Power, Sex, Suicide: Mitochondria and the Meaning of Life (45 page)

The third aspect of mitochondrial DNA that the Berkeley team drew on is its steady rate of evolution: the mutation rate, though fast, remains approximately constant over thousands or millions of years. This is ascribed to neutral evolution, the assumption that there is little selective pressure on mitochondrial genes, which serve a restricted and menial purpose (so the argument goes). Sporadic mutations occur at random over generations, and as averages balance out, accumulate at a steady, metronomic speed, leading to a gradual divergence between the daughters of Eve. This assumption is perhaps open to question, and later refinements of the technique have concentrated on the ‘control region’, a string of 1000 DNA letters that does not code for proteins, and so is claimed not be subject to natural selection (we will return to this assumption later).
¹

So how fast does the mitochondrial clock tick? On the basis of relatively recent, approximately known colonization dates (a minimum of 30 000 years ago for New Guinea, 40 000 years ago for Australia, and 12 000 years ago for the Americas), Wilson and colleagues were able to calculate a divergence rate of about 2 per cent to 4 per cent every million years. This figure matches the rate estimated on the basis of divergence from chimpanzees, which began about six million years ago.

If this speed is correctly calibrated, then the actual measured differences between the 147 mitochondrial DNA samples give a date for their last common ancestor of about 200 000 years ago. Furthermore, in agreement with nuclear DNA studies, the deepest divergences were found among African populations, implying that our last common ancestor was indeed African. A third important conclusion of the 1987 paper related to migration patterns. Most populations from outside Africa had ‘multiple origins’, in other words, peoples living in the same place had different mitochondrial DNA sequences, implying that many areas were colonized repeatedly. In sum, Wilson’s group concluded that Mitochondrial Eve lived fairly recently in Africa, and the rest of the world was populated by repeated waves of migration from that continent, lending support to the ‘Out of Africa’ hypothesis.

Not surprisingly these unprecedented findings gave birth to a dynamic new field, which dominated genealogy in the 1990s. The unresolved questions raised by skeletal morphology, by linguistic and cultural studies, by anthropology and population genetics, could at last all be answered with ‘hard’ scientific objectivity. Many technical refinements have been introduced, and calibrated dates modified (Mitochondrial Eve is now dated to about 170 000 years ago), but the basic tenets presented by Wilson and his colleagues underpinned the entire edifice. Wilson himself, an inspiring figure, sadly died of leukaemia at the height of his powers, at the age of 56, in 1991.

Surely Wilson would have been proud of the achievements of the field he helped found. Mitochondrial DNA has answered many questions that had seemed eternally controversial. One such question is the identity of the people living in the remote Pacific archipelagos of Polynesia. According to the famous Norwegian explorer Thor Heyerdahl, the Polynesian islands were populated from South America. To prove it he built a traditional balsa-wood raft, the
Kon-Tiki
, and set sail with five companions from Peru in 1947, arriving in the Tuamotus archipelago, 8000 km away, after 101 days. Of course, proving that a feat is possible is not the same as proving that it actually happened. Mitochondrial DNA sequences speak otherwise, corroborating earlier linguistic studies. The results suggest that the Polynesians originated from the west in at least three waves of migration. About 94 per cent of the people tested had DNA sequences similar to the peoples of Indonesia and Taiwan; 3.5 per cent seemed
to have come from Vanuatu and Papua New Guinea; and 0.6 per cent from the Philippines. Interestingly, 0.3 per cent had mitochondrial DNA matching some tribes of South American Indians, so there is still a remote chance that there could have been some prehistoric contact.

Another difficult question apparently resolved was the identity of the Neanderthals. Mitochondrial DNA taken from a mummified Neanderthal corpse (found in 1856 near Düsseldorf) showed that their sequence is distinct from modern humans, and no traces of Neanderthal sequence have been found in
Homo sapiens
. This implies that the Neanderthals were a separate subspecies, which fell extinct without ever interbreeding with humans. In fact, the last common ancestor of Neanderthals and humans probably lived about 500 to 600 thousand years ago.

