A bayesian heterogeneous analysis of variance approach to inferring recent selective sweeps

Genetics

Volumn 173, Issue 4, 2006, Pages 2357-2370

  Marshall, John M ^a   Weiss, Robert E ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICA; ALLELE; ANOPHELES GAMBIAE; ARTICLE; BAYES THEOREM; BOTTLENECK POPULATION; GENE FREQUENCY; GENETIC ANALYSIS; GENETIC HETEROGENEITY; GENETIC PARAMETERS; GENOME ANALYSIS; INSECT GENETICS; NONHUMAN; PRIORITY JOURNAL;

ALLELES; ANIMALS; ANOPHELES GAMBIAE; CHROMOSOMES; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GENOME, INSECT; MICROSATELLITE REPEATS; MODELS, GENETIC; QUANTITATIVE TRAIT LOCI; RECOMBINATION, GENETIC; SELECTION (GENETICS);

ANOPHELES GAMBIAE;

EID: 33747854119     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.105.053314     Document Type: Article

References (46)

1. AYALA, F. J., and M. COLUZZI, 2005 Chromosome speciation: humans, Drosophila and mosquitoes. Proc. Natl. Acad. Sci. USA 102: 6535-6542.
2. BRINKMANN, B., M. KLINTSCHAR, F. NEUHUBER, J. HUHNE and B. ROLF, 1998 Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat. Am. J. Hum. Genet. 62: 1408-1415.
3. BROWN, K. M., L. M. BURK, L. M. HENAGAN and M. A. F. NOOR, 2004 A test of the chromosomal rearrangement model of speciation in Drosophila pseudoobscura. Evolution 58: 1856-1860.
4. COLUZZI, M., 1982 Spatial distribution of chromosomal inversions and speciation in Anopheline mosquitoes, pp. 143-153 in Mechanisms of Speciation, edited by C. BARIGOZZI. A. R. Liss, New York.
5. COLUZZI, M., A. SABATINI, A. DELLA TORRE, M. DI DECO and V. PETRARCA, 2002 A polytene chromosome analysis of the Anopheles gambiae complex. Science 298: 1415-1418.
6. COOK, R., and S. WEISBERG, 1982 Residuals and Influence in Regression. Chapman & Hall, New York.
7. DIB, C., S. FAURE, C. FIZAMES, D. SAMSON, N. DROUOT et al., 1996 A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380: 152-154.
8. DI RIENZO, A., A. C. PETERSON, J. C. GARZA, A. M. VALDES, M. SLATKIN et al., 1994 Mutational processes of simple-sequence repeat loci in human populations. Proc. Natl. Acad. Sci. USA 91: 3166-3170.
9. EWENS, W. J., 1972 The sampling theory of selectively neutral alleles. Theor. Popul. Biol. 3: 87-112.
10. GELMAN, J., J. CARLIN, H. STERN and D. RUBIN, 1995 Bayesian Data Analysis. Chapman & Hall, New York.
11. GEMAN, S., and D. GEMAN, 1984 Stochastic relaxation, Gibbs distributions and the Bayesian restoration of images. IEEE Trans. Patt. Anal. Machine Intell. 6: 721-741.
12. GOLDMAN, N., and Z. YANG, 1994 A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11: 725-736.
13. GOLDSTEIN, D. B., A. RUIZ LINEARES, L. L. CAVALLI-SFORZA and M. W. FELDMAN, 1995 An evaluation of genetic distances for use with microsatellite loci. Genetics 139: 463-471.
14. HARR, B., and C. SCHLÖTTERER, 2000 Long microsatellite alleles in Drosophila melanogaster have a downward mutation bias and short persistence times, which cause their genome-wide underrepresentation. Genetics 155: 1213-1220.
15. HARR, B., B. ZANGERL, G. BREM and C. SCHLÖTTERER, 1998 Conservation of locus specific microsatellite variability across species: a comparison of two Drosophila sibling species D. melanogaster and D. simulans. Mol. Biol. Evol. 15: 176-184.
16. HASTINGS, W. K., 1970 Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97-109.
17. HUDSON, R. R., 1990 Gene genealogies and the coalescent process, pp. 1-44 in Oxford Surveys in Evolutionary Biology, edited by D. FUTUYAMA and J. ANTONOVICS. Oxford University Press, Oxford.
18. HUDSON, R. R., M. KRIETMAN and M. AGUADE, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
19. KIRKPATRICK, M., and N. BARTON, 2006 Chromosome inversions, local adaptation and speciation. Genetics 173: 419-434.
20. LANGE, K., 1997 Mathematical and Statistical Methods for Genetic Analysis. Springer-Verlag, New York.
