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Cited by 200Pleistocene-Era Hominins and ArchaeologyForensic and Genetic ResearchGenetic diversity and population structure

Signatures of Archaic Adaptive Introgression in Present-Day Human Populations

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Racimo, Fernando, Marnetto, Davide, Huerta-Sánchez, Emilia·2016·Molecular Biology and Evolution
DOI 10.1093/molbev/msw216PMC PMC5400396

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Abstract

Comparisons of DNA from archaic and modern humans show that these groups interbred, and in some cases received an evolutionary advantage from doing so. This process-adaptive introgression-may lead to a faster rate of adaptation than is predicted from models with mutation and selection alone. Within the last couple of years, a series of studies have identified regions of the genome that are likely examples of adaptive introgression. In many cases, once a region was ascertained as being introgressed, commonly used statistics based on both haplotype as well as allele frequency information were employed to test for positive selection. Introgression by itself, however, changes both the haplotype structure and the distribution of allele frequencies, thus confounding traditional tests for detecting positive selection. Therefore, patterns generated by introgression alone may lead to false inferences of positive selection. Here we explore models involving both introgression and positive selection to investigate the behavior of various statistics under adaptive introgression. In particular, we find that the number and allelic frequencies of sites that are uniquely shared between archaic humans and specific present-day populations are particularly useful for detecting adaptive introgression. We then examine the 1000 Genomes dataset to characterize the landscape of uniquely shared archaic alleles in human populations. Finally, we identify regions that were likely subject to adaptive introgression and discuss some of the most promising candidate genes located in these regions.

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  1. Akira S Uematsu S Takeuchi O. 2006 Pathogen recognition and innate immunity. Cell 124: 783– 801. 16497588
  2. Aslanidis C Ries S Fehringer P Büchler C Klima H Schmitz G. 1996 Genetic and biochemical evidence that CESD and wolman disease are distinguished by residual lysosomal acid lipase activity. Genomics 33: 85– 93. 8617513
  3. Barreiro LB Ben-Ali M Quach H Laval G Patin E Pickrell JK Bouchier C Tichit M Neyrolles O Gicquel B, 2009 Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense. PLoS Genet. 5: e1000562. 19609346 PMC2702086
  4. Beall CM Cavalleri GL Deng L Elston RC Gao Y Knight J Li C Li JC Liang Y McCormack M, 2010 Natural selection on EPAS1 (hif2α) associated with low hemoglobin concentration in Tibetan highlanders. Proc Natl Acad Sci U S A. 107: 11459– 11464. 20534544 PMC2895075
  5. Berisa T Pickrell JK. 2016 Approximately independent linkage disequilibrium blocks in human populations. Bioinformatics 32: 283– 285. 26395773 PMC4731402
  6. Bigham A Bauchet M Pinto D Mao X Akey JM Mei R Scherer SW Julian CG Wilson MJ Herráez DL, 2010 Identifying signatures of natural selection in Tibetan and Andean populations using dense genome scan data. PLoS Genet. 6: e1001116., 20838600 PMC2936536
  7. Cabral A Fischer DF Vermeij WP Backendorf C. 2003 Distinct functional interactions of human Skn-1 isoforms with Ese-1 during keratinocyte terminal differentiation. J Biol Chem. 278: 17792– 17799. 12624109
  8. Candille S Van Raamsdonk CD Chen C Kuijper S Chen-Tsai Y Russ A Meijlink F Barsh GS. 2004 Dorsoventral patterning of the mouse coat by Tbx15. PLoS Biol. 2: E3. 14737183 PMC314463
