Skeleton Lake

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This is Unexplainable.

I'm Noam Hasenfeld.

For most of human history, which goes back hundreds of thousands of years, our past has been close to a black box.

Slowly, we develop tools.

Fossils and archaeological evidence tell us a little about the deep past.

Carbon dating can tell us about the age of something.

Altogether, though, the story they tell is incomplete.

Then, just about a decade ago, we came up with a new tool.

Scientists drilled into 40,000-year-old bones and were finally able to sequence the entire genome of an ancient person.

This was an earthquake.

All of a sudden, there was a brand new way of analyzing our past, our extremely ancient past, and it gave us a huge amount of new information.

But it also just blew up a lot of what we thought we understood.

Over the last decade, it's forced scientists to rewrite a wide swath of history.

And one of these rewrites, which started near an icy lake in the mountains of northern India, has generated even more questions.

Douglas Preston reported on this rewrite for The New Yorker.

Well, in 1942, an Indian forest ranger was following a herd of rare antelope very high up in the Himalaya mountains.

And he came across something incredible.

He came across a lake at 16,500 feet amidst glaciers and barren peaks.

The lake was called Rupkund.

Rup meaning beautiful shape, kund meaning lake.

And the slopes around the lake were covered with human skeletons.

Some of which still had hair on them and flesh.

It was just an enormous number of human remains.

These dead bodies were everywhere, and no one knew where they came from.

People were worried they were evidence of a failed Japanese invasion or maybe even a mass ritual suicide, but no theory held up.

So it remained a mystery for several years until in 1956, the Anthropological Survey of India sent several expeditions up there to collect bones and to try to figure out who these people were, how they died, and what were they doing up there.

They used a technique called carbon dating, which allowed them to look at a radioactive timestamp in the bones.

It was still a pretty new technique in the 50s, but they were able to roughly date the bones to somewhere between the 12th and 15th centuries.

But it didn't really solve the mystery of who the people were or where they came from.

The only real clue was that a very ancient pilgrimage trail to the goddess Nanda Devi ran through that area on a ridge above this lake.

It's actually the longest and and most arduous pilgrimage in all of Hinduism.

Locals near Rupkund had a legend about this pilgrimage.

It started when Nandadevi, this Hindu goddess, had gone to visit a distant kingdom, but she was treated with disrespect.

And so in order to appease the goddess, the king and queen of this kingdom decided to undertake this pilgrimage.

But the king was a man who liked his entertainment, so on this pilgrimage he took along a bunch of dancing courtesans, and this so enraged Nanda Devi, who sent a terrific whirlwind with giant hailstones and pummeled the king and queen and their entourage to death.

And that was the origin of all these bones at the lake.

Scientists started thinking that the locals were onto something here with this Nanda Devi story.

So in the early 2000s, more research was done on the bones.

Several of the skulls had depressed fractures on the top that were made by a heavy object.

Like a hailstone.

This particular research project concluded that in fact this legendary story of Nanda Devi sending down these hailstones was actually based in a real event.

And that sometime in the 8th, 9th century, a group of pilgrims was actually killed by giant hailstones.

I know it seems pretty unlikely that you would have these hailstones that were big enough to bash in somebody's skull, but apparently in this area of the Himalayas, vicious hailstorms like that are not unknown.

So that was it?

It appeared that the mystery had been solved.

That was the early 2000s.

In 2010, we got the first fully sequenced genome of ancient DNA, and it opened a world of new possibilities.

So in 2015, an Indian scientist, Dr.

K.

Tangaraj, started a new study.

By looking at genetic aspects of the bone sample, we can assign the ancestry of these populations.

Tangiraj worked with a geneticist at Harvard named David Reich, and they did a more thorough analysis.

They took powder that had been drilled out from the bones and all these little vials of bone powder and tooth powder were sent all over the world to Germany, to the United States, and to other labs in India for analysis.

I had heard of the skeletons of Rupkund Lake, and when I realized that we had DNA from these individuals and could potentially solve this mystery, I was really excited.

A.

Dean Harney headed up this new DNA analysis project for the Reich Lab at Harvard.

You know, our initial assumption was that these individuals would probably look similar to populations from around the area, but instead, what we found was a much more complicated picture.

When we analyzed, we found there are three distinct groups.

They called these three groups Rupkund A, Rupkund B, and Rupkund C.

With Rupkund A, the scientists found what they were expecting.

Rupkund A

were people who showed the typical genetic heritage of India.

Similar to the populations that are living very close to Rupkund.

Rubkund C was just a single person resembling someone from Cambodia.

