Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Jan 13;17(1):15.
doi: 10.1186/s12862-016-0857-z.

A Genome-Wide Scan for Genes Under Balancing Selection in Drosophila Melanogaster

Affiliations
Free PMC article

A Genome-Wide Scan for Genes Under Balancing Selection in Drosophila Melanogaster

Myriam Croze et al. BMC Evol Biol. .
Free PMC article

Abstract

Background: In the history of population genetics balancing selection has been considered as an important evolutionary force, yet until today little is known about its abundance and its effect on patterns of genetic diversity. Several well-known examples of balancing selection have been reported from humans, mice, plants, and parasites. However, only very few systematic studies have been carried out to detect genes under balancing selection. We performed a genome scan in Drosophila melanogaster to find signatures of balancing selection in a derived (European) and an ancestral (African) population. We screened a total of 34 genomes searching for regions of high genetic diversity and an excess of SNPs with intermediate frequency.

Results: In total, we found 183 candidate genes: 141 in the European population and 45 in the African one, with only three genes shared between both populations. Most differences between both populations were observed on the X chromosome, though this might be partly due to false positives. Functionally, we find an overrepresentation of genes involved in neuronal development and circadian rhythm. Furthermore, some of the top genes we identified are involved in innate immunity.

Conclusion: Our results revealed evidence of genes under balancing selection in European and African populations. More candidate genes have been found in the European population. They are involved in several different functions.

Keywords: Balancing selection; Drosophila melanogaster; Genome scan; Population genetics.

Figures

Fig. 1
Fig. 1
Proportion of candidate windows as a function of window size (in bp) for each chromosome arm (2L, 2R, 3L, 3R and X) in the African and the European populations
Fig. 2
Fig. 2
Power analysis for different window sizes (in bp) for the two statistics θw and Tajima’s D for the African and European populations. The overlap between the distributions of simulations with and without selection is represented on the y-axis
Fig. 3
Fig. 3
Map of the genes CG15818 and chm. In a, the green bar represents the region of interest in the African population and the red bar represents the region of interest in the European population. In the case of the African population, the region of interest is larger as two contiguous candidate windows are significant. The Tajima’s D (b) and θw (c) values are plotted for a 1-kb sliding window across the genes CG15818 and chm for both the European and African populations. Plot of θw for a 1-kb window across the gene CG15818 and chm for the European and African populations. The x-axis represents the position on the chromosome and the y-axis, the values of θw. Plot of Tajima\'s D for a 1-kb window across the gene CG15818 and chm for the European and African populations. The x-axis represents the position on the chromosome and the y-axis, the values of Tajima\'s D. Map of the genes CG15818 and chm. the green bar represents the region of interest in the African population and the red bar represents the region of interest in the European population

Similar articles

See all similar articles

Cited by 7 articles

See all "Cited by" articles

References

    1. Dobzhansky T. A review of some fundamental concepts and problems of population genetics. Cold Spring Harb Symp Quant Biol. 1955;20:1–15. doi: 10.1101/SQB.1955.020.01.003. - DOI - PubMed
    1. Soejima M, Tachida H, Tsuneoka M, Takenaka O, Kimura H, Koda Y. Nucleotide sequence analyses of human complement 6 (C6) gene suggest balancing selection. Ann Hum Genet. 2005;69(Pt 3):239–252. doi: 10.1046/J.1469-1809.2005.00165.x. - DOI - PubMed
    1. Grigorova M, Rull K, Laan M. Haplotype structure of FSHB, the beta-subunit gene for fertility-associated follicle-stimulating hormone: possible influence of balancing selection. Ann Hum Genet. 2007;71(Pt 1):18–28. doi: 10.1111/j.1469-1809.2006.00299.x. - DOI - PMC - PubMed
    1. Andrés AM, Hubisz MJ, Indap A, Torgerson DG, Degenhardt JD, Boyko AR, Gutenkunst RN, White TJ, Green ED, Bustamante CD, et al. Targets of balancing selection in the human genome. Mol Biol Evol. 2009;26(12):2755–2764. doi: 10.1093/molbev/msp190. - DOI - PMC - PubMed
    1. Thomas JC, Godfrey PA, Feldgarden M, Robinson DA. Candidate targets of balancing selection in the genome of Staphylococcus aureus. Mol Biol Evol. 2012;29(4):1175–1186. doi: 10.1093/molbev/msr286. - DOI - PMC - PubMed

LinkOut - more resources

Feedback