An investigation.

In 1911, Marcellin Boule, a French paleontologist, published the first scientific description of the Neanderthal species. And let’s just say it didn’t have a lot of sex appeal.

The skeleton in Boule’s volume, dubbed the “Old Man of La Chapelle,” was a wretched creature: a hunched-over, brutish, dim-witted, primitive man clearly destined to fail in the game of “survival of the fittest.”

Since Boule’s analysis, our view of Neanderthals has shifted, from a caricature of a caveman to a remarkably sophisticated species. We’ve learned about how they built tools. That they made jewelry. That they, at times, buried their dead. We learned they were possibly stronger than us, and maybe just as smart.

And Neanderthals just might have been sexy after all. Well, at least, we’ve learned that we had sex with them.

Neanderthal genomes recently sequenced by scientists have revealed that we humans mated with Neanderthals over thousands of years. These couplings are believed to have been rare and sporadic. But they were meaningful: Just about every human today (except those of solely African ancestry) has around 1 to 4 percent Neanderthal genes in every cell of their body.

That’s epic. Humans have been around for 200,000 years. But only 6,000 years of it has been recorded. New genetic science is starting to fill in the gaps. And the story it’s starting to tell is gripping.

“It’s sort of like discovering the Game of Thrones,” John Hawks, a University of Wisconsin anthropologist, tells me. “There’s this plot that we didn’t know. These people were interacting with each other, and they survived for thousands of years with those interactions. When you put that together, there’s going to be this incredible story.”

So, yes, humans and Neanderthals had sex. But that’s not the most interesting question, the one I’ve become somewhat obsessed with.

It’s this: Could a human and a Neanderthal fall in love?

Early depictions of Neanderthals portrayed them as more savage and ape-like than they likely were. This illustration appeared in a 1909 edition of Illustrated London News.

Checking out Neanderthals

Would a Neanderthal be attractive by today’s standards? I decided to get a look for myself.

On a sweaty July day, I meet Bernard Wood, a paleoanthropologist at George Washington University, in the lobby of the Smithsonian’s National Museum of Natural History.

Wood is white-haired, white-bearded, and affable, with circular black glasses and the hint of an underbite. I was delighted to find out his voice is a near dead ringer for David Attenborough’s.

We set off toward the Hall of Human Origins, where dozens of skulls and skeletons of humans or human-like creatures are on display. Their hollow eye sockets stare blankly outward, beckoning us to imagine their flesh, their personalities, their desires and pains. I think about how they might have stared upward at the same stars as us with similar wide-eyed wonder.

There’s a common misconception that Neanderthals were our ancestors, that we evolved from them. We did not. Neanderthals and modern humans are believed to have diverged from a common ancestor in the genus Homo sometime around 500,000 years ago. The Neanderthal ancestors moved up to Europe before us, and continued to evolve there.

The possible pathways of evolution. (solid lines show temporal — time — ranges, and dotted lines are the inferred relationships between species) Encyclopaedia Britannica/UIG Via Getty Image

The possible pathways of evolution. Solid lines show temporal — time — ranges, and dotted lines are the inferred relationships between species.

It’s easy to think of evolution as being like that ubiquitous illustration of an ape transitioning into an animal that stands upright, shedding fur, and then finally walking as a proud human.

But evolution doesn’t follow a straight line. It’s messy, a many-forked path with more dead ends than living branches. Nature is like a jazz musician, trying out slightly tweaked versions of a similar riff to find one just a bit catchier than the rest. Neanderthals are one of the failed branches, a tune that played out.

I asked Wood if it’s right to think that because we survived and they didn’t, we humans are more “evolved” than Neanderthals.

“What do you mean by evolved?” he asked, and pointed toward a skull of a creature called Paranthropus boisei, a hominid that looks more like an ape than an accountant.

“These guys lasted a million years,” he says of the Paranthropus. When Neanderthals went extinct around 40,000 years ago, he said, they likely had been on Earth longer than we have been now. We can start feeling truly superior in about 750,000 years, he says.

Wood and I walk past a case that contains the remains of a 40- to 50-year-old Neanderthal man who died around 45,000 years ago in Iraq. He’s laid out like Lenin in a glass sarcophagus, but fossilized and missing most of his bones. We turn and then arrive at an artist’s sculptural rendering of what such a man might have looked like.

He’s about 5-foot-5 with ruddy skin and a surprisingly on-trend man bun and beard.

This is the Smithsonian’s rendering of what a Neanderthal man might have looked like. With a shower, he could fit in in Brooklyn, right?

“[Neanderthals] are not as tall as we are, their limbs aren’t as long, the surfaces of their joints are bigger, their bones are bigger, their bones are generally stronger,” Wood says. Then he points out their defining characteristic: thick, spherical skulls, protruding brows, and a very small forehead.

