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Lollar MJ, Kim E, Stern DL, Pool JE. Courtship song differs between African and European populations of Drosophila melanogaster and involves a strong effect locus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594231. [PMID: 38798463 PMCID: PMC11118343 DOI: 10.1101/2024.05.14.594231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The courtship song of Drosophila melanogaster has long served as excellent model system for studies of animal communication and differences in courtship song have been demonstrated among populations and between species. Here, we report that flies of African and European origin, which diverged approximately 13,000 years ago, show significant genetic differentiation in the use of slow versus fast pulse song. Using a combination of quantitative trait mapping and population genetic analysis we detected a single strong QTL underlying this trait and we identified candidate genes that may contribute to the evolution of this trait. Song trait variation between parental strains of our recombinant inbred panel enabled detection of genomic intervals associated with six additional song traits, some of which include known courtship-related genes. These findings improve the prospects for further genetic insights into the evolution of reproductive behavior and the biology underlying courtship song.
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Affiliation(s)
- Matthew J Lollar
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Elizabeth Kim
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147 USA
| | - David L Stern
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147 USA
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, WI, 53705, USA
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2
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Stazione L, Sambucetti PD, Norry FM. Mating success at elevated temperature is associated to thermal adaptation in a set of recombinant inbred lines of Drosophila melanogaster. JOURNAL OF INSECT PHYSIOLOGY 2023; 144:104468. [PMID: 36528089 DOI: 10.1016/j.jinsphys.2022.104468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/30/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
In insects, mating ability at elevated temperature can be relevant for adaptation to heat-stressed environments and global warming. Here, we examined copulation latency (T1), copulation duration (T2), and mating frequency (T3, an index of mating success) in two related sets of recombinant inbred lines (RIL) in Drosophila melanogaster at both elevated (33 °C) and benign (25 °C) temperatures. One of these RIL sets (RIL-SH2) was shown to be consistently more resistant in both heat knockdown and heat-shock survival assays than its related set (RIL-D48) in previous studies. Negative correlations across RILs were found between T1 and T3 in this study. Flies from the heat-resistant set of RIL (RIL-SH2) were better able to mate at elevated temperature than flies from the heat-susceptible set (RIL-D48). Quantitative trait locus (QTL) mapping identified temperature-dependent QTLs for all traits (T1, T2 and T3) on all the three major chromosomes. Mating success at elevated temperature was found to be influenced by multiple QTLs. At elevated temperature, several QTLs for mating traits co-localized with QTLs that were previously associated with thermotolerance. The genetic basis for T1, T2 and T3 at the elevated temperature was found to be largely different from the genetic basis controlling the variation for mating success at benign temperature, as there was only a very low (or even null) number of QTLs overlapping across temperatures.
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Affiliation(s)
- Leonel Stazione
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA) - CONICET, Universidad de Buenos Aires, C-1428-EHA Buenos Aires, Argentina; Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, C-1428-EHA Buenos Aires, Argentina
| | - Pablo D Sambucetti
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA) - CONICET, Universidad de Buenos Aires, C-1428-EHA Buenos Aires, Argentina; Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, C-1428-EHA Buenos Aires, Argentina
| | - Fabian M Norry
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA) - CONICET, Universidad de Buenos Aires, C-1428-EHA Buenos Aires, Argentina; Facultad de Ciencias Exactas y Naturales, Departamento de Ecología, Genética y Evolución, Universidad de Buenos Aires, C-1428-EHA Buenos Aires, Argentina.
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MacPherson RA, Shankar V, Sunkara LT, Hannah RC, Campbell MR, Anholt RRH, Mackay TFC. Pleiotropic fitness effects of the lncRNA Uhg4 in Drosophila melanogaster. BMC Genomics 2022; 23:781. [PMID: 36451091 PMCID: PMC9710044 DOI: 10.1186/s12864-022-08972-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/26/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are a diverse class of RNAs that are critical for gene regulation, DNA repair, and splicing, and have been implicated in development, stress response, and cancer. However, the functions of many lncRNAs remain unknown. In Drosophila melanogaster, U snoRNA host gene 4 (Uhg4) encodes an antisense long noncoding RNA that is host to seven small nucleolar RNAs (snoRNAs). Uhg4 is expressed ubiquitously during development and in all adult tissues, with maximal expression in ovaries; however, it has no annotated function(s). RESULTS We used CRISPR-Cas9 germline gene editing to generate multiple deletions spanning the promoter region and first exon of Uhg4. Females showed arrested egg development and both males and females were sterile. In addition, Uhg4 deletion mutants showed delayed development and decreased viability, and changes in sleep and responses to stress. Whole-genome RNA sequencing of Uhg4 deletion flies and their controls identified co-regulated genes and genetic interaction networks associated with Uhg4. Gene ontology analyses highlighted a broad spectrum of biological processes, including regulation of transcription and translation, morphogenesis, and stress response. CONCLUSION Uhg4 is a lncRNA essential for reproduction with pleiotropic effects on multiple fitness traits.
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Affiliation(s)
- Rebecca A MacPherson
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Vijay Shankar
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Lakshmi T Sunkara
- Present adress: Clemson Veterinary Diagnostic Center, Livestock Poultry Health, Clemson University, 500 Clemson Road, Columbia, SC, 29229, USA
| | - Rachel C Hannah
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Marion R Campbell
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Robert R H Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA.
| | - Trudy F C Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA.
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4
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Jin B, Barbash DA, Castillo DM. Divergent selection on behavioural and chemical traits between reproductively isolated populations of Drosophila melanogaster. J Evol Biol 2022; 35:693-707. [PMID: 35411988 PMCID: PMC9320809 DOI: 10.1111/jeb.14007] [Citation(s) in RCA: 1] [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: 07/26/2021] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 11/29/2022]
Abstract
Speciation is driven by traits that can act to prevent mating between nascent lineages, including male courtship and female preference for male traits. Mating barriers involving these traits evolve quickly because there is strong selection on males and females to maximize reproductive success, and the tight co-evolution of mating interactions can lead to rapid diversification of sexual behaviour. Populations of Drosophila melanogaster show strong asymmetrical reproductive isolation that is correlated with geographic origin. Using strains that capture natural variation in mating traits, we ask two key questions: which specific male traits are females selecting, and are these traits under divergent sexual selection? These questions have proven extremely challenging to answer, because even in closely related lineages males often differ in multiple traits related to mating behaviour. We address these questions by estimating selection gradients for male courtship and cuticular hydrocarbons for two different female genotypes. We identify specific behaviours and particular cuticular hydrocarbons that are under divergent sexual selection and could potentially contribute to premating reproductive isolation. Additionally, we report that a subset of these traits are plastic; males adjust these traits based on the identity of the female genotype they interact with. These results suggest that even when male courtship is not fixed between lineages, ongoing selection can act on traits that are important for reproductive isolation.