  9. Carvill GL Heavin SB Yendle SC McMahon JM O’Roak BJ Cook J Khan A Dorschner MO Weaver M Calvert S, 2013 Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1. Nat Genet. 45: 825– 830. 23708187 PMC3704157
  10. Casey JP McGettigan P Lynam-Lennon N McDermott M Regan R Conroy J Bourke B O’Sullivan J Crushell E Lynch S, 2012 Identification of a mutation in LARS as a novel cause of infantile hepatopathy. Mol Genet Metab. 106: 351– 358. 22607940
  11. Curry G. 1959 Genetical and developmental studies on droopy-eared mice. J Embryol Exp Morphol. 7: 39– 65. 13654621
  12. Deschamps M Laval G Fagny M Itan Y Abel L Casanova JL Patin E Quintana-Murci L. 2016 Genomic signatures of selective pressures and introgression from archaic hominins at human innate immunity genes. Am J Hum Genet. 98: 5– 21. 26748513 PMC4716683
  13. Ding Q Hu Y Xu S Wang J Jin L. 2013 Neanderthal introgression at chromosome 3p21. 31 was under positive natural selection in East Asians. Mol Biol Evol. 31: 683– 695. 24336922
  14. Dong XY Sun X Guo P Li Q Sasahara M Ishii Y Dong JT. 2010 ATBF1 inhibits estrogen receptor (ER) function by selectively competing with AIB1 for binding to the ER in ER-positive breast cancer cells. J Biol Chem. 285: 32801– 32809. 20720010 PMC2963406
  15. Durand EY Patterson N Reich D Slatkin M. 2011 Testing for ancient admixture between closely related populations. Mol Biol Evol. 28: 2239– 2252. 21325092 PMC3144383
  16. Fedetz M Matesanz F Caro-Maldonado A Fernandez O Tamayo J Guerrero M Delgado C López-Guerrero J Alcina A. 2006 OAS1 gene haplotype confers susceptibility to multiple sclerosis. Tissue Antigens 68: 446– 449. 17092260
  17. Fumagalli M Cagliani R Riva S Pozzoli U Biasin M Piacentini L Comi GP Bresolin N Clerici M Sironi M. 2010 Population genetics of IFIH1: ancient population structure, local selection, and implications for susceptibility to type 1 diabetes. Mol Biol Evol. 27: 2555– 2566. 20538742
  18. Fumagalli M Moltke I Grarup N Racimo F Bjerregaard P Jørgensen ME Korneliussen TS Gerbault P Skotte L Linneberg A, 2015 Greenlandic Inuit show genetic signatures of diet and climate adaptation. Science 349: 1343– 1347. 26383953
  19. Gburcik V Cawthorn WP Nedergaard J Timmons JA Cannon B. 2012 An essential role for Tbx15 in the differentiation of brown and “brite” but not white adipocytes. Am J Physiol Endocrinol Metab. 303: E1053– E1060. 22912368
  20. Giles RE Shimizu N Ruddle FH. 1980 Assignment of a human genetic locus to chromosome 5 which corrects the heat sensitive lesion associated with reduced leucyl-tRNA synthetase activity in ts025Cl Chinese hamster cells. Somatic Cell Genet. 6: 667– 687. 6933703
  21. Gravel S. 2012 Population genetics models of local ancestry. Genetics 191: 607– 619. 22491189 PMC3374321
  22. Green RE Krause J Briggs AW Maricic T Stenzel U Kircher M Patterson N Li H Zhai W Fritz MHY, 2010 A draft sequence of the Neandertal genome. Science 328: 710– 722. 20448178 PMC5100745
  23. Hackinger S Kraaijenbrink T Xue Y Mezzavilla M van Driem G Jobling MA de Knijff P Tyler-Smith C Ayub Q, 2016 Wide distribution and altitude correlation of an archaic high-altitude-adaptive EPAS1 haplotype in the Himalayas. Hum Genet. 135: 393– 402. 26883865 PMC4796332
  24. Hamano E Hijikata M Itoyama S Quy T Phi NC Long HT Van Ban V Matsushita I Yanai H Kirikae F, 2005 Polymorphisms of interferon-inducible genes oas-1 and MxA associated with SARS in the Vietnamese population. Biochem Biophys Res Commun. 329: 1234– 1239. 15766558 PMC7092916
  25. Hašová M Crhák T Šafránková B Dvořáková J Muthn` T Velebn` V Kubala L. 2011 Hyaluronan minimizes effects of UV irradiation on human keratinocytes. Arch Dermatol Res. 303: 277– 284. 21448660
  26. Hedrick PW. 2013 Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation. Mol Ecol. 22: 4606– 4618. 23906376
  27. Heid IM Jackson AU Randall JC Winkler TW Qi L Steinthorsdottir V Thorleifsson G Zillikens MC Speliotes EK Mägi R, 2010 Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Nat Genet. 42: 949– 960. 20935629 PMC3000924
