NATURE PODCAST

Podcast: Denisovan DNA in modern Europeans, and the birth of an unusual celestial object

Listen to the latest from the world of science, brought to you by Nick Howe and Shamini Bundell.

This week, evidence of ancient hominin DNA in modern human genomes, and the origin of a snowman-shaped object at the edge of the solar system.

In this episode:

00:45 Intermixing of ancient hominins

By combing through the DNA of over 27,000 modern day Icelanders, researchers have uncovered new insights about the ancient hominin species who interbred with Homo sapiens. Research Article: Skov et al.

08:05 Research Highlights

The scent of lemur love, a hidden Viking trade route, and ‘gargantuan’ hail. Research Highlight: Lemurs’ love language is fragrance; Research Highlight: Vikings’ lost possessions mark a long-hidden early trade route; Research Highlight: Enormous hailstones inspire a new scientific size category: ‘gargantuan’

11:44 The origin of Arrokoth

In 2019, the New Horizon Spacecraft took images of Arrokoth - an unusual, bi-lobal object found in the Kuiper belt. Now, researchers believe they’ve figured out how it formed. Research Article: Grishin et al.

17:29 Pick of the Briefing

We pick some highlights from the Nature Briefing. This week we discuss why the Universe may be lopsided, and why water could actually be two different liquid states. Scientific American: Do We Live in a Lopsided Universe?; Chemistry World: The weirdness of water

Subscribe to Nature Briefing, an unmissable daily round-up of science news, opinion and analysis free in your inbox every weekday.

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Transcript

This week, evidence of ancient hominin DNA in modern human genomes, and the origin of a snowman-shaped object at the edge of the solar system.

Host: Nick Howe

Welcome back to the Nature Podcast. This week, the ancient hominins in your DNA…

Host: Shamini Bundell

And the origin of an unusual object at the edge of the Solar System. I’m Shamini Bundell.

Host: Nick Howe

And I’m Nick Howe.

[Jingle]

Interviewer: Nick Howe

First up on the show, how the genomes of modern humans can tell us about our past. You’re probably a little bit Neanderthal. Once upon a time, you may have considered that an insult, but these days, a lot of people are familiar with the idea that all humans outside of Africa can trace a little bit of their DNA – around 2% – to these now extinct hominins. And scientists are able to take advantage of that fact to learn more about Neanderthals.

Interviewee: Laurits Skov

And one way you can do that is you can sequence a lot of modern humans, and because our ancestors, when they left Africa, met and exchanged with these Neanderthals, looking at a lot of samples you can actually reconstruct what a Neanderthal population looked like.

Interviewer: Nick Howe

This is Laurits Skov, a bioinformatician with an interest in ancient hominins. This week in Nature, to get a better understanding of our Neanderthal cousins, he and his colleagues have been looking at genomic data from over 27,000 modern-day Icelanders. The samples were collected by their collaborators, a company called deCODE. So, how do you use modern DNA to work out what Neanderthals were like? Well, first, you have to find the ancient bits of DNA hidden in our genomes. To do that, you could start with the genome sequences of ancient hominins and then match them up with the sequences in modern humans. But this assumes that any DNA that doesn’t match isn’t ancient, which may not be the case. Besides, good-quality ancient genomes are, let’s face it, pretty hard to come by, so Laurits used a different strategy.

Interviewee: Laurits Skov

What we do here is that we say we don’t use any Neanderthal-Denisovan genomes, but we use the expectations that we have about what these fragments would look like. One, they are very different from other human fragments, and two, they should be fairly long.

Interviewer: Nick Howe

By looking for these characteristics, Laurits could identify what regions of the DNA were likely from an ancient hominin. Then he could go about working out where they were from by finding similarities with existing ancient genomes.

Interviewee: Laurits Skov

So, we actually learned quite a few things from sequencing this many individuals. One, we do find Neanderthal fragments but we also surprisingly found Denisovan fragments.

