Population size changes reshape genomic patterns of diversity

Evolution

Volumn 61, Issue 12, 2007, Pages 3001-3006

  Pool, John E ^a   Nielsen, Rasmus ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Autosomal variation; Human genome diversity; Population bottleneck; Population history; X linked variation

Indexed keywords

EMPIRICAL ANALYSIS; EVOLUTION; GENETIC VARIATION; GENOMICS; POPULATION BOTTLENECK; POPULATION SIZE;

ANIMAL; ARTICLE; BIODIVERSITY; BIOLOGICAL MODEL; GENETIC VARIABILITY; GENOME; HUMAN; MOUSE; POPULATION DENSITY; POPULATION DYNAMICS;

ANIMALS; BIODIVERSITY; GENOME; HUMANS; MICE; MODELS, GENETIC; POPULATION DENSITY; POPULATION DYNAMICS; VARIATION (GENETICS);

EID: 36549065630     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2007.00238.x     Document Type: Article

References (38)

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. Aquadro, C. F., D. J. Begun, and E. C. Kindahl. 1994. Selection, recombination and DNA polymorphism in Drosophila. Pp. 46 56 in B. Golding, ed. Non-neutral evolution. Chapman & Hall, New York.
3. Baines, J. F., and B. Harr. 2007. Reduced X-linked diversity in derived populations of house mice. Genetics 175 : 1911 1921.
4. Bauer, V. L., and C. F. Aquadro. 1997. Rates of DNA sequence evolution are not sex-biased in Drosophila melanogaster and D. simulans. Mol. Biol. Evol. 14 : 1252 1257.
5. Betancourt, A. J., Y. Kim, and H. A. Orr. 2004. A pseudohitchhiking model of X vs. autosomal diversity. Genetics 168 : 2261 2269.
6. Caballero, A. 1995. On the effective size of populations with separate sexes, with particular reference to sex-linked genes. Genetics 139 : 1007 1011.
7. Charlesworth, B. 1996. Background selection and patterns of genetic diversity in Drosophila melanogaster. Genet. Res. 134 : 1289 1303.
8. Charlesworth, B. 2001. The effect of life-history and mode of inheritance on neutral genetic variability. Genet. Res., Camb. 77 : 153 166.
9. Charlesworth, B., J. A. Coyne, and N. H. Barton. 1987. The relative rates of evolution of sex chromosomes and autosomes. Am. Nat. 130 : 113 146.
10. Fay, J. C., and C.-I. Wu. 1999. A human population bottleneck can account for the discordance between patterns of mitochondrial versus nuclear DNA variation. Mol. Biol. Evol. 16 : 1003 1005.
11. Fischer, A., J. Pollack, O. Thalmann, B. Nikel, and S. Pääbo. 2006. Demographic history and genetic differentiation in apes. Curr. Biol. 16 : 1133 1138.
12. Haddrill, P., 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.
13. Hey, J. 1997. Mitochondrial and nuclear genes present conflicting portraits of human origins. Mol. Bio. Evol. 14 : 166 172.
14. Hey, J., and E. Harris. 1999. Population bottlenecks and patterns of human polymorphism. Mol. Biol. Evol. 16 : 1423 1426.
15. Hudson, R. R. 1983. Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23 : 183 201.
16. Jesus, F. F., J. F. Wilkins, V. N. Solferini, and J. Wakeley. 2006. Expected coalescence times and segregating sites in a model of glacial cycles. Genet. Mol. Res. 5 : 466 474.
17. Kaessmann, H., V. Wiebe, G. Weiss, and S. Pääbo. 2001. Great ape DNA sequences reveal a reduced diversity and an expansion in humans. Nat. Genet. 27 : 155 156.
18. 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.
19. Kauer, M., D. Dieringer, and C. Schlötterer. 2003. A microsatellite variability screen for positive selection associated with the "out of Africa" habitat expansion of Drosophila melanogaster. Genetics 165 : 1137 1148.
20. Kimura, M. 1969. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutation. Genetics 61 : 893 903.
21. Kingman, J. F. C. 1982a. The coalescent. Stochastic Process. Appl. 13 : 235 248.
22. Kingman, J. F. C. 1982b. On the genealogy of large populations. J. Appl. Probab. 19A : 27 43.
23. Laporte, V., and B. Charlesworth. 2002. Effective population size and population subdivision in demographically structured populations. Genetics 162 : 501 519.
24. Lawson Handley, L. J., L. Berset-Brändli, and N. Perrin. 2006. Disentangling reasons for low Y chromosome variation in the greater white-toothed shrew Crocidura russula. Genetics 173 : 935 942.
25. Li, W.-H. 1977. Distribution of nucleotide differences between two randomly chosen cistrons in a finite population. Genetics 85 : 331 337.
26. Li, W.-H., S. Yi, and K. Makova. 2002. Male-driven evolution. Curr. Op. Gen. Dev. 12 : 650 656.
27. 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 : 2219 2230.
28. Orr, H. A., and A. J. Betancourt. 2001. Haldane's sieve and adaptation from the standing genetic variation. Genetics 157 : 875 884.
29. Pascual, M., M. P. Chapuis, F. Mestres, J. Balanya, R. B. Huey, G. W. Gilchrist, L. Serra, and A. Estoup. 2007. Introduction history of Drosophila subobscura in the New World: a microsatellite-based survey using ABC methods. Mol. Ecol. 16 : 3069 3083.
30. Polanski, A., M. Kimmel, and R. Chakraborty. 1998. Application of a time-dependent coalescence process for inferring the history of population size changes from DNA sequence data. Proc. Natl. Acad. Sci. USA 95 : 5456 5461.
31. Prevosti, A., G. Ribo, L. Serra, M. Aguade, J. Balana, M. Monclus, and F. Mestres. 1988. Colonization of America by Drosophila subobscura: Experiment in natural populations that supports the adaptive role of chromosomal-inversion polymorphism. Proc. Natl. Acad. Sci. USA 85 : 5597 5600.
32. Reiland, J., S. Hodge, and M. A. F. Noor. 2002. Strong founder effect in Drosophila pseudoobscura colonizing New Zealand from North America. J. Heredity 93 : 415 420.
33. Rhesus Macaque Genome Sequencing and Analysis Consortium. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316 : 222 234.
34. Rogers, A. R., and H. C. Harpending. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9 : 552 569.
35. Slatkin, M., and R. R. Hudson. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129 : 555 562.
36. Thornton, K., D. Bachtrog, and P. Andolfatto. 2006. X chromosomes and autosomes evolve at similar rates in Drosophila: no evidence for faster-X protein evolution. Genome Res. 16 : 498 504.
37. Wall, J. D., P. Andolfatto, and M. Przeworski. 2002. Testing models of selection and demography in Drosophila simulans. Genetics 162 : 203 216.
38. Yu, N., F.-C. Chen, S. Ota, L. B. Jorde, P. Pamilo, L. Patthy, M. Ramsey, T. Jenkins, S.-K. Shyue, and W.-H. Li. 2002. Larger genetic differences within Africans than between Africans and Eurasians. Genetics 161 : 269 274.