Genomic and genetic tools for the helmeted honeyeater, Victoria’s endangered state bird

A team led by scientists from Monash University have completed a major milestone towards achieving the rescue of the critically endangered helmeted honeyeater. They have deciphered the bird’s genome and created a high-density genetic linkage map, thereby introducing new tools that will be helpful in conservation efforts.

You can read the GigaScience Data Note, presenting the genome and linkage map, here and a press release here .

For GigaBlog, two of the authors, Alexandra Pavlova and Paul Sunnucks, explain below in a bit more detail how genetics and genomics can contribute to the ongoing efforts to rescue the helmeted honeyeater. Also don’t miss the embedded videos with first author Diana Robledo-Ruiz, explaining why the “HeHo” is such a great system, how genetic rescue works, and what is so exciting about now having a full genome sequence and a genetic linkage map.


Why did you choose the helmeted honeyeater for sequencing?

The helmeted honeyeater is Victoria’s bird emblem. Occurring only in Victoria, Australia, this rare bird is subject to an exceptionally broad and deep array of conservation approaches, including a rare case of genetic rescue from a neighboring subspecies.

The helmeted honeyeater is a distinct subspecies of a widely distributed species – the yellow-tufted honeyeater. The bird’s range and populations contracted over the 200 years since non-indigenous humans came to Australia, until there were only ~50 of the birds left in the 1980s, at a single location at Yellingbo Nature Conservation Reserve.

The lead author on this paper, Diana Robledo-Ruiz, produced a short video explaining why the helmeted honeyeater (nicknamed HeHo by people involved with it) is a great study system:

Much has been done to restore this population, including habitat restoration, a captive breeding program at Healesville Sanctuary with release of captive-bred birds, supplementary feeding from 2012, and genetic rescue from 2019.

The latter intends to improve the health and fitness of the helmeted honeyeater by reducing inbreeding. Extensive field data collected over three decades revealed that the sole remaining helmeted honeyeater population experiences strong decline in health and fitness due to inbreeding, with the most inbred birds having only 10% fitness lifetime reproductive success of the least inbred ones (Harrisson et al 2019). Previous research showed that without adding new genetic variation, this bird will likely become extinct in the near future even if other threats to the population’s existence were removed (Harrisson et al 2016).

What exactly is “genetic rescue” and how do the genome sequence and linkage map help with this effort?

Genetic rescue is a conservation genetic approach to managing small, inbred populations, whereby genetic variation is added to the population to address genetic problems caused by human impacts.

In this award-winning video, Diana Robledo-Ruiz explains the general concept behind genetic rescue, which she adopted in her PhD:

Addition of genetically diverse individuals to the population helps to alleviate inbreeding and increase genetic diversity, which in turn equips the population with material for adaptation to changing environments.

A broad definition of genetic rescue includes any form of augmenting genetic variation with the purpose of increasing the genetic health of a population and improving its chances of avoiding extinction. Improved genetic health might encompass reversing inbreeding, replacing faulty genetic variants with better ones, and adding genetic variation that might be useful for future adaptation to changing conditions.

Because the helmeted honeyeater is the last population of its kind, genetic augmentation must come from a different subspecies. However, this kind of genetic mixing is not common: managers generally avoid crossing subspecies for fears of losing local adaptation and distinctiveness.
The genome sequence and the genetic map are important resources for truly understanding these processes at the genomic level and will be used to get the right balance between rescuing the helmeted honeyeater from extinction through inbreeding, while retaining unique features that make it a helmeted honeyeater.

What is rare about this assembly is its combination of being chromosome-length and having a linkage map. The latter was possible only because the population has been studied for so long. This combination of features will be central to our work going forward. In her recently submitted PhD thesis, Diana Robledo-Ruiz has trialled new analyses, requiring a good assembly with a linkage map, that will characterize which parts of the helmeted honeyeater genome are damaged by inbreeding, and which encode characteristics unique to this subspecies. This knowledge will help us to monitor the effects of genetic rescue on the genomes of the helmeted honeyeater and manage the ongoing rescue so that important unique features are not lost from this population.

Here Diana Robledo-Ruiz presents the genome and linkage map:

Which challenges did you have to overcome for the sequencing project?

Production of a high quality genome, its annotation and linkage maps required a collaborative effort of a large international team of researchers with diverse expertise, affiliated with 14 organizations from five countries. For example, researchers from Deakin Genomics Centre led initial sequencing and draft genome assembly, the international DNA Zoo Consortium led the Hi-C work transforming the draft genome into a chromosomal-length assembly, while the linkage map was generated by the Monash University team based on field data collection led by our collaborators from the Department of Environment, Land, Water and Planning.

Another challenge included collecting fresh tissue samples for DNA and RNA sequencing. This had to be done opportunistically, because killing members of a critically endangered species for research purposes would not be ethical. Because helmeted honeyeaters are closely monitored by a team of vets from our collaborators Zoos Victoria, we set up systems so that when a bird had to be euthanized because of suffering, fresh tissues would be sampled shortly after it was put down.

Anything else you’d like to mention?

The problems faced by the helmeted honeyeater are not unique, and solutions will be useful for other threatened species. For example, based on helmeted honeyeaters, we have already developed a novel analytical framework for designing and modifying breeding management strategies to counteract inbreeding (Robledo-Ruiz et al 2022).

Without the passion and commitment and work of hundreds of people and many organizations, the helmeted honeyeater would be extinct. This support includes state government, the Department of Environment, Land, Water and Planning (DELWP) and Zoos Victoria. Some individuals such as Bruce Quin of DELWP have devoted 30 years or more to conservation efforts of the species, and a highly effective community group, The Friends of the Helmeted Honeyeater, has provided a range of assistance for the conservation program for more than three decades. It is an inspiring case of people caring and making a real difference to biodiversity outcomes.

Read the GigaScience Data Note:

Diana A Robledo-Ruiz, Han Ming Gan, Parwinder Kaur, Olga Dudchenko, David Weisz, Ruqayya Khan, Erez Lieberman Aiden, Ekaterina Osipova, Michael Hiller, Hernán E Morales, Michael J L Magrath, Rohan H Clarke, Paul Sunnucks, Alexandra Pavlova 2022. Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater

Further reading:

Friends of Helmeted Honeyeater website:

Harrisson, K. A., M. J. Magrath, J. D. Yen, A. Pavlova, N. Murray, B. Quin, P. Menkhorst, K. A. Miller, K. Cartwright, and P. Sunnucks. 2019. Lifetime fitness costs of inbreeding and being inbred in a critically endangered bird. Current Biology 29:2711–2717.

Harrisson, K. A., A. Pavlova, A. Gonçalves da Silva, R. Rose, J. J. Bull, M. Lancaster, N. Murray, B. Quin, P. Menkhorst, M. J. L. Magrath, and P. Sunnucks. 2016. Scope for genetic rescue of an endangered subspecies though re-establishing natural gene flow with another subspecies. Molecular Ecology 25:1242–1258.

Robledo-Ruiz, D. A., A. Pavlova, R. H. Clarke, M. J. Magrath, B. Quin, K. A. Harrisson, H. M. Gan, G. Low, and P. Sunnucks. 2022. A novel framework for evaluating in-situ breeding management strategies in endangered populations. Molecular Ecology Resources 22:239-25