Identifying signatures of positive selection in human populations from North Africa.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
20 05 2023
20 05 2023
Historique:
received:
15
11
2022
accepted:
16
05
2023
medline:
22
5
2023
pubmed:
21
5
2023
entrez:
20
5
2023
Statut:
epublish
Résumé
Because of its location, North Africa (NA) has witnessed continuous demographic movements with an impact on the genomes of present-day human populations. Genomic data describe a complex scenario with varying proportions of at least four main ancestry components: Maghrebi, Middle Eastern-, European-, and West-and-East-African-like. However, the footprint of positive selection in NA has not been studied. Here, we compile genome-wide genotyping data from 190 North Africans and individuals from surrounding populations, investigate for signatures of positive selection using allele frequencies and linkage disequilibrium-based methods and infer ancestry proportions to discern adaptive admixture from post-admixture selection events. Our results show private candidate genes for selection in NA involved in insulin processing (KIF5A), immune function (KIF5A, IL1RN, TLR3), and haemoglobin phenotypes (BCL11A). We also detect signatures of positive selection related to skin pigmentation (SLC24A5, KITLG), and immunity function (IL1R1, CD44, JAK1) shared with European populations and candidate genes associated with haemoglobin phenotypes (HPSE2, HBE1, HBG2), other immune-related (DOCK2) traits, and insulin processing (GLIS3) traits shared with West and East African populations. Finally, the SLC8A1 gene, which codifies for a sodium-calcium exchanger, was the only candidate identified under post-admixture selection in Western NA.
Identifiants
pubmed: 37210386
doi: 10.1038/s41598-023-35312-3
pii: 10.1038/s41598-023-35312-3
pmc: PMC10199912
doi:
Substances chimiques
Insulins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
8166Informations de copyright
© 2023. The Author(s).
Références
Hum Immunol. 1994 Aug;40(4):267-78
pubmed: 7528188
Nature. 2007 Oct 18;449(7164):913-8
pubmed: 17943131
Nat Rev Genet. 2014 Jun;15(6):379-93
pubmed: 24776769
Am J Hum Genet. 2013 Aug 8;93(2):278-88
pubmed: 23910464
Science. 2005 Dec 16;310(5755):1782-6
pubmed: 16357253
Nature. 2017 Jun 7;546(7657):293-296
pubmed: 28593967
Am J Hum Genet. 2004 May;74(5):898-916
pubmed: 15077204
Nat Genet. 2019 Sep;51(9):1321-1329
pubmed: 31477933
Lancet. 2021 Sep 11;398(10304):957-980
pubmed: 34450083
Nature. 2017 Jun 7;546(7657):289-292
pubmed: 28593953
PLoS Genet. 2005 Dec;1(6):e82
pubmed: 16429165
Nature. 2012 Sep 20;489(7416):443-6
pubmed: 22895189
Science. 2018 May 4;360(6388):548-552
pubmed: 29545507
Ann Hum Genet. 2007 May;71(Pt 3):354-69
pubmed: 17233754
Hum Genet. 2023 Feb;142(2):305-320
pubmed: 36441222
Science. 2010 Jul 2;329(5987):75-8
pubmed: 20595611
Am J Hum Genet. 2001 Apr;68(4):1019-29
pubmed: 11254456
PLoS Genet. 2018 Jan 30;14(1):e1007172
pubmed: 29381699
Pharmacol Ther. 2020 Nov;215:107632
pubmed: 32693112
J Med Virol. 2022 Feb;94(2):752-760
pubmed: 34741549
Mol Ecol. 2015 Jul;24(14):3529-45
pubmed: 25943689
Proc Natl Acad Sci U S A. 2010 May 11;107 Suppl 2:8962-8
pubmed: 20445093
Hypertens Res. 2017 Oct 5;40(10):876-884
pubmed: 28446801
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61
pubmed: 14681407
Mol Diagn Ther. 2019 Apr;23(2):235-244
pubmed: 30478714
Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1620-5
pubmed: 18245381
J Infect Dis. 2015 Oct 1;212 Suppl 2:S329-35
pubmed: 26209680
Genomics. 1992 Mar;12(3):616-7
pubmed: 1559714
Evol Anthropol. 2017 May;26(3):119-135
pubmed: 28627786
PLoS One. 2010 Oct 21;5(10):e13378
pubmed: 20975840
PLoS Genet. 2012 Jan;8(1):e1002397
pubmed: 22253600
Ann Hum Biol. 2018 Feb;45(1):98-104
pubmed: 29382280
Genome Res. 2009 May;19(5):826-37
pubmed: 19307593
Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):6774-6779
