NATURE PODCAST

Podcast: Fox aggression, microbiota and geoengineering

Join Adam Levy and Benjamin Thompson for the latest news from the world of science.

This week, shaping the gut microbiota, geoengineering’s effect on farming, and the genetics of fox aggression.

In this episode:

00:45 Geoengineering and your food

A new study suggests that undoing some of the warming from greenhouse gases wouldn’t undo the effects on agriculture: Research paper: Proctor et al.

07:12 Gut bacteria vs the immune system

An insight into how the immune system affects the gut microbiota of mice: Research paper: Fulde et al.

11:57 Research Highlights

Modern humans aren’t at all hobbit; and mapping microbes on the metro: Research Highlight: A single island spawned two populations of miniature humans; Research Highlight: Transport network’s handrails teem with a mix of microbes during evening rush hour

13:33 Fox genetics

Over half a century of studying tame and wild foxes uncovers some genetic clues to aggression: Research paper: Kukekova et al.

19:42 News Chat

The winners of a prestigious maths prize; and a new look at the origins of language: News: Number-theory prodigy among winners of most coveted prize in mathematics; News: Diverse genome study upends understanding of how language evolved

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Transcript

This week, shaping the gut microbiota, geoengineering’s effect on farming, and the genetics of fox aggression.

[Jingle]

Host: Adam Levy

Welcome back to the Nature Podcast. This week we’ll hear how the immune system affects gut bacteria, and the side effects of a procedure to cool the planet.

Host: Benjamin Thompson

Plus, the latest results from a 60-year study of fox behaviour. I’m Benjamin Thompson.

Host: Adam Levy

And I’m Adam Levy.

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Interviewer: Adam Levy

What can we learn from disaster… from one disaster in particular? On Saturday June 15th 1991, the second largest volcanic eruption of the 20th century took place - Mount Pinatubo in the Philippines.

Clip from a news report

In the shadow of Mount Pinatubo, towns and villages lie covered in a thick blanket of volcanic ash and mud. More bodies are still being discovered while volcano experts here argue about Pinatubo’s future behaviour, the people below continue to move out. It’s estimated half a million people have fled their homes.

Interviewer: Adam Levy

The effects of this devastating eruption were felt far beyond the Philippines. The volcano pumped millions of tonnes of sulfur dioxide into the atmosphere. This chemical formed ‘sulfate aerosols’, which thanks to their size and chemical composition, scattered sunlight. Here’s agricultural economist, Jon Proctor.

Interviewee: Jon Proctor

The earth cooled by about 0.5 °C, and that’s because more solar radiation or sunlight was being bounced into space.

Interviewer: Adam Levy

These aerosols and their cooling effect wear off after a couple of years. So, fast forward to summer 2018, and we’re not currently experiencing the cooling from a big volcano like Pinatubo. Instead, the planet has continued to heat up as we’ve continued to pump increasing amounts of greenhouse gases into the atmosphere. Now, though, some researchers are asking whether we could one day mimic volcanoes like Pinatubo to cool the globe. Such proposals are called ‘solar geoengineering’.

Interviewee: Jon Proctor

The main goal of solar geoengineering technologies, is to cool the Earth by reflecting sunlight back into space, and this is similar to how you might stand under a tree during a hot day in the shade to cool yourself off.

Interviewer: Adam Levy

The idea is that this technique could be used to offset some of the warming caused by the carbon dioxide and other greenhouse gases. The most common suggestion is to pump the same kinds of aerosols produced by volcanoes into the upper atmosphere. And while researchers are confident this would cool the globe, many other effects are less certain. Importantly, it’s remained unclear how these solar radiation management techniques would affect farming.

Interviewee: Jon Proctor

Because solar radiation management both cools the Earth and reduces the amount of sunlight that hits the Earth, we were unsure about what the net effect of these forces might be.

