High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation.
Adaptation, Physiological
/ genetics
Antiporters
/ genetics
Black People
/ genetics
Data Management
Ethiopia
/ epidemiology
Female
Genetic Variation
/ genetics
Genetics, Population
Genome, Human
/ genetics
Haplotypes
/ genetics
Humans
Male
Membrane Glycoproteins
/ genetics
Oxidoreductases
/ genetics
Polymorphism, Single Nucleotide
/ genetics
Selection, Genetic
/ genetics
Skin Pigmentation
/ genetics
Sorting Nexins
/ genetics
Tumor Suppressor Proteins
/ genetics
Uganda
/ epidemiology
Nilo-Saharan
population genetic variation
signatures of selection
Journal
American journal of human genetics
ISSN: 1537-6605
Titre abrégé: Am J Hum Genet
Pays: United States
ID NLM: 0370475
Informations de publication
Date de publication:
03 09 2020
03 09 2020
Historique:
received:
03
07
2020
accepted:
13
07
2020
pubmed:
12
8
2020
medline:
21
10
2020
entrez:
12
8
2020
Statut:
ppublish
Résumé
Africa contains more human genetic variation than any other continent, but the majority of the population-scale analyses of the African peoples have focused on just two of the four major linguistic groups, the Niger-Congo and Afro-Asiatic, leaving the Nilo-Saharan and Khoisan populations under-represented. In order to assess genetic variation and signatures of selection within a Nilo-Saharan population and between the Nilo-Saharan and Niger-Congo and Afro-Asiatic, we sequenced 50 genomes from the Nilo-Saharan Lugbara population of North-West Uganda and 250 genomes from 6 previously unsequenced Niger-Congo populations. We compared these data to data from a further 16 Eurasian and African populations including the Gumuz, another putative Nilo-Saharan population from Ethiopia. Of the 21 million variants identified in the Nilo-Saharan population, 3.57 million (17%) were not represented in dbSNP and included predicted non-synonymous mutations with possible phenotypic effects. We found greater genetic differentiation between the Nilo-Saharan Lugbara and Gumuz populations than between any two Afro-Asiatic or Niger-Congo populations. F3 tests showed that Gumuz contributed a genetic component to most Niger-Congo B populations whereas Lugabara did not. We scanned the genomes of the Lugbara for evidence of selective sweeps. We found selective sweeps at four loci (SLC24A5, SNX13, TYRP1, and UVRAG) associated with skin pigmentation, three of which already have been reported to be under selection. These selective sweeps point toward adaptations to the intense UV radiation of the Sahel.
Identifiants
pubmed: 32781046
pii: S0002-9297(20)30237-8
doi: 10.1016/j.ajhg.2020.07.007
pmc: PMC7477016
pii:
doi:
Substances chimiques
Antiporters
0
Membrane Glycoproteins
0
SLC24A5 protein, human
0
SNX13 protein, human
0
Sorting Nexins
0
Tumor Suppressor Proteins
0
UVRAG protein, human
0
Oxidoreductases
EC 1.-
TYRP1 protein, human
EC 1.14.18.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
473-486Subventions
Organisme : Wellcome Trust
Pays : United Kingdom
Investigateurs
Enock Matovu
(E)
Issa Sidibe
(I)
Dieuodonne Mumba
(D)
Mathurin Koffi
(M)
Gustave Simo
(G)
John Chisi
(J)
Vincent P Alibu
(VP)
Annette Macleod
(A)
Bruno Bucheton
(B)
Christianne Hertzfowler
(C)
Alison Elliot
(A)
Mamadou Camara
(M)
Ozlem Bishop
(O)
Julius Mulindwa
(J)
Oscar Nyangiri
(O)
Magambo Phillip Kimuda
(MP)
Elvis Ofon
(E)
Bernadin Ahouty
(B)
Justin Kabore
(J)
Informations de copyright
Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.
