Everyone Is African (6 page)

Our current understanding of mitochondrial DNA diversity is extensive, highly reliable, and derived from complete mitochondrial DNA sequences from thousands of indigenous people from various parts of the world. Moreover, Neanderthal mitochondrial DNA sequences have been obtained from the remains of several individuals, allowing for comparison of modern human and Neanderthal mitochondrial DNA. In an earlier book I authored,
Evolving: The Human Effect and Why It Matters
, I devoted most of a chapter to the details of how mitochondrial DNA evidence reveals ancient human emigrations. Here, we'll focus on a few of the major conclusions.

First, the highest mitochondrial DNA diversity in the world is found in people whose maternal ancestry is African.
⁸
These highly diverse African mitochondrial DNAs can be classified into several large and diverse ancient groups, called mitochondrial
haplogroups
. Seven major haplogroups are found in people whose maternal ancestry is African: haplogroups L0, L1, L2, L3, L4,
L5, and L6. L0 is the most distinct, and it diverged from the ancestral type for all the others very early in Africa, probably more than 190,000 years ago. People who carry the L0 haplogroup belong mostly to indigenous African groups who speak Khoisan languages and reside predominantly in the south of Africa. The remaining haplogroups diverged at various times from a common ancestral type and are found in Africa, largely among people who speak other African languages.

Although each haplogroup has its own intriguing history, the L2 and L3 haplogroups are two of the most relevant in terms of emigration out of Africa, both ancient and modern. People carrying L2 in ancient times (beginning about ninety thousand years ago) immigrated to the western regions of Africa but later spread throughout Africa. Today, L2 is the most prevalent African haplogroup among people whose recent maternal ancestry is African, both within and outside of Africa, including people whose maternal ancestors were taken from west Africa as slaves. For instance, most people who identify themselves as African American (in the North and South American continents and Caribbean islands) carry the L2 haplogroup.

People carrying haplogroup L3 spread anciently throughout the northern parts of Africa. It is here that we find powerful evidence supporting the single-origin hypothesis for humans whose ancestry lies outside Africa. All non-African mitochondrial haplogroups, from all people anywhere in the world outside Africa, trace their origin to L3. Because this observation points to a single African origin for all non-African mitochondrial haplogroups, it contradicts the multiple-origins hypothesis. It points to a group of people (or perhaps several groups) who carried L3 and emigrated out of northeastern Africa about sixty thousand to seventy thousand years ago. Their descendants immigrated into west-central Asia and became the genetic founders of people who populated the rest of the world in ancient times.

Newer variants arose against the L3 background in people who lived in the Middle East and had descended from ancestors who left Africa, causing L3 to diverge into two major haplogroups, called M and N. A third major haplogroup, called R, then diverged from N. Even though they originated from the African haplogroup L3, we'll refer to M, N, and R as
non-African
from this point forward because the variants that define them arose outside Africa and
were the founding haplogroups for all other haplogroups that arose outside Africa. The map in
figure 2.2
is a simplified version showing the major routes of migration and the mitochondrial haplogroups.

Figure 2.2. Major migration routes for early human diasporas, as revealed by mitochondrial DNA analysis. The area in white represents the approximate ancient landmasses and ice sheets when sea levels were lower during the last major ice age, when these migrations took place. The modern continents are outlined in black.

 

As an example, let's focus on people whose maternal ancestry is Native American—from the northern regions of Alaska and Canada to the southern tip of South America. As shown in
figure 2.2
, they carry five mitochondrial haplogroups, called A, B, C, D, and X. The first four (A, B, C, and D) are prevalent and widespread throughout the Americas. A relatively small number of people with ancient North American ancestry carry the haplogroup X, which is always rare wherever it is found. All five of these haplogroups are also present in Asia, and the patterns of variants in Native Americans make it clear that people carrying them emigrated from Asia to North America about fifteen thousand years ago, probably in more than one emigration event, across a land bridge called Beringia that connected what are now northeastern Siberia and Alaska.
⁹
Ancient emigrations from Asia to the Americas ceased when the land bridge was inundated by rising sea levels at the end of the most recent ice age, about eleven thousand years ago.
¹⁰
Thus, the ancient ancestry of Native
Americans is undoubtedly Asian. Interestingly, these five haplogroups that are present in people from both Asia and the Americas arose from all three major non-African haplogroups, M, N, and R: M was the source of C and D, N was the source of A and X, and R was the source of B.

