The Evolutionary Genetics of Life History in Drosophila Melanogaster

Life history traits are critical components of fitness and frequently reflect adaptive responses to environmental pressures. Natural populations of Drosophila melanogaster exhibit patterns of lifespan, fecundity, development time, body size and stress resistance that vary predictably along environmental gradients. Artificial selection studies, genetic correlation analyses, and quantitative trait mapping efforts have demonstrated a genetic basis for the observed phenotypic variation, but few genes have been identified that contribute to natural life history variation. This work employs a candidate gene approach to discover genes and specific polymorphisms that contribute to genetic variance for D. melanogaster life history. Three aging genes, which have been characterized to mediate longevity, reproduction and stress tolerance, have been evaluated for natural genetic variation from samples derived from the wild. Allelic variation at one gene, methuselah (mth), shows functional effects on lifespan, lifetime fecundity and resistance to oxidative stress. A polymorphism in the mth promoter has been identified which may contribute to variation in these traits by affecting levels of gene expression. Natural genetic variation at two genes in the insulin signaling pathway reveals a history of positive selection at the Insulin-like Receptor (InR), but evidence of neutral evolution at the InR substrate, chico. Furthermore, an indel polymorphism in the first exon of InR shows striking, nonrandom distributions on two continents, a sign that it may contribute to the observed patterns of phenotypic variation across these same habitats. Functional evaluation of alternate InR alleles demonstrates predictable effects on phenotype and levels of insulin signaling, which implicates this polymorphism in the adaptive evolution of wild D. melanogaster populations. These findings provide novel examples of how allelic variation underlies adaptive changes in life history evolution, and contribute complementary characterization of genetic function to the biology of aging

Cryptic Genetic Variation in Evolutionary Developmental Genetics

Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits

Functional significance of allelic variation at methuselah, an aging gene in Drosophila.

BACKGROUND: Longevity and age-specific patterns of mortality are complex traits that vary within and among taxa. Multiple candidate genes for aging have been identified in model systems by extended longevity mutant phenotypes, including the G-protein coupled receptor methuselah (mth) in D. melanogaster. These genes offer important insights into the mechanisms of lifespan determination and have been major targets of interest in the biology of aging. However, it is largely unknown whether these genes contribute to genetic variance for lifespan in natural populations, and consequently contribute to lifespan evolution. METHODOLOGY/PRINCIPLE FINDINGS: For a gene to contribute to genetic variance for a particular trait, it must meet two criteria: natural allelic variation and functional differences among variants. Previous work showed that mth varies significantly among wild populations; here we assess the functional significance of wild-derived mth alleles on lifespan, fecundity and stress resistance using a quantitative complementation scheme. Our results demonstrate that mth alleles segregating in nature have a functional effect on all three traits. CONCLUSIONS/SIGNIFICANCE: These results suggest that allelic variation at mth contributes to observed differences in lifespan and correlated phenotypes in natural populations, and that evaluation of genetic diversity at candidate genes for aging can be a fruitful approach to identifying loci contributing to lifespan evolution

Data from: A highly pleiotropic amino acid polymorphism in the Drosophila insulin receptor contributes to life history adaptation

Finding the specific nucleotides that underlie adaptive variation is a major goal in evolutionary biology, but polygenic traits pose a challenge because the complex genotype-phenotype relationship can obscure the effects of individual alleles. However, natural selection working in large wild populations can shift allele frequencies and indicate functional regions of the genome. Previously, we showed that the two most common alleles of a complex amino acid insertion-deletion polymorphism in the Drosophila insulin receptor show independent, parallel clines in frequency across the North American and Australian continents. Here, we report that the cline is stable over at least a five-year period and that the polymorphism also demonstrates temporal shifts in allele frequency concurrent with seasonal change. We tested the alleles for effects on levels of insulin signaling, fecundity, development time, body size, stress tolerance, and lifespan. We find that the alleles are associated with predictable differences in these traits, consistent with patterns of Drosophila life history variation across geography that likely reflect adaptation to the heterogeneous climatic environment. These results implicate insulin signaling as a major mediator of life history adaptation in Drosophila, and suggest that life history tradeoffs can be explained by extensive pleiotropy at a single locus

A portable, low-cost device for precise control of specimen temperature under stereomicroscopes.

