1
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Choy YMM, Walter GM, Mirth CK, Sgrò CM. Within-population plastic responses to combined thermal-nutritional stress differ from those in response to single stressors, and are genetically independent across traits in both males and females. J Evol Biol 2024; 37:717-731. [PMID: 38757509 DOI: 10.1093/jeb/voae061] [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: 03/15/2023] [Revised: 03/25/2024] [Accepted: 05/16/2024] [Indexed: 05/18/2024]
Abstract
Phenotypic plasticity helps animals to buffer the effects of increasing thermal and nutritional stress created by climate change. Plastic responses to single and combined stressors can vary among genetically diverged populations. However, less is known about how plasticity in response to combined stress varies among individuals within a population or whether such variation changes across life-history traits. This is important because individual variation within populations shapes population-level responses to environmental change. Here, we used isogenic lines of Drosophila melanogaster to assess the plasticity of egg-to-adult viability and sex-specific body size for combinations of 2 temperatures (25 °C or 28 °C) and 3 diets (standard diet, low caloric diet, or low protein:carbohydrate ratio diet). Our results reveal substantial within-population genetic variation in plasticity for egg-to-adult viability and wing size in response to combined thermal-nutritional stress. This genetic variation in plasticity was a result of cross-environment genetic correlations that were often < 1 for both traits, as well as changes in the expression of genetic variation across environments for egg-to-adult viability. Cross-sex genetic correlations for body size were weaker when the sexes were reared in different conditions, suggesting that the genetic basis of traits may change with the environment. Furthermore, our results suggest that plasticity in egg-to-adult viability is genetically independent from plasticity in body size. Importantly, plasticity in response to diet and temperature individually differed from plastic shifts in response to diet and temperature in combination. By quantifying plasticity and the expression of genetic variance in response to combined stress across traits, our study reveals the complexity of animal responses to environmental change, and the need for a more nuanced understanding of the potential for populations to adapt to ongoing climate change.
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Affiliation(s)
- Yeuk Man Movis Choy
- School of Biological Sciences, Monash University, Wellington Rd, Clayton, Melbourne, Victoria, Australia
| | - Greg M Walter
- School of Biological Sciences, Monash University, Wellington Rd, Clayton, Melbourne, Victoria, Australia
| | - Christen K Mirth
- School of Biological Sciences, Monash University, Wellington Rd, Clayton, Melbourne, Victoria, Australia
| | - Carla M Sgrò
- School of Biological Sciences, Monash University, Wellington Rd, Clayton, Melbourne, Victoria, Australia
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2
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Pennell TM, Sharma MD, Sutter A, Wilson DT, House CM, Hosken DJ. The condition-dependence of male genital size and shape. Ecol Evol 2024; 14:e11180. [PMID: 38495435 PMCID: PMC10944674 DOI: 10.1002/ece3.11180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 02/12/2024] [Accepted: 03/05/2024] [Indexed: 03/19/2024] Open
Abstract
The male genitals of internal fertilisers evolve rapidly and divergently, and sexual selection is generally responsible for this. Many sexually selected traits are condition-dependent-with their expression dependent upon the resources available to be allocated to them-as revealed by genetic or environmental manipulations of condition. However, it is not clear whether male genitals are also condition-dependent. Here we manipulate condition in two ways (via inbreeding and diet) to test the condition-dependence of the genital arch of Drosophila simulans. We found that genital size but not genital shape suffered from inbreeding depression, whereas genital size and shape were affected by dietary manipulation of condition. The differential effects of these treatments likely reflect underlying genetic architecture that has been shaped by past selection: inbreeding depression is only expected when traits have a history of directional selection, while diet impacts traits regardless of historical selection. Nonetheless, our results suggest genitals can be condition-dependent like other sexually selected traits.
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Affiliation(s)
- Tanya M. Pennell
- Centre for Ecology & Conservation, Faculty of Environment, Science and Economy (ESE)University of ExeterExeterUK
| | - Manmohan D. Sharma
- Centre for Ecology & Conservation, Faculty of Environment, Science and Economy (ESE)University of ExeterExeterUK
| | - Andreas Sutter
- Centre for Ecology & Conservation, Faculty of Environment, Science and Economy (ESE)University of ExeterExeterUK
| | - Drew T. Wilson
- Centre for Ecology & Conservation, Faculty of Environment, Science and Economy (ESE)University of ExeterExeterUK
| | - Clarissa M. House
- School of ScienceWestern Sydney UniversityRichmondNew South WalesAustralia
| | - David J. Hosken
- Centre for Ecology & Conservation, Faculty of Environment, Science and Economy (ESE)University of ExeterExeterUK
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3
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Desbiez-Piat A, Ressayre A, Marchadier E, Noly A, Remoué C, Vitte C, Belcram H, Bourgais A, Galic N, Le Guilloux M, Tenaillon MI, Dillmann C. Pervasive G × E interactions shape adaptive trajectories and the exploration of the phenotypic space in artificial selection experiments. Genetics 2023; 225:iyad186. [PMID: 37824828 DOI: 10.1093/genetics/iyad186] [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: 07/27/2023] [Revised: 07/27/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023] Open
Abstract
Quantitative genetics models have shown that long-term selection responses depend on initial variance and mutational influx. Understanding limits of selection requires quantifying the role of mutational variance. However, correlative responses to selection on nonfocal traits can perturb the selection response on the focal trait; and generations are often confounded with selection environments so that genotype by environment (G×E) interactions are ignored. The Saclay divergent selection experiments (DSEs) on maize flowering time were used to track the fate of individual mutations combining genotyping data and phenotyping data from yearly measurements (DSEYM) and common garden experiments (DSECG) with four objectives: (1) to quantify the relative contribution of standing and mutational variance to the selection response, (2) to estimate genotypic mutation effects, (3) to study the impact of G×E interactions in the selection response, and (4) to analyze how trait correlations modulate the exploration of the phenotypic space. We validated experimentally the expected enrichment of fixed beneficial mutations with an average effect of +0.278 and +0.299 days to flowering, depending on the genetic background. Fixation of unfavorable mutations reached up to 25% of incoming mutations, a genetic load possibly due to antagonistic pleiotropy, whereby mutations fixed in the selection environment (DSEYM) turned to be unfavorable in the evaluation environment (DSECG). Global patterns of trait correlations were conserved across genetic backgrounds but exhibited temporal patterns. Traits weakly or uncorrelated with flowering time triggered stochastic exploration of the phenotypic space, owing to microenvironment-specific fixation of standing variants and pleiotropic mutational input.
