AMplify: Episode 1, Dr Rebecca Johnson
For the debut episode, Kim McKay talks to Dr Rebecca Johnson, Director of AMRI, about what motivated her to become a wildlife geneticist.
"I look at the DNA of pretty much any species of animal, wildlife in our world here at the Australian Museum basically means all animals but not typically plants, and that also excludes humans... There's so many reasons why you'd want to know about animal DNA..."
Kim McKay: Hi, I'm Kim McKay, the director and CEO at the Australian Museum and today I'm going to take you on a journey looking inside the Australian Museum. You'll hear about our extraordinary collection which has more than 18.5 million objects and species, and also about our scientific research. The collection and our floor exhibitions are looked after by some 300 staff, and sitting opposite me today is one of the most important of those, it's the director of the Australian Museum Research Institute, Dr Rebecca Johnson. Welcome Rebecca.
Rebecca Johnson: Thanks for having me, Kim, it's a pleasure to be here.
Kim McKay: That's great, well look, we're going to have a great conversation which I'm sure the listeners are going to just love today because apart from leading the Australian Museum Research Institute, which is a role you've had for almost a year now, you're also a wildlife geneticist. Can you tell us what a wildlife geneticist does?
Rebecca Johnson: Yes, it's…well, I think that I have, when you count both of them, the two best jobs in the world. Leading the Research Institute is incredible and something I never thought that I would be doing. But being a wildlife geneticist is also pretty amazing. It's a very broad title, it means that I look at the DNA of pretty much any species of animal. So wildlife in our world here at the Australian Museum basically means all animals but not typically plants, and that also kind of excludes humans. So wildlife genetics, anything you can think of out there in the wild.
Kim McKay: Now, we know why humans want to know about their DNA because it helps us understand why we are the way we are and maybe can help us with our medical conditions. But why do we need to know animals' DNA?
Rebecca Johnson: There's so many reasons why you would want to know about animal DNA. The obvious ones might be that you can understand how diverse a population is, and through those types of information you can then understand if there are certain ones that need to be conserved as opposed to others, how things are related to each other at the DNA level. We are all related…when you come down to it, we all have a common ancestor of a multicellular organism, and so we all actually share a lot of DNA.
Kim McKay: I've never invited that ancestor over. Is that a relative I don't want to know?
Rebecca Johnson: Only after a very long day perhaps. So we are actually all related at the molecular level, and DNA can be very informative in that sense because it helps us understand how things are related and how deeply they are related.
Kim McKay: You have really spearheaded a project which has come to global attention, and that is sequencing the DNA of the koala for the first time, and you did that I think as part of a consortium. What was that called?
Rebecca Johnson: The Koala Genome Consortium, very aptly named I suppose, and that's a really exciting project because it's something that is multidisciplinary, so we are working with colleagues from all around Australia to start with, but now we have welcomed a few international collaborators, which is very exciting. It's also really exciting for a museum to be involved in spearheading a really big project like that, that hadn't really been done at that level in a museum in Australia before.
Kim McKay: The koala is one of our iconic species, obviously, people love koalas. It's sort of like the kangaroo and the emu. I think Australians like to think of themselves as fuzzy koalas sometimes when we travel. So we love this animal, but it is under threat, isn't it.
Rebecca Johnson: Yes, they are really interesting little creatures too. They have no close relatives, so their closest living relative is the wombat. There used to be other species that went…
Kim McKay: The closest relative is the wombat?
Rebecca Johnson: Yes, that's right. And they are very distant, it's millions and millions of years since they've shared a common ancestor. So they have no other…there's no other species of koala, so it is what it is. And so coming with that, because we love them so much, sometimes we think of them as honorary humans really, with their big long limbs and their big eyes, and they are quite sedate really. Because they have no close relatives, it is really important to understand how to conserve them. And population genetics is very important in that way, so that we can understand what is the genetic diversity of each population, ensure that we are maximising that diversity so we don't inadvertently lose a whole chunk of the population and with that might be some adaptive potential.
So an example that I often use is the Tasmanian devil, for example. They were isolated on an island for a long time, and as a consequence one of the things that happened is they have very low diversity in their immune genes, and they have this very well characterised transmissible cancer that causes the facial tumour that we know from those terrible photos that causes them to die effectively from starvation. And because they have no…one hypothesis is that due to no immune gene diversity, when this novel unusual cancer came along they didn't really have any response to it. And so we really don't want koalas to end up the same way, particularly through things that humans might be introducing through habitat loss or roads or dogs.