  28. Hill W Robertson A. 1968 Linkage disequilibrium in finite populations. Theor Appl Genet. 38: 226– 231. 24442307
  29. Huerta-Sanchez E Casey FP. 2015 Archaic inheritance: supporting high altitude life in Tibet. J Appl Physiol. 119: 1129– 1134. 26294746
  30. Huerta-Sánchez E Jin X Bianba Z Peter BM Vinckenbosch N Liang Y Yi X He M Somel M Ni P, 2014 Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 512: 194– 197. 25043035 PMC4134395
  31. Jeong C Alkorta-Aranburu G Basnyat B Neupane M Witonsky DB Pritchard JK Beall CM Di Rienzo A. 2014 Admixture facilitates genetic adaptations to high altitude in Tibet. Nat Commun. 5: 3281. 24513612 PMC4643256
  32. Kamalati T Jolin HE Mitchell PJ Barker KT Jackson LE Dean CJ Page MJ Gusterson BA Crompton MR. 1996 Brk, a breast tumor-derived non-receptor protein-tyrosine kinase, sensitizes mammary epithelial cells to epidermal growth factor. J Biol Chem. 271: 30956– 30963. 8940083
  33. Kato T Sato H Emi M Seino T Arawaka S Iseki C Takahashi Y Wada M Kawanami T. 2011 Segmental copy number loss of SFMBT1 gene in elderly individuals with ventriculomegaly: a community-based study. Intern Med. 50: 297– 303. 21325761
  34. Khrameeva EE Bozek K He L Yan Z Jiang X Wei Y Tang K Gelfand MS Prufer K Kelso J, 2014 Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. Nat Commun. 5: 3584. 24690587 PMC3988804
  35. Kim BY Lohmueller KE. 2015 Selection and reduced population size cannot explain higher amounts of Neandertal ancestry in East Asian than in European human populations. Am J Hum Genet. 96:454–461. PMC4375557 25683122
  36. Kim Y Nielsen R. 2004 Linkage disequilibrium as a signature of selective sweeps. Genetics 167: 1513– 1524. 15280259 PMC1470945
  37. Kim Y Stephan W. 2002 Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765– 777. 11861577 PMC1461968
  38. Klima H Ullrich K Aslanidis C Fehringer P Lackner K Schmitz G. 1993 A splice junction mutation causes deletion of a 72-base exon from the mRNA for lysosomal acid lipase in a patient with cholesteryl ester storage disease. J Clin Invest. 92: 2713–2718. 8254026 PMC288469
  39. Knapp S Yee L Frodsham A Hennig B Hellier S Zhang L Wright M Chiaramonte M Graves M Thomas H, 2003 Polymorphisms in interferon-induced genes and the outcome of hepatitis C virus infection: roles of MxA, OAS-1 and PKR. Genes Immun. 4: 411– 419. 12944978
  40. Krause M Moradi J Coleman S D’Souza D Liu C Kronenberg M Rowe D Hawke T Hadjiargyrou M. 2013 A novel GFP reporter mouse reveals Mustn1 expression in adult regenerating skeletal muscle, activated satellite cells and differentiating myoblasts. Acta Physiol. 208: 180– 190. 23506283
  41. Kronforst MR Hansen ME Crawford NG Gallant JR Zhang W Kulathinal RJ Kapan DD Mullen SP. 2013 Hybridization reveals the evolving genomic architecture of speciation. Cell Rep. 5: 666– 677. 24183670 PMC4388300
  42. Lausch E Hermanns P Farin HF Alanay Y Unger S Nikkel S Steinwender C Scherer G Spranger J Zabel B, 2008 TBX15 mutations cause craniofacial dysmorphism, hypoplasia of scapula and pelvis, and short stature in cousin syndrome. Am J Hum Genet. 83: 649– 655. 19068278 PMC2668032
  43. Lewontin R. 1964 The interaction of selection and linkage. I. general considerations; heterotic models. Genetics 49: 49. 17248194 PMC1210557
  44. Lim JK Lisco A McDermott DH Huynh L Ward JM Johnson B Johnson H Pape J Foster GA Krysztof D, 2009 Genetic variation in OAS1 is a risk factor for initial infection with West Nile virus in man. PLoS Pathog. 5: e1000321. 19247438 PMC2642680
  45. Lin S Shen H Li JL Tang S Gu Y Chen Z Hu C Rice JC Lu J Wu L. 2013 Proteomic and functional analyses reveal the role of chromatin reader SFMBT1 in regulating epigenetic silencing and the myogenic gene program. J Biol Chem. 288: 6238– 6247. 23349461 PMC3585059
