S3.12 Out Standing in the Field: the highs and lows of genetics fieldwork

Kat: Hello, and welcome to Genetics Unzipped - the Genetics Society podcast with me, Dr Kat Arney. In this episode we’re off on our virtual travels, finding out about the highs and lows of fieldwork. From chasing butterflies up mountains to artificially inseminating kakapos with the help of drones and putting angry birds in paper bags until they poo, we talk to the researchers studying genetics and evolution in action.

Every year The Genetics Society runs the Heredity Fieldwork Grant scheme, awarding up to £1,500 to cover the travel and accommodation costs for researchers wanting to carry out a fieldwork project in genetics.

Our stay-at-home roving reporter Georgia Mills caught up with four intrepid explorers who’ve been off on their travels in locations as exotic as New Zealand, Lanzarote and the Lake District to hear more about their research and what they learned out in the field.

The Great British Butterfly Hunt

Kat: Melissa Minter, a PhD student at the University of York, is studying how the UK’s most secretive butterfly species - the mountain ringlet is coping with climate change - and whether there is any hope that they might be saved. 

The mountain ringlet is the UK’s only montane butterfly, and as the name suggests, they live right at the top of mountains, so there aren’t any more places for it to go as the climate warms. If there’s enough genetic diversity in the butterfly populations that still remain, they might be able to adapt and survive in the future.

But before Melissa could answer that question, she first had to find them. It was time to put on her hiking boots and go on a butterfly hunt.

Melissa: I did some really excellent fieldwork where I went and found this butterfly all over the UK. Which means I actually went to some of the most beautiful places in the country. 

This butterfly only occurs in the Lake District in England and in the Scottish Highlands, so between the Cairngorms and Loch Lomond National Park there's a belt of mountains there which is where they occur.

So, my field work was basically me climbing up a mountain and sampling this butterfly so that I can do some genetic testing on it. So, it was tiring but really fantastic fieldwork.

Georgia: Wow! So how did your calves compare at the beginning and at the end of all this mountain climbing?

Melissa: I think I weighed myself before and afterwards and I think I lost a stone over my fieldwork season.

Georgia: Oh my goodness! So how did you catch the butterflies?

Melissa: You would spend maybe between an hour or three hours climbing, then when you start to come into the area where you know they are, you start getting excited. Then you see this brown, very small butterfly fly in the distance and you just absolutely leg it with your net. (Laughing) That's basically it. A lot of sprinting and trying not to fall over.

Georgia: Was the butterfly net like the net I'm imagining, the sort of stick with a hoop on the end?

Melissa: Oh yes, definitely.

Georgia: And how common were these butterflies? How long did it take to spot them and then chase them down in an average day?

Melissa: Once you are in the area where there are mountain ringlets, there are loads of them. It's actually amazing because I've never seen so many of one species of butterfly. 

Because normally, you go in your garden and you see maybe one small tortoiseshell. You go to the woods and you might see a few speckled woods, but to see the amount I saw in these areas was amazing.

You'd get into the area and you'd start seeing them flying around and they would be everywhere. So most of the time, it didn't take me longer than an hour to collect the males that I needed to collect. 

That would be a struggle, an hour, most of the time it would be in 20 minutes. Then after that I'd sit and have my lunch and watch more and more mountain ringlets flying around. There were just so many of them.

Georgia: Have you managed to do any of the genetic analysis yet?

Melissa: I've done some mitochondrial DNA sequencing of some of the UK populations along with the European populations, which I managed to get hold of to try and see whether the UK was unique in terms of the kind of genetic diversity we have here in comparison to Europe, which it does. 

The Lake District has really high genetic diversity in comparison to Europe. You can see that Scotland and the Lake District don't really share that much genetic information. 

This suggests that potentially they came from different areas of Europe or they colonised the UK separately after the last ice age, which is really interesting because you would think that because they were both in the UK, that they came from the same area and split off after the last glacial, but it looks as though that might not be the case.

Georgia: Okay, so is it good news or bad news for the butterflies, for climate change?

Melissa: Well, because there is so much genetic diversity in the mountain ringlet across all of Europe, because they've been separated into these distinct mountain regions, it is more likely that they may be able to lose genetic diversity. 

