A unified genealogy of modern and ancient genomes.
Africa
Chromosomes, Human, Pair 20
/ genetics
Computer Simulation
DNA, Ancient
Databases, Nucleic Acid
Datasets as Topic
Evolution, Molecular
Genetic Variation
Genetics, Population
Genome, Human
Genomics
Geography
Haplotypes
Human Migration
Humans
Mutation
Pedigree
Sequence Analysis, DNA
Spatio-Temporal Analysis
Statistics, Nonparametric
Journal
Science (New York, N.Y.)
ISSN: 1095-9203
Titre abrégé: Science
Pays: United States
ID NLM: 0404511
Informations de publication
Date de publication:
25 02 2022
25 02 2022
Historique:
entrez:
24
2
2022
pubmed:
25
2
2022
medline:
12
3
2022
Statut:
ppublish
Résumé
The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.
Identifiants
pubmed: 35201891
doi: 10.1126/science.abi8264
pmc: PMC10027547
mid: NIHMS1876052
doi:
Substances chimiques
DNA, Ancient
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
eabi8264Subventions
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NIGMS NIH HHS
ID : R01 GM100233
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG012287
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Commentaires et corrections
Type : CommentIn
Type : CommentIn
Références
Curr Biol. 2018 Apr 2;28(7):1157-1165.e7
pubmed: 29501328
Curr Biol. 2017 Jun 19;27(12):1801-1810.e10
pubmed: 28552360
Proc Biol Sci. 2019 Jan 30;286(1895):20182288
pubmed: 30963949
Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11917-22
pubmed: 26351665
Nat Commun. 2018 Sep 11;9(1):3547
pubmed: 30206220
Curr Biol. 2017 Nov 6;27(21):3396-3402.e5
pubmed: 29107554
Nat Genet. 2019 Sep;51(9):1321-1329
pubmed: 31477933
Proc Natl Acad Sci U S A. 2018 Mar 27;115(13):3494-3499
pubmed: 29531040
Nature. 2017 Jun 7;546(7657):289-292
pubmed: 28593953
Ann Hum Genet. 2001 Jan;65(Pt 1):43-62
pubmed: 11415522
Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):7485-90
pubmed: 27325755
Nat Commun. 2018 Jan 30;9(1):442
pubmed: 29382937
Science. 2018 Jul 6;361(6397):88-92
pubmed: 29976827
Sci Rep. 2015 Dec 07;5:17875
pubmed: 26639839
Evolution. 2010 Sep;64(9):2701-15
pubmed: 20408876
Science. 2018 May 4;360(6388):548-552
pubmed: 29545507
Trends Genet. 2021 Aug;37(8):717-729
pubmed: 33199048
Nature. 2014 Sep 18;513(7518):409-13
pubmed: 25230663
Nat Commun. 2016 Jun 30;7:12065
pubmed: 27356984
Science. 2019 Nov 8;366(6466):731-734
pubmed: 31601705
Proc Natl Acad Sci U S A. 2019 May 7;116(19):9469-9474
pubmed: 30988179
Sci Rep. 2018 Oct 5;8(1):14879
pubmed: 30291256
Cell. 2020 Feb 20;180(4):677-687.e16
pubmed: 32004458
Am J Hum Genet. 2007 Nov;81(5):1084-97
pubmed: 17924348
Nature. 2017 Aug 10;548(7666):214-218
pubmed: 28783727
Theor Popul Biol. 1999 Oct;56(2):183-201
pubmed: 10544068
Genetics. 1943 Mar;28(2):114-38
pubmed: 17247074
Syst Biol. 2015 Mar;64(2):205-14
pubmed: 25378436
Brief Bioinform. 2013 Mar;14(2):144-61
pubmed: 22908213
Nat Commun. 2019 Aug 20;10(1):3670
pubmed: 31431628
