title: Adaptation to infectious disease exposure in indigenous Southern African populations.
abstract: Genetic analyses can provide information about human evolutionary history that cannot always be gleaned from other sources. We evaluated evidence of selective pressure due to introduced infectious diseases in the genomes of two indigenous southern African San groups-the ‡Khomani who had abundant contact with other people migrating into the region and the more isolated Ju|'hoansi. We used a dual approach to test for increased selection on immune genes compared with the rest of the genome in these groups. First, we calculated summary values of statistics that measure genomic signatures of adaptation to contrast selection signatures in immune genes and all genes. Second, we located regions of the genome with extreme values of three selection statistics and examined these regions for enrichment of immune genes. We found stronger and more abundant signals of selection in immune genes in the ‡Khomani than in the Ju|'hoansi. We confirm this finding within each population to avoid effects of different demographic histories of the two populations. We identified eight immune genes that have potentially been targets of strong selection in the ‡Khomani, whereas in the Ju|'hoansi, no immune genes were found in the genomic regions with the strongest signals of selection. We suggest that the more abundant signatures of selection at immune genes in the ‡Khomani could be explained by their more frequent contact with immigrant groups, which likely led to increased exposure and adaptation to introduced infectious diseases.
authors.affiliation: Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden.|Department of Epidemiology of Microbial Diseases, Yale University School of Public Health, New Haven, CT, USA.
authors.forename: Katharine A
authors.identifier: http://orcid.org/0000-0002-5323-5079
authors.initials: KA
authors.lastname: Owers
authors.affiliation: Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden.
authors.forename: Per
authors.initials: P
authors.lastname: Sjödin
authors.affiliation: Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden.
authors.forename: Carina M
authors.identifier: http://orcid.org/0000-0002-8160-9621
authors.initials: CM
authors.lastname: Schlebusch
authors.affiliation: Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden.
authors.forename: Pontus
authors.identifier: http://orcid.org/0000-0002-3021-5913
authors.initials: P
authors.lastname: Skoglund
authors.affiliation: Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa.
authors.forename: Himla
authors.initials: H
authors.lastname: Soodyall
authors.affiliation: Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden mattias.jakobsson@ebc.uu.se.|Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Mattias
authors.identifier: http://orcid.org/0000-0001-7840-7853
authors.initials: M
authors.lastname: Jakobsson
mesh_terms: D000222:Adaptation, Physiological; D044383:Black People; D003141:Communicable Diseases; D004781:Environmental Exposure; D005006:Ethnicity; D005828:Genetics, Population; D023281:Genomics; D006801:Humans; D007109:Immunity / Q000235:genetics*; D012641:Selection, Genetic; D013019:South Africa
keywords: adaptation; human migrations; immune genes; introduced diseases; population genetics