Quantitative trait loci affecting life span in replicated populations of Drosophila melanogaster. I. Composite interval mapping

Genetic, Environmental, and Stochastic Components of Lifespan Variability: The Drosophila Paradigm

Lifespan is a complex quantitative trait involving genetic and non-genetic factors as well as the peculiarities of ontogenesis. As with all quantitative traits, lifespan shows considerable variation within populations and between individuals. Drosophila, a favourite object of geneticists, has greatly advanced our understanding of how different forms of variability affect lifespan. This review considers the role of heritable genetic variability, phenotypic plasticity and stochastic variability in controlling lifespan in Drosophila melanogaster. We discuss the major historical milestones in the development of the genetic approach to study lifespan, the breeding of long-lived lines, advances in lifespan QTL mapping, the environmental factors that have the greatest influence on lifespan in laboratory maintained flies, and the mechanisms, by which individual development affects longevity. The interplay between approaches to study ageing and lifespan limitation will also be discussed. Particular attention will be paid to the interaction of different types of variability in the control of lifespan.

Genetic Basis of Increased Lifespan and Postponed Senescence in Drosophila melanogaster

Limited lifespan and senescence are near-universal phenomena. These quantitative traits exhibit variation in natural populations due to the segregation of many interacting loci and from environmental effects. Due to the complexity of the genetic control of lifespan and senescence, our understanding of the genetic basis of variation in these traits is incomplete. Here, we analyzed the pattern of genetic divergence between long-lived (O) Drosophila melanogaster lines selected for postponed reproductive senescence and unselected control (B) lines. We quantified the productivity of the O and B lines and found that reproductive senescence is maternally controlled. We therefore chose 57 candidate genes that are expressed in ovaries, 49 of which have human orthologs, and assessed the effects of RNA interference in ovaries and accessary glands on lifespan and reproduction. All but one candidate gene affected at least one life history trait in one sex or productivity week. In addition, 23 genes had antagonistic pleiotropic effects on lifespan and productivity. Identifying evolutionarily conserved genes affecting increased lifespan and delayed reproductive senescence is the first step toward understanding the evolutionary forces that maintain segregating variation at these loci in nature and may provide potential targets for therapeutic intervention to delay senescence while increasing lifespan.

Genetic analysis of variation in lifespan using a multiparental advanced intercross Drosophila mapping population

BACKGROUND

Considerable natural variation for lifespan exists within human and animal populations. Genetically dissecting this variation can elucidate the pathways and genes involved in aging, and help uncover the genetic mechanisms underlying risk for age-related diseases. Studying aging in model systems is attractive due to their relatively short lifespan, and the ability to carry out programmed crosses under environmentally-controlled conditions. Here we investigate the genetic architecture of lifespan using the Drosophila Synthetic Population Resource (DSPR), a multiparental advanced intercross mapping population.

RESULTS

We measured lifespan in females from 805 DSPR lines, mapping five QTL (Quantitative Trait Loci) that each contribute 4-5 % to among-line lifespan variation in the DSPR. Each of these QTL co-localizes with the position of at least one QTL mapped in 13 previous studies of lifespan variation in flies. However, given that these studies implicate >90 % of the genome in the control of lifespan, this level of overlap is unsurprising. DSPR QTL intervals harbor 11-155 protein-coding genes, and we used RNAseq on samples of young and old flies to help resolve pathways affecting lifespan, and identify potentially causative loci present within mapped QTL intervals. Broad age-related patterns of expression revealed by these data recapitulate results from previous work. For example, we see an increase in antimicrobial defense gene expression with age, and a decrease in expression of genes involved in the electron transport chain. Several genes within QTL intervals are highlighted by our RNAseq data, such as Relish, a critical immune response gene, that shows increased expression with age, and UQCR-14, a gene involved in mitochondrial electron transport, that has reduced expression in older flies.

CONCLUSIONS

The five QTL we isolate collectively explain a considerable fraction of the genetic variation for female lifespan in the DSPR, and implicate modest numbers of genes. In several cases the candidate loci we highlight reside in biological pathways already implicated in the control of lifespan variation. Thus, our results provide further evidence that functional genetics tests targeting these genes will be fruitful, lead to the identification of natural sequence variants contributing to lifespan variation, and help uncover the mechanisms of aging.