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Affiliation(s)
- Arnaud Desbiez-Piat
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
- Université Montpellier, INRAE, Institut Agro Montpellier, LEPSE, Montpellier 34000, France
| | - Adrienne Ressayre
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Elodie Marchadier
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Alicia Noly
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institut of Plants Sciences Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Carine Remoué
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Clémentine Vitte
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Harry Belcram
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Aurélie Bourgais
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Nathalie Galic
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Martine Le Guilloux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Maud I Tenaillon
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
| | - Christine Dillmann
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette 91190, France
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4
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Arnqvist G, Sayadi A. A possible genomic footprint of polygenic adaptation on population divergence in seed beetles? Ecol Evol 2022; 12:e9440. [PMID: 36311399 PMCID: PMC9608792 DOI: 10.1002/ece3.9440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 09/14/2022] [Accepted: 09/29/2022] [Indexed: 11/25/2022] Open
Abstract
Efforts to unravel the genomic basis of incipient speciation are hampered by a mismatch between our toolkit and our understanding of the ecology and genetics of adaptation. While the former is focused on detecting selective sweeps involving few independently acting or linked speciation genes, the latter states that divergence typically occurs in polygenic traits under stabilizing selection. Here, we ask whether a role of stabilizing selection on polygenic traits in population divergence may be unveiled by using a phenotypically informed integrative approach, based on genome‐wide variation segregating in divergent populations. We compare three divergent populations of seed beetles (Callosobruchus maculatus) where previous work has demonstrated a prominent role for stabilizing selection on, and population divergence in, key life history traits that reflect rate‐dependent metabolic processes. We derive and assess predictions regarding the expected pattern of covariation between genetic variation segregating within populations and genetic differentiation between populations. Population differentiation was considerable (mean FST = 0.23–0.26) and was primarily built by genes showing high selective constraints and an imbalance in inferred selection in different populations (positive Tajima's DNS in one and negative in one), and this set of genes was enriched with genes with a metabolic function. Repeatability of relative population differentiation was low at the level of individual genes but higher at the level of broad functional classes, again spotlighting metabolic genes. Absolute differentiation (dXY) showed a very different general pattern at this scale of divergence, more consistent with an important role for genetic drift. Although our exploration is consistent with stabilizing selection on polygenic metabolic phenotypes as an important engine of genome‐wide relative population divergence and incipient speciation in our study system, we note that it is exceedingly difficult to firmly exclude other scenarios.
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Affiliation(s)
- Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, EBCUppsala UniversityUppsalaSweden
| | - Ahmed Sayadi
- Animal Ecology, Department of Ecology and Genetics, EBCUppsala UniversityUppsalaSweden,Rheumatology, Department of Medical SciencesUppsala UniversityUppsalaSweden
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5
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Kokate PP, Smith M, Hall L, Zhang K, Werner T. Inter- and intraspecific variation in mycotoxin tolerance: A study of four Drosophila species. Ecol Evol 2022; 12:e9126. [PMID: 35898423 PMCID: PMC9309036 DOI: 10.1002/ece3.9126] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/11/2022] [Accepted: 06/23/2022] [Indexed: 12/03/2022] Open
Abstract
Many mycophagous Drosophila species have adapted to tolerate high concentrations of mycotoxins, an ability not reported in any other eukaryotes. Although an association between mycophagy and mycotoxin tolerance has been established in many Drosophila species, the genetic mechanisms of the tolerance are unknown. This study presents the inter‐ and intraspecific variation in the mycotoxin tolerance trait. We studied the mycotoxin tolerance in four Drosophila species from four separate clades within the immigrans‐tripunctata radiation from two distinct locations. The effect of mycotoxin treatment on 20 isofemale lines per species was studied using seven gross phenotypes: survival to pupation, survival to eclosion, development time to pupation and eclosion, thorax length, fecundity, and longevity. We observed interspecific variation among four species, with D. falleni being the most tolerant, followed by D. recens, D. neotestacea, and D. tripunctata, in that order. The results also revealed geographical variation and intraspecific genetic variation in mycotoxin tolerance. This report provides the foundation for further delineating the genetic mechanisms of the mycotoxin tolerance trait.
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Affiliation(s)
- Prajakta P Kokate
- Department of Biological Sciences Michigan Technological University Houghton Michigan USA
| | - Morgan Smith
- Department of Biological Sciences Michigan Technological University Houghton Michigan USA
| | - Lucinda Hall
- Department of Biological Sciences Michigan Technological University Houghton Michigan USA
| | - Kui Zhang
- Department of Mathematical Sciences Michigan Technological University Houghton Michigan USA
| | - Thomas Werner
- Department of Biological Sciences Michigan Technological University Houghton Michigan USA
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6
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Christodoulaki E, Nolte V, Lai WY, Schlötterer C. Natural variation in Drosophila shows weak pleiotropic effects. Genome Biol 2022; 23:116. [PMID: 35578368 PMCID: PMC9109288 DOI: 10.1186/s13059-022-02680-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 04/26/2022] [Indexed: 11/12/2022] Open
Abstract
Background Pleiotropy describes the phenomenon in which a gene affects multiple phenotypes. The extent of pleiotropy is still disputed, mainly because of issues of inadequate power of analyses. A further challenge is that empirical tests of pleiotropy are restricted to a small subset of all possible phenotypes. To overcome these limitations, we propose a new measurement of pleiotropy that integrates across many phenotypes and multiple generations to improve power. Results We infer pleiotropy from the fitness cost imposed by frequency changes of pleiotropic loci. Mixing Drosophila simulans populations, which adapted independently to the same new environment using different sets of genes, we show that the adaptive frequency changes have been accompanied by measurable fitness costs. Conclusions Unlike previous studies characterizing the molecular basis of pleiotropy, we show that many loci, each of weak effect, contribute to genome-wide pleiotropy. We propose that the costs of pleiotropy are reduced by the modular architecture of gene expression, which facilitates adaptive gene expression changes with low impact on other functions. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02680-4.
