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Kākāpō in good genetic health despite inbreeding

Analysis of almost 50 kākāpō genomes has found the current population on Rakiura/Stewart Island is more in-bred – but shows fewer harmful mutations – than a now-extinct mainland population.

One explanation is that Rakiura kākāpō may have “purged” more harmful mutations than their mainland relatives, from whom they separated around 10,000 years ago. The international research team, which includes New Zealanders, says their analysis shows small populations can survive even when isolated for hundreds of generations.

The SMC asked experts to comment on the research.

Dr Ang McGaughran, Senior Lecturer, Te Aka Mātuatua – School of Science, University of Waikato, comments:

“I got really excited when I saw just the title of this paper. And, upon reading it, I wasn’t disappointed! It’s got a little bit of everything: a focus on a precious taonga species (the kākāpō), the use of genome sequencing to understand the current status of this endangered bird, ‘museomics’ – the use of historical specimens – to ‘go back in time’ and tell us about the kākāpō’s evolutionary history, and the finding of some cool results that have strong conservation implications and challenge our way of thinking in the evolutionary space.

“We expect small, inbred populations to be at high risk of extinction, but these authors found that actually, these small populations have less mutations of negative effect than anticipated. This challenges our expectations and means that small populations can sometimes be better at coping with the associated genetic effects than we’d thought.

“Another key finding is that kākāpō on Stewart Island likely became isolated there before it separated from the South Island – we had previously thought that humans introduced the birds to Stewart Island in the last ~500 years. But this tells us that instead, kākāpō have a longer independent history in the South of New Zealand than expected, adding another line of evidence to the authors’ hypothesis that small populations can survive well, even in isolation and over long time periods.

“Just as the COVID pandemic has outlined the strength of genome sequencing for telling us about relationships among viral strains, this paper emphasises the importance of genomic tools in telling us about how treasured birds of Aotearoa are related to each other. It also provides us with vital information about how to proceed with future conservation efforts to give the kākāpō the best chance of survival into the future. I hope that this paper paves the way for future genomic work on endangered species, both in New Zealand and beyond.”

No conflict of interest

Dr Phillip Wilcox, Senior Lecturer in Quantitative Genetics, Kaiawhina Māori, Department of Mathematics and Statistics, and Affiliate Faculty, Bioethics Centre, University of Otago, comments:

“In the context of Western Science and use of genomics for conservation of a rare and critically endangered unique species, this work demonstrates that island populations may have improved resilience owing to mild population bottlenecks purging deleterious genetic load. As the authors point out, similar results have been observed in other studies. Collectively, these results have implications for structuring breeding populations and prioritising specific lineages for managing deleterious impacts of inbreeding.

“However, from a context of indigenous knowledge and indigenous utilisation of genomics, there is no evidence of any deliberative or thorough effort to obtain and incorporate mātauranga Māori (traditional Māori knowledge) nor are the results interpreted in terms of application by takata tiaki (Māori environmental managers/guardians), thus this research sits entirely within – and for – a monocultural context. The study is therefore of limited value to Māori and reflects a monocultural bias in the conservation genomics sub-discipline. Ironically, access to data generated in this project (as stated in the ‘data and code availability’ section) require these aspects to be covered (including benefit to Māori) – but there is no evidence of addressing these in the study reported here.”

Conflict of interest statement: “I work in the same University (but not departments) as some of the authors and receive funding from an entity (Genomics Aotearoa) that one of the authors (Dearden) is the current Director of.”

Karaitiana Taiuru (Ngāi Tahu, Ngāti Kahungunu, Ngāti Rārua), Research Fellow/Pou Tikanga at the University of Otago, Christchurch Campus, comments:

Note: Karaitiana Taiuru is a former: Ngāi Tahu Development Corporation staff member 2002-04, Te Rūnanga o Ngāi Tahu – Koukourarata Alternate Representative 2016-2018, Contractor at Arowhenua Runanga 2018.

“As with the Tuatara genome research, this is another Taonga Species to Māori that has been researched without Te Tiriti and Māori Data Sovereignty considerations and it ignores mātauranga Māori. In addition, the lack of Iwi consultation and engagement is alarming, with primary Iwi and manawhenua not mentioned.

“The benefits of science/academia working together with Māori and Iwi, recognising mātauranga Māori, is essential to developing western science and for western science to assist mātauranga Māori. In this research, mātauranga Māori may have provided important information about the harmful mutations in current species as opposed to the now-extinct populations and confirmed mātauranga Māori pertaining to the sacred Kākāpō.

