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Are you my father? Population-wide genome analysis confirms kākāpō parentage

Having a whole genome sequence has opened the possibilities for understanding the health and fertility of kākāpō - one of New Zealand’s most critically-endangered species, and now it’s helped to confirm parentage.

Unusual mating biology complicates paternity assignment

Many birds mate for life, which makes tracing lineages straightforward, but that’s not the case for kākāpō; they are nocturnal and solitary, many female kākāpō mate with two or three males, and males have no part in incubation or rearing.

This complex mating system makes it hard to confirm paternal identity based on observations alone.


Photo: Kākāpō by Andrew Digby

Understanding parentage is important to conservation; it helps plan breeding programmes to avoid inbreeding and maintain genetic diversity. Genetic diversity is essential to buffer a population to the impact of changing environments and resist disease. Low numbers of breeding kākāpō confined to a small area of Aotearoa means they have already lost considerable genetic diversity, and fertility is a problem.

Parentage testing, which identifies parents and offspring based on shared similarities in their DNA, is therefore important to understand how to manage a breeding programme and preserve critical DNA variation.

Fortunately, the kākāpō has the genome of almost an entire living population sequenced (169 in total). This is thanks to the Kākāpō125+ project, a collaboration between DOC, Genetic Rescue Foundation, Ngāi Tahu, Science Exchange,, University of Otago, Duke University, Rockefeller University and Genomics Aotearoa.

That genome information was used to confirm the paternity of kākāpō chicks.

A species-wide approach to genomics

Genomes are complete datasets of DNA. Most of genetic information is common across all of the populations of a species, it’s the genetic variants that make individuals unique, and populations diverse. Parentage testing traditionally uses a few very variable parts of the genome (microsatellites) to identify relationships between individuals.

University of Otago PhD student Marissa Le Lec took a different route, making use of the kākāpō population genomes to compare DNA variation between a chick and all the possible fathers in the rest of the population.

Using computational methods, she looked at 130,000 genetic variants from the whole genome sequence to find the crucial DNA data common to parent and chick.

This is the first time this whole genome sequence data has been used to establish kākāpō parentage. The method confirmed one of the chicks produced via artificial insemination is the offspring of a Sinbad, a male kākāpō who had not yet bred. this way, the technique also verified success of the pioneering kākāpō artificial insemination programme.

The value of genomics approaches for conservation and mating systems research

The work has highlighted the value of using genome sequence datasets and genomic approaches to understand the hidden parentage of a species with a complex mating system.

This level of genetic information also allows difficult problems to be understood and questions to be answered in more depth in conservation, to estimate population structure and genetic diversity, as well as infertility and disease resistance.

Adapting and developing new genomic approaches such as this paves the way for analysing genomes from other species. For kākāpō conservation, the genome data will now be used to support accuracy and consistency in managed matings, which are crucial to ensure all adults are represented in future generations to minimise further genetic loss. It will also help to understand the diseases affecting kākāpō, particularly aspergillosis.