Our African “gastric” companion?

[Jacques Cinq-Mars]

Already all over the place, this is a story in which it is “demonstrated”, thanks to “simulations” making use of a broad range of genetic data, that Helicobacter pylori, a not-so-friendly parasitic bug that feasts on human stomachs, left Africa 60,000 years ago and eventually reached South America about 52,000 years later. And since “we” were the carriers, we had to come out of Africa at the same time, etc. … QER.

The Max Planck Society press release on this can be read HERE.

As I have already made clear before, I am really not in a position to argue about the increasingly contradictory and confusing molecular biology “solutions” that purport to deal with the origin(s), direction, and chronology of global human palaeo-dispersals. What I can do, however, is note that the latter show an annoying ignorance (avoidance?) of complementary information emanating from other modes of investigation such as, for example, prehistory (sensu lato).

A good example of this can be seen in the caricatural, outdated map presented in the press release (see link). Assuming that the very few dates listed are based on some molecular clock derived from the studies of Helicobacter pylori, they can only be taken as indicative that the “bug” didn’t travel with the early migrants, but only caught up very slowly with some of the human groups that have been studied. This is especially well illustrated by their rendition of the sequence of events that led to the dispersal of humanity in northeastern Eurasia, Beringia, and the lower latitudes of the New World.

Finally, I should note that, from a scientific point-of-view, and contrary to what is written in the press release, “simulations” (check out the definition) do not “demonstrate” anything. They can only be used, in iterative and testable ways, to develop hypotheses that, hopefully, will end up being better approximations of what may have happened. 

The reference to the actual article is:

Bodo Linz, François Balloux, Yoshan Moodley, Andrea Manica, Hua Liu, Philippe Roumagnac, Daniel Falush, Christiana Stamer, Franck Prugnolle, Schalk W. van der Merwe, Yoshio Yamaoka, David Y. Graham, Emilio Perez-Trallero, Torkel Wadstrom, Sebastian Suerbaum1, and Mark Achtman. 2007. An African origin for the intimate association between humans and Helicobacter pylori. Nature

And here is the Abstract:

Infection of the stomach by Helicobacter pylori is ubiquitous among humans. However, although H. pylori strains from different geographic areas are associated with clear phylogeographic differentiation1–4, the age of an association between these bacteria with humans remains highly controversial5,6. Here we show, using sequences from a large data set of bacterial strains that, as in humans, genetic diversity in H. pylori decreases with geographic distance from east Africa, the cradle of modern humans. We also observe similar clines of genetic isolation by distance (IBD) for both H. pylori and its human host at a worldwide scale. Like humans, simulations indicate that H. pylori seems to have spread from east Africa around 58,000 yr ago. Even at more restricted geographic scales, where IBD tends to become blurred, principal component clines in H. pylori from Europe strongly resemble the classical clines for Europeans described by Cavalli-Sforza and colleagues 7. Taken together, our results establish that anatomically modern humans were already infected by H. pylori before their migrations from Africa and demonstrate that H. pylori has remained intimately associated with their human host populations ever since.

Those of you interested in the full article (AOP) can click HERE or look around for a free PDF copy.

Jacques

PS   Note (in the Abstract) the contradiction between “Helicobacter pylori is ubiquitous among humans” and “over half of all humans are infected by Helicobacter pylori”.

PPS   And what about the poor Neanderthals? How about a good “simulation” that could "demonstrate" that they were eradicated by stomach ulcers following their contacts with the infested African invaders?

PPPS   And, if  you look at the list of the authors of the article and their affiliation(s), you will note that none of them appear in a position to know much about the complementary information I mentioned above. It does make one wonder about the significance of peer-review.

[lagarvelho]

Jacques:

None of the authors are familiar to me at all.  I'm not entirely sure, from the press release or the abstract(I don't have any way of getting a PDF, as yet, that would demonstrate their thesis more fully), exactly how the Helicobacter pylorii organism would have followed people out of Africa, or how they determined that it originiated in Africa in the first place.  Whether or not prehistory would enlighten us, I'm not in a position to know.  As for Neandertals being killed off by stomach ulcers brought in by "invading Africans", I'm sure somebody will soon come up with such a scenario, either as bad science fiction, or as some sort of idiotic bad press that gets disseminated here, there, and everywhere. But then, maybe I'm just getting cynical in my old age or something.
Anne G

[Daryl Habel]

Well, I won't even make an attempt to comment on the new article, since I've only read the Max Planck press release and the Nature abstact.   However, while googling more information about the origin of H. pylori , I did find another article authored by some of the same authors and published March 7, 2003 in the journal Science.

Science 7 March 2003:
Vol. 299. no. 5612, pp. 1582 - 1585
DOI: 10.1126/science.1080857

Traces of Human Migrations in Helicobacter pylori Populations
 
Daniel Falush,1 Thierry Wirth,1 Bodo Linz,1 Jonathan K. Pritchard,2 Matthew Stephens,3 Mark Kidd,4 Martin J. Blaser,5 David Y. Graham,6 Sylvie Vacher,7 Guillermo I. Perez-Perez,5 Yoshio Yamaoka,6 Francis Mégraud,7 Kristina Otto,8 Ulrike Reichard,1 Elena Katzowitsch,8 Xiaoyan Wang,1 Mark Achtman,1* Sebastian Suerbaum8

Helicobacter pylori, a chronic gastric pathogen of human beings, can be divided into seven populations and subpopulations with distinct geographical distributions. These modern populations derive their gene pools from ancestral populations that arose in Africa, Central Asia, and East Asia. Subsequent spread can be attributed to human migratory fluxes such as the prehistoric colonization of Polynesia and the Americas, the neolithic introduction of farming to Europe, the Bantu expansion within Africa, and the slave trade.

For those signed up for the free content offered from the journal Science website, the article is free in html from
CLICK HERE
or pdf download (Adobe Reader required):
PDF HERE

In this earlier article, the authors suggest two sources for the entry of two variants of  H pylori into Europe, correlating these with, for one variant, human dispersal occurring with Neolithic agriculturists 8500 BP, and for the other, the arrival of Uralic speakers in Europe (dated by them as "?").  Here, they suggest neither variant  "was harbored by the original Paleolithic hunter-gatherers in Europe" (p. 1584).

Now that the Nature article published this week suggests that H. pylori entered Europe c. 40-25 ka, simultaneous with the arrival of anatomically modern humans, I'm most curious about the reason(s) for this change in the European ancestral chronology.   But not so curious I'll lose sleep over it.   

Dar   

[lagarvelho]

Dar:

Well, it's obvious I'm going to have to go out and get some more black ink jet ink, so I can read the article(sigh).  But I'm not going to do that today.  Have too much else to attend to.  But I too, would be interested to know exacly how they determined these dates.
Anne G