Neanderthal introgression at chromosome 3p21.31 was under positive natural selection in east asians

Molecular Biology and Evolution

Volumn 31, Issue 3, 2014, Pages 683-695

  Ding, Qiliang ^a   Hu, Ya ^a   Xu, Shuhua ^b   Wang, Jiucun ^a   Jin, Li ^a,b  

^a FUDAN UNIVERSITY   (China)

^b MAX PLANCK INSTITUTE   (Germany)

Author keywords

East Asians; HYAL; introgression; Neanderthals; positive selection

Indexed keywords

ALLELE; ARTICLE; ASIAN; CHROMOSOME 3P; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; HAPLOTYPE; HOMO NEANDERTHALENSIS; HOMOZYGOSITY; INTROGRESSION; NATURAL SELECTION; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; SINGLE NUCLEOTIDE POLYMORPHISM; ULTRAVIOLET B RADIATION;

EAST ASIANS; HYAL; INTROGRESSION; NEANDERTHALS; POSITIVE SELECTION;

ADAPTATION, PHYSIOLOGICAL; ALLELES; ANIMALS; ASIAN CONTINENTAL ANCESTRY GROUP; CHROMOSOMES, HUMAN, PAIR 3; FAR EAST; GENETIC VARIATION; GEOGRAPHY; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; NEANDERTHALS; PAN TROGLODYTES; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC; SELECTION, GENETIC; TIME FACTORS;

EID: 84895737920     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mst260     Document Type: Article

References (43)

