome, we then extracted species-specific DNA from soil. We combined long read-based haplotype phasing with known individual genomic variation in the kakapo population to identify the presence of individuals, and were able to confirm the genomically informed identifications using detailed metadata on kakapo distributions. This study shows that individual identification is feasible through nanopore sequencing of environmental DNA, with important implications for future efforts in the application of genomics to the conservation of rare and elusive species, potentially expanding the application of environmental DNA research from monitoring species distribution to inferring fitness-related parameters such as genomic diversity, inbreeding, and adaptive potential.