  46. Lin SE Oyama T Nagase T Harigaya K Kitagawa M. 2002 Identification of new human mastermind proteins defines a family that consists of positive regulators for notch signaling. J Biol Chem. 277: 50612– 50620. 12386158
  47. Liu CT Buchkovich ML Winkler TW Heid IM Borecki I Fox CS Mohlke KL North KE Cupples LA, A. A. A. G. Consortium, 2014 Multi-ethnic fine-mapping of 14 central adiposity loci. Hum Mol Genet. 23: 4738– 4744. 24760767 PMC4119415
  48. Liu CT Monda KL Taylor KC Lange L Demerath EW Palmas W Wojczynski MK Ellis JC Vitolins MZ Liu S, 2013 Genome-wide association of body fat distribution in African ancestry populations suggests new loci. PLoS Genet. 9: e1003681. 23966867 PMC3744443
  49. Liu S Wang H Jin Y Podolsky R Reddy MPL Pedersen J Bode B Reed J Steed D Anderson S, 2009 IFIH1 polymorphisms are significantly associated with type 1 diabetes and IFIH1 gene expression in peripheral blood mononuclear cells. Hum Mol Genet. 18: 358– 365. 18927125 PMC2638779
  50. Liu SY Aliyari R Chikere K Li G Marsden MD Smith JK Pernet O Guo H Nusbaum R Zack JA, 2013 Interferon-inducible cholesterol-25-hydroxylase broadly inhibits viral entry by production of 25-hydroxycholesterol. Immunity 38: 92– 105. 23273844 PMC3698975
  51. Lund EG Kerr TA Sakai J Li WP Russell DW. 1998 cDNA cloning of mouse and human cholesterol 25-hydroxylases, polytopic membrane proteins that synthesize a potent oxysterol regulator of lipid metabolism. J Biol Chem. 273: 34316– 34327. 9852097
  52. Martin SH Davey JW Jiggins CD. 2015 Evaluating the use of ABBA–BABA statistics to locate introgressed loci. Mol Biol Evol. 32: 244– 257. 25246699 PMC4271521
  53. Mendez FL Watkins JC Hammer MF. 2013 Neandertal origin of genetic variation at the cluster of OAS immunity genes. Mol Biol Evol. 30: 798– 801. 23315957
  54. Messer PW. 2013 SLiM: simulating evolution with selection and linkage. Genetics 194: 1037– 1039. 23709637 PMC3730910
  55. Mochida GH Ganesh VS de Michelena MI Dias H Atabay KD Kathrein KL Huang HT Hill RS Felie JM Rakiec D, 2012 CHMP1A encodes an essential regulator of BMI1-INK4A in cerebellar development. Nat Genet. 44: 1260– 1264., 23023333 PMC3567443
  56. Myers S Bottolo L Freeman C McVean G Donnelly P. 2005 A fine-scale map of recombination rates and hotspots across the human genome. Science 310: 321– 324. 16224025
  57. Pallares LF Carbonetto P Gopalakrishnan S Parker CC Ackert-Bicknell CL Palmer AA Tautz D. 2015 Mapping of craniofacial traits in outbred mice identifies major developmental genes involved in shape determination. PLOS Genet. 11: e1005607. 26523602 PMC4629907
  58. Peng Y Yang Z Zhang H Cui C Qi X Luo X Tao X Wu T Chen H Shi H, 2011 Genetic variations in Tibetan populations and high-altitude adaptation at the Himalayas. Mol Biol Evol. 28: 1075– 1081. 21030426
  59. Persson B Kallberg Y Bray JE Bruford E Dellaporta SL Favia AD Duarte RG Jörnvall H Kavanagh KL Kedishvili N, 2009 The SDR (short-chain dehydrogenase/reductase and related enzymes) nomenclature initiative. Chem Biol Interact. 178: 94– 98. 19027726 PMC2896744
  60. Pickrell JK Coop G Novembre J Kudaravalli S Li JZ Absher D Srinivasan BS Barsh GS Myers RM Feldman MW, 2009 Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 19: 826– 837. 19307593 PMC2675971
  61. Pool JE Nielsen R. 2009 Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics 181: 711– 719. 19087958 PMC2644959
  62. Prüfer K Racimo F Patterson N Jay F Sankararaman S Sawyer S Heinze A Renaud G Sudmant PH de Filippo C, 2014 The complete genome sequence of a Neanderthal from the Altai mountains. Nature 505: 43– 49. 24352235 PMC4031459
  63. Pruitt KD Harrow J Harte RA Wallin C Diekhans M Maglott DR Searle S Farrell CM Loveland JE Ruef BJ, 2009 The consensus coding sequence (CCDS) project: identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 19: 1316– 1323. 19498102 PMC2704439
