Australasian Science Magazine

By the 1980s there were as few as 40 individual northern hairy-nosed wombats. Credit: Alan Horsup

By Lauren White & Jeremy Austin

Creative sampling and DNA techniques have allowed scientists to keep track of one of Australia’s most endangered and elusive marsupials.

The northern hairy-nosed wombat is an elusive and critically endangered marsupial. Despite their large size, northern hairy-nosed wombats are surprisingly difficult to see and count reliably. They live in large underground burrow systems that are hundreds of metres long, with multiple entrances and many passageways, and only emerge for a few hours each night.

Sighting one is therefore difficult. Sighting enough to get an accurate population count is almost impossible.

To figure out how many wombats are left, we have been using an unusual and somewhat low-tech technique – sticky tape placed across burrow entrances – to collect wombat hair for DNA analysis. This non-invasive sampling allows us to identify individual wombats and estimate population size without ever having to actually see or catch one.

Conserving a Species

Before European arrival, the species is thought to have been widely distributed in eastern Australia, from southern NSW to central Queensland. However, loss of habitat, competition with grazing stock and a string of droughts in the 1900s saw the species contract to just a single surviving population at Epping Forest in central Queensland. By the 1980s their numbers were as low as 40 individuals. Without intervention the species faced almost certain extinction.

To save northern hairy-nosed wombats from extinction, the Queensland Government began to carefully manage the sole surviving population in the 1980s when it became apparent just how endangered they were. To do so Epping Forest was declared a national park and cattle were excluded from the area. This ensures that the wombat’s remaining habitat and food supply is preserved, and prevents cattle from competing with them for food. Additionally, a large mesh fence was erected in 2009 to keep out wombat predators, such as dingoes and foxes, and feed and water stations were set up for use during times of drought.

Most importantly, the wombat population is monitored. Regular population counts are vital to inform the park managers about whether or not their efforts are working. A decrease in population size might prompt additional action to help the species survive. On the other hand, if the population at Epping Forest reaches a large enough size, a group of wombats could be selected to start a new insurance population elsewhere.

It is also important to monitor the sex ratio of the population. Any gender bias would mean that the number of breeding individuals is considerably smaller than the actual number of wombats. If this is the case, a population’s size would provide misleading information about its recovery.

However, monitoring wombats is not easy. Night vision cameras set at burrow entrances can be used, but wombats have very few markings that can distinguish them from a burrow-mate. Trapping is also not ideal: it is labour-intensive and can negatively affect the health of the trapped animals. It is also not very effective: while cages can be set at the entrance to the burrow, wombats have been known to simply dig themselves under or around them. How, then, can we monitor the wombats effectively?

Genetic Monitoring

DNA provides a way to work around the wombats’ secretive nature. Faecal pellets, shed skin, saliva, feathers and hair are all easily gathered sources of DNA for difficult-to-observe animals.

For our work with the northern hairy-nosed wombat, hair is collected non-invasively by stringing double-sided sticky tape across their burrow entrances. As the wombats enter or exit their burrows, hair sticks to the tape and leaves behind a DNA fingerprint of each individual wombat.

Many hairs can be collected over several nights. For example, in 2013 we collected 1260 individual hairs over 7 nights. Every hair was carefully placed in its own small tube, a task that involved tweezers, good eyesight and no small amount of patience.

DNA extracted from this hair is then analysed in a laboratory using several genetic markers that enable us to distinguish one wombat from another, in much the same way DNA is analysed in human forensic cases.

There are many types of genetic markers, but those used for our wombat study are called microsatellites. These consist of short sequence of DNA bases repeated multiple times. The number of repeats in each microsatellite varies, not only between wombats but also within a single wombat. This is because almost all animals have two copies of each non-sex chromosome. Therefore each wombat will have two copies of each microsatellite, and these may be of different lengths. By determining the size of both copies of multiple microsatellites, we produce a pattern that is specific to a single wombat, much like a barcode (Fig. 1).

A wombat’s gender can also be determined using DNA. Using a marker that is only present on the male Y chromosome, we can figure out whether a hair came from a male or female simply by observing if the gender marker is present or absent.

By collecting hair over several nights, population size estimates are then calculated by seeing how many unique wombat barcodes we find, and estimating what proportion of the population we are likely to have sampled. These hair censuses for the northern hairy-nosed wombats have been conducted every 2–3 years, and a steady increase in population size has been observed since they began in 2000.

Last year we once again collected hair samples from the wombats of Epping Forest and conducted genetic analyses. A population size of roughly 200 wombats was estimated – a fantastic result showing that the northern hairy-nosed wombat population is continuing to grow.

However, the analysis also revealed a male bias within the population. It is important that further investigations are conducted to determine the cause of this skew and, if it increases, actions are taken to mitigate it.

Nevertheless, a growing population size is something to celebrate. If this trend continues it may give the green light for translocations of wombats to other areas. This is exactly what happened in 2009 when 15 wombats were moved to Richard Underwood Nature Reserve in southern Queensland. Although this is only a small group at the moment, future translocation could allow this population to become self-sustaining like the one at Epping Forest.

Such insurance populations are very important as low numbers at Epping Forest make the wombats extremely vulnerable to disease, inbreeding and natural disasters. Without other self-sustaining populations at different sites, any one of these events could cause total extinction of the species in the wild.

Using DNA analyses as part of the conservation effort has additional benefits. For example, work is underway to amass the samples and data from several years of wombat hair censuses. This will give us unprecedented insight into the lifespan of wild wombats, their dispersal habits, and also identify any important changes in genetic diversity through time.

The future of the northern hairy-nosed wombat is highly precarious, and population censuses are vital to assist park managers conserve the species. Hopefully, the next population estimate will show that the northern hairy-nosed wombat population is continuing to grow and, using DNA analyses as part of the conservation effort, we hope to make sure they are here to stay.

Lauren White is a PhD student supervised by Jeremy Austin at the Australian Centre for Ancient DNA, The University of Adelaide.