Références
Am J Phys Anthropol. 2004 Nov;125(3):292-302
pubmed: 15386260
PLoS Biol. 2003 Oct;1(1):E27
pubmed: 14551921
Nat Rev Genet. 2010 Feb;11(2):149-60
pubmed: 20084087
Nucleic Acids Res. 2016 Jan 4;44(D1):D313-6
pubmed: 26578587
J Allergy Clin Immunol. 2006 Jul;118(1):214-9
pubmed: 16815158
Bioinformatics. 2012 Apr 15;28(8):1176-7
pubmed: 22402612
Nat Commun. 2017 Feb 27;8:14519
pubmed: 28240266
Proc Biol Sci. 2014 Oct 22;281(1793):
pubmed: 25209939
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Am J Phys Anthropol. 1963 Sep;21(3):341-70
pubmed: 14159970
Science. 2009 May 22;324(5930):1035-44
pubmed: 19407144
Am J Hum Genet. 2018 Apr 5;102(4):547-556
pubmed: 29526279
Dermatol Clin. 2014 Apr;32(2):113-21
pubmed: 24679998
Nature. 2015 Jan 15;517(7534):327-32
pubmed: 25470054
Cold Spring Harb Perspect Med. 2013 Jul 01;3(7):
pubmed: 23613366
Nature. 2010 Oct 28;467(7319):1061-73
pubmed: 20981092
Ann Hum Genet. 2001 Jan;65(Pt 1):1-26
pubmed: 11415519
Int J Nanomedicine. 2017 Jul 06;12:4823-4833
pubmed: 28740388
Nat Commun. 2013;4:2739
pubmed: 24253340
Eur J Hum Genet. 2017 Nov;25(11):1282-1285
pubmed: 28875980
Am J Hum Genet. 2015 Jun 4;96(6):986-91
pubmed: 26027499
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Genome Res. 2016 Mar;26(3):279-90
pubmed: 26888263
Elife. 2017 May 24;6:
pubmed: 28537557
Heredity (Edinb). 2015 Nov;115(5):426-36
pubmed: 25990878
BMC Genomics. 2020 Apr 10;21(1):289
pubmed: 32272904
Cell. 2012 Aug 3;150(3):457-69
pubmed: 22840920
Front Immunol. 2020 Jan 24;10:3103
pubmed: 32038633
PLoS Biol. 2007 Jul;5(7):e171
pubmed: 17579516
Am J Hum Genet. 2010 Mar 12;86(3):479-84
pubmed: 20170898
Nature. 2007 Oct 18;449(7164):913-8
pubmed: 17943131
Cell. 2017 Nov 30;171(6):1340-1353.e14
pubmed: 29195075
Clin Chem. 2013 Jan;59(1):225-33
pubmed: 23136245
Nucleic Acids Res. 2020 Jan 8;48(D1):D971-D976
pubmed: 31584086
BMC Bioinformatics. 2013 Oct 02;14:289
pubmed: 24088262
PLoS Biol. 2006 Mar;4(3):e72
pubmed: 16494531
Science. 2014 Jun 20;344(6190):1346-8
pubmed: 24948725
Curr Opin Genet Dev. 2014 Dec;29:120-32
pubmed: 25461616
PLoS Genet. 2017 Aug 24;13(8):e1006976
pubmed: 28837655
Nature. 2002 Oct 24;419(6909):832-7
pubmed: 12397357
Nature. 2016 Oct 13;538(7624):201-206
pubmed: 27654912
Nature. 1950 Aug 12;166(4215):247-9
pubmed: 15439261
Front Pharmacol. 2015 Nov 20;6:276
pubmed: 26635606
Genetics. 2012 Nov;192(3):1065-93
pubmed: 22960212
PLoS Genet. 2015 Aug 20;11(8):e1005397
pubmed: 26291793
Bioinformatics. 2011 Nov 1;27(21):2987-93
pubmed: 21903627
Am J Hum Genet. 2012 Jul 13;91(1):83-96
pubmed: 22726845
Immunology. 2004 May;112(1):136-42
pubmed: 15096192
Front Genet. 2016 Jun 01;7:98
pubmed: 27313599
J Transl Med. 2018 Nov 19;16(1):316
pubmed: 30454063
Sci Rep. 2019 Dec 11;9(1):18811
pubmed: 31827175
Genome Biol. 2019 Apr 26;20(1):82
pubmed: 31023338
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
PLoS Negl Trop Dis. 2017 Jun 1;11(6):e0005438
pubmed: 28570558
Front Oncol. 2019 Aug 27;9:824
pubmed: 31508375
J Immunol. 2006 Jan 15;176(2):1090-7
pubmed: 16393997
Bioinformatics. 2019 Sep 1;35(17):3194-3195
pubmed: 30668635
Nat Genet. 2012 Nov;44(11):1227-30
pubmed: 23042117
Nature. 2015 Oct 1;526(7571):68-74
pubmed: 26432245
Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2584-9
pubmed: 14983052
Nat Genet. 2009 Jun;41(6):657-65
pubmed: 19465909
J Stroke Cerebrovasc Dis. 2020 Jan;29(1):104502
pubmed: 31744764
Autophagy. 2016 Sep;12(9):1677-8
pubmed: 27439570
Am J Hum Genet. 2007 Sep;81(3):559-75
pubmed: 17701901
BMC Med Genomics. 2015 Oct 15;8:66
pubmed: 26470881
Mol Genet Genomic Med. 2020 May;8(5):e1147
pubmed: 32142224
Genome Res. 2009 Sep;19(9):1655-64
pubmed: 19648217
J Biol Chem. 2008 Nov 28;283(48):33211-20
pubmed: 18826954
Front Genet. 2014 Aug 26;5:293
pubmed: 25206364
Autophagy. 2019 Feb;15(2):366-367
pubmed: 30209981
Nat Methods. 2013 Jan;10(1):5-6
pubmed: 23269371
Nat Genet. 2009 Oct;41(10):1110-5
pubmed: 19734900
Genome Res. 2009 May;19(5):850-8
pubmed: 19299565
Hum Genet. 2020 Apr;139(4):513-519
pubmed: 31960134
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Genetics. 1989 Nov;123(3):585-95
pubmed: 2513255