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Affiliation(s)
- Bozhou Jin
- Department of Molecular Biology and GeneticsCornell UniversityIthacaNew YorkUSA
| | - Daniel A. Barbash
- Department of Molecular Biology and GeneticsCornell UniversityIthacaNew YorkUSA
| | - Dean M. Castillo
- Department of BiologyUniversity of Nebraska at OmahaOmahaNebraskaUSA
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5
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Rihani K, Sachse S. Shedding Light on Inter-Individual Variability of Olfactory Circuits in Drosophila. Front Behav Neurosci 2022; 16:835680. [PMID: 35548690 PMCID: PMC9084309 DOI: 10.3389/fnbeh.2022.835680] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/29/2022] [Indexed: 12/25/2022] Open
Abstract
Inter-individual differences in behavioral responses, anatomy or functional properties of neuronal populations of animals having the same genotype were for a long time disregarded. The majority of behavioral studies were conducted at a group level, and usually the mean behavior of all individuals was considered. Similarly, in neurophysiological studies, data were pooled and normalized from several individuals. This approach is mostly suited to map and characterize stereotyped neuronal properties between individuals, but lacks the ability to depict inter-individual variability regarding neuronal wiring or physiological characteristics. Recent studies have shown that behavioral biases and preferences to olfactory stimuli can vary significantly among individuals of the same genotype. The origin and the benefit of these diverse “personalities” is still unclear and needs to be further investigated. A perspective taken into account the inter-individual differences is needed to explore the cellular mechanisms underlying this phenomenon. This review focuses on olfaction in the vinegar fly Drosophila melanogaster and summarizes previous and recent studies on odor-guided behavior and the underlying olfactory circuits in the light of inter-individual variability. We address the morphological and physiological variabilities present at each layer of the olfactory circuitry and attempt to link them to individual olfactory behavior. Additionally, we discuss the factors that might influence individuality with regard to olfactory perception.
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Affiliation(s)
- Karen Rihani
- Research Group Olfactory Coding, Max Planck Institute for Chemical Ecology, Jena, Germany
- Max Planck Center Next Generation Insect Chemical Ecology, Jena, Germany
| | - Silke Sachse
- Research Group Olfactory Coding, Max Planck Institute for Chemical Ecology, Jena, Germany
- Max Planck Center Next Generation Insect Chemical Ecology, Jena, Germany
- *Correspondence: Silke Sachse,
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6
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Mueller JM, Zhang N, Carlson JM, Simpson JH. Variation and Variability in Drosophila Grooming Behavior. Front Behav Neurosci 2022; 15:769372. [PMID: 35087385 PMCID: PMC8787196 DOI: 10.3389/fnbeh.2021.769372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/13/2021] [Indexed: 01/23/2023] Open
Abstract
Behavioral differences can be observed between species or populations (variation) or between individuals in a genetically similar population (variability). Here, we investigate genetic differences as a possible source of variation and variability in Drosophila grooming. Grooming confers survival and social benefits. Grooming features of five Drosophila species exposed to a dust irritant were analyzed. Aspects of grooming behavior, such as anterior to posterior progression, were conserved between and within species. However, significant differences in activity levels, proportion of time spent in different cleaning movements, and grooming syntax were identified between species. All species tested showed individual variability in the order and duration of action sequences. Genetic diversity was not found to correlate with grooming variability within a species: melanogaster flies bred to increase or decrease genetic heterogeneity exhibited similar variability in grooming syntax. Individual flies observed on consecutive days also showed grooming sequence variability. Standardization of sensory input using optogenetics reduced but did not eliminate this variability. In aggregate, these data suggest that sequence variability may be a conserved feature of grooming behavior itself. These results also demonstrate that large genetic differences result in distinguishable grooming phenotypes (variation), but that genetic heterogeneity within a population does not necessarily correspond to an increase in the range of grooming behavior (variability).
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Affiliation(s)
- Joshua M. Mueller
- Interdepartmental Graduate Program in Dynamical Neuroscience, University of California, Santa Barbara, Santa Barbara, CA, United States
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Neil Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Jean M. Carlson
- Department of Physics, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Julie H. Simpson
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA, United States
- *Correspondence: Julie H. Simpson,
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Mollá-Albaladejo R, Sánchez-Alcañiz JA. Behavior Individuality: A Focus on Drosophila melanogaster. Front Physiol 2021; 12:719038. [PMID: 34916952 PMCID: PMC8670942 DOI: 10.3389/fphys.2021.719038] [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: 06/01/2021] [Accepted: 10/11/2021] [Indexed: 12/02/2022] Open
Abstract
Among individuals, behavioral differences result from the well-known interplay of nature and nurture. Minute differences in the genetic code can lead to differential gene expression and function, dramatically affecting developmental processes and adult behavior. Environmental factors, epigenetic modifications, and gene expression and function are responsible for generating stochastic behaviors. In the last decade, the advent of high-throughput sequencing has facilitated studying the genetic basis of behavior and individuality. We can now study the genomes of multiple individuals and infer which genetic variations might be responsible for the observed behavior. In addition, the development of high-throughput behavioral paradigms, where multiple isogenic animals can be analyzed in various environmental conditions, has again facilitated the study of the influence of genetic and environmental variations in animal personality. Mainly, Drosophila melanogaster has been the focus of a great effort to understand how inter-individual behavioral differences emerge. The possibility of using large numbers of animals, isogenic populations, and the possibility of modifying neuronal function has made it an ideal model to search for the origins of individuality. In the present review, we will focus on the recent findings that try to shed light on the emergence of individuality with a particular interest in D. melanogaster.