All mitochondrial haplogroups from throughout the world—both African and non-African—have accumulated distinct, more recent variants that allow scientists to clearly distinguish subtypes within each haplogroup. I'll use the variants present in my own mitochondrial DNA as an example. According to a DNA test, I carry haplogroup U5, one of the most widespread and ancient mitochondrial haplogroups in Europe and in people whose maternal ancestry traces to Europe. It arose by mutation approximately thirty-six thousand years ago and was carried by people who spread throughout Europe at that time. My particular subtype is most prevalent in Scandinavia, the British Isles, and the northern parts of the European subcontinent. It also was found in ancient DNA extracted from a Stone Age individual who lived approximately 8,700 years ago and whose remains were discovered in the Hohlenstein-Stadel cave near the city of Ulm in Germany.
¹¹
My mitochondrial lineage, when traced back to Africa, is the following: U5 (Europe) < U (Northern Middle East) < R (Middle East) < N (Middle East) < L3 (Africa).

The sort of hierarchical clustering evident in mitochondrial haplogroups allows scientists to extrapolate back to the trunk of the human mitochondrial family tree. Through comparison of mitochondrial DNA sequences from thousands of living people and the remains of ancient people and Neanderthals, scientists have reconstructed the original ancestral mitochondrial DNA sequence for all humans. This original mitochondrial DNA is no longer present in anyone alive today because variants have accumulated in everyone's ancestry, but everyone alive now traces her or his mitochondrial ancestry to a single woman who carried it long ago.
¹²

Because each variant arose at one time in one person, any variant that is present in all people today but is not present in other closely related species, such as Neanderthals, chimpanzees, and gorillas, typically traces to one person. (There are rare exceptions, when the same variant arose on different occasions in different individuals, and these repeated variants can be identified by their presence against different genetic backgrounds.) For this
reason, all ancestral lines of the human mitochondrial family ultimately lead to this one woman who lived in Africa nearly two hundred thousand years ago, according to a recent estimate, close to the time when anatomically modern humans first appeared.
¹³
She is famously known as the
mitochondrial Eve
, and there is no doubt she was African. The oldest variant in mitochondrial DNA that is inherited by all humans alive today, and by no other species, arose in her and was inherited by at least one of her daughters. She was not the first human female, however. Her mother, her mother's mother, her mother's mother's mother, and so on were all ancient humans and all mitochondrial Eves—ancient mothers of all humanity.

The Y chromosome in males is very different genetically from mitochondrial DNA, but its pattern of inheritance mirrors that of mitochondrial DNA: it is inherited through purely
paternal
lineages, exclusively from father to son. Like mitochondrial DNA, it does not recombine, so the same sort of hierarchical grouping of mitochondrial variants can also be done with Y chromosome variants.
¹⁴
And the same general patterns of diversity are present in DNA from the Y chromosome. Not surprisingly, the greatest diversity is in Africa, and the same general patterns of emigration within Africa and throughout the rest of the world are also apparent in Y chromosome DNA.

It is also possible to extrapolate back to the ancestral trunk of the Y chromosome family tree. All human males trace the DNA in their Y chromosome to a single man who lived in Africa probably a few tens of thousands of years later than the mitochondrial Eve—possibly about 142,000 years ago, according to a recent estimate, although dating methods for Y chromosome DNA are less reliable than for mitochondrial DNA.
¹⁵
He is known as the
Y chromosome Adam
. Obviously, given the time period in which he lived, he never met the mitochondrial Eve. In fact, there is a good chance he was one of her distant descendants, having inherited his mitochondrial DNA from her hundreds of generations later.

Although the most extensive studies of human diversity to date are from mitochondrial and Y chromosome DNA, scientists in recent years have extensively characterized human genetic diversity throughout all our DNA. The vast majority of our DNA is inherited from both parents and does recombine, so superimposition of recent variants on a background of ancient variants does
not persist indefinitely as it does in mitochondrial and Y chromosome DNA. Nonetheless, some layering of variants that are near one another in each DNA molecule does persist for many generations, so each new variant, regardless of where it resides, is superimposed on a genetic background. And this variation throughout our DNA adds a mountain of evidence to the mitochondrial and Y chromosome evidence that our ancient origins are African.

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.
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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.
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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.”
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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.
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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: