A detailed eucalypt family tree helps us see how they came to dominate Australia



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In Australia you can have any tree you want, as long as it’s a eucalypt.
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Andrew Thornhill, James Cook University

Eucalypts dominate Australia’s landscape like no other plant group in the world.

Europe’s pine forests consist of many different types of trees. North America’s forests change over the width of the continent, from redwood, to pine and oak, to deserts and grassland. Africa is a mixture of savannah, rainforest and desert. South America has rainforests that contain the most diversity of trees in one place. Antarctica has tree fossils.

But in Australia we have the eucalypts, an informal name for three plant genera: Angophora, Corymbia and Eucalyptus. They are the dominant tree in great diversity just about everywhere, except for a small region of mulga, rainforest and some deserts.

My research, published today, has sequenced the DNA of more than 700 eucalypt species to map how they came to dominate the continent. We found eucalypts have been in Australia for at least 60 million years, but a comparatively recent explosion in diversity 2 million years ago is the secret to their spread across southern Australia.

Hundreds of species

The oldest known Eucalyptus macrofossil, from Patagonia in South America, is 52 million years old. The fossil pollen record also provides evidence of eucalypts in Australia for 45 million years, with the oldest specimen coming from Bass Strait.

Despite the antiquity of the eucalypts, researchers assumed they did not begin to spread around Australia until the continent began drying up around 20 million years ago, when Australia was covered in rainforests. But once drier environmental conditions kicked in, the eucalypts seized their chance and took over, especially in southeastern Australia.

Eucalypts are classified by their various characteristics, including the number of buds.
Mary and Andrew/flickr, CC BY-NC-SA

There are over 800 described species of eucalypts. Most of them are native only to Australia, although some have managed to naturally escape further north to New Guinea, Timor and Indonesia. Many eucalypts have been introduced to other parts of the world, including California, where Aussie eucalypts make cameos in Hollywood movies.

Eucalypts can grow as tall trees, as various multi-trunk or single-trunk trees, or in rare cases as shrubs. The combination of main characteristics – such as leaf shape, fruit shape, bud number and bark type – provided botanists with enough evidence to describe 800 species and estimate how they were all related to each other, a field of science known as “taxonomy”.

Since the 1990s and early 2000s, taxonomy has been slightly superseded by a new field called “phylogenetics”. This is the study of how organisms are related to each other using DNA, which produces something akin to a family tree.

Phylogenetics still relies on the species to be named though, so there is something to sample. New scientific fields rely on the old. There have been a number of eucalypt phylogenetic studies over the years, but none have ever sampled all of the eucalypt species in one phylogeny.




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Our new paper in Australian Systematic Botany aimed to change that. We attempted to genetically sample every described eucalypt species and place them in one phylogeny to determine how they are related to each other. We sampled 711 species (86% of all eucalypts) as well as rainforest species considered most closely related to the eucalypts.

We also dated the phylogeny by time-stamping certain parts using the ages of the fossils mentioned above. This allowed us to estimate how old eucalypt groups are and when they separated from each other in the past.

Not so ancient

We found that the eucalypts are an old group that date back at least 60 million years. This aligns with previous studies and the fossil record. However, a lot of the diversification in the Eucalyptus genus has happened only in the last 2 million years.

Gum trees are iconic Australian eucalypts.
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Hundreds of species have appeared very recently in evolutionary history. Studies on other organisms have shown rapid diversification, but none of them compare to the eucalypts. Many species of the eucalypt forests of southeastern Australia are new in evolutionary terms (10 million years or less).

This includes many of the tall eucalypts that grow in the wet forests of southern Australia. They are not, as was previously assumed, ancient remnants from Gondwana, a supercontinent that gradually broke up between 180 million and 45 million years ago and resulted in the continents of Australia, Africa, South America and Antarctica, as well as India, New Zealand, New Guinea and New Caledonia.

The eucalypts that grow natively overseas have only made it out from Australia in the last 2 million years or less. Other groups in the eucalypts such as Angophora and Corymbia didn’t exhibit the same rapid diversification as the Eucalyptus species.




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What we confirmed with the fossil record using our phylogeny is that until very recently, and I mean in terms of the Earth being 4 billion years old, the vegetation of southeastern Australia was vastly different.

At some point in the last 2-10 million years the Eucalyptus arrived in new environmental conditions. They thrived, they most likely helped spread fire to wipe out their competition, and they then rapidly changed their physical form to give us the many species that we see today.

Very few other groups in the world have made this amount of change so quickly, and arguably dramatically. The east coast of Australia would look very different if it wasn’t dominated by gum trees.

The next time you’re in a eucalypt forest, take a look around and notice all of the different types of bark and gumnuts and leaves on the trees, and know that all of that diversity has happened quite recently, but with a deep and long link to trees that once grew in Gondwana.

They have been highly advantageous, highly adaptable and, with the exception of a small number of species, are uniquely Australian. They are, as the press would put it, “a great Australian success story”.The Conversation

Andrew Thornhill, Research botanist, James Cook University

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Koalas sniff out juicy leaves and break down eucalypt toxins – it’s in their genome


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Koalas spend a large part of the day sleeping – while their digestive enzymes get to work.
emmanueleragne/flickr , CC BY

Jenny Graves, La Trobe University

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.




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We now have a high quality read-out of the koala genome. Video thanks to the Australian Academy of Science.

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.




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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.




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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).

Koalas have 16 chromosomes per cell.
chrisfithall/flickr, CC BY

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.




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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.




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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.

Koalas are the sole surviving member of the Phascolarctidae marsupial family group.
Photo by Holger Link on Unsplash, CC BY

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.


The Conversation


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Jenny Graves, Distinguished Professor of Genetics, La Trobe University

This article was originally published on The Conversation. Read the original article.