Perspective An Adaptive Allelic Series Featuring Complex Gene Rearrangements Joshua M. Schmidt, Charles Robin* Genetics Department, The University of Melbourne, Melbourne, Australia An intriguing observation from some studies of adaptive change is allelic series, where adaptive alleles successive- ly replace each other at a single locus. For instance, at the Cyp6g1 locus of Drosophila melanogaster, transposable ele- ment insertions and a gene duplication event have combined to create at least two adaptive alleles in which the more derived the allele, the greater the insecticide resistance of its bearer [1]. Similarly, insecticide-resistant alleles in Culex mosquitoes have been observed replacing each other within the period of a decade [2]. Another case of an allelic series is presented in the paper by Magwire et al. [3], which identifies a new locus affect- ing sigma virus resistance in D. melano- gaster. Multiple alleles exist at this locus and they differ in their extent of gene copy number polymorphism and feature a transposable element thought to gen- erate novel transcripts. Thus, this study contributes to an emerging picture that the mutations associated with recent adaptive events may not involve regula- tory SNPs or coding SNPs, but complex gene rearrangements [1,4,5]. Further- more, the nested nature of these rear- rangements means that the order in which they arose can be deduced. The genes featured in the particular rearrangement described by Magwire etal. [3] were originally identified via a novel genome-wide screen to identify transposable element insertions at high frequencies in natural populations [6]. Unlike the situation in humans and many other vertebrates, particular trans- posable element insertions are rarely at high frequencies in Drosophila popula- tions. A survey of insertion site occu- pancy led Aminetzach and colleagues [6] to a gene, which they dubbed CHKov1, that has a DOC transposable element inserted into the coding region. This gene is one of a large cluster of 27 paralogs that encode proteins with distant similarity to choline kinases. The pattern of polymorphism around the DOC insertion suggests it was at the center of a very recent and strong selective sweep dating to between 25 and 240 years ago. What selective agent could result in such strong selection on an insect species, so recently? The link to ‘‘choline’’ motivated Aminetzach et al. [6] to test whether a commonly used class of insecticides, the organophos- phates (OPs), which target the insect nervous system by inhibiting the enzyme acetylcholine esterase, could be the selective agent driving this selective sweep at a locus implied in choline metabolism. They found that a line bearing the DOC allele had greater resistance to an OP than a control line with a similar genetic background. The new study of Magwire et al. [3] links another adaptive phenotype, viral resistance, to the CHKov genes. The sigma virus has been found to infect up to 20% of D. melanogaster flies in field populations. At least six separate genes that reduce infection rates have been mapped in D. melanogaster [7]. Sigma- resistant alleles of the ref(2)P locus of D. melanogaster have previously been char- acterized and display patterns of poly- morphism consistent with a selective sweep [8]. Magwire et al. [3] used a positional cloning approach involving some of the genetic tools available for D. melanogaster to molecularly character- ize the second of the six genes, ref(3)D. The resistant mutation involves a com- plex rearrangement of the CHKov1 and CHKov2 genes, with gene duplications derived from the allele originally char- acterized by Aminetzach et al. [6]. Thus the naturally occurring allelic series involves three alleles: the ancestral allele that is purportedly susceptible to an OP insecticide and the sigma virus, the DOC insertion allele characterized as resistant to an OP and moderately resistant to sigma viruses, and a derived, highly virus-resistant allele (alleles A, B, and C, respectively, in Figure 1). As in the case of Cyp6g1, it appears that the next step in an allelic series has arisen before the previous step has swept to fixation. What is the significance of this? We might expect that in a species with high population substructure, inde- pendent alleles may arise and compete against each other depending on the degree of gene flow. However, D. melanogaster populations are not thought of as highly structured and the fact the alleles in an allelic series are not independent, but are nested, indicates that D. melanogaster populations are large enough to increase the probability of subsequent mutation, even while the previous allele is at a low to moderate frequency. On the other hand, these results suggest mutation may still be limiting. The most adaptive allele at a gene may be two, three, or more mutational steps away. This may be because the initial adaptive allele is negatively correlated with other important traits, while the subsequent alleles ameliorate these trade offs or costs. Alternatively, the allelic series may reflect a ‘‘Red Queen’’ phenomenon, where a molecular arms race between host and pathogen means that new alleles must arise in the host species, to counter the new alleles in the pathogen species. In Citation: Schmidt JM, Robin C (2011) An Adaptive Allelic Series Featuring Complex Gene Rearrangements. PLoS Genet 7(10): e1002347. doi:10.1371/journal.pgen.1002347 Editor: David J. Begun, University of California Davis, United States of America Published October 20, 2011 Copyright: 2011 Schmidt, Robin. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The authors received no specific funding for this article. Competing Interests: The authors have declared that no competing interests exist. * E-mail: crobin@unimelb.edu.au PLoS Genetics | www.plosgenetics.org 1 October 2011 | Volume 7 | Issue 10 | e1002347