by Meave Leakey
Either way, we clearly overcame many hardships to become what we are today—inhabiting every corner of every continent and altering habitats to such an extent that no other species on land or sea remains untouched by our reach.
Only two things could have decimated the population so dramatically: a ferocious outbreak of disease or rapid and extreme climate change. Of the two, climate change is more likely because a disease can no longer spread when it becomes so virulent that it wipes out its host (outbreaks of lethal diseases such as Ebola tend to fire up quickly and then peter out). We’ve already witnessed the huge role that the earth’s usually erratic climate has played in our evolution up to this point, and it is certain that climate change will remain a major force in our future too. In 2019, the United Nations released a report on the state of biodiversity on earth that summed up 15,000 scientific papers. The staggering findings are that the earth is set to lose one million species within decades due to human activity unless we change our habits. Man-made climate change is a huge and inexorable part of this equation.
On a rushed visit to Washington, D.C., in March 2007, I bumped into Spencer Wells during a brief break from an annual symposium of National Geographic’s Explorer-in-Residence program. Louise and I had become “explorers” in 2002, and the symposia offer an opportunity to meet and learn more about the varied and extremely interesting people and projects under the Explorer program. Spencer, who is completely committed to his work and always gushing with new and exciting ideas, was even more buoyant than usual.
Spencer is a geneticist who has had an illustrious career, and he is the mastermind behind the National Geographic’s Genographic Project, which was launched in 2005. This was an ambitious enterprise that looked at the bloodlines of people to trace the migration of Homo sapiens around the world. As Spencer is wont to say, “Every drop of human blood contains a history book.” This history book is a genetic record of our past encrypted in an elaborate code that we pass down to later generations through our DNA. These days, so many words are bandied about concerning our human genome and our DNA, that it is all too easy to casually use these terms without fully comprehending them. Permit me a brief digression into the nitty-gritty of cellular biology courtesy of my discussion with Spencer because deciphering this genetic code is now a mainstay of our tracing our recent past.
The makeup of our cells is fascinating. More than a billion years ago, a wayward bacterium found itself enclosed within the walls of another single-celled organism, and so began a long and fruitful association that facilitated the development of complex life-forms made of multiple cells. The descendants of that original bacterium prisoner are mitochondria, and they serve as an army of battery packs that literally give us life as they use the nutriments we ingest and the oxygen we breathe to generate energy. In return, they are housed in a safe, warm environment where these raw materials are conveniently delivered in a constant stream for processing. But this endosymbiosis has changed little over time: mitochondria still operate like quasiseparate organisms complete with their own DNA, RNA, and ribosomes, and their own schedule for reproduction quite independent of the cell they are enclosed in. Thus there are two independent sets of DNA within each of our cells. The cell nucleus houses our own much more complex set of nuclear DNA, which is the sequence or code that controls how our bodies form and function (more on this later). And outside the nucleus of each cell, thousands of mitochondria share a mitochondrial DNA (mtDNA) sequence that is likely to be identical across all the cells in one human body.
Two qualities of mitochondria help us trace historical populations. The first is that mitochondrial DNA mutates far faster than our own nuclear DNA: it contains roughly ten times as many polymorphs (mutation errors that alter the sequence on the DNA chain) as our nuclear DNA. While all the mtDNA in one human is likely to be identical, there is so much variation between humans that there may even be mutations or sequences specific to individual families. This is a good thing for geneticists because the greater the degree of variation, the better our ability to distinguish between individuals. The second quality is that mtDNA is passed down only through the mother because the mitochondria in sperm are concentrated in the tail region of the cell. Once the tail has propelled the sperm on its epic swim up the Fallopian tube to meet the egg, it is summarily dispensed with along with its mitochondria. If you are born male, you are basically an mtDNA evolutionary dead end. These two characteristics of mtDNA make it possible to trace the ancestry of every single woman alive back in time to an original woman. It was she who provided the mitochondria we carry in our cells today.