Interviewer: Adam Levy

So, reversing some of the temperature rise caused by greenhouse gases reduces heat stresses on crops, and so would be expected to benefit agriculture. But by scattering sunlight, these aerosols would both reduce this light, and make it more diffuse, and it’s unclear how this might impact crops’ ability to photosynthesise. Modelling studies have attempted to weigh these factors against each other, but it’s hard to be certain what a computer model may have missed. So, in a study out this week, Jon took a different approach.

Interviewee: Jon Proctor

A key innovation in this study was to use the volcanic eruptions that, in some ways, inspired geoengineering technologies to study the effect that the technology might have on agricultural production.

Interviewer: Adam Levy

To do this, Jon looked at how crop yields varied within individual countries as levels of sulfate aerosols varied overhead in the years before and after eruptions. This allowed him to tease out how cooling and reduced sunlight were affecting agriculture. Environmental scientist Alan Robock, who didn’t work on this study, was impressed by its approach.

Interviewee: Alan Robock

I think it was a very nice paper because it actually used observations of what actually happened, rather than using models of agriculture, models of amount of sunlight from aerosols.

Interviewer: Adam Levy

But what did the observations reveal? The study found that yes, the cooling from sulfate aerosols is positive for agriculture. But John found that the reduced, scattered sunlight had net negative effects, cancelling out the benefits of cooling.

Interviewee: Jon Proctor

Put another way, if we imagine geoengineering as an experimental surgery, our results suggest that the side effects of the treatment are just as bad as the original disease.

Interviewer: Adam Levy

And Alan stresses how important understanding the outcomes of this operation are.

Interviewee: Alan Robock

One of the impacts of global warming, probably the most important one, is how it will affect our food supply. If you’re trying to solve that problem of reduction of agriculture with geoengineering, this study tells you that it’s not going to work.

Interviewer: Adam Levy

While Alan has confidence in Jon’s approach, he points out that farming techniques will continue to change over the coming decades, potentially altering how crops respond to the effects of these aerosols. He also stresses that due to limited observations, the results of this study stem mainly from a single eruption - Mount Pinatubo.

Interviewee: Alan Robock

They did the best that they could with the available data but it was a one-off, and so we really need to look at it in more detail.

Interviewer: Adam Levy

Jon agrees that more detail is needed to understand the effects that solar geoengineering might have on the globe. And while his study suggests that dimming sunlight might cancel out any benefits to agriculture from cooling, he believes that it’s not time to stop investigating this procedure just yet.

Interviewee: Jon Proctor

Just because the first test of an experimental surgery had side effects for a specific part of the human body, doesn’t mean that the procedure should be immediately abandoned. There are many sort of illnesses that are so harmful, that procedures known to cause side effects are sometimes still worth the risk. And so, kind of similarly, research into geoengineering should not be entirely abandoned because our analysis has demonstrated one adverse side effect. There may be many good reasons to eventually pursue such a strategy despite some costs.

Interviewer: Adam Levy

That was Jon Proctor who’s at the University of California, Berkeley, and before him Alan Robock of Rutgers University, both in the US. Check out the study in the usual place.

Interviewer: Benjamin Thompson

Listeners, we often talk about the gut microbiota on the podcast, and this is of course the community of microbes that live in our intestines. The formation of the early gut microbiota, which happens after birth and during early infancy, is believed to be a particularly important window of time that could have long-lasting effects on our immune system. However, while a lot of research has looked at the effects that colonising microbes have on the developing immune system, there has been less research on the other side of the coin - namely, how the immune system affects the microbes. Well, in a Nature paper this week, Mathias Hornef has been redressing that balance. He is looking at how the immune system shapes which bacteria become part of the microbiota in mice. This shaping is an important process, as he explains.

Interviewee: Mathias Hornef

The current kind of information that we have indicates that after birth, any type of bacteria can colonise the gut, and it is hard to imagine that this would be beneficial for the host. So, we would think that the host organism actually prefers a certain type of bacteria to colonise, and that the host should try to regulate this process and limit maybe colonisation by some and favour colonisation by other bacteria that are more beneficial.

