Demographic inference reveals african and european admixture in the north american drosophila melanogaster population

Genetics

Volumn 193, Issue 1, 2013, Pages 291-301

  Duchen, Pablo ^a   Živković, Daniel ^a   Hutter, Stephan ^a   Stephan, Wolfgang ^a   Laurent, Stefan ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DEMOGRAPHY; DROSOPHILA MELANOGASTER; FEMALE; HISTORY; MALE; NETHERLANDS; NONHUMAN; PRIORITY JOURNAL; UNITED STATES; ZIMBABWE;

AFRICA; ANIMALS; BAYES THEOREM; COMPUTER SIMULATION; CROSSES, GENETIC; DEMOGRAPHY; DROSOPHILA MELANOGASTER; EUROPE; GENETICS, POPULATION; MODELS, GENETIC; NORTH AMERICA; POLYMORPHISM, SINGLE NUCLEOTIDE;

DROSOPHILA MELANOGASTER;

EID: 84871785145     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.145912     Document Type: Article

References (54)

1. Andolfatto, P., 2001 Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans. Mol. Biol. Evol. 18: 279-290.
2. Baudry, E., B. Viginier, and M. Veuille, 2004 Non-African populations of Drosophila melanogaster have a unique origin. Mol. Biol. Evol. 21: 1482-1491.
3. Beaumont, M. A., W. Zhang, and D. J. Balding, 2002 Approximate Bayesian Computation in population genetics. Genetics 162: 2025-2035.
4. Begun, D. J., and C. F. Aquadro, 1993 African and North American populations of Drosophila melanogaster are very different at the DNA level. Nature 365: 548-550.
5. Caracristi, G., and C. Schlötterer, 2003 Genetic differentiation between American and European Drosophila melanogaster populations could be attributed to admixture of African alleles. Mol. Biol. Evol. 20: 792-799.
6. Csilléry, K., M. G. B. Blum, and O. François, 2012 abc: an R package for approximate Bayesian computation (ABC). Methods Ecol. Evol. 3: 475-479.
7. David, J. R., and P. Capy, 1988 Genetic variation of Drosophila melanogaster natural populations. Trends Genet. 4: 106-111.
8. 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.
9. Edgar, R. C., 2004 MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797.
10. Excoffier, L., M. Foll, and R. J. Petit, 2009 Genetic consequences of range expansions. Annu. Rev. Ecol. Evol. Syst. 40: 481-501.
11. Fagundes, N. J. R., N. Ray, M. A. Beaumont, S. Neuenschwander, F. M. Salzano et al., 2007 Statistical evaluation of alternative models of human evolution. Proc. Natl. Acad. Sci. USA 104: 17614-17619.
12. Fu, Y.-X., 1995 Statistical properties of segregating sites. Theor. Popul. Biol. 48: 172-197.
13. 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.
14. Griffiths, R. C., and S. Tavaré, 1998 The age of a mutation in a general coalescent tree. Stoch. Models 14: 273-295.
15. 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.
16. Hedrick, P. W., 2011 Genetics of Populations. Jones & Bartlett, Boston.
17. Hernandez, R. D., S. H. Williamson, and C. D. Bustamante, 2007 Context dependence, ancestral misidentification, and spurious signatures of natural selection. Mol. Biol. Evol. 24: 1792-1800.
18. Howard, L. O., 1900 A contribution to the study of the insect fauna of human excrement. Proc. Washington Acad. Sci. 2: 541-604.
19. Hudson, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
20. Hutter, S., H. Li, S. Beisswanger, D. De Lorenzo, and W. Stephan, 2007 Distinctly different sex ratios in African and European populations of Drosophila melanogaster inferred from chromosomewide single nucleotide polymorphism data. Genetics 177: 469-480.
21. Jensen, J. D., Y. Kim, V. B. DuMont, C. F. Aquadro, and C. D. Bustamante, 2005 Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170: 1401-1410.
22. Jensen, J. D., K. R. Thornton, and P. Andolfatto, 2008 An approximate Bayesian estimator suggests strong, recurrent selective sweeps in Drosophila. PLoS Genet. 4: e1000198.
23. Johnson, C. W., 1913 The distribution of some species of Drosophila. Psyche 20: 202-205.
24. Kauer, M., B. Zangerl, D. Dieringer, and C. Schlötterer, 2002 Chromosomal patterns of microsatellite variability contrast sharply in African and non-African populations of Drosophila melanogaster. Genetics 160: 247-256.
