News is out today that the entire genome of the koala has been sequenced. This means we now have a complete read-out of the genes and other DNA sequences of this iconic marsupial mammal.
Knowing the full set of koala genes deepens our knowledge of koalas (and other Australian mammals) in many ways. Now we can understand how koalas manage to survive on such a toxic diet of gum leaves. Now we can follow the fortunes of historic koala populations and make good decisions about how to keep remaining koala populations healthy. Now we have a new point of comparison that we can use to understand how the mammal genome evolved.
This is important for science – but also economically. Koalas are incredibly well loved, with their baby-faces, shiny noses and big fluffy ears. Millions of visitors line up each year to spot them snoozing in gum trees – indeed, they are worth A$3.2 billion in tourist dollars.
Koalas are listed as a vulnerable species in some parts of Australia, affected by habitat destruction, disease and other stresses.
The koala genome
Koala DNA was sequenced with new “long-read” technology that delivers a complete and well-assembled genome. As far as quality of the read-out goes, it’s as good as the human genome, with continuous sequences now known over huge (almost chromosome-scale) spans. New technology enabled us to achieve this at a tiny fraction of the $2.7 billion it cost to sequence the first human.
The obtained koala genome sequence is much better quality than that for other sequenced marsupials – opossum, tammar wallaby and Tasmanian devil – and will really help us to assemble and compare genomes from all marsupials.
The koala has a genome a bit bigger than that of humans, with 3.5 billion DNA base-pairs. This amounts to about a metre of DNA, which is divided and packaged into eight large bits that we recognise as chromosomes.
An animal has a set of chromosomes from mother and a set from father, so koalas have 16 large chromosomes in each cell. This is similar to other marsupials; as a group they seem to have a low chromosome number and a very stable genome arrangement. In placental mammals the number and arrangement of chromosomes is much more varied: for example, humans have 46, and rhinos 82 chromosomes.
The source of junk DNA
New findings from the koala genome help us to understand how mammal genomes evolved and how they work.
A lot (sometimes more than 50%) of animal genomes seem to be “junk DNA” – these are repeated sequences, many deriving from ancient viral infections. The koala, uniquely, seems to be in the middle of one such invasion. A DNA sequence derived from a retrovirus is present in different numbers and sites in different koala populations, testifying to its recent movement and amplification. This helps us learn how the genomes of humans and other mammals got so puffed up with junk DNA.
Like the human genome, the koala genome contains about 26,000 genes. These are stretches of DNA that code for or control proteins. Indeed, most koala genes are present in humans and other mammals – these are the same genes doing the same basic jobs in different animals.
So why is it important to sequence different species if their genomes are so similar? Well, it’s the special genes that have evolved to adapt the koala to its unique lifestyle that give us new and valuable information.
How to survive on gum leaves
How koalas exist on an exclusive low-calorie and toxin-laced diet of eucalyptus leaves has been somewhat of a science mystery.
The genome provides answers. The koala has multiplied a family of genes that code for enzymes (members of the cytochrome P450 family) that break down the toxins of gum leaves. Evolution of these additional gene copies has enabled the koala to outstrip its competition, even at the cost of sleeping most of the day.
The genome also gives us clues to the koala’s picky eating habits. The koala genome contains many additional copies of genes that enable them to taste and avoid bitter flavours and even to “smell” water and choose juicy leaves (they don’t drink water).
The genome also gives us new information about how koalas develop. Like other marsupials, they are born about the size of a pea, and complete most of their growth and differentiation in the pouch. Developing koalas are nurtured by milk with a complex composition that changes with the stage of development.
Saving an iconic Australian
Managing koala populations is very fraught, and there has long been a need for a holistic, scientifically-grounded approach to koala conservation.
Today’s koalas are the “last stand” of the marsupial family Phascolarctidae – and the koala genome contains new information about this evolutionary history. It also tells us that koala populations peaked about 100,000 years ago, then plunged to about 10% of their numbers 30-40,000 years ago, at the same time that the megafauna became extinct. This population was fairly stable until European settlement, when it plunged again to its present numbers (about 300,000).