The Genomic Basis of Postponed Senescence in Drosophila melanogaster

Natural populations harbor considerable genetic variation for lifespan. While evolutionary theory provides general explanations for the existence of this variation, our knowledge of the genes harboring naturally occurring polymorphisms affecting lifespan is limited. Here, we assessed the genetic divergence between five Drosophila melanogaster lines selected for postponed senescence for over 170 generations (O lines) and five lines from the same base population maintained at a two week generation interval for over 850 generations (B lines). On average, O lines live 70% longer than B lines, are more productive at all ages, and have delayed senescence for other traits than reproduction. We performed population sequencing of pools of individuals from all B and O lines and identified 6,394 genetically divergent variants in or near 1,928 genes at a false discovery rate of 0.068. A 2.6 Mb region at the tip of the X chromosome contained many variants fixed for alternative alleles in the two populations, suggestive of a hard selective sweep. We also assessed genome wide gene expression of O and B lines at one and five weeks of age using RNA sequencing and identified genes with significant (false discovery rate < 0.05) effects on gene expression with age, population and the age by population interaction, separately for each sex. We identified transcripts that exhibited the transcriptional signature of postponed senescence and integrated the gene expression and genetic divergence data to identify 98 (175) top candidate genes in females (males) affecting postponed senescence and increased lifespan. While several of these genes have been previously associated with Drosophila lifespan, most are novel and constitute a rich resource for future functional validation.

Genomic response to selection for postponed senescence in Drosophila

Limited lifespan and senescence are quantitative traits, controlled by many interacting genes with individually small and environmentally plastic effects, complicating genetic analysis. We performed genome wide analysis of gene expression for two Drosophila melanogaster lines selected for postponed senescence and one control, unselected line to identify candidate genes affecting lifespan as well as variation in lifespan. We obtained gene expression profiles for young flies of all lines, all lines at the time only 10% of the control lines survived, and the time at which 10% of the selected lines survived. Transcriptional responses to aging involved 19% of the genome. The transcriptional signature of aging involved the down-regulation of genes affecting proteolysis, metabolism, oxidative phosphorylation, and mitochrondrial function; and the up-regulation of genes affecting protein synthesis, immunity, defense responses, and the detoxification of xenobiotic substances. The transcriptional signature of postponed senescence involved the up-regulation of proteases and phosphatases and genes affecting detoxification of xenobiotics; and the down-regulation of genes affecting immunity, defense responses, metabolism and muscle function. Functional tests of 17 mutations confirmed 12 novel genes affecting Drosophila lifespan. Identification of genes affecting longevity by analysis of gene expression changes in lines selected for postponed senescence thus complements alternative genetic approaches.

Fine-scale mapping of natural variation in fly fecundity identifies neuronal domain of expression and function of an aquaporin

To gain insight into the molecular genetic basis of standing variation in fitness related traits, we identify a novel factor that regulates the molecular and physiological basis of natural variation in female Drosophila melanogaster fecundity. Genetic variation in female fecundity in flies derived from a wild orchard population is heritable and largely independent of other measured life history traits. We map a portion of this variation to a single QTL and then use deficiency mapping to further refine this QTL to 5 candidate genes. Ubiquitous expression of RNAi against only one of these genes, an aquaporin encoded by Drip, reduces fecundity. Within our mapping population Drip mRNA level in the head, but not other tissues, is positively correlated with fecundity. We localize Drip expression to a small population of corazonin producing neurons located in the dorsolateral posterior compartments of the protocerebrum. Expression of Drip–RNAi using both the pan-neuronal ELAV-Gal4 and the Crz-Gal4 drivers reduces fecundity. Low-fecundity RILs have decreased Crz expression and increased expression of pale, the enzyme encoding the rate-limiting step in the production of dopamine, a modulator of insect life histories. Taken together these data suggest that natural variation in Drip expression in the corazonin producing neurons contributes to standing variation in fitness by altering the concentration of two neurohormones.

A major goal of modern evolutionary biology is to elucidate the genetic basis of standing genetic variation underlying fitness traits. This goal is important for a comprehensive picture of the evolutionary process, because it allows us to understand the mode of natural selection on fitness traits and identify the molecular and physiological processes that affect fitness traits. Here, we describe our work to identify the molecular genetic and physiological basis for natural variation in a core life history trait, fecundity, of Drosophila melanogaster. Using a variety of mapping techniques, we show that differential expression of the aquaporin Drip in nervous tissue affects natural variation in female fecundity. We further go on to describe a novel domain of expression of Drip in neurons that produce the insect stress hormone corazonin and demonstrate that differential expression of Drip in these neurons affects female fecundity putatively through modulating the concentration of corazonin and dopamine. This surprising and novel observation highlights the benefit of exploiting natural genetic variation to identify the molecular processes underlying phenotypic traits.

