The Ghosts of Africa

Africa had its own Neanderthals.

Written by Peter Frost.

At the dawn of recorded history, Black Africans were still absent from most of Africa. South of the Sahara, the continent was largely home to hunter-gatherers who were small in stature, childlike in build and light reddish-brown in color. Many were archaic humans and not true Homo sapiens.

Most Americans think of native Africans as black and of white Africans as recent intruders; and when they think of Africa's racial history they think of European colonialism and slave trading. But very different types of peoples occupied much of Africa until as recently as a few thousand years ago. (Diamond, 1994)

When Jared Diamond penned those words, no one had yet retrieved DNA from ancient human remains, let alone African ones. Even when retrieval became possible, it still seemed impractical in a tropical climate that can quickly degrade complex organic molecules, like DNA.

Nonetheless, DNA has been retrieved from the remains of four long-dead individuals at a Cameroonian site. Two of them lived 8,000 years ago and the other two 3,000 years ago. Genetically, they were most like the Pygmies of the Congo rainforests, and not at all like the Bantu who today dominate central, eastern, and southern Africa (Lipson et al., 2020).

Those four individuals had substantial ancestry from a “ghost population” that split from the modern human lineage at about the same time as the Neanderthals (Lipson et al., 2020). That finding is borne out by two other studies:

• Skoglund et al. (2017), using ancient and modern DNA from West Africans, found admixture from archaic humans who were as divergent from modern humans as the Neanderthals were. Archaic ancestry persists today at a level of 9% among the Yoruba and 13% among the Mende.

• Durvasula and Sankararaman (2020) found that present-day West Africans derive 2 to 19% of their ancestry from unknown archaic humans. Unlike the other two research teams, they concluded that the ghost population split from the modern human lineage before the Neanderthals did.

The timing of the “ghost African” split will be settled only when we sequence that archaic genome. But the big picture is clear. Modern humans arose in the east of Africa and spread into the west and the south, where they encountered archaic humans. They also spread north into Eurasia and encountered other archaic humans—Neanderthals and Denisovans.

The Neanderthals of Africa

Africa was home to several archaic peoples when modern humans began to push out of East Africa. Some were more archaic than others, and some survived until recent times. Signs of late survival and late admixture have been found in human remains and even in present-day humans:

• Present-day genomes: The genomes of Biaka and Baka Pygmies show signs of archaic admixture that occurred during the last 30,000 years (Hammer et al., 2011; Hsieh et al., 2016; Wall et al., 2019). The Khoisan genome shows signs of archaic admixture from 20,000 years ago. The admixture came from a population that split from the modern human lineage some 700,000 years ago (Hammer et al., 2011; Wall et al., 2019).

• Present-day dentitions: Sub-Saharan Africans have 9 high-frequency and 2 low-frequency dental traits that are absent in other modern humans but present in extinct hominids and even nonhuman primates (Irish, 1998; Irish, 2013; Irish and Guatteli-Steinberg, 2003).

• Ancient skeletal remains: A skull from a Nigerian site (Iwo Eleru) has been dated to 11,700-16,300 years ago, yet it is intermediate in shape between the skull of a Homo sapiens and that of a Homo neanderthalensis or a Homo erectus. In fact, it falls outside the range of modern human variation. It resembles the skull of the Skhul-Qafzeh hominins, who preceded modern humans and lived in the Middle East 80,000 to 100,000 years ago (Harvati et al., 2011; Stojanowski, 2014).

  A Zambian site (Kabwe) yielded the remains of an apparent Homo erectus (Bada et al., 1974; Grün et al., 2020; Stringer, 2011). One research team has dated the skull to 110,000 years ago (Bada et al., 1974). Another research team has proposed a range of dates: 299,000 years ago for the basioccipital skull fragments; 216,000 years ago for the dentition; 130,000-191,000 years ago for other skeletal fragments; and 100,000-150,000 years ago for small mammal bones inside and outside the skull (Grün et al., 2020). This individual seems to have come from one of the last relict populations of Homo erectus.

  A South African site (Klasies River) yielded jawbone fragments that vary significantly in size and shape, a sign of admixture from archaic humans. The fragments are dated to a range of 60,000 to 110,000 years ago (Malekfar, 2012).

• Ancient artefacts and technology: A Senegalese site shows persistence of Middle Stone Age technology until at least 12,000 years ago. The authors of the study conclude: “Africa was until recently, more culturally and biologically diverse than has typically been considered” (Scerri et al., 2017).

