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Shpak M, Lawrence KN, Pool JE. The Precision and Power of Population Branch Statistics in Identifying the Genomic Signatures of Local Adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594139. [PMID: 38798330 PMCID: PMC11118325 DOI: 10.1101/2024.05.14.594139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Population branch statistics, which estimate the branch lengths of focal populations with respect to two outgroups, have been used as an alternative to FST-based genome-wide scans for identifying loci associated with local selective sweeps. In addition to the original population branch statistic (PBS), there are subsequently proposed branch rescalings: normalized population branch statistic (PBSn1), which adjusts focal branch length with respect to outgroup branch lengths at the same locus, and population branch excess (PBE), which also incorporates median branch lengths at other loci. PBSn1 and PBE have been proposed to be less sensitive to allele frequency divergence generated by background selection or geographically ubiquitous positive selection rather than local selective sweeps. However, the accuracy and statistical power of branch statistics have not been systematically assessed. To do so, we simulate genomes in representative large and small populations with varying proportions of sites evolving under genetic drift or background selection (approximated using variable Ne), local selective sweeps, and geographically parallel selective sweeps. We then assess the probability that local selective sweep loci are correctly identified as outliers by FST and by each of the branch statistics. We find that branch statistics consistently outperform FST at identifying local sweeps. When background selection and/or parallel sweeps are introduced, PBSn1 and especially PBE correctly identify local sweeps among their top outliers at a higher frequency than PBS. These results validate the greater specificity of rescaled branch statistics such as PBE to detect population-specific positive selection, supporting their use in genomic studies focused on local adaptation.
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Affiliation(s)
- Max Shpak
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI, USA
| | - Kadee N. Lawrence
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI, USA
| | - John E. Pool
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI, USA
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2
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Wynne NE, Applebach E, Chandrasegaran K, Ajayi OM, Chakraborty S, Bonizzoni M, Lahondère C, Benoit JB, Vinauger C. Aedes albopictus colonies from different geographic origins differ in their sleep and activity levels but not in the time of peak activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585187. [PMID: 38559099 PMCID: PMC10980008 DOI: 10.1101/2024.03.15.585187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Mosquitoes occupy a wide range of habitats where they experience various environmental conditions. The ability of some species, such as the tiger mosquito, Aedes albopictus, to adapt to local conditions certainly contributes to their invasive success. Among traits that remain to be examined, mosquitoes' ability to time their activity with that of the local host population has been suggested to be of significant epidemiological importance. However, whether different populations display heritable differences in their chronotype has not been examined. Here, we compared laboratory strains originating from 8 populations from 3 continents, monitored their spontaneous locomotor activity patterns, and analyzed their sleep-like states. Overall, all strains showed conserved diurnal activity concentrated in the hours preceding the crepuscule. Similarly, they all showed increased sleep levels during the morning and night hours. However, we observed strain-specific differences in the activity levels at each phase of the day. We also observed differences in the fraction of time that each strain spends in a sleep-like state, explained by variations in the sleep architecture across strains. Human population density and the latitude of the site of geographic origin of the tested strain showed significant effects on sleep and activity patterns. Altogether, these results suggest that Ae. albopictus mosquitoes adapt to local environmental conditions via heritable adaptations of their chronotype.
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Affiliation(s)
- Nicole E Wynne
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Emilie Applebach
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Karthikeyan Chandrasegaran
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Oluwaseun M Ajayi
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Souvik Chakraborty
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Mariangela Bonizzoni
- Department of Biology and Biotechnology, University of Pavia, Pavia 27100, Italy
| | - Chloé Lahondère
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Clément Vinauger
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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3
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Shpak M, Ghanavi HR, Lange JD, Pool JE, Stensmyr MC. Genomes from historical Drosophila melanogaster specimens illuminate adaptive and demographic changes across more than 200 years of evolution. PLoS Biol 2023; 21:e3002333. [PMID: 37824452 PMCID: PMC10569592 DOI: 10.1371/journal.pbio.3002333] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/11/2023] [Indexed: 10/14/2023] Open
Abstract
The ability to perform genomic sequencing on long-dead organisms is opening new frontiers in evolutionary research. These opportunities are especially notable in the case of museum collections, from which countless documented specimens may now be suitable for genomic analysis-if data of sufficient quality can be obtained. Here, we report 25 newly sequenced genomes from museum specimens of the model organism Drosophila melanogaster, including the oldest extant specimens of this species. By comparing historical samples ranging from the early 1800s to 1933 against modern-day genomes, we document evolution across thousands of generations, including time periods that encompass the species' initial occupation of northern Europe and an era of rapidly increasing human activity. We also find that the Lund, Sweden population underwent local genetic differentiation during the early 1800s to 1933 interval (potentially due to drift in a small population) but then became more similar to other European populations thereafter (potentially due to increased migration). Within each century-scale time period, our temporal sampling allows us to document compelling candidates for recent natural selection. In some cases, we gain insights regarding previously implicated selection candidates, such as ChKov1, for which our inferred timing of selection favors the hypothesis of antiviral resistance over insecticide resistance. Other candidates are novel, such as the circadian-related gene Ahcy, which yields a selection signal that rivals that of the DDT resistance gene Cyp6g1. These insights deepen our understanding of recent evolution in a model system, and highlight the potential of future museomic studies.
