Characterizing recurrent positive selection at fast-evolving genes in Drosophila miranda and Drosophila pseudoobscura

Genome Biology and Evolution

Volumn 2, Issue 1, 2010, Pages 371-378

  Jensen, Jeffrey D ^a,b   Bachtrog, Doris ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

Adaptation; Fast evolving genes; Genetic hitchhiking; Natural selection; Recurrent positive selection

Indexed keywords

DNA; DROSOPHILA PROTEIN;

ADAPTATION; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER SIMULATION; DROSOPHILA; GENE; GENETIC POLYMORPHISM; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SPECIES DIFFERENCE; TIME;

ADAPTATION, BIOLOGICAL; ANIMALS; BASE SEQUENCE; COMPUTER SIMULATION; DNA; DROSOPHILA; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; GENES, INSECT; GENETIC VARIATION; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; SELECTION, GENETIC; SPECIES SPECIFICITY; TIME FACTORS;

DROSOPHILA MIRANDA; DROSOPHILA PSEUDOOBSCURA;

EID: 77958489006     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evq028     Document Type: Article

References (26)

1. Andolfatto P. 2007. Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome. Genome Res. 17:1755-1762.
2. Bachtrog D. 2008. Similar rates of protein adaptation in Drosophila miranda and D. melanogaster, two species with different current effective population sizes. BMC Evol Biol. 8:334.
3. Bachtrog D, Jensen JD, Zhang Z. 2009. Accelerated adaptive evolution on a newly formed X chromosome. PLoS Biol. 7: e82.
4. Beaumont MA, Zhang W, Balding DJ. 2002. Approximate Bayesian computation in population genetics. Genetics. 162:2025-2035.
5. Hudson R. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 18:337-338.
6. Hudson RR, Kreitman M, Aguade M. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics. 116:153-159.
7. Jensen JD, Kim Y, Bauer DuMont V, Aquadro CF, Bustamante CD. 2005. Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics. 170:1401-1410.
8. Jensen JD, Thornton KR, Andolfatto P. 2008. An approximate Bayesian estimator suggests strong recurrent selective sweeps in Drosophila. PLoS Genet. 4(9):e1000198.
9. Jensen JD, Thornton KR, Aquadro CF. 2008. Inferring selection in partially sequenced regions. Mol Biol Evol. 25:438-446.
10. Jensen JD, Thornton KR, Bustamante CD, Aquadro CF. 2007. On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in non-equilibrium populations. Genetics. 176:2371-2379.
11. Jensen JD, Wong A, Aquadro CF. 2007. On statistical and functional approaches for identifying targets of positive selection. Trends Genet. 23:484-491.
12. Kim Y, Nielsen R. 2004. Linkage disequilibrium as a signature of selective sweeps. Genetics. 167:1513-1524.
13. Kim Y, Stephan W. 2002. Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics. 160:765-777.
14. Loewe L, Charlesworth B, Bartolome B, Noel V. 2006. Estimating selection on nonsynonymous mutations. Genetics. 172:1079-1092.
15. Macpherson JM, Sella G, Davis JC, Petrov DA. 2007. Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila. Genetics. 177:2083-2099.
16. McDonald JH, Kreitman M. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 351:652-654.
17. Nielsen R. 2005. Molecular signatures of natural selection. Annu Rev Genet. 39:197-218.
18. Nielsen R, et al. 2005. Genomic scans for selective sweeps using SNP data. Genome Res. 15:1566-1575.
19. Orengo DJ, Aguade M. 2010. Uncovering the footprint of positive selection on the X chromosome of Drosophila melanogaster. Mol Biol Evol. 27:153-160.
20. Przeworski M. 2002. The signature of positive selection at randomly chosen loci. Genetics. 160:1179-1189.
21. Sella G, Petrov DA, Przeworski M, Andolfatto P. 2009. Pervasive natural selection in the Drosophila genome? PLoS Genet. 5: e1000495.
22. Stephan W, Song Y, Langley CH. 2006. The hitchhiking effect on linkage disequilibrium between linked neutral loci. Genetics. 172:2647-2663.
23. Thornton KR. 2009. Automating approximate Bayesian computation by local linear regression. BMC Genet. 10:35.
24. Thornton KR, Jensen JD. 2007. Controlling the false positive rate in multi-locus genome scans for selection. Genetics. 175:737-750.
25. Wiehe TH, Stephan W. 1993. Analysis of a genetic hitchhiking model, and its application to DNA polymorphism data from Drosophila melanogaster. Mol Biol Evol. 10:842-854.
26. Wright SI, Charlesworth B. 2004. The HKA test revisited: a maximumlikelihood-ratio test of the standard neutral model. Genetics. 168:1071-1076.