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Ancient WorldsAncient Worlds

In a controversial study, DNA from today’s southern Africans hints at possible “homeland” for modern humans

But many questions remain about the true origin of the Homo sapiens species.

ByKatherine J. WuNOVA NextNOVA Next
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Members of a Khoesan hunter gatherer population in Botswana region of the Kalahari Desert. Image Credit: DavorLovincic, iStock

With 7.7 billion members and counting, humankind has yet to run its course. But a controversial new study argues it’s possible all of us can trace our roots back to the same starting line: a single spot on the African continent where the ancestors of today’s people arose roughly 200,000 years ago, before dispersing in waves and populating the rest of the world.

Where exactly modern humans came to be remains a topic of intense contention, as does the question of whether it even is just one point. Now, an interdisciplinary team of researchers has entered the fray with a new theory that one place was of certain significance: The “homeland” of modern humans, they argue, might lie south of the Zambezi River, in what’s now northern Botswana.

Their study, published last week in the journal Nature, intertwines genetic, geological, and climatological data to map out the probable migratory routes of one of the earliest groups of modern humans identified.

The early group, known as L0, was the first to diverge away from the enigmatic population that included “Mitochondrial Eve”—the hypothetical maternal ancestor of all living humans—and is considered the oldest branch on our species’ evolutionary tree. Pinpointing the place where L0 first emerged, the researchers say, may be one of our best bets for identifying the elusive geographic origins of Homo sapiens itself.

But other experts stress an important distinction: While the new study helps to position the L0 lineage in time and space, it can’t do the same for the earlier group that Mitochondrial Eve belonged to, says Vagheesh Narasimhan, a genomicist studying human evolution at Harvard University who wasn’t involved in the study. That leaves the biggest question of all—the one that addresses the true origin of all modern humans—unanswered, he says.

All humans inherit a form of genetic information known as mitochondrial DNA exclusively from their mothers. Trace all those maternal lines far back enough, and you’ll end up at what scientists call Mitochondrial Eve: The woman all living humans supposedly descended from.

But Mitochondrial Eve is long gone, and in the 200,000 years since, her lineage has splintered substantially. The closest we can get to rewinding the clock with modern data is tracing the roots of the oldest mitochondrial lineage that still survives today: L0, says study author Vanessa Hayes, a genomicist at the Garvan Institute of Medical Research and the University of New South Wales in Australia.

To home in on where L0 got its start, Hayes and her colleagues compared 1,217 modern mitochondrial genomes, 198 of which they collected from living southern Africans.

Since it first arose, L0 has diverged into its own set of subgroups. But the vast majority of its members have remained on the African continent, Hayes says, some never straying more than a few miles from the land their ancestors occupied for generations. That’s effectively created genetic sublineages that are also culturally, linguistically, and geographically distinct, she says, allowing the researchers to map out not just when different L0 subgroups had last shared a common ancestor, but where.

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Geographical distribution of the 1,217 L0 mitochondrial genomes used in the study, 198 of which were newly collected. The map on the right shows the distribution of KhoeSan populations, which tend to be genetically, culturally, linguistically, and geographically distinct. Most KhoeSan individuals reside south of the Zambezi river, while non-KhoeSan individuals live north of the river. Image Credit: Chan et al., Nature, 2019

Remarkably, Hayes says, all the genomes seemed to unspool from a single knot: A population that once resided in the Kalahari region of the Zambezi river basin, about 200,000 years ago. This group, she says, is ancestral to all humans alive on Earth today.

Having tied these threads together, the researchers then spun them out again, this time overlaying geologic and paleontologic data that suggested that this early group’s biggest migrations—and resulting genetic splits—had been driven by changes in the region’s climate.

Nowadays, the Zambezi river basin is arid and inhospitable, speckled with the salty remnants of long-gone lakes. But hundreds of thousands of years ago, it was a wetland that blanketed much of the northern part of modern Botswana, says study author Axel Timmermann, a researcher at the Institute for Basic Science and Pusan National University in South Korea. While nearby regions were plagued with frequent droughts, this resource-rich oasis was sustained by the (inland) Okavango delta and the fragments of a once-gargantuan lake called Makgadikgadi, he says, creating prime real estate for humans and animals alike.

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Botswana's Makgadikgadi salt pans, the remnants of what was once a vast lake that covered much of the country's northern region. Image Credit: JJ Vos, flickr

This “homeland” appears to have hosted an early population of modern humans for about 70,000 years, Timmermann says. Then, around 130,000 years ago, as Earth wobbled on its axis, the landscape began to shift. Previously parched conditions to the northeast gave way to warmer, wetter climes, prompting at least one subgroup to leave and subsequently branch into their own lineage. About 20,000 years later, a second hospitable corridor emerged to the southwest, sparking another wave of dispersal—and another round of genetic fracture.