Koalas once occupied a swathe of timbered habitat from Queensland to South Australia; now, only fragmented populations survive in the south. These are intensively managed, and small numbers of koalas are translocated to other sites, producing dangerously inbred populations. Bizarrely, one of the greatest problems is overbreeding in isolated populations – for example, on South Australia’s Kangaroo Island – which leads to animals eating themselves out of house and home.
The enemies of koalas in the north are habitat destruction and fragmentation by urbanisation and climate change.
The koala genome paper reports sequence comparisons of different populations and identifies barriers to gene flow. With the information from the koala genome, we can now monitor genetic diversity in the surviving populations, and maximise gene flow between connected populations.
Maintaining genetic diversity is important because different animals can mount different responses to environmental threats and diseases such as chlamydia, a bacteria that affects koala reproduction and eye health.
The koala genome provides us with information about the immune genes of the koala, and the changes in activity of these genes in infected animals. This will help us understand the different responses of animals, vital for developing vaccines and treatments.
The koala genome also identifies powerful anti-bacterials in milk that protect the baby koala from disease – and may provide humans with the next generation of antibiotics.
So sequencing the koala genome is good for science and good for koalas, an iconic species at the top of the tree for conservation efforts.
Tony Abbott has called for Australia to pull out of the Paris climate agreement, in a swingeing attack on Malcolm Turnbull’s National Energy Guarantee.
Abbott said the NEG was not about reducing prices but about cutting emissions. “The only certainty that the National Energy Guarantee as it stands would provide is the certainty of emissions reduction.”
Delivering the Bob Carter Commemorative Lecture in Melbourne, Abbott said: “Withdrawing from the Paris agreement that is driving the National Energy Guarantee would be the best way to keep prices down and employment up – and to save our party from a political legacy that could haunt us for the next decade at least”.
“As long as we remain in the Paris agreement – which is about reducing emissions, not building prosperity – all policy touching on emissions will be about their reduction, not our well-being. It’s the emissions obsession that’s at the heart of our power crisis and it’s this that has to end for our problems to ease.”
Abbott played down the importance of the government’s much-vaunted tax cuts in comparison with the implications of energy policy.
“These are strange times in Canberra when there’s a hullaballoo over modest tax cuts that only take effect fully in six or seven years’ time, while mandatory emissions cuts that start sooner, that mean more for the economy, and whose ramifications will be virtually impossible to reverse are expected more or less to be waved through”.
In the party room last week Abbott had little support for his attack on the NEG. But his constant agitation is unhelpful for the government as it tries to win backing from the states and territories for the scheme. It also reinforces the impression of division in government ranks, even though the majority of the backbenchers now just want the energy policy settled.
Abbott said that his government in 2015 had set a 2030 emissions reduction target “on the basis that this was more or less what could be achieved without new government programs and without new costs on the economy.
‘’There was no advice then to the effect that it would take a Clean Energy Target or a National Energy Guarantee to get there,” he said.
“My government never put emissions reduction ahead of the wellbeing of families and the prosperity of industries”.
When the world’s leading country exited the Paris agreement “it can hardly be business as usual,” he said. “Absent America, my government would not have signed up to the Paris treaty, certainly not with the current target”.
Abbott said he could understand “the government would like to crack the so-called trilemma of keeping the lights on, getting power prices down and reducing emissions in line with our Paris targets – it’s just that there’s no plausible evidence all three can be done at the same time”.
“If you read the National Energy Guarantee documentation, there’s a few lines about lower prices, a few pages about maintaining supply, and page after impenetrable page about reducing emissions.
’‘The government is kidding us when it says it’s all about reducing prices when there ’s an emissions reduction target plus a reliability target but no price target”.
The government said it wanted to give certainty but the only certainty was that any NEG approved by state ALP governments at COAG would be “massively ramped up to deliver even more emissions reduction under the next Labor government”.
Abbott repeated his call for the government to subsidise the boosting of baseload power. He again suggested threatening to compulsorily acquire Liddell coal-fired power station, which AGL is refusing either to keep going or to sell.
