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In the 1970s most molecular biologists and most taxonomists had little interest in each other’s work. Among the few taxonomists who appreciated the potential power of the new DNA hybridization technique was Charles Sibley, an ornithologist then serving as Professor of Ornithology and Director at Yale’s Peabody Museum of Natural History. Bird taxonomy is a difficult field because of the severe anatomical constraints imposed by flight. There are only so many ways to design a bird capable, say, of catching insects in mid-air, with the result that birds of similar habits tend to have very similar anatomies, whatever their ancestry. For example, American vultures look and behave much like Old World vultures, but biologists have come to realize that the former are related to storks, the latter to hawks, and that their resemblances result from their common lifestyle. Frustrated by the shortcomings of traditional methods for deciphering bird relationships, Sibley and Jon Ahlquist turned in 1973 to the DNA clock, in the most massive application to date of the methods of molecular biology to taxonomy. Not until 1980 were Sibley and Ahlquist ready to begin publishing their results, which eventually came to encompass applying the DNA clock to about 1,700 bird species – nearly one-fifth of all living birds.
While Sibley’s and Ahlquist’s achievement was a monumental one, it initially caused much controversy because so few other scientists possessed the blend of expertise required to understand it. Here are typical reactions I heard from my scientist friends:
‘I’m sick of hearing about that stuff. I no longer pay attention to anything those guys write,’ (an anatomist).
‘Their methods are okay, but why would anyone want to do something so boring as all that bird taxonomy?’ (a molecular biologist).
‘Interesting, but their conclusions need a lot of testing by other methods before we can believe them,’ (an evolutionary biologist).
‘Their results are The Revealed Truth, and you better believe it,’ (a geneticist).
My own assessment is that the last view will prove to be the most nearly correct one. The principles on which the DNA clock rests are unassailable; the methods used by Sibley and Ahlquist are state-of-the-art; and the internal consistency of their genetic-distance measurements from over 18,000 hybrid pairs of bird DNA testifies to the validity of their results.
Just as Darwin had the good sense to marshal his evidence for variation in barnacles before discussing the explosive subject of human variation, Sibley and Ahlquist similarly stuck to birds for most of the first decade of their work with the DNA clock. Not until 1984 did they publish their first conclusions from applying the same DNA methods to human origins, and they refined their conclusions in later papers. Their study was based on DNA from humans and from all of our closest relatives: the common chimpanzee, pygmy chimpanzee, gorilla, orangutan, two species of gibbons, and seven species of Old World monkeys. The figure on this page summarizes the results.
As any anatomist would have predicted, the biggest genetic difference, expressed in a big DNA melting point lowering, is between monkey DNA and the DNA of humans or of any ape. This simply puts a number on what everybody has agreed ever since apes first became known to science: that humans and apes are more closely related to each other than either are to monkeys. The actual statistic is that monkeys share ninety-three per cent of their DNA structure with humans and apes, and differ in seven per cent.
Trace back each pair of modern higher primates to the black dot connecting them. The numbers to the left then give the percentage difference between the DNAs of those modern primates, while the numbers to the right give the estimated number of millions of years since they last shared a common ancestor. For example, the common and pygmy chimps differ in about 0.7% of their DNA and diverged about three million years ago; we differ in 1.6% of our DNA from both chimps and diverged from their common ancestor about seven million years ago; gorillas differ in about 2.3% of their DNA from us or from chimps and diverged from the common ancestor leading to us and the two chimps about ten million years ago.
Equally unsurprising is the next biggest difference, one of five per cent between gibbon DNA and the DNA of other apes or humans. This too confirms the accepted view that gibbons are the most distinct apes, and that our affinities are instead with gorillas, chimpanzees, and orangutans. Among those latter three groups of apes, most recent anatomists have considered the orangutan as somewhat separate, and that conclusion too fits the DNA evidence: a difference of 3.6% between orangutan DNA and that of humans, gorillas, or chimpanzees. Geography confirms that the latter three species parted from gibbons and orangutans quite some time ago: living and fossil gibbons and orangutans are confined to Southeast Asia, while living gorillas and chimpanzees plus early fossil humans are confined to Africa.
