Einzeltreffer — DigiBib

We conduct high coverage (>30×) whole-genome sequencing of 180 individuals from 12 indigenous African populations. We identify millions of unreported variants, many predicted to be functionally important. We observe that the ancestors of southern African San and central African rainforest hunter-gatherers (RHG) diverged from other populations >200 kya and maintained a large effective population size. We observe evidence for ancient population structure in Africa and for multiple introgression events from "ghost" populations with highly diverged genetic lineages. Although currently geographically isolated, we observe evidence for gene flow between eastern and southern Khoesan-speaking hunter-gatherer populations lasting until ∼12 kya. We identify signatures of local adaptation for traits related to skin color, immune response, height, and metabolic processes. We identify a positively selected variant in the lightly pigmented San that influences pigmentation in vitro by regulating the enhancer activity and gene expression of PDPK1.

Competing Interests: Declaration of interests The authors declare that they have no competing interests.

Titel:	Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation.
Autor/in / Beteiligte Person:	Fan, S ; Spence, JP ; Feng, Y ; Hansen, MEB ; Terhorst, J ; Beltrame, MH ; Ranciaro, A ; Hirbo, J ; Beggs, W ; Thomas, N ; Nyambo, T ; Mpoloka, SW ; Mokone, GG ; Njamnshi, A ; Folkunang, C ; Meskel, DW ; Belay, G ; Song, YS ; Tishkoff, SA
Link:	Zum Volltext
Zeitschrift:	Cell, Jg. 186 (2023-03-02), Heft 5, S. 923
Veröffentlichung:	Cambridge, Ma : Cell Press ; <i>Original Publication</i>: Cambridge, MIT Press., 2023
Medientyp:	academicJournal
ISSN:	1097-4172 (electronic)
DOI:	10.1016/j.cell.2023.01.042
Schlagwort:	Humans Whole Genome Sequencing Population Density Africa 3-Phosphoinositide-Dependent Protein Kinases Acclimatization Skin Pigmentation
Sonstiges:	Nachgewiesen in: MEDLINE Sprachen: English Publication Type: Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural Language: English [Cell] 2023 Mar 02; Vol. 186 (5), pp. 923-939.e14. MeSH Terms: Acclimatization* ; Skin Pigmentation* ; Humans ; Whole Genome Sequencing ; Population Density ; Africa ; 3-Phosphoinositide-Dependent Protein Kinases References: Nucleic Acids Res. 2022 Jul 5;50(W1):W216-W221. (PMID: 35325185) ; Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943) ; Curr Biol. 2022 Apr 25;32(8):1852-1860.e5. (PMID: 35271793) ; Nat Hum Behav. 2021 Apr;5(4):436-446. (PMID: 33398143) ; Genome Biol. 2012 Jan 20;13(1):R1. (PMID: 22264333) ; Nat Genet. 2018 Nov;50(11):1593-1599. (PMID: 30349118) ; Bioinformatics. 2012 Sep 15;28(18):i333-i339. (PMID: 22962449) ; J Comput Graph Stat. 2017;26(1):182-194. (PMID: 28239248) ; Orphanet J Rare Dis. 2007 Nov 02;2:43. (PMID: 17980020) ; J Biol Chem. 2017 Apr 7;292(14):5981-5991. (PMID: 28232488) ; Bioinformatics. 2009 Jul 15;25(14):1754-60. (PMID: 19451168) ; Nat Genet. 2014 Nov;46(11):1173-86. (PMID: 25282103) ; Nature. 2017 Jun 7;546(7657):289-292. (PMID: 28593953) ; Science. 2009 May 22;324(5930):1035-44. (PMID: 19407144) ; Dev Biol. 2007 Dec 15;312(2):572-81. (PMID: 17997399) ; Bioinformatics. 2014 Oct 15;30(20):2843-51. (PMID: 24974202) ; Am J Hum Genet. 2011 Aug 12;89(2):289-94. (PMID: 21782149) ; Sci Adv. 2019 Oct 23;5(10):eaaw9206. (PMID: 31681842) ; Proc Natl Acad Sci U S A. 1996 Nov 12;93(23):13206-11. (PMID: 8917569) ; Nucleic Acids Res. 2001 Jan 1;29(1):308-11. (PMID: 11125122) ; Curr Biol. 2010 Feb 23;20(4):R166-73. (PMID: 20178763) ; Malar J. 2012 Apr 05;11:109. (PMID: 22480186) ; Hum Mol Genet. 