New experiments for an undivided genetics

There used to be a broad split within the experimental genetics research community between those who did mechanistic research using homozygous laboratory strains and those who studied patterns of genetic variation in wild populations. The former benefited from the advantage of reproducible experiments, but faced difficulties of interpretation given possible genomic and evolutionary complexities. The latter research approach featured readily interpreted evolutionary and genomic contexts, particularly phylogeny, but was poor at determining functional significance. Such burgeoning experimental strategies as genome-wide analysis of quantitative trait loci, genotype-phenotype associations, and the products of experimental evolution are now fostering a unification of experimental genetic research that strengthens its scientific power.

Mutations and quantitative genetic variation: lessons from Drosophila

A central issue in evolutionary quantitative genetics is to understand how genetic variation for quantitative traits is maintained in natural populations. Estimates of genetic variation and of genetic correlations and pleiotropy among multiple traits, inbreeding depression, mutation rates for fitness and quantitative traits and of the strength and nature of selection are all required to evaluate theoretical models of the maintenance of genetic variation. Studies in Drosophila melanogaster have shown that a substantial fraction of segregating variation for fitness-related traits in Drosophila is due to rare deleterious alleles maintained by mutation-selection balance, with a smaller but significant fraction attributable to intermediate frequency alleles maintained by alleles with antagonistic pleiotropic effects, and late-age-specific effects. However, the nature of segregating variation for traits under stabilizing selection is less clear and requires more detailed knowledge of the loci, mutation rates, allelic effects and frequencies of molecular polymorphisms affecting variation in suites of pleiotropically connected traits. Recent studies in D. melanogaster have revealed unexpectedly complex genetic architectures of many quantitative traits, with large numbers of pleiotropic genes and alleles with sex-, environment- and genetic background-specific effects. Future genome wide association analyses of many quantitative traits on a common panel of fully sequenced Drosophila strains will provide much needed empirical data on the molecular genetic basis of quantitative traits.

Quantitative trait locus mapping of genes under selection across multiple years and sites in Avena barbata: epistasis, pleiotropy, and genotype-by-environment interactions

The genetic architecture of variation in evolutionary fitness determines the trajectory of adaptive change. We identified quantitative trait loci (QTL) affecting fitness in a mapping population of recombinant inbred lines (RILs) derived from a cross between moist- and dry- associated ecotypes of Avena barbata. We estimated fitness in 179 RILs in each of two natural environments in each of 4 years. Two loci account for over half of the variation in geometric mean fitness across environments. These loci are associated in repulsion phase in the wild ecotypes, suggesting the potential for strong transgressive segregation, but also show significant epistasis giving hybrid breakdown. This epistasis is the result of sharply lower fitness in only one of the recombinant genotypes, suggesting that the loci may contain synergistically acting mutations. Within each trial (year/site combination), we can explain less of the variation than for geometric mean fitness, but the two major loci are associated with variation in fitness in most environments. Tests for pleiotropic effects of QTL on fitness in different environments reveal that the same loci are under selection in all trials. Genotype-by-environment interactions are significant for some loci, but this reflects variation in the strength, not the direction of selection.

Integrating evolutionary and molecular genetics of aging

Aging or senescence is an age-dependent decline in physiological function, demographically manifest as decreased survival and fecundity with increasing age. Since aging is disadvantageous it should not evolve by natural selection. So why do organisms age and die? In the 1940s and 1950s evolutionary geneticists resolved this paradox by positing that aging evolves because selection is inefficient at maintaining function late in life. By the 1980s and 1990s this evolutionary theory of aging had received firm empirical support, but little was known about the mechanisms of aging. Around the same time biologists began to apply the tools of molecular genetics to aging and successfully identified mutations that affect longevity. Today, the molecular genetics of aging is a burgeoning field, but progress in evolutionary genetics of aging has largely stalled. Here we argue that some of the most exciting and unresolved questions about aging require an integration of molecular and evolutionary approaches. Is aging a universal process? Why do species age at different rates? Are the mechanisms of aging conserved or lineage-specific? Are longevity genes identified in the laboratory under selection in natural populations? What is the genetic basis of plasticity in aging in response to environmental cues and is this plasticity adaptive? What are the mechanisms underlying trade-offs between early fitness traits and life span? To answer these questions evolutionary biologists must adopt the tools of molecular biology, while molecular biologists must put their experiments into an evolutionary framework. The time is ripe for a synthesis of molecular biogerontology and the evolutionary biology of aging.