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8
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Davis JS, Pearcy MJ, Yew JY, Moyle LC. A shift to shorter cuticular hydrocarbons accompanies sexual isolation among Drosophila americana group populations. Evol Lett 2021; 5:521-540. [PMID: 34621538 PMCID: PMC8484720 DOI: 10.1002/evl3.246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 04/08/2021] [Accepted: 06/13/2021] [Indexed: 12/15/2022] Open
Abstract
Because sensory signals often evolve rapidly, they could be instrumental in the emergence of reproductive isolation between species. However, pinpointing their specific contribution to isolating barriers, and the mechanisms underlying their divergence, remains challenging. Here, we demonstrate sexual isolation due to divergence in chemical signals between two populations of Drosophila americana (SC and NE) and one population of D. novamexicana, and dissect its underlying phenotypic and genetic mechanisms. Mating trials revealed strong sexual isolation between Drosophila novamexicana males and SC Drosophila americana females, as well as more moderate bi-directional isolation between D. americana populations. Mating behavior data indicate SC D. americana males have the highest courtship efficiency and, unlike males of the other populations, are accepted by females of all species. Quantification of cuticular hydrocarbon (CHC) profiles-chemosensory signals that are used for species recognition and mate finding in Drosophila-shows that the SC D. americana population differs from the other populations primarily on the basis of compound carbon chain-length. Moreover, manipulation of male CHC composition via heterospecific perfuming-specifically perfuming D. novamexicana males with SC D. americana males-abolishes their sexual isolation from these D. americana females. Of a set of candidates, a single gene-elongase CG17821-had patterns of gene expression consistent with a role in CHC differences between species. Sequence comparisons indicate D. novamexicana and our Nebraska (NE) D. americana population share a derived CG17821 truncation mutation that could also contribute to their shared "short" CHC phenotype. Together, these data suggest an evolutionary model for the origin and spread of this allele and its consequences for CHC divergence and sexual isolation in this group.
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Affiliation(s)
- Jeremy S. Davis
- Department of BiologyIndiana UniversityBloomingtonIndiana47405
- Department of BiologyUniversity of KentuckyLexingtonKentucky40508
| | | | - Joanne Y. Yew
- Pacific Biosciences Research CenterUniversity of Hawaii at MānoaHonoluluHawaii96822
| | - Leonie C. Moyle
- Department of BiologyIndiana UniversityBloomingtonIndiana47405
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9
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RNA-binding protein syncrip regulates starvation-induced hyperactivity in adult Drosophila. PLoS Genet 2021; 17:e1009396. [PMID: 33617535 PMCID: PMC7932510 DOI: 10.1371/journal.pgen.1009396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/04/2021] [Accepted: 02/03/2021] [Indexed: 11/28/2022] Open
Abstract
How to respond to starvation determines fitness. One prominent behavioral response is increased locomotor activities upon starvation, also known as Starvation-Induced Hyperactivity (SIH). SIH is paradoxical as it promotes food seeking but also increases energy expenditure. Despite its importance in fitness, the genetic contributions to SIH as a behavioral trait remains unexplored. Here, we examined SIH in the Drosophila melanogaster Genetic Reference Panel (DGRP) and performed genome-wide association studies. We identified 23 significant loci, corresponding to 14 genes, significantly associated with SIH in adult Drosophila. Gene enrichment analyses indicated that genes encoding ion channels and mRNA binding proteins (RBPs) were most enriched in SIH. We are especially interested in RBPs because they provide a potential mechanism to quickly change protein expression in response to environmental challenges. Using RNA interference, we validated the role of syp in regulating SIH. syp encodes Syncrip (Syp), an RBP. While ubiquitous knockdown of syp led to semi-lethality in adult flies, adult flies with neuron-specific syp knockdown were viable and exhibited decreased SIH. Using the Temporal and Regional Gene Expression Targeting (TARGET) system, we further confirmed the role of Syp in adult neurons in regulating SIH. To determine how syp is regulated by starvation, we performed RNA-seq using the heads of flies maintained under either food or starvation conditions. RNA-seq analyses revealed that syp was alternatively spliced under starvation while its expression level was unchanged. We further generated an alternatively-spliced-exon-specific knockout (KO) line and found that KO flies showed reduced SIH. Together, this study demonstrates a significant genetic contribution to SIH as a behavioral trait, identifies syp as a SIH gene, and highlights the significance of RBPs and post-transcriptional processes in the brain in regulating behavioral responses to starvation. Animals living in the wild often face periods of starvation. How to physiologically and behaviorally respond to starvation is essential for survival. One behavioral response is Starvation-Induced Hyperactivity (SIH). We used the Drosophila melanogaster Genetic Reference Panel, derived from a wild population, to study the genetic basis of SIH. Our results show that there is a significant genetic contribution to SIH in this population, and that genes encoding RNA binding proteins (RBPs) are especially important. Using RNA interference and the TARGET system, we confirmed the role of an RBP Syp in adult neurons in SIH. Using RNA-seq and Western blotting, we found that syp was alternatively spliced under starvation while its expression level was unchanged. Further studies from syp exon-specific knockout flies showed that alternative splicing involving two exons in syp was important for SIH. Together, this study identifies syp as a SIH gene and highlights an essential role of post-transcriptional modification in regulating this behavior.
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10
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Anholt RRH, O'Grady P, Wolfner MF, Harbison ST. Evolution of Reproductive Behavior. Genetics 2020; 214:49-73. [PMID: 31907301 PMCID: PMC6944409 DOI: 10.1534/genetics.119.302263] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/04/2019] [Indexed: 12/20/2022] Open
Abstract
Behaviors associated with reproduction are major contributors to the evolutionary success of organisms and are subject to many evolutionary forces, including natural and sexual selection, and sexual conflict. Successful reproduction involves a range of behaviors, from finding an appropriate mate, courting, and copulation, to the successful production and (in oviparous animals) deposition of eggs following mating. As a consequence, behaviors and genes associated with reproduction are often under strong selection and evolve rapidly. Courtship rituals in flies follow a multimodal pattern, mediated through visual, chemical, tactile, and auditory signals. Premating behaviors allow males and females to assess the species identity, reproductive state, and condition of their partners. Conflicts between the "interests" of individual males, and/or between the reproductive strategies of males and females, often drive the evolution of reproductive behaviors. For example, seminal proteins transmitted by males often show evidence of rapid evolution, mediated by positive selection. Postmating behaviors, including the selection of oviposition sites, are highly variable and Drosophila species span the spectrum from generalists to obligate specialists. Chemical recognition features prominently in adaptation to host plants for feeding and oviposition. Selection acting on variation in pre-, peri-, and postmating behaviors can lead to reproductive isolation and incipient speciation. Response to selection at the genetic level can include the expansion of gene families, such as those for detecting pheromonal cues for mating, or changes in the expression of genes leading to visual cues such as wing spots that are assessed during mating. Here, we consider the evolution of reproductive behavior in Drosophila at two distinct, yet complementary, scales. Some studies take a microevolutionary approach, identifying genes and networks involved in reproduction, and then dissecting the genetics underlying complex behaviors in D. melanogaster Other studies take a macroevolutionary approach, comparing reproductive behaviors across the genus Drosophila and how these might correlate with environmental cues. A full synthesis of this field will require unification across these levels.
