Accurate and fast methods to estimate the population mutation rate from error prone sequences

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages 247-

  Knudsen, Bjarne ^a   Miyamoto, Michael M ^b  

^a CLC bio   (Denmark)

^b UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; MAXIMUM LIKELIHOOD ESTIMATION; RANDOM ERRORS;

ACCURATE ESTIMATION; DATA COLLECTION; EVOLUTIONARY BIOLOGY; EVOLUTIONARY SIMULATIONS; EXPERIMENTAL ERRORS; EXPRESSED SEQUENCE TAGS; POLYMORPHIC SITES; SAMPLED SEQUENCES;

POPULATION STATISTICS;

ACCURACY; ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; AUTOGRAPHA CALIFORNICA; CONTROLLED STUDY; DATA ANALYSIS; EXPRESSED SEQUENCE TAG; GENE MUTATION; GENE SEQUENCE; GENEALOGY; GENETIC CONSERVATION; GENETIC POLYMORPHISM; MATHEMATICAL ANALYSIS; MAXIMUM LIKELIHOOD METHOD; METHODOLOGY; MUTATION RATE; MUTATIONAL ANALYSIS; POPULATION GENETICS; SEQUENCE ANALYSIS; SIMULATION; UNITED STATES;

APLYSIA CALIFORNICA;

EID: 70349751765     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-247     Document Type: Article

References (45)