At the opposite extreme but equally unsurprising, the most similar DNAs are those of common chimpanzees and pygmy chimpanzees, which are 99.3% identical and differ by only 0.7%. So similar are these two chimp species in appearance that it was not until 1929 that anatomists even bothered to give them separate names. Chimps living on the equator in central Zaire rate the name ‘pygmy chimps’ because they are on average slightly smaller (and have more slender builds and longer legs) than the widespread ‘common chimps’ ranging across Africa just north of the equator. However, with the increased knowledge of chimp behaviour acquired in recent years, it has become clear that the modest anatomical differences between pygmy and common chimps mask considerable differences in reproductive biology. Unlike common chimps but like ourselves, pygmy chimps assume a wide variety of positions for copulation, including face-to-face; copulation can be initiated by either sex, not just by the male; females are sexually receptive for much of the month, not just for a briefer period in mid-month; and there are strong bonds among females or between males and females, not just among males. Evidently, those few genes (0.7%) that differ between pygmy and common chimps have big consequences for sexual physiology and roles. That same theme – a small percentage of gene differences having great consequences – will recur later in this and the next chapter in regard to the gene differences between humans and chimps.
In all the cases that I have discussed so far, anatomical evidence of relationships was already convincing, and the DNA-based conclusions confirmed what the anatomists had already concluded. But DNA was also able to resolve the problem at which anatomy had failed – the relationships between humans, gorillas, and chimpanzees. As the figure on here shows, humans differ from both common chimps and pygmy chimps in about 1.6% of their (our) DNA, and share 98.4%. Gorillas differ somewhat more, by about 2.3%, from us and from both of the chimps.
Let us pause to let some of the implications of these momentous numbers sink in.
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The gorilla must have branched off from our family tree slightly before we separated from the common and pygmy chimpanzees. The chimpanzees, not the gorilla, are our closest relatives. Put another way, the chimpanzees’ closest relative is not the gorilla but the human. Traditional taxonomy has reinforced our anthropocentric tendencies by claiming to see a fundamental dichotomy between mighty man, standing alone on high, and the lowly apes all together in the abyss of bestiality. Now future taxonomists may see things from the chimpanzees’ perspective: a weak dichotomy between slightly higher apes (the three chimpanzees, including the ‘human chimpanzee’) and slightly lower apes (gorilla, orangutan, gibbons). The traditional distinction between ‘apes’ (defined as chimps, gorillas, etc.) and humans misrepresents the facts.
The genetic distance (1.6%) separating us from pygmy or common chimps is barely double that separating pygmy from common chimps (0.7%). It is less than that between two species of gibbons (2.2%), or between such closely related North American bird species as red-eyed vireos and white-eyed vireos (2.9%), or between such closely related and hard-to-distinguish European bird species as willow warblers and chiffchaffs (2.6%). The remaining 98.4% of our genes are just normal chimp genes. For example, our principal haemoglobin, the oxygen-carrying protein t
hat gives blood its red colour, is identical in all 287 units with chimp haemoglobin. In this respect as in most others, we are just a third species of chimpanzee, and what is good enough for common and pygmy chimps is good enough for us. Our important visible distinctions from the other chimps – our upright posture, large brains, ability to speak, sparse body hair, and peculiar sexual lives (of which I will say more in Chapter Three) – must be concentrated in a mere 1.6% of our genes.
If genetic distances between species accumulated at a uniform rate with time, they would function as a smoothly ticking clock. All that would be required to convert genetic distance into absolute time since the last common ancestor would be a calibration, furnished by a pair of species for which we know both the genetic distance and the time of divergence as dated independently by fossils. In fact, two independent calibrations are available for higher primates. On the one hand, monkeys diverged from apes between twenty-five and thirty million years ago according to fossil evidence, and now differ in about 7.3% of their DNA. On the other hand, orangutans diverged from chimps and gorillas between twelve and sixteen million years ago and now differ in about 3.6% of their DNA. Comparing these two examples, a doubling of evolutionary time, as one goes from twelve or sixteen to twenty-five or thirty million years, leads to a doubling of genetic distance (3.6 to 7.3% of DNA). Thus, the DNA clock has ticked relatively steadily among higher primates.
