Nucleotide variation in the triosephosphate isomerase (Tpi) locus of Drosophila melanogaster and Drosophila simulans

Hasson, Esteban; Wang, I N; Zeng, Lingwen; Kreitman, Martin; Eanes, Walter F.

doi:10.1093/oxfordjournals.molbev.a025979

Cited by 50 publications

(25 citation statements)

References 57 publications

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“…This gene also appears to be involved in hybrid sterility in crosses between Heliconius sister species (Jiggins et al, 2001). Tpi has previously been used in studies of Drosophila evolution and population genetics as well as the molecular evolution of introns (Hasson et al, 1998;Kwiatowinski et al, 1995;Logsdon et al, 1995). The Tpi primers we used were designed by Owen McMillan and Dave Heckel for Heliothis (Beltr a an et al, in press;Jiggins et al, 2001).…”

Section: Pcr and Sequencingmentioning

confidence: 99%

A molecular phylogeny of the neotropical butterfly genus Anartia (Lepidoptera: Nymphalidae)

Blum

Bermingham

Dasmahapatra

2003

Molecular Phylogenetics and Evolution

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Section: Pcr and Sequencingmentioning

confidence: 99%

A molecular phylogeny of the neotropical butterfly genus Anartia (Lepidoptera: Nymphalidae)

Blum

Bermingham

Dasmahapatra

2003

Molecular Phylogenetics and Evolution

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“…Estimates of (41) for X-linked genes have been multiplied by 4/3 to make them directly comparable to estimates from autosomal loci. *Previously published data (42)(43)(44)(45)(46)(47)(48)(49)(50). For G6pd, runt, and v, a haphazardly selected subsample of eight published D. simulans alleles was used.…”

Section: ϫ5mentioning

confidence: 99%

Reduced X-linked nucleotide polymorphism inDrosophila simulans

Begun

Whitley

2000

Proc. Natl. Acad. Sci. U.S.A.

166

105

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Population genetic theory predicts that selectively driven changes of allele frequency for both beneficial and deleterious mutants reduce polymorphism at tightly linked sites. All else being equal, these reductions in polymorphism are expected to be greater when recombination rates are lower. Therefore, the empirical observation of a positive correlation between recombination rates and amounts of DNA polymorphism across the Drosophila melanogaster genome can be explained by two very different types of natural selection. Here, we evaluate alternative models of effects of selection on linked sites by comparison of X-linked and autosomal variation. We present polymorphism data from 40 genes distributed across chromosome arms X and 3R of Drosophila simulans, a sibling species of D. melanogaster. We find significantly less silent polymorphism in D. simulans on the X chromosome than on 3R, but no difference between arms for silent divergence between species. This pattern is incompatible with predictions from theoretical studies on the effect of negative selection on linked sites. We propose that some form of positive selection having greater effects on sex chromosomes than on autosomes is the better explanation for the D. simulans data.T he amount of nucleotide polymorphism in a given region of the Drosophila melanogaster genome is positively correlated with the regional recombination rate (1, 2), which varies several-fold from one part of the genome to another (e.g., ref.3). The absence of a detectable effect of varying recombination rates on amounts of nucleotide divergence between species (1, 2) rules out variation in neutral mutation rates (4) across the genome as the explanation for the polymorphism data from D. melanogaster. Two kinds of population genetic models, both of which invoke effects of natural selection on linked neutral sites, have dominated the debate as to the cause of these patterns. One model (5-7) invokes effects of selection for beneficial mutants on linked neutral sites (i.e., hitchhiking effects), whereas a second model (8-10) invokes effects of selection against deleterious mutants on linked neutral sites (i.e., background selection). Both models predict that selection reduces polymorphism at linked neutral sites and that the magnitude of this reduction is greater when recombination rates are lower. Finally, for both models there is no expectation that variation in recombination rates affects divergence between species at neutral sites (11). The qualitatively similar predictions of the two models have made it difficult to determine their relative importance. The background selection model can provide a reasonably good fit to the polymorphism data, given certain parameters of deleterious mutation rate and recombination rate in D. melanogaster (9, 10). Similarly, a simple hitchhiking model also fits the D. melanogaster polymorphism data quite well (7, 12). Attempts to distinguish hitchhiking effects from background selection based on the frequency spectrum of variation in regions of very low cr...

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“…Along with discoveries from other laboratories, we had begun a project using PCR-cloning strategies to recover the primary gene sequences for most of the pathway members (Verrelli and Eanes, 2000;Eanes, 1999;Duvernell and Eanes, 2000;Eanes et al, 1993;Hasson et al, 1998;Merritt et al, 2005). Of course, this approach became irrelevant when the genome sequence of D. melanogaster became available.…”

Section: Introductionmentioning

confidence: 99%

Molecular population genetics and selection in the glycolytic pathway

Eanes

2011

Journal of Experimental Biology

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SummaryIn this review, I discuss the evidence for differential natural selection acting across enzymes in the glycolytic pathway in Drosophila. Across the genome, genes evolve at very different rates and possess markedly varying levels of molecular polymorphism, codon bias and expression variation. Discovering the underlying causes of this variation has been a challenge in evolutionary biology. It has been proposed that both the intrinsic properties of enzymes and their pathway position have direct effects on their molecular evolution, and with the genomic era the study of adaptation has been taken to the level of pathways and networks of genes and their products. Of special interest have been the energy-producing pathways. Using both population genetic and experimental approaches, our laboratory has been engaged in a study of molecular variation across the glycolytic pathway in Drosophila melanogaster and its close relatives. We have observed a pervasive pattern in which genes at the top of the pathway, especially around the intersection at glucose 6-phosphate, show evidence for both contemporary selection, in the form of latitudinal allele clines, and inter-specific selection, in the form of elevated levels of amino acid substitutions between species. To further explore this question, future work will require corroboration in other species, expansion into tangential pathways, and experimental work to better characterize metabolic control through the pathway and to examine the pleiotropic effects of these genes on other traits and fitness components.

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Nucleotide variation in the triosephosphate isomerase (Tpi) locus of Drosophila melanogaster and Drosophila simulans

Cited by 50 publications

References 57 publications

A molecular phylogeny of the neotropical butterfly genus Anartia (Lepidoptera: Nymphalidae)

A molecular phylogeny of the neotropical butterfly genus Anartia (Lepidoptera: Nymphalidae)

Reduced X-linked nucleotide polymorphism inDrosophila simulans

Molecular population genetics and selection in the glycolytic pathway

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