Everyone Is African
Page 4
The reason people with entirely African ancestry have the highest diversity in the world is straightforward and can be illustrated with a simple analogy. When I was in grade school, my friends and I used to play games with marbles, and I had a large collection of them. They were highly diverse, with a multitude of colors and patterns. Some marbles in my collection were identical to others, especially those with solid colors—and I had numerous copies of those, lots of solid red, green, blue, orange, yellow, black, and white marbles. Several were much more varied in their coloration but also more rare, represented just once or a few times in my collection. Now, imagine thousands of these marbles, both common and rare types, are mixed randomly in a large container. Imagine reaching into this large container with a cup and scooping out about fifty marbles. The overall diversity of marbles in the cup is not likely to be the same as in the container. Some of the rare types will almost certainly be absent from the cup, remaining only in the large container. Most, and perhaps all, of the more common types are likely to be in the cup, albeit in somewhat different proportions than in the container. In any case, the collection of marbles in the cup is likely to be less diverse than the one in the large container, and the reason has to do with sampling a less diverse subset of individuals from a much larger and more diverse collection.
This same sampling phenomenon happens genetically when a group of people emigrates from a region. Those who leave the original population constitute a subset of that population, and they carry a subset of the overall genetic diversity of the original population. They become the founders of a new population containing the more limited genetic diversity of the emigrants. Now, imagine that several generations later, another group of people emigrates away from the descendants of the first group of emigrants. The diversity diminishes even further in these secondary emigrants. Each group of subsequent emigrants carries a less diverse subset of the diversity that was present in the population from which they originated. Thus, the greatest diversity should be among people whose ancestors constituted the original population, and the region where they live typically represents the region of origin. For humans, that region unquestionably is sub-Saharan Africa.
Studies of human genetic diversity consistently show the diversity in people of African ancestry is the highest in the world. And the evidence from both anthropology and DNA strongly supports a scenario in which people emigrated out of Africa about sixty thousand to seventy thousand years ago and founded what ultimately became the rest of the world's human population, carrying with them a subset of the diversity in Africa. Although far more people in the world's current human population are descended from these out-of-Africa emigrants than from people who remained in Africa, the majority of the world's genetic diversity is still indigenous African.
This observation explains and augments the major conclusion of Lewontin's 1972 study, discussed in the previous chapter. His observation that there is more diversity within major geographic groups than among them is largely a result of the original diversity that was present in Africa more than one hundred thousand years ago, when all humans lived there. The emigrants who left Africa carried a subset of that original diversity in their DNA, and, as a result, many of the same variants are present in people throughout the world, both African and non-African. Thus, much of the variation within major groupings of people is original African variation predating the out-of-Africa diaspora.5 More recent variants—those that originated after the dispersal of humans throughout the rest of the world—should be more rare and concentrated in geographically localized populations. The more recent these variants are, the more rare and geographically localized they should be. And, consistent with Edwards’ description of correlation, these more recent variants tend to be correlated with one another according to the region of more recent geographic origin.6
Patterns of genetic diversity are evident in all types of DNA, but they have been most extensively documented in what is called mitochondrial DNA, and for some very good reasons. In general, each of us inherits about half our DNA from our mother and half from our father. But mitochondrial DNA is a very important exception. It resides in different compartments of our cells than the rest of our DNA, compartments called mitochondria, and each of us inherits our mitochondrial DNA exclusively from our mothers. Thus, variants in mitochondrial DNA are inherited purely through the maternal lineage, from a mother to all her children, but transmitted to the following generation only through females—from mother to daughter. Although males have mitochondrial DNA, it is a hereditary dead end; they do not pass it on to their offspring.7
Mitochondrial DNA is relatively small compared to the rest of our DNA—only 16,569 base pairs, compared to slightly more than six billion base pairs in the rest of our DNA (slightly more than three billion inherited from each parent). Thus, it is relatively easy for scientists to track and sequence it. However, it has one feature that makes it especially useful for studying diversity: mitochondrial DNA does not recombine.
For most of your DNA, you inherited half from your mother and half from your father. Go back a generation, and each of them inherited essentially half of their DNA from each of their parents, so about one quarter of your DNA is from each of your four grandparents. During the formation of an egg cell in your mother, the DNA molecules from her parents came together and exchanged segments, shuffling the information they carried. This same type of shuffling also happens during the development of sperm cells in males. And this shuffling recombines maternal and paternal DNA in every generation.
Mitochondrial DNA, however, does not recombine. It is replicated faithfully each generation and inherited through multiple generations exclusively through maternal lineages. If a mutation happens in mitochondrial DNA, it may end up being transmitted as a variant from mother to daughter through subsequent generations. Then, in a later generation, a new variant may originate against the background of the first variant. Some people inherit just the first variant, and others inherit the second variant on the background of the first. This pattern then repeats itself for additional variants that arise at various times and places through many generations. Because there is no recombination, new variants are superimposed on backgrounds of previous variants.
A simple analogy illustrates how these various layers of variants that originated as mutations at different times in mitochondrial DNA allow scientists to reconstruct ancient human genetic history. Before the printing press became available, scribes made handwritten copies of valuable manuscripts. In most cases, the original manuscript had been lost or was not available, so scribes made copies from other copies. Occasionally, a scribe made an error—perhaps a word copied incorrectly or left out—and other scribes subsequently copied the change. Then, later, another scribe made yet another error, adding it to a manuscript with the previous error that had persisted through several rounds of copying, so now two errors were present. Later, another scribe added yet another error to these two. Over time, errors accumulated, more recent ones added to earlier ones. The earlier errors tend to be more widespread, whereas the more recent errors are localized among fewer copies. Modern literary scholars can compare all existing copies of a particular work and hierarchically group them, ultimately extrapolating back to determine much of the original wording.
Scientists who examine the sequences from mitochondrial DNA can reconstruct the same sorts of hierarchical groupings based on the variants they find. Widespread variants in large numbers of people from diverse geographic origins must be the most ancient. Rarer variants in smaller groups of people with a more limited geographic origin must be more recent. And, in each case, newer sets of variants are superimposed on identifiable sets of older variants, allowing scientists to classify different sequences of human mitochondrial DNA hierarchically into numerous small groups clustered within sets of larger groups, and yet again within sets of even larger groups. Ultimately, the variants coalesce into a single group of the most ancient variants, which is the trunk of the maternal human f
amily tree. Furthermore, many of the mitochondrial DNAs examined are from people who belong to indigenous populations, groups of people who have been geographically and reproductively isolated for many generations. By comparing mitochondrial DNA sequences with the geographic regions where these indigenous people live, scientists can reconstruct the geographic migration patterns of ancient humans.
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.