So many Nigerians: why is Nigeria overrepresented as the ancestral genetic homeland of Legacy African North Americans?

Summary

The genetics of African North Americans are complex amalgamations of various West and Central African peoples with modest gene flow from specific European and Amerindian peoples. A comprehensive understanding of African North American biohistory is a prerequisite for accurate interpretations of the ancestral genetics of this population. Too often, genetic interpretations falter with ahistorical reconstructions. The recently reported overrepresentation of Nigerian lineages in African North Americans reflects pronounced limitations in the African genomic database, the artificiality of the colonial maps of Africa, the contributions of multiple African empires and kingdoms into the transatlantic trade in enslaved Africans, and the overrepresentation of Yoruba peoples in the existing limited representation of West Africans in public genomic databases. This Matters Arising paper is in response to Micheletti et al. (2020), published in The American Journal of Human Genetics. See also the response by Micheletti et al. (2020), published in this issue.

Introduction

In a recent paper in The American Journal of Human Genetics entitled “Genetic Consequences of the Transatlantic Slave Trade in the Americas,” Micheletti and colleagues¹ detail the “overrepresentation” of genetic lineages designated as Nigerian in the ancestry of Legacy African North Americans. Legacy African North Americans are US-born African North Americans with the heritage of approximately 16 generations of exposure to a history of enslavement and institutional racism in the United States. This socio-residential pattern has influenced their genetic ancestry as well as their epigenome.^2,3 However, even after 401 years of residence in North America, this population remains primarily genetically African with modest gene flow from non-Africans.

The overrepresentation of Nigerian lineages identified by Micheletti et al.¹ reflects the confluence of many factors, beginning with the inadequacies of the existing African reference genomic database⁴ as well as weaknesses in comprehensively accounting for the geospatial history of modern Nigeria and that of contemporary Legacy African Americans. To fully understand the current ancestral presentations of African North American genomes in general and Legacy African Americans in particular, researchers must integrate salient historical factors into their robust genetic and evolutionary interpretations of these complex populations. This paper reviews the relevant historical and epidemiological factors that have shaped aspects of African North American populations, particularly those events that have seemingly amplified the genetic signals of their Nigerian ancestry.

Results and discussion

The artificiality of the colonial map in Africa

The borders of modern Nigeria are a post-colonial construction encompassing lands traditionally occupied by highly diverse ethnic groups with distinct languages, traditions, and cultures. Many of these groups formed highly organized empires that influenced areas beyond the current borders of modern Nigeria. In the southeast of modern Nigeria, there were 45–50 independent Igbo states or kingdoms during the period of the transatlantic trade in enslaved Africans. The northern part of modern Nigeria includes part of the Hausa-Fulani Empire. The southwest part of modern Nigeria includes part of the Oyo-Yoruba Empire. Before colonization by the British in the late 19^th century, the region now known as modern Nigeria was war ravaged with kings competing for the resources offered by the European powers and African prisoners of war feeding the transatlantic trade in enslaved Africans. The region saw a succession of fluctuating ascendancies of expansive empires, such as those of Oyo, Benin, Kanem-Bornu, and Sokoto, whose descendants are now all part of modern Nigeria. In the middle regions of modern Nigeria, there has historically been intermingling of diverse ethnic groups (see Figure 1). Modern Nigeria currently includes more than 200 distinct ethnic groups; greater Nigeria includes even more because many of these groups also “spill over” across colonial borders. Table 1 lists the relevant empires and kingdoms of Nigeria that were present during the period of the transatlantic trade in enslaved Africans.

Figure 1.

Ethnic groups of modern Nigeria with subgroups noted, many extending into surrounding countries

Map courtesy of QuadGRID (see Web Resources).

Table 1.

Listing of historic empires and kingdoms now in or adjacent to modern Nigeria who participated in the transatlantic trade in enslaved Africans as either victims, perpetrators, or both

Empire or kingdom	Time frame	Location	Ethnic groups	Activities related to transatlantic slave trade
Kingdom of Nri	1043–1911 CE	southeastern Nigeria	Igbo subgroup	refuge for enslaved Africans; non-militaristic, 45–50 kingdom states
Oyo Empire	1300–1836 CE	western Nigeria	Yoruba peoples	powerful calvary and active traders; dominated Fon kingdom of Dahomey; actively engaged in enslavement
Kingdom of Allada (Arda)	1100–1724 CE	southwestern Nigeria, modern Republic of Benin	Fon and Aja peoples	founded by a group of Aja migrants from Tado; maintained control of key seaports for the growing slave trade business, which gave Allada the economic means to pay its tribute to Oyo; between 1640 and 1690, about 125,000 enslaved Africans were sold from Allada, peaking at about 55,000 during the 1680s alone
Kingdom of Akwamu (Akuambo)	1600–1900 CE	modern Ghana	subset of the Akan peoples	migrants from Bono state, the Akan founders settled in Twifo-Heman; Akwamu expansion started between 1629 and 1710 all the way to Ouidah in present-day southern Benin
Kingdom of Ouidah (Whydah)	1580–1728 CE	southern modern Republic of Benin	Fon and Aja peoples	major slave trading area; enslaved Africans were housed prior to transport to the Americas and forced to make reverse circumambulation around the Tree of Forgetfulness to lose their memories of Africa
Kingdom of Dahomey	1600–1904 CE	southwestern Nigeria, southern modern Republic of Benin	Fon and Aja peoples	major center in the Atlantic slave trade until 1852; In 1724, the Kingdom of Dahomey invaded the Kingdom of Allada; in 3 days, the king of Dahomey’s troops slaughtered thousands of Allada’s warriors and citizens; more than 8,000 of Allada’s population were taken as prisoners and sold into slavery in the Americas
Benin Empire	1240–1897 CE	central Nigeria	Edo peoples	first West African empire to significantly interact with Europeans on Atlantic coast (Bight of Bonny)
Kaabu Empire	1536–1867 CE	northeastern border with Nigeria	Mandinka peoples	former province of the Mali Empire; ties to Senegambia
Aro Confederacy	1690–1902 CE	southeastern Nigeria	Igbo subgroup	aggregate of Igbo-related peoples
Bonoman State	1000–1800CE	southern modern Ghana	Akan-associated groups	gold and kola nut traders with Saharan traders
Ashanti Empire	1701–1957 CE	Ashanti region of southern modern Ghana	Ashanti peoples	known as fierce warriors, gold traders, contact with the coast, and the important slave and gun trade
Kong or Wattara Empire	1712–1896 CE	northeastern Côte d’Ivoire and Burkina Faso	Dyala immigrants from Mali Empire	Islamic state ruled by the Kulubali or Coulibaly dynasty
Bamana or Ségou Empire	1712–1896 CE	Ségou area of modern Mali	Bambara peoples	established after the fall of the Mali Empire and the Keita dynasty, conquered by the Toucouleur
Sokoto Caliphate	1804–1903 CE	northeast area of modern Nigeria	Fulani and Hausa peoples	Islamic state founded during the jihad of the Fulani War in 1804 by Sheik Usman dan Fodio; destroyed by the British army; slavery was a large part of the economy; significant trade over the trans-Saharan routes.
Wassoulou Empire	1878–1898 CE	Bissandugu, southwest modern Guinea	Mandinka peoples	Islamic state, destroyed by the French army
Hausa-Fulani Empire	1300 –1800 CE	northeast area of modern Nigeria	Hausa and Fulani peoples	Islamic state; traders with North Africa, Nile Valley, and Africa south of Sahara
Kanem-Bornu Empire	700–1893 CE	northeast modern Nigeria, Chad, Libya, and west of Lake Chad to Sudan	Tebu-speaking Kanembu. Kanuri, and Fulani peoples	Kanem was located at the southern end of the trans-Saharan trade route between Tripoli and the region of Lake Chad
Songhai Empire	1375–1591 CE	Sahel region	Songhai, Malinké, Mandinka, Fulani, Bozo, Soninke, Hausa, and Mossi peoples	Songhai controlled trade routes and the sources of salt and gold

The European colonial masters and their post-war agreements contrived Africa’s current national borders, creating fragile units in which ethnic, religious, and linguistic groups are haphazardly thrown together or separated without any recourse to those groups’ peculiarities, priorities, and aspirations.5, 6, 7 Often colonial borders still cut through African ethnic nations. This is part of the reason that these borders are not valid demarcation points in human genetic studies. There was never any logical reason for the current ethnic constellations of modern Nigeria to be grouped together except that it suited the priorities of Britain. Each of the pre-colonial African empires whose descendants currently reside in modern Nigeria were significant perpetrators of slavery and were, at other times, themselves enslaved. All disproportionately contributed Africans to the Americas because it was at their ports in the Bight of Benin and the Bight of Bonny that European slave ships docked.

Regional variation in the proportions of Africans brought from different regions into the staging areas of North America

Slavery was a legal institution in eastern North America in the 16^th through 19^th centuries. A large proportion (38%) of the enslaved Africans brought into Chesapeake Bay were from the Bight of Bonny (Biafra).^8,9 This demographic distinction contrasts with the smaller proportions of Nigerian-derived Africans brought to either the Carolina Coast or the Mississippi Delta regions. Figure 2 contrasts the varying proportions of Africans from diverse catchment regions transported to these three disembarkation sites in North America. This immigration bias by itself, however, does not fully account for the current overrepresentation of Nigeria as the ancestral genetic homeland of so many African North Americans. To explain that, we must look at what happened in the United States in 1808.

