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MBE Advance Access published online on January 22, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh060
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted November 18, 2003
© 2004 Society for Molecular Biology and Evolution

Original Articles

Rapid Sequence Turnover at an Intergenic Locus in Drosophila

Nadia D. Singh 1* and Dmitri A. Petrov 1

1 Department of Biological Sciences, Stanford University, 371 Serra Mall, Stanford, CA 94305-5020

* To whom correspondence should be addressed. E-mail: ndsingh{at}stanford.edu.


  Abstract

Closely related species of Drosophila tend to have similar genome sizes. The strong imbalance in favor of small deletions relative to insertions implies that the unconstrained DNA in Drosophila is unlikely to be passively inherited from even closely related ancestors, and yet the majority of DNA in Drosophila genomes is intergenic and potentially unconstrained. In an attempt to investigate the maintenance of this intergenic DNA, we studied the evolution of an intergenic locus on the fourth chromosome of the Drosophila melanogaster genome. This 1.2 Kb locus is marked by two distinct, large insertion events: a nuclear transposition of a mitochondrial sequence as well as a transposition of a non-autonomous DNA transposon DNAREP1_DM. Because we could trace the evolutionary histories of these sequences, we were able to reconstruct the length evolution of this region in some detail. We sequenced this locus in all four species of the D. melanogaster species complex: D. melanogaster, D. simulans, D. sechellia, and D. mauritiana. Although this locus is similar in size in these four species, less than ten percent of the sequence from the most recent common ancestor remains in D. melanogaster and all of its sister species. This region appears to have increased in size through several distinct insertions in the ancestor of the D. melanogaster species complex and has been shrinking since the split of these lineages. In addition, we found no evidence suggesting that the size of this locus has been maintained over evolutionary time; these results are consistent with the model of a dynamic equilibrium between persistent DNA loss through small deletions and more sporadic DNA gain through less frequent but longer insertions. The apparent stability of genome size in Drosophila may belie very rapid sequence turnover at intergenic loci.

Key Words: DNAREP1_DM, numt, intergenic, insertions, deletions, genome evolution


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