Kim McKay: Is this how chlamydia got into the koala population?
Rebecca Johnson: I actually can't answer that question because we actually don't know yet, but it is a possibility that it had been introduced via domesticated animals to Australia. But it may have been here much, much longer. And so the genome is really important because we can understand the genetic basis of how they might react to a disease. So we can again understand at the molecular level what is really important when they are working through things like perhaps a vaccine for chlamydia, for example.
Kim McKay: How big is the koala genome?
Rebecca Johnson: It's the same size as humans roughly…
Kim McKay: Wow.
Rebecca Johnson: So it's quite big. And so it is a lot of work because it is quite a large genome. To put it into perspective, the human genome cost billions and billions of dollars and it took over 10 years to put together. What we know about humans is actually quite useful for translating to other animals because we share a lot of DNA in common, as I mentioned earlier. However, because koalas don't have any close ancestors who have had their genome sequenced, there is only three other marsupials have that have been done to date…
Kim McKay: What are they?
Rebecca Johnson: Those are the tammar wallaby, so the first kangaroo, the American opossum, so that's a marsupial from South America and North America, and the Tasmanian devil. So those are the three that have been done to date.
Kim McKay: So you've done this initial work by sequencing the DNA, but you are continuing, I know, with this work. What are you doing now?
Rebecca Johnson: So we are looking at…sequencing technology evolves incredibly fast, even faster than computing technology. It's hard to keep track of the latest phones and the latest devices that can help you do your work, DNA technology evolves even quicker. And so we have had the fortune of being able to do some really new DNA sequencing methods which give us really, really long reads of DNA, and that's what we are doing at the moment, and that's going to give us a really incredible genome. And that is helpful for things like the immune genes which are actually expanded gene families. They probably started off with a single version a long time ago and have expanded so that what they look like on the chromosome, for example, is pieces of DNA repeated over and over and over again, but they are all slightly different because they all have a slightly different function. But when you sequence them, they end up all jumbled up because they all look similar enough that it's hard to know exactly where they go in the sequence. So this new technology actually sequences big, big long strings of DNA, almost like they are on the chromosome, and that means we don't have to assemble so much and we can get a really good idea of where the immune genes sit in relation to each other and how many there are.
Kim McKay: So will this work, Rebecca, actually help save the koala?
Rebecca Johnson: Yes, we very much hope so. The more information the better really, to understand how diverse they are, what kind of diversity we need to maintain going forward, what their immune genes look like, how this would actually interact with any vaccines in development. Some of our collaborators are quite involved in chlamydial vaccine development. And they also have this retrovirus which is…it's a virus that actually jumps into the genome and then disrupts the DNA around it. So we are trying to understand what this retrovirus is doing at the genome level in koalas because it is actually happening in real-time, which is quite unusual. We all have retroviruses in our genome and they jump into our DNA and then they just kind of sit there and do nothing. And I think it is estimated about 8% of our DNA is viruses that have jumped in and then just kind of died. But this one actually appears to be active.
Kim McKay: I mean, to do this work it must cost money, more than sort of a normal allocation to a museum. Where do you get that funding?
Rebecca Johnson: It's a great question, and science funding is a tough environment, for sure. So we've been very fortunate for things like the Koala Genome Project, for example, we've had funding from another of sources. So places like Bioplatforms Australia who are a federally funded organisation who allow us to access infrastructure like DNA sequences. We have been very fortunate to receive funding from the Australian Museum Foundation, which is philanthropic gifts and donations, and we've also received a number of other grants to do specialty projects on the koala, for example. And for our other wildlife genomics work we receive similar grants, donations and other contract work to fund that type of work, which is a little out of the ordinary.
Kim McKay: And some organisations like Customs or Quarantine who use the facilities actually pay fees too, so you are actually like operating a mini consulting service on the side.
Rebecca Johnson: That's right, they pay for our expertise and to access the specialty infrastructure that we have for us to produce those types of results.
Kim McKay: I know that one of the unusual things about you and one of your collaborators there is that you are both forensically qualified. I've watched CSIon television, like a lot of people. What does that actually mean?