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Affiliation(s)
- Robert R H Anholt
- Center for Human Genetics, Clemson University, Greenwood, South Carolina 29646
- Department of Genetics and Biochemistry, Clemson University, Greenwood, South Carolina 29646
| | - Patrick O'Grady
- Department of Entomology, Cornell University, Ithaca, New York 14853
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Susan T Harbison
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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11
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Baxter CM, Yan JL, Dukas R. Genetic variation in sexual aggression and the factors that determine forced copulation success. Anim Behav 2019. [DOI: 10.1016/j.anbehav.2019.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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12
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Young HK, Denecke SM, Robin C, Fournier-Level A. Sublethal larval exposure to imidacloprid impacts adult behaviour in Drosophila melanogaster. J Evol Biol 2019; 33:151-164. [PMID: 31637792 DOI: 10.1111/jeb.13555] [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: 06/14/2019] [Revised: 10/07/2019] [Accepted: 10/11/2019] [Indexed: 12/27/2022]
Abstract
Pesticides are now chronically found in numerous ecosystems incurring widespread toxic effects on multiple organisms. For insects, the larvae are very exposed to pesticide pollution and the acute effect of insecticides on larvae has been characterized in a range of species. However, the carry-on effects in adults of sublethal exposure occurring in larvae are not well characterized. Here, we use a collection of strains of Drosophila melanogaster differing in their larval resistance to a commonly used insecticide, imidacloprid, and we test the effect of larval exposure on behavioural traits at the adult stage. Focusing on locomotor activity and on courtship and mating behaviour, we observed a significant carry-on effect of imidacloprid exposure. The heritability of activity traits measured in flies exposed to imidacloprid was higher than measured in controls and in these, courtship traits were genetically less correlated from mating success. Altogether, we did not observe a significant effect of the larval insecticide resistance status on adult behavioural traits, suggesting that selection for resistance in larvae does not involve repeatable behavioural changes in adults. This lack of correlation between larval resistance and adult behaviour also suggests that resistance at the larval stage does not necessarily result in increased behavioural resilience at a later life stage. These findings imply that selection for resistance in larvae as well as for behavioural resilience to sublethal exposure in adult will combine and impose a greater evolutionary constraint. Our conclusions further substantiate the need to encompass multiple trait measures and life stages in toxicological assays to properly assess the environmental impact of pesticides.
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Affiliation(s)
- Helen K Young
- School of BioSciences, The University of Melbourne, Parkville, Vic., Australia
| | - Shane M Denecke
- Institute of Molecular Biology and Biotechnology FORTH, Heraklion, Greece
| | - Charles Robin
- School of BioSciences, The University of Melbourne, Parkville, Vic., Australia
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Watanabe LP, Riddle NC. New opportunities: Drosophila as a model system for exercise research. J Appl Physiol (1985) 2019; 127:482-490. [DOI: 10.1152/japplphysiol.00394.2019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Because of the growing rates of obesity in much of the world, exercise as a treatment option for obesity and as part of a healthy lifestyle is of great interest to the general public, health policy makers, and scientists alike. Despite the long history of exercise promotion and exercise research, there are still significant gaps in our understanding of how exercise impacts individuals and what role genetics plays in determining an individual’s response to exercise. Model organisms are positioned uniquely to help address these questions because of the challenges associated with carrying out large-scale, well-controlled studies in humans. The fruit fly model system, Drosophila melanogaster, has joined the models used for exercise research only recently but already has made significant contributions to the field. In this review, we highlight the opportunities for exercise research in Drosophila. We review the resources available to researchers interested in using Drosophila for exercise research, focusing on the existing systems to induce exercise in Drosophila, to measure the amount of exercise performed, and to assess physical fitness. We illustrate the potential of the Drosophila system by drawing attention to pioneering studies in Drosophila exercise research and emphasize the unique opportunities this model system represents.
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Affiliation(s)
- Louis P. Watanabe
- Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Nicole C. Riddle
- Department of Biology, The University of Alabama at Birmingham, Birmingham, Alabama
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14
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Brenman-Suttner DB, Yost RT, Frame AK, Robinson JW, Moehring AJ, Simon AF. Social behavior and aging: A fly model. GENES BRAIN AND BEHAVIOR 2019; 19:e12598. [PMID: 31286644 DOI: 10.1111/gbb.12598] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 07/02/2019] [Accepted: 07/05/2019] [Indexed: 12/16/2022]
Abstract
The field of behavioral genetics has recently begun to explore the effect of age on social behaviors. Such studies are particularly important, as certain neuropsychiatric disorders with abnormal social interactions, like autism and schizophrenia, have been linked to older parents. Appropriate social interaction can also have a positive impact on longevity, and is associated with successful aging in humans. Currently, there are few genetic models for understanding the effect of aging on social behavior and its potential transgenerational inheritance. The fly is emerging as a powerful model for identifying the basic molecular mechanisms underlying neurological and neuropsychiatric disorders. In this review, we discuss these recent advancements, with a focus on how studies in Drosophila melanogaster have provided insight into the effect of aging on aspects of social behavior, including across generations.
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Affiliation(s)
- Dova B Brenman-Suttner
- Department of Biology, Faculty of Science, Western University, London, Ontario, Canada.,Department of Biology, York University, Toronto, Ontario, Canada
| | - Ryley T Yost
- Department of Biology, Faculty of Science, Western University, London, Ontario, Canada
| | - Ariel K Frame
- Department of Biology, Faculty of Science, Western University, London, Ontario, Canada
| | - J Wesley Robinson
- Department of Biology, Faculty of Science, Western University, London, Ontario, Canada
| | - Amanda J Moehring
- Department of Biology, Faculty of Science, Western University, London, Ontario, Canada
| | - Anne F Simon
- Department of Biology, Faculty of Science, Western University, London, Ontario, Canada
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15
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Robin C, Battlay P, Fournier-Level A. What can genetic association panels tell us about evolutionary processes in insects? CURRENT OPINION IN INSECT SCIENCE 2019; 31:99-105. [PMID: 31109681 DOI: 10.1016/j.cois.2018.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
If we are to fully comprehend the evolution of insect diversity at a genomic level we need to understand how natural selection can alter genetically encoded characters within populations. Genetic association panels have the potential to be standard bearers in this endeavour. They enable the mapping of phenotypes to genotypes at unprecedented resolution while simultaneously providing population genomic samples that can be interrogated for the tell-tale signs of selection. Analyses of these panels promise to elucidate the entanglement of gene ontologies, pathways, developmental processes and evolutionary constraints, and inform how these are shaped by adaptation.
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Affiliation(s)
- Charles Robin
- The School of BioSciences, The University of Melbourne, Parkville 3010, Australia.
| | - Paul Battlay
- The School of BioSciences, The University of Melbourne, Parkville 3010, Australia
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16
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The Sleep Inbred Panel, a Collection of Inbred Drosophila melanogaster with Extreme Long and Short Sleep Duration. G3-GENES GENOMES GENETICS 2018; 8:2865-2873. [PMID: 29991508 PMCID: PMC6118319 DOI: 10.1534/g3.118.200503] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Understanding how genomic variation causes differences in observable phenotypes remains a major challenge in biology. It is difficult to trace the sequence of events originating from genomic variants to changes in transcriptional responses or protein modifications. Ideally, one would conduct experiments with individuals that are at either extreme of the trait of interest, but such resources are often not available. Further, advances in genome editing will enable testing of candidate polymorphisms individually and in combination. Here we have created a resource for the study of sleep with 39 inbred lines of Drosophila-the Sleep Inbred Panel (SIP). SIP lines have stable long- and short-sleeping phenotypes developed from naturally occurring polymorphisms. These lines are fully sequenced, enabling more accurate targeting for genome editing and transgenic constructs. This panel facilitates the study of intermediate transcriptional and proteomic correlates of sleep, and supports genome editing studies to verify polymorphisms associated with sleep duration.
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17
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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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18
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Everman ER, Delzeit JL, Hunter FK, Gleason JM, Morgan TJ. Costs of cold acclimation on survival and reproductive behavior in Drosophila melanogaster. PLoS One 2018; 13:e0197822. [PMID: 29791517 PMCID: PMC5965859 DOI: 10.1371/journal.pone.0197822] [Citation(s) in RCA: 16] [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: 11/30/2017] [Accepted: 05/09/2018] [Indexed: 12/27/2022] Open
Abstract
Fitness is determined by the ability of an organism to both survive and reproduce; however, the mechanisms that lead to increased survival may not have the same effect on reproductive success. We used nineteen natural Drosophila melanogaster genotypes from the Drosophila Genetic Reference Panel to determine if adaptive plasticity following short-term acclimation through rapid cold-hardening (RCH) affects mating behavior and mating success. We confirmed that exposure to the acclimation temperature is beneficial to survival following cold stress; however, we found that this same acclimation temperature exposure led to less efficient male courtship and a significant decrease in the likelihood of mating. Cold tolerance and the capacity to respond plastically to cold stress were not correlated with mating behavior following acclimation, suggesting that the genetic control of the physiological effects of the cold temperature exposure likely differ between survival and behavioral responses. We also tested whether the exposure of males to the acclimation temperature influenced courtship song. This exposure again significantly increased courtship duration; however, courtship song was unchanged. These results illustrate costs of short-term acclimation on survival and reproductive components of fitness and demonstrate the pronounced effect that short-term thermal environment shifts can have on reproductive success.
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Affiliation(s)
- Elizabeth R. Everman
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Jennifer L. Delzeit
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - F. Kate Hunter
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Jennifer M. Gleason
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Theodore J. Morgan
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail:
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19
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Abstract
Recent years have seen an increase in studies that associate genomic loci with behavioral variation both within and across animal species. Ryan York compiles and analyzes over 1,000 of these loci, finding that the genetic... Although most animal behaviors are associated with some form of heritable genetic variation, we do not yet understand how genes sculpt behavior across evolution, either directly or indirectly. To address this, I here compile a data set comprised of over 1000 genomic loci representing a spectrum of behavioral variation across animal taxa. Comparative analyses reveal that courtship and feeding behaviors are associated with genomic regions of significantly greater effect than other traits, on average threefold greater than other behaviors. Investigations of whole-genome sequencing and phenotypic data for 87 behavioral traits from the Drosophila Genetics Reference Panel indicate that courtship and feeding behaviors have significantly greater genetic contributions and that, in general, behavioral traits overlap little in individual base pairs but increasingly interact at the levels of genes and traits. These results provide evidence that different types of behavior are associated with variable genetic bases and suggest that, across animal evolution, the genetic landscape of behavior is more rugged, yet predictable, than previously thought.
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20
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Golov Y, Rillich J, Harari A, Ayali A. Precopulatory behavior and sexual conflict in the desert locust. PeerJ 2018; 6:e4356. [PMID: 29507823 PMCID: PMC5834936 DOI: 10.7717/peerj.4356] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/21/2018] [Indexed: 11/28/2022] Open
Abstract
Studies of mating and reproductive behavior have contributed much to our understanding of various animals' ecological success. The desert locust, Schistocerca gregaria, is an important agricultural pest. However, knowledge of locust courtship and precopulatory behavior is surprisingly limited. Here we provide a comprehensive study of the precopulatory behavior of both sexes of the desert locust in the gregarious phase, with particular emphasis on the conflict between the sexes. Detailed HD-video monitoring of courtship and mating of 20 locust pairs, in a controlled environment, enabled both qualitative and quantitative descriptions of the behavior. A comprehensive list of behavioral elements was used to generate an eight-step ethogram, from first encounter between the sexes to actual copulation. Further analyses included the probability of each element occurring, and a kinematic diagram based on a transitional matrix. Eleven novel behavioral elements are described in this study, and two potential points of conflict between the sexes are identified. Locust sexual interaction was characterized by the dominance of the males during the pre-mounting stage, and an overall stereotypic male courtship behavior. In contrast, females displayed no clear courtship-related behavior and an overall less organized behavioral sequence. Central elements in the sexual behavior of the females were low-amplitude hind-leg vibration, as well as rejecting males by jumping and kicking. Intricate reciprocal interactions between the sexes were evident mostly at the mounting stage. The reported findings contribute important insights to our knowledge of locust mating and reproductive behavior, and may assist in confronting this devastating agricultural pest.
