Ancient DNA from West Africa Adds to Picture of Humans’ Rise

In October 2015, scientists reconstructed the genome of a 4,500-year-old man who lived in Ethiopia. It was the first time that anyone had created a complete genetic snapshot of an African from an ancient skeleton.

Since then, other researchers have recovered DNA from skeletons unearthed in other regions of the continent. Now researchers have found the first genetic material from West Africa. On Wednesday a team reported that they had recovered DNA from four individuals in Cameroon, dating back as far as 8,000 years.

These ancient genomes contain vital clues to the history of the continent that have largely disappeared in the past few thousand years. Taken together, they are giving scientists a new vision of our species since it arose in Africa.

In the new study, published in Nature, the researchers reported that modern humans diverged into four major populations between 200,000 and 250,000 years ago. One of those populations is new to scientists; few traces of it remain in the DNA of living Africans.

The vanished population may have consisted of bands of hunter-gatherers who lived south of the Sahara from Mali to Sudan until just a few thousand years ago.

“We are so limited by the information we can get from living people,” said Jessica Thompson, an archaeologist at Yale University who was not involved in the new study. “It’s pretty clear that there’s been a huge transformation in the genetic landscape in Africa just recently.”

Scientists have been studying the genetic diversity of living Africans since the 1970s. As it became possible to sequence more DNA, the additional data revealed that the genetic variation among living Africans was much greater than that among the rest of the world combined.

This insight made it clear that our species arose in Africa and stayed there for most of its history. Small groups of people expanded out to give rise to non-African populations.

But scientists have struggled to draw the older branches of the human family tree with much precision. Looking for fresh clues, they tried drilling into ancient bones.

The odds seemed low. Many researchers assumed that ancient, fragile DNA molecules would not have survived the hot climate across much of Africa.

The discovery in 2015 of Mota, an Ethiopian skeleton with DNA to offer, proved otherwise. Geneticists and archaeologists began investigating other skeletons from across Africa, and found a few that still contained genetic material.

Mary Prendergast, an archaeologist at Saint Louis University in Madrid, considered the skeletons found at Shum Laka, a rock shelter in Cameroon, among of the top candidates to test for DNA. “People working all over the continent are aware of this site,” she said.

Archaeologists have dug into the floor of Shum Laka since the 1980s, and have found layers of human remains as old as 30,000 years. The surrounding region has long been viewed as the origin of one of the most important expansions in African history. About 4,000 years ago, the Bantu people started farming oil palm and grains. They later expanded for thousands of miles to the east and south, across a vast swath of Africa.

Dr. Prendergast wondered if DNA from Shum Laka would show a kinship with living Bantu people. But finding that genetic material would be a long shot, she knew: Shum Laka is close to the Equator and has a heavy rainy season each year.

“My hopes were not high at all,” she said. “I went into this project thinking, ‘Will this work?’”

In the end, it did. The researchers recovered abundant DNA from four individuals, two of whom were buried in the rock shelter 8,000 years ago, and another pair 3,000 years ago.

One of the 8,000-year-old skeletons was especially rich with human DNA. “It’s of a quality of a modern medical genome,” said David Reich, a Harvard Medical School geneticist and a co-author with Dr. Prendergast.

To Dr. Prendergast’s surprise, none of the people at Shum Laka were closely related to Bantu speakers at all. In fact, they had a strong kinship to the Aka, a group of hunter-gatherers with a pygmy body type who live today in rain forests 1,000 miles to the east.

To make sense of this paradox, the researchers carried out a large-scale comparison of all the ancient African DNA gathered so far, along with living people from across Africa and beyond. The team found a scenario that best explains how different groups of Africans ended up with their particular combinations of DNA.

Dr. Reich and his colleagues can trace the major lineages of people back to common ancestors who lived in Africa between 200,000 and 250,000 years ago.

“It seems we have four lineages splitting at the same time,” said Mark Lipson, a postdoctoral researcher at Harvard and an author of the new study.

One lineage passed down their DNA to living hunter-gatherers in southern Africa. A second group were ancestors of the Aka and other central African hunter-gatherers.

A third group became hunter-gatherers in East Africa, as evidenced by the fact that many living Africans in that region have inherited some of that DNA.

The fourth group, which Dr. Reich and his colleagues call “Ghost Modern,” is far more mysterious.

The ancient Shum Laka people have a substantial amount of Ghost Modern ancestry. So does the ancient Mota man from Ethiopia. But ancient remains from Morocco and South Africa had none. Today some people in Sierra Leone have a tiny trace of Ghost Modern ancestry, the researchers found.

It’s possible that the Ghost Moderns were hunter-gatherers who lived across the southern edge of the Sahara. They remained isolated from other Africans for tens of thousands of years. Later, they bred with people from other groups at the eastern and western edges of their range.

Most people in Africa — and the rest of the planet — can trace much of their ancestry to the East African hunter-gatherers. Less than 100,000 years ago, this group split into new lineages.

One group gave rise to many of today’s East African tribes. Another group included the Mota man. They were closely related to the people who expanded east out of East Africa and into the rest of the world.

A separate group of East Africans moved west, encountering and mixing with Central African hunter-gatherers and eventually becoming the first West Africans. The people of Shum Laka may be the descendants of this group.

Many thousands of years passed before a different group of the West Africans gave rise to the Bantu people. Their population discovered agriculture, grew and took over larger areas of land.

But the Bantu farmers didn’t swiftly drive hunter-gatherers to oblivion. The Shum Laka people survived for at least 1,000 years in the heart of Bantu country.

But after a couple thousand years, the society reached a tipping point, and the hunter-gatherers were marginalized. East African tribes that also began farming and grazing livestock applied additional pressure.

It’s possible that this pressure brought an end to many groups of hunter-gatherers, including the Mota and the Shum Laka — perhaps even the ancient Ghost Modern people.

The surviving hunter-gatherers interbred with neighboring farmers. The new study finds that the Aka, for instance, can trace 59 percent of their ancestry to the Bantu.

“Their results have some big implications for us archaeologists,” Dr. Thompson said.

It’s conceivable that researchers could find skeletons of Ghost Modern individual in areas those people once lived. The bones might even hold some DNA that could confirm the hypothesis.

“If we could get really old samples from there, that would be amazing,” Dr. Lipson said.