“Little red men”

An earlier people is remembered in West African oral tradition. Such folk memories have been recorded in different countries of the region:

Côte d’Ivoire:

Pygmies may have been the first inhabitants of Côte d'Ivoire. In their oral tradition, most of the present-day peoples, in particular the Dan-Yacouba, recount that their ancestors, on arriving in the country, found "little red men" whom they pushed back into the forest. Others speak of "little brown men," who had supernatural powers and to whom presents were given to win them over. (Mantongouine, 2012)

According to some authors like Allou and Gonnin, the presence of these mysterious beings appears in the oral traditions. They are presented as short beings about 1 m 44 cm to 1 m 55 cm according to J.N. Loucou, with reddish skin, abundant hair, and feet pointing backwards. They appear in almost all of the regions of prehistoric Côte d’Ivoire in the sense that almost all of the oral traditions of Côte d’Ivoire’s ethnic groups affirm that they found Pygmies in the area before they became established. (Afri, 2013; see also Gonnin and Allou, 2006; Loucou, 1984, p. 18)

Who, before the Guérés, occupied the forest between the Sassandra and Cavally rivers? Everything suggests that they were these men of short stature and reddish color, called Négrilles and considered to be the ancestors of the present-day Pygmies of central Africa. The Guérés have preserved in their legends the memory of the “little red men” who are considered to be a tribe of malevolent forest spirits. Even today, some deserted parts of the rainforest are reputed to be sheltering some of their descendants. Simply encountering them brings death within a year to whomever they meet. (Viard, 1934, p. 11)

Burkina Faso:

The “konton-bili” are sometimes lumped together with the pygmies who are supposed to live in caves. They are red with their feet turned backwards. His misshapen male member is so long that he winds it around his neck. If someone succeeds in capturing him in the bush, he can obtain all the secrets of nature. … But who occupied this region before the Pougouli, the Sissala, the Yèri, and the Bwa? We will not go back to antediluvian times, be reassured, nor will we go back to the time when the region was inhabited by little red men hidden in the caves whom we call Kontonbili! Some will even tell you they still exist nowadays hidden in the caves of the mountains! (Dagara, 2017)

Mali:

A legend, reported by Desplagnes, who was told it by the old hogon of the Bankass, has the cliff being inhabited a long time ago by little red men, fishermen or hunters, who lived in the bushes and in the hollows of rocks. (Arnaud, 1921, p. 273)

Liberia:

The Mano of Liberia say that the forested area used to contain only “talking chimpanzees.” These small creatures, called Lam, inhabited the area when the Mano first came. A Lam and his family would live in a hole in the ground. (Riddell, 1970, p. 27)

Western and Central Africa in general:

Everywhere, but mainly in the countries from which the Négrilles have long disappeared, the Blacks who are considered to be the oldest occupants of the land say that it does not really belong to them and that when their distant ancestors, coming from the East, established themselves, they found it in the possession of little men with reddish complexions and large heads who were the real natives and who, in exchange for fulfilment of certain agreements, permitted the Negroes who first arrived on a piece of land to enjoy its use and cultivate it. Eventually, those little men disappeared, but the memory of them has remained alive. Generally, they have been deified and identified with the gods or spirits of the soil, the forest, the mountains, the great trees, the stones, and the waters; often, it is claimed that they live again in strangely behaving animal species, such as the manatee and varieties of small, semi-aquatic antelopes (Limnotragus Gratus and Hyæmoschus Aquaticus). Sometimes, as among the Mandinka, the same word (man or mâ) is used to designate those antelopes, the manatee, the bush spirits, and the legendary little red men. It also means “ancestor” and “master” and more particularly “master of the soil.” Thus, the native traditions tend to establish that the Négrilles preceded the Negroes on African soil and recognize the former’s eminent rights of ownership to the soil, whose current occupants consider themselves only to be precarious property holders and usufructuaries. (Delafosse, 1922, p. 14; see note #1)

Those folk memories may explain a passage about the “land of Pigmies” in The Travels of Sir John Mandeville, a medieval work written between 1357 and 1381:

This little folk neither labour in lands ne in vines; but they have great men amongst them of our stature that till the land and labour amongst the vines for them (Mandeville, 1915, p. 138).