Interviewer: Benjamin Thompson

To work out how this might be happening, Mathias and his colleagues focused on a particular immune molecule that’s known to impact the gut microbiota in mice – it’s called TLR5. Now, broadly speaking, TLR5’s job is to recognise a protein found on the outside of some bacteria called flagellin. If detected, TLR5 then switches on an immune response to deal with the invading bacteria. During the first two weeks of a mouse’s life, Mathias and his colleagues found high levels of TLR5 in the cells that line the small intestine. Although these levels quickly dropped off, this short window of time made a big difference, as these mice had far fewer flagellated bacteria present in their gut microbiota. Mathias also looked at mice which had been engineered to not have TLR5 in their intestines, and their gut microbiota looked very different, containing a lot more flagellated bacteria. And that’s not all…

Interviewee: Mathias Hornef

This seems to persist for 150 days - that’s what we looked at. And this is much longer than the 30 days TLR5 is actually expressed in the gut epithelium.

Interviewer: Benjamin Thompson

This short-lived mechanism seems to have a long-lasting influence. These results offer a new insight into how the early gut microbiota is shaped.

Interviewee: Mathias Hornef

I think the take-home message is that there does exist a mechanism in the neonate that favours the colonisation of certain bacteria, and disfavours the colonisation of others. And interestingly, this mechanism only exists in the neonate, but the effect actually persists throughout life, at least in mice.

Interviewer: Benjamin Thompson

Knowing how the immune system shapes bacterial colonisation will give researchers a

better understanding of what’s going on in early life. This window of opportunity is really

important, as Lizzie Mann, a gut microbiome microbiota researcher, who was not part of the

study, explains.

Interviewee: Lizzie Mann

I think there’s been a whole load of evidence showing that it’s a really critically important window during development where microbiota interactions shape immune homeostasis and immune function, but also susceptibility to disease later in life. And we know that the microbiota that establishes then plays a really big role on how the immune system develops in the gut, what diseases we get, but the mechanisms are still quite unclear. So, I think what’s great about this paper is it really starts to unravel how that actually happens.

Interviewer: Benjamin Thompson

This work might begin to unravel how the early immune system modifies the gut

microbiota, but it’s by no means the end of the conversation – we are just beginning to learn how one affects the other. It’s a fantastically nuanced system, with many environmental and genetic factors at play. Not to mention of course, this current work is in mice, and the mechanisms involved might be completely different in humans. Here’s Mathias again.

Interviewee: Mathias Hornef

I think definitely that it may be different in humans. The interesting thing here is that this type of mechanism does exist, because we previously didn’t know this. So, I’m sure in humans there are also mechanisms that kind of shape the early microbiome, whether they are TLR5 or any other TLR or any other mechanism, I don’t know. But the human has the same kind of problems to deal with.

Interviewer: Benjamin Thompson

That was Mathias Hornef from the RWTH Aachen University in Germany. You also heard from Lizzie Mann from the University of Manchester in the UK. You can read Mathias’ paper over at nature.com/nature.

Host: Adam Levy

The News Chat is still to come at the end of the show, where we’ll find out about the mathematicians that picked up this year’s Fields Medals. Now, though, Shamini Bundell is here for this week’s Research Highlights.

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Interviewer: Shamini Bundell

The island of Flores in Indonesia became famous in 2003, after the discovery of a remarkably small, extinct human species nicknamed ‘the hobbit’. Ever since the fossilised remains of Homo floresiensis were found, scientists have wondered whether the hobbit’s genes could live on in certain local people of unusually short stature. Now, the question has been answered. Genetic analysis of these modern Homo sapiens has revealed no trace of hobbit DNA. Instead, the short height of these modern islanders may have evolved in response to the same evolutionary pressures that created the original Hobbit, tens of thousands of years ago. Read more in Science.

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It’s maybe no surprise that microbes mingle on the metro, but which ones are present and where do they come from? A team in Hong Kong studied the bacteria found on handrails in the city’s Mass Transit Railway System. They found that during morning rush hour, each railway line had a microbiota characteristic of the neighbourhood it served, but by the evening, bacteria from the whole city had mixed together. Their work helps illuminate the ways in which microbial species and antibiotic resistance genes spread around a city. Find out more in Cell Reports.

