Better living through informatics: in search of koalas

In 2015, I’d like to write, think and do more about things that I care about. One of those things happens to be the koala. Now, this being a blog about bioinformatics and computational biology, I can’t just start writing about any old thing that takes my fancy…I guess. So in this post I’m going to stretch the definition to include ecological informatics and tell you the story of how I achieved a long-held ambition using one of my favourite online resources, The Atlas of Living Australia. And then we’ll wrap up with a quick survey of the (sorry) state of marsupial genomics.

No longer a Koala Place

I would bet that if I asked many people for words associated with “Australia”, “koala” would be at or near the top of the list. Like the popular myth – or is it? – of “kangaroos bouncing down every street”, people outside of Australia might imagine koalas hanging from every tree.

This is very much not the case. I’m fortunate to live next to Berowra Valley National Park on the northern fringes of Sydney, surrounded by what looks like prime koala habitat – relatively large tracts of eucalyptus forest. Pictured right is a street not far from where I live, Koala Place. Maybe there were once koalas there – but not any more. In fact, very few people will have seen a koala in the region in recent years and very many Australians will confess to never having seen a koala outside of the zoo.

There are essentially two major reasons for this. First, koalas are not very easy to see. They’re thinly-distributed; more about that later on. They are quite well camouflaged, ranging from grey to chocolate-brown in colour. They spend much of the day barely moving, often high in a tree.

The second reason is that human activity has taken a terrible toll on koala populations. Over 80% of their habitat has been lost to land clearing. In the early part of the twentieth century they were hunted in their millions for their pelts. As humans encroach further into the edges of remaining koala habitat, death comes in the form of roads and attacks by domestic or feral animals. Environmental stress increases their susceptibility to diseases: particularly chlamydia and Koala retrovirus. We don’t know how many there were before 1788 – perhaps 10 million or more. We don’t know for sure how many remain – it may be considerably fewer than 100 000.

It’s interesting to note that even in the early years of European colonisation, koalas were difficult to observe. The first written record describes an encounter on what is now Australia Day with a “cullawine” near Bargo, exactly 10 years after the first fleet sailed into Port Jackson. This has led some authors to speculate that koalas have always been distributed sparsely in much of the Sydney basin.

Which brings me to my own story.

I’ve lived in Australia for almost 15 years. I’ve always been a keen amateur naturalist – that’s how I came to biology – and I’ve spent a lot of time walking in the bush. One day, I figured, surely I’d see a koala.
Years passed. It’s fair to say that my desire to see one in the wild became something of an obsession. I began to wonder whether there might be a medical condition named “koala blindness.” What was needed, clearly, was a more scientific approach. Enter The Atlas of Living Australia (ALA).

There are many entry points into the ALA. For this search I started at the datasets page and simply typed “Koala” in the search occurrences records box. This returns 45 342 records and a map. More powerful features are available by clicking on the button that says “view in spatial portal”.

Koala density in New South Wales & Victoria

Zooming into the state of New South Wales and selecting “Display as: Density grid” results in a view like the one shown at the left. Things to notice: first, koalas live around the eastern and southern coasts. Second, a lot of yellow which corresponds to the lowest density of records: 0-100 per grid square (1×1 km). Third, several orange and red “hotspots” of higher density, particularly along the central and northern coast of New South Wales. These are the last remaining fragments of high-quality environment for koalas.

Koala density around Sydney

Let’s zoom in to the NSW coast and centre on Sydney (image right). Now we see three density hotspots. From the top down they are:

• The Tilligerry Peninsula near Port Stephens
• An area south of Bathurst
• The Campbelltown region of south-west Sydney

Recent koala sightings near Campbelltown NSW

Campbelltown is the easiest day trip for me so the final step is to zoom into that region and switch from density grid view to points. We can also colour and highlight the points choosing from a large selection of variables. In this view (image left) more recent records are orange and red, with circles around the most recent records from the current decade (the 2010s). Using satellite view suggests that many recent sightings occurred around a network of fire trails between south-east Campbelltown and the Georges River.

See anything? Look closely.

Armed with this information and the public transport timetables, I arrived in Campbelltown on January 2 2015 and began walking the trails, neck craned toward the tree tops. After two and a half hours without success, the humidity rising and temperature passing 30 °C, I was contemplating return to the train station. I headed south for one more pass of a wide fire trail and as I rounded a bend, glanced up into the branches of a large gum tree.

My first koala in the wild

And there, after almost 15 years, looking back down at me – was this female with her youngster above her head (light-grey fur just visible in this image). There are some more images from the day over at my Flickr account.

Mission accomplished. Location of my sighting shown by the yellow arrow on the map, below-right. Thanks Atlas of Living Australia! There are many, many more ways to use the ALA, including programmatic access and I encourage you to go and play with it – and to campaign for its continued funding.

Location of “my” koalas

To finish, some brief words on the koala genome. There isn’t one. This might be confusing if you, like me, searched for “koala genome” using Google and found articles with titles such as “Aussie scientists sequence koala genome.’ In fact this is a partial transcriptome, assembled from RNA-Seq reads, translated to putative ORFs and used to BLAST search the NCBI NR protein database and some other marsupial sequences. I’ve long bemoaned the state of genome research in Australia and now that we’re well into the era of plentiful, cheap genomes, I think it’s shameful that we can’t raise the funds or resources to research our own iconic and important species.

Having said that: a koala genome might be beneficial in population or disease research, but it isn’t going to be much use in preventing road deaths, dog attacks or habitat loss. So if you love these animals as I do, put some dollars to good use. I’d suggest the Australian Koala Foundation is a good option and/or, given the importance of habitat conservation, the Wilderness Society.