Evidence Of An Amerindian Population Bottleneck Seen Through Heliobacter pylori Genetics

As you know, we have many symbiotic relationships with bacteria. In fact, the average human gut contains about 1 kilogram (2.2 pounds) of these microscopic cells, some of which are beneficial. If you’ve ever had to take antibiotics, you may have come to learn how dependent we are on certain strains of bacteria to process plant materials… albeit through a rather uncomfortable experience. Certain flora, like E. coli, live in our intestines and help us synthesize vitamins K and B-complex, which are then absorbed by the body.

But microbes provide us with more than just dietary aide. Actually, microbes offer a unique line of evidence into investigating human migrations, which is crucial to have in anthropology. Since they evolve faster due to their exponentially expedited life span, we can trace how human population diverged from one another. One of my favorite papers on the subject was last year’s support for the Out of Africa model of human migrations using the genetics of Helicobacter pylori, another gut dwelling bacterial species.

Helicobacter pylori
Helicobacter pylori

A similar study on the topic was published today in the open access journal PLoS One. The title, “Amerindian Helicobacter pylori Strains Go Extinct, as European Strains Expand Their Host Range,” does a great job at explaining the main results of the paper. But I’ll try to provide a bit more detail in this post.

First, let me introduce the microbe to you. Unlike some of the other flora that reside inside of us, H. pylori, is more or less a parasite and a nasty one at that — known to cause stomach and intestinal cancers because of the chronic inflammation it causes. The inflammation stems off of the reaction of a component of its gram-negative staining walls, a lipopolysaccharide that initiates an immune response. However, most of us play host to this species and do a good job at keeping it under control. Inflammation only becomes a problem when combined with other deficiencies in the health and immune system of the individual.

The authors of this study made 131 bacterial cultures, 19 of which came from from Africans, 36 from Spanish, 11 from Koreans, 43 from Amerindians and 22 from South American Mestizos. They lysed the cells from the cultures and did lots of PCR and sequencing reactions for 7 housekeeping genes from each of the 131 cultures. When they did a comparison of the sequences they noted an interesting, but consistent result: decreased diversity of H. pylori strains in the human group with the least genomic diversity.

In other words, Native American human populations, who experienced a population bottleneck while crossing Beringia, also inadvertently caused a H. pylori bottleneck! We’ve suspected that Native American populations have undergone a bottleneck because looking at their ABO blood group diversity, they show a remarkable dominance of O blood type — something not seen in European and African populations.

Among Mestizo people, H. pylori genetic diversity was high. That’s cause Mestizos are people of mixed ancestry — a hodgepodge of Spanish and Native American hybrids. In fact, the authors could see the hybridization in the H. pylori from these people. Although bacteria reproduce asexually, they have this phenomenon, called recombination, which is effectively a sharing of parts of DNA. Mestizo H. pylori had some signatures from Amerindian H. pylori and some from European H. pylori indicating their was a sharing of H. pylori genes from these two different populations, just as there was a sharing of human genes.

Even though I’ve made this point before, similar to languages, material culture, and our own genetics, the genetics of organisms associated with humans, be it bacteria, rats, etc. can effectively tell us a lot about human migrations. This paper documents how a founder effect of sorts, a decrease of genetic variation of H. pylori among Native Americans due the effects of crossing Beringia some 15,000 years ago. It also documents the increase in genetic diversity of H. pylori as these Native American groups mixed with European ones.

    Maria G. Domínguez-Bello, Maria E. Pérez, Maria C. Bortolini, Francisco M. Salzano, Luis R. Pericchi, Orlisbeth Zambrano-Guzmán, Bodo Linz, Angus Buckling (2008). Amerindian Helicobacter pylori Strains Go Extinct, as European Strains Expand Their Host Range PLoS ONE, 3 (10) DOI: 10.1371/journal.pone.0003307

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