So if the populations suffer under huge climate change, it means that we'll also lose genetic diversity in the mountain ringlet; which is really important because as we've discussed before, genetic diversity is really important for them to be able to adapt, not only to climate change but any other environmental threats.

Georgia: So, it's bad news either way really but we're possibly not going to see them completely gone, at least?

Melissa: Hopefully not. Hopefully not.

Endangered Angry Birds

Kat: Ewan Stenhouse is a PhD student at Cardiff University, who’s got his eye on a different elusive UK species: hawfinches. He’s finding out whether differences in diet between UK and European hawfinch populations might be behind their decline in the British Isles, putting them on the red list for threatened species here while their continental cousins in Europe are thriving. 

Rather than trudging up mountains or through muddy fields, his fieldwork experience was rather cushy. But to start with, for those of us who’ve never seen a hawfinch, what are they like?

Ewan: So, a hawfinch is the biggest species of finch in the UK. They are found in North Wales, the New Forest and the border, so the Wye Valley and the Forest of Dean. They look pretty evil. I think the best way to describe them would be - you know the little red birds out of Angry Birds?

Georgia: Yeah?

Ewan: They look a little bit -- they've got this kind of evil glint in their eye. They are amazing, really cool looking birds. They've got massive bills. And their name in Greek, or the Latin name is Coccothraustes coccothraustes, and that actually means the one that can actually break the kernel. So they can crack cherry stones and olive stones. They're pretty powerful.

Georgia: Do you know what? I'm just looking up pictures of them online at the moment and you're absolutely right. They do have angry eyebrows, don't they? They look like they're going to go for your eyes.

Ewan: Yes, they look absolutely furious, yes.

Georgia: But saying that, we still want to save them. So tell me about your fieldwork. How did that come into it?

Ewan: Okay. So my European fieldwork basically involved me initially sending off loads and loads of emails to different bird ringers in continental Europe to say what my project was about and what I was doing and if they could help me.

A few people from Denmark got in contact with me initially and said yes, we ring hawfinches in the woods by my house or in my back garden, you're more than welcome to come out and do some fieldwork here. It was the same in Germany as well.

It was really interesting because when I initially went out there, I didn't know what to expect at all. I thought it was going to be very much like ringing was here in the UK, which is you get up at 4.00am in the morning, you're sitting in a freezing cold car or even worse, standing in the middle of the woods just kind of waiting. But because these birds visit back gardens really regularly in continental Europe which they don't here, it was great.

It didn't really feel like fieldwork to be honest, Georgia. It was me sat in a nice warm house, getting fed. Especially in Denmark. A bit of breakfast, all the cups of tea that I could handle and we just sat and waited for them to go into the nets in the back garden.

Once they were there we just went out, extracted them. We'd take biometric data and then the really strange bit is - I put it into a brown paper bag and then I'd wait for it to do a poo, it's really glamorous. So it was basically from that faecal sample that I would do all my genetic work with.

Georgia: Okay, so how are the genetics of the poo coming into things?

Ewan: The best way to describe it would be - this poo is my entire PhD really. And that's a sentence I never thought I would say. Because you want to look at the diet of an animal but you want to do it non-invasively, collecting faecal samples is a really good way of doing that because we don't have to harm the birds.

So faecal sample collection is a really good non-invasive way of collecting dietary information. Because obviously, what the bird has been eating recently will be passed out in its poo.

Georgia: Brilliant. So what kind of things did you find in the poo? What had they been eating?

Ewan: I'm currently working through the main analysis of my results. What we've found so far is that the number of different things, the number of dietary items that we've found in Europe is a lot higher than in the UK.

The most common thing we found was sunflower seeds. That's because in order to bait the site, to get the hawfinches to come down from the trees (because they're notoriously shy and secretive) you basically have to give them an all-you-can-eat sunflower seed buffet for weeks and weeks and weeks before you even put up any traps.

We also got - beech was there, European beech, hornbeam and then when I did the same analysis for invertebrates, it was just a lot of caterpillars. Which makes sense because they're big and squishy and full of nutrients and water.