With those calibrations, Sibley and Ahlquist estimated the following time scale for our evolution. Since our own genetic distance from chimps (1.6%) is about half the distance of orangutans from chimps (3.6%), we must have been going our separate way for about half of the twelve to sixteen million years that orangutans had to accumulate their genetic distinction from chimps. That is, the human and ‘other chimp’ evolutionary lines diverged around six to eight million years ago. By the same reasoning, gorillas parted from the common ancestor of us three chimpanzees around nine million years ago, and the pygmy and common chimps diverged around three million years ago. In contrast, when I took physical anthropology as a college freshman in 1954, the assigned textbooks said that humans diverged from apes fifteen to thirty million years ago. Thus, the DNA clock strongly supports a controversial conclusion also drawn from several other molecular clocks based on amino acid sequences of proteins, mitochondrial DNA, and globin pseudogene DNA. Each clock indicates that humans have had only a short history as a species distinct from other apes, much shorter than paleontologists used to assume.
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What do these results imply about our position in the animal kingdom? Biologists classify living things in hierarchical categories, each less distinct than the next: subspecies, species, genus, family, superfamily, order, class, and phylum. The Encyclopaedia Britannica and all the biology texts on my shelf say that humans and apes belong to the same order, called Primates, and the same superfamily, called Hominoidea, but to separate families, called Hominidae and Pongidae. Whether Sibley’s and Ahlquist’s work changes this classification depends on one’s philosophy of taxonomy. Traditional taxonomists group species into higher categories by making somewhat subjective evaluations of how important the differences between species are. Such taxonomists place humans in a separate family because of distinctive functional traits like large brain and bipedal posture, and this classification would remain unaffected by measures of genetic distance.
However, another school of taxonomy, called cladistics, argues that classification should be objective and uniform, based on genetic distance or times of divergence. All taxonomists agree now that red-eyed and white-eyed vireos belong together in the genus Vireo, willow warblers and chiffchaffs in the genus Phylloscopus, the various species of gibbons in the genus Hylobates. Yet the members of each of these pairs of species are genetically more distant from each other than are humans from the other two chimpanzees, and diverged longer ago. On this basis, then, humans do not constitute a distinct family, nor even a distinct genus, but belong in the same genus as common and pygmy chimps. Since our genus name Homo was proposed first, it takes priority, by the rules of zoological nomenclature, over the genus name Pan coined for the ‘other’ chimps. Thus, there are not one but three species of genus Homo on Earth today: the common chimpanzee, Homo troglodytes; the pygmy chimpanzee, Homo paniscus; and the third chimpanzee or human chimpanzee, Homo sapiens. Since the gorilla is only slightly more distinct, it has almost equal right to be considered a fourth species of Homo.
Even taxonomists espousing cladistics are anthropocentric, and the lumping of humans and chimps into the same genus will undoubtedly be a bitter pill for them to swallow. There is no doubt, however, that whenever chimpanzees learn cladistics, or whenever taxonomists from outer space visit Earth to inventory its inhabitants, they will unhesitatingly adopt the new classification.
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Which particular genes are the ones that differ between humans and chimps? Before we can consider this question, we need first to understand what it is that DNA, our genetic material, does.
Much or most of our DNA has no function and may just constitute ‘molecular junk’: that is, DNA molecules that have become duplicated or have lost former functions, and that natural selection has not eliminated from us because they do us no harm. Of our DNA that does have known functions, the main ones have to do with the long chains of amino acids called proteins. Certain proteins make up much of our body’s structure (such as the proteins keratin, of hair, or collagen, of connective tissue), while other proteins, termed enzymes, synthesize and break down most of our body’s remaining molecules. The sequences of the component small molecules (nucleotide bases) in DNA specify the sequence of amino acids in our proteins. Other parts of our functional DNA regulate protein synthesis.
