Evolutionary genomics in Africa

To the Editor

We bring together a series of reviews on human evolutionary genetics reflecting a journey through time by featuring studies on the genomes of ancient and extant humans in, and recently from, Africa. New approaches using genome-wide variation for thousands of individuals are providing the means to re-envision the history of our species, pushing forward the debate on the possible scenarios that have brought us to where we are today. There is a global call for more African data and population geneticists are starting to explore the extensive genomic data generated from disease-related studies in Africa, supported by initiatives such as the H3Africa Consortium.

This special issue of Human Molecular Genetics was planned to coincide with the 14th International Congress of Human Genetics (ICHG), to be hosted in Africa for the first time. It would provide a backdrop to the proceedings providing insights from genetic, anthropological, paleoarchaeological and linguistic data into our current understanding of the origins of modern humans, the peopling of the continent and the recent African diaspora. Plans for the March 2021 Congress were scuppered by the COVID-19 pandemic, and the meeting has been postponed to February 2022 with high hopes for an in-person welcoming back of the international human genetics community to Africa (https://www.ichg2022.com/). We did however decide to stick to course and publish this issue, which will now coincide with the March 2021 pre-ICHG Symposium.

Firstly, two papers review our current understanding of the deep population history of Africa and what we can learn from African genomes about evolutionary processes such as recombination. This is followed by seven reviews that provide insights into the complex migration and admixture events that shaped populations of different regions and countries across Africa, including Egypt, Ethiopia, the north African region, Sudan, Sahelian populations, the Khoe and San of southern Africa, and southern African Bantu-speaker migrations. Information from some of the geographic gaps and omissions can be found in Schlebusch and Jakobsson 2018 (Tales of Human Migration, Admixture, and Selection in Africa. Annu. Rev. Genomics Hum. Genet. 2018;19:405–428) and Choudhury et al. 2020 (High-depth African genomes inform human migration and health. Nature 2020;586(7831):741–748). The latter reporting on genetic variation in whole genome sequences from 426 individuals from 50 ethnolinguistic groups. Furthermore, the more recent history of the African diaspora is reviewed in the context of the transatlantic slave trade and the populations of the Canary Islands and Madagascar. Finally, there are seven papers that review our current understanding of the role of adaptation in shaping the distribution and frequency of genetic variants in extant African populations. They include descriptions of the genetics underlying lactase persistence, skin pigmentation, susceptibility to diabetes, hypertension and kidney disease and adaptation to infectious diseases, such as malaria and tuberculosis.

Our planning for this special issue started well before the shadow of COVID-19 crept across every corner of the world. It did not take long for several papers and preprints to appear, describing genetic variants that may protect from or exacerbate serious consequences of infection by the novel coronavirus, SARS-CoV-2. African genome data have contributed to understanding the potential impact of such gene variants.

The reviews published here reflect our current understanding and bring together many of the recently published advances in evolutionary genomics in Africa. Many more insights and stories are buried in the treasure trove of African genomes and, together with archaeological, paleoanthropological and linguistic studies, will sharpen the focus on the events that shaped the history and adaptation of our species on the continent of our origin.