These findings are just two of the many fascinating insights into human prehistory afforded by mitochondrial DNA studies. But every silver lining has a cloud. A rather simplistic view of mitochondria has become the mantra, which is repeated ever more succinctly, and ever more misleadingly; the provisos are lost in the telling. We are told that mitochondrial DNA is inherited exclusively down the maternal line. There is no recombination. It is not subject to much selection because it codes for only a handful of menial genes. The mutation rate is roughly constant. The mitochondrial genes represent the true phylogeny of people and peoples because they reflect individual inheritance, not a kaleidoscope of genes.

This mantra generated unease in some quarters from the beginning, but only recently have these misgivings found substance. In particular, we now have evidence of genetic recombination between maternal and paternal mitochondria, of discrepancies in the ticking of the mitochondrial ‘clock’, and of strong selection on some mitochondrial genes (including the supposedly ‘neutral’ control region). These exceptions, while raising some doubts about the validity of our inferences into the past, sharpen our ideas of mitochondrial inheritance, and help us to grasp the real difference between the sexes.

If mitochondria are passed down the maternal line exclusively, then there would seem to be little possibility for recombination. Sexual recombination refers to the random swapping of DNA between two equivalent chromosomes, to make up two new chromosomes, each of which contains a mixture of genes from both sources. Clearly DNA from two distinct sources—two parents—is needed to make recombination possible, or at least meaningful: swapping genes from two identical chromosomes makes little sense, unless one of the two chromosomes is damaged; and this, as we shall see, does raise a spectre. In
general, however, during sexual reproduction, the pairs of chromosomes in the nucleus are recombined to generate new groupings of genes, mixing up genes from different parents or grandparents, but this does not happen with mitochondrial DNA, as all the mitochondrial genes are derived from the mother. Thus, according to orthodoxy, mitochondrial DNA does not recombine: we don’t see a mixture of mitochondrial DNA from both the father and the mother.

Even so, for a decade some primitive eukaryotes like yeast have been known to fuse their mitochondria and recombine mitochondrial DNA. Yeast, of course, is a poor substitute for a human being, as any anthropologist will tell you, and this behaviour was no challenge to reigning orthodoxy. Other curiosities, like mussels, also showed evidence of recombination, but again these were quite easily dismissed as irrelevant to human evolution. So it came as a surprise in 1996 when Bhaskar Thyagarajan and colleagues at the University of Minnesota showed that rats too recombine mitochondrial DNA. Rats, as fellow mammals, are a little too close for comfort. It got worse. In 2001, recombination of mitochondrial DNA was shown to take place in the heart muscle of humans.

Even these studies did not rock the boat too violently, because they were limited in scope. Most mitochondria have five to ten copies of their chromosome, which act as an insurance policy against free-radical damage; it is unlikely that the same gene will be damaged on all copies so normal proteins can still be produced. But just hoarding spare copies is an inefficient method of dealing with damage, as a mixture of normal and abnormal proteins would be produced from the raggedy chromosomes. Better to repair the damage, in the standard bacterial fashion, by recombining undamaged bits of chromosomes to regenerate clean working copies. Such recombination between equivalent chromosomes in the same mitochondrion is known as ‘homologous’ recombination, and does not undermine the principle of uniparental inheritance—it is simply a method of repairing the damage that occurs within a single individual, as we have just noted. So even when mitochondria fuse together, and recombine DNA from different copies of their chromosome, all their DNA is still inherited only from the mother.

Nonetheless, if paternal mitochondria manage to survive in the egg, then recombination of paternal and maternal mitochondrial DNA is possible, at least in principle. We know that in humans the paternal mitochondria do get into the egg cell, so it is always possible that some survive. Does it happen? In the absence of direct evidence, various research groups tried looking for signs of mitochondrial recombination—and found them. The first evidence came in 1999 from Adam Eyre-Walker, Noel Smith, and John Maynard Smith, at the University of Sussex. Their findings were basically statistical. They argued that if mitochondrial DNA really is clonal, its sequences should continue to diverge in different populations, as they pick up new mutations. In fact this does not
always happen: sometimes an ‘atavistic’ sequence re-emerges, which bears an uncanny resemblance to the ancestral type. There are only two ways this could happen: either by random ‘back’ mutations to the original sequence, which sounds inherently implausible, or else by recombination with someone who happened to have retained the original sequence. Such unexpected sequence reincarnations are known as
homoplasies
, and Eyre-Walker and colleagues found a lot of them—far more than could be realistically put down to chance. They took this to be evidence of recombination.

