So, the answer to our question about dates – how to reconcile 200,000 and 2 million – is that Homo erectus, despite its clear similarity to us, did not evolve into modern Homo sapiens independently in the far corners of the earth. Coon was wrong. Rather, the conclusion from the mitochondrial data is that modern humans evolved very recently in Africa, and subsequently spread to populate the rest of the globe, replacing our hominid cousins in the process. It’s a ruthless business, and only the winners leave a genetic trace. Unfortunately, Homo erectus appears to have lost.
As we’ll see, other genetic data corroborates the mitochondrial results, placing the root of the human family tree – our most recent common ancestor – in Africa within the past few hundred thousand years. Consistent with this result, all of the genetic data shows the greatest number of polymorphisms in Africa – there is simply far more variation in that continent than anywhere else. You are more likely to sample extremely divergent genetic lineages within a single African village than you are in whole of the rest of the world. The majority of the genetic polymorphisms found in our species are found uniquely in Africans – Europeans, Asians and Native Americans carry only a small sample of the extraordinary diversity that can be found in any African village.
Why does diversity indicate greater age? Thinking back to our hypothetical Provencal village, why do the bouillabaisse recipes change? Because in each generation, a daughter decides to modify her soup in a minor way. Over time, these small variations add up to an extraordinary amount of diversity in the village’s kitchens. And – critically – the longer the village has been accumulating these changes, the more diverse it is. It is like a clock, ticking away in units of rosemary and thyme – the longer it has been ticking, the more differences we see. It is the same phenomenon Emile Zuckerkandl noted in his proteins – more time equals more change. So, when we see greater genetic diversity in a particular population, we can infer that the population is older – and this makes Africa the oldest of all.
But does the placement of the root of our family tree in Africa mean that Coon was right, and Africans are frozen in some sort of ancestral evolutionary limbo? Of course not – all of the branches on the family tree change at the same rate, both within and outside of Africa, so there are derived lineages on each continent. That is the reason we see greater diversity within Africa – each branch has continued to evolve, accumulating additional changes. One of the interesting corollaries of inferring a single common ancestor is that each descendant lineage continues to change at the same rate, and therefore all of the lineages are the same age. The time that has elapsed between my mitochondrial DNA type and Eve’s is exactly the same as that of an African cattle herder, or a Thai boat captain, or a Yanomami hunter from Brazil – we are all the recent descendants of a single woman who lived in Africa less than 150,000 years ago.
This result begs the question of where Eve actually lived – where in Africa was the Garden of Eden? In one sense this is a red herring, since we know that there were many women alive all over Africa at this time. But, phrasing the question slightly differently, we can ask which populations in Africa retain the clearest traces of our genetic ancestors. Although the diversity within Africa has not by any means been sampled exhaustively, the picture that has emerged is that the oldest genetic lineages are found in people living in eastern and southern Africa. What we can infer from this is that these populations have maintained a direct mitochondrial link back to Eve, while the rest of us have lost some of these genetic signals along the way. We’ll pursue our search for Eden, using Adam as a guide, in the next chapter.
* Parsimony here is simply the application of methods which infer evolutionary history in such a way as to minimize complexity. It is not necessarily the method known as ‘maximum parsimony’ used by many population geneticists.
* Cavalli-Sforza and Edwards also developed other methods of analysing the relationship between populations on the basis of gene frequencies which rely less on absolute minimization of evolutionary change. Parsimony, however, is still widely used in the field.
3
Eve’s Mate
A woman without a man is like a fish without a bicycle.
Gloria Steinem
In the last chapter we met ‘Eve’ – the female ancestor of everyone alive today, who lived in Africa around 150,000 years ago. Based on the populations that seem to have retained the clearest genetic signals from our distant grandmother, we’ve begun our search for the location of the Garden of Eden. But before we go any further, we need to clarify Eve’s uniqueness. She represents the root of the mitochondrial family tree, and as such she unites everyone around the world in a shared maternal history. However, it isn’t necessarily the case that every part of our DNA should tell the same story. Because of sexual recombination, our genome is composed of a large number of blocks that have each evolved pretty much independently. Perhaps one region of DNA traces back to an origin in Indonesia, while another began its journey in Mexico. So is Eve’s lineage unique in tracing a recent journey out of Africa?
The answer is that the test of our genome shows essentially the same pattern as the mtDNA, although it tends to have a lower degree of resolution. Studies of polymorphisms in the beta-globin gene (which encodes the oxygen-carrying component of blood), the CD4 gene (which encodes a protein that helps to regulate the immune system) and a region of DNA on chromosome 21 all show that African populations are much more diverse than those living outside of Africa, and provide dates that are substantially less than 2 million years for the age of our common African ancestor. But the problem with using markers like these – from the 22 pairs of chromosomes that comprise the majority of our genome – is that the information tends to be shuffled over time. The further apart the polymorphisms are, the more likely it is that they have been shuffled. And because shuffling obscures the historical signal, this means that most of our genome isn’t terribly useful for tracing migrations.