Interviewer: Nick Howe

Around 3% of all the ancient parts of the genome appear to be Denisovan in origin. The Denisovans – another branch of ancient hominins – are generally considered to have lived in Asia, compared to the more Eurocentric Neanderthals. In fact, Denisovan remains have only been discovered in Siberia and the Tibetan Plateau, so you might wonder how Denisovan DNA ended up in modern-day Icelanders. Well, John Capra, a computational geneticist who wasn’t associated with this work, was intrigued by this finding, but he wasn’t especially surprised.

Interviewee: John Capra

Over the past couple of years, there have been enough studies showing that these archaic groups moved around quite a bit, and that there were other events of interbreeding, for example, between Neanderthals and Denisovans in other places, so it’s not so surprising to me that we’re seeing here the potential after effects of another such interbreeding event.

Interviewer: Nick Howe

It appears that ancient hominins quite readily, well, spread their genes around, but John says that this study shows the strongest evidence so far that Denisovan DNA is, in fact, in Europeans. For Laurits, he thinks that it might show that ancient humans were spread a lot more widely than previously thought.

Interviewee: Laurits Skov

So, there might have been a Neanderthal population in the Middle East somewhere when Denisovans came over or, which is perhaps even more interesting, there could have been a Denisovan-like population all the way in the Middle East, which greatly expands the range where we think Denisovans lived.

Interviewer: Nick Howe

Laurits and his colleagues didn’t want to just use these samples to learn about ancient hominins. They also wanted to ask how ancient bits of DNA – Neanderthal or otherwise – might be impacting modern humans.

Interviewee: Laurits Skov

We thought there would actually be quite a significant amount of Neanderthal genes that did something, but it turns out that most DNA that we got from Neanderthals doesn’t have a huge effect.

Interviewer: Nick Howe

Now, Laurits did find some effects, but according to their analysis, they were very small. John isn’t so sure though. What researchers are looking for is associations between gene variants and physical traits, and John thinks that the criteria Laurits used to determine those associations were too strict. Also, John’s latest research suggests that, due to human interbreeding, these associations may not be direct.

Interviewee: John Capra

We discovered an interesting pattern that in many cases, the Neanderthal variant was not causing the association, but other variants that came into modern human populations through interbreeding that had actually been present in an ancestral population and then lost in human populations were causing the association. And so, it’s sort of a complex thing where interbreeding with Neanderthals introduced these causal genetic variants, but those genetic variants were not created in Neanderthals. They were present in a population that was ancestral to both Neanderthals and modern humans, and the Neanderthals gave them back.

Interviewer: Nick Howe

Whether or not these ancient genes are having their effect on modern humans, Laurits could still use them to gain insights about what Neanderthals themselves were like.

Interviewee: Laurits Skov

The type of mutations that Neanderthal fragments have compared to human fragments is different, and these types of differences, you can actually explain by a difference in generation time in Neanderthals. So, in this case, on average, their mothers were older and the fathers were younger, compared to modern humans.

Interviewer: Nick Howe

Laurits hopes that many more insights will come out of this huge dataset, and he’s excited for new archaeological finds to help us build a better picture of human history – Homo sapiens and otherwise. And what’s clear to both Laurits and John is that human history is far from straightforward.

Interviewee: Laurits Skov

We tend to think of populations being separate, like Neanderthals live in Africa and the Neanderthals in Europe, Denisovans in Asia, humans in Africa and there’s no mixing between these populations, but that certainly seems not to be true. We already know of Neanderthals and humans meeting, of course, but now there’s also Denisovans meeting with modern-day non-Africans, so in that sense, I actually think that’s quite nice, that human evolutionary history is much more complicated than we previously thought.

Interviewer: Nick Howe

That was Laurits Skov from the University of Aarhus in Denmark and the Max Planck Institute in Germany. You also heard from John Capra from Vanderbilt University in the US. Laurits’ paper is out now, and there’s a link to that in the show notes.

Host: Shamini Bundell

Later on, we’ll be finding out about paired asteroids at the edge of the Solar System. Right now, though, it’s time for the Research Highlights, read to you this week by Dan Fox.

