Scientists have revealed a surprisingly complex origin of our species, rejecting the long-standing argument that modern humans arose from one place in Africa over a period of time.

By analyzing the genomes of 290 living people, the researchers concluded that modern humans descend from at least two populations that coexisted in Africa for a million years before merging in various independent events across the continent. The findings were published Wednesday in Nature.

“There is no single birthplace,” said Eleanor Scerri, an evolutionary archaeologist at the Max Planck Institute for Geoarchaeology in Jena, Germany, who was not involved in the new study. “She really puts a nail in the coffin of that idea.”

Paleoanthropologists and geneticists have found evidence that points to Africa as the origin of our species. The oldest fossils that may belong to modern humans have been unearthed there, dating back 300,000 years. So were the oldest stone tools used by our ancestors.

Human DNA also points to Africa. Living Africans have a huge amount of genetic diversity compared to other people. That’s because humans lived and evolved in Africa for thousands of generations before small groups, with comparatively small gene pools, began expanding to other continents.

Within the vast expanse of Africa, researchers have proposed several locations as the birthplace of our species. The first human-like fossils in Ethiopia led some researchers to look to eastern Africa. But some living groups of people in South Africa appeared to be very distantly related to other Africans, suggesting that humans might have a deep history there.

Brenna Henn, a geneticist at the University of California, Davis, and her colleagues developed software to run large-scale simulations of human history. The researchers created many scenarios of different populations existing in Africa during different time periods and then looked at which ones might produce the DNA diversity found in people alive today.

“We might ask what kinds of models are really plausible for the African continent,” Dr. Henn said.

The researchers analyzed the DNA of a variety of African groups, including the Mende, farmers who live in Sierra Leone in West Africa; the Gumuz, a descendant group of hunter-gatherers in Ethiopia; the Amhara, a group of Ethiopian farmers; and the Nama, a group of hunter-gatherers from South Africa.

The researchers compared the DNA of these Africans with the genome of a person from Great Britain. They also looked at the genome of a 50,000-year-old Neanderthal found in Croatia. Previous research had found that modern humans and Neanderthals shared a common ancestor that lived 600,000 years ago. Neanderthals spread across Europe and Asia, interbred with modern humans from Africa, and then went extinct around 40,000 years ago.

The researchers concluded that for a million years, the ancestors of our species existed in two different populations. Dr. Henn and her colleagues call them Stem1 and Stem2.

Around 600,000 years ago, a small group of humans emerged from Stem1 and became the Neanderthals. But Stem1 persisted in Africa for hundreds of thousands of years after that, just like Stem2.

If Stem1 and Stem2 had been completely separated from each other, they would have accumulated a large number of different mutations in their DNA. Instead, Dr. Henn and her colleagues found that they had remained only moderately different, almost as different as Europeans and West Africans are today. The scientists concluded that people had moved between Stem1 and Stem2, mating to have children and mixing their DNA.

The model does not reveal where Stem1 and Stem2 people lived in Africa. And it is possible that the bands of these two groups moved around a lot during the vast periods of time during which they existed on the continent. Around 120,000 years ago, the model indicates, African history changed dramatically.

In southern Africa, the people of Stem1 and Stem2 merged, giving rise to a new lineage that would lead to the Nama and other humans living in that region. In other parts of Africa, a separate merger of the Stem1 and Stem2 groups took place. That merger produced a lineage that would give rise to people living in West Africa and East Africa, as well as people who spread out of Africa.

It is possible that climatic upheavals forced Stem1 and Stem2 people to live in the same regions, leading them to merge into unique groups. Some hunter-gatherer bands may have had to withdraw from the coast when sea levels rose, for example. Some regions of Africa became arid, potentially sending people looking for new homes.

Even after these mergers 120,000 years ago, people with either only Stem1 or only Stem2 ancestry appear to have survived. The DNA of the Mende people showed that their ancestors had interbred with the Stem2 people only 25,000 years ago. “It suggests to me that Stem2 was somewhere in West Africa,” Dr. Henn said.

She and her colleagues are now adding more genomes from people in other parts of Africa to see if they affect the models.

They may uncover other populations that endured in Africa for hundreds of thousands of years and ultimately helped produce our species as we know it today.

Dr. Scerri speculated that living in a network of mixed populations in Africa might have allowed modern humans to survive while Neanderthals died out. In that arrangement, our ancestors could have held on to greater genetic diversity, which in turn could have helped them withstand changes in climate, or even develop new adaptations.

“This diversity at the root of our species may have ultimately been the key to our success,” Dr. Scerri said.