There is one piece of DNA, though, that has recently proven to be an invaluable tool for inferring details about human history – providing us with far greater resolution than we ever thought possible about the paths followed by our ancestors during their wanderings. It is the male equivalent of mtDNA, in that it is only passed from father to son. For this reason, it defines a uniquely male lineage – a counterpart to the female line illuminated by studying mtDNA. It is the patrimoine in our Provencal village, and the details of lineage extinction and diversification that went on with the soup recipes also apply to this piece of DNA. It is known as the Y-chromosome.
Now wait a minute, you might be saying – what’s going on with all of this maternal and paternal lineage gibberish? I thought that the whole idea of sex was to mix the mother’s and father’s genomes in a 50 : 50 ratio to produce the child? Why do we have these oddities that break the rules? For the mitochondrial DNA the answer is easy – it is actually outside of what we think of as the human genome, an evolutionary remnant of a time when it was a parasitic bacterium living inside the earliest cells. The story for the Y is a bit more complicated.
One of the quirky features of sexual reproduction is that the chromosomes that actually determine our sex – the so-called sex chromosomes – are exceptions to the 50 : 50 sexual mixing rule. The double layout of our genomes, with two copies of each chromosome, fails us when we get to these chromosomes. This is because of the way in which sex is determined in most animals, through the presence of a mismatched sex chromosome. In the case of mammals, it is the male that is mismatched, with one X and one Y-chromosome. In females, the X-chromosome is present in two copies, like the other chromosomes, allowing normal recombination. In males, however, the Y only matches with the X in short regions at either end, which serve to align the sex chromosomes properly during cell division. The rest of the Y-chromosome, known as the non-recombining portion of the Y, is pretty much completely unrelated to the X. Thus it has no paired chromosome with which it can recombine, and so it doesn’t. It is passed uns
huffled from one generation to the next, for ever – exactly like the mitochondrial genome.
The Y turns out to provide population geneticists with the most useful tool available for studying human diversity. Part of the reason for this is that, unlike mtDNA, a molecule roughly 16,000 nucleotide units long, the Y is huge – around 50 million nucleotides. It therefore has many, many sites at which mutations may have occurred in the past. As we saw in the last chapter, more polymorphic sites give us better resolution – if we only had Landsteiner’s blood types to work with, everyone would be sorted into four categories: A, B, AB and O. To put it another way, the landscape of possible polymorphisms is simply much larger for the Y. And critically, because of its lack of recombination, we are able to infer the order in which the mutations occurred on the Y – just like mtDNA. Without this feature, we can’t use Zuckerkandl and Pauling’s methods to define lineages, and Ock the Knife can’t help us with the ancestors.
How does the Y manage to exist without recombination – doesn’t this contradict the idea that we need to create diversity in case it’s necessary to react to a changing environment? The short answer is that there almost certainly are negative evolutionary consequences to the lack of recombination – part of the reason for the low number of functional genes found on the Y. The number of active genes varies greatly among different parts of the genome. In the mitochondrion, for instance, there are thirty-seven. The total number of genes in the nuclear genome is around 30,000 – approximately 1,500 per chromosome, on average. Most of the thousands of genes that would have been found in the bacterial ancestor of the mitochondria have been lost over the past few hundred million years as mitochondria have become more parasitic, giving up autonomy for a cosseted life inside another cell. Some have actually been inserted into the nuclear DNA, leaving us in the odd situation of having small pieces of our genome that are bacterial in origin. So in the case of mitochondrial DNA, it does look like there was pressure for it to lose its genes, transferring the critical ones to the nucleus where recombination can keep them in shape for the evolutionary race.
We see the same pattern of gene loss for the Y-chromosome. Although the average human chromosome has roughly 1,500 active genes, only twenty-one have been identified on the Y. Some of these are present in multiple, tandem copies – as though the copying machine stuttered as it was duplicating that gene at some point in the past; these are counted as a single gene in our tally. Interestingly, all of the twenty-one genes on the Y are involved in some way in the creation of ‘maleness’ – particularly the gene known as SRY, for ‘Sex-determining Region of the Y, which is the master switch for creating a male out of an undifferentiated embryo. The rest have secondary functions involved in making men look (and act) like men. For the most part, though, the DNA that makes up the Y is devoid of any discernible function. It is so-called ‘junk DNA’, which means that it is transmitted from one generation to the next without conferring any utility. But while it may be biological junk, it is like gold dust to population geneticists.
As we have seen, we can only study human diversity by looking at differences – the language of population genetics is written in the polymorphisms that we all carry around with us. These differences define all of us as unique individuals – unless we have a twin, no other person in the world has an identical pattern of genetic polymorphisms. This is the insight behind a DNA ‘fingerprint’, used to identify criminals. Applied to the Y-chromosome, it allows us to trace a unique male lineage back in time, from son to father to grandfather, and so on. Taken to the extreme, it allows us to travel back in time from the DNA of any man alive today to our first male ancestor – Adam. But how does it link unrelated men to each other in regional patterns? Surely each man must trace his own unique Y-chromosome line back to Adam?