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Host: Benjamin Thompson

In the 1950s, a pair of Russian scientists by the name of Dmitry Belyaev and Lyudmila Trut started an experiment. They wanted to create a population of tame foxes. The foxes came from fur farms all over Eastern Europe. Although farmed, these animals hadn’t lost their natural aggression towards humans. Belyaev and Trut gradually began selective breeding, choosing foxes with the least aggressive traits. The experiment has now been running for over 50 years and has created foxes with a range traits, from tame animals which wag their tails and dote on their humans to foxes specifically selected for aggressive behaviour. Anna Kukekova from the University of Illinois in the United States has taken a particular interest in the fox farm experiment. She wants to understand more about the genetic basis of aggressive and tame behaviour, and the foxes provide an intriguing model. Noah Baker called her up to find out more.

Interviewer: Noah Baker

Why are researchers interested in studying the fox genome? What is it about it that’s particularly interesting to them?

Interviewee: Anna Kukekova

I think first of all, we were interested about that because this particular population of foxes which was selected in Siberia for friendly response to humans and for aggressive response to humans, and we really want to figure out what’s going on in their genome which makes them to behave so differently.

Interviewer: Noah Baker

And how long has this Russian fox farm experiment been going on for?

Interviewee: Anna Kukekova

Since 1959.

Interviewer: Noah Baker

And so, now, the foxes that they’re getting, would you classify those as fully domesticated?

Interviewee: Anna Kukekova

I would not classify them as pets. They definitely don’t really show any aggression to people, but at the same time they will never be selected to be adopted to live in human houses, right. So, it’s kind of quite difficult to house-break them. I would say that they are domesticated, but they are not necessarily pets.

Interviewer: Noah Baker

Before your study, what was known about the genetics of fox behaviour, in particular when it comes to aggressive and tame behaviours?

Interviewee: Anna Kukekova

So, they did quite a bit of studies of their behaviour that demonstrated that differences in the behaviour of these foxes are genetically determined. But, it was very limited abilities to actually understand what kind of genetic differences make foxes to behave that way. We started to do some molecular genetics in these foxes in the early 2000s, and we were able to identify regions on fox chromosomes which contribute to fox behaviour, but these regions were very broad. We included tens of hundreds of genes and we could not really say which particular gene may have a certain behaviour.

Interviewer: Noah Baker

What is it you’ve done in this particular study?

Interviewee: Anna Kukekova

So, first of all we assembled the fox genome, and then we used this as a reference for our studies. And we sequenced 10 individuals from each population: tame, aggressive, and conventional farm-bred population which is kind of ancestral populations of both tame and aggressive to see which regions in genomes of foxes from these three populations actually differentiate them. In the early kind of computational techniques, we identified 103 regions which seem to differentiate these populations. You know, some of them may not do anything that is selection for behaviour, but we think that many, many of them are actually are indeed selected for behaviour.

Interviewer: Noah Baker

Tell me a little bit about the gene assemblies. What do you think the front runners are for tame behaviour, I suppose, which genes are most likely to be associated with tame behaviour?

Interviewee: Anna Kukekova

So, there’s 103 regions. Some of them have one gene, some of them have several genes and we pulled up on this study just one region, which contained gene SorCS1, and we tested if this gene actually has an effect on behaviour. We see that there is particular variants of this gene which make foxes more friendly. I want to emphasise that that’s not a single gene, and this study just pulled up on this particular gene because each region is a lot of work. So, actually to find specific gene and variants and so on, we could not do more.

Interviewer: Noah Baker

SorCs1 that you’ve highlighted – how do you suggest that that might have an impact on tame behaviour? What does it do and why might that make behaviour more tame?

Interviewee: Anna Kukekova

We didn’t do any functional studies yet, but taking into account that SorCs1 is the main trafficking protein for AMPA glutamate receptors is definitely something which is very important for how neural systems function. But exact mechanism still needs to be investigated.

Interviewer: Noah Baker

How have studies into aggressive or tame behaviour been done in the past? Fox is an odd model for this – it hasn’t really been a common model for this?

Interviewee: Anna Kukekova

Yes, most common model to study genetics of behaviour is mice. But to say the truth, the number of behavioural phenotypes, behaviours which can be studied in mice in particular to genetic level, are quite limited in terms of social behaviour.

Interviewer: Noah Baker

This study has been specifically in foxes to understand aggressive behaviour, but could it have implications outside of foxes?

Interviewee: Anna Kukekova

Yes, it’s again, because, you know, in mice we can study only very specific elements of aggressive behaviour, but aggressive behaviour is much broader, right. And in foxes, again, we cannot study any type of aggression behaviour, but we can study something different. And if we find the genes we know more genes which are involved in aggressive behaviour, and I think it’s also very important for human studies in this way, our work is supported by the National Institute of Health because there is not much information about the genes which are involved in social behaviour.

Host: Adam Levy

That was Anna Kukekova, speaking with Noah Baker. Her paper was published in Nature Ecology and Evolution. You can find it at nature.com/nee.

Interviewer: Benjamin Thompson

Right then listeners, finally this week it’s time for the News Chat, and I’m joined here in the studio by Davide Castelvecchi, maths and physics reporter here at Nature. Hi Davide.

Interviewee: Davide Castelvecchi

Hello Ben.

Interviewer: Benjamin Thompson

Well, first up this week then, this is a story that just missed out on last week’s show, but I think it was an important one nevertheless. Every four years, the Fields Medals are awarded. Davide, maybe you could tell our listeners what the Fields Medals are?

Interviewee: Davide Castelvecchi

They are the most coveted awards for a mathematician, especially or actually exclusively, for a young mathematician, because they are only given to people who are 40 years old or younger.

Interviewer: Benjamin Thompson

Well, we’ve got four winners this year, and let’s talk about them in turn. The first one is Peter Scholze, and if I was a gambling man, Davide, I think he was probably odds on to be one of the recipients this time round.

Interviewee: Davide Castelvecchi

Yes, although you probably wouldn’t make a lot of money because he was everyone’s favourite. As a matter of fact, the question most often heard, you know, in the math community was not who’s going to win the medal, it was who do you think will win, apart from Scholze?

Interviewer: Benjamin Thompson

Oh my goodness, well let’s talk about what he’s actually won it for then. What, sort of in overarching terms, is his field of research?

Interviewee: Davide Castelvecchi

It’s a very abstract field called arithmetic geometry. He’s famous for devising this kind of mysterious concept called ‘perfectoid space’, and it’s, loosely speaking, number theory and specifically, these number fields called p-adic numbers.

Interviewer: Benjamin Thompson

And as I understand, he was quite the wiz as a graduate student?

Interviewee: Davide Castelvecchi

Indeed, and he became the youngest person ever in Germany to rise to the level of full professor at the age of 24.

Interviewer: Benjamin Thompson

Well, so seemingly a deserved winner then. The next winner has got a very interesting backstory, and this is Caucher Birkar.

Interviewee: Davide Castelvecchi

Indeed, Birkar, who is a UK citizen, he first came to this country as a refugee. He is Kurdish, from the predominantly Kurdish region of Iran. He works in algebraic geometry which is the study of geometric figures that are defined by polynomial equations.

Interviewer: Benjamin Thompson

And it sounds like he had rather an exciting time during the awards ceremony as well.

Interviewee: Davide Castelvecchi

Yes, the poor fellow. Soon after he received the medal, he put it in his briefcase but his briefcase was stolen. And then the organisers decided to award him a replacement medal which happened just a couple of days later.

Interviewer: Benjamin Thompson

So, he’s actually got the medal in hand?

Interviewee: Davide Castelvecchi

Yes.

Interviewer: Benjamin Thompson

Well, let’s keep going Davide, we’re halfway through now, and the next winner is Akshay Venkatesh.

Interviewee: Davide Castelvecchi

He’s described as a very versatile mathematician, and probably his most famous work was also done in number theory, on problems that date back to the 1800s but they have been almost intractable until now.

Interviewer: Benjamin Thompson

Alright then, well the last one then, and I have to get his name right, Alessio Figalli.

Interviewee: Davide Castelvecchi

Alessio Figalli, yes. He’s only the second Italian to win the Fields Medal in history, and he is, probably you could describe it as, the only one among the four who works on problems closer to applications, like the differential equations that arise in physics, for example.

Interviewer: Benjamin Thompson

Well, there are our four winners then Davide, and obviously, this sort of represents quite an early peak for these young mathematicians. Where do they go from here?

Interviewee: Davide Castelvecchi

Well some people say that mathematics is a young person’s game. The truth is there’s plenty of examples of people who have done incredible work after getting a Fields Medal, and perhaps one example could be Edward Witten, who is the only physicist who ever got the Fields Medal because he’s also a top-notch mathematician, and he’s done some really important contributions to mathematics after he got the Fields Medal.

Interviewer: Benjamin Thompson

Well finally then on this one then Davide, and I think it’s important that it’s raised - four men, yet again.

Interviewee: Davide Castelvecchi

Yes, there’s only been one woman so far who won. It was the late Maryam Mirzakhani who won in 2014 and then tragically died of cancer soon after that. There’s been some calls for the awards committee to look into potential bias, because surely there are other women in mathematics who are deserving of a Fields Medal.

Interviewer: Benjamin Thompson

Well Davide, let’s move on to our second story. And earlier in the podcast Noah was talking about actual foxes, and in this one we’re talking about the FOXP2 gene. Now, maybe you could tell our listeners at home what that gene is involved in.

Interviewee: Davide Castelvecchi

We know that it’s a gene that has something to do with language. There’s been studies on certain mutations in families that have speech impediments, and there’s also been studies that have suggested that it could play a crucial role in giving humans their unique ability to talk,? which is obviously something that sets us apart from all other primates.

Interviewer: Benjamin Thompson

I mean, Davide, this is kind of a superstar gene, I guess, and there was the thought that because it was so special, it spread through the human population very quickly.

Interviewee: Davide Castelvecchi

Yeah, so there was evidence that this gene had spread quickly around 100,000 years ago across human populations. This is something that usually happens when a gene gives you a particular edge over the people who don’t have it. And it’s a study that’s been cited hundreds of times. It seemed like oh, finally we’ve found the gene for language, but now there’s a second study, or new study, that can kind of puts that into question.

Interviewer: Benjamin Thompson

And what’s this new study saying then?

Interviewee: Davide Castelvecchi

Well, it’s putting into question the very basis of the earlier claims. The 2002 study was based on a small number of people of about 20, and most of them were of European backgrounds, so it turns out that if you broaden your search, then you’ll find that perhaps there wasn’t such a quick spread. And in fact, also there’s been studies that show that similar mutations in the FOXP2 gene were also seen in Neanderthals, and we know that Neanderthals split from humans long before maybe half a million years ago.

Interviewer: Benjamin Thompson

Well, does this mean kind of the end of the road then for FOXP2, that it’s not involved in language at all?

Interviewee: Davide Castelvecchi

It seems that there’s no question that it is involved in language, but as with many traits and even diseases, it’s usually hard to pin something down to a single gene. Things are always more complex than that, or almost always.

Interviewer: Benjamin Thompson

Well, what are some of the researchers behind the original 2002 work saying about this new study, Davide?

Interviewee: Davide Castelvecchi

So, yeah, the authors of the original study are welcoming this new evidence, and they say that even if there was no, you know, such quick spread of the gene, it’s still clear that the gene plays an important role in our language skills.

Interviewer: Benjamin Thompson

Thank you, Davide. To read all the latest and greatest science news from around the world, head over to nature.com/news.

Host: Adam Levy

That’s all we’ve got time for this week, but before you go, make sure to give us a review and some stars wherever you get your podcast. It helps us get the latest science news to all the greatest science listeners. Until next time, I’m Adam Levy.

Host: Benjamin Thompson

And I’m Benjamin Thompson. Thanks for listening.

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