New Reich Lab paper on ancient West Africa finds missing 4th branch of humanity

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Ancient West African foragers in the context of African population history

Abstract

Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children—two of whom were buried approximately 8,000 years ago and two 3,000 years ago—from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today—as well as speakers of Bantu languages from across the continent—are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans.


The article is behind a paywall, but it has been explained in Nature News (Ancient African genomes offer glimpse into early human history) and in the New York Times (Ancient DNA from West Africa Adds to Picture of Humans’ Rise).

Here is the Supplementary information.

The study found that the genomes of the four Shum Laka children tested were remarkably similar despite the 5000 years gap between some of them.

The major surprise was that none of the people at Shum Laka were closely related to the Bantu speakers, even though the mainstream theory is that Proto-Bantu language originated in Cameroon between 1000 and 500 BCE. The four skeletons analysed had a strong kinship to the Aka, a group of hunter-gatherers with a pygmy body type who live today in rain forests 1,500 km to the east. It may simply be because the region was home to Proto-Bantu farmers as well as Shum Laka-like hunter-gatherers and that the samples analysed happened to belong to the latter.
 
The genealogical trees of humanity redrawn in the paper:

41586_2020_1929_Fig8_ESM.jpg



Schematic of first alternative admixture graph.

41586_2020_1929_Fig9_ESM.jpg



Schematic of the second alternative admixture graph.

41586_2020_1929_Fig11_ESM.jpg


Mark Lipson explains the above graphs in an interview with the New York Times in the article linked above.

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.
"
 
Screen%20Shot%202020-01-22%20at%205.16.38%20PM.png


The signals of deep ancestry in groups related to the
West African clade (Fig. 3a) can be explained by two admixture events:
one along the ancestral West African lineage, and a second, smaller
contribution (about 4%) to Mende from the same source (Fig. 4a).
Accordingly, f4-statistics testing for ancestry basal to southern African
hunter-gatherers (Fig. 3a, bottom) are well-correlated with the inferred
proportions of ancestry from the West African clade (Extended Data
Fig. 6).

We estimate the shared admixture to introduce 10% deep modern
human and 2% archaic ancestry, although the first proportion is not
well-constrained (Extended Data Table 3). An alternative model with
no archaic component—in which the West African clade receives deep
ancestry from a single source22 that splits before point (1) in Fig. 4a—
also provides a reasonable fit to the data, although it does not account
for previous evidence of archaic ancestry in sub-Saharan Africans27–31.

https://reich.hms.harvard.edu/sites...inline-files/Shum_Laka_published_online_2.pdf

The full text of the study is publicly available at Harvard Medical School's Reich lab website: https://reich.hms.harvard.edu/
 
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I always thought the Bantu languages arose in the area of the lower Niger River.
 
Maciamo what is your input on Iberomaurusian and Ancient North African (ANA) component in relation to this paper?
 

I've read this paper. This study suggests that archaic admixture in West Africans took place before the Out-of-Africa event, which implies that Non-Africans also likely have this kind of admixture, or at least some/a component of the admixture. However, the paper also says that it’s possible that this archaic admixture was diluted or lost during the Out-of-Africa bottleneck. We need more genetic research on the deep ancestry in Africa. Besides the range of the suggested archaic admixture (~2-19%), I personally find difficult to understand or to make a sense out of it. Besides, IF all humans, West Africans, and non-Africans have this Ghost DNA why does the study only talk about West Africans? Were Non-Africans tested for this archaic admixture in the same study? Once again when Non-Africans have this kind of archaic genetic input what is so special about West Africans or the Yoruba then? And what about East Africans?

Besides, this archaic Ghost ancestry in West Africans is very likely from Homo heidelbergensis.
 
Does anyone that has read the paper about Shum Laka agree with the claim this genetic study makes the term “Eurasian” or “SSA” obsolete? There are people who claim that the Shum Laka study shows that ANA is on the same branch as Basal West African and that this paper concludes that the component that constituent the largest component of West Africans (Basal West African) is on the same level and radiated with Eurasian. So basically West Africans are in the same branch with Eurasians with Khoisan as an outgroup. These people argue that the “exclusivity” of the so-called Eurasians in Africa, got a heavy blow with the Shuma study since any “Eurasians” who back migrated back to Africa wouldn‘t have been “Special”. They just would have met African people who were not that different from them, people who later picked up other ancestries with time. Hence the terms like “Subsaharan African” and “Eurasian” are totally meaningless genetically, especially in Africa.
 
Does anyone that has read the paper about Shum Laka agree with the claim this genetic study makes the term “Eurasian” or “SSA” obsolete? There are people who claim that the Shum Laka study shows that ANA is on the same branch as Basal West African and that this paper concludes that the component that constituent the largest component of West Africans (Basal West African) is on the same level and radiated with Eurasian. So basically West Africans are in the same branch with Eurasians with Khoisan as an outgroup. These people argue that the “exclusivity” of the so-called Eurasians in Africa, got a heavy blow with the Shuma study since any “Eurasians” who back migrated back to Africa wouldn‘t have been “Special”. They just would have met African people who were not that different from them, people who later picked up other ancestries with time. Hence the terms like “Subsaharan African” and “Eurasian” are totally meaningless genetically, especially in Africa.

That's a bullshit claim.
 
Does anyone that has read the paper about Shum Laka agree with the claim this genetic study makes the term “Eurasian” or “SSA” obsolete? There are people who claim that the Shum Laka study shows that ANA is on the same branch as Basal West African and that this paper concludes that the component that constituent the largest component of West Africans (Basal West African) is on the same level and radiated with Eurasian. So basically West Africans are in the same branch with Eurasians with Khoisan as an outgroup. These people argue that the “exclusivity” of the so-called Eurasians in Africa, got a heavy blow with the Shuma study since any “Eurasians” who back migrated back to Africa wouldn‘t have been “Special”. They just would have met African people who were not that different from them, people who later picked up other ancestries with time. Hence the terms like “Subsaharan African” and “Eurasian” are totally meaningless genetically, especially in Africa.

I call bullshit on this. Going by that token, there is no use clustering human populations at all because they all ultimately are linked to each other in a prior common population group. The ancestors of West Africans and those of Eurasians split from each and drifted apart (as well as adding admixture from archaic hominins) around 100 kya. That's almost 50-55 ky before the divergence between West and East Eurasians. So honestly they were definitely not similar populations.

There is perhaps some truth in that "SSA" is a bit too vague and imprecise because it encompasses several very distinct population clusters that mixed or partially replaced each other in varying proportions. But I'd say that much like saying "Eurasian" ancestry is good enough for the purposes of a genetic analysis on Central Africans or Southern Africans, because the overwhelming majority of the local gene pool will be non-Eurasian, "SSA" is good enough for genetic analysis of populations that harbor negligible non-Eurasian and non-North African admixture, so there is no need to get a higher-resolution, more detailed determination of those admixtures, which are virtually at "noise" proportions.
 

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