The answer is no, but the reason is a bit complicated. It’s because we’re not as unrelated as we think. Imagine the situation for the majority of our genome – the parts that don’t come uniquely from our mother or our father. Since we inherit half of this DNA from each of our parents, the pattern of polymorphisms it contains can be used to infer paternity, since it connects us to both our mother and our father. If my DNA is shown in court to have a 50 per cent match with that of a child I’ve never met, it is likely that I will be paying for the support of that child for many years to come – the probability of a match occurring by chance is infinitesimally small. So polymorphisms define us, and our parents, as part of a unique genealogical branch. No other group of people on earth has exactly the same story written in its DNA.
If we extend this further, and begin to think about our grandparents, and their grandparents, and so on, we lose some of the signal in each generation. I have a 50 per cent match with my father, but only a 25 per cent match with my grandfather, and only a 6 per cent match with his grandfather. This is because we acquire new ancestors in each generation as we go back in time, and they start to pile up pretty quickly. Each of my parents had two parents, and each of them had two parents, and so on. The geneticist Kenneth Kidd, of Yale University, has pointed out that if we double the number of ancestors in each generation (around twenty-five years), when we go back in time about 500 years each of us must have had over a million living ancestors. If we go back to the time of the Norman invasion of England, around a thousand years, our calculation tells us that we must have had over one trillion (1,000,000,000,000) ancestors – far more than the total number of people that have existed in the whole of human history. So what’s going on? Is our calculation flawed in some way?
The answer is yes and no. The maths is certainly correct – the power of exponential growth has been known since at least the time of the Greeks, and we’re all acquainted with the real-world phenomenon of ‘breeding like rabbits’. The error in our ancestor tally stems not from a malfunctioning calculator, but from the assumption that each of the people in our genealogy is completely unrelated to the others. Clearly, people must share quite a bit of their ancestry, or we can’t make the numbers work. This would have the effect of multiplying by a number smaller than two in each generation – in fact, for most people the number is pretty close to one. And the reason for this can be found by doing a bit of poetic bird-watching.
Water, water everywhere …
Samuel Taylor Coleridge, Romantic poet, failed classicist and drug addict, spent 1797–8 living in a small Dorset village. In between vigorous walks in the hills and long discussions with his neighbour, William Wordsworth, Coleridge found time for a fit of literary activity that was to produce his two greatest pieces of work, Kubla Khan and The Rime of the Ancient Mariner. The former, composed subconsciously while in an opium-induced dream state – how better to conjure up the ‘stately pleasure dome’ – is an extraordinary exercise in literary imagery. The latter, written during a more sober period, follows the travails of a ship in the South Seas. The mariner in the poem callously violates one of the unwritten laws of the sea by killing an albatross, and the entire crew are made to suffer the consequences, ending up becalmed in the sweltering sun, surrounded by ‘water, water everywhere, nor any drop to drink’. The mariner survives the ordeal, but the crew are not so lucky, falling prey to the ship of Death. In penance, the mariner is doomed to spend the rest of his life as a nomad, proselytizing on the dangers of environmental destruction.
The most enduring piece of imagery in the Ancient Mariner is that of the albatross, symbol of good fortune. But why was this bird thought to bring good luck? Basically, it was due to a misinterpretation. Sailors spent many weeks at sea, out of sight of land and dreaming of reaching port. Often one of the early signs that they would be making landfall in the near future was the sighting of birds, which indicated – like Noah’s dove and its olive branch – that dry ground must be near by. The albatross, as one of the most noticeable birds on the planet (some have a wingspan of over 3.5 metres), was a major omen. The only problem is that the albatross, uniquely among birds, spends the majority of its life out at sea. Some birds have
actually spent more than two years wandering around, often sleeping in flight as they glide effortlessly over thousands of kilometres of open ocean. So while the sailors thought they were seeing Noah’s dove, they were in fact being duped by a peripatetic juggernaut.
The only problem with spending your life flying around the world’s oceans is that, if you are a terrestrial species – even an amazingly adapted one like the albatross – you still need to return to land to have your babies. The albatross has a characteristically albatross-like solution to this problem, providing us with a fascinating bit of natural history. Despite its peripatetic lifestyle, and despite having a lifespan of over fifty years, the albatross always returns to the same island in order to mate. It mates for life, and its mate returns to the island as well, where they meet up to raise their single chick, splitting the chores equally. After a few months, when the young albatross is ready to head out into the world, they say their goodbyes, jot down the date of next year’s rendezvous in their diaries and head back out to sea.
The evolutionary effect of always returning to the same island is that, while it encourages speciation between islands – with each island evolving into its own species over time – it tends to homogenize the birds that breed on any particular island. When the young albatrosses get together on their birth-island for the first time as adults, the males perform a ritual courtship dance to impress the females, who make their choice of mate without noting which part of the island the male hails from. As long as you are an albatross and you are on the island at the right time (natural selection takes a rather dim view of ‘running a bit late’ in this case), you’ve got a good chance of getting lucky.
The Journey of Man: A Genetic Odyssey Page 6