Rebecca Johnson: Yes, so we are forensically qualified, which is not something, again, you might typically think of at a museum. We are forensically qualified in wildlife forensics. What wildlife forensics means in our world here at the Australian Museum is that we might get a sample brought in to us that is, say, a seized bird egg or something…
Kim McKay: Do you mean by Customs or Quarantine?
Rebecca Johnson: It could be by Customs, it could be by Quarantine.
Kim McKay: So when we see those people being inspected at the airport, it actually does mean something?
Rebecca Johnson: Yes indeed, and it's very important. It's sadly not uncommon for us to be brought in samples that might be from an endangered species. So there's a lot of legislation around protecting illegal trade of endangered species because of course we want to keep them alive and not put them in the illegal trade. But also quarantine is important to remember because things that have been brought in illegally are going outside of the normal channels of understanding if there's any potential infectious diseases and introduced species risk with that type of introduction.
Kim McKay: So you can actually go to court and give evidence based around the research work you do?
Rebecca Johnson: Yes, and I think that's something that's really special about places like museums and other collecting institutions because we have the scientific expertise. So my background in genetics has allowed me to understand how things are related based on their DNA. But what we have here at the museum is the most extraordinary natural science collection of animals and tissues that relate to those animals that I can draw upon as my reference material.
Kim McKay: How many DNA samples do you have in that fridge? I know, I've seen in there, I've seen literally tens of thousands of test tubes.
Rebecca Johnson: We have about 100,000. So it's fairly small compared to most of our other collections, and it's because it's a much younger collection than the rest of the extraordinary things we have here.
Kim McKay: So it's extraordinary, once upon a time a specimen would be an actual example of a particular species, but now it's the DNA samples that become the specimens as well.
Rebecca Johnson: Yes, your best specimen has both. So your best specimen has your entire body still intact, possibly a skeleton if it's a vertebrate, for example, and also it has a DNA sample or a tissue sample that is taken from that individual. So the best ones have all three.
Kim McKay: Now, in your work with customs and quarantine looking at these illegally imported or exported species, what's the most extraordinary thing you've come across?
Rebecca Johnson: Gosh, they are always unusual…
Kim McKay: I mean, I know you get a lot of birds through.
Rebecca Johnson: You do get a lot of birds.
Kim McKay: It's extraordinary when someone can keep an egg on their body, isn't it.
Rebecca Johnson: People are very creative about where they might illegally transport wildlife…
Kim McKay: In their underwear.
Rebecca Johnson: It helps to keep them warm to keep them alive, so no warmer place than in your underwear I suppose. You might also be delicate about those areas because you don't want to crack these eggs that you're transporting. People do all sorts of strange things, from transporting things in ground coffee, to in their underpants, to strapped to their legs…
Kim McKay: But you've also picked up very rare objects as well and also things that are completely illegal to trade, like rhino horn.
Rebecca Johnson: Yes, sometimes you just think, man, how did they even get hold of this specimen, these things that you can almost count the number of these things in the wild on a couple of hands, and it's really quite sobering and quite sad that people are trading things because basically they can make a few dollars out of it, or a lot of dollars in some cases.
Kim McKay: And of course importing or exporting ivory is also illegal now, correct?
Rebecca Johnson: That is correct, yes.
Kim McKay: But I know you've got a lot of specimens that come in from time to time, even jewellery.
Rebecca Johnson: Yes, all sorts of things are carved out of ivory. I think it's a desirable substance because you can work it to carve all sorts of things into it. But I personally prefer to see it on the elephant, it looks good on the elephant.
Kim McKay: It does, doesn't it. But what if you've got a historic object made out of ivory?
Rebecca Johnson: That is a good question. So if you can demonstrate that it's pre-convention, so if you can demonstrate that the ivory is collected before the endangered species legislation came into force, then it is legal to keep as antique ivory.
Kim McKay: Rebecca, I could keep talking to you forever and I wanted to talk to you all about AMRI in general and women in science because of course you're the first woman to lead the Australian Museum Research Institute, but we're going to have to keep that for another day. Rebecca Johnson, it's been fantastic to have you on the Australian Museum podcast.
Every week, join Executive Director & CEO Kim McKay in conversation with scientists from the Australian Museum Research Institute (AMRI) and experts in Indigenous Australian and Pacific cultures.