Recently, tools have become available that allow scientists to examine DNA sequences on a massive scale in thousands of people, thanks to recent advances in large-scale DNA sequencing and computer technology. These large-scale studies have shown that humans carry an extraordinary number of extremely rare variants. Many of these rare variants are found in only one person of the thousands included in each study. These rare variants have recent origins, and the reason there are so many of them is simple and predictable: the worldwide human population has exploded in recent times, so the number of opportunities for new mutations to appear and become inherited variants has been greater in recent times than at any other time in human history.16 Although they reveal much about recent human genetics, these extremely rare variants contribute very little to overall human diversity. It is the more ancient variants, distributed more widely throughout human populations, that account for the bulk of genetic diversity among humans and reveal continental-scale ancestry.
Jorde and Wooding, whose research we reviewed in the previous chapter, sum it up nicely. Referring to the DNA variants they examined, they state,
All of these findings, which are in accord with many other studies based on different types of genetic variation assessed in different samples of humans, support an evolutionary scenario in which anatomically modern humans evolved first in Africa, accumulating genetic diversity. A small subset of the African population then left the continent, probably experienced a population bottleneck and founded anatomically modern human populations in the rest of the world. Of special importance to discussions of race, our species has a recent, common origin.17
According to the scientific evidence, the biblical Eve and Adam mentioned at the beginning of this chapter as the first parents of all humanity are mythical. Ancient human remains as well as DNA evidence show that humans were widespread throughout the world long before six thousand years ago, when, according to a literal interpretation of biblical history, Adam and Eve supposedly lived. The mitochondrial Eve and the Y chromosome Adam, however, were real, and they were African. Furthermore, they were not the only “Eves” and “Adams”—common ancestors of all humanity. All uniquely human variants in DNA present in all people alive today trace their origins to countless common ancestors, all of whom lived in Africa more than sixty thousand years ago. As humans, everyone is related by common ancient ancestry, and, ultimately, everyone is African.
The Founding Fathers of the United States are widely revered for their intellect, courage, and foresight, which allowed them to lay the foundations of modern democracy. They lived during the Enlightenment—the age of reason—a period of intellectual thought based on the ideals of rationality, equality, and human rights that inspired the framework of democratic government and the philosophies that underlie modern scientific methods and inference.
Thomas Jefferson was among the most influential of the Founders. As author of the Declaration of Independence, congressman, minister to France, governor, secretary of state, vice president, and two-term third president of the United States, his mark on American history and modern political thought is unquestioned. That Jefferson was a champion of freedom and equality while being a slaveholder is one of the great enigmas of his life. After his wife, Martha, died, he inherited her slaves, one of them a woman named Sarah Hemings, who went by the name Sally. She was legally a slave, even though three of her four grandparents were of European ancestry; her maternal grandmother was an African slave, whereas her father and maternal grandfather were both European American slave owners. Interestingly, her father was also Martha's father, so Sally and Martha were half sisters even though Martha owned Sally as a slave. One of Sally's sons, Eston, took on the name Jefferson, and his descendants have carried the name for generations. A quiet tradition passed on for generations among Sally Hemings's descendants held that after Martha Jefferson's death, Thomas Jefferson cohabited with Sally and fathered all six of her children.
Powerful confirmation of this tradition came to light more than two centuries after Sally's death. The Jefferson Y chromosome haplogroup is a very rare one, called T, which is found most often in Egyptian men but also in a very small fraction of European men. The European subtype is in Thomas Jefferson's paternal ancestry, and its prevalence is very rare among men of European ancestry. Eston Hemings Jefferson was Sally Hemings's last child, and he is the only one of Sally's children whose documented paternal lineage remains to the present. A paternal descendant of Eston Hemings Jefferson carries the same Y chromosome as Thomas Jefferson.
Historical information regarding Thomas Jefferson and Sally Hemings, particularly coincidence of the dates when Thomas was in the same place as Sally and the times when Sally's children were conceived, offers historical evidence that he was the most probable father of all six of Sally's children. The DNA evidence is consistent with this historical evidence.1
Sally Hemings's descendants are illustrative of how problematic definitions of race can be. All six of her children had substantial European ancestry but were still legally classified as slaves. Of the four who lived to adulthood, two left Thomas Jefferson's Monticello home as “fugitives” while in their twenties. The word “fugitives” is in quotation marks because there is good evidence that they were not only allowed but encouraged to leave and live in freedom, likely by Thomas Jefferson himself. Both changed their names and lived prosperously as members of white society. Eston eventually moved to Madison, Wisconsin, taking on the surname Jefferson, and his descendants were considered white, largely because of where they lived, how they were raised, and how they appeared. By contrast, some of his brother Madison's descendants were considered as colored and others as white. For instance, two of Madison's sons, Thomas and William, enlisted as Union soldiers in the US Civil War; Thomas was designated as colored and William as white.
