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The World’s Most Interesting Genome

Sandy at 3 weeks of age. Credit: Barry Eggleton

Sandy at 3 weeks of age. Credit: Barry Eggleton

By Bill Ballard

Sequencing of the genome of a pure-bred dingo pup rescued from the side of a remote desert track will enable scientists to examine one of Charles Darwin’s few remaining untested theories.

In 2014, animal-lovers Barry and Lyn Eggleton were travelling near the Strzelecki Track in the South Australian desert when their four-wheel drive went over the top of two furballs lying in the middle of the road. Barry and Lyn stopped, jumped out and discovered a pair of 2-week-old dingoes. They then found a third pup on the side of the road that was too weak to move.

Barry and Lyn gave the pups water and scoured the surrounds to see if a parent could be found. After several hours in the baking sun, they decided to take the pups with them rather than let them die.

Back at their NSW home, the pups were defleaed, deloused and then hand-raised with a critical eye and attention to detail. Barry and Lyn then decided to see if the three amigos were genetically pure.

I received a blood sample from Sandy on 29 September 2014 with a simple note saying that three pups had been found east of the Moomba gas facility in South Australia. DNA analyses, using a test initially developed by Alan Wilton, showed that Sandy was a pure dingo with no sign of any dog genes.

Alan was the face of dingo genetic research for more than a decade and was awarded the Australian Science Communicators Unsung Hero of Science Award in 2004. Sadly, he passed-away on 14 October 2011 after a 20-month battle with cancer. Following Alan’s death, I embraced his work on dingoes.

Although not completely unexpected, given the remote locality where Sandy was found, the discovery of a wild-born pure desert dingo living within cooee of The University of NSW presented a unique opportunity. At the time I didn’t know exactly what that opportunity would be, nor how she and her siblings would turn out to be such a gift to science.

Variation Under Domestication

In 2015, Prof Claire Wade of the University of Sydney and I received an Australian Research Council Discovery grant. Our proposal was heavily influenced by a 2013 Nature publication (http://tinyurl.com/y92fgpbh) which proposed that novel genetic adaptations enabled the early ancestors of modern dogs to thrive on a diet that was rich in starch relative to the carnivorous diet of wolves, and this constituted a crucial step in the early domestication of dogs.

It has subsequently been shown that activity of amylase, an enzyme that helps digest carbohydrates such as rice, is associated with copy numbers of the AMY2B gene in canids. Amylase is made in the pancreas and the glands that make saliva.

We now know that dingoes do not have AMY2B copy gain. This suggests that AMY2B was never duplicated in dingoes or that AMY2B duplications have been lost. Ockham’s Razor suggests that the former hypothesis is preferred, and that dingoes have never been domesticated. However, further research is needed to answer the question.

I hypothesised that dingoes could be used to test one of the few remaining untested postulates published in Charles Darwin’s 1868 book The Variation of Animals and Plants under Domestication. Dingoes are likely to be intermediate between wolves and domestic dogs or are an ancient dog breed.

Darwin states that the principles of selection may be conveniently divided into methodical, unconscious and natural selection. In Darwin’s view, “Methodical selection is that which guides a man who systematically endeavours to modify a breed according to some predetermined standard. Unconscious selection is that which follows from men naturally preserving the most valued and destroying the less valued individuals, without any thought of altering the breed.”

As a part of our ARC grant, we began exploring the possibilities of sequencing the dingo genome. A lingering issue was the question of how similar dingoes are to domestic dogs. Could we simply map the dingo genome to that of the domestic dog, or would this resequencing approach make too many assumptions?

Resequencing is relatively inexpensive (~$2,600) while de novo sequencing is more expensive (~$50,000) and the necessary downstream bioinformatics analyses even more extensive.

A Last Minute Grant Bid

At 1:49 pm on 31 January 2017, Dr Mark Cowley of the Garvan Institute of Medical Research in Sydney sent an email message to me that simply said: “Did you see this?”. The email included notice of a final reminder to enter the Pacific Biosciences long-read single molecule real-time (SMRT) grant program. The deadline for proposals was that same day!

At 2:54 pm I sent Mark a draft of a SMRT grant application that proposed to test Darwin’s 1868 hypothesis. The plan was to use Sandy the desert dingo as an intermediate between the wild wolf and domestic dogs. Mark improved my draft and the proposal was submitted by 5:00 pm. Mark later joked that this was the most productive hour of my research career!

On 28 February 2017 I received an email from Emily Hatas at Pacific Biosciences that we had been selected as one of the five finalists for the PacBio SMRT Grant. The email said:

Among 200+ proposals yours stood out as particularly compelling, and we’re excited to promote it. Per the program outline, the five finalists will be featured on the PacBio website and will be open to community vote for several weeks in March to decide the winner. The proposal that receives the most votes during the open voting period will be awarded PacBio SMRT Sequencing and genome assembly for their organism of interest.

A collegial team from The University of Sydney (Prof Claire Wade), Garvan Institute (Dr Andre Minoche), Vineyard Veterinary Hospital (Dr Rob Zammit) and UNSW (Dr Rich Melvin and myself) was assembled for the voting challenge. At the end of the contest, one vote per email address per 24-hour period was scored. This reset each day at midnight in California. Each person (by entered name) could vote under three different email addresses.

This non-traditional grant required us to engage with the wider community, including through Facebook and Twitter. A highlight of our publicity campaign was an event we held where two alpine dingoes and a pink poodle came onto the UNSW campus, to the delight of students and staff. Being a wild-born dingo Sandy did not come onto campus. The dingoes were from the Bargo Dingo Sanctuary and the coloured poodle, “Sir Walter”, belonged to vet Rob Zammit.

Why did we illustrate the proposal with a pink poodle? Because it visually illustrated (hypothetical) ongoing methodological selection.

The good news that Sandy had won came through on 12 April 2017, with 2-year old Sandy polling 35,781 valid electronic votes. She was closely followed by a temple pit viper snake, a solar-powered sea slug, an explosive bombardier beetle and a pink pigeon.

Winning the competition will enable Sandy’s genome to be sequenced with Pacific Biosciences’ SMRT technology. Sequencing will be completed in Arizona and de novo compilation and annotation of the genome by Computomics in Germany.

Our participation and victory in the competition engaged the community, students and staff of multiple institutions and global sets of canine and conservation groups. It has also raised public awareness of science and genomics, and enabled new scientific collaborations that we fully expect will result in a superior publication, perhaps in 2018.


Bill Ballard is Professor of Evolutionary Genetics in the UNSW School of Biotechnology and Biomolecular Sciences.