A comparison of three estimators of the population-scaled recombination rate: Accuracy and robustness

Genetics

Volumn 171, Issue 4, 2005, Pages 2051-2062

  Smith, Nick G C ^a   Fearnhead, Paul ^a  

^a LANCASTER UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENETIC RECOMBINATION; HUMAN; MATHEMATICAL ANALYSIS; MATHEMATICAL GENETICS; MATHEMATICAL MODEL; METHODOLOGY; POPULATION GENETICS; PRIORITY JOURNAL; SEQUENCE DATABASE; SIMULATION; STATISTICAL MODEL;

COMPUTER SIMULATION; GENETICS, POPULATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MUTATION; POPULATION DENSITY; RECOMBINATION, GENETIC;

EID: 27244456489     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.104.036293     Document Type: Article

References (29)

1. CRAWFORD, D. C., T. BHANGALE, N. LI, G. HELLENTHAL, M. J. RIEDER et al., 2004 Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat. Genet. 36: 700-706.
2. FEARNHEAD, P., 2003 Consistency of estimators of the population-scaled recombination rate. Theor. Popul. Biol. 64: 67-79.
3. FEARNHEAD, P., and P. DONNELLY, 2001 Estimating recombination rates from population genetic data. Genetics 159: 1299-1318.
4. FEARNHEAD, P., and P. DONNELLY, 2002 Approximate likelihood methods for estimating local recombination rates (with discussion). J. R. Soc. Sci. Ser. B 64: 657-680.
5. FEARNHEAD, P., R. M. HARDING, J. A. SCHNEIDER, S. MYERS and P. DONNELLY, 2004 Application of coalescent methods to reveal fine-scale variation and recombination hotspots. Genetics 167: 2067-2081.
6. FRISSE, L., R. R. HUDSON, A. BARTOSZEWICZ, J. D. WALL, J. DONFACK et al., 2001 Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am. J. Hum. Genet. 69: 831-843.
7. GRIFFITHS, R. C., and P. MARJORAM, 1996 Ancestral inference from samples of DNA sequences with recombination. J. Comput. Biol. 3: 479-502.
8. HUDSON, R. R., 2001 Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
9. HUDSON, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
10. HUDSON, R. R., M. SLATKIN and W. P. MADDISON, 1992 Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
11. JEFFREYS, A. J., and C. A. MAY, 2004 Intense and highly localized gene conversion activity in human meiotic crossover hot spots. Nat. Genet. 36: 151-156.
12. JEFFREYS, A. J., L. KAUPPI and R. NEUMANN, 2001 Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet. 29: 217-222.
13. KUHNER, M. K., J. YAMATO and J. FELSENSTEIN, 2000 Maximum likelihood estimation of recombination rates from population data. Genetics 156: 1393-1401.
14. LI, N., and M. STEPHENS, 2003 Modeling LD and identifying recombination hotspots from SNP data. Genetics 165: 2213-2233.
15. MCVEAN, G. A. T., 2002 A genealogical interpretation of linkage disequilibrium. Genetics 162: 987-991.
16. MCVEAN, G. A. T., P. AWADALLA and P. FEARNHEAD, 2002 A coalescent method for detecting recombination from gene sequences. Genetics 160: 1231-1241.
17. MCVEAN, G. A. T., S. R. MYERS, S. HUNT, P. DELOUKAS, D. R. BENTLEY et al., 2004 The fine-scale structure of recombination rate variation in the human genome. Science 304: 581-584.
18. NIELSEN, R., and J. SIGNOROVITCH, 2003 Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. Theor. Popul. Biol. 63: 245-255.
19. PRITCHARD, J. K., and M. PRZEWORSKI, 2001 Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69: 1-14.
20. PTAK, S. E., K. VOELPEL and M. PRZEWORSKI, 2004 Insights into recombination from patterns of linkage disequilibrium in humans. Genetics 167: 387-397.
21. RAMBAUT, A., and N. C. GRASSLY, 1997 Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13: 235-238.
22. SPENCER, G. C. A., and G. COOP, 2004 SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics 20: 3673-3675.
23. STEPHENS, M., and P. DONNELLY, 2003 A comparison of Bayesian methods for haplotype reconstruction. Am. J. Hum. Genet. 70: 1162-1169.
24. STEPHENS, M., N. J. SMITH and P. DONNELLY, 2001 A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68: 978-989.
25. STUMPF, M. P. H., and G. A. T. MCVEAN, 2003 Estimating recombination rates from population-genetic data. Nat. Rev. Genet. 4: 959-968.
26. WALL, J. D., 2000 A comparison of estimators of the population recombination rate. Mol. Biol. Evol. 17: 156-163.
27. WALL, J. D., 2004 Estimating recombination rates using three site likelihoods. Genetics 167: 1461-1473.
28. WALL, J. D., and J. K. PRITCHARD, 2003 Haplotype blocks and LD in the human genome. Nat. Rev. Genet. 4: 587-597.
29. WALL, J. D., and M. PRZEWORSKI, 2000 When did the human population size start increasing? Genetics 155: 1865-1874.