Hitchhiker's Guide to a small planet

Around 60,000 years ago, small bands of modern human beings were moving out of their east African homelands and into the vast grasslands of the central Asia steppes in pursuit of game.

From Asia Minor, the emigrants reached India and island-hopped through the Indonesian archipelago to enter Australia around 50,000 years ago.

By 40,000 years ago, modern humans had colonised Europe and east Asia, and by 30,000 had begun moving into the islands of the south-west Pacific. Around 15kya they crossed the Beringian ice bridge to enter the Americas.

The nomads carried with them a mark of their east African origins: alleles of mitochondrial and nuclear genes, that, despite millennia of random mutation, still set their descendants apart from those of the more genetically diverse populations who stayed at home in Africa.

Some unwanted hitchhikers accompanied the diaspora: microbial pathogens that exhibit similarly restricted genetic diversity to their human hosts.

In February this year, British, German and French researchers published a paper in Nature presenting evidence for an African origin for Helicobacter pylori, which causes peptic ulcers, and acts as an agent provocateur for stomach cancer.

The team, led by Max Planck molecular biologist Bodo Linz, found that genetic diversity in H. pylori declines with distance from east Africa - just as it does in modern Homo sapiens. The study independently pointed to an east African origin for modern, non-African peoples.

At the Australian Society of Microbiology annual conference in Adelaide shortly, French molecular geneticist Dr Phillip Supply, of the Institut Pasteur in Lille, will present even more persuasive microbial evidence for the out-of-east Africa hypothesis.

Supply led a study that investigated the origins of the Mycobacterium tuberculosis complex - a group of intracellular parasites that includes M. tuberculosis, the agent of human tuberculosis; M. africanum (TB in humans from some African regions); M. bovis (TB mostly in cattle); and M. microtii (TB in voles).

These bacteria belong to the genus Mycobacterium, which also includes M. leprae, the agent of leprosy, and several other species with mammalian or bird hosts, including M. microtii in voles, and M. avium (birds).

M. avium ssp paratuberculosis causes Johne's disease, a chronic infection of the digestive tract in cattle and sheep, and is a prime suspect for Crohn's disease in humans.

Supply says the microbes of the M. tuberculosis complex are very successful human pathogens. Collectively, they cause eight million new human infections annually, and cause around two million deaths.

"It has been estimated that a third of the world's population is infected," he says.

"However, only a small minority of people infected develop the disease over their lifetime - the infection remains dormant in most of the other cases. This indicates M. tuberculosis is highly adapted to its host, which in turn suggests a long history of association between the pathogen and humans.

"But there is a paradox: genetically, M. tuberculosis is highly homogeneous, which suggests the pathogen is quite recent, in evolutionary terms.

"When we and other colleagues sequenced corresponding 'housekeeping' genes from different M. tuberculosis complex strains from around the world, there was so little nucleotide variation that it looks as if the entire complex emerged recently from a single ancestor."

Common ancestor

Another virulent human pathogen, Yersinia pestis, exhibits a similar, near-clonal lack of variation, but the agent of bubonic plaque has a far more limited distribution than the M. tuberculosis complex.

When another collaborating team led by Dr Roland Brosh performed a comparative analysis of deletions in the genomes of the complex it obtained a very similar result.

"It shows all these strains descend from a common ancestor, and there has been insufficient time for the lineages to become differentiated," Supply says. "They are almost clonal."

Based on the minimal variation, one research team estimated that the complex originated around 40,000 years ago.

"We might have predicted a more ancient age, based on what we know on the adaptation of the pathogen to its host. The question was: did the complex arise from an earlier human pathogen, and if not, where did it come from?"

The answer came from tuberculosis patients at one of the two French military hospitals in Djibouti, in east Africa, between Eritrea and Somalia. (M. africanum occurs in western and central Africa, and has characteristics that mark it as a classical member of the Mycobacterium complex. Supply says the Djibouti strains are clearly distinct).

Military doctors sent samples of the Djibouti strains to Supply's group in Paris and Lille, which genotyped them using the molecular markers used in the earlier study.

The Djibouti strain was distinct: all classical tubercle bacilli. Cultured on agar plates, it formed smooth-surfaced colonies, where the species normally has a rough appearance.

Supply says different isolates from Djibouti exhibited much greater variation in housekeeping genes than had previously been found within the entire M. tuberculosis species complex found worldwide. The east African isolates were definitely non-clonal.

"They are fundamentally different, and we found evidence for recombination or horizontal gene transfer. That's interesting, because in other bacterial species, horizontal transfer of evolutionarily advantageous genes is an important adaptive mechanism. Horizontal transfer allows species to acquire combinations of advantageous alleles necessary for a successful clone to emerge.

"We believe the isolates we have characterised from east Africa are extant representatives of the ancestral species from which a clone emerged and founded the M. tuberculosis complex. We believe we have identified the ancestral bacterial gene pool for the complex."

Different lineages of the M. tuberculosis complex show significant associations with particular human populations, indicating that the clone has undergone microevolution as it followed various human lineages in their migrations around the planet, he says.

There is also some evidence that other human pathogens, including M. leprae, have followed a similar evolutionary pattern. M. leprae also appears to have originated as a clone in east Africa. It is not a member of the M. tuberculosis complex, but a closely related species.

Based on some speculative hypotheses on molecular evolution, Supply's team put the age of the ancestral species of the M. tuberculosis complex at around three million years, suggesting that tuberculosis might have already affected early hominids present in East Africa at that time.

But there is currently no way of correlating the estimated molecular dates with the archaeological record for human pathogens, so the timing of the emergence of the microbial pathogens - and by implication, the timing of their export from Africa, in company with modern human migrations out of east Africa - remains uncertain.

The ASM conference is being held in Adelaide from July 9 to 13. See www.asm2007.org for more.