Closer to Southeast Asian populations.

But Rupkund B was a complete mystery.

Rupkund B absolutely floored everyone.

It's totally different.

We were just a little bit baffled.

It turned out that these bones, their genetic makeup most closely resembled Greeks from the island of Crete.

Crete is over 3,000 miles away from Rupkund, and it's not exactly walkable.

When I checked online, even Google Maps couldn't find directions.

Yeah, it was a bit surprising why

they're supposed to come to Rupkund.

Our first reaction was that we needed to prove to ourselves that this wasn't some sort of mistake.

So working with labs around the world, they began to ask new questions to confirm the finding.

What diet they ate, because now you can analyze bones and you can tell what food they were eating during the last 10 or 20 years of their life by analyzing carbon isotopes.

You don't actually need to know this, but it's just pretty cool.

There are two basic ways plants perform photosynthesis.

So after you die, depending on what you eat, you'll end up with a different ratio of carbon isotopes in your bones.

I mean, it's incredible the stories that the dead can now tell us about who they were and what they did and how they died and how they lived.

And the diet test backed up the DNA results.

The genetically Greek looking group ate a Mediterranean diet.

And then they did one more test, a new carbon dating process to find the age of the bones.

We got these two wildly different dates.

All of the individuals that belonged to this South Asian kind of cluster died a thousand plus years ago.

So the Hailstone folktales still might have been true, although maybe just for the older group that looked genetically Indian.

But Rupkin Benetically Greek looking individuals dated from the 18th century.

Here was yet another mystery layered on top.

Somehow the genetically Greek looking group was way more recent than the other bones.

Still, remember, at this point, there were no cars, no planes.

To get from Greece to Rupkund, you'd have to walk.

And this wasn't exactly a trade route.

I think first we were shocked and we were kind of in disbelief.

And I just got this forwarded email from David.

I forget exactly what it said, but it had a lot of exclamation points, which can this be real?

So it was definitely a really exciting time.

So this place is about 5,000 meters above the sea level.

And all the time you'll see snow, and it's all the time frozen.

But the question is, why did the people go there?

Not everyone was convinced this was even the right question to ask.

I called up William Sachs, who

is an expert on this whole pilgrimage and this area of India.

And he said, I think that this is crazy.

Eastern Mediterranean, 1800?

He said, it's impossible.

He said, I spent years,

decades with people who have gone on the pilgrimage.

And he said, I didn't hear a whisper.

Not a whisper.

Not a word.

Nothing.

Nothing about a group of Europeans or anybody going up there in the 18th century and dying in some mass death event.

Neither I nor any of my colleagues can come up with any hypothesis that might make sense of it.

He said, I simply don't believe it.

He said, I think the bones were mixed up.

It's the only hypothesis I've got.

You know, we spent a long time, probably a year, just kind of going over all of our analyses, making sure that we were confident in the results.

When the carbon dates came back with these two distinct ages, we spent a lot of time emailing our collaborators who were experts in carbon dating, just asking, you know, is there any way that this is some sort of contamination event?

The consistency of the diet, consistency of the dating, the consistency of the genetics.

It's very unlikely that this could have resulted from bones being mixed up in a storage area.

You would not see this kind of consistency.

All of the different tests that we could do really showed that this data was reliable and that we did have all these different groups of times of when individuals died and these different genetic clusters.

When Adine and her team published their surprising paper on the Rubkoon groups in 2019, she thought someone somewhere might come forward, someone who had some document or some evidence to make sense of it.

I'm still hoping that maybe there's a historian who has access to this document and hasn't known how to interpret it.

And we'd love to hear from them.

But no such information was forthcoming.

When you're writing for the magazine article, you want to give the readers an answer.

And unfortunately, at the end of this article, I could not give the readers any answer.

It's still a profound mystery.

The reason I got interested in ancient DNA work is I found history kind of overwhelming, and I wanted to get back to a time period when it was simple and we could understand, you know, really, really simple patterns.

And then maybe we could, you know, see things get more complex over time.

And I think that what ancient DNA is showing us again and again is that we're underestimating how complex the past was.

And I think Rupkund is just an amazing example of this.

That we thought that, you know, something mysterious, but probably fairly simple, happened at Rupkund Lake.

And then as we dig into it, we're finding out that it's even more of a mystery than we expected.

This whole story, Rupkund, Nanda Devi, Crete, at most we're talking about a thousand or so years of history potentially being rewritten.

After the break, that rewrite goes way, way deeper.

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The bones at Rupgund range from a couple hundred to around a thousand years old.