Once they reached their respective destinations north and south of home base, many of these early migrants settled for good, Hayes says, establishing family lines that have endured for more than 100,000 years. There’s even a population she believes may have never left the homeland at all: the Kalahari KhoeSan, who have maintained many aspects of their hunter-gatherer way of life and complex, click-consonant language since, it seems, L0 first arose. “Genetically, this is the oldest population on the planet,” Hayes says.

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The first people Hayes and her team shared their data with were the participants themselves. Many of Hayes’ KhoeSan contacts were unsurprised by the findings, which affirmed their oral histories, she says. “The first thing one of them said was...‘We know we’ve always been here,’” she says.

Brenna Henn, a population geneticist at the University of California, Davis who was not involved in the study, calls the team’s findings striking. “This really fits the pattern for a single origin in Africa,” she says.

But a “homeland” shouldn’t be confused with an origin—a term that might imply the discovery of one individual, the first Homo sapiens, who gave rise to us all, Hayes says.

That means we’re still a long way off from finding where modern humans really got their start, Narasimhan says. And, given the complexities of human history, more research could reveal a drastically different, and far less simple, answer. It’s still possible, for instance, that a more ancient group arose in East Africa before migrating southwest and segregating into distinct genetic lineages. Just last month, Naramsimhan authored a study that profiled a diverse set of lineages that had branched in South Asia, but actually emerged thousands of miles away. “Where a population diverges isn’t always where it originates,” he says.

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Study author Vanessa Hayes learning how to make fire with Juǀ’hoansi hunters in the greater Kalahari of Namibia. From left to right: Nǂamce Sao, ǀkun Nǂamce, Vanessa Hayes, and ǀkunǀkunta. Image Credit: Chris Bennett, Evolving Picture

Really nailing our origins will take more data, says Charles Rotimi, director of the National Institutes of Health’s Center for Research on Genomics and Global Health, who was not involved in the study. If the study’s findings are correct, the authors have found only “the geographical origin of the woman who carried the L0 lineage.”

But our timeline stretches further back than the root of L0. And while L0 is the oldest branch on our tree, most living humans aren’t a part of it, belonging instead to one of six other groups that emerged from the original lineage (that is, the trunk) after L0 peeled off. The ultimate goal, Narasimhan says, is identifying the common ancestor of all these groups.

This would be a difficult task, Hayes says. Right now, researchers don’t have an easy and ethical way to even collect such a comprehensive set of modern mitochondrial genomes, let alone the computational tools to systematically analyze all of them at once.

For now, scientists might have more success going beyond just mitochondrial DNA, which makes up just a small fraction of the genome, Rotimi says. There’s a paternal lineage, too—one that endures in the Y chromosome. Researchers have also had luck tracing ancestry by comparing mutations that occur across individuals’ entire genomes, as well as by extracting ancient DNA from fossils.

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Study author Vanessa Hayes speaking with ǀkunǀkunta, one of the many participants who donated a mitochondrial genome to the research. ǀkunǀkunta comes from an extended Juǀ’hoansi family that lives in the semi-desert Kalahari region of Namibia. "They know the stories of themselves," Hayes says. "The most important part of this process isn’t talking… it’s listening. It’s their project, at the end of the day." Image Credit: Chris Bennett, Evolving Picture

The new findings may also have a bone to pick with fossil finds that point to an alternative to the “single origin” story, Henn says. Fossils with a wide array of Homo sapiens features speckle the African landscape, including some 195,000-year-old remains from the Omo Kibish rock formation in Ethiopia, the 260,000-year-old Florisbad skull from South Africa, and a 315,000-year-old skull unearthed from Morocco’s Jebel Irhoud site. The age and far-flung locales of these fossils, researchers argue, show that multiple disparate populations arose in different spots, then mixed and mingled until our exact mishmash of contemporary features arose. The Homo sapiens tree, in other words, may not be a tree at all, but a tangle of vines that crisscross later in our timeline.

The so-called multiregionalism hypothesis isn’t well supported by genetics, which seem to bat instead for Team Mitochondrial Eve, Timmermann says. Perhaps many populations existed, then died out, he says, leaving behind only one that successfully seeded today’s humans.

That remains to be seen. But whatever their answers, Hayes says, these questions will keep researchers busy for some time. Understanding our past, after all, is key to understanding our future, she says. “Ancestry fascinates all of us,” she says. “It’s where we come from...it’s who we are.”

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