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Affiliation(s)
- Max Shpak
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | | | - Jeremy D. Lange
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - John E. Pool
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Marcus C. Stensmyr
- Department of Biology, Lund University, Lund, Scania, Sweden
- Max Planck Center on Next Generation Insect Chemical Ecology, Lund, Sweden
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4
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Cridland JM, Contino CE, Begun DJ. Selection and geography shape male reproductive tract transcriptomes in Drosophila melanogaster. Genetics 2023; 224:iyad034. [PMID: 36869688 PMCID: PMC10474930 DOI: 10.1093/genetics/iyad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 01/25/2023] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
Transcriptome analysis of several animal clades suggests that male reproductive tract gene expression evolves quickly. However, the factors influencing the abundance and distribution of within-species variation, the ultimate source of interspecific divergence, are poorly known. Drosophila melanogaster, an ancestrally African species that has recently spread throughout the world and colonized the Americas in the last roughly 100 years, exhibits phenotypic and genetic latitudinal clines on multiple continents, consistent with a role for spatially varying selection in shaping its biology. Nevertheless, geographic expression variation in the Americas is poorly described, as is its relationship to African expression variation. Here, we investigate these issues through the analysis of two male reproductive tissue transcriptomes [testis and accessory gland (AG)] in samples from Maine (USA), Panama, and Zambia. We find dramatic differences between these tissues in differential expression between Maine and Panama, with the accessory glands exhibiting abundant expression differentiation and the testis exhibiting very little. Latitudinal expression differentiation appears to be influenced by the selection of Panama expression phenotypes. While the testis shows little latitudinal expression differentiation, it exhibits much greater differentiation than the accessory gland in Zambia vs American population comparisons. Expression differentiation for both tissues is non-randomly distributed across the genome on a chromosome arm scale. Interspecific expression divergence between D. melanogaster and D. simulans is discordant with rates of differentiation between D. melanogaster populations. Strongly heterogeneous expression differentiation across tissues and timescales suggests a complex evolutionary process involving major temporal changes in the way selection influences expression evolution in these organs.
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Affiliation(s)
- Julie M Cridland
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| | - Colin E Contino
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| | - David J Begun
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
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5
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Abstract
Sleep is a fundamental, evolutionarily conserved, plastic behavior that is regulated by circadian and homeostatic mechanisms as well as genetic factors and environmental factors, such as light, humidity, and temperature. Among environmental cues, temperature plays an important role in the regulation of sleep. This review presents an overview of thermoreception in animals and the neural circuits that link this process to sleep. Understanding the influence of temperature on sleep can provide insight into basic physiologic processes that are required for survival and guide strategies to manage sleep disorders.
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Huang Y, Lack JB, Hoppel GT, Pool JE. Parallel and Population-specific Gene Regulatory Evolution in Cold-Adapted Fly Populations. Genetics 2021; 218:6275754. [PMID: 33989401 PMCID: PMC8864734 DOI: 10.1093/genetics/iyab077] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/10/2021] [Indexed: 11/15/2022] Open
Abstract
Changes in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have assayed within- and between-population variation in gene regulatory traits at a transcriptomic scale, and therefore inferences about the characteristics of adaptive regulatory changes have been elusive. Here, we assess quantitative trait differentiation in gene expression levels and alternative splicing (intron usage) between three closely related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. The cold-adapted populations were known to show population genetic evidence for parallel evolution at the SNP level, and here we find evidence for parallel expression evolution between them, with stronger parallelism at larval and adult stages than for pupae. We also implement a flexible method to estimate cis- vs trans-encoded contributions to expression or splicing differences at the adult stage. The apparent contributions of cis- vs trans-regulation to adaptive evolution vary substantially among population pairs. While two of three population pairs show a greater enrichment of cis-regulatory differences among adaptation candidates, trans-regulatory differences are more likely to be implicated in parallel expression changes between population pairs. Genes with significant cis-effects are enriched for signals of elevated genetic differentiation between cold- and warm-adapted populations, suggesting that they are potential targets of local adaptation. These findings expand our knowledge of adaptive gene regulatory evolution and our ability to make inferences about this important and widespread process.
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Affiliation(s)
- Yuheng Huang
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Justin B Lack
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Grant T Hoppel
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Souto-Maior C, Serrano Negron YL, Harbison ST. Natural selection on sleep duration in Drosophila melanogaster. Sci Rep 2020; 10:20652. [PMID: 33244154 PMCID: PMC7691507 DOI: 10.1038/s41598-020-77680-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/10/2020] [Indexed: 11/30/2022] Open
Abstract
Sleep is ubiquitous across animal species, but why it persists is not well understood. Here we observe natural selection act on Drosophila sleep by relaxing bi-directional artificial selection for extreme sleep duration for 62 generations. When artificial selection was suspended, sleep increased in populations previously selected for short sleep. Likewise, sleep decreased in populations previously selected for long sleep when artificial selection was relaxed. We measured the corresponding changes in the allele frequencies of genomic variants responding to artificial selection. The allele frequencies of these variants reversed course in response to relaxed selection, and for short sleepers, the changes exceeded allele frequency changes that would be expected under random genetic drift. These observations suggest that the variants are causal polymorphisms for sleep duration responding to natural selection pressure. These polymorphisms may therefore pinpoint the most important regions of the genome maintaining variation in sleep duration.
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Affiliation(s)
- Caetano Souto-Maior
- Laboratory of Systems Genetics, Systems Biology Center, National Heart Lung and Blood Institute, Bethesda, MD, USA
| | - Yazmin L Serrano Negron
- Laboratory of Systems Genetics, Systems Biology Center, National Heart Lung and Blood Institute, Bethesda, MD, USA
| | - Susan T Harbison
- Laboratory of Systems Genetics, Systems Biology Center, National Heart Lung and Blood Institute, Bethesda, MD, USA.
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Sarikaya DP, Cridland J, Tarakji A, Sheehy H, Davis S, Kochummen A, Hatmaker R, Khan N, Chiu J, Begun DJ. Phenotypic coupling of sleep and starvation resistance evolves in D. melanogaster. BMC Evol Biol 2020; 20:126. [PMID: 32962630 PMCID: PMC7507639 DOI: 10.1186/s12862-020-01691-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/13/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND One hypothesis for the function of sleep is that it serves as a mechanism to conserve energy. Recent studies have suggested that increased sleep can be an adaptive mechanism to improve survival under food deprivation in Drosophila melanogaster. To test the generality of this hypothesis, we compared sleep and its plastic response to starvation in a temperate and tropical population of Drosophila melanogaster. RESULTS We found that flies from the temperate population were more starvation resistant, and hypothesized that they would engage in behaviors that are considered to conserve energy, including increased sleep and reduced movement. Surprisingly, temperate flies slept less and moved more when they were awake compared to tropical flies, both under fed and starved conditions, therefore sleep did not correlate with population-level differences in starvation resistance. In contrast, total sleep and percent change in sleep when starved were strongly positively correlated with starvation resistance within the tropical population, but not within the temperate population. Thus, we observe unexpectedly complex relationships between starvation and sleep that vary both within and across populations. These observations falsify the simple hypothesis of a straightforward relationship between sleep and energy conservation. We also tested the hypothesis that starvation is correlated with metabolic phenotypes by investigating stored lipid and carbohydrate levels, and found that stored metabolites partially contributed towards variation starvation resistance. CONCLUSIONS Our findings demonstrate that the function of sleep under starvation can rapidly evolve on short timescales and raise new questions about the physiological correlates of sleep and the extent to which variation in sleep is shaped by natural selection.
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Affiliation(s)
- Didem P Sarikaya
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA.
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California, USA.
| | - Julie Cridland
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
| | - Adam Tarakji
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
| | - Hayley Sheehy
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
| | - Sophia Davis
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
| | - Ashley Kochummen
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
| | - Ryan Hatmaker
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
| | - Nossin Khan
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
| | - Joanna Chiu
- Department of Nematology and Entomology, University of California Davis, Davis, California, USA
| | - David J Begun
- Department of Evolution and Ecology, University of California Davis, Davis, California, USA
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9
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R. Smith B, J. Macdonald S. Dissecting the Genetic Basis of Variation in Drosophila Sleep Using a Multiparental QTL Mapping Resource. Genes (Basel) 2020; 11:genes11030294. [PMID: 32168738 PMCID: PMC7140804 DOI: 10.3390/genes11030294] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/07/2020] [Accepted: 03/09/2020] [Indexed: 12/27/2022] Open
Abstract
There is considerable variation in sleep duration, timing and quality in human populations, and sleep dysregulation has been implicated as a risk factor for a range of health problems. Human sleep traits are known to be regulated by genetic factors, but also by an array of environmental and social factors. These uncontrolled, non-genetic effects complicate powerful identification of the loci contributing to sleep directly in humans. The model system, Drosophila melanogaster, exhibits a behavior that shows the hallmarks of mammalian sleep, and here we use a multitiered approach, encompassing high-resolution QTL mapping, expression QTL data, and functional validation with RNAi to investigate the genetic basis of sleep under highly controlled environmental conditions. We measured a battery of sleep phenotypes in >750 genotypes derived from a multiparental mapping panel and identified several, modest-effect QTL contributing to natural variation for sleep. Merging sleep QTL data with a large head transcriptome eQTL mapping dataset from the same population allowed us to refine the list of plausible candidate causative sleep loci. This set includes genes with previously characterized effects on sleep and circadian rhythms, in addition to novel candidates. Finally, we employed adult, nervous system-specific RNAi on the Dopa decarboxylase, dyschronic, and timeless genes, finding significant effects on sleep phenotypes for all three. The genes we resolve are strong candidates to harbor causative, regulatory variation contributing to sleep.
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Affiliation(s)
- Brittny R. Smith
- Department of Molecular Biosciences, 4043 Haworth Hall, 1200 Sunnyside Avenue, University of Kansas, Lawrence, KS 66045, USA
| | - Stuart J. Macdonald
- Department of Molecular Biosciences, 4043 Haworth Hall, 1200 Sunnyside Avenue, University of Kansas, Lawrence, KS 66045, USA
- Center for Computational Biology, University of Kansas, Lawrence, KS 66047, USA
- Correspondence: ; Tel.: +1-785-864-5362
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Raphael KA, Sved JA, Pearce S, Oakeshott JG, Gilchrist AS, Sherwin WB, Frommer M. Differences in gene regulation in a tephritid model of prezygotic reproductive isolation. INSECT MOLECULAR BIOLOGY 2019; 28:689-702. [PMID: 30955213 DOI: 10.1111/imb.12583] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The two tephritid fruit fly pests, Bactrocera tryoni and Bactrocera neohumeralis, are unusually well suited to the study of the genetics of reproductive isolating mechanisms. Sequence difference between the species is no greater than between a pair of conspecific Drosophila melanogaster populations. The two species exist in close sympatry, yet do not hybridize in the field, apparently kept separate by a strong premating isolation mechanism involving the time of day at which mating occurs. This spurred us to search for key genes for which time of day expression is regulated differently between the species. Using replicated, quantitative transcriptomes from head tissues of males of the two species, sampled in the day and night, we identified 141 transcripts whose abundance showed a significant interaction between species and time of day, indicating a difference in gene regulation. The brain transcripts showing this interaction were enriched for genes with a neurone function and 90% of these were more abundant at night than day in B. tryoni. Features of the expression patterns suggest that there may be a difference in the regulation of sleep-wake cycles between the species. In particular several genes, which in D. melanogaster are expressed in circadian pacemaker cells, are promising candidates to further explore the genetic differentiation involved in this prezygotic reproductive isolation mechanism.
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Affiliation(s)
- K A Raphael
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - J A Sved
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - S Pearce
- CSIRO Land & Water Flagship, Canberra, ACT, Australia
| | - J G Oakeshott
- CSIRO Land & Water Flagship, Canberra, ACT, Australia
| | - A S Gilchrist
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - W B Sherwin
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - M Frommer
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
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Brown EB, Slocumb ME, Szuperak M, Kerbs A, Gibbs AG, Kayser MS, Keene AC. Starvation resistance is associated with developmentally specified changes in sleep, feeding and metabolic rate. ACTA ACUST UNITED AC 2019; 222:jeb.191049. [PMID: 30606795 DOI: 10.1242/jeb.191049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/11/2018] [Indexed: 11/20/2022]
Abstract
Food shortage represents a primary challenge to survival, and animals have adapted diverse developmental, physiological and behavioral strategies to survive when food becomes unavailable. Starvation resistance is strongly influenced by ecological and evolutionary history, yet the genetic basis for the evolution of starvation resistance remains poorly understood. The fruit fly Drosophila melanogaster provides a powerful model for leveraging experimental evolution to investigate traits associated with starvation resistance. While control populations only live a few days without food, selection for starvation resistance results in populations that can survive weeks. We have previously shown that selection for starvation resistance results in increased sleep and reduced feeding in adult flies. Here, we investigate the ontogeny of starvation resistance-associated behavioral and metabolic phenotypes in these experimentally selected flies. We found that selection for starvation resistance resulted in delayed development and a reduction in metabolic rate in larvae that persisted into adulthood, suggesting that these traits may allow for the accumulation of energy stores and an increase in body size within these selected populations. In addition, we found that larval sleep was largely unaffected by starvation selection and that feeding increased during the late larval stages, suggesting that experimental evolution for starvation resistance produces developmentally specified changes in behavioral regulation. Together, these findings reveal a critical role for development in the evolution of starvation resistance and indicate that selection can selectively influence behavior during defined developmental time points.
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Affiliation(s)
- Elizabeth B Brown
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Melissa E Slocumb
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Milan Szuperak
- Departments of Psychiatry and Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arianna Kerbs
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Allen G Gibbs
- Department of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Matthew S Kayser
- Departments of Psychiatry and Neuroscience, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alex C Keene
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL 33458, USA
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12
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Yang Y, Edery I. Parallel clinal variation in the mid-day siesta of Drosophila melanogaster implicates continent-specific targets of natural selection. PLoS Genet 2018; 14:e1007612. [PMID: 30180162 PMCID: PMC6138418 DOI: 10.1371/journal.pgen.1007612] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 09/14/2018] [Accepted: 08/06/2018] [Indexed: 11/18/2022] Open
Abstract
Similar to many diurnal animals, Drosophila melanogaster exhibits a mid-day siesta that is more robust as ambient temperature rises, an adaptive response aimed at minimizing exposure to heat. Mid-day siesta levels are partly regulated by the thermosensitive splicing of a small intron (termed dmpi8) found in the 3’ untranslated region (UTR) of the circadian clock gene period (per). Using the well-studied D. melanogaster latitudinal cline along the eastern coast of Australia, we show that flies from temperate populations sleep less during the day compared to those from tropical regions. We identified combinations of four single nucleotide polymorphisms (SNPs) in the 3’ UTR of per that yield several different haplotypes. The two most abundant of these haplotypes exhibit a reciprocal tropical-temperate distribution in relative frequency. Intriguingly, transgenic flies with the major tropical isoform manifest increased daytime sleep and reduced dmpi8 splicing compared to those carrying the temperate variant. Our results strongly suggest that for a major portion of D. melanogaster in Australia, thermal adaptation of daily sleep behavior included spatially varying selection on ancestrally derived polymorphisms in the per 3’ UTR that differentially control dmpi8 splicing efficiency. Prior work showed that African flies from high altitudes manifest reduced mid-day siesta levels, indicative of parallel latitudinal and altitudinal adaptation across continents. However, geographical variation in per 3’ UTR haplotypes was not observed for African flies, providing a compelling case for inter-continental variation in factors targeted by natural selection in attaining a parallel adaptation. We propose that the ability to calibrate mid-day siesta levels to better match local temperature ranges is a key adaptation contributing to the successful colonization of D. melanogaster beyond its ancestral range in the lowlands of Sub-Saharan Africa. In warm climates many animals, including humans, exhibit a mid-day siesta, almost certainly a behavior meant to minimize the harm from prolonged exposure to the hot mid-day sun. But what about animals that adapted to cooler more temperate climates, might they have a less pronounced siesta? Indeed, we show that in the common fruit fly, Drosophila melanogaster, those from temperate regions in Australia exhibit less mid-day siesta compared to their tropical counterparts. Prior work showed that mid-day sleep levels are partially regulated by a ‘clock’ gene called period (per), which controls the timing of wake-sleep cycles in addition to other daily rhythms. We identified several DNA differences in the per gene that show geographical variation and contribute to the daytime sleep differences in flies from tropical and temperate regions via a mechanism that involves how well a temperature-sensitive intron in per is removed. A similar reduction in mid-day sleep was previously observed in African flies that adapted to the cooler temperatures found at high altitudes. Together, our findings provide a rare example where latitude and altitude lead to a similar behavioral adaptation to temperature. Moreover, the results suggest inter-continental differences in the evolutionary solutions used to attain the same thermal adaptation to cooler climates.
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Affiliation(s)
- Yong Yang
- Rutgers University, Center for Advanced Biotechnology and Medicine, New Jersey, United States of America
| | - Isaac Edery
- Rutgers University, Center for Advanced Biotechnology and Medicine, New Jersey, United States of America
- Department of Molecular Biology and Biochemistry, Rutgers University, Center for Advanced Biotechnology and Medicine, New Jersey, United States of America
- * E-mail:
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13
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Abstract
Sleep is nearly ubiquitous throughout the animal kingdom, yet little is known about how ecological factors or perturbations to the environment shape the duration and timing of sleep. In diverse animal taxa, poor sleep negatively impacts development, cognitive abilities and longevity. In addition to mammals, sleep has been characterized in genetic model organisms, ranging from the nematode worm to zebrafish, and, more recently, in emergent models with simplified nervous systems such as Aplysia and jellyfish. In addition, evolutionary models ranging from fruit flies to cavefish have leveraged natural genetic variation to investigate the relationship between ecology and sleep. Here, we describe the contributions of classical and emergent genetic model systems to investigate mechanisms underlying sleep regulation. These studies highlight fundamental interactions between sleep and sensory processing, as well as a remarkable plasticity of sleep in response to environmental changes. Understanding how sleep varies throughout the animal kingdom will provide critical insight into fundamental functions and conserved genetic mechanisms underlying sleep regulation. Furthermore, identification of naturally occurring genetic variation regulating sleep may provide novel drug targets and approaches to treat sleep-related diseases.