  64. Qu HQ Marchand L Grabs R Polychronakos C. 2008 The association between the IFIH1 locus and type 1 diabetes. Diabetologia 51: 473– 475. 18071670
  65. Racimo F Gokhman D Fumagalli M Hansen T Moltke I Albrechtsen A Carmel L Huerta-Sanchez E Nielsen R. 2016 Archaic adaptive introgression in TBX15/WARS2. bioRxiv 033928. PMC5430617 28007980
  66. Racimo F Sankararaman S Nielsen R Huerta-Sánchez E. 2015 Evidence for archaic adaptive introgression in humans. Nat Rev Genet. 16: 359– 371. 25963373 PMC4478293
  67. Rauch A Wieczorek D Graf E Wieland T Endele S Schwarzmayr T Albrecht B Bartholdi D Beygo J Di Donato N, 2012 Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 380: 1674– 1682. 23020937
  68. Sankararaman S Mallick S Patterson N Reich D. 2016 The combined landscape of Denisovan and Neanderthal ancestry in present-day humans. Curr Biol. 26: 1241– 1247. 27032491 PMC4864120
  69. Shibata N Kawarai T Lee JH Lee HS Shibata E Sato C Liang Y Duara R Mayeux RP St George-Hyslop PH, 2006 Association studies of cholesterol metabolism genes (CH25H, ABCA1 and CH24H) in Alzheimer’s disease. Neurosci Lett. 391: 142– 146. 16157450
  70. Sigma Type 2 Diabetes Consortium. 2014 Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico. Nature 506: 97– 101. 24390345 PMC4127086
  71. Singh MK Petry M Haenig B Lescher B Leitges M Kispert A. 2005 The t-box transcription factor Tbx15 is required for skeletal development. Mech Dev. 122: 131– 144. 15652702
  72. Skoglund P Jakobsson M. 2011 Archaic human ancestry in East Asia. Proc Natl Acad Sci U S A. 108: 18301– 18306. 22042846 PMC3215044
  73. Smith J Kronforst MR. 2013 Do Heliconius butterfly species exchange mimicry alleles? Biol Lett. 9: 20130503. 23864282 PMC3730661
  74. Spilker C Kreutz MR. 2010 Rapgaps in brain: multipurpose players in neuronal Rap signalling. Eur J Neurosci. 32: 1– 9. 20576033
  75. Sun X Frierson HF Chen C Li C Ran Q Otto KB Cantarel BM Vessella RL Gao AC Petros J, 2005 Frequent somatic mutations of the transcription factor ATBF1 in human prostate cancer. Nat Genet. 37: 407– 412. 15750593
  76. Surapureddi S Yu S Bu H Hashimoto T Yeldandi AV Kashireddy P Cherkaoui-Malki M Qi C Zhu YJ Rao MS, 2002 Identification of a transcriptionally active peroxisome proliferator-activated receptor α-interacting cofactor complex in rat liver and characterization of PRIC285 as a coactivator. Proc Natl Acad Sci U S A. 99: 11836– 11841. 12189208 PMC129355
  77. Takemoto H Tamai K Akasaka E Rokunohe D Takiyoshi N Umegaki N Nakajima K Aizu T Kaneko T Nakano H, 2010 Relation between the expression levels of the POU transcription factors Skn-1a and Skn-1n and keratinocyte differentiation. Jo Dermatol Sci. 60: 203– 205. 21074976
  78. Tomaru T Satoh T Yoshino S Ishizuka T Hashimoto K Monden T Yamada M Mori M. 2006 Isolation and characterization of a transcriptional cofactor and its novel isoform that bind the deoxyribonucleic acid-binding domain of peroxisome proliferator-activated receptor-γ. Endocrinology 147: 377– 388. 16239304
  79. Vanhoutteghem A Djian P. 2006 Basonuclins 1 and 2, whose genes share a common origin, are proteins with widely different properties and functions. Proc Natl Acad Sci U S A. 103: 12423– 12428. 16891417 PMC1567895
  80. Vernot B Akey JM. 2014 Resurrecting surviving Neandertal lineages from modern human genomes. Science 343: 1017– 1021. 24476670
  81. Vernot B Tucci S Kelso J Schraiber JG Wolf AB Gittelman RM Dannemann M Grote S McCoy RC Norton H, 2016 Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science. DOI: 10.1126/science.aad9416. PMC6743480 26989198 · DOI · Paper page
  82. Voight BF Kudaravalli S Wen X Pritchard JK. 2006 A map of recent positive selection in the human genome. PLoS Biol. 4: e72. 16494531 PMC1382018
