UH Hilo conservation geneticist Jolene Sutton and colleagues awarded grant for research on endangered birds

The team of genetic researchers from Hilo, California, New Zealand, and Australia will collaborate on a genetics study to address the hatching failure of two endangered bird species: the ‘alalā (Hawaiian crow) and the kākāpō of New Zealand.

By Alyssa Mathews.

Jolene Sutton
Jolene Sutton

Jolene Sutton, a conservation geneticist and assistant professor of biology at the University of Hawai‘i at Hilo, along with colleagues from New Zealand, Australia, and California, were recently awarded a three-year grant from the Marsden Fund. The grant will fund research that will help discover the reason behind the hatching failure of two iconic endangered bird species—the ‘alalā (Hawaiian crow) and the kākāpō of New Zealand—through whole genome sequencing data.

Sutton’s colleagues on the project are Bruce Robertson, an associate professor of biology at the University of Otago, Catherine Grueber, a research fellow at the University of Sydney, and Oliver Ryder, the Kleberg Endowed Director of Conservation Genetics at San Diego Zoo Global.

The project is titled, “Resolving the genomic architecture of hatching failure to improve conservation of endangered birds” (abstract). The Marsden award will provide 933,000$NZD (~630,000$USD) over three years. Marsden grants are the main large-sum funding method used by the government of New Zealand to fund science and research.

Sutton is part of the Conservation Genomics Research Group at UH Hilo.

“Our lab has been working with the ‘alalā since late 2015,” says Sutton. “In August of this year, we published the genome assembly of this species, and we’re really excited about that.”

In publishing the genome assembly, the team of researchers from UH Hilo, San Diego Zoo Global, and Pacific Biosciences released a public resource that is now being used to benefit conservation management and help the recovery of the endangered bird species.

“A genome is basically all of the DNA for an individual, so this gives us a tool that we can start to use for conservation management,” explains Sutton.

Two photos. The one the left is of a Kākāpō, New Zealand, a green and brown bird, eating berries in a bush. On the right is a photo of ‘Alalā, Hawai‘i, a blacj crow, sitting on branches of a fallen tree fern in the forest.
Left: Kākāpō, New Zealand (Photo Dept. of Conservation via Wikimedia). Right: ‘Alalā, Hawai‘i (Photo U.S. Fish and Wildlife via Wikimedia). Click to enlarge.

“We’re also going to do something unique for both ‘alalā and kākāpō,” says Sutton. “In addition to sequencing every living individual and some of the birds that are no longer alive today, we’re going to sequence embryos as well. Genetic material has been saved from eggs that didn’t hatch, and we’re interested in establishing whole genome resources for those. By comparing genomes of eggs that didn’t hatch to genomes of individuals that did successfully hatch, we hope to identify genes associated with hatching failure.”

In discovering why eggs fail to hatch, conservation scientists will be able to overcome one of the most challenging barriers in conserving the species.

“Their hatching failure is about 60 percent in ‘alalā and about 50 percent in kākāpō, and if you compare that to most wild species, hatching failure is only around 10 to 20 percent. This inability to make it from an egg to a chick is one of the biggest barriers to their recovery, at least from a genetic basis,” says Sutton.

The high rates of hatching failure can be attributed to inbreeding because of the low populations of both species.

“If you start with an egg that has been produced from a pair of birds that are closely related, that egg is an inbred egg,” explains Sutton. “Eggs that are more inbred than others have a worse chance of hatching. With this grant, we hope to find out specifically why that happens.”

In releasing birds back into the wild, the inbreeding of a bird is one of the important factors in deciding mating pairs.

“What we’ve started to do is add molecular genetic data to the pedigree genetic data, which gives us a finer-scale estimate of an individual egg’s inbreeding level,” says Sutton. “We think that this will help breeding in captivity, but it will also help to inform the reintroduction program, so which birds get released into the wild to help make up this new wild population of ‘alalā. By whole genome sequencing every living member of the species, along with a subset those that are no longer alive, we will generate a tremendous amount of data. As far as I know, the ‘alalā will become the third species for which the entire population will be sequenced this way. The other two species are the kākāpō and Spix’s macaw.”

When the ‘alalā is released back into the wild, there also will be a benefit on the local ecosystem as a whole.

“The ‘alalā itself is an agent of its own recovery,” explains Sutton. “If we can recover and help the ‘alalā, in turn, that species is going to help the Native Hawaiian forests because it’s going to help disperse Native Hawaiian plant seeds.”

In addition to having a positive impact ecologically and culturally, the research in recovering the two bird species will also have an educational benefit both at UH Hilo and the University of Otago.

“A lot of our research is being done with students,” Sutton says. “With the Marsden Funds, we’ll continue to involve graduate as well as undergraduate students in this research—there’s going to be a lot of data generated, so we’re going to involve a lot of students in that research. Our work will be facilitated our excellent lab facilities and big data computer resources at UH Hilo. Students and staff will get hands-on experience doing cutting-edge research with the latest bioinformatics tools, the latest genomics tools, and two species that are very iconic worldwide.”

In improving conservation management with the ‘alalā and kākāpō as model species, Sutton hopes that the research done with the bird species can serve to eventually help other endangered species.

“This work should inform conservation species efforts here in Hawai‘i, as well as New Zealand, but an additional component of the grant is to adapt our results to other species as well,” says Sutton. “One of the objectives in this project is to take the results generated from ‘alalā and kākāpō, and to do comparative genomic analysis with other bird species. This will help us assess the likelihood that variation the same genomic regions could explain variation in hatching outcome in multiple birds. The most direct benefits of the research will probably affect ‘alalā and kākāpō conservation, but certainly we expect this information to be applied to endangered birds world-wide.”

Sutton and her colleagues at the University of Otago, University of Sydney, and San Diego Zoo Global hope to continue to benefit communities through remaining dedicated to conservation efforts.

“The future goals are to continue to do the kinds of research that we think will benefit local species and local communities because they can be applied to local conservation management actions,” says Sutton. “Conservation takes an entire village, it takes a lot of agencies and a lot of people being very dedicated for a long period of time.”


Story by Alyssa Mathews, a freshman at UH Hilo. She graduated from Waiakea High School and is a UH Hilo Chancellor’s Scholar.

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