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Affiliation(s)
- Alex C Keene
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458, USA
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Erik R Duboue
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458, USA
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
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Brown EB, Torres J, Bennick RA, Rozzo V, Kerbs A, DiAngelo JR, Keene AC. Variation in sleep and metabolic function is associated with latitude and average temperature in Drosophila melanogaster. Ecol Evol 2018; 8:4084-4097. [PMID: 29721282 PMCID: PMC5916307 DOI: 10.1002/ece3.3963] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/18/2018] [Accepted: 01/31/2018] [Indexed: 01/05/2023] Open
Abstract
Regulation of sleep and metabolic homeostasis is critical to an animal's survival and under stringent evolutionary pressure. Animals display remarkable diversity in sleep and metabolic phenotypes; however, an understanding of the ecological forces that select for, and maintain, these phenotypic differences remains poorly understood. The fruit fly, Drosophila melanogaster, is a powerful model for investigating the genetic regulation of sleep and metabolic function, and screening in inbred fly lines has led to the identification of novel genetic regulators of sleep. Nevertheless, little is known about the contributions of naturally occurring genetic differences to sleep, metabolic phenotypes, and their relationship with geographic or environmental gradients. Here, we quantified sleep and metabolic phenotypes in 24 D. melanogaster populations collected from diverse geographic localities. These studies reveal remarkable variation in sleep, starvation resistance, and energy stores. We found that increased sleep duration is associated with proximity to the equator and elevated average annual temperature, suggesting that environmental gradients strongly influence natural variation in sleep. Further, we found variation in metabolic regulation of sleep to be associated with free glucose levels, while starvation resistance associates with glycogen and triglyceride stores. Taken together, these findings reveal robust naturally occurring variation in sleep and metabolic traits in D. melanogaster, providing a model to investigate how evolutionary and ecological history modulate these complex traits.
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Affiliation(s)
- Elizabeth B. Brown
- Department of Biological SciencesFlorida Atlantic UniversityJupiterFLUSA
| | - Joshua Torres
- Department of Biological SciencesFlorida Atlantic UniversityJupiterFLUSA
- Wilkes Honors CollegeFlorida Atlantic UniversityJupiterFLUSA
| | - Ryan A. Bennick
- Division of SciencePennsylvania State University BerksReadingPAUSA
| | - Valerie Rozzo
- Department of Biological SciencesFlorida Atlantic UniversityJupiterFLUSA
- Lifelong Learning SocietyFlorida Atlantic UniversityJupiterFLUSA
| | - Arianna Kerbs
- Department of Biological SciencesFlorida Atlantic UniversityJupiterFLUSA
- Dwyer High SchoolPalm Beach GardensFLUSA
| | | | - Alex C. Keene
- Department of Biological SciencesFlorida Atlantic UniversityJupiterFLUSA
- Wilkes Honors CollegeFlorida Atlantic UniversityJupiterFLUSA
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15
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Selection for long and short sleep duration in Drosophila melanogaster reveals the complex genetic network underlying natural variation in sleep. PLoS Genet 2017; 13:e1007098. [PMID: 29240764 PMCID: PMC5730107 DOI: 10.1371/journal.pgen.1007098] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 11/01/2017] [Indexed: 12/16/2022] Open
Abstract
Why do some individuals need more sleep than others? Forward mutagenesis screens in flies using engineered mutations have established a clear genetic component to sleep duration, revealing mutants that convey very long or short sleep. Whether such extreme long or short sleep could exist in natural populations was unknown. We applied artificial selection for high and low night sleep duration to an outbred population of Drosophila melanogaster for 13 generations. At the end of the selection procedure, night sleep duration diverged by 9.97 hours in the long and short sleeper populations, and 24-hour sleep was reduced to 3.3 hours in the short sleepers. Neither long nor short sleeper lifespan differed appreciably from controls, suggesting little physiological consequences to being an extreme long or short sleeper. Whole genome sequence data from seven generations of selection revealed several hundred thousand changes in allele frequencies at polymorphic loci across the genome. Combining the data from long and short sleeper populations across generations in a logistic regression implicated 126 polymorphisms in 80 candidate genes, and we confirmed three of these genes and a larger genomic region with mutant and chromosomal deficiency tests, respectively. Many of these genes could be connected in a single network based on previously known physical and genetic interactions. Candidate genes have known roles in several classic, highly conserved developmental and signaling pathways—EGFR, Wnt, Hippo, and MAPK. The involvement of highly pleiotropic pathway genes suggests that sleep duration in natural populations can be influenced by a wide variety of biological processes, which may be why the purpose of sleep has been so elusive. One of the biggest mysteries in biology is the need to sleep. Sleep duration has an underlying genetic basis, suggesting that very long and short sleep times could be bred for experimentally. How far can sleep duration be driven up or down? Here we achieved extremely long and short night sleep duration by subjecting a wild-derived population of Drosophila melanogaster to an experimental breeding program. At the end of the breeding program, long sleepers averaged 9.97 hours more nightly sleep than short sleepers. We analyzed whole-genome sequences from seven generations of the experimental breeding to identify allele frequencies that diverged between long and short sleepers, and verified genes and genomic regions with mutation and deficiency testing. These alleles map to classic developmental and signaling pathways, implicating many diverse processes that potentially affect sleep duration.