A major QTL affects temperature sensitive adult lethality and inbreeding depression in life span in Drosophila melanogaster

BACKGROUND

The study of inbreeding depression has major relevance for many disciplines, including conservation genetics and evolutionary biology. Still, the molecular genetic basis of this phenomenon remains poorly characterised, as knowledge on the mechanistic causes of inbreeding depression and the molecular properties of genes that give rise to or modulate its deleterious effects is lacking. These questions warrant the detailed study of genetic loci giving rise to inbreeding depression. However, the complex and polygenic nature of general inbreeding depression makes this a daunting task. Study of inbreeding effects in specific traits, such as age-specific mortality and life span, provide a good starting point, as a limited set of genes is expected to be involved.

RESULTS

Here we report on a QTL mapping study on inbreeding related and temperature sensitive lethality in male Drosophila melanogaster. The inbreeding effect was expressed at moderately high temperature, and manifested itself as severe premature mortality in males, but not in females. We used a North Carolina crossing design 3 to estimate average dominance ratio and heritability. We found the genetic basis of the lethal effect to be relatively simple, being due mainly to a single recessive QTL on the left arm of chromosome 2. This locus colocalised with a QTL that conditioned variation in female life span, acting as an overdominant locus for this trait. Male life span was additionally affected by variation at the X-chromosome.

CONCLUSION

This demonstrates that analysis of large conditional lethal effects is a viable strategy for delineating genes which are sensitive to inbreeding depression.

No influence of Indy on lifespan in Drosophila after correction for genetic and cytoplasmic background effects

To investigate whether alterations in mitochondrial metabolism affect longevity in Drosophila melanogaster, we studied lifespan in various single gene mutants, using inbred and outbred genetic backgrounds. As positive controls we included the two most intensively studied mutants of Indy, which encodes a Drosophila Krebs cycle intermediate transporter. It has been reported that flies heterozygous for these Indy mutations, which lie outside the coding region, show almost a doubling of lifespan. We report that only one of the two mutants lowers mRNA levels, implying that the lifespan extension observed is not attributable to the Indy mutations themselves. Moreover, neither Indy mutation extended lifespan in female flies in any genetic background tested. In the original genetic background, only the Indy mutation associated with altered RNA expression extended lifespan in male flies. However, this effect was abolished by backcrossing into standard outbred genetic backgrounds, and was associated with an unidentified locus on the X chromosome. The original Indy line with long-lived males is infected by the cytoplasmic symbiont Wolbachia, and the longevity of Indy males disappeared after tetracycline clearance of this endosymbiont. These findings underscore the critical importance of standardisation of genetic background and of cytoplasm in genetic studies of lifespan, and show that the lifespan extension previously claimed for Indy mutants was entirely attributable to confounding variation from these two sources. In addition, we saw no effects on lifespan of expression knockdown of the Indy orthologues nac-2 and nac-3 in the nematode Caenorhabditis elegans.

A CENTENNIAL CELEBRATION FOR QUANTITATIVE GENETICS

Quantitative genetics is at or is fast approaching its centennial. In this perspective I consider five current issues pertinent to the application of quantitative genetics to evolutionary theory. First, I discuss the utility of a quantitative genetic perspective in describing genetic variation at two very different levels of resolution, (1) in natural, free-ranging populations and (2) to describe variation at the level of DNA transcription. Whereas quantitative genetics can serve as a very useful descriptor of genetic variation, its greater usefulness is in predicting evolutionary change, particularly when used in the first instance (wild populations). Second, I review the contributions of Quantitative trait loci (QLT) analysis in determining the number of loci and distribution of their genetic effects, the possible importance of identifying specific genes, and the ability of the multivariate breeder's equation to predict the results of bivariate selection experiments. QLT analyses appear to indicate that genetic effects are skewed, that at least 20 loci are generally involved, with an unknown number of alleles, and that a few loci have major effects. However, epistatic effects are common, which means that such loci might not have population-wide major effects: this question waits upon (QTL) analyses conducted on more than a few inbred lines. Third, I examine the importance of research into the action of specific genes on traits. Although great progress has been made in identifying specific genes contributing to trait variation, the high level of gene interactions underlying quantitative traits makes it unlikely that in the near future we will have mechanistic models for such traits, or that these would have greater predictive power than quantitative genetic models. In the fourth section I present evidence that the results of bivariate selection experiments when selection is antagonistic to the genetic covariance are frequently not well predicted by the multivariate breeder's equation. Bivariate experiments that combine both selection and functional analyses are urgently needed. Finally, I discuss the importance of gaining more insight, both theoretical and empirical, on the evolution of the G and P matrices.