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Affiliation(s)
- Eirini Christodoulaki
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210, Vienna, Austria
| | - Wei-Yun Lai
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
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7
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Yushkova E. Radiobiological features in offspring of natural populations of Drosophila melanogaster after Chernobyl accident. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2022; 63:84-97. [PMID: 35275441 DOI: 10.1002/em.22476] [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: 01/21/2022] [Revised: 02/24/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
In their natural habitats, populations of organisms are faced with different levels of chronic low-intensity radiation, causing a wide range of radiobiological effects (from radiosensitivity to radioadaptive response and hormesis). In this study, specimens of Drosophila melanogaster were selected from territories of the Chernobyl nuclear power plant with different levels of radioactive contamination. The isogenic stocks derived from these specimens represent the genetic systems of current populations and make it possible to study radioresistance and its mechanisms in future generations under controlled laboratory conditions. Previous studies have shown that transgenerational radiation effects at the level of lethal mutations and survival rate are unstable and depend not only on the level of chronic low-intensity irradiation, but also on other factors. A single acute irradiation exposure of offspring whose parents inhabited a site with a higher level of chronic irradiation made it possible to reveal pronounced radioresistant features in the offspring. And the offspring whose parents were exposed to radiation levels close to the natural radiation background, on the contrary, acquired radiosensitive features. Their response to acute exposure includes a high-frequency of lethal mutations and a short lifespan. The differential response to different levels of chronic parental exposure is caused by differences in the activities of certain transposons that destabilize the genome. Our data contribute to the understanding of genetic and epigenetic mechanisms (via transposon activity) of the effect of parental radiation exposure on the health and adaptive potential of populations affected by the technogenically increased radiation background.
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Affiliation(s)
- Elena Yushkova
- Institute of Biology of Komi Scientific Centre of the Ural Branch of the Russian Academy of Science, Syktyvkar, Russia
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8
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Desbiez-Piat A, Le Rouzic A, Tenaillon MI, Dillmann C. Interplay between extreme drift and selection intensities favors the fixation of beneficial mutations in selfing maize populations. Genetics 2021; 219:6339583. [PMID: 34849881 DOI: 10.1093/genetics/iyab123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/21/2021] [Indexed: 11/13/2022] Open
Abstract
Population and quantitative genetic models provide useful approximations to predict long-term selection responses sustaining phenotypic shifts, and underlying multilocus adaptive dynamics. Valid across a broad range of parameters, their use for understanding the adaptive dynamics of small selfing populations undergoing strong selection intensity (thereafter High Drift-High selection regime, HDHS) remains to be explored. Saclay Divergent Selection Experiments (DSEs) on maize flowering time provide an interesting example of populations evolving under HDHS, with significant selection responses over 20 generations in two directions. We combined experimental data from Saclay DSEs, forward individual-based simulations, and theoretical predictions to dissect the evolutionary mechanisms at play in the observed selection responses. We asked two main questions: How do mutations arise, spread, and reach fixation in populations evolving under HDHS? How does the interplay between drift and selection influence observed phenotypic shifts? We showed that the long-lasting response to selection in small populations is due to the rapid fixation of mutations occurring during the generations of selection. Among fixed mutations, we also found a clear signal of enrichment for beneficial mutations revealing a limited cost of selection. Both environmental stochasticity and variation in selection coefficients likely contributed to exacerbate mutational effects, thereby facilitating selection grasp and fixation of small-effect mutations. Together our results highlight that despite a small number of polymorphic loci expected under HDHS, adaptive variation is continuously fueled by a vast mutational target. We discuss our results in the context of breeding and long-term survival of small selfing populations.
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Affiliation(s)
- Arnaud Desbiez-Piat
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Arnaud Le Rouzic
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91120 Gif-sur-Yvette, France
| | - Maud I Tenaillon
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Christine Dillmann
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190 Gif-sur-Yvette, France
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9
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Kulikov AM, Sorokina SY, Melnikov AI, Gornostaev NG, Seleznev DG, Lazebny OE. The effects of the sex chromosomes on the inheritance of species-specific traits of the copulatory organ shape in Drosophila virilis and Drosophila lummei. PLoS One 2020; 15:e0244339. [PMID: 33373382 PMCID: PMC7771703 DOI: 10.1371/journal.pone.0244339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022] Open
Abstract
The shape of the male genitalia in many taxa is the most rapidly evolving morphological structure, often driving reproductive isolation, and is therefore widely used in systematics as a key character to distinguish between sibling species. However, only a few studies have used the genital arch of the male copulatory organ as a model to study the genetic basis of species-specific differences in the Drosophila copulatory system. Moreover, almost nothing is known about the effects of the sex chromosomes on the shape of the male mating organ. In our study, we used a set of crosses between D. virilis and D. lummei and applied the methods of quantitative genetics to assess the variability of the shape of the male copulatory organ and the effects of the sex chromosomes and autosomes on its variance. Our results showed that the male genital shape depends on the species composition of the sex chromosomes and autosomes. Epistatic interactions of the sex chromosomes with autosomes and the species origin of the Y-chromosome in a male in interspecific crosses also influenced the expression of species-specific traits in the shape of the male copulatory system. Overall, the effects of sex chromosomes were comparable to the effects of autosomes despite the great differences in gene numbers between them. It may be reasonably considered that sexual selection for specific genes associated with the shape of the male mating organ prevents the demasculinization of the X chromosome.
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Affiliation(s)
- Alex M. Kulikov
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Svetlana Yu. Sorokina
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Anton I. Melnikov
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Nick G. Gornostaev
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
| | - Dmitriy G. Seleznev
- Department of Ecology of Aquatic Invertebrates, Papanin Institute for Biology of Inland Waters of the Russian Academy of Sciences, Borok village, Yaroslavl Region, Russia
| | - Oleg E. Lazebny
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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Zhang H, Liang Q, Wang N, Wang Q, Leng L, Mao J, Wang Y, Wang S, Zhang J, Liang H, Zhou X, Li Y, Cao Z, Luan P, Wang Z, Yuan H, Wang Z, Zhou X, Lamont SJ, Da Y, Li R, Tian S, Du Z, Li H. Microevolutionary Dynamics of Chicken Genomes under Divergent Selection for Adiposity. iScience 2020; 23:101193. [PMID: 32554187 PMCID: PMC7303556 DOI: 10.1016/j.isci.2020.101193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/19/2020] [Accepted: 05/19/2020] [Indexed: 01/01/2023] Open
Abstract
Decades of artificial selection have significantly improved performance and efficiency of animal production systems. However, little is known about the microevolution of genomes due to intensive breeding. Using whole-genome sequencing, we document dynamic changes of chicken genomes under divergent selection on adiposity over 19 generations. Directional selection reduced within-line but increased between-line genomic differences. We observed that artificial selection tended to result in recruitment of preexisting variations of genes related to adipose tissue growth. In addition, novel mutations contributed to divergence of phenotypes under selection but contributed significantly less than preexisting genomic variants. Integration of 15 generations genome sequencing, genome-wide association study, and multi-omics data further identified that genes involved in signaling pathways important to adipogenesis, such as autophagy and lysosome (URI1, MBL2), neural system (CHAT), and endocrine (PCSK1) pathways, were under strong selection. Our study provides insights into the microevolutionary dynamics of domestic animal genomes under artificial selection.
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Affiliation(s)
- Hui Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing 10089, P. R. China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Qigui Wang
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China
| | - Li Leng
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Jie Mao
- Novogene Bioinformatics Institute, Beijing 10089, P. R. China
| | - Yuxiang Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Shouzhi Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Jiyang Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Hao Liang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Xun Zhou
- Novogene Bioinformatics Institute, Beijing 10089, P. R. China
| | - Yumao Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Zhiping Cao
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Peng Luan
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Zhipeng Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Hui Yuan
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
| | - Zhiquan Wang
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2C8, Canada
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames 50011, USA
| | - Yang Da
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing 10089, P. R. China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing 10089, P. R. China.
| | - Zhiqiang Du
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China.
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China.
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Flatt T. Life-History Evolution and the Genetics of Fitness Components in Drosophila melanogaster. Genetics 2020; 214:3-48. [PMID: 31907300 PMCID: PMC6944413 DOI: 10.1534/genetics.119.300160] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/03/2019] [Indexed: 12/28/2022] Open
Abstract
Life-history traits or "fitness components"-such as age and size at maturity, fecundity and fertility, age-specific rates of survival, and life span-are the major phenotypic determinants of Darwinian fitness. Analyzing the evolution and genetics of these phenotypic targets of selection is central to our understanding of adaptation. Due to its simple and rapid life cycle, cosmopolitan distribution, ease of maintenance in the laboratory, well-understood evolutionary genetics, and its versatile genetic toolbox, the "vinegar fly" Drosophila melanogaster is one of the most powerful, experimentally tractable model systems for studying "life-history evolution." Here, I review what has been learned about the evolution and genetics of life-history variation in D. melanogaster by drawing on numerous sources spanning population and quantitative genetics, genomics, experimental evolution, evolutionary ecology, and physiology. This body of work has contributed greatly to our knowledge of several fundamental problems in evolutionary biology, including the amount and maintenance of genetic variation, the evolution of body size, clines and climate adaptation, the evolution of senescence, phenotypic plasticity, the nature of life-history trade-offs, and so forth. While major progress has been made, important facets of these and other questions remain open, and the D. melanogaster system will undoubtedly continue to deliver key insights into central issues of life-history evolution and the genetics of adaptation.
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Affiliation(s)
- Thomas Flatt
- Department of Biology, University of Fribourg, CH-1700, Switzerland
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12
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Unpredictable Effects of the Genetic Background of Transgenic Lines in Physiological Quantitative Traits. G3-GENES GENOMES GENETICS 2019; 9:3877-3890. [PMID: 31540975 PMCID: PMC6829147 DOI: 10.1534/g3.119.400715] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Physiology, fitness and disease phenotypes are complex traits exhibiting continuous variation in natural populations. To understand complex trait gene functions transgenic lines of undefined genetic background are often combined to assess quantitative phenotypes ignoring the impact of genetic polymorphisms. Here, we used inbred wild-type strains of the Drosophila Genetics Reference Panel to assess the phenotypic variation of six physiological and fitness traits, namely, female fecundity, survival and intestinal mitosis upon oral infection, defecation rate and fecal pH upon oral infection, and terminal tracheal cell branching in hypoxia. We found continuous variation in the approximately 150 strains tested for each trait, with extreme values differing by more than four standard deviations for all traits. In addition, we assessed the effects of commonly used Drosophila UAS-RNAi transgenic strains and their backcrossed isogenized counterparts, in the same traits plus baseline intestinal mitosis and tracheal branching in normoxia, in heterozygous conditions, when only half of the genetic background was different among strains. We tested 20 non-isogenic strains (10 KK and 10 GD) from the Vienna Drosophila Resource Center and their isogenized counterparts without Gal4 induction. Survival upon infection and female fecundity exhibited differences in 50% and 40% of the tested isogenic vs. non-isogenic pairs, respectively, whereas all other traits were affected in only 10–25% of the cases. When 11 isogenic and their corresponding non-isogenic UAS-RNAi lines were expressed ubiquitously with Gal4, 4 isogenic vs. non-isogenic pairs exhibited differences in survival to infection. Furthermore, when a single UAS-RNAi line was crossed with the same Gal4 transgene inserted in different genetic backgrounds, the quantitative variations observed were unpredictable on the basis of pure line performance. Thus, irrespective of the trait of interest, the genetic background of commonly used transgenic strains needs to be considered carefully during experimentation.
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13
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Neyhart JL, Lorenz AJ, Smith KP. Multi-trait Improvement by Predicting Genetic Correlations in Breeding Crosses. G3 (BETHESDA, MD.) 2019; 9:3153-3165. [PMID: 31358561 PMCID: PMC6778794 DOI: 10.1534/g3.119.400406] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/25/2019] [Indexed: 12/22/2022]
Abstract
The many quantitative traits of interest to plant breeders are often genetically correlated, which can complicate progress from selection. Improving multiple traits may be enhanced by identifying parent combinations - an important breeding step - that will deliver more favorable genetic correlations (rG ). Modeling the segregation of genomewide markers with estimated effects may be one method of predicting rG in a cross, but this approach remains untested. Our objectives were to: (i) use simulations to assess the accuracy of genomewide predictions of rG and the long-term response to selection when selecting crosses on the basis of such predictions; and (ii) empirically measure the ability to predict genetic correlations using data from a barley (Hordeum vulgare L.) breeding program. Using simulations, we found that the accuracy to predict rG was generally moderate and influenced by trait heritability, population size, and genetic correlation architecture (i.e., pleiotropy or linkage disequilibrium). Among 26 barley breeding populations, the empirical prediction accuracy of rG was low (-0.012) to moderate (0.42), depending on trait complexity. Within a simulated plant breeding program employing indirect selection, choosing crosses based on predicted rG increased multi-trait genetic gain by 11-27% compared to selection on the predicted cross mean. Importantly, when the starting genetic correlation was negative, such cross selection mitigated or prevented an unfavorable response in the trait under indirect selection. Prioritizing crosses based on predicted genetic correlation can be a feasible and effective method of improving unfavorably correlated traits in breeding programs.
