Sunday, August 12, 2012

fastIBD analysis of Africans and African Americans

Individuals from the following populations have been included in this analysis:
African_American_D Somali_D Moroccan_D Algerian_D North_African_Jews_D Tunisian_D East_African_Various_D Yoruba_D Sudan_D Egyptian_D Chad_D
These were analyzed in the context of a large set of African populations. CEU European Americans were also added to account for the European admixture present in some African American individuals.
This is the first time I have included African American Dodecad participants in this type of analysis.

A few quick points:
  • fastIBD was run with default parameters over a dataset of 679 individuals/255020 SNPs
  • fastIBD identifies segments of relatively recent origin that are shared by individuals. These results should not be construed as measures of overall genetic similarity or origins. Rather, they suggest which populations have exchanged genes in the relative recent past.
With that said, you can get:
  • Spreadsheet of numeric results, showing median sharing (in centi-Morgans, cM)
  • Population-level graphical results, showing an ordering of other populations based on median IBD sharing.

IBD sharing was assessed only for populations with 5+ individuals.

The following heat map allows for a quick appraisal of populations sharing an excess of IBD sharing (read row-by-row). The grouping of populations by language group and/or region is clearly manifested. There are some interesting details that jump off the screen (but do consult the spreadsheet for details). For example, notice that: 
  • within the Bantu group (Bantu_NE, LWK/Luhya, and Bantu_S), only the South Bantu have an excess of IBD sharing with San.
  • Of the North Africans, Egyptans show an excess of IBD sharing with Tigray
  • Notice that of the Ethiopians/East Africans it is the Omotic speaking Wolayta that seem to especially share IBD with the Ari people who are also Ethiopian Omotic speakers.

Some visualizations (see graphical results above for full set):

Mozabites showing a high degree of within-population IBD sharing, and secondarily with other NW African groups.

The Dodecad Project Somali sample shows high degree of sharing within itself and also with the Pagani et al. Somali and Ethiopian Somali samples, and then with various other East African groups.
Sources of data are listed at the bottom left of this blog.

1 comment:

  1. Interesting to see that both North Aficans and East Africans have low sharing with West africans (Yoruba/Mandenka at 3-4).

    This confirms why it is meaningless to have just one "sub-saharan component" in Admixture/Structure analysis as in this case African diversity that is not present in the panel populations is more likely to be assigned to the more diverse, Sub-Saharan African ancestry which is wrong most of the time for these populations.