Nature. 2018 Mar 8;555(7695):190-196
pubmed: 29466337
Nature. 2019 Jan;565(7741):640-644
pubmed: 30700871
Science. 2018 Jul 6;361(6397):92-95
pubmed: 29773666
Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):E11248-E11255
pubmed: 30397125
Nature. 2016 Oct 27;538(7626):510-513
pubmed: 27698418
Am J Hum Genet. 2017 Aug 3;101(2):274-282
pubmed: 28757201
Nature. 2010 Feb 11;463(7282):757-62
pubmed: 20148029
Science. 2014 Nov 28;346(6213):1113-8
pubmed: 25378462
Genetics. 1931 Mar;16(2):97-159
pubmed: 17246615
PLoS Biol. 2018 Jan 9;16(1):e2003703
pubmed: 29315301
Nature. 2020 Jun;582(7810):78-83
pubmed: 32494067
Nat Commun. 2017 Feb 21;8:14115
pubmed: 28221340
Nature. 2019 Jun;570(7760):236-240
pubmed: 31168094
Science. 2012 Oct 12;338(6104):222-6
pubmed: 22936568
Nature. 2005 Feb 17;433(7027):733-6
pubmed: 15716951
Nature. 2014 Mar 20;507(7492):354-7
pubmed: 24476815
Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):6774-6779
pubmed: 29895688
Sci Adv. 2020 Jun 12;6(24):eaaz0183
pubmed: 32582847
PLoS Comput Biol. 2021 Jan 6;17(1):e1008561
pubmed: 33406072
Sci Rep. 2019 Dec 20;9(1):19544
pubmed: 31863024
Science. 1991 Sep 27;253(5027):1503-7
pubmed: 1840702
Nat Genet. 2019 Sep;51(9):1306-1307
pubmed: 31477932
Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):E4006-E4012
pubmed: 29632188
Science. 2018 Dec 7;362(6419):
pubmed: 30409807
Sci Adv. 2016 Apr 01;2(4):e1501385
pubmed: 27051878
Cell. 2012 Dec 21;151(7):1431-42
pubmed: 23260136
Wellcome Open Res. 2019 Mar 11;4:50
pubmed: 32175479
Curr Biol. 2013 Apr 8;23(7):553-559
pubmed: 23523248
Nature. 2014 Jan 2;505(7481):43-9
pubmed: 24352235
Nat Commun. 2016 Jan 19;7:10408
pubmed: 26783965
Nature. 2020 Sep;585(7825):357-362
pubmed: 32939066
Curr Biol. 2017 Feb 20;27(4):576-582
pubmed: 28162894
Nature. 2014 Mar 13;507(7491):225-8
pubmed: 24463515
Nature. 2019 Jun;570(7760):182-188
pubmed: 31168093
Curr Biol. 2017 Jul 24;27(14):2185-2193.e6
pubmed: 28712569
Nat Genet. 2020 Jul;52(7):646-654
pubmed: 32601475
Proc Natl Acad Sci U S A. 2020 Jun 30;117(26):15132-15136
pubmed: 32546518
Nat Commun. 2012 Feb 28;3:698
pubmed: 22426219
Nat Commun. 2018 Nov 27;9(1):5018
pubmed: 30479341
Science. 2014 Aug 29;345(6200):1255832
pubmed: 25170159
Nat Methods. 2020 Mar;17(3):261-272
pubmed: 32015543
Science. 2020 Mar 20;367(6484):
pubmed: 32193295
Nature. 2018 May;557(7705):369-374
pubmed: 29743675
Nat Commun. 2019 Feb 4;10(1):590
pubmed: 30713341
Nat Commun. 2017 Mar 03;8:14615
pubmed: 28256537
PLoS Genet. 2009 Oct;5(10):e1000695
pubmed: 19851460
Nat Commun. 2016 Jan 19;7:10326
pubmed: 26783717
Nat Commun. 2014 Oct 21;5:5257
pubmed: 25334030
Ann Hum Biol. 2019 Mar;46(2):145-149
pubmed: 31184205
Hum Biol. 1963 Feb;35:61-89
pubmed: 13968819
PLoS Comput Biol. 2016 May 04;12(5):e1004842
pubmed: 27145223
Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2341-2346
pubmed: 29463742
Genetics. 2020 Jul;215(3):779-797
pubmed: 32357960