“They probably needed about another 600 or 700 calories a day more than a modern human” to feed their hardier bodies, he explains — great in times of plenty but catastrophic in a famine. They were the gas-guzzling pickup truck of the hominids. We were the smart car.

And the verdict on their attractiveness? Maybe, if you squint.

Regardless, we must have seen something in them.

“There are lots of ways of defining species,” Wood tells me. “But there is one that I find particularly intuitive and practical, and it’s called the ‘specific mate recognition system.’ You mate with individuals who you are comfortable with, who you recognize. The ‘specific mate recognition systems’ of Neanderthals and humans must have overlapped, to the extent that we were willing to mate with a Neanderthal.”

But “did modern humans look over there and see a Neanderthal and say, ‘Hmm, not bad’?” Maybe, he says.

But romantic love? “Frankly, I don’t know.”

Everything we know about human-Neanderthal sex

We know for sure humans and Neanderthals had sex because of a Swedish scientist named Svante Pääbo, who “more or less invented the field of paleogenetics,” Elizabeth Kolbert wrote in a terrific New Yorker article in 2011.

When a mammal dies — human, Neanderthal, or woolly mammoth — microbes and the body’s own enzymes quickly start to break down the flesh. For scientists to salvage to genetic information from remains tens of thousands of years later, the remains have to be protected from heat, moisture, and contamination. And even then, “the DNA preserved in these bones is far from intact,” Beth Shapiro, a biologist who specializes in extracting ancient DNA, tells me in an email.

And the genomes the scientists find are never complete. They’re diced up into fragments. “Think of the DNA [extraction] as a zillion-piece puzzle that has not been assembled,” Shapiro says. “All the pieces are in there, but they are in no particular order.” What’s more, the puzzle set is often contaminated with genetic pieces from other organisms, like bacteria, and is easily contaminated by cells from the scientists’ own bodies.

In 1997, Pääbo’s team became the first to extract Neanderthal DNA from a tiny slice of a 40,000-year-old humerus. That discovery kicked off the “Neanderthal genome project,” an effort to decode the entirety of Neanderthals’ genetics from their fossils. In 2014, the team published an entire Neanderthal genome (sourced from the big toe of a female who lived 50,000 years ago in Siberia) in the journal Nature.

As the scientists assembled the puzzle of the Neanderthal genome, they began to notice something incredibly odd: Specific genes looked oddly similar to human genes, more similar than they ought to have looked considering how long ago both species diverged from the same ancestor.

“I don’t think anyone seriously believed, at least in genetics … that hybridization had happened,” Josh Akey, a genome scientist at the University of Washington who has co-authored papers with Pääbo, tells me. Yet that’s what the evidence was pointing toward. The genes looked so similar because some time after Neanderthals and humans diverged, they swapped some.

How different were the Neanderthals from us?  Encyclopaedia Britannica/UIG Via Getty Image

How different were the Neanderthals from us? “If you were to compare two random modern human chromosomes, you’d see a difference every thousand base pairs,” Josh Akey, a genetics researcher at University of Washington, told me. With Neanderthals, you’d see a difference once every 750 base pairs.

Using this insight, researchers began to speculate about when and where this mating happened. That is, they could begin to write about this chapter in human history.

We all know DNA contains the instructions for life. But it is also a historical volume. Regularly, mutations in the genome pop up in a community in a particular corner of the world and then get passed on to the next generation. Many of these mutations are meaningless when it comes to our health and biology, but they function as a sort of serial number for the manufacturing of humans. You can look at a person’s smattering of mutations and determine what regions of the world his ancestors came from, and when.

“Knowing how many of these mutations have accumulated in those segments that look Neanderthal-like, and based on the rate at which human mutations accumulate, we can say approximately how long ago that interbreeding must have happened,” Adam Siepel, a genetics researcher at the Cold Spring Harbor Laboratory, says. “When you do that calculation, you come up with something on the order of 50,000 to 60,000 years ago, which fits pretty well with all of the other evidence.” That’s when our ancestors were first venturing out of Africa.

What makes this evidence particularly compelling is that people of only sub-Saharan African ancestry don’t have Neanderthal genes. And it helps to confirm the finding: Neanderthals never lived in Africa.

Siepel has also found evidence of an even earlier mating than those that took place around 50,000 years ago. In the fully sequenced Neanderthal genome published in 2014, he found some human genes dating back to 100,000 years ago. “Instead of finding Neanderthal segments in modern human genomes, we identified modern, human-like segments in one of the Neanderthal genome,” he says.

