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Wild Genomes: Conservation Genomics Of New Zealand’s Largest Flightless Rail

By January 11, 2021January 20th, 2021Wild Genomes

This post is written by Dr. Lara Urban, PI for the takahē project, as part of our Wild Genomes banking and sequencing program.

Fieldwork to count the number of wild takahē takes place in the remote Murchison Mountains where the species was rediscovered in 1948.

A blood sample is taken from the takahē chick “Kohika.”  Her DNA will serve as the basis of the reference genome. Kohika means “ancestor” in Māori, a name that acknowledges her important role in the conservation of the entire species.

A party of juvenile takahē. Blood samples of the 84 to-be-sequenced individuals were collected in collaboration with the Takahē Recovery Programme as an integral part of their routine health monitoring.

A truly wild takahē. This curious female has hooked up with Moss, a male takahē recently released into the wild. Takahē are very much like humans, mostly monogamous, but changing their partners from time to time.

The takahē (Porphyrio hochstetteri) has literally risen from the dead. This flightless rail species, which is endemic to New Zealand, was considered extinct until the rediscovery of a remnant population in the remote Murchison Mountains in 1948. This was considered by some to be “one of the greatest ornithological moments in history.”  The Takahē Recovery Programme was subsequently initiated and captive rearing, health monitoring, translocations, and control of invasive species that threaten the takahē through competition for food (deer) and predation (stoat), was begun. The takahē, however, remains highly endangered.

I, therefore, seek to establish and apply a suite of genomic tools to rapidly accelerate and transform takahē recovery. We are currently producing an annotated platinum quality reference genome in collaboration with the Vertebrate Genomes Project and Revive & Restore, and are undertaking the genome sequencing of altogether 84 individuals that are representative of the extant population.

We propose to use these data to leverage cutting-edge genomic approaches to investigate and understand the genomic, phenotypic, microbial, and environmental factors that affect takahē fitness, persistence, and adaptive potential. Insights from such analyses will inform decisions concerning managed breeding, health monitoring, and translocations of the takahē, to increase genetic diversity and enhance fitness traits such as fertility, offspring survival, and disease resistance amongst the species.

The only wild takahē population continues to persist in the Murchison Mountains (N<200), with some individuals recently released to the iconic Kahurangi National Park. The remaining takahē are maintained in sanctuaries. My collaboration with the Takahē Recovery Programme includes health monitoring of the wild populations and number and distribution assessments of individuals. While this work includes arduous fieldwork through steep mountains, thick grassland, and freezing rivers, this is where the fun begins. While hiking through the amazing landscape is a reward in itself, this is where one can find the last truly wild takahe—which have never encountered humans and therefore approach us with curiosity.

In order to monitor the wild population in a non-invasive manner, we will trial novel approaches to obtain takahē genomic data from their faeces instead of their blood. This might allow us to gather information about takahē relatedness, inbreeding, and resilience without interfering with their lifestyle. Even more importantly, we will understand if any genetic diversity remains in the wild population that is not yet represented in the sanctuary populations.

The next critical step for takahē conservation is the establishment of more wild territories. We look forward to applying our genomic research to assist the takahē’s return to their ancient habitat, which will require a resilient species with reduced inbreeding effects and increased reproduction success.

The re-establishment of takahē across the New Zealand South Island would be a milestone in modern conservation, but also has important ecological ramifications for the tussock ecosystems this species inhabits. Tussock grasses are keystone species that provide important ecosystem functions, including prevention of soil erosion and flooding due to efficient water retention. Thus, as takahē numbers increase, so must the fragile New Zealand tussock ecosystems, leading to spill-over benefits for other threatened species such as falcon (Falco novaeseelandiae), mōhua (Mohoua ochrocephala), and kākā (Nestor meridionalis).

This project is a collaboration between Lara Urban and the Takahē Recovery Programme, Ngāi Tahu, the Kaitiaki Rōpū (guardian) of the species, the Vertebrate Genomes Project, and Revive & Restore. Key collaborators are Glen Greaves, Andrew Digby, Deidre Vercoe, Estelle Leask, Alana Alexander, Joanne Gillum, Neil Gemmell, Olivier Fedrigo and Erich Jarvis.