The author seems to have never seen the peoples of his book, relying instead on a mix of hearsay and eyewitness accounts. Perhaps he knew a Jewish merchant who had crossed the Sahara, traveled down the Niger, and traded with the “great men” and the “little folk.”  

Pygmy carrying a dead crane, c. 450-450 BC. Source.

West Africans thus remember their ancestors as farmers who came from “the East” and replaced an earlier population of hunter-gatherers. The “little red men” must have survived into recent times because they are still mentioned in oral tradition.

All of this is consistent with a scenario proposed by George Murdock, an American anthropologist. He argued that Black Africans were once absent from most of the continent. They began as a small farming population around the Niger's headwaters, near the Mali-Guinea border, a fertile region that has given us such crops as fonio, sorghum, pearl millet, cowpea, Guinea yam, and watermelon (Murdock, 1959, pp. 64-68).

That is where farming began in West Africa, perhaps with assistance from the warmer, wetter climate of 12,000 to 10,000 years ago (Blench, 2006, pp. 123-126). There then followed a long transition during which hunter-gatherers learned how to manage wild food sources. By 4,000 to 3,000 years ago, there was already some form of cultivation (Harris, 1976, p. 352). Words in proto-Bantu (5,000 BP) indicate the domestication of some plants, like the yam, and the semi-domestication of others, like the oil palm, the bush candle, and the cola nut tree (Bostoen, 2020).

Murdock’s scenario is backed by other linguistic evidence. All languages in West Africa descend from proto-Niger-Congo. Around 10,000 years ago, its speakers began to increase in number and break up into different groups. The oldest group were the Mande speakers, whose descendants still inhabit the Niger's headwaters (Bennett and Sterk, 1977; Blench, 1993, pp. 128-129; Ehret, 1984; Murdock, 1959, pp. 44, 64-68, but see Blench 2006, pp. 111-118).

In summary:

• Some 60,000 years ago, modern humans began to expand out of East Africa. In the West and the South of the continent, they replaced earlier, more archaic humans, while intermixing with them to varying degrees. A semi-archaic population arose in the forested regions of West Africa.

• Some 10,000 years ago, a community of modern humans settled around the Niger’s headwaters and increased in number, thanks to the warmer, wetter climate at the onset of the Holocene. They gradually learned how to manage and domesticate their food sources, thus becoming proto-farmers.

• Their numbers continued to increase. By 7,000 years ago, they were spreading farther and farther down the Niger.

• Eventually, they reached the rainforest of southern Nigeria. They worked out a modus vivendi with the local hunter-gatherers, whose ownership of the land was acknowledged in exchange for the right to farm it as tenants.

• That arrangement allowed the proto-farmers to spread westward through the forest zone along the Atlantic coast and up the rivers of West Africa.

• With the passage of time, the modus vivendi became more and more theoretical, and the hunter-gatherers were pushed farther and farther into the forest… until they were no more.

Meanwhile, there was a similar push eastwards from the lower Niger. Some 4,000 to 5,000 years ago, proto-farmers fanned out into central, eastern, and southern Africa (Bostoen, 2020; Pakendorf et al., 2011; Rocha and Fehn, 2016). They became the Bantu peoples, and their demographic expansion appears to have continued the earlier one that began at the Niger’s headwaters (de Filippo et al., 2011).

There may have been a second eastward push from the middle Niger to the Nile and then northward and southward. Those proto-farmers (eventually pastoralists) spoke Nilo-Saharan languages, including Nubian. Pictorial and skeletal evidence suggests that ancient Egyptians began to encounter black-skinned Nubians to the south of their kingdom only 3,500 years ago (Junker, 1921). An eastward migration from the Niger to the Nile is suggested by the continuing presence of Nilo-Saharan speakers along the middle Niger (i.e., the Songhay).

Year-round farming by women → more polygyny → bigger, stronger men

Farming brought changes to behavior and morphology by intensifying intra-sexual competition among men:

• In Sub-Saharan Africa, farming can be done year-round and is overwhelmingly women’s work (Boserup et al., 2007, pp. 19-40; Goody, 1973; Guyer, 1991). A woman is thus largely self-reliant in feeding herself and her children.

• Because a man can more easily support a second wife and her children, polygyny accounts for 20 to 50% of all marriages in traditional Sub-Saharan farming societies (Bourguignon and Greenbaum, 1973, p. 51; Goody, 1973; Pebley and Mbugua, 1989; van den Berghe, 1979, p. 65; Welch and Glick, 1981; White, 1988). In contrast, the rate of polygyny is low among hunter-gatherers, like the Khoisans, the Pygmies, and the Hadza (Bourguignon and Greenbaum, 1973, p. 171; Butovskaya et al., 2015; Cavalli-Sforza, 1986a).