This woman has been anointed with the loaded name of “Mitochondrial Eve”—and it would be easy to suppose that she was the only woman alive when she began propagating her mitochondria. This is a mistaken deduction. It is mathematical logic that leads us to the conclusion that we all share an original “mother.” All the women from the same generation descended from a smaller number of women—as some of our mothers’ generation, for example, either had no offspring or only produced boys, and this happened in their mothers’ generation and the one before that. This logic forces us inexorably up a pyramid of ever-diminishing numbers of ancestral women, a process called coalescence, which cannot continue indefinitely. Eventually, there will be just two women, and they must have shared a single mother, the so-called Mitochondrial Eve. All the earlier lineages of mtDNA—including Eve’s mother’s—are now extinct. But Eve obviously did not live alone; she just happened to be the one whose mtDNA made it through.
Specific mutations are like flags on the mtDNA sequence. Although these mutations are random errors in the copying of DNA, they can be averaged over time to give a mutation rate for a gene (such as mtDNA) that can be used as a molecular clock. By comparing the sequence of two individuals, or two species, scientists can establish how different they are, and using a known historical event (such as a fossil), they can calculate how long in years those differences took to accumulate—in other words, scientists can calibrate the clock. Using a calibrated clock, researchers are able to map the history of individuals, populations, and species.
By looking at which populations share particular markers, geneticists can decipher the timing and path of the dispersal of Homo sapiens out of Africa, and this work began using mtDNA. Two very early markers on mtDNA are called the L0 and L1. These flags trace migrations of African peoples before the exodus out of the continent. Both groups lived in Africa more than 130,000 years ago, and today L0 is found in highest frequencies among geographically diverse populations such as the Central African Pigmies and the Khoisan of Southern Africa, but it has low frequencies in West and North Africa. L1 markers, on the other hand, are found in higher frequencies in West Africa but exhibit the greatest diversity (and thus age) in Central and East Africa. These two ancient markers only made their way out of Africa with the forced migration of Africans to the New World in the barbarous Atlantic slave trade.
By tracing the mutations on mtDNA back in time, geneticists now believe that Eve lived in Africa sometime around 170,000 years ago. It is interesting to note that the process of coalescence is much more likely to occur when a population is small and their genes are passed through what is called a genetic bottleneck—as when our population was reduced to a mere ten thousand souls.
Unlike mtDNA, nuclear DNA undergoes a huge shake-up with each generation—rather like a shuffling and splitting of two decks of cards so the child ends up with a random half of each parent’s genetic makeup. When we procreate, we make unique reproductive cells—the eggs and sperm. These gametes contain only one of each of the twenty-three pairs of chromosomes, so that they have twenty-three single chromosomes, rather than the usual paired forty-six. Genes are sequences of nucleotides (basic building blocks) on a strand of DNA, and human genes are located along the strands of DNA in twenty-three different pairs of chromosomes. We inherit half of our genes from our mother and half from our father, but the combinations are almost endless—the
twenty-three chromosomes in each human sperm or egg cell contain about three billion nucleotides, which are the basic building blocks of genes.
There are roughly 1,500 active genes on the average human chromosome, but the Y chromosome has only twenty-one genes, and all of them are involved in making a boy instead of a female, the mammalian default. The rest of the Y chromosome appears to be biological junk with no discernable function. Spencer Wells calls this junk DNA “gold dust to population geneticists” because mutations in the Y chromosome are handed down through the generations and can serve as markers to trace our gene tree.
Since women have two X chromosomes and men inherit a Y chromosome only from their father, we can trace an ancestral Adam from mutations in the Y chromosome just as we followed mtDNA mutations back in time to a Mitochondrial Eve. The Y chromosome equivalent to the earliest female markers, L0 and L1, carry particular mutations such as the M91 and M60 markers. Men bearing the M91 marker are found today in non-Bantu populations in Ethiopia, the Sudan, and the southern regions of Africa. The M60 marker is widely dispersed across the African continent today and shared by many different African people. Our common Y chromosome ancestor lived in Africa between 160,000 and 300,000 years ago, although it is unclear whether Adam and Eve ever had the pleasure of making each other’s acquaintance! The discrepancy in age sounds implausible at first—for where were the men that Eve and her group were procreating with?
