As genomics technology has continued to advance, so too has our ability to map and understand key kākāpō survival traits.
The kākāpō is a unique, critically endangered parrot living in the wild only on predator-free islands in Aotearoa. Intensive conservation management saw the population recover from a low of 51 individuals in 1995 to about 150 adults in 2019. Sequencing of the genomes of every kākāpō was completed in late 2018 through the kākāpō 125+ project, established by the Department of Conservation with funding organised by the Genetic Rescue Foundation.
Our work
In 2022 the Genomics Aotearoa High Quality Genomes and Population Genomics (HQG+PG) project produced a second genome for kākāpō, with a total of 169 inidivudal datasets.
Dr Joseph Guhlin and his team from around the country developed state-of-the-art methods to detect variation among individuals to a quality that meets the rigorous standards of human genome mapping.
This new high-quality variant genome offers researchers the tools needed to identify specific genetic characteristics that are critical to species survival. It linked a range of variants to physical differences among individuals, producing a wealth of information on genetic variations affecting growth, fertility, embryo survival, and clutch size. This new knowledge has:
- Revealed genetic contributions to egg shape, which provides a baseline test to validate that methods are appropriate for the small sample size and agrees with findings for other bird species.
- Identified variants of interest to make it easier to identify chicks most at-risk from other diseases and conditions, such as aspergillosis susceptibility and egg fertility.
- Helped understand how genetics contribute to early growth. This understanding can lead to more targeted monitoring, the potential for intervention if a chick is not thriving, and prioritising chicks for special care.
The implications
The kākāpō high-quality genetic variant resource provides a much-needed foundation for understanding and translating genomics for future generations of these precious birds.
The depth of genetic information now available enables conservation biologists to use genomics as a practical tool to estimate population structure and genetic diversity, as well as respond to problems like infertility and diseases.
“This new tool assists conservationists to identify potential illness at an earlier stage if a chick deviates from their expected growth rate,” Lydia Uddstrom, Veterinary Advisor, Kākāpō at the Department of Conservation said.
The high-quality variant dataset is available for kākāpō researchers to use through the Aotearoa Genomic Data Repository.
The variant calling pipeline developed for kākāpō is also being further developed into reusable code for all researchers to use. Adapting and developing these new genomic approaches therefore has promise for managing other threatened species in more powerful ways than ever before.
Read more about High Quality Genomes and Population Genomics here