2018 Oct 15;27(20):3641-3649. (PMID: 30124842) ; Nat Genet. 2019 Jun;51(6):957-972. (PMID: 31152163) ; Science. 2012 Oct 12;338(6104):222-6. (PMID: 22936568) ; Science. 2012 Oct 19;338(6105):374-9. (PMID: 22997136) ; Genome Res. 2010 Sep;20(9):1297-303. (PMID: 20644199) ; Development. 1999 Dec;126(24):5611-20. (PMID: 10572038) ; Genome Res. 2016 Mar;26(3):279-90. (PMID: 26888263) ; Pigment Cell Melanoma Res. 2010 Aug;23(4):496-513. (PMID: 20444197) ; Mol Biol Evol. 2011 Sep;28(9):2491-500. (PMID: 21436121) ; Nature. 2020 May;581(7809):434-443. (PMID: 32461654) ; Cell. 2012 Aug 3;150(3):457-69. (PMID: 22840920) ; Proc Natl Acad Sci U S A. 2014 Sep 2;111(35):E3596-603. (PMID: 25136101) ; Nat Genet. 2018 Jul;50(7):906-908. (PMID: 29892013) ; Genome Biol Evol. 2013;5(11):2075-81. (PMID: 24162011) ; Elife. 2017 Sep 19;6:. (PMID: 28923166) ; Gigascience. 2015 Feb 25;4:7. (PMID: 25722852) ; Cell. 2019 May 2;177(4):1080. (PMID: 31051100) ; Proc Natl Acad Sci U S A. 2019 Mar 5;116(10):4166-4175. (PMID: 30782801) ; Trends Mol Med. 2006 Sep;12(9):406-14. (PMID: 16899407) ; Nature. 2014 Jan 2;505(7481):43-9. (PMID: 24352235) ; Dis Model Mech. 2016 Nov 1;9(11):1257-1269. (PMID: 27491074) ; Am J Hum Genet. 1963 Sep;15:259-64. (PMID: 13985019) ; Cell. 2017 Nov 30;171(6):1340-1353.e14. (PMID: 29195075) ; Proc Natl Acad Sci U S A. 2010 Jan 19;107(3):1160-5. (PMID: 20080661) ; Mol Biol Evol. 2014 Oct;31(10):2824-7. (PMID: 25015648) ; Mech Dev. 2005 Feb;122(2):131-44. (PMID: 15652702) ; PLoS Biol. 2006 Mar;4(3):e72. (PMID: 16494531) ; N Engl J Med. 2019 Feb 28;380(9):833-841. (PMID: 30763140) ; Curr Opin Genet Dev. 2014 Dec;29:120-32. (PMID: 25461616) ; PLoS Genet. 2019 Jun 10;15(6):e1008204. (PMID: 31181058) ; Nature. 2010 Feb 18;463(7283):943-7. (PMID: 20164927) ; Science. 2016 Oct 7;354(6308):54-59. (PMID: 27846491) ; Nucleic Acids Res. 2010 Sep;38(16):e164. (PMID: 20601685) ; Nature. 2022 Mar;603(7900):290-296. (PMID: 35197631) ; PLoS Genet. 2009 Jul;5(7):e1000564. (PMID: 19609347) ; Nature. 2016 Oct 13;538(7624):201-206. (PMID: 27654912) ; BMC Genet. 2019 Jul 17;20(1):59. (PMID: 31315583) ; Int J Biol Sci. 2012;8(2):272-88. (PMID: 22298955) ; Science. 2017 Nov 17;358(6365):. (PMID: 29025994) ; Science. 2019 Jul 5;365(6448):. (PMID: 31147405) ; Malar J. 2020 Jan 13;19(1):15. (PMID: 31931834) ; J Clin Endocrinol Metab. 2017 Jan 1;102(1):10-14. (PMID: 27778639) ; Bioinformatics. 2014 Sep 1;30(17):2503-5. (PMID: 24812344) ; Sci Adv. 2020 Feb 12;6(7):eaax5097. (PMID: 32095519) ; Nat Genet. 2013 Jun;45(6):580-5. (PMID: 23715323) ; Dev Biol. 2016 Oct 1;418(1):189-203. (PMID: 27546376) ; Mol Biol Evol. 2007 Mar;24(3):757-68. (PMID: 17194802) ; Nature. 2012 Sep 6;489(7414):57-74. (PMID: 22955616) ; Genetics. 2012 Nov;192(3):1065-93. (PMID: 22960212) ; Curr Opin Genet Dev. 2016 Dec;41:159-166. (PMID: 27810637) ; Genome Res. 2011 Jun;21(6):830-9. (PMID: 21460062) ; N Engl J Med. 2016 Aug 18;375(7):655-65. (PMID: 27532831) ; Science. 2017 Nov 3;358(6363):652-655. (PMID: 28971970) ; Curr Biol. 2019 Nov 18;29(22):3953-3959.e4. (PMID: 31679935) ; Science. 2022 Feb 25;375(6583):eabi8264. (PMID: 35201891) ; Science. 2019 Sep 6;365(6457):. (PMID: 31488661) ; J Am Stat Assoc. 2020;115(531):1472-1487. (PMID: 33012903) ; PLoS Genet. 2012;8(11):e1002967. (PMID: 23166502) ; Genome Biol. 2019 Apr 26;20(1):82. (PMID: 31023338) ; Bioinformatics. 