Spencer explains this as a product of the hierarchy of traditional patriarchal societies. Having many wives and children is an expensive privilege, and in many instances, polygamy is reserved for an elite few, and some men cannot afford any wives at all because of the costly bride price. The current king of Swaziland, Mswati III, has 15 wives and 35 children at last count, and his father, King Sobhuza II, had 70 wives and 210 children before his death at age 82 in 1982.
We obviously can’t speculate on whether Adam was a rich chieftain who paid a generous bride price for his mates, but in most primate societies, it is the dominant males who enjoy most of the sexual action and pass down their genes. There is, therefore, far more equal opportunity in the evolutionary fate of mtDNA than there is for Y chromosomes because many more females will pass down their genes than their male counterparts. Effectively, most of the older lineages of Y chromosomes have become extinct, although a few survive and give us precious insights into earlier periods in our species African history. So far, the molecular evidence is firmly in the single-origin court of the splitters.
At this point, deciphering DNA gets much more complicated. A vast amount of information is contained on our chromosomes, but until only very recently, this library has been inaccessible to us. DNA is a double-stranded molecule with each strand consisting of a linear sequence of nucleotides that can be one of four types: adenine (A), thymine (T), cytosine (C), and guanine (G). The combination of A, T, C and G nucleotides is remarkably uniform in all people—it is 99.9 percent identical throughout the world. The remaining 0.1 percent of variation is responsible for the individual characteristics that make each of us unique. This sequence in our nuclear DNA and our mtDNA makes up the human genome, and when scientists succeeded in mapping it in 2003, they at last found a key to unlock the vast secrets contained in our nuclear DNA.
Copying errors that alter one of the nucleotides in the sequence—changing an A to a G, for instance—are what make evolution possible. These mutations account for the 0.1 percent of variance in the genetic makeup of the more than seven and a half billion people alive today. What happens after a mutation occurs depends partly on how it affects the body. Some of this DNA is responsible for individual characteristics—the most glaringly obvious physical trait in my family is the “Epps chin,” which is about as far from a chinless Neanderthal as one can get. The Leakeys don’t have very distinctive chins, but they carry a particularly dominant gene for very prominent ears that on young Leakeys seem to be placed at right angles to the side of the head rather than laid flat against it. Other famous Leakey genetic traits include what could politely be called extreme tenacity, a zealous missionary streak, and an obsession with punctuality that makes the military a sound career option. Richard has every single one of these genetic traits.
Our cells have complex ways of fixing mistakes that may occur when DNA is being copied, and the most common mutations that persist are those that have no effect on us. Such mutations carry on from generation to generation as harmless variants. Second-most common are mutations that are harmful, and nature’s solution is usually to terminate the pregnancy. At least one-fifth of all conceptions end in miscarriages, many of them because the genetic mutations are fatal to the foetus. Much rarer are mutations that are beneficial to an individual in a given environment. These mutations confer a reproductive advantage and are the basis for Darwin’s theory of natural selection as a driving evolutionary force.
Mutations in mtDNA and the Y chromosome are easy to trace because they are passed down intact from generation to generation. If the same mutation can be identified generations later in two individuals, it indicates a common ancestor. By comparing markers in different populations, scientists can trace ancestral affinities along a single line of descent (maternal or paternal) until all living lines can be traced to the mtDNA Eve or Y chromosome Adam (coalescence). But for the vast majority of our genes, the number of ancestors grows and grows (two parents, four grandparents, sixteen great-great-grandparents, and so on), and we receive a random configuration of their genes. This is made all the more variable by the fact that there is some gene mixing—known as crossing over or recombination—before an egg or a sperm is produced. In other words, not only does each child receive a random set of genes from each parent, but each set is a reshuffle of the child’s maternal and paternal grandparents’ genes. And this reshuffling is repeated at every generation. This makes it all but impossible to trace mutations along ancestral lineages because it is hard to sort out which novel combinations have arisen from gene reshuffling and which are mutations.