  83. Von Holstein SL Fehr A Heegaard S Therkildsen MH Stenman G. 2012 CRTC1-MAML2 gene fusion in mucoepidermoid carcinoma of the lacrimal gland. Oncol Rep. 27: 1413– 1416. 22323114
  84. Vrijenhoek T Buizer-Voskamp JE van der Stelt I Strengman E Risk G Sabatti C van Kessel AG Brunner HG Ophoff RA Veltman JA, 2008 Recurrent CNVs disrupt three candidate genes in schizophrenia patients. Am J Hum Genet. 83: 504– 510. 18940311 PMC2561936
  85. Wang B Zhang YB Zhang F Lin H Wang X Wan N Ye Z Weng H Zhang L Li X, 2011 On the origin of Tibetans and their genetic basis in adapting high-altitude environments. PLoS One 6: e17002. 21386899 PMC3046130
  86. Wang KS Liu XF Aragam N. 2010 A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. Schizophr Res. 124: 192– 199. 20889312
  87. Warner TG Dambach LM Shin JH O’Brien JS. 1980 Separation and characterization of the acid lipase and neutral esterases from human liver. Am J Hum Genet 32: 869. 7446527 PMC1686149
  88. Winnes M Mölne L Suurküla M Andrén Y Persson F Enlund F Stenman G. 2007 Frequent fusion of the CRTC1 and MAML2 genes in clear cell variants of cutaneous hidradenomas. Genes Chromosomes Cancer 46: 559– 563. 17334997
  89. Wood DS Zeviani M Prelle A Bonilla E Salviati G Miranda AF DiMauro S Rowland LP. 1987 Is nebulin the defective gene product in Duchenne muscular dystrophy? N Engl J Med. 1987: 107– 108. 3785354
  90. Woodage T Basrai MA Baxevanis AD Hieter P Collins FS. 1997 Characterization of the CHD family of proteins. Proc Natl Acad Sci U S A. 94: 11472– 11477. 9326634 PMC23509
  91. Wu L Liu J Gao P Nakamura M Cao Y Shen H Griffin JD. 2005 Transforming activity of MECT1-MAML2 fusion oncoprotein is mediated by constitutive CREB activation. EMBO J. 24: 2391– 2402. 15961999 PMC1173159
  92. Xu S Li S Yang Y Tan J Lou H Jin W Yang L Pan X Wang J Shen Y, 2011 A genome-wide search for signals of high-altitude adaptation in Tibetans. Mol Biol Evol. 28: 1003– 1011. 20961960
  93. Yotova V Lefebvre JF Moreau C Gbeha E Hovhannesyan K Bourgeois S Bédarida S Azevedo L Amorim A Sarkisian T, 2011 An X-linked haplotype of neandertal origin is present among all non-African populations. Mol Biol Evol. 28: 1957– 1962. 21266489

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Authors
Racimo, F., Marnetto, D., & Huerta-Sánchez, E.
Affiliations
  • University of California, Berkeley (US)
  • University of Turin (IT)
ORCID
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2016-10-18
Volume
34
Issue
2
Pages
msw216
ISSN
  • 0737-4038 (ISSN-L)
  • 1537-1719
DOI
10.1093/molbev/msw216
PMC
PMC5400396
OpenAlex
W2534489581
Cited by
200
References
16
Citations by year
2026: 13 · 2025: 18 · 2024: 23 · 2023: 23 · 2022: 17 · 2021: 30 · 2020: 17 · 2019: 19 · 2018: 18 · 2017: 17 · 2016: 5
FWCI
76.90
Type
journal article
Language
en
Open access
Locations
  • Molecular Biology and Evolution (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • Institutional Research Information System University of Turin (University of Turin) (submittedVersion, other-oa)
Funders
  • National Science Foundation (1557151)
  • National Institutes of Health
  • University of California Merced
  • National Human Genome Research Institute (R01HG003229)
  • Division of Environmental Biology
Topics
  • Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Keywords
adaptive introgression, archaic human admixture, Neanderthal introgression, Denisovan introgression, positive selection detection, haplotype structure, allele frequency distribution, 1000 Genomes Project, human population genomics, candidate genes
MeSH terms
DNA, Ancient, Adaptation, Biological, Alleles, Animals, Computer Simulation, Biological Evolution, Gene Frequency, Genetics, Population, Haplotypes, Humans, Phylogeny, Selection, Genetic, Sequence Analysis, DNA, Evolution, Molecular, Databases, Nucleic Acid, Neanderthals

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