It goes to show these matings weren’t a one-time event in our history. (And it adds a wrinkle to the common story that humans left Africa around 50,000 to 60,000 years ago. Human DNA found its way into Neanderthals 100,000 years ago, so there must have been an earlier human incursion into Europe. Those humans, though, did not survive.)

How many of these matings happened? “We tried to estimate this, actually, and it’s incredibly difficult,” Akey says. The number would depend on the size of the human and Neanderthal populations, which are also difficult to estimate from the fossil record. “It could vary from a couple of hundred matings to thousands of matings, and we just don’t know where that number is right now,” he says.

What was the sex like?

At this point, you’re probably wondering about the dirty details. Were humans and Neanderthals compatible physically?

On this question, we do know one thing: Neanderthal penises were probably very similar to human penises.

“You see, most primates, and indeed many mammals, have at least some spines on their penises,” Hawks explains on his website. “‘Spine’ means more or less what you would expect: little projections that are covered in hard material, generally keratin, curving toward the base of the penis. These spines are sometimes called ‘horny papillae.’”

Like humans, Neanderthals were missing the genes that codes for spiny penises.

I also asked Philip Reno, a Penn State anthropologist who was part of the team that analyzed the Neanderthal genome for the spiny penis gene, if there’s anything we can learn about female Neanderthal sexual organs. “Unfortunately, I am not aware of much evidence on the soft tissue anatomy of [female] Neanderthals,” he wrote me in an email.

Human females are one of the few apes that don’t have an obvious outward display to show they are ovulating. Reno speculates Neanderthals probably were the same. “I don’t have any reason to doubt that Neanderthals would show the human-like pattern of concealed ovulation,” he writes.

Still, we do have the evidence that these couplings happened.

Let’s talk about feelings. Were the couplings true love? Or was it abuse?

A photographer takes pictures of a Neanderthal reconstruction, displayed in a show of the Prehistoric Museum in Halle, eastern Germany.

I started to wonder about stories of forbidden interspecies love, or perhaps of an innocent Neanderthal child getting mixed up in a human tribe and ultimately being accepted as an equal. The genetics data seems almost trivial to this fact: “These are actual events that happened to actual people,” Akey says.

When modern humans first left Africa, we traveled to a Europe and Middle East that Neanderthals had colonized some thousands of years before.

“Meeting up with Neanderthals when modern humans first expanded out of Africa must have been an incredible shock,” Pat Shipman, an anthropologist and author who has written about the demise of Neanderthals, told me a few days after my museum visit. “They [modern humans] had never seen anything like themselves or not like themselves,” she says.

(Shipman stressed that because all this happened at least 40,000 years ago, the best she could do is speculate. That caveat is true for many of the conversations I held reporting this piece. The past teases us with a few clues, but in truth, we can never fully know what happened.)

This was a time when you lived your whole life perhaps never knowing more than a few dozen people. Anywhere you traveled, you traveled on foot. The world must have seemed impossibly immense.

Meeting a Neanderthal must have been an uncanny experience: like Star Trek characters encountering Vulcans for the first time. Here’s a species that looks remarkably like us, but it is not us.

“If you think about what it’s like when you see a chimpanzee up close, you feel this immediate sense of kinship; you recognize a lot of its mannerisms and see things in its face. Neanderthals would have been 10 times as much like us as chimps,” Siepel says. “There would have been a strong feeling of kinship, but there would have also been a strong sense of otherness.”

How would we have dealt with that uncanny otherness?

Human history suggests there are two options: We would have empathized with them, or we would have met them with aggression.

We don’t know much about Neanderthal behavior — or their capacity for emotional connection. But we do know a lot about human behavior, and in it a particularly disturbing historical pattern. When humans arrive in new lands with an eye for exploration, they usually end up cruelly conquering the foreign-looking people they encounter.

“When we look at history and see what Australian aboriginals went through, what Native American people went through, what Easter Islanders went through, it’s hard to say that the Neanderthals would have been better off than these historical cases,” Hawks says. “It’s probably the case that Neanderthals went through the Paleolithic version of the contacts we know about through history.” (It could also be the case, Hawks says, that we just didn’t really notice Neanderthals were different from us.)

Horrors like the Holocaust, the Rwandan genocide, and so many other atrocities show how easily humans can dehumanize humans. What would we do to an entirely different species easily mistaken as an inferior? In this country, the Supreme Court didn’t establish a right for interracial marriage until 1967.

It’s also not hard to imagine that if Neanderthals were around today, we wouldn’t treat them very well. They’d activate all of our psychological systems that divide the world into us versus them.

But there is a case to be made that we might have been compassionate toward them.