Figure 2.

Proportions of Africans leaving from specific African ports for disembarkment at three North American sites during the transatlantic trade in enslaved Africans

Map courtesy of QuadGRID (see Web Resources).

Domestic slave trade introduces distortions into the African ancestries of African North Americans

In 1794, US-born inventor Eli Whitney patented the cotton gin, a machine that revolutionized the production of cotton by accelerating the process of removing seeds from cotton fiber, thus allowing for more cotton to be grown but requiring fewer numbers of enslaved people to process the cotton. Prior to this, the effort involved in processing the cotton was rate limiting.

In 1807, King George III of Britain signed into law the Act for the Abolition of the Slave Trade, banning trading in enslaved people throughout the British Empire. In response to these new limitations to the transatlantic trade and shifts in the agricultural economy, the US Congress barred the importation of enslaved Africans into the United States in 1808. However, it left the internal or domestic trade in enslaved Africans intact. Thus, the internal trade took on a new importance as the slave-holding states of the Old South (e.g., Virginia, Delaware, Maryland, Georgia, North Carolina, and South Carolina) recognized that holding large numbers of imported enslaved Africans in reserve was too expensive.¹⁰ Plantation owners desired the free labor but sought to locally produce it rather than import it from continental Africa. As the transatlantic African slave trade diminished, an “abominable” new trade emerged in the Americas.^11,12 In the United States, the internal slave trade was centered in state of Virginia. At this time, the large agricultural concerns shifted to the New South (e.g., Kentucky, Tennessee, Alabama, Florida, Mississippi, Missouri, Arkansas, Louisiana, and Texas), where cotton and sugar plantations needed the cheap labor provided by the institution of slavery.

As this transition intensified, Richmond, Virginia, became a central slave market that facilitated the interstate slave trade. Planters in the Old South chose to breed and sell enslaved Africans and African Americans as a commodity rather than freeing them.¹⁰ This domestic slave trade, also known as the Second Middle Passage (see Web Resources) and the interregional slave trade made enslaved Africans of the Chesapeake Bay the primary targets of this new strategy.¹³ The main African ethnic groups of this region were the Ibo and Ibo-related peoples from what is now modern Nigeria. These groups disproportionately bore the brunt of this cruel and inhumane activity. Yet it is their lineages now that are so abundantly represented among African North Americans. The state of Virginia was the center of the domestic internal slave trade and was the prime site for the breeding colonies established to increase the numbers of the enslaved without incurring the problems associated with transport on the high seas (and possible intervention by the [British] Royal Navy and renegade pirates).

The role of rebellions in distorting African survivorship patterns

Rebellions among enslaved Africans and African Americans were a reoccurring source of European and European-American fear and a basis for restrictive legislation in slave-holding states. As early as 1934, J.A. Rogers¹⁴ had identified 33 slave revolts, and this was undoubtedly just the tip of the iceberg. In the early decades of American slavery, participation in slave rebellions was often spiritually based and ethnically demarcated and may have initiated African ethnicity-based selection against certain groups. The African ethnicities that dominated the leadership of the numerous acts of resistance during American slavery include the Ashanti, Bakongo, Fon, Mandinka, and Mbundu peoples. Participation in the early rebellions was most often along African ethnic lines.^15,16 Unsuccessful rebellions, which were the majority, invariably ended in loss of life for the identified perpetrators, particularly those in the leadership, and loss of biological fitness if the rebel’s life was spared.

The immediate post-emancipation period created opportunities for the emergence of African North American microethnic groups

Remnants of state-sponsored chattel slavery and draconian segregation laws relegated a large proportion of Legacy African Americans to populate the Southeastern part of the United States densely and disproportionately. These include the contemporary states of Alabama, Florida, Georgia, Kentucky, Maryland, Mississippi, North Carolina, South Carolina, Tennessee, Virginia, and West Virginia. It is within these settings that various Legacy African American microethnic groups have emerged and proliferated.⁸ Generations later, descendants of enslaved Africans are still clustered in the Southeastern states. They represent local clusters of amalgamations of African peoples (i.e., intra-African admixture) with varying degrees of genetic admixture with non-Africans (i.e., continental admixture).¹⁷ Although the bulk of genetic admixture studies of African North Americans has focused on the extent of continental admixture, it is the intra-African admixture (both in Africa¹⁸ and in the Americas) that comprises the most significant admixture events in this population. Variations in these admixture proportions across the range of African North Americans contributes to population substructure in this group. By the time African North Americans were able to form communities of banded lineages that are the foundations for these microethnic groups, the “Nigerian ancestral component” was already well represented.¹⁹

