Confidence intervals for population allele frequencies: The general case of sampling from a finite diploid population of any size

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Fung, Tak ^a,b   Keenan, Kevin ^b  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CELL STRUCTURE; CONTROLLED STUDY; DIPLOIDY; FINLAND; GENETIC ASSOCIATION; GENETIC VARIABILITY; HOMOZYGOSITY; LEPIDOPTERA; MATHEMATICAL MODEL; MELITAEA CINXIA; NONHUMAN; POPULATION GENETIC STRUCTURE; RESOURCE MANAGEMENT; RISK MANAGEMENT; SAMPLE SIZE;

ANIMALS; BUTTERFLIES; CONFIDENCE INTERVALS; DIPLOIDY; GENE FREQUENCY; GENETICS, POPULATION; HOMOZYGOTE; POPULATION DENSITY; SAMPLE SIZE;

EID: 84908181121     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0085925     Document Type: Article

References (39)

1. Bowcock AM, Kidd JR, Mountain JL, Hebert JM, Carotenuto L, et al. (1991) Drift, admixture, and selection in human evolution: A study with DNA polymorphisms. Proc Natl Acad Sci USA 88: 839-843. (Pubitemid 21916119)
2. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Res 12: 1805-1814. (Pubitemid 35469929)
3. Luikart G, England PR, Tallmon D, Jordan S, Taberlet P (2003) The power and promise of population genomics: from genotyping to genome typing. Nature 4: 981-994. (Pubitemid 37474645)
4. de Kovel CGF (2006) The power of allele frequency comparisons to detect the footprint of selection in natural and experimental situations. Genet Sel Evol 38: 3-23.
5. Friedlander SM, Herrmann AL, Lowry DP, Mepham ER, Lek M, et al. (2013) ACTN3 allele frequency in humans covaries with global latitudinal gradient. PLoS ONE 8(1):e52282.
6. Nei M (1972) Genetic distance between populations. Am Nat 106: 283-292.
7. Nei M, Chesser RK (1983) Estimation of fixation indices and gene diversities. Ann Hum Genet, 47: 253-259. (Pubitemid 13000183)
8. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370. (Pubitemid 16277759)
9. Jost L (2008) GST and its relatives do not measure differentiation. Mol Ecol 17: 4015-4026
10. Weir BS (1996) Genetic data analysis II. Sunderland, USA, Sinauer Associates. 445 p.
11. Eanes WF, Koehn RK (1978) An analysis of genetic structure in the Monarch butterfly, Danaus plexippus L. Evolution 32: 784-797.
12. Forbes SH, Hogg JT, Buchanan FC, Crawford AM, Allendorf FW (1995) Microsatellite evolution in congeneric mammals: domestic and bighorn sheep. Mol Biol and Evol 12: 1106-1113.
13. Palo J, Varvio S-L, Hanski I, Väinölä R (1995) Developing microsatellite markers for insect population structure: complex variation in a checkerspot butterfly. Hereditas 123: 295-300. (Pubitemid 26162573)
14. Luikart G, Allendorf FW, Cournuet J-M, Sherwin WB (1998) Distortion of allele frequency distributions provides a test for recent population bottlenecks. J Hered 89:238-247. (Pubitemid 28292519)
15. Rank NE, Dahlhoff EP (2002) Allele frequency shifts in response to climate change and physiological consequences of allozyme variation in a montane insect. Evolution 56: 2278-2289. (Pubitemid 35436833)
16. Hugnet C, Bentjen SA, Mealey KL (2004) Frequency of the mutant MDR1 allele associated with multidrug sensitivity in a sample of collies from France. J Vet Pharmacol Ther 27: 227-229. (Pubitemid 39141607)
17. Seider T, Fimmers R, Betz P, Lederer T (2010) Allele frequencies of the five miniSTR loci D1S1656, D2S441, D10S1248, D12S391 and D22S1045 in a German population sample. Forensic Sci Int Genet 4: e159-e160.
18. Petrejčíková E, Soták M, Bernasovská J, Bernasovský I, Rȩbała K, et al. (2011) Allele frequencies and population data for 11 Y-chromosome STRs in samples from Eastern Slovakia. Forensic Sci Int Genet 5: e53-e62.
19. Hale ML, Burg TM, Steeves TE (2012) Sampling for microsatellite-based population genetic studies: 25 to 30 individuals per population is enough to accurately estimate allele frequencies. PLoS ONE 7(9): e45170.
20. Gillespie JH (2004) Population genetics: a concise guide, second edition. Baltimore, USA, The John Hopkins University Press. 217 p.
21. Laplace PS (1812) Théorie analytique des probabilités. Paris, France, Courcier. 464 p.
22. Agresti A, Coull BA (1998) Approximate is better than "exact" for interval estimation of binomial proportions. Am Stat 52: 119-126.
23. Cai Y, Krishnamoorthy K (2005) A simple improved inferential method for some discrete distributions. Comput Stat Data Anal 48: 605-621.
24. Clopper CJ, Pearson ES (1934) The use of confidence or fiducial limits illustrated in the case of the binomial. Biometrika 26: 404-413.
25. Frankham R (1996) Relationship of genetic variation to population size in wildlife. Conserv Biol 10: 1500-1508.
26. Green DM (2003) The ecology of extinction: population fluctuation and decline in amphibians. Biol Conserv 111: 331-343.
27. Vredenberg VT, Knapp RA, Tunstall TS, Briggs CJ (2010) Dynamics of an emerging disease drive large-scale amphibian population extinctions. Proc Natl Acad Sci USA 107: 9689-9694.
28. Johnson NL, Kotz S, Balakrishnan N (1997) Discrete multivariate distributions. Hoboken, USA, Wiley-Blackwell. 328 p.
29. Cox DR, Hinkley DV (1974) Theoretical statistics. London, UK, Chapman and Hall. 511 p.
30. Talens E (2005) Statistical auditing and the AOQL-Method. Ridderkerk, The Netherlands, Labyrint Publications. 164 p.
31. Wolfram Research Inc. (2003) Mathematica Edition: Version 5.0. Champaign, Illinois, USA, Wolfram Research Inc.
32. The MathWorks Inc. (2012) MATLAB version 8.0. Natick, Massachusetts, ,USA, The MathWorks Inc.
33. R Development Core Team (2010) R: a language and environment for statistical computing. Vienna, Austria, R Foundation for Statistical Computing. 1731 p.
34. Rice JA (1995) Mathematical statistics and data analysis, second edition. Belmont, USA, Duxbury Press. 651 p.
35. Chakraborty R (1992) Sample size requirements for addressing the population genetic issues of forensic use of DNA typing. Hum Biol 64: 141-159.
36. Gregorius H-R (1980) The probability of losing an allele when diploid genotypes are sampled. Biometrics 36: 643-652.
37. Sjögren P, Wyöni P-I (1994) Conservation genetics and detection of rare alleles in finite populations. Conserv Biol 8: 267-270.
38. DeGiorgio M, Rosenberg NA (2009) An unbiased estimator of gene diversity in samples containing related individuals. Mol Biol Evol 26: 501-512.
39. DeGiorgio M, Jankovic I, Rosenberg NA (2010) Unbiased estimation of gene diversity in samples containing related individuals: exact variance and arbitrary ploidy. Genetics 186: 1367-1387.