Evidence for the fixation of gene duplications by positive selection in Drosophila

Margarida Cardoso-Moreira, J. Roman Arguello, Srikanth Gottipati, Lawrence G Harshman, Jennifer K. Grenier, Andrew G. Clark

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

Gene duplications play a key role in the emergence of novel traits and in adaptation. But despite their centrality to evolutionary processes, it is still largely unknown how new gene duplicates are initially fixed within populations and later maintained in genomes. Long-standing debates on the evolution of gene duplications could be settled by determining the relative importance of genetic drift vs. positive selection in the fixation of new gene duplicates. Using the Drosophila Global Diversity Lines (GDL), we have combined genome-wide SNP polymorphism data with a novel set of copy number variant calls and gene expression profiles to characterize the polymorphic phase of new genes. We found that approximately half of the roughly 500 new complete gene duplications segregating in the GDL lead to significant increases in the expression levels of the duplicated genes and that these duplications are more likely to be found at lower frequencies, suggesting a negative impact on fitness. However, we also found that six of the nine gene duplications that are fixed or close to fixation in at least one of the five populations in our study show signs of being under positive selection, and that these duplications are likely beneficial because of dosage effects, with a possible role for additional mutations in two duplications. Our work suggests that in Drosophila, theoretical models that posit that gene duplications are immediately beneficial and fixed by positive selection are most relevant to explain the long-term evolution of gene duplications in this species.

Original languageEnglish (US)
Pages (from-to)787-798
Number of pages12
JournalGenome Research
Volume26
Issue number6
DOIs
StatePublished - Jun 1 2016

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Gene Duplication
Drosophila
Duplicate Genes
Genome
Genetic Drift
Transcriptome
Population
Single Nucleotide Polymorphism
Theoretical Models
Mutation
Genes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Cardoso-Moreira, M., Arguello, J. R., Gottipati, S., Harshman, L. G., Grenier, J. K., & Clark, A. G. (2016). Evidence for the fixation of gene duplications by positive selection in Drosophila. Genome Research, 26(6), 787-798. https://doi.org/10.1101/gr.199323.115

Evidence for the fixation of gene duplications by positive selection in Drosophila. / Cardoso-Moreira, Margarida; Arguello, J. Roman; Gottipati, Srikanth; Harshman, Lawrence G; Grenier, Jennifer K.; Clark, Andrew G.

In: Genome Research, Vol. 26, No. 6, 01.06.2016, p. 787-798.

Research output: Contribution to journalArticle

Cardoso-Moreira, M, Arguello, JR, Gottipati, S, Harshman, LG, Grenier, JK & Clark, AG 2016, 'Evidence for the fixation of gene duplications by positive selection in Drosophila', Genome Research, vol. 26, no. 6, pp. 787-798. https://doi.org/10.1101/gr.199323.115
Cardoso-Moreira M, Arguello JR, Gottipati S, Harshman LG, Grenier JK, Clark AG. Evidence for the fixation of gene duplications by positive selection in Drosophila. Genome Research. 2016 Jun 1;26(6):787-798. https://doi.org/10.1101/gr.199323.115
Cardoso-Moreira, Margarida ; Arguello, J. Roman ; Gottipati, Srikanth ; Harshman, Lawrence G ; Grenier, Jennifer K. ; Clark, Andrew G. / Evidence for the fixation of gene duplications by positive selection in Drosophila. In: Genome Research. 2016 ; Vol. 26, No. 6. pp. 787-798.
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