But scientists have discovered that there are small chunks of nuclear DNA that don’t get broken up by recombination very often and are passed down from generation to generation like mtDNA. Any changes in these sections, called haplotypes, will be the result of mutation, so they too can be used to build gene trees. One such haplotype lies within a gene called PDHA1 (which with a gene called PDHB produces two proteins that combine into an enzyme that is involved in the chemical pathway that converts energy from food into something the cells can use), and in the modern population, there are a number of variations that can be grouped into two basic types of sequences. It is interesting to note that these last shared a common ancestor 1.8 million years ago—when Homo erectus first appears in Africa. An even more startling revelation followed: one of these two lineages then split a second time at 200,000 years, which coincides with the appearance of Homo sapiens in Africa.
This is just one of a growing number of genetic studies that have found genes that mutated long ago. An intriguing finding relates to a gene called microcephalin—mutations in this gene lead to microcephaly, which is the explanation some attributed to the very small brain of the Flores Hobbit. There are two variants of this gene, and they are so different that Bruce Lahn, the scientist who studied them, concluded that they must have diverged about 1.1 million years ago—either in H. erectus or in the ancestor of H. sapiens and Neanderthals. The second variant found in modern humans can be traced back only about 37,000 years. As most of our genes are there to make us function—genes that make us a multicellular organism, a vertebrate, a mammal, a primate, an ape—we share them with other creatures at each ring in our particular evolutionary chain. Now we are beginning to discover those genes that mutated at the time of H. erectus and, through them, some of the genetic code for being Homo.
It is remarkable that scientists have managed to recover DNA from Neanderthal remains. Extracting DNA from fossils is extremely difficult because so little remains and contamination from mo
dern DNA is difficult to contain. Scientists work in hermetically sealed labs and endure lengthy procedures so every wayward cell from their bodies is tightly contained in protective clothing and masks. But this work on ancient DNA has transformed the study of recent human evolution.
Since those early discoveries using mtDNA and Y chromosome markers, geneticists have moved in giant leaps. The entire human genome was sequenced in 2003; the chimpanzee genome in 2005; and, most astonishing of all, the Neanderthal genome was pieced together from tiny fragments of ancient DNA in 2010. Since the mapping of the first complete human genome, geneticists have sequenced thousands of others from across the world as well as those of hundreds of ancient humans, twelve Neanderthals, and six Denisovans, an elusive new hominin. This extraordinary library of genetic variation has given us unparalleled insights into the history, adaptation, and behaviour of recent hominins.
Geneticists have been able to compare our DNA to that of Neanderthals and Denisovans in detail. These comparisons show that the “out of Africa” model was mostly correct—all H. sapiens have their origin in Africa between 300,000 and 200,000 years ago, and the Neanderthals (and Denisovans), with whom we share an African ancestor around 500,000 years ago, are our closest relatives. This means that African populations expanded and colonised Eurasia at least twice in the last million years—once 500,000 years ago, which gave rise to the Neanderthals in the west and the Denisovans in the east, and once 70,000 to 60,000 years ago when humans progressively settled the entire world. And there are genomic signatures for possible further “out of Africa” events in between. It is easy to see these expansions as something uniquely special to hominins, but they are not. They were fuelled by climate change. The glacial cycles of the last 800,000 years had hotter and colder extremes than earlier climatic shifts. One consequence of those extremes was a very wet beginning to interglacials, the “green Sahara” events. It was during these that the African ancestors of Neanderthals and modern humans increased in numbers, crossed the Sahara, and dispersed into Eurasia.