The evolutionary history of the amylase multigene family in Drosophila pseudoobscura

In Drosophila pseudoobscura, the amylase (Amy) multigene family iscontained within a series of inversions, or gene arrangements, on the thirdchromosome. The Standard (ST), Santa Cruz (SC), and Tree Line (TL)inversions are central to the phylogeny of arrangements, and have clustersof other arrangements derived from them. The gene arrangements belonging toeach of these three clusters have a characteristic number of Amy genes,ranging from three in ST to two in SC to one in TL. This distributionpattern can reflect a history of either duplications or deletions, althoughthe data available in the past did not permit a decision between thesealternatives. We provide unambiguous evidence that three Amy genes werepresent before the divergence of the ST, SC, and TL arrangements. Thus, thecurrent status of the Amy multigene family is the result of deletions inthe TL and SC arrangements, which created three new pseudogenes: TLAmy2-psi, TL Amy3-psi, and SC Amy3- psi. Analysis of pseudogene sequencesrevealed that, in the SC and ST arrangements, pseudogene evolution has beenretarded, most likely due to the homogenization effect of gene conversion.Finally, by determining the original copy number, we have reconstructed theevolutionary history of the Amy multigene family and linked it with theevolution of the central gene arrangements.