Classification of people into discrete racial categories has a long history dominated by the dogma of white supremacy, based on interpretations of biblical history that were popular at the time. For example, a belief common to Christianity, Judaism, and Islam during medieval times was the notion that Africans are the descendants of Noah's son Ham and dark skin is the “curse of Ham” or “Hamitic curse.”2 Adherents of this belief divided the known world into three regions—Africa, Asia, and Europe—and assigned the supposed three major races to these regions as the posterity of the three sons of Noah: Africans to Ham, Europeans to Japheth, and Asians to Shem (figure 3.1). Dark skin was thought to be God's curse on Ham for looking upon Noah when he was drunk and naked, as recounted in Genesis 9:18–25. This quasi-biblical scheme with its three-race classification was often used as justification for subjecting those who had supposedly inherited the curse of Ham to slavery.
Figure 3.1. Mappa mundi (map of the world) from Etymologiae by Isidorus, printed in 1472. The known world was thought to be surrounded by the ocean, with three continents populated by the descendants of Noah's three sons: Asia, populated by the descendants of Shem; Europe, populated by the descendants of Japheth; and Africa, populated by the descendants of Ham. Dark skin of Africans was supposedly the curse imposed on the descendants of Ham. Image from the Harry Ransom Center, University of Texas at Austin.
Also common in Europe and the Americas from the seventeenth century well into the twentieth century was the conjecture that the biblical mark of Cain is dark skin and that people with African ancestry are the seed of Cain. Connecting the mark of Cain to the curse of Ham was the presumption that Ham married a descendant of Cain, thus propagating the curse of Cain in his descendants after the great flood.3 Adherents of these conjectures supported slavery based on the claim that God had cursed people with African ancestry and, by inheritance of this curse, they were inferior.
In the eighteenth century, scientists and scholars attempted to classify humans into distinct races, although on purely geographic rather than biblical grounds. The founder of modern biological taxonomy, Carl von Linné (better known by his Latinized name, Carolus Linnaeus), proposed
in his 1758 work Systema naturae a Latinized classification of four human races: Americanus, Europeus, Asiaticus, and Afer—essentially the same as the three medieval classifications but with Native Americans added as a fourth category (the Americas were unknown to Europeans during medieval times). His follower, Johann Friedrich Blumenbach, expanded this classification into five so-called human varieties: Caucasian, Mongolian, Ethiopian, American, and Malaysian.4
Racial, ethnic, and cultural classification have persisted to the present. For example, the 2010 US Census listed five “racial categories” and allowed people to classify themselves into one or more than one category: 1) White, 2) Black or African American, 3) American Indian or Alaska Native, 4) Asian, and 5) Native Hawaiian or Other Pacific Islander. Regardless of which racial category a person chose, the census also allowed each individual to self-classify as Hispanic or non-Hispanic. It also included the following caveat: “The racial categories included in the census questionnaire generally reflect a social definition of race recognized in this country and not an attempt to define race biologically, anthropologically, or genetically.”5 This caveat is consistent with current scientific evidence suggesting that discrete racial classification is predominantly a social construct and does not reflect an accurate biological classification.
Complex ancestries often complicate attempts to biologically classify people by race. North Africa, the Middle East, and central and south Asia were anciently the crossroads of major civilizations, with people from various regions of the world traveling through, emigrating, or entering as traveling merchants or invading armies for thousands of years. As a consequence, genetic diversity for people with ancestry from this broad region is second only to sub-Saharan Africa. And there is so much overlap in the genetic variants carried by people from this region that genetic classification fails to place people into discrete racial categories.
In the postcolonial Americas, most people trace at least some of their ancestry to immigrant populations, often with varied ancestries. In Brazil, where immigrants from many regions of the world have converged and cultural taboos against so-called interracial marriage were not as powerful as in other cultures, ancestry is highly diverse. People in the United States who today classify themselves as African American often have some European ancestry—in many cases, significant European ancestry. For example, about 26 percent of African American men carry a Y chromosome of European origin.6 Most people who classify themselves as Hispanic have European and Native American ancestry, and a large proportion have African ancestry. The same is true for many who self-identify as Native American. In fact, membership in Native American tribes in the United States is often disputed because of varied ancestry. Likewise, some who classify themselves as white or Caucasian (usually a catchall term to include people of European, Middle Eastern, and north African ancestry) have some African, Native American, or Asian ancestry. It is not unusual for someone who self-classifies as “white,” “European American,” or “Caucasian” to discover from a DNA test that his or her ancestry is varied. Had DNA tests been available and widely applied during the time of the antimiscegenation laws and the “one-drop rule” in the United States, a significant number of marriages considered valid at the time would have been technically illegal.
