Key points
- The Night Parrot (Pezoporus occidentalis) was a missing species for most of the 20th century but is now known to live in remote spinifex grasslands in critically low numbers.
- Using advanced long read DNA sequencing we’ve now published the first fully annotated Night Parrot genome.
- The genome sequence will help understand and conserve the recently rediscovered species.
The Night Parrot (Pezoporus occidentalis) is one of Australia’s most mysterious species.
Habitat loss and predation by cats and foxes dramatically reduced its numbers and it went missing for most of the 20th century.
Night Parrots are now known to exist in only a few locations in southwest Queensland and the Pilbara.
Sequencing the genome of this mysterious bird offers new hope for understanding the biology of this nocturnal parrot and saving the species.
Beak-a-boo
The Night Parrot is serious about ghosting.
Dr Leo Joseph is Director of our Australian National Wildlife Collection. He says the once widespread species went missing in 1912.
“There were no confirmed sightings for nearly 80 years, until they began showing up in southwest Queensland.”
“A Night Parrot killed on a road was found in 1990 by the Australian Museum. Then in 2006 another bird was found dead under a fence,” Leo says.
“Finally, a live Night Parrot was reported in the same part of Queensland in 2013 and a live Night Parrot was caught and tagged in 2015.”
Night club
The Night Parrot is a ground-dwelling parrot that lives in spinifex. Spinifex is a dense, clumping native grass with sharp, spiky leaves that offers some protection for nests.
It is one of only a few nocturnal parrot species in the world. However, some of the Night Parrot’s close relatives are active at dawn and dusk.
But the Night Parrot is not particularly good at living the nocturnal life – at least when it comes to night vision. Instead, its ear openings are asymmetrical. Similar to an owl’s, they amplify and determine the direction of sound to compensate for limited night vision.
Leo says its colouring is like New Zealand’s Kākāpō or owl-parrot.
“The Night Parrot has distinctive yellow, green and black flecked colouring, likely related to its need to camouflage on the ground in its spinifex habitat.”
Night Parrot populations are severely fragmented and the species is classified as critically endangered. There may be fewer than 250 individuals remaining.
A bird in the hand
We received a small tissue sample from a single deceased specimen from Traditional Owners in the Pilbara. It has allowed us to assemble the first genome sequence for this species.
The specimen recently went on display at the Western Australian Museum Boola Bardip.
Leo wasn’t sure if he’d ever see the day when this species had its DNA sequenced and genome assembled.
“There have been so few specimens collected over the years – fewer than 30 are known to exist in collections worldwide and most date from the 1800s,” Leo says.
“The Night Parrot really is one of the holy grails in ornithology. I was amazed when I found out we would be able to add this tissue sample to our wildlife collection, thanks to the support and permission of the Aboriginal community in the Pilbara and our colleagues at the Western Australian Museum.”
Sequencing from super small samples
Dr Rahul Rane is co-lead of our Applied Genomics Initiative. He says next generation high throughput sequencing technology is bringing big advances from tiny samples.
“Back in the day it would have been hard to do anything with such a small tissue sample,” Rahul says.
“Ten years ago, if you wanted to get a genome assembly of this quality, we would have needed about half a bird in terms of tissue sample size.”
“Now we can generate genomes from a tiny tissue sample the size of an ant’s head. And our team is working on being able to produce a genome from a single hair.”
A detailed roadmap
Dr Gunjan Pandey is leader of the Night Parrot genomics project. He says the annotated genome would show the location of individual genes like a detailed road map.
“The annotated genome will provide critical information on the genetic code of the Night Parrot. This includes the identification and characterisation of genes, their functions, and regulatory elements,” Gunjan says.
“This comprehensive insight into the bird's genome is pivotal for unravelling mysteries surrounding its biology such as its sight, hearing, feeding, drinking, and flight mechanisms. It opens the door to a deeper understanding of how its genes influence various aspects of its biology and behaviour.”
Small populations need big conservation
Rahul says that the genome is crucial for the Night Parrot's genetic rescue and marks another feather in Australia's cap. The nation is already a global leader thanks to previous projects for threatened species such as the eastern barred bandicoot and the mountain pygmy-possum.
“Genetic rescue is one of the most informed forms of rescue that you can do,” Rahul says.
“Knowing if a species has a genetic Achilles heel means you can make sure that any future conservation programs are resilient and maximise the long-term survival of the species.”
“We need to look at how much genetic diversity there is in Night Parrot populations because reduced genetic diversity is a major reason for species collapse.”
“For example, overseas, when cheetah conservation programs started people had no idea what the genetic diversity was, nor a way to assess it.
"And so, they mixed populations form southern and eastern Africa, with the hope that they might just survive. But they happened to sample a low genetic diversity, and saw very low reproductive success.
"This wasn’t the end though, because they also found that on a genetic level all the populations had a single critical shortfall in their immune system. When a feline coronavirus came in it just swept through the whole breeding population, and they lost 60 per cent of the cheetahs in three years."
“Being able to know the genetic makeup of a species is hence critical to conservation rescue programs.”
Solving the genome puzzle
The next step is to produce an even more detailed genome using the new Revio long-read sequencing machine.
“We’re going to come up with version 2.0 of the genome where we'll have all the chromosomes sorted,” Gunjan says.
“Currently, we have chunks of the genome, like puzzle pieces. However, we're unsure how these fit together to reveal the complete structure of each chromosome.”
“This allows us to compare the chromosome structures of the endangered Night Parrot with those of thriving birds, offering insights that can help develop strategies for the conservation and protection of the Night Parrot.”
“This genome isn’t our property. We want to make it available for everyone researching this bird so that we can all go out and save this bird. That’s the main goal – to save the bird.”
The National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM) in the USA annotated the genome sequence of the Night Parrot. The names of individual genes were found using NCBI’s Eukaryotic Annotation Pipeline (EGAP). The annotated genome is now available online as part of the NCBI Reference Sequence (RefSeq) Database through NCBI Datasets.