The paper raised an immediate storm and was attacked by establishment figures, who discovered errors in the DNA sequences that had been sampled, but not the statistical technique. After excluding these errors, they found no evidence for recombination. ‘No need to panic’ was the retort of Vincent Macauley and his colleagues at Oxford, and the field took a collective sigh of relief: the great edifice stood firm. But Eyre-Walker and colleagues, while accepting that there had indeed been some sampling errors, stuck to their guns. Even disregarding the errors, they said, the data were still suggestive of recombination, which ‘may not lead some to panic, but surely they should, because there is a very real possibility that an assumption we have held for so long is incorrect.’

That same year, 1999 (indeed in the very same issue of the
Proceedings of the Royal Society
), Erika Hagelberg, a former student in the Oxford group and her colleagues put forward their own challenge. Their argument was based on a particular oddity, the recurrence of a rare mutation in several otherwise unrelated groups living on the Pacific island of Nguna, in the Vanuatu archipelago. As their mitochondrial DNA was clearly inherited from different stocks, and yet the same mutation occurred repeatedly, then either it had arisen independently on several occasions, which seemed improbable, or it was evidence that the mutation arose only once, but had then been passed around to other populations—which is only possible by recombination. On closer inspection the edifice was again saved. This time the error turned out to be attributable to the sequencing machine, which had somehow become misaligned by 10 letters. After correction the mystery vanished. Hagelberg and colleagues were forced to publish a retraction, and she herself now refers to the unfortunate affair as her ‘infamous mistake.’

By 2001, the evidence for recombination looked muddy, to say the least. The two major studies had both been discredited, and although the authors of both papers maintained that the rest of their data still raised doubts, that was only to be expected; they had to defend their tattered reputations. For an unbiased observer, it seemed that recombination had been disproved.

Then in 2002, a fresh challenge emerged. Marianne Schwartz and John Vissing, at Copenhagen University Hospital, reported that one of their patients, a 28-year-old man suffering from a mitochondrial disorder, had actually inherited
some mitochondrial DNA from his father, and so had a mixture of both maternal and paternal DNA—the dreaded heteroplasmy. The mixture occurred as a mosaic, such that the mitochondrial DNA in his muscle cells was 90 per cent paternal and only 10 per cent maternal, whereas in his blood cells it was nearly 100 per cent maternal. This was the first time that paternal mitochondrial DNA had been shown unequivocally to be inherited in humans. Clearly some degree of ‘seepage’ of paternal DNA in the egg is possible, and in this case it was picked up because it caused a disease. But the study raised one overriding question: as two populations of mitochondria from the father and the mother exist in the same person, do they recombine?

The answer is:
they do
. In 2004, Konstantin Khrapko’s group at Harvard reported in
Science
that 0.7 per cent of the disparate mitochondrial DNA in the patient’s muscles had indeed recombined. So, given the opportunity, human mitochondrial DNA really does recombine. But that is not to say that the recombinants will be passed on. No matter if recombinant DNA is formed in the muscles, it can only influence posterity if it recombines in the fertilized egg. Only then can the recombinant form be inherited. So far, there is no evidence of this, although that is at least partly because very few groups have actually looked. On balance, the statistical evidence from population studies suggests that recombination is extremely rare. Of course, very rare recombination events might explain otherwise mystifying deviations in genetic makeup, even if such rare events are unlikely to topple the whole edifice.

But the point I want to make is that, in evolutionary terms, some degree of recombination probably does occur. Is this just a fluke, an occasional accident, or is there a deeper meaning? We’ll return to this question later, but first let’s consider the other exceptions to the mantra, for they, too, have a bearing on the matter.