Clusters Galore analysis of East Africans

I have included the new data from Pagani et al. (2012) together with various other East African datasets available to me, including various East African Dodecad Project participants.

The first four PCA dimensions can be seen below:

Project participants can find their co-ordinates in the first four dimensions below:

I have also run MCLUST over the first 4 dimensions, which resulted in 12 clusters inferred:

All Project participants fall in the expected clusters, so there is no need to report any individual clustering results.

Assessing East Africans of Pagani et al. (2012) using 'weac2'

Thanks to the publication of new data from Pagani et al. (2012), we now have 235 more individuals from East Africa, mainly Ethiopians, but also Somalis and South Sudanese with dense genotype data.

Naturally, I wanted to make sure that everything was in order, so I applied the 'weac2' calculator on the new data. Here are the normalized median admixture proportions:

I have also created population portraits for the 12 different populations, which appear to show rather homogeneous samples.

Here are the descriptions of the data from the original paper:

The populations sampled (numbers) were the Semitic-speaking Amhara (26) and Tigray (21); the Cushitic-speaking Oromo (21), Ethiopian Somali (17), and Afar (12); the Omotic-speaking Ari Cultivators (24), Ari Blacksmiths (17), and Wolayta (8); and the Nilotic-speaking Gumuz (19) and Anuak (23). In addition to these groups, we also generated South Sudanese data from mixed populations (24) and Somali data from Somali populations (23).

Newer versions of the Dodecad tools will of course take into account the new samples, which ought to  help better define the "East_African" component that often arises at higher levels of detail.

And, of course kudos to all researchers who make their data publicly available and hence provide genome bloggers such as myself with much appreciated "fuel" for their inquiries.

Ancient DNA provides clues to donkey domestication

Proceedings of the Royal Society B doi: 10.1098/rspb.2010.0708

Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication

Birgitta Kimura et al.

Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass.

Link