Dying Breeds
How Scientists Can Save Species Through Genetics
Hoki, Queenie, Basil, Dobbie, Joe, Stumpy, Bluster Murphy… the Kākāpō Recovery Team know each of their flightless parrots by name. It’s not so difficult when there are less than 150 left: 148, to be exact, with the recent death of Jane, whose genome was the first of the parrots to be fully sequenced.
They are now getting to know the endangered birds even more intimately, thanks to an ambitious crowd-funded project to sequence the DNA of each living (and some recently deceased) member of the indigenous New Zealand species.
Launched in 2016, the Kākāpō 125 Project has already sequenced 80 birds with $45,000 raised on PacBio’s Genome Galaxy Initiative hosted by Experiment.com, a scientific crowdfunding platform, and an additional 90 will now be sequenced with funding by Science Exchange.
The kākāpō (Strigops habroptila) is the world’s only flightless parrot and the heaviest. It may also be one of the longest living birds, with many reaching the ripe old age of 95. Endemic to New Zealand, the large, nocturnal bird has finely blotched yellow-green plumage, a distinct facial disc of sensory, vibrissa-like feathers, a large grey beak, short legs, large feet and wings, and a short tail.
But they only breed in seasons when there’s a good supply of fruit of the rimu tree (Dacrydium cupressinum), about every three years. And because of Polynesian and European colonization and the introduction of predators such as cats, rats, ferrets, and stoats, the kākāpō was almost wiped out.
With so few parrots remaining, descended from just a few individuals that narrowly escaped extinction a few decades ago, conservationists are eager to use any tool available to boost breeding success and salvage genetic diversity. Comprehensive blueprints of the genetic underpinnings of individual birds could provide vital information for future breeding decisions.
The DNA assemblies could be used to identify critical genes relevant to fertility, adaptation and disease resistance, for instance. They could also help to pinpoint individuals carrying genetic variants that might be beneficial in the preservation of the species — both those that should be reinforced to contribute to genetic diversity, and those that should be bred out to maintain the species’ health.
Jason Howard at Duke University sequenced the first kākāpō genome, creating a high-quality de novo reference assembly using PacBio SMRT Sequencing, and other collaborators, including Andrew Digby of the New Zealand Department of Conservation, Bruce Robertson of Otago University in Dunedin, and The Kinghorn Centre for Clinical Genomics in Sydney, Australia, carried out sequencing and analysis of the rest of DNA.
“Detailed genetic data for every individual in an entire species is a world first and represents a genomics-focused paradigm shift in modern conservation efforts,” said David Iorns, the New Zealand native and founder of Genetic Rescue who launched the crowd-funding campaign, in the latest project update. “It is my hope that this data will steer kākāpō conservation decisions for years and decades to come. It may prove to be the deciding factor in saving this species.”
Few and Far Between: Rare Hawaiian Crow
Although the kākāpō project is the first to digitally capture the genetics of every extant member of a species, it may not be the last. Another endangered indigenous bird, the ‘alalā crow (Corvus hawaiiensis), is getting the comprehensive PacBio profiling treatment in an effort to save the remaining 140 members of the Hawaiian species, and boost the breeding efforts of more.
Similarly struck by disease, predators and shrinking habitats, the ‘alalā was actually completely lost in the wild, and saved only by a captive breeding program led by San Diego Zoo Global. But, as highlighted in this recent blog post, the captive birds also face challenges, including low hatching success and signs of poor genetic diversity due to inbreeding, with the majority of the population linked to a single founding pair.
A research team from the San Diego Zoo Institute for Conservation Research, the University of Hawaii, and other organizations have produced a high-quality genome assembly based on SMRT Sequencing to provide a more detailed picture of population-level genomic diversity and genetic load of the crow, as well as more accurate estimates of molecular relatedness to guide breeding decisions. The result is one of the very best avian genomes assembled to date, which has already provided valuable insights into inbreeding and disease susceptibility.
“Whole genome sequencing of threatened and endangered taxa enables conservation geneticists to transition from a reliance on limited numbers of genetic markers toward increased resolution of genome-wide genetic variation. Such genome-level data offer unprecedented precision to examine the causes and genetic consequences of population declines, and to apply these results to conservation management”
Jolene Sutton, assistant professor at the University of Hawaii, Hilo
Odd Ones Out: Cuddly Koalas
In Australia, an iconic tree-dwelling marsupial is the animal under particular threat of extinction. The deadly trifecta of disease, predators and shrinking habitats have similarly struck the koala. Add to that an extremely limited diet — a particular type of eucalyptus that is toxic to most other animals — and you have a very vulnerable species.
So scientists have been keen to parse out the 27,000 genes in the koala genome to discover any clues that might shed light on koala biology, explain its unique features, and inform future conservation schemes.
Rebecca Johnson, Director of the Australian Museum Research Institute, and colleagues Matthew Hobbs and Andrew King, have been particularly devoted to the cause, publishing several papers recently about discoveries they have made thanks to chromosome-level assembly of the koala genome using PacBio long-read sequencing.
The first, highlighted in this blog post, involved insight into a species-specific retrovirus threatening the cuddly tree-huggers: KoRV, which can cause chlamydia and blindness, hindering the animals’ ability to forage and defend themselves.
The second, recently released in Nature Genetics, explains how the koala manages its eucalyptus-exclusive diet using special enzymes that break down the toxic molecules and expel them.
“They’re super-detoxers compared to all other species that have had their genomes sequenced,” Johnson told WIRED.
This information could be helpful in koala rehabilitation (identifying koalas based on their local cuisine) or relocation (finding an area with similar foliage).
“Long-term survival of the species depends on understanding the impacts of disease and management of genetic diversity, as well as the koala’s ability to source moisture and select suitable foraging trees,” Johnson writes in the Nature paper. “This is particularly important given the koala’s narrow food range, which makes it especially vulnerable to a changing climate.”
“Sequencing the genome has advanced our understanding of the unique biology of the koala, including detoxification pathways and innovations in taste and smell to enable food choices in an obligate folivore,” she adds. “A greater understanding of genetic diversity across the species will guide the selection of individuals from genetically healthy northern populations to augment genetically restricted populations in the south.”