But ancient DNA analysis can get way more ancient.

And the further back scientists reach with this new analysis, the more history they end up rewriting.

At this point, they've been forced to rewrite the basic origin story of humanity that so many of us grew up with.

In the early textbooks that I was reading and the articles that my dad was giving me when I was a little kid, the map of human evolution is pretty well understood.

Adam Rutherford is a geneticist who studies extremely ancient history.

We've got this nice branching tree structure which goes, we've got Lucy Australopithecus afarensis, and then from there it branches out and we have Heidelbergensis and Hermoneander talensis, and eventually you get to us.

And I guess sort of, you know, one of those branches ends on us and all the other branches just kind of fizzle out?

Exactly.

They all peter out.

Anything with the genus title homo is referred to as humans, and we are the last remaining species of humans.

And was this based on DNA analysis, or was it just like looking at the bones?

It's all entirely based on bones.

So it's all physical anthropology, which determines the relationship between those organisms.

How much does ancient DNA shake all this up 10 years ago?

Well, that was, you know, a revolutionary moment in the history of biology.

It's like discovering the Dead Sea Scrolls or something.

We know the Bible.

We've got the Bible.

We've got various versions of the Bible over the years.

And then suddenly you just go, oh, we've just found a brand new.

tablet with missing chapters.

Yeah, and what do those missing chapters do to the tree that we had in the textbook, that neat tree with all the branches slowly dying off?

They dug it up and we threw the tree away at that point.

So if it's not a tree anymore, how do we describe it?

What shape is the history of our evolution now?

It's a matted web is the best way I like to describe it.

So just to go back in time a little bit, Homo sapiens and Homo Neanderthalensis split around maybe 600,000 years ago.

A group ended up as the Neanderthals in Europe and A group ended up as Homo sapiens in Africa.

And then 45,000 years ago, the Homo sapiens had migrated out of Africa and into Europe and they'd gone into the Neanderthals domain, right?

So we think that there's roughly a 5,000-year period where Neanderthals and Homo sapiens overlapped in time and space.

So the question then becomes, well, did they get it on?

And the answer by genomics was absolutely yes.

So your question was about whether there's a tree and whether it's branching.

Well, yeah, there was a branching point when the Andatos and Homo sapiens split, but then when they met again, that became a loop.

So there are just tons and tons of these little loops all over the place?

Well, yeah, I mean,

evolutionary trees are sort of right in principle, but wrong in almost every detail, because it's all loops.

We know this within families, we know this within species.

And now we know it outside of species.

Because we're seeing the same thing in primates and birds and insects and various other things.

Okay, so I guess if you've got European ancestry, you're carrying around at least some Neanderthal DNA.

Are there other kinds of ancient humans that people are carrying around in their genes?

Yeah, the field just, it turned into a sort of continual revolution because as soon as we'd done one,

within a year of that publication there was the discovery of two tiny bones actually one bone and one tooth because a tooth isn't a bone because we're now in the era of ancient dna

this tiny little fingertip bone was enough to get the full genome out of this girl and lo and behold it's not Neanderthal and it's not Homo sapiens.

So it's something else.

And we call them the Denisovans and you can ask the same question again.

I assume they had sex with our ancestors too?

Well, very much so.

Definitely, yes.

And so, in general, we talk about gene flow events, right?

And that's a euphemism for sex, basically, right?

That's a new one.

I've never heard of that one before.

It's not a great chat upline, but you know, we are the results of gene flow events between our parents.

And you asked me the question a minute ago, which was, well, what do you call it if it's not a tree?

And I said, a web or a net.

But a much better way of describing human evolution is a sort of hundred thousand year cluster fuck

because

every time we met another type of human, we had sex with them and we carry their genetic legacy in our genomes to this day.

You know, we're just seeing this massive sort of melee of human species that all interbred with each other.

So it's not a tree at all.

It's a, yeah, it's a cluster fuck.

So, so some of us have Neanderthal DNA, some of us have Denisovan DNA.

Is that it?

Oh, no.

I don't know.

I think it it may be my favorite bit of science in the last 10 years.

When you compare the genomes of Denisovans with Homo sapiens, with Neanderthals,

and what we find is there's bits of the Denisovan sequence which look like they don't fit into any of those other two, right?

And it looks like they've been introduced into the Denisovans from another type of human, and we don't know what that was.

So we call this a ghost population or a phantom species.

Phantom species.

We don't have any physical remains for them.

We don't have any bones for them.

But their legacy is right there in the Denisovan DNA and indeed in the DNA of living people in their Denisovan portions.

