Y Chromosome Lineages in Men of West African Descent

The early African experience in the Americas is marked by the transatlantic slave trade from ∼1619 to 1850 and the rise of the plantation system. The origins of enslaved Africans were largely dependent on European preferences as well as the availability of potential laborers within Africa. Rice production was a key industry of many colonial South Carolina low country plantations. Accordingly, rice plantations owners within South Carolina often requested enslaved Africans from the so-called “Grain Coast” of western Africa (Senegal to Sierra Leone). Studies on the African origins of the enslaved within other regions of the Americas have been limited. To address the issue of origins of people of African descent within the Americas and understand more about the genetic heterogeneity present within Africa and the African Diaspora, we typed Y chromosome specific markers in 1,319 men consisting of 508 west and central Africans (from 12 populations), 188 Caribbeans (from 2 islands), 532 African Americans (AAs from Washington, DC and Columbia, SC), and 91 European Americans. Principal component and admixture analyses provide support for significant Grain Coast ancestry among African American men in South Carolina. AA men from DC and the Caribbean showed a closer affinity to populations from the Bight of Biafra. Furthermore, 30–40% of the paternal lineages in African descent populations in the Americas are of European ancestry. Diverse west African ancestries and sex-biased gene flow from EAs has contributed greatly to the genetic heterogeneity of African populations throughout the Americas and has significant implications for gene mapping efforts in these populations

History and genetics in Africa: Multidisciplinary efforts

Population studies that integrate genetics and aspects of culture in order to examine historical topics, or that use history or archaeology to help explain geographical patterns of genetic variation, have become more common in the literature. This body of work includes, but is not restricted to, the exploration of the relationship between patterns of genetic and linguistic differentiation, genetic variation in societies defined as politically simple or complex (even if they fall within the boundaries of states), and the possible association of genetic variation and the spread of cultural innovations such as the practice of plant and animal domestication. In all of these examples, geography and/or migration are major background themes because genes and aspects of culture are evaluated in terms of movement across space and/or time. Such work at its best in theory requires the effective use of historical linguistics, archaeology, ethnology, and written and oral historical texts in the context of population genetics data and theory. The term population history” is not necessarily used consistently. The subject - population” - may vary in its referent. Genetics and other fields would likely be better understood as having different roles to play in any writing of history from any region in the world. This leads to the question of what kind of data/evidence should lead the construction of a historical narrative, and when: This interesting question may be obvious in some cases, but not so obvious in others. Ideas about identity and whether culture, with or without language, may be more important than ancestry or phenotype in a narrative are points of contestation. In some models of research, genetic profiles could be interpreted in terms of ideas about the geographical origins of genes found in a population, which may give us a history” of interactions of gene bearers, but it must be kept in mind that gene history is not the same as population or culture history: The mediators (i.e., gene bearers”) of particular genes may not be the population, or from the region, of the ultimate origin of the genes. Time and geography are important. The genetic profile at one time or place for a society does not necessarily tell you about its population’s total cultural or biological origins” - a notion that is not always used consistently or clearly: Different fields may bring different assumptions to the analysis of the data. It also does not tell you about its descendants. Although statistical modeling might be helpful, it is clear that it has real limits: Statistics, Bayesian or otherwise, could not have predicted the change in population in North and South America, or the subsequent history that led to numerous admixed” communities. (We have to remember that admixture” is not a new phenomenon.) It is important to say that genetic history” is not the same as social or political history, and to ask how or if genetics would help understand various historical events versus the other data. This chapter will explore some concepts related to these issues

Ancient Egyptian Genomes from northern Egypt: Further discussion

Schuenemann et al.1 seemingly suggest, based largely on the results of an ancient DNA study of later period remains from northern Egypt, that the ‘ancient Egyptians’ (AE) as an entity came from Asia (the Near East, NE), and that modern Egyptians “received additional sub-Saharan African (SSA) admixtures in recent times” after the latest period of the pharaonic era due to the “trans-Saharan slave trade and Islamic expansion.” In spite of the implied generalization about ‘origins’ the authors do offer the caveat that their findings may have been different if samples had been used from southern Egypt, and this is a significant admission. Their conclusions deserve further discussion from multiple perspectives which cannot be fully developed due to space limitations. There are alternative interpretations of the results but which were not presented as is traditionally done, with the exception of the admission that results from southern Egyptians may have been different. The alternative interpretations involve three major considerations: 1) sampling and methodology, 2) historiography and 3) definitions as they relate to populations, origins and evolution

Y Chromosome Lineages in Men of West African Descent

The early African experience in the Americas is marked by the transatlantic slave trade from ~1619 to 1850 and the rise of the plantation system. The origins of enslaved Africans were largely dependent on European preferences as well as the availability of potential laborers within Africa. Rice production was a key industry of many colonial South Carolina low country plantations. Accordingly, rice plantations owners within South Carolina often requested enslaved Africans from the so-called ‘‘Grain Coast’’ of western Africa (Senegal to Sierra Leone). Studies on the African origins of the enslaved within other regions of the Americas have been limited. To address the issue of origins of people of African descent within the Americas and understand more about the genetic heterogeneity present within Africa and the African Diaspora, we typed Y chromosome specific markers in 1,319 men consisting of 508 west and central Africans (from 12 populations), 188 Caribbeans (from 2 islands), 532 African Americans (AAs from Washington, DC and Columbia, SC), and 91 European Americans. Principal component and admixture analyses provide support for significant Grain Coast ancestry among African American men in South Carolina. AA men fromDC and the Caribbean showed a closer affinity to populations from the Bight of Biafra. Furthermore, 30–40% of the paternal lineages in African descent populations in the Americas are of European ancestry. Diverse west African ancestries and sexbiased gene flow from EAs has contributed greatly to the genetic heterogeneity of African populations throughout the Americas and has significant implications for gene mapping efforts in these populations

Estimates of European paternal ancestry (%) in African descent populations in the Americas.

<p>Estimates of European paternal ancestry (%) in African descent populations in the Americas.</p

Partitions of Y chromosome molecular variance.

<p> <b>Φ_ST = Within populations; Φ_CT = Among groups; Φ_SC = Among populations within groups; %V = Percent of the variance.</b></p

Expansion Times of West African Y Chromosome Groups.

<p>Expansion Times of West African Y Chromosome Groups.</p

Plot of the first two principal components of a Y chromosome genetic distance matrix estimated for 17 populations.

<p>Plot of the first two principal components of a Y chromosome genetic distance matrix estimated for 17 populations.</p

Summary of Y chromosome diversity and frequency of YAP and M89 alleles.

<p><b>Note</b>. n = number of Y-chromosomes, <i>k</i> = observed number of haplotypes, H = haplotype diversity, <i>h</i> = allelic diversity, MPD = mean pairwise differences of haplotypes.</p

Maps showing location of (A) 5 populations in the Americas and (B) 12 West African populations sampled in the study.

<p>Maps showing location of (A) 5 populations in the Americas and (B) 12 West African populations sampled in the study.</p