[Jingle]

Dan Fox

A little perfume or aftershave might be the finishing touch you apply as you get ready for a hot date. But maybe that isn’t limited to humans, as a team of researchers from Japan have found that lemurs also up their smell game to attract mates. Male lemurs produce a floral scent from glands on their wrists that they use to attract females. And much like a Lothario applying cologne, the lemurs want to make sure any perspective mates smelt them coming, so they rub their scent glands over their tails to waft the fragrance even further. The scent was made up of three pheromones – compounds that animals emit to communicate with each other. As it got closer to mating season, the levels of the pheromones emitted from their scent glands increased, changing their aroma from bitter and leathery to floral and fruity. Find that fragrant research over at Current Biology.

[Jingle]

Dan Fox

What could we learn about you from the objects you’ve lost on long journeys? Depending on what you take with you, perhaps not much, but we might at the very least get an idea of what route you were travelling. The same idea has allowed researchers to reveal an ancient Viking trade route by uncovering a trove of artefacts from a glacier. A team from the UK collected hundreds of artefacts, including horseshoes, arrows and walking sticks from the receding ice patch at Lendbreen glacier in the mountains of southern Norway. By dating 60 of these objects, the team determined that Lendbreen pass was used for both local travel and long-distance trading from around 300 to 1000 AD. Their findings suggest that travellers use the pass in spring and early summer, when thick snow would have made the rocky terrain easier to navigate with pack horses. After 1000 AD, traffic started to decline as economic changes, colder winters and the bubonic plague took their toll. Pick up that trail over at Antiquity.

[Jingle]

Dan Fox

An otherwise unremarkable thunderstorm in 2018 may have yielded the largest hailstones ever recorded, with some as big as footballs. Researchers from Pennsylvania State University collected photographs, videos and stories from residents of Córdoba province in Argentina where the storm struck. The biggest hailstone recorded measured an estimated 18.8-23.7 centimetres wide, potentially bigger than the current record-holder – a 20-centimetre-wide hailstone that fell in South Dakota in 2010. The scientists propose a new classification for hail larger than 15 centimetres in diameter – gargantuan hail. But despite the size of the hailstones, weather radar failed to detect any reason for this storm to produce such extreme precipitation. The researchers suggest that meteorologists should work closely with the public to document future cases of gargantuan hail in order to understand the conditions that lead to it. Avoid any hailstones by staying inside while you read that paper in full at Bulletin of the American Meteorological Society.

[Jingle]

Host: Shamini Bundell

In 2006, the New Horizons spacecraft left Earth on its mission to explore what was then the furthest planet in our Solar System – Pluto. By the time it arrived nine years later, Pluto had been demoted to a dwarf planet. Nevertheless, the space probe successfully completed its flyby, gathering a wealth of data and some incredible images of the dwarf’s surface. But the mission wasn’t over yet. The spacecraft’s next target was a strange-looking object a billion miles from Pluto, which would turn out to have some rather unusual properties. This week in Nature, researchers have modelled how this object called Arrokoth might have formed. Anand Jagatia investigates.

Interviewer: Anand Jagatia

On 1 January last year, New Horizons flew past Arrokoth, the most distant object ever visited by a spacecraft.

Interviewee: Evgeni Grishin

Arrokoth is an object in what is known as the Kuiper Belt beyond the orbit of Neptune, and in 2014, it seemed like Arrokoth had a really unique shape – mainly, it looks like a snowman.

Interviewer: Anand Jagatia

This is Evgeni Grishin, a PhD student at the Technion in Israel, and he’s right – Arrokoth really does look like the head and body of a space snowman. It’s made up of two lobes – one bigger and one smaller – connected by a narrow neck. Researchers think that Arrokoth is a contact binary. It was made from two separate objects rotating around each other in a binary system which eventually moved closer together until they touched. The data that New Horizons gathered about Arrokoth in 2019 confirmed that it’s shape wasn’t the only unusual thing about it.

Interviewee: Evgeni Grishin

Arrokoth completes a revolution around its axis roughly once per 16 hours, and that’s surprisingly slow because usually other similar objects closer in decibels, they actually tend to rotate much, much faster.