Post-enslavement migrations were significant initiators of displacement in African North Americans

During the period of enslavement, the mobility of the average enslaved African North American was geospatially restricted. With emancipation, the migrations of previously enslaved individuals were pronounced, often to find lost family members, to seek employment opportunities, and to avoid the deadly backlash of white supremacist racial terrorism. Immediately after the Civil War, poor rural Legacy African Americans often relied upon labor recruiters to facilitate their interstate travel.²⁰ Later, chain migration characterized the interstate movements of African North Americans. These migrations, called the Great Migrations, were significant geospatial relocators of African North American lineages. Recent 20^th century migrations, such as the Great Migrations between 1916 and 1970, relocated 6 million Legacy African Americans out of the rural Southern United States to the urban Northeast, Midwest, and West. The migrations of Legacy African Americans increased intra-group gene flow,²¹ despite the source populations’ being previously geospatially distinct. For example, Detroit, MI attracted Legacy African American migrants from Louisiana and the Mississippi Delta. Chicago, IL disproportionately attracted Legacy African Americans from five counties in Mississippi. Los Angeles, CA attracted Legacy African Americans from east Texas, Louisiana, and Missouri, and some migrants stopped to found new, predominantly African American towns such as Dearfield, CO, Nicodemus, KS, and McNary, AZ. Not taking into account the structure of these migrations could introduce an additional source of misrepresentation among an African North American sample.

Yoruba bias in public genetic databases

Finally, there is Yoruba domination in the early genetic databases, such as 1000 Genomes and HapMap,^22,23 that creates a deeply embedded Yoruba bias in our reconstructions of continental African diversity,¹⁸ evolutionary history,24, 25, 26 and African North American ancestry.¹ The use of continent-incomplete datasets to represent all of Africa introduces biases in principle, including overrepresentation of high-allele frequencies, artifacts of small samples, over-extrapolations of Yoruba-specific patterns to other unrelated Africans, and analysis of short genomic regions that underestimate long-range linkage disequilibrium (LD). Moreover, specific genomic regions examined may not be representative of genome-wide patterns for LD¹⁷ or copy number variation (CNV), potentially because of extreme natural selection at these regions. The Yoruba are not prototypical Africans,²⁷ and assumptions that their demographic history is less complex than other groups⁹ is simply not true and not consistent with Yoruba traditional history.

The history of the Yoruba people begins in 4^th-century Ile-Ife. By the 7^th century, the people who lived in Yorubaland were not initially known as the Yoruba, although they shared a common ethnicity and language group. The historical Yoruba develop in situ, out of earlier (Mesolithic) Volta-Niger populations, by the 1^st millennium BC. Therefore, the Yoruba have not been a static population and, like every other African groups, cannot be considered the category for adequately representing the entire African continent. Africans maintain the highest levels of genetic diversity; the continent is the site of human origins. No existing African group can adequately represent all Africans in human genetic studies. The fact that the current public databases are inadequately comprehensive regarding African genomic variation means that each time the Yoruba is substituted for “African,” this caveat must be noted. For researchers, scientific thought must go into each aspect of our genetic studies in Africa, beginning with the collection of representative samples. Africa must be sampled with non-reductionist paradigms guiding the research.

Conclusions

Emerging genetic knowledge has the potential to transform contemporary notions of group identity, provide insights into the past, identify strategies to optimize the present and future, and foster the foundations of social coherence.²⁸ A comprehensive understanding of African North American biohistory is thus an essential prerequisite for accurate interpretations of the ancestral genetics of this population. This is particularly important because this population has been genetically understudied, historically defamed, and biologically mischaracterized in the past. Too often, genetic interpretations falter with incomplete, ahistorical reconstructions of this complex and diverse American macroethnic group. Knowledge of a people’s past is critical for reconstructing that past with the tools of genetics and genomics, identifying the status of their current biological fitness, and predicting their future susceptibilities.

Although groups from modern Nigeria appear to loom large in African North American ancestry, as Micheletti and colleagues have indicated,¹ there are specific reasons for and limitations to this observation. Only when armed with the proper historical and cultural context data can we rely upon the genetics and genomics to faithfully reconstruct a people’s population biology. From these accurate and comprehensive reconstructions, we can then develop useful applied models of human evolutionary biology for this segment of humanity.

Data and code availability

This study did not generate unique data. All data used in this paper (e.g., Table 1, Figures 1 and 2) are publicly available through the existing historical record. Data sources are also available from the corresponding author on request.

Declaration of interests

The author declares no competing interests.

Web resources

• QuadGRID, quadgrid.com

• “What Was the 2nd Middle Passage? The Root,” https://www.theroot.com/what-was-the-2nd-middle-passage-1790895016