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Affiliation(s)
- Jeffrey L Neyhart
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | - Aaron J Lorenz
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108
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14
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Genome-Wide Association Analysis of Anoxia Tolerance in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2019; 9:2989-2999. [PMID: 31311780 PMCID: PMC6723132 DOI: 10.1534/g3.119.400421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
As the genetic bases to variation in anoxia tolerance are poorly understood, we used the Drosophila Genetics Reference Panel (DGRP) to conduct a genome-wide association study (GWAS) of anoxia tolerance in adult and larval Drosophila melanogaster Survival ranged from 0-100% in adults exposed to 6 h of anoxia and from 20-98% for larvae exposed to 1 h of anoxia. Anoxia tolerance had a broad-sense heritability of 0.552 in adults and 0.433 in larvae. Larval and adult phenotypes were weakly correlated but the anoxia tolerance of adult males and females were strongly correlated. The GWA identified 180 SNPs in adults and 32 SNPs in larvae associated with anoxia tolerance. Gene ontology enrichment analysis indicated that many of the 119 polymorphic genes associated with adult anoxia-tolerance were associated with ionic transport or immune function. In contrast, the 22 polymorphic genes associated with larval anoxia-tolerance were mostly associated with regulation of transcription and DNA replication. RNAi of mapped genes generally supported the hypothesis that disruption of these genes reduces anoxia tolerance. For two ion transport genes, we tested predicted directional and sex-specific effects of SNP alleles on adult anoxia tolerance and found strong support in one case but not the other. Correlating our phenotype to prior DGRP studies suggests that genes affecting anoxia tolerance also influence stress-resistance, immune function and ionic balance. Overall, our results provide evidence for multiple new potential genetic influences on anoxia tolerance and provide additional support for important roles of ion balance and immune processes in determining variation in anoxia tolerance.
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15
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Rech GE, Bogaerts-Márquez M, Barrón MG, Merenciano M, Villanueva-Cañas JL, Horváth V, Fiston-Lavier AS, Luyten I, Venkataram S, Quesneville H, Petrov DA, González J. Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. PLoS Genet 2019; 15:e1007900. [PMID: 30753202 PMCID: PMC6372155 DOI: 10.1371/journal.pgen.1007900] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/16/2018] [Indexed: 11/30/2022] Open
Abstract
Most of the current knowledge on the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions annotated in the reference genome of Drosophila melanogaster, in 91 samples from 60 worldwide natural populations. We identified a set of 300 polymorphic TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. Besides, we identified a set of 21 fixed TEs also likely to be adaptive. Indeed, we, and others, found evidence of selection for 84 of these reference TE insertions. The analysis of the genes located nearby these 84 candidate adaptive insertions suggested that the functional response to selection is related with the GO categories of response to stimulus, behavior, and development. We further showed that a subset of the candidate adaptive TEs affects expression of nearby genes, and five of them have already been linked to an ecologically relevant phenotypic effect. Our results provide a more complete understanding of the genetic variation and the fitness-related traits relevant for adaptive evolution. Similar studies should help uncover the importance of TE-induced adaptive mutations in other species as well.
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Affiliation(s)
- Gabriel E. Rech
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - María Bogaerts-Márquez
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Maite G. Barrón
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Miriam Merenciano
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Vivien Horváth
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Anna-Sophie Fiston-Lavier
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | | | - Sandeep Venkataram
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | | | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, CA, United States of America
| | - Josefa González
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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16
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Kodama M, Naish KA, Devlin RH. Influence of a growth hormone transgene on the genetic architecture of growth-related traits: A comparative analysis between transgenic and wild-type coho salmon. Evol Appl 2018; 11:1886-1900. [PMID: 30459836 PMCID: PMC6231474 DOI: 10.1111/eva.12692] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 07/26/2018] [Accepted: 07/28/2018] [Indexed: 12/20/2022] Open
Abstract
Genetic engineering has been increasingly applied to many commercially important plant and animal species, generating phenotypic changes that are not observed in natural populations and creating genetic interactions that have not experienced natural selection. The degree to and way in which such human-induced genetic variation interacts with the rest of the genome is currently largely unknown. Integrating such information into ecological and risk assessment frameworks is crucial to understand the potential effects of genetically modified organisms in natural environments. Here, we performed QTL mapping to investigate the genetic architecture of growth-related traits in nontransgenic (NT) and growth hormone transgenic (T) coho salmon with large changes in growth and related physiology, with the aim of identifying how an inserted transgene might influence the opportunity for selection. These fish shared the same parental genetic background, thus allowing us to determine whether the same or different loci influence these traits within the two groups. The use of over 1,700 loci, derived from restriction site-associated DNA sequencing, revealed that different genomic regions were linked with growth over time between the two groups. Additionally, the effect sizes of detected QTL appear to have been influenced by the transgene. Direct comparison of QTL between the T and NT fish during two size-matched periods identified little overlap in their location. Taken together, the results showed that the transgene altered the genetic basis of growth-related traits in this species. The study has important implications for effective conservation and management of wild populations experiencing introduction of transgenes. Evolutionary changes and their ecological consequences may occur at different rates and in different directions in NT versus T individuals in response to selection. Thus, assessments of phenotypic change, and hence ecological risk, should be determined periodically to evaluate whether initial estimates made with founder strains remain valid.