Interviewer: Anand Jagatia

The other strange think about Arrokoth is the orientation of its spin. As it orbits the Sun, Arrokoth rotates as if the snowman is doing cartwheels in the snow, like the propeller on the front of an old aeroplane. This is odd because if it was formed from two bodies that are slowly spiralled in towards each other, losing energy because of the friction with gas and dust in between them, then we’d expect Arrokoth to spin on its axis much more quickly and in a different orientation, more like the propeller on top of a helicopter. So, how did Arrokoth form? To work it out, Evgeni and colleagues have used simulations of a three-body system. A familiar example of this would be the Earth, Moon and Sun. The Earth and the Moon rotate around each other, while both of them orbit the Sun.

Interviewee: Evgeni Grishin

We know that the orbital plane of the Moon is roughly misaligned by roughly 5 degrees compared to the orbital plane of the Earth and the Sun, and the orbit of the Moon seems to be pretty stable, right. Instead, if the angle between these two planes would have been 90 degrees and not 5 degrees, actually because of the perturbations induced by the Sun, the Moon would have collided with the Earth a long time ago.

Interviewer: Anand Jagatia

Simulating this process with the two parents of Arrokoth, the team showed that if they were rotating around each other in a plane that was misaligned enough from their orbit around the Sun, the Sun’s gravitational pull could eventually lead to a collision between them, producing an object that rotates like Arrokoth. And the relatively small size of the two parents would have helped them merge into a celestial snowman.

Interviewee: Evgeni Grishin

The collision looks to be gentle. So, in this case, a collision usually happens on a velocity which is very close to the escape velocity. So, for these bodies, these bodies are relatively small. The large one is roughly the size of London, probably smaller, and the escape velocity from the surface is roughly a few metres, I think 4 metres per second, so it’s really a very slow jogging.

Interviewer: Anand Jagatia

The small mass means that the gravity at play is pretty weak, so the two bodies that formed Arrokoth were able to collide relatively gently and fuse together rather than smashing into each other and breaking apart. The simulations also showed that the angle of impact is important for Arrokoth’s formation.

Interviewee: Evgeni Grishin

What’s important is what we call the impact parameter or the impact angle. In this case, you can imagine that the collision, in the two extremes, it could either happen head on or you can have almost like an edge-on collision or some kind of a grazing collision, and collisions that are more head-on, they generate much less of the spin period.

Interviewer: Anand Jagatia

Arrokoth has a slow rotation on its axis, so it’s this latter, more head-on collision that would have formed it. Arrokoth is the first confirmed contact binary that researchers have observed, but they think there could be many more lurking in the Kuiper Belt and beyond, so this process could be used to explain the formation of other objects in the Solar System too, including what New Horizons set out to explore in the first place – Pluto and its moon, Charon.

Interviewee: Evgeni Grishin

What’s weird is that Charon’s pretty close to Pluto. They’re what’s called tidally locked, meaning that Plutonians will see only one side of Charon and it’s like we see only one side of the Moon. It’s the same. Also, the angle between the orbit of Pluto and Charon and the orbit of Pluto around the Sun is almost 120 degrees. It’s really puzzling how we could have formed the system, and we really believe that probably the Pluto-Charon system was also formed by some kind of collision. Maybe on some similar mechanism, they will not become a contact binary like Arrokoth, but they will probably have some bouncing off and will be stuck eventually.

Host: Shamini Bundell

That was Evgeni Grishin from Technion in Israel. You can find Evgeni’s paper over at nature.com, and we’ll put a link in the show notes.

Host: Nick Howe

Finally on the show, you might be familiar with the Nature Briefing, Nature’s daily or weekly pick of science news and stories delivered directly to your inbox. Well, Shamini and I have been scouring it to bring you some non-corona science news. Shamini, what’s caught your eye this week?

Host: Shamini Bundell

So, the story I looked at is about the Universe being lopsided – that’s how Scientific American described it anyway – and what they’re talking about is lopsided in the rate of it expanding. So, you know the cosmic microwave background radiation…

Host: Nick Howe

Yeah, yeah.