It’s generally thought that humans have been essentially the same, in terms of biology, for around 200,000 years. We can project ourselves onto the people of the past because they are us. And that can give us hope to root for human-Neanderthal true love. “We all know people who have tragic love stories, and people who are very happy and contented their whole lives with one partner, and I imagine that we’re not looking at anything different in the past,” Hawks says.

(And while one theory of Neanderthal extinction is that they died by our hands, their population numbers were already in decline by the time we encountered them. So maybe we didn’t kill them. Some scientists say we absorbed them).

One piece of scientific data that will help clear up whether these encounters were consensual or not would be the direction of the gene flow. That is, whether it was Neanderthal males impregnating human females, or human males impregnating Neanderthal females. The former would suggest that we were less conquering tyrants and more open-minded lovers. This is an open question in the science.

“All we really know is that some offspring of humans and Neanderthals eventually got incorporated into human populations, because what we see is small fragments of genomes in human populations,” Siepel says.

Which is really quite profound, if you think about it: These hybrid individuals, stuck between two species and probably a little less healthy for the intermixing, were accepted into our human society enough to start families. To kick off the chain of moms and dads that has left its mark on so many of us.

What it was like to be a human-Neanderthal hybrid

What do we know about these first bi-species people?

It’s likely that they were less healthy than their single-species peers, the geneticists I spoke to said. It’s possible not all hybrid offspring were fertile. And there’s evidence that the Neanderthal genes actually introduced disadvantageous traits into the population.

In his work, Akey has determined that a full 20 percent of the Neanderthal genome can be found scattered in humans around the world today. But what’s more interesting is figuring out what Neanderthal genes didn’t get passed on. These would be Neanderthal traits that are not advantageous for survival.

These Neanderthal-gene-less regions are involved in speech, language, and neural functions. “It is interesting to speculate that maybe hybrid individuals had deficits in speech or language or something like that,” Akey says, and therefore those genes didn’t survive natural selection.

Today, there’s some evidence that Neanderthal genes increase the risk for diseases like depression and blood clots. But the genes may also have provided some evolutionary advantages: Many of the surviving genes are found in regions that code for proteins in skin and hair.

What’s also fascinating is that we didn’t just mate with Neanderthals. Genetics are finding evidence of gene flows between humans and the recently discovered Denisovans, and I’m told there’s emerging evidence for gene flows between us and a mystery species we haven’t even discovered yet.

Yes, if two species of the genus Homo are similar enough, life will find a way.

This schematic shows the gene flows (i.e., mating) among species closely related to us: the Neanderthals, the Denisovans, and a yet-to-be-discovered species. You can see the Neanderthal “injection” of genes skipped humans of African descent.

And that shakes up the way we’ve traditionally viewed how evolution works.

“For a long time, the field of human evolution has imagined a fictional world where distinct human groups separated from one another and then remained distinct for long periods of time,” Siepel tells me. “And we’re just finding out on multiple time scales that’s just not true.”

Evolution is a messy business. Species split at a certain point. But then, for thousands of years on, each lineage’s decedents can be swapping spit and influencing the other’s gene pool. The branches of the tree of life split and then braid again together, before splitting apart again.

Why I’m rooting for human-Neanderthal true love

We don’t know the answer to the love question. But if we could fall in love with Neanderthals, a wholly separate species, wouldn’t that make modern debates over same-sex marriage or insignificant differences between people of different races just seem less important?

Robert Sawyer is a science fiction author who won the Hugo Award — one of sci-fi’s highest honors — for his 2002 book Hominids, a story that imagines a parallel world where Neanderthals survived and we didn’t. In the book (which spawned a trilogy), a Neanderthal physicist opens up a rift between the worlds and falls in love with a human.

Sawyer believes the actual history between humans and Neanderthals probably wasn’t consensual. “I wish I could paint a more romantic tale of candlelit dinners over mammoth steak, but it seems much more likely that the gene flow was mostly unintentional,” he tells me.

But he too can’t resist the hope that love could have existed between the groups.

“I think absolutely they could fall in love,” he says. “The emotion of love clearly exists in lesser primates: chimpanzees, Bonobos in particular … and gorillas clearly show love for their children and love for their mates. Given that our common ancestors had that ability, our common ancestor of Neanderthals had that ability, then obviously Neanderthals had it as well as we had it.”

When I asked Akey, the University of Washington genome scientist, why he was interested in studying this, he recalled tucking his 4-year-old son into bed one night. The little one asked the question no parent is really ever prepared to answer: “Dad, where did I come from?”

“You came from Mom and Dad.”

“But where did you come from?” the child replied.

“Even at that age,” Akey says, “we start wondering about all the things that had to happen for us to be where we’re at today.”

Knowing where we come from teaches us what it means to be human. I hope we came from love.