The Helmeted Honeyeater Lichenostomus melanops cassidix, named for its ‘helmet’ of head feathers, is a critically endangered subspecies of the yellow-tufted honeyeater (L. melanops) that is widespread in south-eastern Australia.
As do most related honeyeaters, it uses its long, brush-tipped tongue to collect nectar, which comprises a quarter of its diet [1]. It also consumes invertebrates, honeydew from bugs, manna (sugary exudate from damaged foliage), lerp (the sugary coating on scale insects) and sap exuding from scars on branches caused by gliding possums [2]. Each breeding pair vigorously defends its territory where it feeds, and helps neighboring pairs to drive out the intruders [3]. Females usually lay two eggs per clutch and attempt three or four clutches per season.
The Helmeted Honeyeater belongs to family Meliphagidae, an iconic Australo-Papuan group that evolved around 20 million years ago. Genus Lichenostomus, as currently recognized, split from other honeyeaters about 8 million years ago [4].
The State of Victoria, Australia, made the beautiful Helmeted honeyeater Victoria’s bird emblem in 1971 [5]. Of the four subspecies of Yellow-tufted honeyeater, the Helmeted Honeyeater is the largest and most colourful [6]. It is also most threatened (critically endangered under IUCN criteria [7]) with only about 250 individuals remaining in the single wild population despite decades of intensive management and supplementation from a captive breeding program at Healesville Sanctuary [8]. It is one of the most intensively monitored bird populations in Australia. Recent results have revealed that the population lost much of its genetic diversity over recent decades [9], with the most-inbred birds producing only one-tenth as many young over their lifetimes compared to the least-inbred birds [8].
To reverse population decline, genetic rescue was recommended. That is, genes from a closely related subspecies, L. m. gippslandicus diverged from the common ancestor up to 50,000 years ago [10], were proposed to be introduced into the Helmeted Honeyeater population. Because the two subspecies historically exchanged genes, this management action would reinstate historical gene flow. Inter-subspecies crosses were successful in captivity and the hybrid young produced from such pairings released into the wild in 2019 [11].
To support ongoing conservation efforts led by a multidisciplinary Recovery Team, including the Department of Environment, Land, Water and Planning, The Friends of the Helmeted Honeyeater and Zoos Victoria, DNA Zoo has been working with Paul Sunnucks and Alexandra Pavlova at Monash University to generate a chromosome-length assembly genome for a female Helmeted Honeyeater.
The chromosome-length assembly we share today is based on the draft assembly available on NCBI generated by Han Ming Gan of the Deakin Genomics Centre, and the Monash University team, with funding from Zoos Victoria and Australian Research Council-funded project LP160100482 (Lichenostomus melanops cassidix isolate B80296). The draft genome assembly was created using MaSuRCA v. 3.3.4 (Zimin et al. 2013), using Oxford Nanopore MinION reads polished with short-insert size Illumina NovaSeq reads. The above draft was scaffolded using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details!
The sample used to generate the Hi-C library was kindly provided by Leanne Wicker (Zoos Victoria). The Hi-C work was supported by resources provided by DNA Zoo Australia, Faculty of Science, The University of Western Australia (UWA), DNA Zoo, Zoos Victoria, Holsworth Wildlife Endowment and Monash University, with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.
The following people contributed to the Hi-C chromosome-length upgrade of the project: Erez Aiden, Olga Dudchenko, David Weisz, Ashling Charles, Ruqayya Khan & Parwinder Kaur.
Blog by: Parwinder Kaur, Alexandra Pavlova and Paul Sunnucks
Citations
3. Smales, I.J. (2004).Population ecology of the Helmeted Honeyeater Lichenostomus melanops cassidix: long-term investigations of a threatened bird. Honours thesis, Melbourne University, Melbourne, Victoria
4. Joseph, L., Toon, A., Nyári, Á.S., Longmore, N.W., Rowe, K., Haryoko, T., Trueman, J., Gardner, J.L., 2014. A new synthesis of the molecular systematics and biogeography of honeyeaters (Passeriformes: Meliphagidae) highlights biogeographical and ecological complexity of a spectacular avian radiation. Zool Scr 43, 235-248.
5. Delacombe, Rohan; Bolte, Henry (10 March 1971). "Faunal Emblems for the State of Victoria" (PDF). Victoria Government Gazette – Online Archive 1836–1997. State Library of Victoria.
6. Wakefield, N., 1958. The Yellow-tufted Honeyeater with a description of a new subspecies. Emu 58, 163–194
7. Garnett, S., Szabo, J., Dutson, G., 2011. Action Plan for Australian Birds 2010. CSIRO Publishing, Melbourne.
8. Harrisson, K.A., Magrath, M.J., Yen, J.D., Pavlova, A., Murray, N., Quin, B., Menkhorst, P., Miller, K.A., Cartwright, K., Sunnucks, P., 2019. Lifetime fitness costs of inbreeding and being inbred in a critically endangered bird. Curr Biol 29, 2711–2717.
9. Harrisson, K.A., Pavlova, A., Gonçalves da Silva, A., Rose, R., Bull, J.J., Lancaster, M., Murray, N., Quin, B., Menkhorst, P., Magrath, M.J.L., Sunnucks, P., 2016. Scope for genetic rescue of an endangered subspecies though re-establishing natural gene flow with another subspecies. Mol Ecol 25, 1242–1258.
10. Pavlova, A., Selwood, P., Harrisson, K.A., Murray, N., Quin, B., Menkhorst, P., Smales, I., Sunnucks, P., 2014. Integrating phylogeography and morphometrics to assess conservation merits and inform conservation strategies for an endangered subspecies of a common bird species. Biol Conserv 174, 136–146.
11. https://www.zoo.org.au/healesville/whats-on/news/helmeted-honeyeater-release/