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16
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Berry DP. Symposium review: Breeding a better cow-Will she be adaptable? J Dairy Sci 2017; 101:3665-3685. [PMID: 29224864 DOI: 10.3168/jds.2017-13309] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/12/2017] [Indexed: 12/12/2022]
Abstract
Adaption is a process that makes an individual or population more suited to their environment. Long-term adaptation is predicated on ample usable genetic variation. Evolutionary forces influencing the extent and dynamics of genetic variation in a population include random drift, mutation, recombination, selection, and migration; the relative importance of each differs by population (i.e., drift is likely to be more influential in smaller populations) and number of generations exposed to selection (i.e., mutation is expected to contribute substantially to genetic variability following many generations of selection). The infinitesimal model, which underpins most genetic and genomic evaluations, assumes that each quantitative trait is controlled by an infinitely large number of unlinked and non-epistatic loci, each with an infinitely small effect. Under the infinitesimal model, selection is not expected to noticeably alter the allele frequencies, despite a potential substantial change in the population mean; the exception is in the first few generations of selection when genetic variance is expected to decline, after which it stabilizes. Despite the common use of the heritability statistic in quantitative genetics as a descriptor of adaption or response to selection, it is arguably the coefficient of genetic variation that is more informative to gauge adaptation potential and should, therefore, always be cited in such studies; for example, the heritability of fertility traits in dairy cows is generally low, yet the coefficient of genetic variation for most traits is comparable to many other performance traits, thus supporting the observed rapid genetic gain in fertility performance in dairy populations. Empirical evidence from long-term selection studies, across a range of animal and plant species, fails to support the premise that selection will deplete genetic variability. Even after 100 yr (synonymous with 100 generations) of selection in corn for high protein or oil content, there appears to be no obvious plateauing in the response to selection. Although populations in several selection experiments did reach a selection limit after multiple generations of directional selection, this does not equate to an exhaustion of genetic variance; such a declaration is supported by the observed rapid responses to reverse selection once implemented in long-term selection studies. New technologies such as genome-wide enabled selection and genome editing, as well as having the potential to accelerate genetic gain, could also increase the genetic variation, or at least reduce the erosion of genetic variance over time. In conclusion, there is no evidence, either theoretical or empirical, to indicate that dairy cow breeding programs will be unable to adapt to evolving challenges and opportunities, at least not because of an absence of ample genetic variability.
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Affiliation(s)
- D P Berry
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland.
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17
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Koritala BSC, Lee K. Natural Variation of the Circadian Clock in Neurospora. ADVANCES IN GENETICS 2017; 99:1-37. [PMID: 29050553 DOI: 10.1016/bs.adgen.2017.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Most living organisms on earth experience daily and expected changes from the rotation of the earth. For an organism, the ability to predict and prepare for incoming stresses or resources is a very important skill for survival. This cellular process of measuring daily time of the day is collectively called the circadian clock. Because of its fundamental role in survival in nature, there is a great interest in studying the natural variation of the circadian clock. However, characterizing the genetic and molecular mechanisms underlying natural variation of circadian clocks remains a challenging task. In this chapter, we will summarize the progress in studying natural variation of the circadian clock in the successful eukaryotic model Neurospora, which led to discovering many design principles of the molecular mechanisms of the eukaryotic circadian clock. Despite the success of the system in revealing the molecular mechanisms of the circadian clock, Neurospora has not been utilized to extensively study natural variation. We will review the challenges that hindered the natural variation studies in Neurospora, and how they were overcome. We will also review the advantages of Neurospora for natural variation studies. Since Neurospora is the model fungal species for circadian study, it represents over 5 million species of fungi on earth. These fungi play important roles in ecosystems on earth, and as such Neurospora could serve as an important model for understanding the ecological role of natural variation in fungal circadian clocks.
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Affiliation(s)
- Bala S C Koritala
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States; Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States
| | - Kwangwon Lee
- Department of Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States; Center for Computational and Integrative Biology, Rutgers, The State University of New Jersey, Camden, NJ, United States.
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18
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Watanabe LP, Riddle NC. Characterization of the Rotating Exercise Quantification System (REQS), a novel Drosophila exercise quantification apparatus. PLoS One 2017; 12:e0185090. [PMID: 29016615 PMCID: PMC5634558 DOI: 10.1371/journal.pone.0185090] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 09/06/2017] [Indexed: 02/06/2023] Open
Abstract
Obesity is a disease that has reached epidemic proportions in the United States and has prompted international legislation in an attempt to curtail its prevalence. Despite the fact that one of the most prescribed treatment options for obesity is exercise, the genetic mechanisms underlying exercise response in individuals are still largely unknown. The fruit fly Drosophila melanogaster is a promising new model for studying exercise genetics. Currently, the lack of an accurate method to quantify the amount of exercise performed by the animals is limiting the utility of the Drosophila model for exercise genetics research. To address this limitation, we developed the Rotational Exercise Quantification System (REQS), a novel apparatus that is able to simultaneously induce exercise in flies while recording their activity levels. Thus, the REQS provides a method to standardize Drosophila exercise and ensure that all animals irrespective of genotype and sex experience the same level of exercise. Here, we provide a basic characterization of the REQS, validate its measurements using video-tracking technology, illustrate its potential use by presenting a comparison of two different exercise regimes, and demonstrate that it can be used to detect genotype-dependent variation in activity levels.
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Affiliation(s)
- Louis Patrick Watanabe
- Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Nicole C. Riddle
- Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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19
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Abstract
Despite its evolutionary importance and apparent ubiquity among animals, the ecological significance of sleep is largely unresolved. The ecology of sleep has been particularly neglected in invertebrates. In insects, recent neurobehavioral research convincingly demonstrates that resting behavior shares several common characteristics with sleep in vertebrates. Laboratory studies have produced compelling evidence that sleep disruption can cause changes in insect daily activity patterns (via "sleep rebound") and have consequences for behavioral performance during active periods. However, factors that could cause insect sleep disruption in nature have not been considered nor have the ecological consequences. Drawing on evidence from laboratory studies, we argue that sleep disruption may be an overlooked component of insect ecology and could be caused by a variety of anthropogenic and nonanthropogenic factors in nature. We identify several candidate sleep-disrupting factors and provide new insights on the potential consequences of sleep disruption on individual fitness, species interactions, and ecosystem services. We propose an experimental framework to bridge the current gap in knowledge between laboratory and field studies. We conclude that sleep disruption is a potential mechanism underpinning variation in behavioral, population, and community-level processes associated with several aspects of global change.