Natural genetic variation in cuticular hydrocarbon expression in male and female Drosophila melanogaster

Cuticular hydrocarbons (CHCs) act as contact pheromones in Drosophila melanogaster and are an important component of several ecological traits. Segregating genetic variation in the expression of CHCs at the population level in D. melanogaster is likely to be important for mate choice and climatic adaptation; however, this variation has never been characterized. Using a panel of recombinant inbred lines (RILs) derived from a natural population, we found significant between-line variation for nearly all CHCs in both sexes. We identified 25 QTL in females and 15 QTL in males that pleiotropically influence CHC expression. There was no evidence of colocalization of QTL for homologous traits across the sexes, indicating that sexual dimorphism and low intersex genetic correlations between homologous CHCs are a consequence of largely independent genetic control. This is consistent with a pattern of divergent sexual and natural selection between the sexes.

High-resolution mapping of quantitative trait loci affecting increased life span in Drosophila melanogaster

Limited life span and senescence are near-universal characteristics of eukaryotic organisms, controlled by many interacting quantitative trait loci (QTL) with individually small effects, whose expression is sensitive to the environment. Analyses of mutations in model organisms have shown that genes affecting stress resistance and metabolism affect life span across diverse taxa. However, there is considerable segregating variation for life span in nature, and relatively little is known about the genetic basis of this variation. Replicated lines of Drosophila that have evolved increased longevity as a correlated response to selection for postponed senescence are valuable resources for identifying QTL affecting naturally occurring variation in life span. Here, we used deficiency complementation mapping to identify at least 11 QTL on chromosome 3 that affect variation in life span between five old (O) lines selected for postponed senescence and their five base (B) population control lines. Most QTL were sex specific, and all but one affected multiple O lines. The latter observation is consistent with alleles at intermediate frequency in the base population contributing to the response to selection for postponed senescence. The QTL were mapped with high resolution and contained from 12 to 170 positional candidate genes.

Survival analysis of life span quantitative trait loci in Drosophila melanogaster

We used quantitative trait loci (QTL) mapping to evaluate the age specificity of naturally segregating alleles affecting life span. Estimates of age-specific mortality rates were obtained from observing 51,778 mated males and females from a panel of 144 recombinant inbred lines (RILs). Twenty-five QTL were found, having 80 significant effects on life span and weekly mortality rates. Generation of RILs from heterozygous parents enabled us to contrast effects of QTL alleles with the means of RIL populations. Most of the low-frequency alleles increased mortality, especially at younger ages. Two QTL had negatively correlated effects on mortality at different ages, while the remainder were positively correlated. Chromosomal positions of QTL were roughly concordant with estimates from other mapping populations. Our findings are broadly consistent with a mix of transient deleterious mutations and a few polymorphisms maintained by balancing selection, which together contribute to standing genetic variation in life span.

Quantitative trait loci affecting life span in replicated populations of Drosophila melanogaster. II. Response to selection

Three selection experiments were used to identify chromosome regions that contain QTL affecting late-life and early-life fitness in Drosophila melanogaster. The selection experiments were initiated by crossing pairs of inbred lines that had been derived from outbred laboratory populations that had different mean life spans. QTL regions were located by association with microsatellite markers that showed significant selection responses. Regions between recombination map positions 54 and 81 on chromosome 2, between 0 and 30 on chromosome 3, and near locations 49 and 81 on chromosome 3 had the strongest support as locations of life-span QTL. There was good general agreement between the life-span QTL regions that were identified by selection and those that were identified in a companion recombination mapping experiment that used the same fly stocks. Many marker loci responded in opposite directions to selection for late- and early-life fitness, indicating negative genetic correlations or trade-offs between those traits. Indirect evidence suggested that some negative genetic correlations were due to antagonistic pleiotropy.

Multilevel analyses of genetic differentiation in Anopheles gambiae s.s. reveal patterns of gene flow important for malaria-fighting mosquito projects

Malaria control projects based on the introduction and spread of transgenes into mosquito populations depend on the extent of isolation between those populations. On the basis of the distribution of paracentric inversions, Anopheles gambiae has been subdivided into five subspecific chromosomal forms. Estimating gene flow between and within these forms of An. gambiae presents a number of challenges. We compared patterns of genetic divergence (F(ST)) between sympatric populations of the Bamako and Mopti forms at five sites. We used microsatellite loci within the j inversion on chromosome 2, which is fixed in the Bamako form but absent in the Mopti form, and microsatellites on chromosome 3, a region void of inversions. Estimates of genetic diversity and F(ST)'s suggest genetic exchanges between forms for the third chromosome but little for the j inversion. These results suggest a role for the inversion in speciation. Extensive gene flow within forms among sites resulted in populations clustering according to form despite substantial gene flow between forms. These patterns underscore the low levels of current gene flow between chromosomal forms in this area of sympatry. Introducing refractoriness genes in areas of the genome void of inversions may facilitate their spread within forms but their passage between forms may prove more difficult than previously thought.