What’s in a scat? Quite a lot, if you’re interested in conservation and environmental genomics. In fact, studying animal diets through DNA analysis of scat material can reveal whether animal populations are genetically healthy, how they are moving around and impacting their environment, and what they’re eating.
But to extract any of this information, you need labs, and to set up and manage those labs, you need a geneticist with a vision.
In 2020, the year of shutdowns and lockdowns - Fenner School Director Dr Saul Cunningham decided to pursue developing genetic labs at the School, and sought out an expert to invite into the School’s scientific community. He found Dr Linda Neaves.
“There was a realisation at Fenner that the School as a whole is across so many environmental and social aspects of conservation science; we have all of these incredible long-term ecological studies, and littlegenetics. But it’s a field many of these studies could do so much with, if the School had a geneticist in the building, directing these inquiries," explains Dr Neaves.
Before arriving at The Fenner School, Dr Neaves was working partly at the Australian Museum doing marsupial genomics work with koala populations in forensic science and trace DNA, and partly between the UK and China, doing population genetics of bamboos and understanding which ones were important for the giant panda. She quickly set to work setting up the lab and building up a genetics base at Fenner.
“Coming to ANU is the coming together of all of these these different things, because I can draw on the Australian mammal genomics and plant work that I’ve been doing, and the eDNA and diet work, and pull these together into a lot of the long-term ecological studies that are happening through researchers at Fenner.”
So what goes on in genetic labs, and who uses them? We took a tour of the new setup to discover everything you need to know about how they work, why you need several isolated rooms to do DNA extraction and analysis, and what DNA can do for conservation work.
The Fenner School labs are made up of three key rooms. Each has colour-coded lab coats. This is because the process of extracting DNA from various samples needs to be a clean, clear and simple process, otherwise DNA can float into other samples and interfere with the testing and findings.
The first room - small, relatively sparse, with a fumes chamber - is a DNA-free-zone. People who use this lab wear a red coat, and the only thing that comes in from the outside, are people - nothing else.
“In this room we have all of the reagents we use, so we can keep them safe, use them, set everything up, and then take it out to the next room to add the DNA to it. Then we know all our reagents are nice and clean, there’s no contamination, so we’re not going to go and have a researcher doing quoll DNA extractions in there one day, and someone doing bettong diet another day, and saying, ‘That’s funny - bettongs are eating quolls! That’s not right.’ Because we know everything’s clean, and we’ve got protocols in the lab that allow us to keep track of these processes," explains Dr Neaves.
The second room - the largest of the three - contains white and occasionally tie-dyed lab coats. PhD Scholar and Research Assistant Brittany Brockett is sitting at a workstation, sampling out bettong DNA to look at diet and trophic interaction. Dr Neaves explains that this lab is where the DNA is introduced to the base materials created in the first lab, to be cleaned and extracted for further analysis.
Then Dr Neaves takes us down a corridor to the third and final room in the DNA extraction process. This time, blue coats hang at the door of the lab, and boxes of latex gloves rest above them. Here, a tiny single-copy of isolated DNA (or DNA barcode) is amplified to become 1-10 million copies of that barcode, with the help of a PCR machine.
“We call them DNA barcodes because they work exactly like a barcode in a shop: it’s a short bit of sequence that we can look at and it’s unique to a given species or genus. We can look for that in the scat, and if it’s there, then we know that’s what the bettong has been eating.”
The PCR machines cycles through different temperatures - up to 95oC, to separate strands of DNA and multiply the number of DNA barcodes that are of interest in the sample. When the process has ended, you’ve got a tube full of teeny tiny droplets that contain an intense number of DNA barcodes. For this reason, to prevent DNA barcodes from spilling into other samples, everything is kept in this third room once the final step of amplification has occurred.
So what’s the use in all this DNA work? Dr Neaves explains that genetic testing of bettong scats revealed that while many thought bettongs at Mulligans Flat mainly ate fungi, it turned out they were also digging up little holes around geophytes and insects and eating them. This work went on to contribute to the studies of PhD Scholar Catherine Ross, whose 3MT explained how her research examined the positive environmental impacts of bettongs’ digging.
"That’s not something that was really predicted. You can’t follow bettongs around without bothering them, and see all of that, so we collect the scats, and they’re really informative because we can get the bettong DNA out of that, we can get the DNA of everything that bettong has been eating out of that. And that gives us a whole insight into their impacts and interaction with the ecosystem, that can help us conserve things," Dr Neaves said.
"I really enjoy that there’s a big push here to do research that makes a difference on the ground. It’s still cutting-edge science, but we’re doing it to inform management and conservation, not just because we can," she adds.
“Every living thing has DNA: DNA defines what we are and what we’re like and how we function in so many ways. If you don’t understand that, you’re missing out on such a big part of the larger picture.”
Thanks to Dr Neaves, the new Conservation and Environmental Genomics Labs offer new possibilities to research projects, students, and researchers, providing a space for a range of genetic analysis to address all kinds of conservation and ecological questions.
Dr Neaves is eager to collaborate and develop new projects within Fenner, and with new students. If you’re interested in participating in labs this year, students can take ENVS3016 Special Topics and work with Dr Neaves to custom-build a genetics project. Dr Neaves is also co-convenor for BIOL3178, a course where students spend the second part of the semester working on small group research projects, two of which are in the lab.