So it's been interesting to look at the diet and to compare the UK and European populations because there's a definite difference.

Georgia: Right, so does this give us any clues as to how to bring back the hawfinch to Britain?

Ewan: Hopefully. What we can do is, working in conjunction with the RSPB who are my case partners, we can look at the diet and say, okay, there's a really high occurrence of say beech or hornbeam or this or that type of tree species or this species of invertebrate. Once we've got this detailed knowledge of the diet, we can start planting certain trees that will hopefully encourage them back.

Georgia: When you were sequencing the DNA, I know sometimes they can crop up with quite surprising things. Did you find anything very weird that they'd been eating?

Ewan: Yes, a few things. Once you got rid of the obvious human contamination like - I don't know - raisins, the most interesting thing I found was that quite a lot of birds had been eating cashews.

Georgia: Oh?

Ewan: Yes. Now, as far as I'm aware, there isn't a lovely plantation of cashew trees growing in the middle of the Forest of Dean or Snowdonia.

So I think it shows that actually, they are visiting garden feeders slightly more often than people think. Because people do make their own bird seed and people put all sorts out for garden birds.

It's almost like I'm getting a sneak peak into people's back gardens through the diet work. It's quite interesting. I think cashew was probably the strangest one. I got some lemons and satsumas as well, oddly enough.

Georgia: And we mentioned earlier they've got a kind of mean look about them and this incredibly powerful beak. How was it, working so closely with them and having to handle them? Were they good partners?

Ewan: No, it was painful.

Georgia: Painful?

Ewan: Yes, it was painful. Because when you handle a bird it's called the ringer's grip. So you basically get its head in between your two index fingers and in a cloth bag, you can usually feel where the bird's head is so you can be really gentle and work your way around without getting your fingers getting bitten off.

But because I'm putting them in these paper bags, it's thicker. So you can't really feel where the bird's head is beforehand. What you've basically got to do is just shove your hand in and then have a little feel around. Obviously, you can't feel the bird's head so you don't know where it's beak is.
I actually showed my lab a video of me trying to extract the hawfinch out of the bag and I didn't realise quite how much swearing was in it. Because once it's actually clamped onto your finger, it hurt.

It leaves a little diamond-shaped scar like this. It's there for a good few hours. It's pretty impressive. They are powerful birds and yes, if they bite you, especially on the knuckles, you know about it.
They've got incredibly flexible necks, I found. So I'd be holding one quite happily and then I'd look away for a second and it would just somehow turn its head nearly --

Georgia: Just full-on Exorcist you?

Ewan: -- yes, nearly 360 degrees and then clamp onto my knuckle. Then I'd look back!

Georgia: Have you still got all your fingers?

Ewan: Yes, just about, just about!

Pipits and Canaries

Kat: Claudia Martin, who’s doing her PhD at the University of East Anglia, ended up in a slightly more glamorous location for her field trip - the Canary Islands, off the coast of west Africa. But she wasn’t studying the eponymous canaries - instead, she had her sights fixed on a different bird. 

Claudia: I study a species called the Berthelot's pipit, which most people haven't heard of. It's a small, brown bird. It diverged from mainland Africa 2 million years ago and spread across the Canary Islands and several other archipelagos including Madeira and the Selvagens.

I'm interested in how these populations have diverged across these islands and how different habitats and selection processes have driven their evolution across these islands.

Georgia: Cool. So is this a similar kind of thing to Darwin's finches?

Claudia: Yes, pretty similar. Quite interestingly, we can see differences in the bill morphology across the different populations. So just like Darwin's finches we're interested to see how different ecological pressures have driven this change in physical appearance that we see, and why that might be advantageous for some individuals.

I'm specifically interested in trying to identify signatures of selection. So across the genome, we can find regions of the genome that give us indications of selection in that region. We can identify what that region does by looking at the genes.

Previously we've found that some of these regions are quite closely related to disease. Across my pipits in the different islands, there's quite a variation in the levels and presence of disease. We were interested in following this up further.

For this particular bit of fieldwork we decided to travel to Lanzarote, which is an island that quite a lot of people will be familiar with. Here on this island, we actually find a really high presence of disease in populations where we'd measured a small number of individuals in previous years.

