July 10, 2008

Campbell & Tishkoff review paper on African genetic diversity

From the paper:
Several studies of nucleotide and haplotype variation have indicated that ancestral African populations were geographically structured prior to the migration of modern humans out of Africa (70, 71, 79, 157, 197, 237). Additionally, a recent study of 800 short tandem repeat polymorphisms (STRPs) and 400 INDELs genotyped in more than 3000 geographically and ethnically diverse Africans indicates the presence of at least 13 genetically distinct ancestral populations in Africa and high levels of population admixture in many regions (F.A. Reed & S.A Tishkoff, unpublished data). Population clusters are correlated with selfdescribed ethnicity and shared cultural and/or linguistic properties (e.g., Pygmies, Khoisanspeaking hunter-gatherers, Bantu speakers, Cushitic speakers). This study reveals extensive admixture between inferred ancestral populations in most African populations. One exception is amongWest African Niger-Kordofanian (i.e., Bantu) speakers who are more genetically homogeneous compared with other African populations, likely reflecting the recent and rapid spread of Bantu speakers from a common origin in Cameroon/Nigeria (although fine-scale genetic structure can be detected amongst these populations). Thus, the pattern of genetic diversity in Africa indicates that African populations have maintained a large and subdivided population structure throughout much of their evolutionary history (Figure 2).
As I have argued before, the great genetic diversity of Sub-Saharan Africans is due to the fact that they are composed of several long-differentiated populations admixed with each other. As Figure 2, mentioned above, indicates, NE Africans are related to Eurasians more closely than other Africans, although there has been subsequent gene flow into NE Africans from other Sub-Saharan Africans. Annual Review of Genomics and Human Genetics Vol. 9 (Volume publication date September 2008) (doi:10.1146/annurev.genom.9.081307.164258) African Genetic Diversity: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping Michael C. Campbell­, Sarah A. Tishkoff­ Comparative studies of ethnically diverse human populations, particularly in Africa, are important for reconstructing human evolutionary history and for understanding the genetic basis of phenotypic adaptation and complex disease. African populations are characterized by greater levels of genetic diversity, extensive population substructure, and less linkage disequilibrium (LD) among loci compared to non-African populations. Africans also possess a number of genetic adaptations that have evolved in response to diverse climates and diets, as well as exposure to infectious disease. This review summarizes patterns and the evolutionary origins of genetic diversity present in African populations, as well as their implications for the mapping of complex traits, including disease susceptibility. Link


Maju said...

Looks like a very interesting paper, pity it's behind a paywall.

13 ancestral populations is quite a good number of them, more than could be infered from mtDNA, for instance. It's no surprise, I'll add, that NE Africans (Horners, I assume) are more closely related to Eurasians than any other group.

terryt said...

"more than could be infered from mtDNA". Maju. Are you implying that mtDNA might not be the perfect measure of population origin and diversity?

Maju said...

I am not implying anything: I haven't read the paper.

Are you implying that autsomal studies are some sort of holy grail? I don't think that certainly, much less without reading the study.

terryt said...

I've been trying to get through to you for ages that mtDNA (or Y-chromosome) on its own is totally inadequate to draw conclusions from. Autosomal studies are a necessary consideration too.

Maju said...

Autosomal studies seem to yield a too recent picture of groupings. They are complementary certainly, at least when they yield sufficiently deep bayesian K-means analysis, but they can't replace halpid genetics at all.

Overall one of the main problems I've seen in autosomal genetic studies is most visible in PC analysis, where locally important components are just ecclipsed by the overall most sampled ones. This also happens in low depth K-means structure, and maybe even in middle depth one.

In other words, if you are studying a region like West Eurasia and there is, say an specifical Saami component that makes up like 80% of their autosomal structure it's very likely that it won't show up in the continental/subcontinental structure at all, except at pretty deep structure. But very few autosomal studies do that. I have only read one of those that reched K=16 and was about Native Americans. Normally they tend to remain at the surface, what obviously only yields very shallow results.

The structure also varies a lot with samples and recently it's been strongly recommended (this month's PLOS Genetics) to expand samples for better results when possible.