A different view on fine-scale population structure in Western African populations

Kridsadakorn Chaichoompu,Verónica Fernandes,Bruno Cavadas,Luísa Pereira,Bertram Müller-Myhsok,Kristel Van Steen,Fentaw Abegaz

doi:10.1007/s00439-019-02069-7

Abstract

Due to its long genetic evolutionary history, Africans exhibit more genetic variation than any other population in the world. Their genetic diversity further lends itself to subdivisions of Africans into groups of individuals with a genetic similarity of varying degrees of granularity. It remains challenging to detect fine-scale structure in a computationally efficient and meaningful way. In this paper, we present a proof-of-concept of a novel fine-scale population structure detection tool with Western African samples. These samples consist of 1396 individuals from 25 ethnic groups (two groups are African American descendants). The strategy is based on a recently developed tool called IPCAPS. IPCAPS, or Iterative Pruning to CApture Population Structure, is a genetic divisive clustering strategy that enhances iterative pruning PCA, is robust to outliers and does not require a priori computation of haplotypes. Our strategy identified in total 12 groups and 6 groups were revealed as fine-scale structure detected in the samples from Cameroon, Gambia, Mali, Southwest USA, and Barbados. Our finding helped to explain evolutionary processes in the analyzed West African samples and raise awareness for fine-scale structure resolution when conducting genome-wide association and interaction studies.

Highlights

IntroductionAfrican languages have been classified into four main linguistic families (reviewed in Campbell and Tishkoff 2010): Niger-Kordofanian spoken by agriculturalist populations across a broad geographic distribution in Africa; Afroasiatic spoken mainly by northern and eastern African pastoralists; Nilo-Saharan spoken predominantly by central and eastern African pastoralists; and the click-consonant Khoisan language spoken by eastern and southern African hunter-gatherers
We observed that ACB and ASW were spread out, unlike the other populations (Figs. 2, 3). These two groups are African descendants living in the American continent, and, as such, are descendants from enslaved Africans that originated from diverse parts of Western Africa
We have reported fine-scale population structure in the Western African populations using IPCAPS as genetic clustering tool

Summary

Introduction

African languages have been classified into four main linguistic families (reviewed in Campbell and Tishkoff 2010): Niger-Kordofanian spoken by agriculturalist populations across a broad geographic distribution in Africa; Afroasiatic spoken mainly by northern and eastern African pastoralists; Nilo-Saharan spoken predominantly by central and eastern African pastoralists; and the click-consonant Khoisan language spoken by eastern and southern African hunter-gatherers These myriads of environments, climates, diets, lifestyles, and exposure to infectious diseases contribute to strong selective pressures (Campbell and Tishkoff 2008; Teo et al 2010) upon the African populations, whose genome-wide characterization has enormous potential in revealing main aspects of human population history and genetic susceptibility to diseases

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Discussion

Conclusion