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Affiliation(s)
- Miyako Kodama
- Fisheries and Oceans CanadaWest VancouverBritish ColumbiaCanada
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattle, Washington
- Present address:
Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
- Present address:
Genome Research and Molecular BiomedicineDepartment of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Kerry A. Naish
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattle, Washington
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17
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Peltier E, Sharma V, Martí Raga M, Roncoroni M, Bernard M, Jiranek V, Gibon Y, Marullo P. Dissection of the molecular bases of genotype x environment interactions: a study of phenotypic plasticity of Saccharomyces cerevisiae in grape juices. BMC Genomics 2018; 19:772. [PMID: 30409183 PMCID: PMC6225642 DOI: 10.1186/s12864-018-5145-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/05/2018] [Indexed: 11/17/2022] Open
Abstract
Background The ability of a genotype to produce different phenotypes according to its surrounding environment is known as phenotypic plasticity. Within different individuals of the same species, phenotypic plasticity can vary greatly. This contrasting response is caused by gene-by-environment interactions (GxE). Understanding GxE interactions is particularly important in agronomy, since selected breeds and varieties may have divergent phenotypes according to their growing environment. Industrial microbes such as Saccharomyces cerevisiae are also faced with a large range of fermentation conditions that affect their technological properties. Finding the molecular determinism of such variations is a critical task for better understanding the genetic bases of phenotypic plasticity and can also be helpful in order to improve breeding methods. Results In this study we implemented a QTL mapping program using two independent cross (~ 100 progeny) in order to investigate the molecular basis of yeast phenotypic response in a wine fermentation context. Thanks to whole genome sequencing approaches, both crosses were genotyped, providing saturated genetic maps of thousands of markers. Linkage analyses allowed the detection of 78 QTLs including 21 with significant interaction with the environmental conditions. Molecular dissection of a major QTL demonstrated that the sulfite pump Ssu1p has a pleiotropic effect and impacts the phenotypic plasticity of several traits. Conclusions The detection of QTLs and their interactions with environment emphasizes the complexity of yeast industrial traits. The validation of the interaction of SSU1 allelic variants with the nature of the fermented juice increases knowledge about the impact of the sulfite pump during fermentation. All together these results pave the way for exploiting and deciphering the genetic determinism of phenotypic plasticity. Electronic supplementary material The online version of this article (10.1186/s12864-018-5145-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emilien Peltier
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France. .,Biolaffort, Bordeaux, France.
| | - Vikas Sharma
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France
| | - Maria Martí Raga
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France.,Departament de Bioquímica i Biotecnologia, Facultat d'Enologia de Tarragona, Tarragona, Spain
| | - Miguel Roncoroni
- Wine Science Programme, University of Auckland, Private Bag, Auckland, 92019, New Zealand
| | - Margaux Bernard
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France.,Biolaffort, Bordeaux, France
| | - Vladimir Jiranek
- Department of Wine and Food Science, University of Adelaide, Urrbrae, South Australia, 5064, Australia
| | - Yves Gibon
- INRA, University of Bordeaux, UMR 1332 Fruit Biology and Pathology, F-33883, Villenave d'Ornon, France
| | - Philippe Marullo
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France.,Biolaffort, Bordeaux, France
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18
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Chen J, Zhou S, Wang Y, Shi M, Chen X, Huang J. Biocontrol characteristics of the fruit fly pupal parasitoid Trichopria drosophilae (Hymenoptera: Diapriidae) emerging from different hosts. Sci Rep 2018; 8:13323. [PMID: 30190608 PMCID: PMC6127308 DOI: 10.1038/s41598-018-31718-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/20/2018] [Indexed: 12/17/2022] Open
Abstract
Trichopria drosophilae (Hymenoptera: Diapriidae) is an important pupal endoparasitoid of Drosophila melanogaster Meigen (Diptera: Drosophilidae) and some other fruit fly species, such as D. suzukii, a very important invasive and economic pest. Studies of T. drosophilae suggest that this could be a good biological control agent for fruit fly pests. In this research, we compared the parasitic characteristics of T. drosophilae reared in D. melanogaster (TDm) with those reared in D. hydei (TDh). TDh had a larger size than TDm. The number of maximum mature eggs of a female TDh was 133.6 ± 6.9, compared with the significantly lower value of 104.8 ± 11.4 for TDm. Mated TDh female wasp continuously produced female offspring up to 6 days after mating, compared with only 3 days for TDm. In addition, the offspring female ratio of TDh, i.e., 82.32%, was significantly higher than that of TDm, i.e., 61.37%. Under starvation treatment, TDh survived longer than TDm. TDh also survived longer than TDm at high temperatures, such as 37 °C, although they both survived well at low temperatures, such as 18 °C and 4 °C. Old-age TDh females maintained a high parasitism rate and offspring female ratio, while they were declined in old-age TDm. Overall, TDh had an advantage in terms of body size, fecundity, stress resistance ability and the parasitism rate compared with TDm. Therefore, T. drosophilae from D. hydei could improve biocontrol efficacy with enormous economic benefits in the field, especially in the control of many frugivorous Drosophilidae species worldwide.
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Affiliation(s)
- Jiani Chen
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, 310058, Hangzhou, China.,Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, 866 Yuhangtang Road, 310058, Hangzhou, China
| | - Sicong Zhou
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, 310058, Hangzhou, China.,Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, 866 Yuhangtang Road, 310058, Hangzhou, China
| | - Ying Wang
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, 310058, Hangzhou, China.,Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, 866 Yuhangtang Road, 310058, Hangzhou, China
| | - Min Shi
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, 310058, Hangzhou, China.,Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, 866 Yuhangtang Road, 310058, Hangzhou, China
| | - Xuexin Chen
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, 310058, Hangzhou, China. .,Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, 866 Yuhangtang Road, 310058, Hangzhou, China. .,State Key Lab of Rice Biology, Zhejiang University, 866 Yuhangtang Road, 310058, Hangzhou, China.
| | - Jianhua Huang
- Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, 310058, Hangzhou, China. .,Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, 866 Yuhangtang Road, 310058, Hangzhou, China.
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Knoll AT, Jiang K, Levitt P. Quantitative trait locus mapping and analysis of heritable variation in affiliative social behavior and co-occurring traits. GENES, BRAIN, AND BEHAVIOR 2018; 17:e12431. [PMID: 29052939 PMCID: PMC5910301 DOI: 10.1111/gbb.12431] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/04/2017] [Accepted: 10/14/2017] [Indexed: 02/06/2023]
Abstract
Humans exhibit broad heterogeneity in affiliative social behavior. Twin and family studies show that individual differences in core dimensions of social behavior are heritable, yet there are knowledge gaps in understanding the underlying genetic and neurobiological mechanisms. Animal genetic reference panels (GRPs) provide a tractable strategy for examining the behavioral and genetic architecture of complex traits. Here, using males from 50 mouse strains from the BXD GRP, 4 domains of affiliative social behavior-social approach, social recognition, direct social interaction (DSI) (partner sniffing) and vocal communication-were examined in 2 widely used behavioral tasks-the 3-chamber and DSI tasks. There was continuous and broad variation in social and nonsocial traits, with moderate to high heritability of social approach sniff preference (0.31), ultrasonic vocalization (USV) count (0.39), partner sniffing (0.51), locomotor activity (0.54-0.66) and anxiety-like behavior (0.36). Principal component analysis shows that variation in social and nonsocial traits are attributable to 5 independent factors. Genome-wide mapping identified significant quantitative trait loci for USV count on chromosome (Chr) 18 and locomotor activity on Chr X, with suggestive loci and candidate quantitative trait genes identified for all traits with one notable exception-partner sniffing in the DSI task. The results show heritable variation in sociability, which is independent of variation in activity and anxiety-like traits. In addition, a highly heritable and ethological domain of affiliative sociability-partner sniffing-appears highly polygenic. These findings establish a basis for identifying functional natural variants, leading to a new understanding typical and atypical sociability.
