The Evolution of an α-Esterase Pseudogene Inactivated in the Drosophila melanogaster Lineage

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Abstract
Previous analyses of the α-esterase cluster of Drosophila melanogaster revealed 10 active genes and the DmαE4a-Ψ 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 DmαE4a-Ψ alleles contain numerous inactivating mutations, suggesting that pseudogene alleles are fixed in natural populations. Several lines of evidence also suggest that DmαE4a 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 θ̂ 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 DmαE4a-Ψ; and there are about half as many transitional polymorphisms as transversional ones. In contrast, the D. simulans and D. yakuba orthologs DsαE4a and DyαE4a do not have the inactivating mutations of DmαE4a-Ψ 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 DyαE4a and DsαE4a are located in sites that typically vary among active α-esterases rather than those that are usually conserved. We argue that the original αE4a gene had a function which it has lost since the divergence of the D. melanogaster and D. simulans lineages.