Human Genetics

, Volume 138, Issue 10, pp 1123–1142 | Cite as

Runs of homozygosity in sub-Saharan African populations provide insights into complex demographic histories

  • Francisco C. CeballosEmail author
  • Scott Hazelhurst
  • Michèle Ramsay
Original Investigation


The study of runs of homozygosity (ROH) can shed light on population demographic history and cultural practices. We present a fine-scale ROH analysis of 1679 individuals from 28 sub-Saharan African (SSA) populations along with 1384 individuals from 17 worldwide populations. Using high-density SNP coverage, we could accurately identify ROH > 300 kb using PLINK software. The genomic distribution of ROH was analysed through the identification of ROH islands and regions of heterozygosity (RHZ). The analyses showed a heterogeneous distribution of autozygosity across SSA, revealing complex demographic histories. They highlight differences between African groups and can differentiate the impact of consanguineous practices (e.g. among the Somali) from endogamy (e.g. among several Khoe and San groups). Homozygosity cold and hotspots were shown to harbour multiple protein coding genes. Studying ROH therefore not only sheds light on population history, but can also be used to study genetic variation related to adaptation and potentially to the health of extant populations.



FCC is a National Research Foundation of South Africa (NRF) postdoctoral fellow and MR holds a South African Research Chair in Genomics and Bioinformatics of African populations hosted by the University of the Witwatersrand, funded by the Department of Science and Technology and administered by the NRF. SH is partially supported by the NRF (IFR160214158079). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Compliance with ethical standards

Conflict of interest

Authors declare that they have no competing interests.

Web resources

1000 Genomes database, Genome Variation Project dataset,

Supplementary material

439_2019_2045_MOESM1_ESM.pdf (4.1 mb)
Supplementary material 1 (PDF 4181 Kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Sydney Brenner Institute for Molecular Bioscience, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
  2. 2.School of Electrical and Information EngineeringUniversity of the WitwatersrandJohannesburgSouth Africa
  3. 3.Division of Human Genetics, School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa

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