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Affiliation(s)
- Yiftach Golov
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Jan Rillich
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Ally Harari
- Department of Entomology, Volcani Center, Bet Dagan, Israel
| | - Amir Ayali
- School of Zoology, Tel Aviv University, Tel Aviv, Israel
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21
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Wu KJ, Kumar S, Serrano Negron YL, Harbison ST. Genotype Influences Day-to-Day Variability in Sleep in Drosophila melanogaster. Sleep 2018; 41:zsx205. [PMID: 29228366 PMCID: PMC6018780 DOI: 10.1093/sleep/zsx205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/27/2017] [Indexed: 12/22/2022] Open
Abstract
Patterns of sleep often vary among individuals. But sleep and activity may also vary within an individual, fluctuating in pattern across time. One possibility is that these daily fluctuations in sleep are caused by the underlying genotype of the individual. However, differences attributable to genetic causes are difficult to distinguish from environmental factors in outbred populations such as humans. We therefore employed Drosophila as a model of intra-individual variability in sleep using previously collected sleep and activity data from the Drosophila Genetic Reference Panel, a collection of wild-derived inbred lines. Individual flies had significant daily fluctuations in their sleep patterns, and these fluctuations were heritable. Using the standard deviation of sleep parameters as a metric, we conducted a genome-wide association study. We found 663 polymorphisms in 104 genes associated with daily fluctuations in sleep. We confirmed the effects of 12 candidate genes on the standard deviation of sleep parameters. Our results suggest that daily fluctuations in sleep patterns are due in part to gene activity.
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Affiliation(s)
- Katherine J Wu
- Laboratory of Systems Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Shailesh Kumar
- Laboratory of Systems Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Yazmin L Serrano Negron
- Laboratory of Systems Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Susan T Harbison
- Laboratory of Systems Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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22
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Lee YCG, Yang Q, Chi W, Turkson SA, Du WA, Kemkemer C, Zeng ZB, Long M, Zhuang X. Genetic Architecture of Natural Variation Underlying Adult Foraging Behavior That Is Essential for Survival of Drosophila melanogaster. Genome Biol Evol 2018; 9:1357-1369. [PMID: 28472322 PMCID: PMC5452641 DOI: 10.1093/gbe/evx089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2017] [Indexed: 01/04/2023] Open
Abstract
Foraging behavior is critical for the fitness of individuals. However, the genetic basis of variation in foraging behavior and the evolutionary forces underlying such natural variation have rarely been investigated. We developed a systematic approach to assay the variation in survival rate in a foraging environment for adult flies derived from a wild Drosophila melanogaster population. Despite being such an essential trait, there is substantial variation of foraging behavior among D. melanogaster strains. Importantly, we provided the first evaluation of the potential caveats of using inbred Drosophila strains to perform genome-wide association studies on life-history traits, and concluded that inbreeding depression is unlikely a major contributor for the observed large variation in adult foraging behavior. We found that adult foraging behavior has a strong genetic component and, unlike larval foraging behavior, depends on multiple loci. Identified candidate genes are enriched in those with high expression in adult heads and, demonstrated by expression knock down assay, are involved in maintaining normal functions of the nervous system. Our study not only identified candidate genes for foraging behavior that is relevant to individual fitness, but also shed light on the initial stage underlying the evolution of the behavior.
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Affiliation(s)
- Yuh Chwen G Lee
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL.,Present address: Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory; Department of Molecular Biology and Cell Biology, University of California, Berkeley
| | - Qian Yang
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Wanhao Chi
- Department of Neurobiology, The University of Chicago, Chicago, IL.,Present address: Committee on Genetics, Genomics & Systems Biology, The University of Chicago, Chicago, IL
| | - Susie A Turkson
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Wei A Du
- Department of Biology, Wayne State University, Detroit, MI
| | - Claus Kemkemer
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL
| | - Zhao-Bang Zeng
- Department of Statistical Genetics and Bioinformatics, North Carolina State University, Raleigh, NC
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL
| | - Xiaoxi Zhuang
- Department of Neurobiology, The University of Chicago, Chicago, IL
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23
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Mackay TFC, Huang W. Charting the genotype-phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2018; 7:10.1002/wdev.289. [PMID: 28834395 PMCID: PMC5746472 DOI: 10.1002/wdev.289] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 11/08/2022]
Abstract
Understanding the genetic architecture (causal molecular variants, their effects, and frequencies) of quantitative traits is important for precision agriculture and medicine and predicting adaptive evolution, but is challenging in most species. The Drosophila melanogaster Genetic Reference Panel (DGRP) is a collection of 205 inbred strains with whole genome sequences derived from a single wild population in Raleigh, NC, USA. The large amount of quantitative genetic variation, lack of population structure, and rapid local decay of linkage disequilibrium in the DGRP and outbred populations derived from DGRP lines present a favorable scenario for performing genome-wide association (GWA) mapping analyses to identify candidate causal genes, polymorphisms, and pathways affecting quantitative traits. The many GWA studies utilizing the DGRP have revealed substantial natural genetic variation for all reported traits, little evidence for variants with large effects but enrichment for variants with low P-values, and a tendency for lower frequency variants to have larger effects than more common variants. The variants detected in the GWA analyses rarely overlap those discovered using mutagenesis, and often are the first functional annotations of computationally predicted genes. Variants implicated in GWA analyses typically have sex-specific and genetic background-specific (epistatic) effects, as well as pleiotropic effects on other quantitative traits. Studies in the DGRP reveal substantial genetic control of environmental variation. Taking account of genetic architecture can greatly improve genomic prediction in the DGRP. These features of the genetic architecture of quantitative traits are likely to apply to other species, including humans. WIREs Dev Biol 2018, 7:e289. doi: 10.1002/wdev.289 This article is categorized under: Invertebrate Organogenesis > Flies.
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Affiliation(s)
- Trudy F C Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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24
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Mackay TFC, Huang W. Charting the genotype-phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2018; 7:10.1002/wdev.289. [PMID: 28834395 PMCID: PMC5746472 DOI: 10.1002/wdev.289+10.1002/wdev.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 01/20/2024]
Abstract
Understanding the genetic architecture (causal molecular variants, their effects, and frequencies) of quantitative traits is important for precision agriculture and medicine and predicting adaptive evolution, but is challenging in most species. The Drosophila melanogaster Genetic Reference Panel (DGRP) is a collection of 205 inbred strains with whole genome sequences derived from a single wild population in Raleigh, NC, USA. The large amount of quantitative genetic variation, lack of population structure, and rapid local decay of linkage disequilibrium in the DGRP and outbred populations derived from DGRP lines present a favorable scenario for performing genome-wide association (GWA) mapping analyses to identify candidate causal genes, polymorphisms, and pathways affecting quantitative traits. The many GWA studies utilizing the DGRP have revealed substantial natural genetic variation for all reported traits, little evidence for variants with large effects but enrichment for variants with low P-values, and a tendency for lower frequency variants to have larger effects than more common variants. The variants detected in the GWA analyses rarely overlap those discovered using mutagenesis, and often are the first functional annotations of computationally predicted genes. Variants implicated in GWA analyses typically have sex-specific and genetic background-specific (epistatic) effects, as well as pleiotropic effects on other quantitative traits. Studies in the DGRP reveal substantial genetic control of environmental variation. Taking account of genetic architecture can greatly improve genomic prediction in the DGRP. These features of the genetic architecture of quantitative traits are likely to apply to other species, including humans. WIREs Dev Biol 2018, 7:e289. doi: 10.1002/wdev.289 This article is categorized under: Invertebrate Organogenesis > Flies.
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Affiliation(s)
- Trudy F C Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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25
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Mackay TFC, Huang W. Charting the genotype-phenotype map: lessons from the Drosophila melanogaster Genetic Reference Panel. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2018; 7:10.1002/wdev.289. [PMID: 28834395 PMCID: PMC5746472 DOI: 10.1002/wdev.289 10.1002/wdev.289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/11/2017] [Accepted: 07/13/2017] [Indexed: 11/30/2023]
Abstract
Understanding the genetic architecture (causal molecular variants, their effects, and frequencies) of quantitative traits is important for precision agriculture and medicine and predicting adaptive evolution, but is challenging in most species. The Drosophila melanogaster Genetic Reference Panel (DGRP) is a collection of 205 inbred strains with whole genome sequences derived from a single wild population in Raleigh, NC, USA. The large amount of quantitative genetic variation, lack of population structure, and rapid local decay of linkage disequilibrium in the DGRP and outbred populations derived from DGRP lines present a favorable scenario for performing genome-wide association (GWA) mapping analyses to identify candidate causal genes, polymorphisms, and pathways affecting quantitative traits. The many GWA studies utilizing the DGRP have revealed substantial natural genetic variation for all reported traits, little evidence for variants with large effects but enrichment for variants with low P-values, and a tendency for lower frequency variants to have larger effects than more common variants. The variants detected in the GWA analyses rarely overlap those discovered using mutagenesis, and often are the first functional annotations of computationally predicted genes. Variants implicated in GWA analyses typically have sex-specific and genetic background-specific (epistatic) effects, as well as pleiotropic effects on other quantitative traits. Studies in the DGRP reveal substantial genetic control of environmental variation. Taking account of genetic architecture can greatly improve genomic prediction in the DGRP. These features of the genetic architecture of quantitative traits are likely to apply to other species, including humans. WIREs Dev Biol 2018, 7:e289. doi: 10.1002/wdev.289 This article is categorized under: Invertebrate Organogenesis > Flies.
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Affiliation(s)
- Trudy F C Mackay
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Wen Huang
- Program in Genetics, W. M. Keck Center for Behavioral Biology and Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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26
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Ørsted M, Rohde PD, Hoffmann AA, Sørensen P, Kristensen TN. Environmental variation partitioned into separate heritable components. Evolution 2017; 72:136-152. [DOI: 10.1111/evo.13391] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Michael Ørsted
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience; Aalborg University; Fredrik Bajers Vej 7H 9220 Aalborg E Denmark
- School of Biosciences, Bio21 Molecular Science and Biotechnology Institute; The University of Melbourne; Parkville Victoria 3052 Australia
| | - Palle Duun Rohde
- Center for Quantitative Genetics and Genomics; Department of Molecular Biology and Genetics; Aarhus University; Blichers Allé 20 8830 Tjele Denmark
- i PSYCH; The Lundbeck Foundation Initiative for Integrative Psychiatric Research; 8000 Aarhus C Denmark
- i SEQ, Center for Integrative Sequencing; Aarhus University; Bartholins Allé 6 8000 Aarhus C Denmark
| | - Ary Anthony Hoffmann
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience; Aalborg University; Fredrik Bajers Vej 7H 9220 Aalborg E Denmark
- School of Biosciences, Bio21 Molecular Science and Biotechnology Institute; The University of Melbourne; Parkville Victoria 3052 Australia
| | - Peter Sørensen
- Center for Quantitative Genetics and Genomics; Department of Molecular Biology and Genetics; Aarhus University; Blichers Allé 20 8830 Tjele Denmark
| | - Torsten Nygaard Kristensen
- Section of Biology and Environmental Science, Department of Chemistry and Bioscience; Aalborg University; Fredrik Bajers Vej 7H 9220 Aalborg E Denmark
- Section of Genetics, Ecology and Evolution, Department of Bioscience; Aarhus University; 8000 Aarhus C Denmark
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27
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Teague C, Youngblood JP, Ragan K, Angilletta MJ, VandenBrooks JM. A positive genetic correlation between hypoxia tolerance and heat tolerance supports a controversial theory of heat stress. Biol Lett 2017; 13:rsbl.2017.0309. [PMID: 29118239 DOI: 10.1098/rsbl.2017.0309] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/18/2017] [Indexed: 11/12/2022] Open
Abstract
We used quantitative genetics to test a controversial theory of heat stress, in which animals overheat when the demand for oxygen exceeds the supply. This theory, referred to as oxygen- and capacity-limited thermal tolerance, predicts a positive genetic correlation between hypoxia tolerance and heat tolerance. We demonstrate the first genetic correlation of this kind in a model organism, Drosophila melanogaster Genotypes more likely to fly under hypoxic stress (12% O2) were also more likely to fly under heat stress (39°C). This finding prompts new questions about mechanisms and limits of adaptation to heat stress.
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Affiliation(s)
- Collin Teague
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | | | - Kinley Ragan
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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28
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The road less traveled: from genotype to phenotype in flies and humans. Mamm Genome 2017; 29:5-23. [DOI: 10.1007/s00335-017-9722-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/05/2017] [Indexed: 12/20/2022]
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29
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Dissecting genetic architecture of startle response in Drosophila melanogaster using multi-omics information. Sci Rep 2017; 7:12367. [PMID: 28959013 PMCID: PMC5620086 DOI: 10.1038/s41598-017-11676-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 08/24/2017] [Indexed: 01/01/2023] Open
Abstract
Startle behavior is important for survival, and abnormal startle responses are related to several neurological diseases. Drosophila melanogaster provides a powerful system to investigate the genetic underpinnings of variation in startle behavior. Since mechanically induced, startle responses and environmental conditions can be readily quantified and precisely controlled. The 156 wild-derived fully sequenced lines of the Drosophila Genetic Reference Panel (DGRP) were used to identify SNPs and transcripts associated with variation in startle behavior. The results validated highly significant effects of 33 quantitative trait SNPs (QTSs) and 81 quantitative trait transcripts (QTTs) directly associated with phenotypic variation of startle response. We also detected QTT variation controlled by 20 QTSs (tQTSs) and 73 transcripts (tQTTs). Association mapping based on genomic and transcriptomic data enabled us to construct a complex genetic network that underlies variation in startle behavior. Based on principles of evolutionary conservation, human orthologous genes could be superimposed on this network. This study provided both genetic and biological insights into the variation of startle response behavior of Drosophila melanogaster, and highlighted the importance of genetic network to understand the genetic architecture of complex traits.