“This research is another exciting genome milestone for the research community, but also another lost opportunity for Iwi and Māori to benefit from any derived traditional knowledge, commercial, or medical products.”

No conflicts of interest declared.

Professor Peter Dearden, University of Otago, comments:

Note: Professor Dearden is a co-author on this paper. The SMC NZ asked Prof Dearden to respond to some of the concerns raised by other experts in their comments.

“The publication of the Dussex et al paper contains analysis of the genome of the Kākāpō Jane and preliminary analysis of a population dataset of living and ancient kākāpō genomes. Genomics Aotearoa played a role in providing data to help annotate genes in Jane’s genome. That data was provided only after we had support from mana whenua and DOC to do so. Genomics Aotearoa also holds the genomics data from the living kākāpō population on behalf of DOC and mana whenua. This is detailed in the Resource Availability section of the manuscript which indicates that this data remains under the stewardship of mana whenua, and access is controlled through a committee of mana whenua and DOC.”

Conflict of interest statement: “I am an author on this paper and Director of Genomics Aotearoa.”

Deidre Vercoe, Operations Manager, Kākāpō/Takahē team, Department of Conservation, comments:

Note: Deidre Vercoe is a co-author on this paper. The SMC asked Vercoe to respond to some of the concerns raised by other experts in their comments.

“The Kākāpō Recovery Programme (KRP) has been primarily involved in this publication through the provision of the population genomic data. The KRP was a principal partner in the Kākāpō125+ project, which sequenced the genomes of all living and recently deceased kākāpō with the aim of furthering kākāpō conservation. These data are available to researchers upon application, provided their intended use meets the requirements of Te Rūnanga o Ngāi Tahu and the Department of Conservation. DOC worked closely with Ngāi Tahu to establish this joint decision-making process regarding access to the data, to safeguard Māori data sovereignty, and to ensure the data are used appropriately from the perspective of mātauranga Māori and for the benefit of kākāpō conservation. Identifying the genetic basis for issues which threaten the future of kākāpō, such as disease and the infertility addressed in this publication, was a primary motivation for this genomic project. The KRP pursues a strong active partnership with Ngāi Tahu, to ensure that mana whenua have a lead role in restoring the mauri of this taonga.”

No conflicts of interest.

Associate Professor Tammy Steeves, Associate Professor in Conservation Genomics, School of Biological Sciences, University of Canterbury, comments:

“The publication of the first high-quality reference genome for kākāpō – Jane’s genome – alongside 35 genomes from the remnant population on Stewart Island and 14 genomes from two extinct populations on the mainland provides invaluable insights regarding the impact of severe population bottlenecks in critically endangered species.

“The finding that Richard Henry – the sole survivor of the now extinct Fiordland population – harbours deleterious mutations not found in the Stewart Island population requires careful consideration by Kākāpō Recovery, especially because the impact of these deleterious mutations on survival and reproduction in kākāpō is unknown.

“One of the main challenges facing kākāpō is high rates of hatching failure – 61 per cent of their eggs fail to hatch, and of these 73 per cent show no sign of development. Dussex and colleagues underscore the need to further investigate the genetic basis of reproductive traits like high hatching failure in kākāpō.

“Given that all genomic data obtained from taonga species in Aotearoa New Zealand have whakapapa and are taonga in their own right, I am delighted to see that the kākāpō genomes generated as part of the Kākāpō125+ project and used by Dussex et al. are being managed in accordance with the CARE Principles for Indigenous Data Governance: Collective Benefit, Authority to Control, Responsibility, and Ethics.”

Conflict of interest statement: “I’m a member of the Kākāpō125+ Consortium. My team and I provide conservation genomic advice to a number of Department of Conservation recovery groups, specialist groups and technical advisory groups to enhance the recovery of some of Aotearoa New Zealand’s most threatened species.”

Dr Emma Carroll, Rutherford Discovery Fellow, University of Auckland, comments:

“New genomic research on kākāpō provides both good and bad news for the species’ conservation and future. A legacy of long-term small population size, kākāpō that historically lived on Rakiura Stewart Island have low genetic diversity. This is often associated with poor outcomes for both populations and species as harmful gene variants or mutations can become more common when genetic diversity is low.

“What is positive is that there is evidence that individuals from the Rakiura population ‘purged’ or expelled some of these harmful mutations from their genomes over time. Whether this is something that the current population, which are descendants of both mainland and Rakiura kākāpō, can continue to do remains to be seen.

“The detailed genomic information on individual kākāpō produced by this work will provide useful information for conservation, for example, guiding the breeding programme and helping to identify which kākāpō need particular attention due to mutations linked with reproductive and immune system problems.”

No conflict of interest.

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