Nature. 2016 Oct 13;538(7624):201-206
pubmed: 27654912
Nat Commun. 2017 May 30;8:15694
pubmed: 28556824
Nature. 2016 May 02;534(7606):200-5
pubmed: 27135931
Nature. 2015 Jul 23;523(7561):455-458
pubmed: 26087396
Evolution. 1983 Jan;37(1):203-217
pubmed: 28568026
Cell. 2019 Oct 17;179(3):729-735.e10
pubmed: 31495572
Science. 2019 Jul 5;365(6448):
pubmed: 31147405
Nature. 2014 Oct 23;514(7523):445-9
pubmed: 25341783
Mol Biol Evol. 2021 Aug 23;38(9):3497-3511
pubmed: 34129037
Sci Adv. 2018 Oct 03;4(10):eaat4457
pubmed: 30417088
Genetics. 2003 Dec;165(4):2213-33
pubmed: 14704198
Nat Biotechnol. 2019 Oct;37(10):1155-1162
pubmed: 31406327
Nat Commun. 2018 Aug 20;9(1):3336
pubmed: 30127404
Am J Phys Anthropol. 2017 Dec;164(4):736-749
pubmed: 28913852
Sci Adv. 2018 Nov 08;4(11):eaau4921
pubmed: 30417096
Proc Biol Sci. 2019 Oct 9;286(1912):20191528
pubmed: 31594508
Nat Genet. 2016 Sep;48(9):1066-70
pubmed: 27455350
Am J Hum Genet. 2019 May 2;104(5):977-984
pubmed: 31006515
Genetics. 2012 Nov;192(3):1065-93
pubmed: 22960212
Nature. 2010 Dec 23;468(7327):1053-60
pubmed: 21179161
PLoS Genet. 2017 Jul 27;13(7):e1006852
pubmed: 28749934
Theor Popul Biol. 1983 Apr;23(2):183-201
pubmed: 6612631
Curr Biol. 2016 Jan 25;26(2):270-275
pubmed: 26748850
Science. 2016 Apr 8;352(6282):235-9
pubmed: 26989198
Algorithms Mol Biol. 2019 Apr 02;14:11
pubmed: 30988694
PLoS Genet. 2014 May 15;10(5):e1004342
pubmed: 24831947
Science. 2017 Nov 3;358(6363):652-655
pubmed: 28971970
Nature. 2017 Jan 18;541(7637):302-310
pubmed: 28102248
Science. 2019 Sep 6;365(6457):
pubmed: 31488661
PLoS Biol. 2020 Jan 17;18(1):e3000586
pubmed: 31951611
PLoS Genet. 2012;8(11):e1002967
pubmed: 23166502
Science. 2014 May 16;344(6185):747-50
pubmed: 24762536
Proc Natl Acad Sci U S A. 2019 May 28;116(22):10705-10710
pubmed: 31061125
Mol Biol Evol. 2016 Oct;33(10):2735-43
pubmed: 27343287
Science. 2019 Nov 8;366(6466):708-714
pubmed: 31699931
Am J Hum Genet. 2021 Feb 4;108(2):219-239
pubmed: 33440170
Nature. 2018 Mar 8;555(7695):197-203
pubmed: 29466330
Curr Biol. 2018 Sep 10;28(17):2730-2738.e10
pubmed: 30146150
Sci Adv. 2021 Jul 16;7(29):
pubmed: 34272242
Nature. 2017 Nov 16;551(7680):368-372
pubmed: 29144465
Curr Biol. 2014 Nov 3;24(21):R1035-7
pubmed: 25455029
Nature. 2018 Oct;562(7726):203-209
pubmed: 30305743
Genetics. 2013 May;194(1):199-209
pubmed: 23410836
Nature. 2015 Dec 24;528(7583):499-503
pubmed: 26595274
Sci Rep. 2020 Oct 29;10(1):18542
pubmed: 33122697
Curr Biol. 2019 Jul 22;29(14):2430-2441.e10
pubmed: 31303491
PLoS Genet. 2006 Dec;2(12):e190
pubmed: 17194218
Science. 2017 Nov 3;358(6363):655-658
pubmed: 28982794
Nat Ecol Evol. 2019 May;3(5):765-771
pubmed: 30988490
Science. 2015 Nov 13;350(6262):820-2
pubmed: 26449472
Nature. 2007 Oct 18;449(7164):851-61
pubmed: 17943122
PLoS Genet. 2012 Jan;8(1):e1002453
pubmed: 22291602
Nature. 2018 Sep;561(7721):113-116
pubmed: 30135579