21. LANZARO, G., Y. TOURE, J. CARNAHAN, L. ZHENG, G. DOLO et al., 1998 Complexities in the genetic structure of Anopheles gambiae populations in West Africa as revealed by microsatellite DNA analysis. Proc. Natl. Acad. Sci. USA 95: 14260-14265.
22. LEWONTIN, R. C., and J. KRAKAUER, 1973 Distribution of gene frequency as a test of the theory of selective neutrality of polymorphisms. Genetics 74: 175-195.
23. LUIKART, G., 2003 The power and promise of population genomics. Nat. Rev. 4: 981-994.
24. MATHIOPOULOS, K. D., and G. C. LANZARO, 1995 Distribution of genetic diversity in relation to chromosomal inversions in the malaria mosquito Anopheles gambiae. J. Mol. Evol. 40: 578-584.
25. MAYNARD SMITH, J., and J. HAIGH, 1974 The hitch-hiking effect of a favorable gene. Genet. Res. 23: 23-35.
26. MCDONALD, J. H., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
27. MORAN, P. A. P., 1975 Wandering distributions and electrophoretic profile. Theor. Popul. Biol. 8: 318-330.
28. NAVARRO, A., and N. H. BARTON, 2003a Accumulating postzygotic isolation genes in parapatry: a new twist on chromosomal speciation. Evolution 57: 447-459.
29. NAVARRO, A., and N. H. BARTON, 2003b Chromosomal speciation and molecular divergence - Accelerated evolution in rearranged chromosomes. Science 300: 321-324.
30. NIELSEN, R., 2001 Statistical tests of selective neutrality in the age of genomics. Heredity 86: 641-647.
31. NIELSEN, R., S. WILLIAMSON, Y. KIM, M. J. HUBISZ, A. G. CLARK et al., 2005 Genomic scans for selective sweeps using SNP data. Genome Res. 15: 1566-1575.
32. OHTA, T., and M. KIMURA, 1973 A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet. Res. 22: 201-204.
33. SCHLÖTTERER, C., 2001 A microsatellite-based multilocus screen for the identification of local selective sweeps. Genetics 160: 753-763.
34. SCHLÖTTERER, C., and T. WIEHE, 1999 Microsatellites, a neutral marker to infer selective sweeps, pp. 238-248 in Microsatellites - Evolution and Applications, edited by D. GOLDSTEIN and C. SCHLÖTTERER. Oxford University Press, Oxford.
35. SCHLÖTTERER, C., C. VOGL and D. TAUTZ, 1997 Polymorphism and locus-specific effects on polymorphism at microsatellite loci in natural Drosophila melanogaster populations. Genetics 146: 309-320.
36. SIMONSEN, K. L., G. A. CHURCHILL and C. F. AQUADRO, 1995 Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 141: 413-429.
37. SLATKIN, M., 1995 Hitchhiking and associative overdominance at a microsatellite locus. Mol. Biol. Evol. 12: 473-480.
38. SPIEGELHALTER, D. J., A. THOMAS, N. G. BEST and D. LUNN, 2004 WinBUGS Version 1.4.1 User Manual. MRC Biostatistics Unit, Cambridge, UK.
39. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
40. TAYLOR, C., and N. MANOUKIS, 2003 Effective population size in relation to genetic modification of Anopheles gambiae sensu stricto, pp. 133-146 in Ecological Aspects for Application of Genetically Modified Mosquitoes, edited by W. TAKKEN and T. W. SCOTT. Kluwer Academic, Dordrecht, The Netherlands.
41. TAYLOR, C., Y. T. TOURE, J. CARNAHAN, D. E. NORRIS, G. DOLO et al., 2000 Gene flow among populations of the Malaria vector Anopheles gambiae, in Mali, West Africa. Genetics 157: 743-750.
42. TRIPET, F., G. DOLO and G. C. LANZARO, 2005 Multilevel analyses of genetic differentiation in Anopheles gambiae s.s. reveal patterns of gene flow important for malaria-fighting mosquito projects. Genetics 169: 313-324.
43. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 10: 256-276.
44. WEBER, J. L., and C. WONG, 1993 Mutation of human short tandem repeats. Hum. Mol. Genet. 2: 1123-1128.
45. WIEHE, T., 1998 The effect of selective sweeps on the variance of allele distribution of a linked multi-allele locus-hitchhiking of microsatellites. Theor. Popul. Biol. 53: 272-283.
46. WIERDL, M., M. DOMINSKA and T. D. PETES, 1997 Microsatellite instability in yeast: dependence on the length of the microsatellite. Genetics 146: 769-779.