1. Achaz G. Testing for neutrality in samples with sequencing errors. Genetics 2008, 179:1409-1424. 10.1534/genetics.107.082198, 2475743, 18562660.
2. Knudsen B, Miyamoto M.M. Incorporating experimental design and error into coalescent/mutation models of population history. Genetics 2007, 176:2335-2342. 10.1534/genetics.106.063560, 1950635, 17565962.
3. Fu Y.X. Statistical properties of segregating sites. Theoretical Population Biology 1995, 48:172-197. 10.1006/tpbi.1995.1025, 7482370.
4. Hein J, Shierup M, Wiuf C. Sequence Variation, Genealogies and Evolution 2005,
5. Wakeley J. Coalescent Theory: An Introduction 2008,
6. Hudson R.R. Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 1990, 7:1-44.
7. Fu Y.X. Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences. Genetics 1994, 138:1375-1386. 1206273, 7896116.
8. Felsenstein J. Inferring Phylogenies 2004,
9. Li W.H, Sadler L.A. Low nucleotide diversity in man. Genetics 1991, 129:513-523. 1204640, 1743489.
10. Clark A.G, Whittam T.S. Sequencing errors and molecular evolutionary analysis. Molecular Biology and Evolution 1992, 9:744-752.
11. Tiffin P, Gaut B.S. Molecular evolution of the wound-induced serine protease inhibitor wip1 in Zea and related genera. Molecular Biology and Evolution 2001, 18:2092-2101.
12. Nabholz B, Jean-Francois M, Bazin E, Galtier N, Glemin S. Determination of mitochondrial genetic diversity in mammals. Genetics 2008, 178:351-361. 10.1534/genetics.107.073346, 2206084, 18202378.
13. Ho S.Y, Phillips M.J, Cooper A, Drummond A.J. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Molecular Biology and Evolution 2005, 22:1561-1568. 10.1093/molbev/msi145, 15814826.
14. Ho S.Y, Heupink T.H, Rambaut A, Shapiro B. Bayesian estimation of sequence damage in ancient DNA. Molecular Biology and Evolution 2007, 24:1416-1422. 10.1093/molbev/msm062, 17395598.
15. Johnson P.L, Slatkin M. Inference of population genetic parameters in metagenomics: A clean look at messy data. Genome Research 2006, 16:1320-1327. 10.1101/gr.5431206, 1581441, 16954540.
16. Johnson P.L, Slatkin M. Accounting for bias from sequencing error in population genetic estimates. Molecular Biology and Evolution 2008, 25:199-206. 10.1093/molbev/msm239, 17981928.
17. Axelsson E, Willerslev E, Gilbert M.T.P, Nielsen R. The effect of ancient DNA damage on inferences of demographic histories. Molecular Biology and Evolution 2008, 25:2181-2187. 10.1093/molbev/msn163, 18653730.
18. Burgess R, Yang Z. Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Molecular Biology and Evolution 2008, 25:1979-1994. 10.1093/molbev/msn148, 18603620.
19. Lynch M. Estimation of nucleotide diversity, disequilibrium coefficients, and mutation rates from high-coverage genome-sequencing projects. Molecular Biology and Evolution 2008, 25:2409-2419. 10.1093/molbev/msn185, 18725384.
20. Lottaz C, Iseli C, Jongeneel C.V, Bucher P. Modeling sequencing errors by combining hidden Markov models. Bioinformatics 2003, 19:i103-i112.
21. Long A.D, Beldade P, Macdonald S.J. Estimation of population heterozygosity and library construction-induced mutation rate from expressed sequence tag collections. Genetics 2007, 176:711-714. 10.1534/genetics.106.063610, 1893025, 17179075.
22. Slatkin M, Pollack J.L. Subdivision in an ancestral species creates asymmetry in gene trees. Molecular Biology and Evolution 2008, 25:2241-2246. 10.1093/molbev/msn172, 18689871.
23. Wesche P.L, Gaffney D.J, Keightley P.D. DNA sequence error rates in Genbank records estimated using the mouse genome as a reference. DNA Sequence 2004, 15:362-364.
24. Shendure J.A, Porreca G.J, Church G.M. Overview of DNA sequencing strategies. Current Protocols in Molecular Biology 2008, 81:7.1.1-7.1.11.
25. Watterson G.A. On the number of segregating sites in genetical models without recombination. Theoretical Population Biology 1975, 7:256-276. 10.1016/0040-5809(75)90020-9, 1145509.
26. Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics 1983, 105:437-460. 1202167, 6628982.
27. Kimura M. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 1969, 61:893-903. 1212250, 5364968.
28. Kimura M. The Neutral Theory of Molecular Evolution 1983,
29. Kingman J.F.C. The coalescent. Stochastic Processes and their Applications 1982, 13:235-248.
30. Donnelly P, Tavaré S. Coalescents and genealogical structure under neutrality. Annual Review of Genetics 1995, 29:401-421. 10.1146/annurev.ge.29.120195.002153, 8825481.
31. Fu Y.X, Li W.H. Statistical tests of neutrality of mutations. Genetics 1993, 133:693-709. 1205353, 8454210.
32. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595. 1203831, 2513255.
33. Simonsen K.L, Churchill G.A, Aquadro C.F. Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 1995, 141:413-429. 1206737, 8536987.
34. Fu Y.X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 1997, 147:915-925. 1208208, 9335623.
35. Fisher R.A. The Genetical Theory of Natural Selection 1930,
36. Wright S. Evolution in Mendelian populations. Genetics 1931, 16:97-159. 1201091, 17246615.
37. Griffiths R.C. Genealogical-tree probabilities in the infinitely-many-sites model. Journal of Mathematical Biology 1989, 27:667-680.
38. Griffiths R.C, Tavaré S. Unrooted genealogical tree probabilities in the infinitely-many-sites model. Mathematical Biosciences 1995, 127:77-98. 10.1016/0025-5564(94)00044-Z, 7734858.
39. Huelsenbeck J.P, Rannala B. Phylogenetic methods come of age: Testing hypotheses in an evolutionary context. Science 1997, 276:227-232. 10.1126/science.276.5310.227, 9092465.
40. Huse S.M, Huber J.A, Morrison H.G, Sogin M.L, Welch D.M. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biology 2007, 8:R143.1-R143.9.
41. Griffiths R.C. Ancestral inference from gene trees. Genes, Fossils, and Behaviour: An Integrated Approach to Human Evolution 2001, 137-172.
42. Kuhner M.K, Felsenstein J. Sampling among haplotype resolutions in a coalescent-based genealogy sampler. Genetic Epidemiology 2000, 19:S15-S21. 10.1002/1098-2272(2000)19:1+<::AID-GEPI3>3.0.CO;2-V, 11055365.
43. Nielsen R. Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 2000, 154:931-942. 1460954, 10655242.
44. Beerli P. Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. Bioinformatics 2006, 22:341-345. 10.1093/bioinformatics/bti803, 16317072.
45. Edwards A.W. Estimation of the branch points of a branching diffusion process. Journal of the Royal Statistical Society 1970, 32:155-174.