The federal government’s National Energy Guarantee aims to reduce greenhouse gas emissions in the electricity industry by 26% of 2005 levels. But for Australia to meet its Paris climate change commitments, this 26% reduction will need to be replicated economy-wide.
In sectors such as aviation this is going to be very costly, if not impossible. Our modelling of the carbon price introduced by the Gillard government shows it had no detectable effect on kilometres flown and hence carbon emitted, despite being levied at A$23-$24 per tonne.
If Australia is to meet its Paris climate commitments, the National Energy Guarantee target will need to be raised or radical measures will be required, such as putting a hard cap on emissions in sectors such as aviation.
Obituary: Australia’s carbon price
Our analysis of domestic aviation found no correlation between the Gillard government’s carbon price and domestic air travel, even when adjusting statistically for other factors that influence the amount Australians fly.
This is despite the carbon price being very effective at reducing emissions in the energy sector.
To reduce aviation emissions, a carbon price must either make flying less carbon intensive, or make people fly less.
In theory, a carbon tax should improve carbon efficiency by increasing the costs of polluting technologies and systems, relative to less polluting alternatives. If this is not possible, a carbon price might reduce emissions by making air travel more expensive, thereby encouraging people to either travel less or use alternative modes of transport.
Why the carbon price failed to reduce domestic aviation
The cost of air travel has fallen dramatically over the last 25 years. As the chart below shows, economy air fares in Australia in 2018 are just 55% of the average cost in 1992 (after adjusting for inflation).
Given this dramatic reduction in fares, many consumers would not have noticed a small increase in prices due to the carbon tax. Qantas, for example, increased domestic fares by between A$1.82 and A$6.86.
The carbon price may have just been too small to reduce consumer demand – even when passed on to consumers in full.
Consumer demand may have actually been increased by the Clean Energy Future policy, which included household compensation.
The cost of jet fuel, which accounts for between 30 and 40% of total airline expenses, has fluctuated dramatically over the last decade.
As the chart below shows, oil were around USD$80-$100 per barrel during the period of the carbon price, but had fallen to around USD$50 per barrel just a year later.
Airlines manage these large fluctuations by absorbing the cost or passing them on through levies. Fare segmentation and dynamic pricing also make ticket prices difficult to predict and understand.
Compared to the volatility in the cost of fuel, the carbon price was negligible.
The carbon price was also unlikely to have been fully passed through to consumers as Virgin and Qantas were engaged in heavy competition at the time, also known as the “capacity wars”.
This saw airlines running flights at well below profitable passenger loads in order to gain market share. It also meant the airlines stopped passing on the carbon price to customers.
A carbon price could incentivise airlines to reduce emissions by improving their management systems or changing plane technology. But such an incentive already existed in 2012-2014, in the form of high fuel prices.
A carbon price would only provide an additional incentive over and above high fuel prices if there is an alternative, non-taxed form of energy to switch to. This is the case for electricity generators, who can switch to solar or wind power.
But more efficient aeroplane materials, engines and biofuels are more myth than reality.
What would meeting Australia’s Paris commitment require?
Given the failure of the carbon price to reduce domestic air travel, there are two possibilities to reduce aviation emissions by 26% on 2005 levels.
The first is to insist on reducing emissions across all industry sectors. In the case of aviation, the modest A$23-$24 per tonne carbon price did not work.
Hard caps on emissions will be needed. Given the difficulty of technological change, this will require that people fly less.
The second option is to put off reducing aviation emissions and take advantage of more viable sources of emissions reduction elsewhere.
By increasing the National Energy Guarantee target to well above 26%, the emission reductions in the energy sector could offset a lack of progress in aviation. This is the most economically efficient way to reduce economy-wide emissions, but does little to reduce carbon pollution from aviation specifically.
Airline emissions are likely to remain a difficult problem, but one that needs to be tackled if we’re to stay within habitable climate limits.
Francis Markham, Research Fellow, College of Arts and Social Sciences, Australian National University; Arianne C. Reis, Senior lecturer, Western Sydney University; James Higham, Professor of Tourism, and Martin Young, Associate Professor, School of Business and Tourism, Southern Cross University