25. Keller, A., 2007 Drosophila melanogaster's history as a human commensal. Curr. Biol. 17: R77-R81.
26. Kelly, J. K., 1997 A test of neutrality based on interlocus associations. Genetics 146: 1197-1206.
27. Kim, Y., and W. Stephan, 2002 Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
28. Kimura, M., 1969 The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61: 893-903.
29. Lachaise, D., M.-L. Cariou, J. R. David, F. Lemeunier, L. Tsacas et al., 1988 Historical biogeography of the Drosophila melanogaster species subgroup. Evol. Biol. 22: 159-225.
30. Laurent, S. J., A. Werzner, L. Excoffier, and W. Stephan, 2011 Approximate Bayesian analysis of Drosophila melanogaster polymorphism data reveals a recent colonization of Southeast Asia. Mol. Biol. Evol. 28: 2041-2051.
31. Li, H., and W. Stephan, 2006 Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet. 2: 1580-1589.
32. Lintner, J. A., 1882 First Annual Report on the Injurious and Other Insects of the State of New York. Weed, Parsons, Albany, NY.
33. Macpherson, J. M., G. Sella, J. C. Davis, and D. Petrov, 2007 Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila. Genetics 117: 2083-2099.
34. Nei, M., and W.-H. Li, 1979 Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76: 5269-5273.
35. 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.
36. 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.
37. Pavlidis, P., S. Hutter, and W. Stephan, 2008 A population genomic approach to map recent positive selection in model species. Mol. Ecol. 17: 3585-3598.
38. Pavlidis, P., J. D. Jensen, and W. Stephan, 2010a Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations. Genetics 185: 907-922.
39. Pavlidis, P., S. Laurent, and W. Stephan, 2010b msABC: a modification of Hudson's ms to facilitate multi-locus ABC analysis. Mol. Ecol. Res. 10: 723-727.
40. Pool, J. E., and C. F. Aquadro, 2006 History and structure of sub-Saharan populations of Drosophila melanogaster. Genetics 174: 915-929.
41. Pritchard, J. K., M. T. Seielstad, A. Perez-Lezaun, and M. W. Feldman, 1999 Population growth of human Y chromosome: a study of Y chromosome microsatellites. Mol. Biol. Evol. 16: 1791-1798.
42. Sabeti, P. C., S. F. Schaffner, B. Fry, J. Lohmueller, P. Varilly et al., 2006 Positive natural selection in the human lineage. Science 312: 1614-1620.
43. Stephan, W., and H. Li, 2007 The recent demographic and adaptive history of Drosophila melanogaster. Heredity 98: 65-68.
44. Sturtevant, A. H., 1920 Genetic studies on Drosophila simulans. I. Introduction: hybrids with Drosophila melanogaster. Genetics 5: 488-500.
45. Tajima, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
46. Tavaré, S., D. J. Balding, R. C. Griffiths, and P. Donnelly, 1997 Inferring coalescence times from DNA sequence data. Genetics 145: 505-518.
47. Tellier, A., P. Pfaffelhuber, B. Haubold, L. Naduvilezhath, L. E. Rose et al., 2011 Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum. PLoS ONE 6: e18155.
48. Wakeley, J., and J. Hey, 1997 Estimating ancestral population parameters. Genetics 145: 847-855.
49. Watterson, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
50. Wegmann, D., C. Leuenberger, and L. Excoffier, 2009 Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood. Genetics 182: 1207-1218.
51. Yukilevich, R., T. L. Turner, F. Aoki, S. V. Nuzhdin, and J. R. True, 2010 Patterns and processes of genome-wide divergence between North American and African Drosophila melanogaster. Genetics 186: 219-239.
52. Zayed, A., and C. W. Whitfield, 2008 A genome-wide signature of positive selection in ancient and recent invasive expansions of the honey bee Apis mellifera. Proc. Natl. Acad. Sci. USA 105: 3421-3426.
53. Živković, D., and T. Wiehe, 2008 Second-order moments of segregating sites under variable population size. Genetics 180: 341-357.
54. Živković, D., and W. Stephan, 2011 Analytical results on the neutral non-equilibrium allele frequency spectrum based on diffusion theory. Theor. Popul. Biol. 79: 184-191.