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30
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Wang JB, Lu HL, St. Leger RJ. The genetic basis for variation in resistance to infection in the Drosophila melanogaster genetic reference panel. PLoS Pathog 2017; 13:e1006260. [PMID: 28257468 PMCID: PMC5352145 DOI: 10.1371/journal.ppat.1006260] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/15/2017] [Accepted: 02/24/2017] [Indexed: 01/01/2023] Open
Abstract
Individuals vary extensively in the way they respond to disease but the genetic basis of this variation is not fully understood. We found substantial individual variation in resistance and tolerance to the fungal pathogen Metarhizium anisopliae Ma549 using the Drosophila melanogaster Genetic Reference Panel (DGRP). In addition, we found that host defense to Ma549 was correlated with defense to the bacterium Pseudomonas aeruginosa Pa14, and several previously published DGRP phenotypes including oxidative stress sensitivity, starvation stress resistance, hemolymph glucose levels, and sleep indices. We identified polymorphisms associated with differences between lines in both their mean survival times and microenvironmental plasticity, suggesting that lines differ in their ability to adapt to variable pathogen exposures. The majority of polymorphisms increasing resistance to Ma549 were sex biased, located in non-coding regions, had moderately large effect and were rare, suggesting that there is a general cost to defense. Nevertheless, host defense was not negatively correlated with overall longevity and fecundity. In contrast to Ma549, minor alleles were concentrated in the most Pa14-susceptible as well as the most Pa14-resistant lines. A pathway based analysis revealed a network of Pa14 and Ma549-resistance genes that are functionally connected through processes that encompass phagocytosis and engulfment, cell mobility, intermediary metabolism, protein phosphorylation, axon guidance, response to DNA damage, and drug metabolism. Functional testing with insertional mutagenesis lines indicates that 12/13 candidate genes tested influence susceptibility to Ma549. Many candidate genes have homologs identified in studies of human disease, suggesting that genes affecting variation in susceptibility are conserved across species.
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Affiliation(s)
- Jonathan B. Wang
- Department of Entomology, University of Maryland College Park, College Park, Maryland, United States of America
| | - Hsiao-Ling Lu
- Department of Entomology, University of Maryland College Park, College Park, Maryland, United States of America
| | - Raymond J. St. Leger
- Department of Entomology, University of Maryland College Park, College Park, Maryland, United States of America
- * E-mail:
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31
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Wangler MF, Hu Y, Shulman JM. Drosophila and genome-wide association studies: a review and resource for the functional dissection of human complex traits. Dis Model Mech 2017; 10:77-88. [PMID: 28151408 PMCID: PMC5312009 DOI: 10.1242/dmm.027680] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Human genome-wide association studies (GWAS) have successfully identified thousands of susceptibility loci for common diseases with complex genetic etiologies. Although the susceptibility variants identified by GWAS usually have only modest effects on individual disease risk, they contribute to a substantial burden of trait variation in the overall population. GWAS also offer valuable clues to disease mechanisms that have long proven to be elusive. These insights could lead the way to breakthrough treatments; however, several challenges hinder progress, making innovative approaches to accelerate the follow-up of results from GWAS an urgent priority. Here, we discuss the largely untapped potential of the fruit fly, Drosophila melanogaster, for functional investigation of findings from human GWAS. We highlight selected examples where strong genomic conservation with humans along with the rapid and powerful genetic tools available for flies have already facilitated fine mapping of association signals, elucidated gene mechanisms, and revealed novel disease-relevant biology. We emphasize current research opportunities in this rapidly advancing field, and present bioinformatic analyses that systematically explore the applicability of Drosophila for interrogation of susceptibility signals implicated in more than 1000 human traits, based on all GWAS completed to date. Thus, our discussion is targeted at both human geneticists seeking innovative strategies for experimental validation of findings from GWAS, as well as the Drosophila research community, by whom ongoing investigations of the implicated genes will powerfully inform our understanding of human disease.
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Affiliation(s)
- Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua M Shulman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
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Travers LM, Garcia-Gonzalez F, Simmons LW. Genetic variation but weak genetic covariation between pre- and post-copulatory episodes of sexual selection in Drosophila melanogaster. J Evol Biol 2016; 29:1535-52. [PMID: 27159063 DOI: 10.1111/jeb.12890] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/20/2016] [Accepted: 04/29/2016] [Indexed: 12/16/2022]
Abstract
When females mate polyandrously, male reproductive success depends both on the male's ability to attain matings and on his ability to outcompete rival males in the fertilization of ova post-copulation. Increased investment in ejaculate components may trade off with investment in precopulatory traits due to resource allocation. Alternatively, pre- and post-copulatory traits could be positively related if individuals can afford to invest heavily in traits advantageous at both episodes of selection. There is empirical evidence for both positive and negative associations between pre- and post-copulatory episodes, but little is known about the genetic basis of these correlations. In this study, we measured morphological, chemical and behavioural precopulatory male traits and investigated their relationship with measures of male fitness (male mating success, remating inhibition and offensive sperm competitiveness) across 40 isofemale lines of Drosophila melanogaster. We found significant variation among isofemale lines, indicating a genetic basis for most of the traits investigated. However, we found weak evidence for genetic correlations between precopulatory traits and our indices of male fitness. Moreover, pre- and post-copulatory episodes of selection were uncorrelated, suggesting selection may act independently at the different episodes to maximize male reproductive success.
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Affiliation(s)
- L M Travers
- Centre for Evolutionary Biology, School of Animal Biology (M092), The University of Western Australia, Crawley, WA, Australia
| | - F Garcia-Gonzalez
- Centre for Evolutionary Biology, School of Animal Biology (M092), The University of Western Australia, Crawley, WA, Australia.,Doñana Biological Station, Spanish Research Council CSIC, Isla de la Cartuja, Seville, Spain
| | - L W Simmons
- Centre for Evolutionary Biology, School of Animal Biology (M092), The University of Western Australia, Crawley, WA, Australia
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