• When some men take a disproportionate share of the women, the other men must compete much more for the remaining ones. The only alternative, aside from celibacy, is to raid neighboring communities and steal their women (van den Berghe, 1979, pp. 50-51). “Polygyny is associated with warfare for plunder and/or female captives” (White and Burton, 1988, p. 882).

Photo by James Johnston, 1893, Reality versus Romance in South Central Africa.

The Datoga and the Hadza

In other animals, male-male rivalry for females leads to natural selection for bigger, stronger, and more muscular males. The same outcome has been observed in a study of two East African peoples: the polygynous Datoga and the monogamous Hadza (Butovskaya et al., 2015). Datoga men are larger and more robust than Hadza men. They also score higher on measures of physical aggression, verbal aggression, anger, and hostility. The two groups see aggression very differently:

There is a negative attitude toward aggression among the Hadza but not among the Datoga. In situations of potential aggression, the Hadza prefer to leave. In contrast, aggression is an instrument of social control — both within the family and in outgroup relations — in Datoga society. Datoga men are trained to compete with each other and to act aggressively in particular circumstances.  (Butovskaya et al., 2015)

The two groups also differ at the androgen receptor gene. Datoga men are more likely to carry an allele that correlates among them with a higher level of aggressiveness and a higher number of children fathered.

Other hunter-gatherers and farmers in Africa

The above findings are consistent with a study of two Namibian peoples, the largely monogamous !Kung hunter-gatherers and the highly polygynous Kavango farmers. The latter have much higher levels of total testosterone and DHT. The authors suggest that the lower testosterone and DHT levels of the !Kung might explain their childlike appearance: sparse body hair; short stature; pedomorphic morphology; and light yellowish skin (Winkler and Christiansen, 1993).

In general, men are more robustly built in the polygynous farming societies of Sub-Saharan Africa. They and their African-American descendants outclass men of European descent in weight, chest size, arm girth, leg girth, muscle fiber properties, and bone density (Ama et al., 1986; Ettinger et al., 1997; Himes, 1988; Hui et al., 2003; Pollitzer and Anderson, 1989; Todd and Lindala, 1928; Wagner and Heyward, 2000; Wolff and Steggerda, 1943; Wright et al., 1995).

Natural selection can make men more robust through higher blood levels of testosterone and DHT and through stronger binding to testosterone/DHT receptors. Both evolutionary trajectories are evident in Sub-Saharan farming peoples and their diaspora:

• Blood levels of testosterone are higher (Pettaway, 1999; Ross et al., 1986; Ross et al., 1992; Winters et al., 2001).

• Androgen receptors show higher activity (Kittles et al., 2001).

• Greater lifetime exposure to testosterone is reflected in the high rate of prostate cancer among African-American men (Powell, 2007). The apparently lower rates among West Indians and Sub-Saharan Africans are now put down to underreporting (Glover et al., 1998; Odedina et al., 2006; Ogunbiyi and Shittu, 1999; Osegbe, 1997).

In African Americans, blood testosterone reaches a peak during early adulthood, declines after the age of 24, and converges on European American levels from 30 onward (Gapstur et al., 2002; Nyborg, 1994, pp. 111-113; Ross et al., 1986; Ross et al., 1992; Winters et al., 2001). The latest study on the subject is worth quoting:

Overall, between the ages of 12 and 15, black males had lower testosterone levels than white males. Testosterone levels increased rapidly with age and reached higher and earlier peak levels in black males compared to white males at 20–30 years of age. After reaching a peak level, testosterone levels declined earlier in blacks than in whites. Further analyses showed that black males had considerably higher levels of testosterone compared to white males aged 20–39 years after adjusting for covariates, including age, body mass index, cigarette smoking, physical activity, and waist circumference; however, no statistically significant differences were observed between the groups at any other age. (Hu et al., 2015)

The peak in young adulthood may be an adaptation to polygyny, specifically to the shortage of women available to young men. Traditionally, that shortage was resolved by giving priority to men who were at least ten years past the age of puberty. Thus, among the Nyakyusa: “… there is a difference of ten years or more in the average marriage-age of girls and men, and it is this differential marriage-age which makes polygyny possible” (Wilson, 1950, p. 112).