pubmed: 29895688
Genome Biol. 2016 Jun 06;17(1):122
pubmed: 27268795
Nucleic Acids Res. 2015 Jan;43(Database issue):D789-98
pubmed: 25428349
N Engl J Med. 2021 Jan 21;384(3):252-260
pubmed: 33283989
Genes Immun. 2011 Oct;12(7):582-8
pubmed: 21593778
EMBO J. 2008 Jan 9;27(1):1-5
pubmed: 18046453
Nat Med. 2004 Nov;10(11):1193-9
pubmed: 15475962
Gigascience. 2015 Feb 25;4:7
pubmed: 25722852
BMC Evol Biol. 2010 May 10;10:138
pubmed: 20459715
Genes Nutr. 2017 Aug 24;12:20
pubmed: 28855970
Eur J Hum Genet. 2020 Apr;28(4):435-444
pubmed: 31784700
iScience. 2021 Sep 16;24(9):102988
pubmed: 34622180
Mol Biol Evol. 2014 Oct;31(10):2824-7
pubmed: 25015648
Cell. 2019 Mar 21;177(1):184-199
pubmed: 30901539
Microbiol Immunol. 2004;48(3):147-54
pubmed: 15031527
PLoS Biol. 2006 Mar;4(3):e72
pubmed: 16494531
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
Am J Hum Genet. 2017 Apr 6;100(4):635-649
pubmed: 28366442
Mol Biol Evol. 2022 Jan 7;39(1):
pubmed: 34626111
Am J Hum Genet. 2012 Jul 13;91(1):180-4
pubmed: 22726844
Am J Hum Genet. 2022 Apr 7;109(4):710-726
pubmed: 35259336
Nat Genet. 2007 Dec;39(12):1443-52
pubmed: 17952075
Nucleic Acids Res. 2017 Jan 4;45(D1):D353-D361
pubmed: 27899662
Trends Genet. 2020 Jun;36(6):415-428
pubmed: 32396835
Nucleic Acids Res. 2016 Jan 4;44(D1):D481-7
pubmed: 26656494
Am J Hum Genet. 2004 Dec;75(6):1059-69
pubmed: 15492926
Nat Genet. 2007 Jan;39(1):31-40
pubmed: 17159977
PLoS Genet. 2010 Sep 09;6(9):e1001116
pubmed: 20838600
J Hum Evol. 2013 Sep;65(3):266-81
pubmed: 23891007
J Invest Dermatol. 2015 Jul;135(7):1735-1742
pubmed: 25705849
Hum Mol Genet. 2021 Apr 26;30(R1):R17-R23
pubmed: 33284971
Am J Hum Genet. 2016 Jan 7;98(1):5-21
pubmed: 26748513
Curr Biol. 2019 Nov 18;29(22):3953-3959.e4
pubmed: 31679935
Nutrients. 2018 Nov 03;10(11):
pubmed: 30400332
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
Eur J Hum Genet. 2012 Nov;20(11):1155-61
pubmed: 22535185
PLoS One. 2018 Oct 3;13(10):e0202021
pubmed: 30281602
Endocrinology. 1997 May;138(5):1979-87
pubmed: 9112396
Sci Rep. 2022 May 25;12(1):8841
pubmed: 35614148
Annu Rev Med. 2015;66:311-28
pubmed: 25587654
PLoS Genet. 2006 Dec;2(12):e190
pubmed: 17194218
Cell. 2021 Sep 2;184(18):4612-4625.e14
pubmed: 34352227
Bioinformatics. 2016 Sep 15;32(18):2817-23
pubmed: 27283948
Mol Biol Evol. 2017 Feb 1;34(2):318-329
pubmed: 27744413
Nature. 2015 Oct 1;526(7571):68-74
pubmed: 26432245
Am J Hum Genet. 2014 Oct 2;95(4):437-44
pubmed: 25242497
PLoS Genet. 2011 Nov;7(11):e1002355
pubmed: 22072984
BMC Evol Biol. 2012 Dec 03;12:234
pubmed: 23206491
PLoS Genet. 2019 Sep 13;15(9):e1008384
pubmed: 31518343
Curr Biol. 2005 Jun 7;15(11):1022-7
pubmed: 15936272
Sci Rep. 2021 Oct 26;11(1):21125
pubmed: 34702931
Cell Biol Int. 2022 Jul;46(7):1109-1127
pubmed: 35521908
Hum Mol Genet. 2021 Apr 26;30(R1):R88-R97
pubmed: 33438000
Int J Evol Biol. 2013;2013:204240
pubmed: 23533945
Libyan J Med. 2016 Jun 22;11:31576
pubmed: 27340011
J Immunol. 2012 Jan 15;188(2):818-23
pubmed: 22174453
Nat Genet. 2014 Jul;46(7):748-52
pubmed: 24880339
Genome Res. 2009 Sep;19(9):1655-64
pubmed: 19648217
Evolution. 1984 Nov;38(6):1358-1370
pubmed: 28563791
Blood Cells Mol Dis. 2008 Nov-Dec;41(3):255-258
pubmed: 18691915
Hum Biol. 1997 Jun;69(3):295-311
pubmed: 9164042
Am J Hum Genet. 2005 Aug;77(2):171-92
pubmed: 16001361
J Infect Dis. 2017 May 1;215(9):1430-1434
pubmed: 28368532
Immunogenetics. 2018 Jan;70(1):5-27
pubmed: 28687858
Bioinformatics. 2014 Apr 1;30(7):1006-7
pubmed: 24351709
J Biol Chem. 2011 Jul 15;286(28):25341-51
pubmed: 21613211
Nucleic Acids Res. 2014 Jan;42(Database issue):D1001-6
pubmed: 24316577
J Bioinform Comput Biol. 2021 Dec;19(6):2140006
pubmed: 34753405
Science. 2016 Nov 11;354(6313):760-764
pubmed: 27738015
Am J Hypertens. 2018 Mar 10;31(4):415-421
pubmed: 29182730
Nat Commun. 2019 Nov 28;10(1):5436
pubmed: 31780650