Challenges of detecting directional selection after a bottleneck: Lessons from Sorghum bicolor

Genetics

Volumn 173, Issue 2, 2006, Pages 953-964

  Hamblin, Martha T ^a   Casa, Alexandra M ^a   Sun, Hong ^a   Murray, Seth C ^a   Paterson, Andrew H ^b   Aquadro, Charles F ^a   Kresovich, Stephen ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BOTTLENECK POPULATION; CONTROLLED STUDY; DNA POLYMORPHISM; GENE SEQUENCE; GENEALOGY; GENETIC ANALYSIS; HAPLOTYPE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SORGHUM; SORGHUM BICOLOR;

AGRICULTURE; ANIMALS; BASE SEQUENCE; DNA, PLANT; DROSOPHILA; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GENOME, PLANT; HAPLOTYPES; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; SELECTION (GENETICS); SORGHUM; VARIATION (GENETICS); ZEA MAYS;

SORGHUM BICOLOR;

EID: 33745423085     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.105.054312     Document Type: Article

References (57)

1. ANDOLFATTO, P., and M. PRZEWORSKI, 2000 A genome-wide departure from the standard neutral model in natural populations of Drosophila. Genetics 156: 257-268.
2. BAUER DUMONT, V., and C. F. AQUADRO, 2005 Multiple signatures of positive selection downstream of Notch on the X chromosome in Drosophila melanogaster. Genetics 171: 639-653.
3. BEISSWANGER, S., W. STEPHAN and D. DE LORENZO, 2006 Evidence for a selective sweep in the wapl region of Drosophila melanogaster. Genetics 172: 265-274.
4. BOWERS, J. E., C. ABBEY, S. ANDERSON, C. CHANG, X. DRAYE et al., 2003 A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses. Genetics 165: 367-386.
5. CASA, A. M., S. E. MITCHELL, M. T. HAMBLIN, H. SUN, J. E. BOWERS et al., 2005 Diversity and selection in sorghum: simultaneous analyses using simple sequence repeats. Theor. Appl. Genet. 111: 23-30.
6. CATANIA, F., and C. SCHLOTTERER, 2005 Non-African origin of a local beneficial mutation in D. melanogaster. Mol. Biol. Evol. 22: 265-272.
7. DEPAULIS, F., and M. VEUILLE, 1998 Neutrality tests based on the distribution of haplotypes under an infinite-site model. Mol. Biol. Evol. 15: 1788-1790.
8. DOEBLEY, J., and A. STEC, 1993 Inheritance of the morphological differences between maize and teosinte: comparison of results for two F2 populations. Genetics 134: 559-570.
9. DOGGETT, H., 1988 Sorghum. Longman Scientific & Technical, Essex, England.
10. DOYLE, J. J., and J. L. DOYLE, 1987 A rapid DNA isolation procedure for small amounts of leaf tissue. Phytochem. Bull. 19: 11-15.
11. FAY, J. C., and C.-I WU, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
12. GLINKA, S., L.OMETTO, S. MOUSSET, W. STEPHAN and D. DE LORENZO, 2003 Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach. Genetics 165: 1269-1278.
13. HADDRILL, P. R., K. R. THORNTON, B. CHARLESWORTH AND P. ANDOLFATTO, 2005 Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res. 15: 790-799.
14. HAMBLIN, M. T., S. E. MITCHELL, G. M. WHITE, J. GALLEGO, R. KUKATLA et al., 2004 Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor. Genetics 167: 471-483.
15. HAMBLIN, M. T., M. G. SALAS FERNANDEZ, A. M. CASA, S. E. MITCHELL, A. H. PATERSON et al., 2005 Equilibrium processes cannot explain high levels of short- and medium-range linkage disequilibrium in the domesticated grass sorghum bicolor. Genetics 171: 1247-1256.
16. HAMMER, M. F., D. GARRIGAN, E. WOOD, J. A. WILDER, Z. MOBASHER et al., 2004 Heterogeneous patterns of variation among multiple human X-linked loci: the possible role of diversity-reducing selection in non-Africans. Genetics 167: 1841-1853.
17. HU, F. Y., D. Y. TAO, E. SACKS, B. Y. FU, P. XU et al., 2003 Convergent evolution of perenniality in rice and sorghum. Proc. Natl. Acad. Sci. USA 100: 4050-4054.
18. HUDSON, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
19. HUDSON, R. R., M. KREITMAN and M. AGUADE, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
20. INNAN, H., and Y. KIM, 2004 Pattern of polymorphism after strong artificial selection in a domestication event. Proc. Natl. Acad. Sci. USA 101: 10667-10672.
21. INNAN, H., K. ZHANG, P. MARJORAM, S. TAVARE and N. A. ROSENBERG, 2005 Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites. Genetics 169: 1763-1777.
22. KAUER, M. O., D. DIERINGER and C. SCHLOTTERER, 2003 A microsatellite variability screen for positive selection associated with the "out of Africa" habitat expansion of Drosophila melanogaster. Genetics 165: 1137-1148.
23. KIM, J. S., M. N. ISLAM-FARIDI, P. E. KLEIN, D. M. STELLY, J. H. PRICE et al., 2005 Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice. Genetics 171: 1963-1976.
24. KIMBER, C., 2000 Origins of domesticated sorghum and its early diffusion to India and China, pp. 3-98 in Sorghum, edited by C. W. SMITH and R. A. FREDERIKSEN. John Wiley, New York.
25. LI, H., and W. STEPHAN, 2005 Maximum-likelihood methods for detecting recent positive selection and localizing the selected site in the genome. Genetics 171: 377-384.