1. Genomes Consortium. 2012. An integrated map of genetic variation from 1,092 human genomes. Nature 491:56-65.
2. Abi-Rached L, Jobin MJ, Kulkarni S, McWhinnie A, Dalva K, Gragert L, Babrzadeh F, Gharizadeh B, Luo M, Plummer FA, et al. 2011. The shaping of modern human immune systems by multiregional admixture with archaic humans. Science 334:89-94.
3. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. 2000. Gene Ontology: tool for the unification of biology. Nat Genet. 25:25-29.
4. Atmuri V, Martin DC, Hemming R, Gutsol A, Byers S, Sahebjam S, Thliveris JA, Mort JS, Carmona E, Anderson JE, et al. 2008. Hyaluronidase 3 (HYAL3) knockout mice do not display evidence of hyaluronan accumulation. Matrix Biol. 27:653-660.
5. Averbeck M, Gebhardt CA, Voigt S, Beilharz S, Anderegg U, Termeer CC, Sleeman JP, Simon JC. 2007. Differential regulation of hyaluronan metabolism in the epidermal and dermal compartments of human skin by UVB irradiation. J Invest Dermatol. 127:687-697.
6. Barrett JC, Fry B, Maller J, Daly MJ. 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263-265.
7. Beuten J, Garcia D, Brand TC, He X, Balic I, Canby-Hagino E, Troyer DA, Baillargeon J, Hernandez J, Thompson IM, et al. 2009. Semaphorin 3B and 3F single nucleotide polymorphisms are associated with prostate cancer risk and poor prognosis. J Urol. 182:1614-1620.
8. Cann RL, Stoneking M, Wilson AC. 1987. Mitochondrial DNA and human evolution. Nature 325:31-36.
9. Castro-Rivera E, Ran S, Thorpe P, Minna JD. 2004. Semaphorin 3B (SEMA3B) induces apoptosis in lung and breast cancer, whereas VEGF165 antagonizes this effect. Proc Natl Acad Sci U S A. 101: 11432-11437.
10. Chowdhury B, Hemming R, Homback-Klonisch S, Flamion B, Triggs- Raine B. 2013. Murine hyaluronidase 2 deficiency results in extracellular hyaluronan accumulation and severe cardiopulmonary dysfunction. J Biol Chem. 288:520-528.
11. Drummond AJ, Rambaut A, Shapiro B, Pybus OG. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 22:1185-1192.
12. Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 29: 1969-1973.
13. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, et al. 2002. The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
14. Gautier M, Vitalis R. 2012. rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics 28:1176-1177.
15. Goodman M. 1999. The genomic record of humankind's evolutionary roots. Am J Hum Genet. 64:31-39.
16. Green RE, Krause J, Briggs AW,Maricic T, StenzelU,KircherM, Patterson N, Li H, Zhai W, Fritz MH, et al. 2010. A draft sequence of the Neandertal genome. Science 328:710-722.
17. Grossman SR, Shlyakhter I, Karlsson EK, Byrne EH, Morales S, Frieden G, Hostetter E, Angelino E, Garber M, Zuk O, et al. 2010. A composite of multiple signals distinguishes casual variants in regions of positive selection. Science 327:883-886.
18. Hammer MF. 1995. A recent common ancestry for human Y chromosomes. Nature 378:376-378.
19. Hasova M, Crhak T, Safrankova B, Dvorakova J, Muthny T, Velebny V, Kubala L. 2011. Hyaluronan minimizes effects of UV irradiation on human keratinocytes. Arch Dermatol Res. 303:277-284.
20. Hesson LB, Cooper WN, Latif F. 2007. Evaluation of the 3p21.3 tumoursuppressor gene cluster. Oncogene 26:7283-7301.
21. Hinch AG, Tandon A, Patterson N, Song Y, Rohland N, Palmer CD, Chen GK,Wang K, Buxbaum SG, Akylbekova EL, et al. 2011. The landscape of recombination in African Americans. Nature 476:170-175.
22. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. 2009. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A. 106:9362-9367.
23. International HapMap 3 Consortium. 2010. Integrating common and rare genetic variation in diverse human populations. Nature 467: 52-58.
24. Kurdykowski S, Mine S, Bardey V, Danoux L, Jeanmaire C, Pauly G, Brabencova E, Wegrowski Y, Maquart FX. 2011. Ultraviolet-B irradiation induces differential regulations of hyaluronidase expression and activity in normal human keratinocytes. Photochem Photobiol. 87:1105-1112.
25. Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P. 2010. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26:2462-2463.
26. Mendez FL, Watkins JC, Hammer MF. 2012a. Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations. Mol Biol Evol. 29:1513-1520.
27. Mendez FL, Watkins JC, Hammer MF. 2012b. A haplotype at STAT2 introgressed from Neanderthals and serves as a candidate of positive selection in Papua New Guinea. Am J Hum Genet. 91:265-274.
28. 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.
29. Meyer LJM, Russell SB, Russell JD, Trupin JS, Egbert BM, Shuster S, Stern R. 2000. Reduced hyaluronan in keloid tissue and cultured keloid fibroblasts. J Invest Dermatol. 114:953-959.
30. Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prufer K, de Filippo C, et al. 2012. A high-coverage genome sequence from an archaic Denisovan individual. Science 338: 222-226.
31. Nakashima M, Chung S, Takahashi A, Kamatani N, Kawaguchi T, Tsunoda T, Hosono N, Kubo M, Nakamura Y, Zembutsu H. 2010. A genome-wide association study identifies four susceptibility loci for keloid in the Japanese population. Nat Genet. 42:768-771.
32. Rajeevan H, Soundararajan U, Kidd JR, Pakstis AJ, Kidd KK. 2012. ALFRED: an allele frequency resource for research and teaching. Nucleic Acids Res. 40:D1010-D1015.
33. Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, et al. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468: 1053-1060.
34. Roach JC, Glusman G, Smit AFA, Huff CD, Hubley R, Shannon PT, Rowen L, Pant KP, Goodman N, Bamshad M, et al. 2010. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328:636-639.
35. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, et al. 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419:832-837.
36. Shi H, Tan SJ, Zhong H, Hu W, Levine A, Xiao CJ, Peng Y, Qi XB, Shou WH, Ma RL, et al. 2009. Winter temperature and UV are tightly linked to genetic changes in the p53 tumor suppressor pathway in Eastern Asia. Am J Hum Genet. 84:534-541.
37. Shuttleworth TL, Wilson MD, Wicklow BA, Willkins JA, Triggs-Raine BL. 2002. Characterization of the murine hyaluronidase gene region reveals complex organization and cotranscription of Hyal1 with downstream genes, Fus2 and Hyal3. J Biol Chem. 277:23008-23018.
38. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739.
39. Tian X, Azpurua J, Hine C, Vaidya A, Myakishev-Rempel M, Ablaeva J, Mao Z, Nevo E, Gorbunova V, Seluanov A. 2013. High-molecularmass hyaluronan mediates the cancer resistance of the naked mole rat. Nature 499:346-349.
40. Triggs-Raine B, Salo TJ, Zhang H, Wicklow BA, Natowicz MR. 1999. Mutations in HYAL1, a member of a tandemly distributed multigene family encoding disparate hyaluronidase activities, cause a newly described lysosomal disorder, mucopolysaccharidosis IX. Proc Natl Acad Sci U S A. 96:6296-6300.
41. Voight BF, Kudaravalli S, Wen X, Pritchard JK. 2006. A map of recent positive selection in the human genome. PLoS Biol. 4:e72.
42. Wall JD, Yang MA, Jay F, Kim SK, Durand EY, Stevison LS, Gignoux C, Woerner A, Hammer MF, Slatkin M. 2013. Higher levels of Neanderthal ancestry in East Asians than in Europeans. Genetics 194:199-209.
43. Ward LD, Kellis M. 2012. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 40:D930-D934.