Host: Shamini Bundell

So, at the Big Bang, you’ve got this radiation. We can still see it today and we can see that it’s really even, so the idea is that it kind of shows that the Universe is expanding all over at an equal rate. But this story – this is a paper from Astronomy and Astrophysics – looks at particular galactic clusters and, using a particular measurement of their luminosity, says actually these ones are less bright than they should be and those ones are more bright than they should be, and therefore it kind of could be because that bit of the Universe is expanding faster and this bit is expanding slower, which would be really weird.

Host: Nick Howe

So, in this case, it’s just the fact that some stars are dimmer than others and some are brighter than they should be if the Universe was expanding equally.

Host: Shamini Bundell

Yeah, exactly. This definitely hasn’t confirmed that the Universe isn’t expanding evenly. If that’s true, that will be like a major big deal, so this is like one hint of it and there have been other studies that have also found hints, but then there have been others studies that have been like no, definitely not, it’s all super equal. So, this is an ongoing debate, but that was the latest headline that I thought was peculiar. And what story did you pick from the Briefing?

Host: Nick Howe

So, you know water, right?

Host: Shamini Bundell

Yeah, I think so.

Host: Nick Howe

It’s sort of an important thing. How do I put this? Water is like well weird. So, most liquids have pretty consistent properties, but water just really doesn’t. It is really unusual compared to every other liquid. So, for example, when you cool things down, typically liquids become more dense, and that happens with water as well, up to a point, to around 4 degrees, but then after that it actually becomes less dense. That’s why things like ice float.

Host: Shamini Bundell

But I’ve heard about this in school and I thought all water’s sort of slightly unusual chemical properties is all because it’s got hydrogen bonding which other liquids don’t have?

Host: Nick Howe

Yeah, and that’s what I thought as well, and it’s what a lot of chemists still think, but there are a group of chemists that are increasingly starting to think that actually, water isn’t just one liquid, it’s made of two separate states of the same liquid that sort of intermix and join together to make these really weird properties that water has.

Host: Shamini Bundell

How does that even make sense? I do not understand that.

Host: Nick Howe

So, basically, some chemists are saying that there is a bit of evidence to suggest that water has a low-density state and a high-density state, and these two states are in competition, and as things get cooled down, the competition between these shifts and so the low-density stuff wins out over the high-density things. Quite exactly how that works, I’m not sure and chemists aren’t either – that’s part of the problem – but there are some sort of hints that water is like that. For example, when you get water really, really cold, to temperatures below 136 Kelvin or -137 degrees Celsius, it becomes this glassy state and there are two different kinds of this glassy state. There is one that is high density and one that is low density, and some scientists are saying that that suggests that water always has these but you can only see them when it gets really, really cold.

Host: Shamini Bundell

Oh, so they haven’t sort of seen this directly? They can’t kind of look and see what the atoms are doing differently, but the various behaviours suggest that this could be an alternative explanation for water’s weirdness.

Host: Nick Howe

Basically, yeah, but you’ve also sort of hit the nail on the crux of the debate because some chemists are saying well, surely you should be able to see this with X-ray scattering experiments and things like that, and that’s proving kind of difficult. And the people who are the proponents of this two-state theory, they say this is because it’s not a simple thing of there just being one bit there and one bit there. They’re shifting all the time so it’s really hard to get an actual picture of it, especially when water is really, really cold.

Host: Shamini Bundell

So, this sounds like another ongoing argument to me then.

Host: Nick Howe

Yeah, and this article – it’s in Chemistry World – also wins the best pun points this week because they say that over the last decade, the academic arguments have reached ‘boiling point’.

Host: Shamini Bundell

Laughs. Okay, not sure about that one. But yeah, two really interesting articles there and you can get bite-sized bits of science like that and others in the Nature Briefing, which is our either daily or weekly newsletter, depending on what you subscribe to, and there’ll be a link to that in the show notes.

Host: Nick Howe

That’s all for now. As always, don’t forget you can reach out to us on Twitter - @NaturePodcast – or send us an email. We’re podcast@nature.com.

Host: Shamini Bundell

And don’t forget, we’ll be back on Friday with another episode of Coronapod with some key pandemic updates from the last week. I’m Shamini Bundell.

Host: Nick Howe

And I’m Nick Howe. Thanks for listening.

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