So that's basically like an empty box of a human, right?

All the signs point to this kind of outline of a human.

We know it should be there.

We haven't found it.

But we're outlining a ghost species and still looking for it.

Yeah.

There's a thing in paleontology called ichno-fossils and what they are are the traces

of organisms in the absence of the organism itself.

So they're things like footprints, right?

So there's loads of really cool footprints where someone walked through

some

like soft lava or some mud and it solidified and

we only have the footprints.

That's what the phantom species is.

We don't have any physical remains of them, but we know that they were there and we can tell loads of stuff about them without actually knowing what they looked like, what they were, who they were.

That's just nuts.

So this is basically like

this ancient species of humans

almost walked through our genetic past, like left footprints in our genetic past.

Well, yeah, I mean, that's a more poetic way of saying that we had sex with them.

I'm just wondering, like, it just sounds like we have this new tool or a new, if not a new tool, a new ability to use this previous tool in a more sophisticated way.

And

we think that it could answer questions.

And instead of answering specific questions, it just like blew up our entire model.

Yeah, that's exactly right.

I mean, it answers loads of questions, such as, you know, were the ante tells our cousins or our ancestors.

But what happens in science is you get these sort of nodal points, right?

Where there's a huge mass of information and it's all pointing in a particular direction.

And then suddenly it fuses into this one big thing, right?

So 1859, it was natural selection.

1953, it was the double helix structure of DNA.

2001, it was the Human Genome Project.

2010, it was ancient DNA in Neanderthals.

And so everything flows into this one point in time and space.

And we all, you know, lose our minds.

And then the whole field massively explodes after that.

Is there any danger of trying to answer questions here that may be outside the scope of ancient DNA or maybe

just beyond what is possible, maybe overreaching?

Yes, I really think there is.

And I think that there's a one of the risks that we've seen a few times is that a minute ago I mentioned that it's like being a historian and you've got a new type of data, you've discovered a new book of the Bible or whatever it is.

2010 comes along, geneticists all suddenly become historians and they all suddenly become paleanthropologists.

And because this is a very molecular data set, the temptation is to go, well, you're dealing with old bones of which you've got only a few.

And they're sort of physical things and they're a little bit flabby around the edges.

Whereas I'm dealing in molecules and DNA and genomes and stuff like that.

So I think there was a temptation for a lot of people to say, you know, my source is better than yours, right?

It's more informative than yours.

And that was an error and it continues to be an error.

These are parallel streams of information and they relate to each other.

You know, you have to continue with straightforward, old-fashioned paleoanthropology, looking at the bones.

But the temptation to, you know, crash into a party and say, hey, I've got this new tool now and it's going to fix everything.

I think a lot of genes,

there's...

Some people did do that.

And then you have to back off and learn some humility and realize that

there's a lot of expertise in not genetics.

Yeah.

and when you start thinking about this humility, I mean, we started thinking Neanderthals were this entirely separate branch.

Then we moved towards a web, then we went towards a giant millennia-old clusterfuck.

I mean, is this sort of a lesson in how we should think about the past, that things can't necessarily be explained as neatly as we might want?

Absolutely.

But I think it also says something about our hubris, that when we think we know things, the point of science is to challenge those.

And we look, we find, and then you have to revise what you thought you knew.

It's an ever-moving target.

Everything in science is only transitionally and conditionally correct.

One thing that we do know about science is that when you have definitely, definitively answered a question, you definitely haven't.

Adam Adam Rutherford is a geneticist and the author of A Brief History of Everyone Who Ever Lived.

For more unsolved mysteries, check out his BBC podcast, The Curious Cases of Rutherford and Fry.

Also, Adam mentioned some of the problems that come up when researchers rely solely on ancient DNA while ignoring other things like archaeology, and we actually spoke with a bioarchaeologist named Elizabeth Sawchuk about this exact problem.

You can find an excerpt of our Q ⁇ A with her in our newsletter, which you can subscribe to at vox.com slash unexplainable.

You can also find a link to subscribe in our show notes, and you should subscribe.

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We're unexplainable at Vox.com.

Unexplainable is made by Noam Hasenfeld, Brian Resnick, Meredith Hodenott, and me, Bird Pinkerton.

Noam wrote the music, Hannah Choi played the music, Liliana Michelena fact-checked this episode, Hannis Brown mixed and sound designed it, and Liz Kelly Nelson is the editorial director of Vox Podcasts.

Special extra thanks goes out this episode to Ayushi Nayek, Jillian Weinberger, and Eliza Barclay.

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