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20
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Pharmacodynamic study on insomnia-curing effects of Shuangxia Decoction in Drosophila melanogaster. Chin J Nat Med 2017; 14:653-660. [PMID: 27667510 DOI: 10.1016/s1875-5364(16)30077-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Indexed: 12/25/2022]
Abstract
The present study aimed to establish a pharmacodynamic method using the pySolo software to explore the influence of freeze-dried powders of Shuangxia Decoction (SXD) on the sleep of normal Drosophila melanogaster and the Drosophila melanogaster whose sleep was divested by light. The dose-effect and the time-effect relationships of SXD on sleep were examined. The effect-onset concentration of SXD was 0.25%, the plateau appeared at the concentration of 2.5% and the total sleep time showed a downtrend when the concentration was greater than 2.5%. The sleep time was the longest on the fourth day after SXD was given. The fruit fly sleep deprivation model was repeated by light stimulation at night. The middle dosage group (2.5%) had the best insomnia-curing effect. In conclusion, using the pySolo software, an approach for the pharmacodynamics study was established with Drosophila melanogaster as a model organism to determine the insomnia-curing effects of the traditional Chinese medicine (TCM). Our results demonstrated the reliability of this method. The freeze-dried powders of SXD could effectively improve the sleep quality of Drosophila melanogaster.
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21
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Mid-day siesta in natural populations of D. melanogaster from Africa exhibits an altitudinal cline and is regulated by splicing of a thermosensitive intron in the period clock gene. BMC Evol Biol 2017; 17:32. [PMID: 28114910 PMCID: PMC5259850 DOI: 10.1186/s12862-017-0880-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 01/11/2017] [Indexed: 01/18/2023] Open
Abstract
Background Many diurnal animals exhibit a mid-day ‘siesta’, generally thought to be an adaptive response aimed at minimizing exposure to heat on warm days, suggesting that in regions with cooler climates mid-day siestas might be a less prominent feature of animal behavior. Drosophila melanogaster exhibits thermal plasticity in its mid-day siesta that is partly governed by the thermosensitive splicing of the 3’-terminal intron (termed dmpi8) from the key circadian clock gene period (per). For example, decreases in temperature lead to progressively more efficient splicing, which increasingly favors activity over sleep during the mid-day. In this study we sought to determine if the adaptation of D. melanogaster from its ancestral range in the lowlands of tropical Africa to the cooler temperatures found at high altitudes involved changes in mid-day sleep behavior and/or dmpi8 splicing efficiency. Results Using natural populations of Drosophila melanogaster from different altitudes in tropical Africa we show that flies from high elevations have a reduced mid-day siesta and less consolidated sleep. We identified a single nucleotide polymorphism (SNP) in the per 3’ untranslated region that has strong effects on dmpi8 splicing and mid-day sleep levels in both low and high altitude flies. Intriguingly, high altitude flies with a particular variant of this SNP exhibit increased dmpi8 splicing efficiency compared to their low altitude counterparts, consistent with reduced mid-day siesta. Thus, a boost in dmpi8 splicing efficiency appears to have played a prominent but not universal role in how African flies adapted to the cooler temperatures at high altitude. Conclusions Our findings point towards mid-day sleep behavior as a key evolutionary target in the thermal adaptation of animals, and provide a genetic framework for investigating daytime sleep in diurnal animals which appears to be driven by mechanisms distinct from those underlying nighttime sleep. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0880-8) contains supplementary material, which is available to authorized users.
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22
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Khericha M, Kolenchery JB, Tauber E. Neural and non-neural contributions to sexual dimorphism of mid-day sleep in Drosophila melanogaster: a pilot study. PHYSIOLOGICAL ENTOMOLOGY 2016; 41:327-334. [PMID: 27840547 PMCID: PMC5091642 DOI: 10.1111/phen.12134] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/03/2016] [Accepted: 01/05/2016] [Indexed: 05/10/2023]
Abstract
Many of the characteristics associated with mammalian sleep are also observed in Drosophila melanogaster Meigen, making the fruit fly a powerful model organism for studying the genetics of this important process. Included among the similarities is the presence of sexual dimorphic sleep patterns, which, in flies, are manifested as increased mid-day sleep ('siesta') in males compared with females. In the present study, targeted mis-expression of the genes transformer (tra) and tra2 is used to either feminize or masculinize specific neural and non-neural tissues in the fly. Feminization of male D. melanogaster using three different GAL4 drivers that are expressed in the mushroom bodies induces a female-like reduced siesta, whereas the masculinization of females using these drivers triggers the male-like increased siesta. A similar reversal of sex-specific sleep is also observed by mis-expressing tra in the fat body, which is a key tissue in energy metabolism and hormone secretion. In addition, the daily expression levels of takeout, an important circadian clock output gene, are sexually dimorphic. Taken together, these experiments suggest that sleep sexual dimorphism in D. melanogaster is driven by multiple neural and non-neural circuits, within and outside the brain.
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Affiliation(s)
| | | | - Eran Tauber
- Department of GeneticsUniversity of LeicesterLeicesterU.K.
