Tuesday, September 30, 2008

Lactose Tolerance Phenotypes in Africa

NY Times [italicized extract below] — On the findings that Sarah Tishkoff and her team found, as have others too, showing that the C−13.9kbT allele which is determined to be a predictor of lactose tolerance in Europe, has not been effective in predicting lactose tolerance in Africa, even though this is a continent where lactose tolerance amongst various groups, particularly those that practice pastoralism, has been well documented. The reason for this phenomenon is 'convergent evolution', wherein several distinct alleles different from the European examples appear to be promoters of lactose tolerance...

Geneticists wondered if the lactose tolerance mutation **in Europeans**, identified in 2002, had arisen among pastoral peoples elsewhere.

But it seemed to be largely absent from Africa, even though pastoral peoples there generally have some degree of tolerance...

After testing for lactose tolerance and genetic makeup among 43 ethnic groups in East Africa, she and her colleagues have found three **new** mutations **all independent of one another** and **of the European mutation**, that keep the lactase gene permanently switched on.

Meanwhile, what needs to be understood when considering lactose tolerance situations in Africa, courtesy Mulcare et al. 2004…

—1) Lactase persistence varies widely in frequency among different human populations, both between and within continents.

Examples of within continents variations...

*E.g. 1 - in Europe itself variation is apparent - Almost all Dutch people and 99 percent of Swedes are lactose tolerant, but the mutation becomes **progressively** less common in Europeans who live at increasing distances from the ancient Funnel Beaker region - NY Times, an article on Sarah Tishkoff's 2004 findings on lactase phenotypes in African samples.

*E.g. 2 - Southern Europeans generally showed lower lactose tolerance phenotypes than regions to their north.

*E.g 3 - After testing for lactose tolerance and genetic makeup among 43 ethnic groups in East Africa, she and her colleagues have found three **new** mutations **all independent of one another

Example of between continents variation:

*E.g. - After testing for lactose tolerance and genetic makeup among 43 ethnic groups in East Africa, she and her colleagues have found three **new** mutations **all independent of one another** and **of the European mutation**, that keep the lactase gene permanently switched on.

—2) To date [as of 2003], there have been no reports of allele frequencies for the C−13.9kbT polymorphism in populations living in Africa.

[as of 2004] The frequency of −13.9kb*T type was low or zero in most of the African groups tested. In relation to this, we have the following examples:

*E.g. 1 - In the African populations, the −13.9kb*T allele was only found in a few individuals; all but one of these individuals were from Cameroon, [and these were in the main, ancestral or paraphyletic R1*-M173 carriers]

*E.g. 2 - It is noteworthy that −13.9kb*T was not found in East Africa at all, even though the data sets included many known pastoralists and groups with a high frequency of lactase persistence.

—3) Previous studies of African populations showed variation in the frequency of lactase persistence among population groups, as well as a complex pattern of distribution (reviewed in Flatz 1987; Holden and Mace 1997; Swallow and Hollox 2000).

African populations display multiple lifestyles, with milk-drinking and non–milk-drinking groups often living in close proximity, and have complex demographic histories. Some examples below:

* E.g. 1 - Pastoralists, such as the Fulbe in Nigeria, typically have higher frequencies of lactase persistence than nonpastoralists in the same country—for example, the Yoruba and Igbo

* E.g. 2 - The lactase-persistence phenotype is usually observed at low frequencies in Bantu- and Khoisan-speaking groups (<20%); Comparisons of the predicted frequencies of lactase persistence, deduced from the frequency of −13.9kb*TT and −13.9kb*CT genotypes, with the reported frequencies obtained from lactose-tolerance testing, showed these were significantly different in all of the African populations except the Fulbe and the Hausa.

—4) Why it is misleading to use reports for African American candidates as representative of lactose tolerance phenotypes amongst Africans:

*Although the −13.9kb*T allele frequency in Americans with African ancestry is consistent with their lactase-persistence frequency (Enattah et al. 2002), there is known to be substantial admixture between African Americans and European Americans (Parra et al. 1998)

So, African American examples of the C-13.9kbT alleles could represent introgression from European Americans, since as already noted above, at the time of Mulcare et al.’s study, “To date, there have been no reports of allele frequencies for the C−13.9kbT polymorphism in populations living in Africa” and Mulcare et al. themselves found that “the frequency of −13.9kb*T is too low to explain the observed frequency of lactase persistence.”

*In relation to point 3 at the top - Though African American gene pool are largely reflective of those of their ancestral African populations, it doesn’t represent the overall gene pool of Africa, and it may well have been subjected to some micro-evolutionary processes, however low, since the time of separation from source African populations, including — as noted above — bidirectional genetic introgression with populations that are otherwise rarely geographically proximate to African populations.

*African American lifestyles may not necessarily parallel those of their respective ancestral populations and other African populations.

And as already noted, but not the least…

—5) While the C−13.9kb*T allele has been proclaimed to be a predictor of lactose tolerance in Europeans [see Enattah and colleagues (2002)], Mulcare et al.’s results show that the −13.9kb*T allele cannot be causal of lactase persistence in most Africans [although it could possibly explain lactase persistence in some Cameroonians].

Other reading:
More on R1*-M173 bearers

2 comments:

The Big Valley said...

solver said:
Geneticists wondered if the lactose tolerance mutation **in Europeans**, identified in 2002, had arisen among pastoral peoples elsewhere.

But it seemed to be largely absent from Africa, even though pastoral peoples there generally have some degree of tolerance...

After testing for lactose tolerance and genetic makeup among 43 ethnic groups in East Africa, she and her colleagues have found three **new** mutations **all independent of one another** and **of the European mutation**, that keep the lactase gene permanently switched on.


African populations display multiple lifestyles, with milk-drinking and non–milk-drinking groups often living in close proximity, and have complex demographic histories...



Wow great info. There you have it. Yet another solid example that all Africans are not alike, and dont necessarily group easily into monolithic blocs, even those living in close proximity to one another. Some however, just can't seem to recognize (or accept) this basic reality.

Mystery Solver said...

^Unfortunately, since many non-Africans, including the African diaspora, tend to get their information from non-African media outlets that have vested interest in only propagating a rigid and "idealized" narrow theme of Africa, many members of these groups tend to have a rigid "idealized" caricature of Africans and what Africa is supposed to look and be like. To get a more sober look at Africa, one would have to have set foot in not just a single area, but several different areas of the continent. Anybody who has done this, and is still not convinced of the magnitude of diversity in Africa, and I mean this not only from a biological standpoint but also social one, then that person would have to re-evaluate the state of his/her judgment.