26. MARTH, G. T., E. CZABARKA, J. MURVAI and S. T. SHERRY, 2004 The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics 166: 351-372.
27. MCDONALD, J. H., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
28. NEI, M., 1987 Molecular Evolutionary Genetics. Columbia University Press, New York.
29. NORDBORG, M., T. T. HU, Y. ISHINO, J. JHAVERI, C. TOOMAJIAN et al., 2005 The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3: e196.
30. OMETTO, L., S. GLINKA, D. DE LORENZO and W. STEPHAN, 2005 Inferring the effects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation. Mol. Biol. Evol. 22: 2119-2130.
31. ORENGO, D. J., and M. AGUADE, 2004 Detecting the footprint of positive selection in a european population of Drosophila melanogaster: multilocus pattern of variation and distance to coding regions. Genetics 167: 1759-1766.
32. ORR, H. A., and A. J. BETANCOURT, 2001 Haldane's sieve and adaptation from the standing genetic variation. Genetics 157: 875-884.
33. PLUZHNIKOV, A., A. DI RIENZO and R. R. HUDSON, 2002 Inferences about human demography based on multilocus analyses of non-coding sequences. Genetics 161: 1209-1218.
34. POOL, J. E., V. BAUER DUMONT, J. L. MUELLER and C. F. AQUADRO, 2006 A scan of molecular variation leads to the narrow localization of a selective sweep affecting both Afrotropical and cosmopolitan populations of Drosophila melanogaster. Genetics 172: 1093-1105.
35. PRZEWORSKI, M., 2002 The signature of positive selection at randomly chosen loci. Genetics 160: 1179-1189.
36. PRZEWORSKI, M., G. COOP and J. D. WALL, 2005 The signature of positive selection on standing genetic variation. Evolution Int. J. Org. Evolution 59: 2312-2323.
37. ROZAS, J., J. C. SANCHEZ-DELBARRIO, X. MESSEGUER and R. ROZAS, 2003 DnaSP, DNA Polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
38. SANTIAGO, E., and A. CABALLERO, 2005 Variation after a selective sweep in a subdivided population. Genetics 169: 475-483.
39. SCHLOTTERER, C., 2002 A microsatellite-based multilocus screen for the identification of local selective sweeps. Genetics 160: 753-763.
40. SCHLOTTERER, C., 2003 Hitchhiking mapping - functional genomics from the population genetics perspective. Trends Genet. 19: 32-38.
41. SCHMID, K. J., S. RAMOS-ONSINS, H. RINGYS-BECKSTEIN, B. WEISSHAAR and T. MITCHELL-OLDS, 2005 A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure froma neutral model of DNA sequence polymorphism. Genetics 169: 1601-1615.
42. SCHMID, K. J., O. TORJEK, R. MEYER, H. SCHMUTHS, M. H. HOFFMANN et al., 2006 Evidence for a large-scale population structure of Arabidopsis thaliana from genome-wide single nucleotide polymorphism markers. Theor. Appl. Genet. 112: 1104-1114.
43. SCHOFL, G., and C. SCHLOTTERER, 2004 Patterns of microsatellite variability among X chromosomes and autosomes indicate a high frequency of beneficial mutations in non-African D. simulans. Mol. Biol. Evol. 21: 1384-1390.
44. SLATKIN, M., and T. WIEHE, 1998 Genetic hitch-hiking in a subdivided population. Genet. Res. 71: 155-160.
45. STAJICH, J. E., and M. W. HAHN, 2005 Disentangling the effects of demography and selection in human history. Mol. Biol. Evol. 22: 63-73.
46. STORZ, J. F., 2005 Using genome scans of DNA polymorphism to infer adaptive population divergence. Mol. Ecol. 14: 671-688.
47. SWIGONOVA, Z., J. LAI, J. MA, W. RAMAKRISHNA, V. LLACA et al., 2004 Close split of sorghum and maize genome progenitors. Genome Res. 14: 1916-1923.
48. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
49. TENAILLON, M. I., M. C. SAWKINS, L. K. ANDERSON, S. M. STACK, J. DOEBLEY et al., 2002 Patterns of diversity and recombination along chromosome 1 of maize (Zea mays ssp. mays L.). Genetics 162: 1401-1413.
50. TENAILLON, M. I., J. U'REN, O. TENAILLONAND B. S. GAUT, 2004 Selection versus demography: a multilocus investigation of the domestication process in maize. Mol. Biol. Evol. 21: 1214-1225.
51. THORNTON, K. R., and P. ANDOLFATTO, 2006 Approximate Bayesian Inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619.
52. VIGOUROUX, Y., M. MCMULLEN, C. T. HITTINGER, K. HOUCHINS, L. SCHULZ et al., 2002 Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc. Natl. Acad. Sci. USA 99: 9650-9655.
53. WAKELEY, J., 2004 Metapopulation models for historical inference. Mol. Ecol. 13: 865-875.
54. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
55. WRIGHT, S. I., and B. S. GAUT, 2005 Molecular population genetics and the search for adaptive evolution in plants. Mol. Biol. Evol. 22: 506-519.
56. WRIGHT, S. I., I. V. BI, S. G. SCHROEDER, M. YAMASAKI, J. F. DOEBLEY et al., 2005 The effects of artificial selection on the maize genome. Science 308: 1310-1314.
57. YAMASAKI, M., M. I. TENAILLON, I. VROH BI, S. G. SCHROEDER, H. SANCHEZ-VILLEDA et al., 2005 A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell 17: 2859-2872.