So we wanted to follow this up further and see if we could actually identify - not only across the populations but also within a particular population - if we were able to get a better idea about what's going on at specific loci that we were interested in, in relation to this disease in this population.

Georgia: Take me through when you first arrived. How was it? Was it exciting, scary?

Claudia: I guess when you first arrive, you've got the whole island to explore. You think, okay, where are we going to collect these birds first? Because they're just fairly non-descript, small, brown, birds, you think, well, how am I going to be able to find that bird hopping around, compared to any other bird?

But we quickly learned that the pipits have a very specific preference for habitat. They quite like low scrubland but also all the way through to desert, where you wouldn't expect there to be much there. They need just the right amount of habitat and it's quite hard to catch pipits in some of these habitats.

So we learned, for example, that there are some small shrubs in Lanzarote that have small yellow flowers, they provide a lot of insects for the birds. So when we'd try and catch the pipits in these small areas, it's almost impossible to entice them into our traps.

I should probably talk about how we try and catch them. We use something called clap traps. As the name suggests, they are pinned open with a baited pin which has a little worm on the end. So we are relying on the birds being excited by the presence of this worm.

They hopefully come and tug the worm and that closes the trap on them and we quickly go and fetch them and release them safely shortly afterwards. In these areas where food is very prevalent, they're not interested in the worms, so it makes it quite hard to catch them.

Georgia: And how did you get the genetic sample from the birds?

Claudia: We take a small blood sample from each of the birds, an absolutely tiny sample, but enough for us to extract the DNA. We also monitor disease in the islands. As I said, we're quite interested in Lanzarote because it's got a high prevalence of disease.

These species are exposed to both avian malaria and also an avian pox, which is a viral pathogen which causes massive legions on the birds feet and also sometimes on their beaks.

So we've taken samples of those as well, which we can later sequence. That will tell us more about the evolution of individuals that do or don't have the diseases.

Georgia: Have you managed to get into any of the data yet? Do you have any idea what is going on with these populations?

Claudia: Yes, it looks quite exciting. We can identify that the malarial strains in Lanzarote are very closely related to those on mainland Africa that we find in the sister species of the pipit, the tawny pipit.

Whilst that's not that surprising, it's quite exciting to see that maybe there hasn't been that much evolution of the viral strain recently.

Also, we found an exceptionally high presence of malaria in the populations, so actually 70 percent of our birds had malaria, which to me was surprisingly high. So this will probably be driving evolution in that island quite strongly, and providing quite a strong selection pressure on the birds.

Georgia: What was this work like? How did it compare to the rest of your PhD?

Claudia: I found it really exciting because it allows you to take the work back to its bare bones.

Going and seeing the environments and the variation that we can see in the genetic data and actually being able to see it on the ground - both in terms of the variation in the ecology of the islands, but also variation in the individuals of the birds - is really exciting.

One day we had a particularly poor day. I'm not quite sure exactly why, but we kept catching lizards in our trap. So instead of catching birds, the lizards were quite enticed by the worm.

Sometimes if we put the traps too close to a pile of rocks, a little lizard would climb out and get the worm instead of a bird. Which gave us quite a disappointment when from far away, you can see the trap is gone. You run up to the trap and what you've got in there is a small lizard which looks rather startled.

Georgia: I'm sure a lot of people listening to this will think it sounds like basically the best thing ever - getting to go to Lanzarote and look at birds all the time. So can you give us a reality check? Was it all sunshine and easy? What were the harder moments?

Claudia: Whilst I do really, really enjoy it, it is exceptionally repetitive. Every day you get up, you may or may not catch many birds. Some days we caught one, probably from being out in the field for 10 hours or so.

So it's a bit hard to keep your morale up when you've been to four locations and caught no birds, and sometimes not even seen any. I generally really enjoy it but I do seem to be pooed on quite a lot, I must admit.

And we repetitively use the same kit, so we have to wash it quite well every night so as not to have so much waste. So yes, cleaning pooey trays at 11.30pm at night after dinner is -- I think most people wouldn't enjoy that part. But I shouldn't complain, we had a fantastic time.