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Affiliation(s)
- A. T. Knoll
- Program in Developmental NeurogeneticsInstitute for the Developing Mind, The Saban Research Institute, Children’s Hospital Los AngelesLos AngelesCA
- Department of PediatricsKeck School of Medicine of the University of Southern CaliforniaLos AngelesCA
| | - K. Jiang
- Department of PediatricsKeck School of Medicine of the University of Southern CaliforniaLos AngelesCA
| | - P. Levitt
- Program in Developmental NeurogeneticsInstitute for the Developing Mind, The Saban Research Institute, Children’s Hospital Los AngelesLos AngelesCA
- Department of PediatricsKeck School of Medicine of the University of Southern CaliforniaLos AngelesCA
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20
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Zajitschek F, Connallon T. Antagonistic pleiotropy in species with separate sexes, and the maintenance of genetic variation in life-history traits and fitness. Evolution 2018; 72:1306-1316. [PMID: 29667189 DOI: 10.1111/evo.13493] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/21/2018] [Accepted: 03/23/2018] [Indexed: 01/01/2023]
Abstract
Antagonistic pleiotropy (AP)-where alleles of a gene increase some components of fitness at a cost to others-can generate balancing selection, and contribute to the maintenance of genetic variation in fitness traits, such as survival, fecundity, fertility, and mate competition. Previous theory suggests that AP is unlikely to maintain variation unless antagonistic selection is strong, or AP alleles exhibit pronounced differences in genetic dominance between the affected traits. We show that conditions for balancing selection under AP expand under the likely scenario that the strength of selection on each fitness component differs between the sexes. Our model also predicts that the vast majority of balanced polymorphisms have sexually antagonistic effects on total fitness, despite the absence of sexual antagonism for individual fitness components. We conclude that AP polymorphisms are less difficult to maintain than predicted by prior theory, even under our conservative assumption that selection on components of fitness is universally sexually concordant. We discuss implications for the maintenance of genetic variation, and for inferences of sexual antagonism that are based on sex-specific phenotypic selection estimates-many of which are based on single fitness components.
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Affiliation(s)
- Felix Zajitschek
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Tim Connallon
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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21
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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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22
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Le Manh H, Guio L, Merenciano M, Rovira Q, Barrón MG, González J. Natural and laboratory mutations in kuzbanian are associated with zinc stress phenotypes in Drosophila melanogaster. Sci Rep 2017; 7:42663. [PMID: 28218276 PMCID: PMC5316978 DOI: 10.1038/srep42663] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 01/13/2017] [Indexed: 11/09/2022] Open
Abstract
Organisms must cope with altered environmental conditions such as high concentrations of heavy metals. Stress response to heavy metals is mediated by the metal-responsive transcription factor 1 (MTF-1), which is conserved from Drosophila to humans. MTF-1 binds to metal response elements (MREs) and changes the expression of target genes. kuzbanian (kuz), a metalloendopeptidase that activates the evolutionary conserved Notch signaling pathway, has been identified as an MTF-1 target gene. We have previously identified a putatively adaptive transposable element in the Drosophila melanogaster genome, named FBti0019170, inserted in a kuz intron. In this work, we investigated whether a laboratory mutant stock overexpressing kuz is associated with zinc stress phenotypes. We found that both embryos and adult flies overexpressing kuz are more tolerant to zinc compared with wild-type flies. On the other hand, we found that the effect of FBti0019170 on zinc stress tolerance depends on developmental stage and genetic background. Moreover, in the majority of the genetic backgrounds analyzed, FBti0019170 has a deleterious effect in unpolluted environments in pre-adult stages. These results highlight the complexity of natural mutations and suggest that besides laboratory mutations, natural mutations should be studied in order to accurately characterize gene function and evolution.
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Affiliation(s)
- Hung Le Manh
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49. 08003 Barcelona. Spain
- Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet st, Hanoi, Vietnam
| | - Lain Guio
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49. 08003 Barcelona. Spain
| | - Miriam Merenciano
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49. 08003 Barcelona. Spain
| | - Quirze Rovira
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49. 08003 Barcelona. Spain
| | - Maite G. Barrón
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49. 08003 Barcelona. Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49. 08003 Barcelona. Spain
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23
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Vertacnik KL, Linnen CR. Evolutionary genetics of host shifts in herbivorous insects: insights from the age of genomics. Ann N Y Acad Sci 2017; 1389:186-212. [DOI: 10.1111/nyas.13311] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/16/2016] [Accepted: 12/22/2016] [Indexed: 12/25/2022]
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24
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Salmela MJ, Ewers BE, Weinig C. Natural quantitative genetic variance in plant growth differs in response to ecologically relevant temperature heterogeneity. Ecol Evol 2016; 6:7574-7585. [PMID: 30128112 PMCID: PMC6093144 DOI: 10.1002/ece3.2482] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/22/2016] [Accepted: 08/28/2016] [Indexed: 01/06/2023] Open
Abstract
Adaptation to large‐scale spatial heterogeneity in the environment accounts for a major proportion of genetic diversity within species. Theory predicts the erosion of adaptive genetic variation on a within‐population level, but considerable genetic diversity is often found locally. Genetic diversity could be expected to be maintained within populations in temporally or spatially variable conditions if genotypic rank orders vary across contrasting microenvironmental settings. Taking advantage of fine‐resolution environmental data, we tested the hypothesis that temperature heterogeneity among years could be one factor maintaining quantitative genetic diversity within a natural and genetically diverse plant population. We sampled maternal families of Boechera stricta, an Arabidopsis thaliana relative, at one location in the central Rocky Mountains and grew them in three treatments that, based on records from an adjacent weather station, simulated hourly temperature changes at the native site during three summers with differing mean temperatures. Treatment had a significant effect on all traits, with 2–3‐fold increase in above‐ and belowground biomass and the highest allocation to roots observed in the treatment simulating the warmest summer on record at the site. Treatment affected bivariate associations between traits, with the weakest correlation between above‐ and belowground biomass in the warmest treatment. The magnitude of quantitative genetic variation for all traits differed across treatments: Genetic variance of biomass was 0 in the warmest treatment, while highly significant diversity was found in average conditions, resulting in broad‐sense heritability of 0.31. Significant genotype × environment interactions across all treatments were found only in root‐to‐shoot ratio. Therefore, temperature variation among summers appears unlikely to account for the observed levels of local genetic variation in size in this perennial species, but may influence family rank order in growth allocation. Our results indicate that natural environmental fluctuations can have a large impact on the magnitude of within‐population quantitative genetic variance.
