Genome-wide analysis in Drosophila reveals age-specific effects of SNPs on fitness traits

Durham, Mary F.; Magwire, Michael M.; Stone, Eric A.; Leips, Jeff

doi:10.1038/ncomms5338

Cited by 127 publications

(173 citation statements)

References 54 publications

(75 reference statements)

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“…Although little is known about the specific functions of senseless-2 , this gene was found to be differentially expressed between strains that had contrasting inbreeding effects on cold tolerance (Vermeulen et al 2013). Other SNPs at this gene have been associated with paraquat resistance and fecundity (Weber et al 2012; Durham et al 2014). senseless-2 was also predicted to regulate neuroanatomy-associated genes (Zwarts et al 2015).…”

Section: Discussionmentioning

confidence: 99%

Parallel Evolution of Cold Tolerance Within Drosophila melanogaster

Pool

Braun²,

Lack

2016

Mol Biol Evol

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Drosophila melanogaster originated in tropical Africa before expanding into strikingly different temperate climates in Eurasia and beyond. Here, we find elevated cold tolerance in three distinct geographic regions: beyond the well-studied non-African case, we show that populations from the highlands of Ethiopia and South Africa have significantly increased cold tolerance as well. We observe greater cold tolerance in outbred versus inbred flies, but only in populations with higher inversion frequencies. Each cold-adapted population shows lower inversion frequencies than a closely-related warm-adapted population, suggesting that inversion frequencies may decrease with altitude in addition to latitude. Using the FST-based “Population Branch Excess” statistic (PBE), we found only limited evidence for parallel genetic differentiation at the scale of ∼4 kb windows, specifically between Ethiopian and South African cold-adapted populations. And yet, when we looked for single nucleotide polymorphisms (SNPs) with codirectional frequency change in two or three cold-adapted populations, strong genomic enrichments were observed from all comparisons. These findings could reflect an important role for selection on standing genetic variation leading to “soft sweeps”. One SNP showed sufficient codirectional frequency change in all cold-adapted populations to achieve experiment-wide significance: an intronic variant in the synaptic gene Prosap. Another codirectional outlier SNP, at senseless-2, had a strong association with our cold trait measurements, but in the opposite direction as predicted. More generally, proteins involved in neurotransmission were enriched as potential targets of parallel adaptation. The ability to study cold tolerance evolution in a parallel framework will enhance this classic study system for climate adaptation.

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Section: Discussionmentioning

confidence: 99%

Parallel Evolution of Cold Tolerance Within Drosophila melanogaster

Pool

Braun²,

Lack

2016

Mol Biol Evol

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“…Functional disruption of scrib causes neoplastic overgrowth and results in manifest neuron development (Albertson and Doe 2003). In addition, scrib also contributes to variation in age-specific fitness traits, olfactory memory, and olfactory perception (Durham et al 2014; Arya et al 2015; Walkinshaw et al 2015; Cervantes-Sandoval et al 2016). DIP-η ( Dpr-interacting protein η ) is one member DIP protein family (Özkan et al 2013), whose interactions with DPR protein family were identified to form a network that is required for synaptic connectivity (Carrillo et al 2015).…”

Section: Discussionmentioning

confidence: 99%

Genetic Architecture of Natural Variation Underlying Adult Foraging Behavior That Is Essential for Survival of Drosophila melanogaster

Ycg

Yang

et al. 2017

Genome Biology and Evolution

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Foraging behavior is critical for the fitness of individuals. However, the genetic basis of variation in foraging behavior and the evolutionary forces underlying such natural variation have rarely been investigated. We developed a systematic approach to assay the variation in survival rate in a foraging environment for adult flies derived from a wild Drosophila melanogaster population. Despite being such an essential trait, there is substantial variation of foraging behavior among D. melanogaster strains. Importantly, we provided the first evaluation of the potential caveats of using inbred Drosophila strains to perform genome-wide association studies on life-history traits, and concluded that inbreeding depression is unlikely a major contributor for the observed large variation in adult foraging behavior. We found that adult foraging behavior has a strong genetic component and, unlike larval foraging behavior, depends on multiple loci. Identified candidate genes are enriched in those with high expression in adult heads and, demonstrated by expression knock down assay, are involved in maintaining normal functions of the nervous system. Our study not only identified candidate genes for foraging behavior that is relevant to individual fitness, but also shed light on the initial stage underlying the evolution of the behavior.

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“…To map a trait of interest, a researcher can order the DGRP flies from the Bloomington Stock Center (http://flystocks.bio.indiana.edu/), measure phenotypes in these lines, and access the genome data to perform analyses (http://dgrp2.gnets.ncsu.edu/). GWAS analyses using these lines have identified significant genomic associations with sleep traits (Harbison et al 2013), life span and fecundity (Durham et al 2014), olfactory behavior (Arya et al 2015), abdominal pigmentation (Dembeck et al 2015), starvation resistance, and startle response (Mackay et al 2012;Ober et al 2012). In several cases, the genes identified in these studies have orthologs implicated in similar phenotypes in humans (e.g., Harbison et al 2013).…”

Section: Evolutionary Genetics and Molecular Evolutionmentioning

confidence: 99%

Genetics on the Fly: A Primer on theDrosophilaModel System

et al. 2015

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Fruit flies of the genus Drosophila have been an attractive and effective genetic model organism since Thomas Hunt Morgan and colleagues made seminal discoveries with them a century ago. Work with Drosophila has enabled dramatic advances in cell and developmental biology, neurobiology and behavior, molecular biology, evolutionary and population genetics, and other fields. With more tissue types and observable behaviors than in other short-generation model organisms, and with vast genome data available for many species within the genus, the fly's tractable complexity will continue to enable exciting opportunities to explore mechanisms of complex developmental programs, behaviors, and broader evolutionary questions. This primer describes the organism's natural history, the features of sequenced genomes within the genus, the wide range of available genetic tools and online resources, the types of biological questions Drosophila can help address, and historical milestones.

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Genome-wide analysis in Drosophila reveals age-specific effects of SNPs on fitness traits

Cited by 127 publications

References 54 publications

Parallel Evolution of Cold Tolerance Within Drosophila melanogaster

Parallel Evolution of Cold Tolerance Within Drosophila melanogaster

Genetic Architecture of Natural Variation Underlying Adult Foraging Behavior That Is Essential for Survival of Drosophila melanogaster

Genetics on the Fly: A Primer on theDrosophilaModel System

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