During those years of early adulthood, men could escape involuntary celibacy only by competing fiercely for the few local women available or by seizing other women as spoils of war.

Divergence in skin color between hunter-gatherers and farmers

In Sub-Saharan Africa, hunter-gatherers are not only shorter than farming peoples but also lighter-skinned (Cavalli-Sforza, 1986b; Schapera, 1930: 51-54, 60; Weiner et al, 1964). Their short stature and light skin are sometimes attributed to the dark, cramped habitat of the rainforest, where the Pygmies live (Turnbull, 1986, p. 121). Yet the Khoisans of the Kalahari are likewise short and light-skinned, and they live in open desert.

Among human groups in general, the polygyny rate correlates with darkness of skin, even if we control for latitude (Manning et al., 2004). This is particularly so in Sub-Saharan Africa, whose polygynous farming peoples are visibly darker than the much more monogamous Pygmy and Khoisan hunter-gatherers. The reason may be a widespread mental association between gender and skin color. Because women are naturally fairer in complexion (i.e., their skin has less melanin and less blood flowing through its outer layers), lighter skin has traditionally been viewed as more feminine and darker skin as more masculine (Frost, 2010; Frost, 2023; van den Berghe and Frost, 1986). Since men have to compete more intensely for women in a polygynous society, sexual selection should favor those men who can defeat their rivals by being physically stronger or psychologically more intimidating — such as through darker skin, or through verbal bombast and higher emission of male odorants (Frost, 2022a).

Different African populations may have evolved different selective compromises between natural selection for darker skin, to protect against solar UV, and sexual selection for lighter-skinned women or darker-skinned men. In polygynous societies, the selective compromise is shifted toward darker hues because the scarcity of available women has favored darker-skinned men, either through male-male rivalry or through female choice (Frost, 1994).

Conclusion

Let’s rewind history. We first see Black Africans retreating from the south of the continent, then from the east and the center, and finally from most of West Africa. It’s now the dawn of history, six millennia ago. Where are they? Perhaps none exist yet. There seem to be only hunter-gatherers of short stature, slight build, and light reddish-brown color. Some of them are modern humans, notably in East Africa. To the west and the south are archaic or semi-archaic groups, similar to the hominins who preceded modern humans in the Middle East. There may even be relict populations of Homo erectus.

Now let’s stop the rewind and go forward in time. Some proto-farmers are settling around the Niger’s headwaters. They then increase in number and spread down the Niger, while evolving to be larger, darker, and more polygynous. Meanwhile, the first city-states appear in Sumer.

It’s the first century. How much of Africa is still home to “little red men”? We ask two scholars. Pliny the Elder replies that the Pygmy homeland is in the “marshes where the Nile rises” [Naturalis Historiae 6.35.188]. Strabo adds that the Pygmies used to dwell along “the entire southern sea-board” of Africa [Geographica 1.2.28]. Perhaps he’s including the Khoisan peoples.

It’s the tenth century. Arab geographers tell us that "in the outer reaches of the land of the Zanj there are cool highlands in which live white Zanj" (Lewis, 1990, p. 121, n. 3). The Zanj are the dark-skinned peoples of East Africa, and the “white Zanj” the lighter-skinned Khoisans who still roam the plateau of southern Africa.

Finally, we’re back in the present. The Africans of today are indeed different from those of the past. Does anything remain of those archaic humans? Perhaps through admixture they provided the incoming modern humans with genes that would help them adapt to later developments, such as the rise of complex societies in parts of West Africa (Frost, 2022b; McIntosh and McIntosh, 1988).

These “ghosts in the genome” are a reminder that the past of our species was a different place, even the relatively recent past. The three great continental races have just begun their hour upon the stage.

Peter Frost has a PhD in anthropology from Université Laval. His main research interest is the role of sexual selection in shaping highly visible human traits. Find his newsletter here.

---

Become a free or paid subscriber:

You can also follow us on Twitter.

---

Notes

1. There is also, allegedly, skeletal evidence:

[The farmers] had been preceded there doubtlessly by Pygmies who seem to have peopled even the forest of Côte d'Ivoire, as has reportedly been established from the skulls kept at the Musée de l'Homme which I brought back from Haut Cavally and which Dr Poutrin had examined. (Chevalier, 1948, p. 107)

If you seek a reference from this essay, please comment below.