Good vibrations: conserving kakapos

Kat: Our last intrepid genetic explorer is Lara Urban, who’s now a conservation researcher at the University of Otago in New Zealand, and previously did her PhD at the University of Cambridge. She used her Heredity Fieldwork grant to go in search of some of New Zealand’s most iconic birds: kakapos and takahes.

While kakapos have a place in science history as the only species to have had all its living members genetically sequenced, that’s not the only thing that’s appealing about these flightless birds.

Lara: They both look quite funny actually, the takahe being often called like a fat blue chicken. If you're already here it might not be so interesting, whereas I actually think its colour is absolutely beautiful - the blue, iridescent colour.

I think what might be more interesting for people is the kakapo though. It's a quiet, large, green parrot. It's also quite fat, at least during breeding season. They gain quite some weight.

You can really imagine it as a large green parrot, a really beautiful green colour. They have very large claws and beaks; they can climb with them. Now that they can't fly anymore, they actually became quite good climbers. So sometimes they also just fall of the tree. But yes, I definitely recommend that everyone look them up online. They are very endearing creatures.

There's actually one kakapo who was called Sirocco. When Stephen Fry and Mark Cawardine visited the kakapo for a documentary, one very famous kakapo called Sirocco started climbing onto Mark Cawardine's shoulders and tried to copulate with his head. He was a little bit too curious, I guess!

That's also I think how the kakapo became famous worldwide. It's really true that some of them are really interested in humans. They just don't know that we could cause any danger for them and they follow you around.

Or if you actually wake them up, they will complain by making a very weird sound which is called the booming sound. They don't really care that we humans might do something to them. They don't really know, which is a good thing, I guess.

Georgia: Tell me about your fieldwork. What were you specifically trying to do and what did a normal day look like?

Lara: So last year when I came here, I got the chance to go to Whenua Hou, which is one of the three or four islands where the kakapo still live nowadays.

I mainly came here to do computational work on the genomics of the kakapo but I was very lucky to be able to be allowed to go to Whenua Hou for a few weeks to do some fieldwork there. Whenua Hou is in the South of New Zealand, so quite close to the Antarctic already. It's really far out there in the wild.

I went there mainly to get to know the kakapo conservation project. When I was there on the island what I mainly did was to help out with supplementary feeding and other technical work, helping out because I went during a very, very busy breeding season.

Last year was the most successful breeding season of the whole kakapo conservation project, so there were a lot of chicks to take care of so I mainly helped out.

However, I also got to talk a lot to the rangers and talk about the problems that exist within the kakapo species, with respect to inbreeding for example. We see that a lot of the eggs that the kakapo lay are infertile, so that's about half of the eggs that are being laid are not fertile at all.

These were very interesting insights, where I can then look from the genomic perspective and try to figure out what's going on. I also helped with some artificial insemination and maybe we can talk a bit more about that later on. But mostly I was just walking across the island.

Georgia: Tell me more about holding the little kakapos to do health checks and the artificial insemination. What did that look like? Sounds a bit chaotic.

Lara: Yes. So holding them was actually already a bit chaotic because you have to be really, really careful of their strong beaks and claws. The rangers showed me a very specific way of how to hold them, so as not to hurt them but also hold them in a firm way. Because if they get loose, they might be able to hurt you quite strongly.

In my case once a claw got loose a little bit and I got a little bit of a wound. I still have it, but I'm really happy about it actually!

So whilst holding them, the rangers, who are much, much more experienced than me would do health checks on them and check their eyes and their feathers, which are representative of their overall fitness.

With respect to the artificial insemination, we had some experts in artificial insemination on the island during the time that I was there. They tried a new approach, basically, to get semen from the male birds.

I guess you can best describe it as being like a quite small vibrator. They would hold it to the cloaca of the kakapo and would then get some sperm - not a lot, most of the time, but a little bit of sperm - that they could then use in a very targeted way to fertilise another female.

So if for example, you knew a certain male and a certain female weren't related at all to each other, but they had territories that were really far away from each other, so they would never meet naturally, we could then fly the sperm of the male over to the female.

I say fly over because that's actually how we did it. We used drones to fly the sperm from one point of the island to the other.