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23
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Nystrand M, Cassidy EJ, Dowling DK. Transgenerational plasticity following a dual pathogen and stress challenge in fruit flies. BMC Evol Biol 2016; 16:171. [PMID: 27567640 PMCID: PMC5002108 DOI: 10.1186/s12862-016-0737-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/08/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Phenotypic plasticity operates across generations, when the parental environment affects phenotypic expression in the offspring. Recent studies in invertebrates have reported transgenerational plasticity in phenotypic responses of offspring when the mothers had been previously exposed to either live or heat-killed pathogens. Understanding whether this plasticity is adaptive requires a factorial design in which both mothers and their offspring are subjected to either the pathogen challenge or a control, in experimentally matched and mismatched combinations. Most prior studies exploring the capacity for pathogen-mediated transgenerational plasticity have, however, failed to adopt such a design. Furthermore, it is currently poorly understood whether the magnitude or direction of pathogen-mediated transgenerational responses will be sensitive to environmental heterogeneity. Here, we explored the transgenerational consequences of a dual pathogen and stress challenge administered in the maternal generation in the fruit fly, Drosophila melanogaster. Prospective mothers were assigned to a non-infectious pathogen treatment consisting of an injection with heat-killed bacteria or a procedural control, and a stress treatment consisting of sleep deprivation or control. Their daughters and sons were similarly assigned to the same pathogen treatment, prior to measurement of their reproductive success. RESULTS We observed transgenerational interactions involving pathogen treatments of mothers and their offspring, on the reproductive success of daughters but not sons. These interactions were unaffected by sleep deprivation. CONCLUSIONS The direction of the transgenerational effects was not consistent with that predicted under a scenario of adaptive transgenerational plasticity. Instead, they were indicative of expectations based on terminal investment.
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Affiliation(s)
- M. Nystrand
- School of Biological Sciences, Monash University, Clayton, VIC 3800 Australia
| | - E. J. Cassidy
- School of Biological Sciences, Monash University, Clayton, VIC 3800 Australia
| | - D. K. Dowling
- School of Biological Sciences, Monash University, Clayton, VIC 3800 Australia
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24
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Svetec N, Cridland JM, Zhao L, Begun DJ. The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster. PLoS Genet 2016; 12:e1005869. [PMID: 26950216 PMCID: PMC4780809 DOI: 10.1371/journal.pgen.1005869] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/22/2016] [Indexed: 01/15/2023] Open
Abstract
Despite decades of work, our understanding of the distribution of fitness effects of segregating genetic variants in natural populations remains largely incomplete. One form of selection that can maintain genetic variation is spatially varying selection, such as that leading to latitudinal clines. While the introduction of population genomic approaches to understanding spatially varying selection has generated much excitement, little successful effort has been devoted to moving beyond genome scans for selection to experimental analysis of the relevant biology and the development of experimentally motivated hypotheses regarding the agents of selection; it remains an interesting question as to whether the vast majority of population genomic work will lead to satisfying biological insights. Here, motivated by population genomic results, we investigate how spatially varying selection in the genetic model system, Drosophila melanogaster, has led to genetic differences between populations in several components of the DNA damage response. UVB incidence, which is negatively correlated with latitude, is an important agent of DNA damage. We show that sensitivity of early embryos to UVB exposure is strongly correlated with latitude such that low latitude populations show much lower sensitivity to UVB. We then show that lines with lower embryo UVB sensitivity also exhibit increased capacity for repair of damaged sperm DNA by the oocyte. A comparison of the early embryo transcriptome in high and low latitude embryos provides evidence that one mechanism of adaptive DNA repair differences between populations is the greater abundance of DNA repair transcripts in the eggs of low latitude females. Finally, we use population genomic comparisons of high and low latitude samples to reveal evidence that multiple components of the DNA damage response and both coding and non-coding variation likely contribute to adaptive differences in DNA repair between populations.
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Affiliation(s)
- Nicolas Svetec
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - Julie M. Cridland
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - Li Zhao
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - David J. Begun
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
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25
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Genomic Patterns of Geographic Differentiation in Drosophila simulans. Genetics 2016; 202:1229-40. [PMID: 26801179 DOI: 10.1534/genetics.115.185496] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 01/16/2016] [Indexed: 11/18/2022] Open
Abstract
Geographic patterns of genetic differentiation have long been used to understand population history and to learn about the biological mechanisms of adaptation. Here we present an examination of genomic patterns of differentiation between northern and southern populations of Australian and North American Drosophila simulans, with an emphasis on characterizing signals of parallel differentiation. We report on the genomic scale of differentiation and functional enrichment of outlier SNPs. While, overall, signals of shared differentiation are modest, we find the strongest support for parallel differentiation in genomic regions that are associated with regulation. Comparisons to Drosophila melanogaster yield potential candidate genes involved in local adaptation in both species, providing insight into common selective pressures and responses. In contrast to D. melanogaster, in D. simulans we observe patterns of variation that are inconsistent with a model of temperate adaptation out of a tropical ancestral range, highlighting potential differences in demographic and colonization histories of this cosmopolitan species pair.
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26
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Adrion JR, Hahn MW, Cooper BS. Revisiting classic clines in Drosophila melanogaster in the age of genomics. Trends Genet 2015; 31:434-44. [PMID: 26072452 PMCID: PMC4526433 DOI: 10.1016/j.tig.2015.05.006] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 12/16/2022]
Abstract
Adaptation to spatially varying environments has been studied for decades, but advances in sequencing technology are now enabling researchers to investigate the landscape of genetic variation underlying this adaptation genome wide. In this review we highlight some of the decades-long research on local adaptation in Drosophila melanogaster from well-studied clines in North America and Australia. We explore the evidence for parallel adaptation and identify commonalities in the genes responding to clinal selection across continents as well as discussing instances where patterns differ among clines. We also investigate recent studies utilizing whole-genome data to identify clines in D. melanogaster and several other systems. Although connecting segregating genomic variation to variation in phenotypes and fitness remains challenging, clinal genomics is poised to increase our understanding of local adaptation and the selective pressures that drive the extensive phenotypic diversity observed in nature.
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Affiliation(s)
- Jeffrey R Adrion
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA; School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Brandon S Cooper
- Center for Population Biology, University of California, Davis, CA 95616, USA; Department of Evolution and Ecology, University of California, Davis, CA 95616, USA.
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