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MBE Advance Access originally published online on February 22, 2008
Molecular Biology and Evolution 2008 25(5):929-938; 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

Research Articles

Adaptive Evolution of Newly Emerged Micro-RNA Genes in Drosophila

Jian Lu*, Yonggui Fu{dagger}, Supriya Kumar*, Yang Shen{dagger}, Kai Zeng{dagger}, Anlong Xu, Richard Carthew{ddagger} and Chung-I Wu*,{dagger}

* Department of Ecology and Evolution, University of Chicago
{dagger} State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen (Zhongshan) University, Guangzhou, People's Republic of China
{ddagger} Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University

E-mail: ciwu{at}uchicago.edu.

Accepted for publication February 4, 2008.

How often micro-RNA (miRNA) genes emerged and how fast they evolved soon after their emergence are some of the central questions in the evolution of miRNAs. Because 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 5 are confirmed to be newly emerged in the genus (although many more can be found in the newly reported data set; e.g., Ruby et al. 2007; Stark et al. 2007; Lu et al. 2008). 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-310s) 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 5 miRNA genes and their neighboring regions from a worldwide collection of Drosophila melanogaster lines. The levels of divergence and polymorphism in these miRNA genes, vis-à-vis those of the neighboring DNA sequences, suggest that these 5 genes are evolving adaptively. Furthermore, the polymorphism pattern of miR-310s 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 • micro-RNAs • Drosophila • new gene

Marta L. Wayne, Associate Editor


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