PMID- 37837965 OWN - NLM STAT- MEDLINE DCOM- 20231127 LR - 20240207 IS - 1879-0445 (Electronic) IS - 0960-9822 (Print) IS - 0960-9822 (Linking) VI - 33 IP - 22 DP - 2023 Nov 20 TI - Diverse African genomes reveal selection on ancient modern human introgressions in Neanderthals. PG - 4905-4916.e5 LID - S0960-9822(23)01315-5 [pii] LID - 10.1016/j.cub.2023.09.066 [doi] AB - Comparisons of Neanderthal genomes to anatomically modern human (AMH) genomes show a history of Neanderthal-to-AMH introgression stemming from interbreeding after the migration of AMHs from Africa to Eurasia. All non-sub-Saharan African AMHs have genomic regions genetically similar to Neanderthals that descend from this introgression. Regions of the genome with Neanderthal similarities have also been identified in sub-Saharan African populations, but their origins have been unclear. To better understand how these regions are distributed across sub-Saharan Africa, the source of their origin, and what their distribution within the genome tells us about early AMH and Neanderthal evolution, we analyzed a dataset of high-coverage, whole-genome sequences from 180 individuals from 12 diverse sub-Saharan African populations. In sub-Saharan African populations with non-sub-Saharan African ancestry, as much as 1% of their genomes can be attributed to Neanderthal sequence introduced by recent migration, and subsequent admixture, of AMH populations originating from the Levant and North Africa. However, most Neanderthal homologous regions in sub-Saharan African populations originate from migration of AMH populations from Africa to Eurasia approximately 250 kya, and subsequent admixture with Neanderthals, resulting in approximately 6% AMH ancestry in Neanderthals. These results indicate that there have been multiple migration events of AMHs out of Africa and that Neanderthal and AMH gene flow has been bi-directional. Observing that genomic regions where AMHs show a depletion of Neanderthal introgression are also regions where Neanderthal genomes show a depletion of AMH introgression points to deleterious interactions between introgressed variants and background genomes in both groups-a hallmark of incipient speciation. CI - Copyright (c) 2023 Elsevier Inc. All rights reserved. FAU - Harris, Daniel N AU - Harris DN AD - Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA. FAU - Platt, Alexander AU - Platt A AD - Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA. FAU - Hansen, Matthew E B AU - Hansen MEB AD - Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA. FAU - Fan, Shaohua AU - Fan S AD - State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai 200438, China. FAU - McQuillan, Michael A AU - McQuillan MA AD - Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA. FAU - Nyambo, Thomas AU - Nyambo T AD - Department of Biochemistry and Molecular Biology, Hubert Kairuki Memorial University, Dar es Salaam, Tanzania. FAU - Mpoloka, Sununguko Wata AU - Mpoloka SW AD - Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag UB 0022, Gaborone, Botswana. FAU - Mokone, Gaonyadiwe George AU - Mokone GG AD - Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Private Bag UB 0022, Gaborone, Botswana. FAU - Belay, Gurja AU - Belay G AD - Department of Microbial Cellular and Molecular Biology, Addis Ababa University, P.O. Box 1176, Addis Ababa, Ethiopia. FAU - Fokunang, Charles AU - Fokunang C AD - Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaounde I, P.O. Box 337, Yaounde, Cameroon. FAU - Njamnshi, Alfred K AU - Njamnshi AK AD - Brain Research Africa Initiative (BRAIN), P.O. Box 25625, Yaounde, Cameroon; Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The University of Yaounde I, Yaounde, Cameroon. FAU - Tishkoff, Sarah A AU - Tishkoff SA AD - Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: tishkoff@pennmedicine.upenn.edu. LA - eng GR - R01 AR076241/AR/NIAMS NIH HHS/United States GR - R35 GM134957/GM/NIGMS NIH HHS/United States GR - T32 DK007314/DK/NIDDK NIH HHS/United States PT - Journal Article DEP - 20231013 PL - England TA - Curr Biol JT - Current biology : CB JID - 9107782 SB - IM CIN - Curr Biol. 2023 Nov 20;33(22):R1197-R1200. PMID: 37989099 MH - Humans MH - Animals MH - *Neanderthals/genetics MH - Genome, Human MH - Gene Flow MH - Genomics MH - Africa South of the Sahara PMC - PMC10841429 MID - NIHMS1936283 OTO - NOTNLM OT - African genomics OT - Neanderthal OT - admixture OT - archaic introgression OT - human evolution OT - natural selection COIS- Declaration of interests The authors declare no competing interests. EDAT- 2023/10/15 05:46 MHDA- 2023/11/27 12:42 PMCR- 2024/11/20 CRDT- 2023/10/14 18:41 PHST- 2023/03/15 00:00 [received] PHST- 2023/07/18 00:00 [revised] PHST- 2023/09/26 00:00 [accepted] PHST- 2024/11/20 00:00 [pmc-release] PHST- 2023/11/27 12:42 [medline] PHST- 2023/10/15 05:46 [pubmed] PHST- 2023/10/14 18:41 [entrez] AID - S0960-9822(23)01315-5 [pii] AID - 10.1016/j.cub.2023.09.066 [doi] PST - ppublish SO - Curr Biol. 2023 Nov 20;33(22):4905-4916.e5. doi: 10.1016/j.cub.2023.09.066. Epub 2023 Oct 13.