Nature. 2015 Oct 1;526(7571):68-74
pubmed: 26432245
Science. 2018 Jun 1;360(6392):1028-1032
pubmed: 29853688
Cell. 2017 Sep 21;171(1):59-71.e21
pubmed: 28938123
Sci Rep. 2018 Dec 4;8(1):17567
pubmed: 30514893
Science. 2019 Mar 15;363(6432):1230-1234
pubmed: 30872528
Science. 2018 Jun 1;360(6392):1024-1027
pubmed: 29853687
Nature. 2018 Mar 29;555(7698):652-656
pubmed: 29562232
PLoS Genet. 2020 Aug 6;16(8):e1008895
pubmed: 32760067
Proc Natl Acad Sci U S A. 2016 Jun 21;113(25):6886-91
pubmed: 27274049
Nature. 2014 Jan 2;505(7481):87-91
pubmed: 24256729
Philos Trans R Soc Lond B Biol Sci. 2005 Jul 29;360(1459):1387-93
pubmed: 16048782
BMC Bioinformatics. 2014 Nov 25;15:356
pubmed: 25420514
Database (Oxford). 2018 Jan 1;2018:
pubmed: 30576484
Nature. 2014 Feb 13;506(7487):225-9
pubmed: 24522598
Curr Biol. 2017 Oct 23;27(20):3202-3208.e9
pubmed: 29033327
Nat Genet. 2019 Sep;51(9):1330-1338
pubmed: 31477934
Cell. 2019 May 2;177(4):1010-1021.e32
pubmed: 30981557
Proc Natl Acad Sci U S A. 2018 Mar 27;115(13):3428-3433
pubmed: 29531053
Nat Commun. 2012;3:1143
pubmed: 23072811
Nat Commun. 2019 Mar 19;10(1):1218
pubmed: 30890703
Curr Biol. 2016 Oct 10;26(19):2659-2666
pubmed: 27498567
Nat Genet. 2003 Mar;33 Suppl:266-75
pubmed: 12610536
Genetics. 2000 Jun;155(2):945-59
pubmed: 10835412
Proc Natl Acad Sci U S A. 2017 Apr 18;114(16):4093-4098
pubmed: 28377518
Cell. 2018 Nov 15;175(5):1185-1197.e22
pubmed: 30415837
Nature. 2018 Jan 11;553(7687):203-207
pubmed: 29323294
Nat Commun. 2015 Nov 16;6:8912
pubmed: 26567969
Curr Biol. 2019 May 20;29(10):1701-1711.e16
pubmed: 31080083
Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):4325-4333
pubmed: 29686065
Science. 2015 Aug 21;349(6250):aab3884
pubmed: 26198033
Science. 2014 Feb 28;343(6174):1017-21
pubmed: 24476670
Am J Hum Genet. 2011 Oct 7;89(4):516-28
pubmed: 21944045
Science. 2016 Jul 29;353(6298):499-503
pubmed: 27417496
Mol Biol Evol. 2015 Dec;32(12):3132-42
pubmed: 26337550
Nature. 2016 Aug 25;536(7617):419-24
pubmed: 27459054
Nat Ecol Evol. 2018 Apr;2(4):731-740
pubmed: 29487365
Science. 2018 Jun 29;360(6396):
pubmed: 29743352
Nature. 2015 Jun 11;522(7555):167-72
pubmed: 26062507
Nature. 2015 Aug 13;524(7564):216-9
pubmed: 26098372
Nature. 2020 Jan;577(7792):665-670
pubmed: 31969706
Nature. 2021 Feb;590(7845):290-299
pubmed: 33568819
Genetics. 2020 May;215(1):193-214
pubmed: 32209569
BMC Genomics. 2019 Aug 16;20(1):620
pubmed: 31416423
PLoS Comput Biol. 2009 Sep;5(9):e1000520
pubmed: 19779555
Elife. 2020 Jun 23;9:
pubmed: 32573438
Nature. 2015 Sep 3;525(7567):104-8
pubmed: 26196601
Curr Biol. 2019 Aug 5;29(15):2526-2532.e4
pubmed: 31353181
Science. 2017 Nov 3;358(6363):659-662
pubmed: 28982795
Sci Adv. 2019 Jul 03;5(7):eaax0061
pubmed: 31281897
J Hum Genet. 2017 Feb;62(2):213-221
pubmed: 27581845
Nat Ecol Evol. 2019 Jun;3(6):966-976
pubmed: 31036896
Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):368-73
pubmed: 26712024