Correcting the site frequency spectrum for divergence-based ascertainment

PLoS ONE

Volumn 4, Issue 4, 2009, Pages

  Kern, Andrew D ^a  

^a Dartmouth College   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; FREQUENCY ANALYSIS; GENE FREQUENCY; GENE LOCATION; GENETIC VARIABILITY; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL PARAMETERS; MAXIMUM LIKELIHOOD METHOD; NATURAL SELECTION; POPULATION GENETICS; PROCESS OPTIMIZATION; SIMULATION; EVOLUTION; GENETIC POLYMORPHISM; GENETIC SELECTION; GENOME; GENOMICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; SPECIES DIFFERENCE;

BASE SEQUENCE; EVOLUTION; GENE FREQUENCY; GENETICS, POPULATION; GENOME; GENOMICS; POLYMORPHISM, GENETIC; SELECTION (GENETICS); SPECIES SPECIFICITY;

EID: 65349168919     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0005152     Document Type: Article

References (16)

1. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, et al. (2004) Ultraconserved elements in the human genome. Science 304: 1321-1325.
2. Pollard KS, Salama SR, King B, Kern AD, Dreszer T, et al. (2006) Forces shaping the fastest evolving regions in the human genome. PLoS Genet 2: 1553-7404.
3. Gillespie JH (1991) The causes of molecular evolution. New York: Oxford University Press.
4. Drake JA, Bird C, Nemesh J, Thomas DJ, Newton-Cheh C, et al. (2005) Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat Genet 38: 223-227.
5. Nielsen R, Bustamante CD, Clark AG, Glanowski S, Sackton TB, et al. (2005) A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 3: 1545-7885.
6. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
7. Nielsen R, Hubisz MJ, Clark AG (2004) Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data. Genetics 168: 2373-82.
8. Hey J (1991) The structure of genealogies and the distribution of fixed differences between DNA sequence samples from natural populations. Genetics 128: 831-40.
9. Press WH, Teukolsky SA, Vetterling WT, Flannery BP (1992) Numerical Recipes in C. Cambridge University Press.
10. Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, et al. (2005) Natural selection on protein-coding genes in the human genome. Nature 437: 1153-1157.
11. Sawyer SA, Hartl DL (1992) Population genetics of polymorphism and divergence. Genetics 132: 1161-1176.
12. Bustamante CD, Wakeley J, Sawyer SA, Hartl DL (2001) Directional selection and the site-frequency spectrum. Genetics 159: 1779-1788.
13. Williamson SH, Hernandez R, Fledel-Alon A, Zhu L, Nielsen R, et al. (2005) Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc Natl Acad Sci U S A 102: 7882-7887.
14. Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, et al. (2007) Human ultraconserved elements are ultraselected. Science 317: 915.
15. Gillespie JH (1997) Junk ain't what junk does: neutral alleles in a selected context. Gene 205: 291-299.
16. Kern AD, Jones CD, Begun DJ (2004) Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex. Genetics 167: 725-735.