So if we were lucky enough, when the male and female were close to each other, it was possible to just directly bring the sperm there and fertilise the female. But sperm quality could deteriorate quite quickly if we were on two other sides of the island.

The island is not large but it is so hilly, it would take a lot of time to walk there. So yes, the takahe recovery team and I think especially Andrew Digby, the leading scientist, had the idea of just using drones.

I think that's one of the examples where we can see how innovative the kakapo conservation team has been in the protection, using all sorts of technology.

Georgia: That's brilliant. I've heard of drones being used for science, but for carrying sperm is not one I'd heard.

Lara: Yes, it was the first time I'd heard of it too.

Kat: Georgia Mills talking to Lara Urban about her work to conserve New Zealand’s iconic flightless birds. There’s a link to an online lecture about these fascinating creatures here.

And in case you’re insatiably curious about how a kakapo might try to copulate with someone’s head, there’s a link to the Youtube video on there to, entitled “Shagged by a rare parrot”. Don’t say I didn’t warn you.

If you’re a genetics researcher and you’d like to apply for a Heredity fieldwork grant, head over to The Genetics Society website, genetics.org.uk and take a look at the grants section.

Conserving Chimps

Kat: And finally, it’s time for a quick look at what’s in the latest episode of the podcast from Heredity, the journal of The Genetics Society. Chimpanzees are our closest cousins, but they are at risk of disappearing from the wild thanks to poaching for bushmeat and the illegal wildlife trade.

James Burgon’s been talking to Peter Frandsen from the University of Copenhagen and Claudia Fontsere from the Barcelona Biomedical Research Park, who have been developing new genetic tools to aid in the conservation of this iconic species.

Peter: The Chimpanzee as a species now live in the troubled regions of equatorial Africa. The species consist of four different sub-species. Where you have the three neighbouring sub-species in the most central part, they are all endangered, while the more isolated western chimpanzees are now listed as critically endangered species.

Most of the threats are -- I mean, they all have a human component to it, like deforestation, transmission of diseases and hunting for bush meat. The illegal wildlife trade has really sparked in recent years.

James: It's interesting, I'm not sure many people had really considered the bush meat angle.

Claudia: Yes and I think diseases are also a major threat for chimpanzees. Since they are our closest relatives, they can also get infected by infectious disease that we as humans get, such as Ebola. And recently there have been some people starting to talk about how SARS can also infect these species.

James: I wonder how you think your study might help in say, chimp conservation efforts and the fight against their exploitation?

Peter: There's about 1,000 individual chimpanzees sitting in centres across Africa at the moment. So if we get a hair sample from any of these sanctuaries, we can pinpoint where that animal was captured. When we can collate all that data together, we get some really good insights to some of the main harvesting farms for the illegal trade.

Of course, it can also be used for relocation if you want to reintroduce the captured individuals into the wild. You can actually find exactly where the chimp originally came from.

Lastly, if you have that information of where it was captured and also, where it was confiscated, you can start putting lines between these points and perhaps get an idea about some of the trafficking routes and hopefully in the future, break those routes.

James: That would be the dream.

Peter: Yes.

Kat: You can find the full interview in the latest Heredity podcast - just search for Heredity in your favourite podcast app, or follow the link here.

• Paper: Frandsen, P., Fontsere, C., Nielsen, S.V. et al. Targeted conservation genetics of the endangered chimpanzee. Heredity (2020). https://doi.org/10.1038/s41437-020-0313-0

That’s all for now. Thanks very much to our stay-at-home roving reporter Georgia Mills.

Next time we’ll be exploring some more stories from the history of genetics. In the meantime, you can find us on Twitter @geneticsunzip and please do take a moment to rate and review us on Apple podcasts - it really makes a difference and helps more people discover the show.

Genetics Unzipped is presented by me, Kat Arney, and produced by First Create the Media for The Genetics Society - one of the oldest learned societies in the world dedicated to supporting and promoting the research, teaching and application of genetics.

You can find out more and apply to join at genetics.org.uk  Our theme music was composed by Dan Pollard, and the logo was designed by James Mayall, transcription is by Viv Andrews and production was by Hannah Varrall. Thanks for listening, and until next time, goodbye.