According to current scientific evidence, everyone's ancestry is ultimately African, and much of the variation in modern human DNA is original African variation dispersed throughout the entire human species rather than being confined to any particular geographic group. An example comes from research my colleagues and I recently conducted and published on the evolution of a human gene called NANOG.7
Biologists who discover a new gene have the honor of naming it, and, in this case, the honor fell to Dr. Ian Chambers of the University of Edinburgh in Scotland, who discovered the gene in mice in 2003.8 He picked one of the best names in the history of gene naming, one that is both appropriate and charming. The name comes from Tir na nÓg, a mythical island in the sea west of Ireland that in Celtic legend is the land of eternal youth (also a popular name for Irish pubs). The gene functions in embryonic stem cells, which arise from cell division shortly after egg and sperm unite. When the NANOG gene is turned on, embryonic stem cells continue to grow and divide to make more embryonic stem cells rather than differentiating into different cell types. In other words, they remain indefinitely in a state of eternal youth, hence the mythical name for the gene.
Our research, however, was not on NANOG's ability to maintain the eternal youth of embryonic stem cells; instead, we focused on the gene's evolutionary history in humans. While conducting our research, we found several ancient variants in this gene that, according to the evidence we discovered, diverged at least two million years ago, before the emergence of anatomically modern humans and at a time when all ancestors of modern humans lived exclusively in Africa. These variants are now spread among people throughout the world—in people native to Africa, Asia, the Middle East, the Pacific Islands, Europe, and the Americas, according to our research. This worldwide diversity persists because it was originally present in Africa.
Perhaps the best documented example of ancient African variation that is spread throughout the world is variation that confers the ABO blood groups: types A, B, AB, and O. There is a good chance you know your ABO blood type. For the purposes of this discussion, we'll ignore the positive and negative types, which arise from a different set of variants in a different gene. The ABO blood types arise from three major variants of one gene; the three variants are named A, B, and O. Divergence of the A and B variants is very ancient, having occurred at least twenty million years ago in a common ancestor of humans, great apes, and Old World monkeys.9 This variation has persisted to the present, not only in humans but in other primates as well. Therefore, both the A and B variants are considered ancestral in humans. The O variant that causes type O blood in humans, however, is human specific. It is a derived variant that arose in one person in ancient Africa before the out-of-Africa diasporas, when the A variant mutated into the O variant. The mutation event deleted a single base pair (boxed) from the A variant to create the O variant:
This deletion completely obliterated any function for the O variant; it could no longer encode production of the substance that causes type A blood. The letter O is from the German word ohne, which means “without.” More than four billion people throughout the world have type O blood, so, obviously, the lack of function conferred by the O variant is not detrimental for survival. In fact, as we'll see momentarily, there is some evidence that it anciently conferred an advantage for survival in some parts of the world.
Although all four blood types—A, B, AB, and O—are distributed among people worldwide, the relative proportions of these types differ geographically. Type O blood is the most common type worldwide, present in about 63 percent of the world's people, even though the O variant is derived from an ancient African mutation. Its predominance is particularly high in people whose ancestry is African, northeast Asian, or Native American, especially in Central and South America, where it approaches 100 percent among indigenous people. Type A is most common in people whose ancestry is Aboriginal Australian, northern European, or from the northern regions of North America. Type B is most frequent in people whose ancestry is from central Asia ranging from northern Russia to the southern tip of India. Type AB is the most rare type everywhere, and it happens only when a person inherits the A variant from one parent and the B variant from the other.
A complex pattern of ancient human emigrations, natural selection, and random fluctuations in the proportions of different variants accounts for the uneven distribution of ABO blood types. Natural selection has apparently been underway for all of human history, with different ABO blood variants conferring resistance or susceptibility to several diseases—in most cases, favoring type O blood and thereby explaining its high worldwide prevalence. The most important is protection against severe malaria. People with type O blood may contract malaria, but, once t
hey have it, they are less likely to develop symptoms as severe as those who have other blood types. This observation may explain why type O blood is the most common type in Africa and other tropical regions, where malaria may have acted as a selective agent favoring survival of those people with type O blood who contracted malaria both before and since the out-of-Africa diasporas.10 By contrast, people with type O blood may be more susceptible to cholera than those with type A, B, or AB, which explains the higher prevalence of the A and B variants in regions where cholera was historically common but malaria was not.11
The uneven yet worldwide distribution of A, B, and O variants is typical of ancient African variation in humans. The variants originated anciently in Africa and have spread throughout the world through complex human migrations. A combination of factors, including migration, natural selection, and random fluctuations, resulted in different proportions of the variants among people in different geographic regions.
Variants in DNA can generally be classified as three different types as a result of ancient human migrations: 1) ancient African variants present in people throughout the world, such as the ABO blood variants and NANOG variants we just discussed; 2) ancient African variants that remained predominantly or exclusively in people who were native to Africa until recent times; and 3) more recent variants that trace to a particular region, found in people with ancestry from that region. A subclass of this third class is very recent variants that are extremely rare and highly localized, and they are exceptionally numerous because of the rapid expansion of the world's population in modern times.12
Although most of the worldwide variants are the legacy of ancient African diversity, the recent localized variants tell us much about how recent diversity originated and what it means. The scientific literature is replete with examples, and my colleagues and I have discovered some of them firsthand in research we conducted with DNA from geographically diverse human populations.13
Everyone Is African Page 5