To facilitate precise and convenient control of biological sample temperature, we developed a low-cost device that can be used independently or with any stereomicroscope. The purpose of the device is to control the thermal environment during experimental intervals in which a specimen must be manipulated outside of an incubator, e.g. for dissection or slide-mounting in preparation for imaging. Sample temperatures can be both cooled to below and heated to above room temperatures, and stably maintained at a precision of +/- 0.1˚C. To demonstrate the utility of this device, we report improved characterization of the penetrance of a short-acting temperature-sensitive allele in C. elegans embryos, and identification of the upper temperature threshold for embryonic viability for six Caenorhabditis species. By controlling the temperature environment even as a specimen is manipulated, this device offers consistency and flexibility, reduces environmental noise, and enables precision timing in experiments requiring temperature shifts

raw data for phenotype assays

This Excel file contains the raw data for the phenotype assays

Data from: Wild worm embryogenesis harbors ubiquitous polygenic modifier variation

Embryogenesis is an essential and stereotypic process that nevertheless evolves among species. Its essentiality may favor the accumulation of cryptic genetic variation (CGV) that has no effect in the wild-type but that enhances or suppresses the effects of rare disruptions to gene function. Here, we adapted a classical modifier screen to interrogate the alleles segregating in natural populations of C. elegans: we induced gene knockdowns and used quantitative genetic methodology to examine how segregating variants modify the penetrance of embryonic lethality. Each perturbation revealed CGV, indicating that wild-type genomes harbor myriad genetic modifiers that may have little effect individually but which in aggregate can dramatically influence penetrance. Phenotypes were mediated by many modifiers, indicating high polygenicity, but the alleles tend to act very specifically, indicating low pleiotropy. Our findings demonstrate the extent of conditional functionality in complex trait architecture

Embryonic lethality data

This is a tab-delimited text file with one header row, 27,360 data rows, and 19 columns. Each data row corresponds to a unique image taken of a well in a 96-well plate, in which there are (potentially) adult worms, dead embryos, and living larvae. The column headers are: adults_man (the number of adults in the image, manually counted by a human); eggs_man (the score of the abundance of dead embryos in the image, from 0 to 9, scored manually by a human); larvae_man (the score of the abundance of living larvae in the image, from 0 to 9, scored manually by a human); strain (the worm strain); vector (the gene targeted by RNAi, or in the case of "empty," the negative control RNAi clone); date (the one of three date batches in which the experiments were conducted); well_row (the row, from A to H, in a 96-well plate, in which the well was located); well_col (the column, from 1 to 12, in a 96-well plate, in which the well was located); fol_strain (the grouping, from a to c, to which the worm strain in this image belonged when it was dispensed into the 96-well plates; strains were dispensed in sets of 8, as each plate has 8 rows); fol_lib (the RNAi library, from 1 to 4, to which the bacteria in this well belonged when it was dispensed); fol_bac_rep (the batch of bacterial culture, either "car," "gre," or "roy" that was dispensed into this well; from a single bacterial library, three replicate culture batches were grown in three deep-well 96-well plates, from which the RNAi bacteria were dispensed into the experimental plates); fol_plate_rep (the replicate plate number, from 1 to 8; each experimental condition of worm strain and RNAi vector was replicated 8 times, across the three replicate batches of bacterial culture); image (the image number, from 1 to 96, in a 96-well plate, assigned by the image capture software); adult_area (the number of pixels assigned to the "adult" category by the DevStaR algorithm); larva_area (the number of pixels assigned to the "larva" category by the DevStaR algorithm); egg_area (the number of pixels assigned to the "embryo" category by the DevStaR algorithm); adults (the count of adults in the image by the DevStaR algorithm); larvae (the count of living larvae in the image by the DevStaR algorithm); eggs (the count of dead embryos in the image, determined by dividing egg_area by 70). NA values in the manually scored columns (adults_man, eggs_man, larvae_man) indicate that the well failed to grow a mature culture of worms. This is often due to somatic lethality of the targeted gene (e.g. the somatic control vector tba-2), or to fungal contamination. Because these images were checked by a human eye, rows with NAs in the manual columns should be excluded from most analyses

Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping.

Pleiotropy-when a single mutation affects multiple traits-is a controversial topic with far-reaching implications. Pleiotropy plays a central role in debates about how complex traits evolve and whether biological systems are modular or are organized such that every gene has the potential to affect many traits. Pleiotropy is also critical to initiatives in evolutionary medicine that seek to trap infectious microbes or tumors by selecting for mutations that encourage growth in some conditions at the expense of others. Research in these fields, and others, would benefit from understanding the extent to which pleiotropy reflects inherent relationships among phenotypes that correlate no matter the perturbation (vertical pleiotropy). Alternatively, pleiotropy may result from genetic changes that impose correlations between otherwise independent traits (horizontal pleiotropy). We distinguish these possibilities by using clonal populations of yeast cells to quantify the inherent relationships between single-cell morphological features. Then, we demonstrate how often these relationships underlie vertical pleiotropy and how often these relationships are modified by genetic variants (quantitative trait loci [QTL]) acting via horizontal pleiotropy. Our comprehensive screen measures thousands of pairwise trait correlations across hundreds of thousands of yeast cells and reveals ample evidence of both vertical and horizontal pleiotropy. Additionally, we observe that the correlations between traits can change with the environment, genetic background, and cell-cycle position. These changing dependencies suggest a nuanced view of pleiotropy: biological systems demonstrate limited pleiotropy in any given context, but across contexts (e.g., across diverse environments and genetic backgrounds) each genetic change has the potential to influence a larger number of traits. Our method suggests that exploiting pleiotropy for applications in evolutionary medicine would benefit from focusing on traits with correlations that are less dependent on context