Population and sex differences in Drosophila melanogaster brain gene expression

Catalán, Ana; Hütter, Stephan; Parsch, John

doi:10.1186/1471-2164-13-654

Cited by 86 publications

(103 citation statements)

References 74 publications

(94 reference statements)

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“…In all of these cases, hundreds of genes differing in expression between populations were identified. However, the overlap among the differentially expressed genes identified by each study was small, suggesting that regulatory evolution often occurs in a sex-and tissue-dependent fashion [42,43].…”

Section: (B) the Demographic History Of Drosophila Melanogastermentioning

confidence: 88%

“…This approach focuses on regulatory divergence. To date, such expression studies have been carried out using whole adult males [9,41], whole adult females [42] and the dissected brains of both sexes [43]. In all of these cases, hundreds of genes differing in expression between populations were identified.…”

Section: (B) the Demographic History Of Drosophila Melanogastermentioning

confidence: 99%

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Adaptive divergence of a transcriptional enhancer between populations ofDrosophila melanogaster

Glaser-Schmitt¹,

Catalán²,

Parsch³

2013

Phil. Trans. R. Soc. B

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ResearchAs species colonize new habitats they must adapt to the local environment. Much of this adaptation is thought to occur at the regulatory level; however, the relationships among genetic polymorphism, expression variation and adaptation are poorly understood. Drosophila melanogaster, which expanded from an ancestral range in sub-Saharan Africa around 15 000 years ago, represents an excellent model system for studying regulatory evolution. Here, we focus on the gene CG9509, which differs in expression between an African and a European population of D. melanogaster. The expression difference is caused by variation within a transcriptional enhancer adjacent to the CG9509 coding sequence. Patterns of sequence variation indicate that this enhancer was the target of recent positive selection, suggesting that the expression difference is adaptive. Analysis of the CG9509 enhancer in new population samples from Europe, Asia, northern Africa and subSaharan Africa revealed that sequence polymorphism is greatly reduced outside the ancestral range. A derived haplotype absent in sub-Saharan Africa is at high frequency in all other populations. These observations are consistent with a selective sweep accompanying the range expansion of the species. The new data help identify the sequence changes responsible for the difference in enhancer activity.

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Section: (B) the Demographic History Of Drosophila Melanogastermentioning

confidence: 88%

Section: (B) the Demographic History Of Drosophila Melanogastermentioning

confidence: 99%

Adaptive divergence of a transcriptional enhancer between populations ofDrosophila melanogaster

Glaser-Schmitt¹,

Catalán²,

Parsch³

2013

Phil. Trans. R. Soc. B

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“…As with other Drosophila studies (Catalan et al 2012;Zhao et al 2015), there was bias in the direction of latitudinal clines. For genes showing a significant effect of latitude in males, expression tended to increase at higher latitudes (southwards) more often than it decreased.…”

Section: Expression Divergence Is Stronger In Males Than In Femalessupporting

confidence: 75%

The evolution of sex-biased gene expression in Drosophila serrata

Allen¹

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Sexual reproduction is an ancient biological process and in most species, has resulted in the evolution of two distinct sexes; females that are typically categorised as producing relatively large and metabolically costly gametes, and males that produce smaller less costly gametes. Such differences between the sexes can result in discordant selection pressures where, for example, males are selected for a fast mating rate, whereas it is beneficial for females to reproduce less often. Because the sexes share a genome, such discordant selection can create an intralocus sexual conflict, where an allele can be simultaneously beneficial in one sex while being detrimental in the other. Ultimately, the resolution of intralocus sexual conflict occurs via the evolution of sexual dimorphism, which allows each sex to approach its individual fitness optimum. A prime mechanism for the evolution of sexual dimorphism is sex-biased gene expression, where males and females express the shared genome differently to produce distinct phenotypes.Sex-biased gene expression (SBGE) appears to be a common feature of dioecious species and during my PhD candidature, I studied the following aspects of the evolution of SBGE in the Australian vinegar fly Drosophila serrata. 1) A deficit of male-biased X-linked genes has been observed in several other species. I assessed the possibility that such a nonrandom distribution of sex-biased genes in D. serrata is a by-product of dosage compensation rather than selection. I found that both selection and dosage compensation likely play a part. 2) While the rapid evolution of male-biased genes is a strikingly consistent pattern of divergence between species, I asked whether the same patterns occur for divergence among populations within species spanning a latitudinal gradient. I found that the patterns are indeed reflective, and I also discovered that many more genes diverged in males than females. Because a lot of the malespecific divergence did not clinally vary with latitude, as might be expected of spatially variable natural selection, I hypothesised that male-driven divergence might be in response to stronger sexual selection on males, which may occur on a population-specific scale. 3) While comparisons of protein coding sequence between species indicate that positive selection is a possible explanation for the rapid evolution of male-biased genes, I found support for several other explanations in relation to the evolution of gene expression of male-biased genes in D.

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“…Challenges faced by Kelly's Z nS and the v statistic Both Kelly's Z nS and v have been used to infer selection in population genetic data (e.g., Catalán et al 2012;Lee et al 2013;Renzette et al 2015). However, both the construction of statistics and properties of molecular evolution may complicate the interpretation of results.…”

Section: Selection Statistics Based On Ldmentioning

confidence: 99%

“…We therefore use the OmegaPlus program to calculate v max values rather than using the standard v-statistic construction. Henceforth we use the notation v minwin;maxwin max to denote an individual run of OmegaPlus with window size flags -minwin and -maxwin set as the specified number of kilobases.Challenges faced by Kelly's Z nS and the v statistic Both Kelly's Z nS and v have been used to infer selection in population genetic data (e.g., Catalán et al 2012;Lee et al 2013; Renzette et al 2015). However, both the construction of statistics and properties of molecular evolution may complicate the interpretation of results.…”

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confidence: 99%

Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps

2016

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During a selective sweep, characteristic patterns of linkage disequilibrium can arise in the genomic region surrounding a selected locus. These have been used to infer past selective sweeps. However, the recombination rate is known to vary substantially along the genome for many species. We here investigate the effectiveness of current (Kelly's Z nS and v max ) and novel statistics at inferring hard selective sweeps based on linkage disequilibrium distortions under different conditions, including a human-realistic demographic model and recombination rate variation. When the recombination rate is constant, Kelly's Z nS offers high power, but is outperformed by a novel statistic that we test, which we call Z a : We also find this statistic to be effective at detecting sweeps from standing variation. When recombination rate fluctuations are included, there is a considerable reduction in power for all linkage disequilibrium-based statistics. However, this can largely be reversed by appropriately controlling for expected linkage disequilibrium using a genetic map. To further test these different methods, we perform selection scans on well-characterized HapMap data, finding that all three statistics-v max ; Kelly's Z nS ; and Z a -are able to replicate signals at regions previously identified as selection candidates based on population differentiation or the site frequency spectrum. While v max replicates most candidates when recombination map data are not available, the Z nS and Z a statistics are more successful when recombination rate variation is controlled for. Given both this and their higher power in simulations of selective sweeps, these statistics are preferred when information on local recombination rate variation is available.KEYWORDS linkage disequilibrium; positive selection; recombination rate; genetic map G ENOME-WIDE selection scans now form part of the standard repertoire of techniques through which to probe the evolutionary past of a population. These attempt to identify genomic regions showing evidence of nonneutral evolution by iteratively calculating a test statistic at different locations for a sample of genetic data. As the availability of genetic data and computational power has increased, so too have the number of scans performed and the range of statistics used. In the case of human genetics, thousands of putative selection signals have been suggested (Akey 2009). For the vast majority of these, it is unclear what phenotypic association may have allowed selection to operate, and a relatively small number of signals are replicated between studies.Given the large number of hypotheses tested in genome scans for selection, many signals are likely to be false positives (Kelley et al. 2006;Akey 2009;Nei et al. 2010). This concern is compounded by systematic biases related to ascertainment or data quality (Mallick et al. 2009). Distinguishing true signatures of selection is challenging, requiring a multifaceted approach (Barrett and Hoekstra 2011), but improving statistics used to infer se...

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Population and sex differences in Drosophila melanogaster brain gene expression

Cited by 86 publications

References 74 publications

Adaptive divergence of a transcriptional enhancer between populations ofDrosophila melanogaster

Adaptive divergence of a transcriptional enhancer between populations ofDrosophila melanogaster

The evolution of sex-biased gene expression in Drosophila serrata

Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps

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