2011 Aug 1;27(15):2156-8. (PMID: 21653522) ; Genome Res. 2002 Jun;12(6):996-1006. (PMID: 12045153) ; Nat Genet. 2014 Aug;46(8):919-25. (PMID: 24952747) ; Nat Protoc. 2020 Aug;15(8):2387-2412. (PMID: 32641802) ; Nat Commun. 2017 Dec 12;8(1):2062. (PMID: 29233967) ; Nat Genet. 2017 Feb;49(2):303-309. (PMID: 28024154) ; Nature. 2020 Oct;586(7831):741-748. (PMID: 33116287) ; PLoS Genet. 2006 Dec;2(12):e190. (PMID: 17194218) ; Science. 2015 Nov 13;350(6262):820-2. (PMID: 26449472) ; Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1596-601. (PMID: 18216239) ; Genome Biol. 2019 Apr 26;20(1):77. (PMID: 31023378) ; Nature. 2015 Oct 1;526(7571):68-74. (PMID: 26432245) ; Cell. 2017 Sep 21;171(1):59-71.e21. (PMID: 28938123) ; Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):E11256-E11263. (PMID: 30413626) ; Nat Biotechnol. 2010 May;28(5):495-501. (PMID: 20436461) ; Cell. 2019 Oct 31;179(4):984-1002.e36. (PMID: 31675503) ; Oncogene. 2014 Aug 21;33(34):4330-9. (PMID: 24037523) ; Nature. 2016 Oct 12;538(7624):161-164. (PMID: 27734877) ; Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4109-14. (PMID: 24591619) ; Nature. 2010 Oct 14;467(7317):832-8. (PMID: 20881960) ; Am J Phys Anthropol. 2008 Nov;137(3):316-23. (PMID: 18618658) ; Mol Biol Evol. 2021 Jun 25;38(7):3022-3027. (PMID: 33892491) ; Am J Hum Genet. 2007 Sep;81(3):559-75. (PMID: 17701901) ; Science. 2003 Apr 25;300(5619):597-603. (PMID: 12714734) ; Dev Biol. 2009 Oct 15;334(2):481-90. (PMID: 19699732) ; Nat Commun. 2014 Dec 04;5:5692. (PMID: 25471224) ; Nat Genet. 2006 Aug;38(8):904-9. (PMID: 16862161) ; Genome Res. 2009 Sep;19(9):1655-64. (PMID: 19648217) ; Nat Commun. 2012;3:1143. (PMID: 23072811) ; Nucleic Acids Res. 2022 Jan 7;50(D1):D988-D995. (PMID: 34791404) ; Nat Methods. 2013 Jan;10(1):5-6. (PMID: 23269371) ; BMC Genomics. 2019 Dec 2;20(1):915. (PMID: 31791255) ; Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45. (PMID: 26553804) ; Postgrad Med J. 2005 Dec;81(962):734-40. (PMID: 16344294) ; Circulation. 2021 Feb 23;143(8):e254-e743. (PMID: 33501848) ; Nature. 2020 Jan;577(7792):665-670. (PMID: 31969706) ; Am J Hum Genet. 2010 Apr 9;86(4):632-8. (PMID: 20346438) ; PLoS Genet. 2012;8(4):e1002641. (PMID: 22570615) ; Nature. 2011 Jul 13;475(7357):493-6. (PMID: 21753753) ; Nat Commun. 2019 Jan 21;10(1):358. (PMID: 30664655) ; Bioinformatics. 2007 Jul 15;23(14):1801-6. (PMID: 17485429) ; Mol Biol Evol. 2022 Oct 7;39(10):. (PMID: 36026493) ; Nucleic Acids Res. 2018 Jan 4;46(D1):D1062-D1067. (PMID: 29165669) ; Clin Transl Immunology. 2020 Dec 22;9(12):e1230. (PMID: 33363734) ; Nat Commun. 2019 Nov 28;10(1):5436. (PMID: 31780650) Grant Information: P30 AR069589 United States AR NIAMS NIH HHS; R01 AR076241 United States AR NIAMS NIH HHS; R35 GM134922 United States GM NIGMS NIH HHS; P30 ES013508 United States ES NIEHS NIH HHS; R35 GM134957 United States GM NIGMS NIH HHS Contributed Indexing: Keywords: African demographic history; African genomics; Khoesan; archaic introgression; gene regulation; human evolution; local adaptation; natural selection; population structure; skin color Substance Nomenclature: EC 2.7.11.1 (PDPK1 protein, human) ; EC 2.7.11.1 (3-Phosphoinositide-Dependent Protein Kinases) Entry Date(s): Date Created: 20230303 Date Completed: 20230307 Latest Revision: 20240303 Update Code: 20240303 PubMed Central ID: PMC10568978

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Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation.