The role of phylogenetically conserved elements in shaping patterns of human genomic diversity

Molecular Biology and Evolution

Volumn 35, Issue 9, 2018, Pages 2284-2295

  Woerner, August E ^a,b   Veeramah, Krishna R ^c   Watkins, Joseph C ^d   Hammer, Michael F ^a  

^a UNIVERSITY OF ARIZONA   (United States)

^b UNIVERSITY OF NORTH TEXAS HEALTH SCIENCE CENTER   (United States)

^c STONY BROOK UNIVERSITY   (United States)

^d The University of Arizona   (United States)

Author keywords

Background selection; Diversity; Genetic hitchhiking; Null model.; Phylogenetic conserved elements; Recombination

Indexed keywords

ARTICLE; AUTOSOME; BACKGROUND SELECTION; DEMOGRAPHY; GENE CONVERSION; GROWTH RATE; HUMAN; HUMAN GENOME; POPULATION SIZE; SELECTIVE SWEEP; X CHROMOSOME; YORUBA (PEOPLE); BIOLOGICAL MODEL; CONSERVED SEQUENCE; GENETIC LINKAGE; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIATION; MUTATION; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; CHROMOSOMES, HUMAN, X; CONSERVED SEQUENCE; GENE CONVERSION; GENETIC LINKAGE; GENETIC VARIATION; GENOME, HUMAN; HUMANS; MODELS, GENETIC; MUTATION; RECOMBINATION, GENETIC; SELECTION, GENETIC;

EID: 85053677637     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msy145     Document Type: Article

References (68)

1. Arbeithuber B, Betancourt AJ, Ebner T, Tiemann-Boege I. 2015. Crossovers are associated with mutation and biased gene conversion at recombination hotspots. Proc Natl Acad Sci U S A. 112(7):2109-2114.
2. Arbiza L, Gottipati S, Siepel A, Keinan A. 2014. Contrasting X-linked and autosomal diversity across 14 human populations. Am J Hum Genet. 94(6):827-844.
3. Arbiza L, Zhong E, Keinan A. 2012. NRE: a tool for exploring neutral loci in the human genome. BMC Bioinformatics 14:1.
4. Barton NH. 1998. The effect of hitch-hiking on neutral genealogies. Genet Res. 72(2):123-133.
5. Begun DJ, Aquadro CF. 1992. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. Melanogaster. Nature 356(6369):519-520.
6. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. 2004. Ultraconserved elements in the human genome. Science 304(5675):1321-1325.
7. Birky CW, Walsh JB. 1988. Effects of linkage on rates of molecular evolution. Proc Natl Acad Sci U S A. 85(17):6414-6418.
8. Braverman JM, Hudson RR, Kaplan NL, Langley CH, Stephan W. 1995. The hitchhiking effect on the site frequency spectrumofDNA polymorphisms. Genetics 140(2):783-796.
9. Cai JJ, Macpherson JM, Sella G, Petrov DA. 2009. Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet. 5(1):e1000336.
10. Charlesworth B, Morgan MT, Charlesworth D. 1993. The effect of deleterious mutations on neutral molecular variation. Genetics 134(4):1289-1303.
11. Charlesworth B. 1996. Background selection and patterns of genetic diversity in Drosophila melanogaster. Genet Res. 68(2):131-149.
12. Charlesworth B. 2009. Effective population size and patterns of molecular evolution and variation. Nat Rev Genet. 10(3):195-205.
13. Chen CT, Wang JC, Cohen BA. 2007. The strength of selection on ultraconserved elements in the human genome. Am J Hum Genet. 80(4):692-704.
14. Chinwalla AT, Cook LL, Delehaunty KD, Fewell GA, Fulton LA, Fulton RS, Graves TA, Hillier LW, Mardis ER, McPherson JD. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420(6915):520-562.
15. Comeron JM. 2017. Background selection as null hypothesis in population genomics: insights and challenges from Drosophila studies. Philos Trans R Soc B 372(1736):20160471.
16. Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A. 2005. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 15(7):901-913.
17. Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, et al. 2010. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327(5961):78-81.
18. Elyashiv E, Sattath S, Hu TT, Strutsovsky A, McVicker G, Andolfatto P, Coop G, Sella G. 2016. A genomic map of the effects of linked selection in Drosophila. PLoS Genet. 12(8):e1006130.
19. Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, et al. 2015. Genome-wide patterns and properties of de novo mutations in humans. Nat Genet. 47(7):822-826.
20. Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, et al. 2007. A second generation human haplotype map of over 3.1 million SNPs. Nature 449(7164):851-861.
21. Fu YX, Li WH. 1993. Statistical tests of neutrality of mutations. Genetics 133(3):693-709.
22. Gillepsie JH. 2000. Genetic drift in an infinite population. The pseudohitchhiking model. Genetics 155:909-919.
23. Goldberg A, Rosenberg NA. 2015. Beyond 2/3 and 1/3: the complex signatures of sex-biased admixture on the X chromosome. Genetics 201(1):263-279.
24. Gottipati S, Arbiza L, Siepel A, Clark AG, Keinan A. 2011. Analyses of Xlinked and autosomal genetic variation in population-scale whole genome sequencing. Nat Genet. 43(8):741-743.
25. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. 2009. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5(10):e1000695.
26. Halligan DL, Kousathanas A, Ness RW, Harr B, Eory L, Keane TM, Adams DJ, Keightley PD. 2013. Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents. PLoS Genet. 9(12):e1003995.
27. Halligan DL, Oliver F, Guthrie J, Stemshorn KC, Harr B, Keightley PD. 2011. Positive and negative selection in murine ultraconserved noncoding elements. Mol Biol Evol. 28(9):2651-2660.
28. Hammer MF, Woerner AE, Mendez FL, Watkins JC, Cox MP, Wall JD. 2010. The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes. Nat Genet. 42(10):830-831.
29. Hernandez RD, Kelley JL, Elyashiv E, Melton SC, Auton A, McVean G, Sella G, Przeworski M. 2011. Classic selective sweeps were rare in recent human evolution. Science 331(6019):920-924.
30. HillWG, Robertson A. 1966. The effect of linkage on limits to artificial selection. Genet Res. 8(3):269-294.
31. Hsieh P, Veeramah KR, Lachance J, Tishkoff SA, Wall JD, Hammer MF, Gutenkunst RN. 2016. Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection. Genome Res. 26(3): 279-290.
32. Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. 2006. The UCSC known genes. Bioinformatics 22(9):1036-1046.
33. Hudson RR, Kaplan NL. 1995. Deleterious background selection with recombination. Genetics 141:1605-1607.
34. Hudson RR. 2007. The variance of coalescent time estimates from DNA sequences. J Mol Evol. 64(6):702.
35. Katzman S, Capra JA, Haussler D, Pollard KS. 2011. Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Genome Biol Evol. 3:614-626.
36. Katzman S, Kern AD, BejeranoG, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D. 2007. Human genome ultraconserved elements are ultraselected. Science 317(5840):915.
37. Keightley PD, Eyre-Walker A. 2012. Estimating the rate of adaptive molecular evolution when the evolutionary divergence between species is small. J Mol Evol. 74(1-2):61-68.
38. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. 2002. The human genome browser at UCSC. Genome Res. 12(6):996-1006.
39. Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, Gudjonsson SA, igurdsson A, Jonasdottir A, Jonasdottir A, et al. 2012. Rate of de novo mutations and the importance of father's age to disease risk. Nature 488(7412):471-475.
40. Lohmueller KE, Albrechtsen A, Li Y, Kim SY, Korneliussen T, Vinckenbosch N, Tian G, Huerta-Sanchez E, Feder AF, Grarup N, et al. 2011. Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet. 7(10):e1002326.
41. Marais G. 2003. Biased gene conversion: implications for genome and sex evolution. Trends Genet. 19(6):330-338.
42. Maynard Smith J, Haigh J. 1974. The hitch-hiking effect of a favourable gene. Genet Res. 23(01):23-35.
43. McGaugh SE, Heil CS, Manzano-Winkler B, Loewe L, Goldstein S, Himmel TL, Noor MA. 2012. Recombination modulates how selection affects linked sites in Drosophila. PLoS Biol. 10(11):e1001422.
44. McVicker G, Gordon D, Davis C, Green P. 2009. Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet. 5(5):e1000471.
45. Meader S, Ponting CP, Lunter G. 2010. Massive turnover of functional sequence in human and other mammalian genomes. Genome Res. 20(10):1335-1343.
46. Messer PW, Petrov DA. 2013. Frequent adaptation and the McDonald-Kreitman test. Proc Natl Acad Sci U S A. 110(21):8615-8620.
47. Nachman MW, Crowell SL. 2000. Estimate of the mutation rate per nucleotide in humans. Genetics 156(1):297-304.
48. NachmanMW. 2001. Single nucleotide polymorphisms and recombination rate in humans. Trends Genet. 17(9):481-485.
49. Nicolaisen LE, Desai MM. 2012. Distortions in genealogies due to purifying selection. Mol Biol Evol. 29(11):3589-3600.
50. Nicolaisen LE, Desai MM. 2013. Distortions in genealogies due to purifying selection and recombination. Genetics 195(1):221-230.
51. Nordborg M, Charlesworth B, Charlesworth D. 1996. The effect of recombination on background selection. Genet Res. 67(2):159-174.
52. O'Fallon BD, Seger J, Adler FR. 2010. A continuous-state coalescent and the impact of weak selection on the structure of gene genealogies. Mol Biol Evol. 27(5):1162-1172.
53. Ponting CP, Hardison RC. 2011. What fraction of the human genome is functional? Genome Res. 21(11):1769-1776.
54. Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, et al. 2013. Great ape genetic diversity and population history. Nature 499(7459):471-475.
55. Pratto F, Brick K, Khil P, Smagulova F, Petukhova GV, Camerini-Otero RD. 2014. Recombination initiation maps of individual human genomes. Science 346(6211):1256442.
56. Rands CM, Meader S, Ponting CP, Lunter G. 2014. 8.2% of the human genome is constrained: variation in rates of turnover across functional element classes in the human lineage. PLoS Genet. 10(7):e1004525.
57. Schrider DR, Kern AD. 2017. Soft sweeps are the dominant mode of adaptation in the human genome. Mol Biol Evol. 34(8):1863-1877.
58. Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. 2005. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15(8):1034-1050.
59. Singh ND, Jensen JD, Clark AG, Aquadro CF. 2013. Inferences of demography and selection in an African population of Drosophila melanogaster. Genetics 193(1):215-228.
60. Spencer CC, Deloukas P, Hunt S, Mullikin J, Myers S, Silverman B, Donnelly P, Bentley D, McVean G. 2006. The influence of recombination on human genetic diversity. PLoS Genet. 2(9):e148.
61. Strathern JN, Shafer BK,McGill CB. 1995. DNA synthesis errors associated with double-strand-break repair. Genetics 140(3):965-972.
62. Tachida H. 2000. DNA evolution under weak selection. Gene 261(1):3-9.
63. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123(3):585-595.
64. Tataru P, Mollion M, Glemin S, Bataillon T. 2017. Inference of distribution of fitness effects and proportion of adaptive substitutions from polymorphism data. Genetics 207(3):1103-1119.
65. Uricchio LH, Zaitlen NA, Ye CJ, Witte JS, Hernandez RD. 2016. Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants. Genome Res. 26(7):863-811.
66. Veeramah KR, Gutenkunst RN, Woerner AE, Watkins JC, Hammer MF. 2014. Evidence for increased levels of positive and negative selection on the X chromosome versus autosomes in humans.Mol Biol Evol. 31(9):2267-2282.
67. Williamson S, Orive ME. 2002. The genealogy of a sequence subject to purifying selection at multiple sites. Mol Biol Evol. 19(8):1376-1384.
68. Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, et al. 2016. Ensembl 2016. Nucleic Acids Res. 44(D1):D710-D716.