Those of our observable features that are easiest to understand genetically are ones arising from single proteins and single genes. For instance, our blood’s oxygen-carrying protein haemoglobin, already mentioned, consists of two amino acid chains, each specified by a single chunk of DNA (a single ‘gene’). These two genes have no observable effects except through specifying the structure of haemoglobin, which is confined to our red blood cells. Conversely, haemoglobin’s structure is totally specified by those genes. What you eat or how much you exercise may affect how much haemoglobin you make, but not the details of its structure.
That is the simplest situation, but there are also genes influencing many observable traits. For example, the fatal genetic disorder known as Tay–Sachs disease involves many behavioural as well as anatomical anomalies: excessive drooling, rigid posture, yellowish skin, abnormal head growth, and other changes. We know in this case that all these observable effects result somehow from changes in a single enzyme specified by the Tay–Sachs gene, but we do not know exactly how. Since that enzyme occurs in many tissues of our bodies and breaks down a widespread cellular constituent, changes in that one enzyme have wide-ranging and ultimately fatal consequences. Conversely, some traits, such as your height as an adult, are influenced simultaneously by many genes and also by environmental factors (for example, your nutrition as a child).
While scientists understand well the function of numerous genes that specify known individual proteins, we know much less about the function of genes involved in more complex determinations of traits, such as most behavioural features. It would be absurd to think that human hallmarks such as art, language, or aggression depend on a single gene. Behavioural differences among individual humans are obviously subject to enormous environmental influences, and what role genes play in such individual differences is a controversial question. However, for those consistent behavioural differences between chimps and humans, genetic differences are likely to be involved in those species’ differences, even though we cannot yet specify the genes responsible. For instance, the ability of humans but not chimps to speak surely depends on differences in genes specifying the anatomy of the voice box and the wiring of the brain. A young chimpanzee brought up in a psychologist’s home along with the psyc
hologist’s human baby of the same age still continued to look like a chimp and did not learn to talk or walk erect. But whether an individual human grows up to be fluent in English or Korean is independent of genes and dependent solely on its childhood linguistic environment, as proved by the linguistic attainments of Korean infants adopted by English-speaking parents.
With this as background, what can we say about the 1.6% of our DNA that differs from chimp DNA? We know that the genes for our principal haemoglobin do not differ, and that certain other genes do exhibit minor differences. In the nine protein chains studied to date in both humans and common chimps, only five out of a total of 1,271 amino acids differ: one amino acid in a muscle protein called myoglobin, one in a minor haemoglobin chain called the delta chain, and three in an enzyme called carbonic anhydrase. But we do not yet know which chunks of our DNA are responsible for the functionally significant differences between humans and chimps to be discussed in Chapters Two to Seven: the differences in brain size, anatomy of the pelvis and voice box and genitalia, amount of body hair, female menstrual cycle, menopause, and other traits. Those important changes certainly do not arise from the five amino acid differences detected to date. At present, all we can say with confidence is this: much of our DNA is junk; at least some of the 1.6% that differs between us and chimps is already known to be junk; and the functionally significant differences must be confined to some as-yet-unidentified small fraction of 1.6%.
While we do not know which particular genes are the crucial ones, there are numerous precedents for one or a few genes having a big impact. I just mentioned the many large and visible differences between Tay–Sachs patients and normal people, all somehow arising from a single change in one enzyme. That is an example of differences among individuals of the same species. As for differences between related species, a good example is provided by the cichlid fishes of Africa’s Lake Victoria. Cichlids are popular aquarium species, of which about two hundred are confined to that one lake, where they evolved from a single ancestor within perhaps the last 200,000 years. Those two hundred species differ among themselves in their food habits as much as do tigers and cows. Some graze on algae, others catch other fish, and still others variously crush snails, feed on plankton, catch insects, nibble the scales off other fish, or specialize in grabbing fish embryos from brooding mother fish. Yet all those Lake Victoria cichlids differ from each other on the average by only about 0.4% of their DNA studied. Thus it took even fewer genetic mutations to change a snail-crusher into a specialized baby-killer than it took to produce us from an ape.