Since the first human reference genome was obtained in 2003 by the Human Genome Project and Celera Corporation -sequencing only a few individuals- a lot of progress has been made. The price of sequencing a whole genome has dropped enormously, and the genomic studies now include hundreds or even thousands of individuals, allowing rare disease research, the development of precision medicine and population genomics studies. Nevertheless, most of this vast amount of genomic data has been coming from Europe and North America with African genomic data accounting for less than 3%.

A large study published this week in the scientific journal Nature is finally paving the way for more broadly representative and relevant studies, containing African genomic data. Researchers from the Human Heredity and Health in Africa (H3Africa) Consortium have made a global large-scale effort to sequence the genomes from regions and countries across Africa. The analysis of 426 individual African genomes, comprising 50 ethnolinguistic groups, provides insights into ancient migrations along the routes of Bantu-speaking populations. The study has counted with the participation of CRAG’s population geneticist Laura R. Botigué, who has brought her expertise to the study of novel and rare genetic variants in this African dataset.

“We found an impressive breadth of genomic diversity among these genomes, and each ethnolinguistic group had unique genetic variants,” explained Neil Hanchard, MD, PhD, Assistant Professor at the Baylor College of Medicine (Houston, Texas, USA). “There was a great deal of variation among people in the same region of Africa, and even among those from the same country. This reflects the deep history and rich genomic diversity across Africa, from which we can learn much about population history, environmental adaptation, and susceptibility to diseases.”, he adds.

“We were able to discover more than 3 million novel variants with just about 300 genomes that we analysed at high depth. This was after an exhaustive comparison that included African genomes in public repositories, suggesting that there are still common genetics variants in African populations that haven’t been discovered”, says Dr. Laura R. Botigué.

This is why, the authors of the study emphasize the necessity for a broader characterization of African genomic diversity — including more individuals and from additional populations — for a more comprehensive understanding of human ancestry and to improve health research.

Other findings of the study were the identification of evidence of natural selection in genes involved in viral immunity, DNA repair and metabolism and the observation of complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that populations from Zambia were likely intermediate settlers along the routes of expansion of Bantu-speaking populations.

Understanding the human history through the domesticated species

Like the African human genomes carry the marks of human history, so they do the genomes of the plants and animals that humans have domesticated. This is precisely what Laura R. Botigué studies at CRAG, with the Genomics of ancient crops and domestication research group she leads. Botigué uses her expertise in bioinformatics and population genetics to study plant domestication and dispersal, sequencing and analysing ancient and modern specimens of cereals (emmer wheat) and legumes (chickpea). 

“These studies have a double interest, from one hand, they are useful to find traits that have been lost in the current cultivated species, and that might be interesting to recover, especially now with the threat of climate change and the need for a more sustainable agriculture and, from the other hand, inform on the history of plant domestication and the development of agriculture, which in turn sheds light into the first agricultural human populations”, explains Laura R. Botigué. 

“We, population geneticists, study demographic events and usually major demographic events are related to the spread of agriculture”, she adds.

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Reference article: Ananyo Choudhury, Shaun Aron, Laura R. Botigué, Dhriti Sengupta, Gerrit Botha, Taoufik Bensellak, Gordon Wells, Judit Kumuthini, Daniel Shriner, Yasmina J. Fakim, Anisah W. Ghoorah, Eileen Dareng, Trust Odia, Oluwadamilare Falola, Ezekiel Adebiyi, Scott Hazelhurst, Gaston Mazandu, Oscar A. Nyangiri, Mamana Mbiyavanga, Alia Benkahla, Samar K. Kassim, Nicola Mulder, Sally N. Adebamowo, Emile R. Chimusa, Donna Muzny, Ginger Metcalf, Richard A. Gibbs, TrypanoGEN Research Group, Charles Rotimi, Michèle Ramsay, H3Africa Consortium, Adebowale A. Adeyemo, Zané Lombard & Neil A. Hanchard. High-depth African genomes inform human migration and health. Nature, October 2020. DOI: 10.1038/s41586-020-2859-7

About the funding of the study:  the H3Africa Consortium is funded by the National Institutes of Health from the USA, the African Academy of Sciences, and the Wellcome Trust. Laura R. Botigué research done at CRAG was supported by the CERCA Programme/Generalitat de Catalunya and by the Spanish Ministry of Economy and Competitiveness, through the ‘Severo Ochoa Programme for Centres of Excellence in R&D’ 2016–2019 (SEV-2015-0533).