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MBE Advance Access published online on February 22, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn040
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Adaptive evolution of newly-emerged microRNA genes in Drosophila

Jian Lu1, Yonggui Fu2, Supriya Kumar1, Yang Shen2, Kai Zeng2, Richard Carthew3 and Chung-I Wu1,2,4

1 Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL, 60637, USA
2 State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen (Zhongshan), University, Guangzhou 510275, People's Republic of China
3 Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern, University, Evanston, IL, 60208, USA

4 Corresponding author. Email: ciwu{at}uchicago.edu; Telephone: 773-702-2565

Received for publication December 4, 2007. Revision received January 25, 2008. Accepted for publication February 4, 2008.

How often microRNA (miRNA) genes emerged and how fast they evolved soon after their emergence are some of the central questions in the evolution of miRNAs. Since most known miRNA genes are ancient and highly conserved, these questions can be best answered by identifying newly emerged miRNA genes. Among the 78 miRNA genes in Drosophila reported before 2007, only five are confirmed to be newly emerged in the genus (although many more can be found in the newly reported dataset; e.g. Lu et al. 2008; Ruby et al. 2007; Stark et al. 2007). These new miRNA genes have undergone numerous changes, even in the normally invariant mature sequences. Four of them (the miR- 310/311/312/313 cluster, denoted miR-310's) were duplicated from other conserved miRNA genes. The fifth one (miR-303) appears to be a very young gene, originating de novo from a non-miRNA sequence recently. We sequenced these five miRNA genes and their neighboring regions from a worldwide collection of D. melanogaster lines. The levels of divergence and polymorphism in these miRNA genes, vis-à-vis those of the neighboring DNA sequences, suggest that these five genes are evolving adaptively. Furthermore, the polymorphism pattern of miR-310's in D. melanogaster is indicative of hitchhiking under positive selection. Thus, a large number of adaptive changes over a long period of time may be essential for the evolution of newly-emerged miRNA genes.

Key Words: Adaptive evolution • microRNAs • Drosophila • new gene


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