Molecular Biology and Evolution 17:563-575 (2000)
© 2000 Society for Molecular Biology and Evolution
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The Evolution of an 
-Esterase Pseudogene Inactivated in the Drosophila melanogaster Lineage
*Commonwealth Scientific and Industrial Research Organisation, Canberra, Australia;
Division of Botany and Zoology, Australian National University, Canberra, Australia;
and
Center for Population Biology, University of California at Davis
Abstract
Previous analyses of the 
-esterase cluster of Drosophila melanogaster revealed 10 active genes and the DmE4a-
pseudogene. Here, we reconstruct the evolution of the pseudogene from the sequences of 12 alleles from widely scattered D. melanogaster populations and single alleles from Drosophila simulans and Drosophila yakuba. All of the DmE4a- alleles contain numerous inactivating mutations, suggesting that pseudogene alleles are fixed in natural populations. Several lines of evidence also suggest that DmE4a is now evolving without selective constraint in the D. melanogaster lineage. There are three polymorphic indels which result in frameshifts; a key nucleotide of the intron splice acceptor is polymorphic; the neutral mutation parameter is the same for replacement and silent sites; one of the nonsilent polymorphisms results in a stop codon; only 1 of the 13 replacement polymorphisms is biochemically conservative; residues that are conserved among active esterases have different states in DmE4a-; and there are about half as many transitional polymorphisms as transversional ones. In contrast, the D. simulans and D. yakuba orthologs DsE4a and DyE4a do not have the inactivating mutations of DmE4a- and appear to be evolving under the purifying selection typical of protein- encoding genes. For instance, there have been more substitutions in the introns than in the exons, and more in silent sites than in replacement sites. Furthermore, most of the amino acid substitutions that have occurred between DyE4a and DsE4a are located in sites that typically vary among active -esterases rather than those that are usually conserved. We argue that the original E4a gene had a function which it has lost since the divergence of the D. melanogaster and D. simulans lineages.
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