Nucleotide Variation at the Gpdh Locus in the Genus Drosophila

Abstract

The Gpdh locus was sequenced in a broad range of Drosophila species. In contrast to the extreme evolutionary constraint seen at the amino acid level, the synonymous sites evolve at rates comparable to those of other genes. Gpdh nucleotide sequences were used to infer a phylogenetic tree, and the relationships among the species of the obscura group were examined in detail. A survey of nucleotide polymorphism within D. pseudoobscura revealed no amino acid variation in this species. Applying a modified McDonald-Kreitman test, the amino acid divergence between species in the obscura group does not appear to be excessive, implying that drift is adequate to explain the patterns of amino acid change at this locus. In addition, the level of polymorphism at the Gpdh locus in D. pseudoobscura is comparable to that found at other loci, as determined by a Hudson-Kreitman-Aguadé test. Thus, the pattern of nucleotide variation within and between species at the Gpdh locus is consistent with a neutral model.

Adaptive Evolution of Genes Duplicated from the Drosophila pseudoobscura neo-X Chromosome

“…None of the species with sequenced genomes are appropriate outgroups for analyzing the 14 duplicated genes described here; D. persimilis is too closely related to D. pseudoobscura, and synonymous sites are saturated between D. pseudoobscura and D. melanogaster (Richards et al 2005) or any of the other nine sequenced species (Drosophila 12 Genomes Consortium 2007). The obscura species subgroup is an ideal outgroup for three reasons: synonymous sites are not saturated between genes sampled from the obscura and pseudoobscura subgroups (Russo et al 1995;Wells 1996), the obscura subgroup is the closest relative to the pseudoobscura subgroup that does not share the D. pseudoobscura neo-X chromosome (Patterson and Stone 1952;Steinemann et al 1984), and the burst of duplication that followed the creation of the neo-X chromosome along the D. pseudoobscura lineage likely occurred after the split between the pseudoobscura and obscura subgroups (Meisel et al 2009). There are no whole-genome sequences available for any species in the obscura subgroup, so we sequenced the orthologs of 10 of the 14 duplicated genes in a strain of D. guanche collected from the Canary Islands, Spain, in 1971 (Drosophila Species Stock Center number 14011-0095.00).…”

Excessive homoplasy in an evolutionarily constrained protein

“…When the sequences of more D. melanogaster Gpdh alleles are available, an analysis of linkage disequilibrium between the K-N site and others in the vicinity should help to discern whether or not this model is correct. It is worth noting that the test of McDonald & Kreitman (1991) failed to find evidence of adaptive amino acid fixation between D. pseudoobscura and other species in the obscura group (Wells 1996). However, this test is not particularly sensitive when the number of amino acid replacements between species is small, and thus may be overly conservative in finding evidence of adaptation.…”

“…A D. miranda genomic library in XEMBL4 was provided by R. Norman, Arizona State University. DNA was extracted from flies and the Gpdh locus of each species was cloned and sequenced as described in Wells (1996). The sequence (line JR45) has been published elsewhere (Wells 1995), and the protein sequence of D. simulans was inferred from the paper ofTakano etal.…”