Sequenced quoll genome a new tool for conservation

European colonists mistakenly labelled quolls as “native cats” when in fact they are among Australia’s last living carnivorous marsupials.

Often overshadowed by their better-known cousins the Tasmanian Devils and the extinct Tasmanian Tiger (thylacine), quolls have a 15 million year history in Australia, successfully balancing shifting ecosystems by suppressing prey species and cleaning up carrion.

But quolls have been hard-hit by humans. Populations of most species have declined drastically in the modern era. One species, the eastern quoll (Dasyurus viverrinus), is even thought to have gone extinct in mainland Australia in the late 20th century due to a combination of disease, being hunted by the introduced red fox and poisoning by humans (baits meant for foxes, feral cats and rodents are also lethal to quolls).

Today, wild populations of this species are isolated to Tasmania. However, an ambitious program is underway to reintroduce eastern quolls to their native range on mainland Australia, by translocating captive-bred animals from Tasmania and mainland sanctuaries.

And the long-term success of this effort may well depend on using genetics to help the eastern quoll re-adapt to the changed mainland environment.

It is why our team of researchers are so excited about having now produced the first-ever genome sequence for the eastern quoll (bioproject: PRJNA758704) using Dovetail Genomic’s Omni-C technology.

Sequencing the genome means that we have been able to map the order of the chemical building blocks of the eastern quoll’s DNA, enabling us to read new information about how the animal’s genetics work.

The research team has spanned several universities including the University of Melbourne, University of Tasmania (UTAS) and the Australian National University (ANU) as part of a research grant from wildlife conservation group Revive and Restore.

We’ve also had crucial help from WWF-Australia’s Rewilding Unit and Taronga Zoo which provided samples collected at Aussie Ark, a captive-breeding centre and semi-wild safe haven for eastern quolls.

The ongoing work to reintroduce the eastern quoll has recently been tested at Booderee National Park on the NSW south coast, which has provided valuable data towards making this goal a reality.

But major challenges to the reestablishment of viable mainland quoll populations remain. One possible challenge is that because the eastern quoll population in Tasmania has adapted to that island State’s unique environment, we don’t know yet how this may affect their re-introduction to the mainland.

Tasmania represents the most southern and coldest part of the eastern quoll’s historical range, and native populations have been evolving in isolation there for around 14,000 years, since the end of the last ice age or Last Glacial Maximum (LGM). While helpful for surviving in Tasmania, these same adaptations may actually be disadvantageous in warmer, drying climates on mainland Australia.

This is why sequencing the genome is important. By mapping all of the quoll’s genes, it is now possible to identify genetic variation across both living and extinct quoll populations in ways that we can use to guide breeding and release programs to boost the chances of these Tasmania quolls re-adapting to the mainland.

This work is part of Revive & Restore’s broader Wild Genomes program that aims to promote genetic rescue in environmentally-critical species through the integration of cutting-edge techniques and technologies into biodiversity conservation.

While eastern quoll genomics is still in its infancy, our team is already using our new genomic resource to begin examining the history of eastern quoll population declines in Australia. We do this using a clever approach.

Most animals have two copies of every chromosome, one from their mother and one from their father. With the exception of the sex chromosomes (X and Y), each pair of chromosomes contains nearly the same DNA. This is because all chromosome pairs ultimately share a common ancestry.

Occasionally though, random mutations create small numbers of changes in the letters of the DNA of one chromosome, making it slightly different from its pair. These mutations accumulate over generations at a fairly steady rate.

By comparing this record of mutations between segments of chromosome pairs in the eastern quoll genome to information about mutation rate (how frequently mutations occur per generation) and the generation time of a species, we should be able to estimate how long ago two chromosomes diverged from each other.

The time periods when many chromosome segments share a common origin represent population bottlenecks, where population sizes decreased.

Using this sort of information we can decipher the genetic fingerprints of why and how the living Tasmanian eastern quolls have diverged from their tragically extinct mainland relatives.

We can then use this knowledge to guide expanded population-genetic studies of eastern quolls to ultimately improve genetic management through the breeding of both wild and captive-bred quolls.

As Rob Brewster, WWF-Australia’s Rewilding Program Manager wrote to me, “By combining applied ecosystem restoration ecology with the latest in DNA science, we may one day see eastern quolls return home to mainland Australia and resume the ecosystem services they’ve provided for millions of years”.

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