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Affiliation(s)
- Matti J Salmela
- Department of Botany University of Wyoming Laramie WY USA.,Present address: Natural Resources Institute Finland Vantaa Finland
| | - Brent E Ewers
- Department of Botany University of Wyoming Laramie WY USA.,Program in Ecology University of Wyoming Laramie WY USA
| | - Cynthia Weinig
- Department of Botany University of Wyoming Laramie WY USA.,Program in Ecology University of Wyoming Laramie WY USA.,Department of Molecular Biology University of Wyoming Laramie WY USA
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25
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Muñoz-Muñoz F, Carreira VP, Martínez-Abadías N, Ortiz V, González-José R, Soto IM. Drosophila wing modularity revisited through a quantitative genetic approach. Evolution 2016; 70:1530-41. [PMID: 27272402 DOI: 10.1111/evo.12975] [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: 12/18/2015] [Accepted: 05/14/2016] [Indexed: 02/03/2023]
Abstract
To predict the response of complex morphological structures to selection it is necessary to know how the covariation among its different parts is organized. Two key features of covariation are modularity and integration. The Drosophila wing is currently considered a fully integrated structure. Here, we study the patterns of integration of the Drosophila wing and test the hypothesis of the wing being divided into two modules along the proximo-distal axis, as suggested by developmental, biomechanical, and evolutionary evidence. To achieve these goals we perform a multilevel analysis of covariation combining the techniques of geometric morphometrics and quantitative genetics. Our results indicate that the Drosophila wing is indeed organized into two main modules, the wing base and the wing blade. The patterns of integration and modularity were highly concordant at the phenotypic, genetic, environmental, and developmental levels. Besides, we found that modularity at the developmental level was considerably higher than modularity at other levels, suggesting that in the Drosophila wing direct developmental interactions are major contributors to total phenotypic shape variation. We propose that the precise time at which covariance-generating developmental processes occur and/or the magnitude of variation that they produce favor proximo-distal, rather than anterior-posterior, modularity in the Drosophila wing.
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Affiliation(s)
- Francesc Muñoz-Muñoz
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Avinguda de l'Eix Central, Edifici C, E-08193 Bellaterra (Cerdanyola del Vallès), Spain.
| | - Valeria Paula Carreira
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA - CONICET) DEGE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Int. Guiraldes 2160, Buenos Aires, Argentina
| | - Neus Martínez-Abadías
- CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Victoria Ortiz
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA - CONICET) DEGE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Int. Guiraldes 2160, Buenos Aires, Argentina
| | - Rolando González-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Argentina
| | - Ignacio M Soto
- Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA - CONICET) DEGE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Int. Guiraldes 2160, Buenos Aires, Argentina
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26
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Sayal R, Dresch JM, Pushel I, Taylor BR, Arnosti DN. Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo. eLife 2016; 5. [PMID: 27152947 PMCID: PMC4859806 DOI: 10.7554/elife.08445] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 04/04/2016] [Indexed: 01/02/2023] Open
Abstract
Enhancers constitute one of the major components of regulatory machinery of metazoans. Although several genome-wide studies have focused on finding and locating enhancers in the genomes, the fundamental principles governing their internal architecture and cis-regulatory grammar remain elusive. Here, we describe an extensive, quantitative perturbation analysis targeting the dorsal-ventral patterning gene regulatory network (GRN) controlled by Drosophila NF-κB homolog Dorsal. To understand transcription factor interactions on enhancers, we employed an ensemble of mathematical models, testing effects of cooperativity, repression, and factor potency. Models trained on the dataset correctly predict activity of evolutionarily divergent regulatory regions, providing insights into spatial relationships between repressor and activator binding sites. Importantly, the collective predictions of sets of models were effective at novel enhancer identification and characterization. Our study demonstrates how experimental dataset and modeling can be effectively combined to provide quantitative insights into cis-regulatory information on a genome-wide scale. DOI:http://dx.doi.org/10.7554/eLife.08445.001 DNA contains regions known as genes, which may be “transcribed” to produce the RNA molecules that act as templates for building proteins and regulate cell activity. Proteins called transcription factors can bind to specific sequences of DNA to influence whether nearby genes are transcribed. For example, so-called enhancer regions of DNA contain several binding sites for transcription factors, and this binding activates gene transcription. Little is known about how the transcription factor binding sites are organized in enhancer regions, which makes it difficult to use DNA sequence information alone to predict the regulation of genes. A transcription factor called Dorsal controls the activity of a network of genes that plays a crucial role in the development of fruit fly embryos. Dorsal binds to the enhancer region of a gene called rhomboid, which has been well studied and is known to be a fairly typical example of an enhancer region. To understand the regulatory information encoded in the DNA sequences of enhancers, Sayal, Dresch et al. have now used a technique called perturbation analysis to investigate the interactions that are likely to occur between Dorsal and other transcription factors as they bind to the rhomboid enhancer. This technique involves systematically mutating the enhancer to remove different combinations of transcription factor binding sites and quantitatively investigating the effect this has on gene activity. A large set of mathematical models were then trained using this data and shown to correctly predict the activity of a range of other gene regulatory regions. The collective predictions of the models identified new enhancer regions and revealed details about how different types of transcription factor binding sites are arranged within enhancers. As we enter an era where the DNA sequences of entire human populations are increasingly accessible, we would like to know the functional significance of changes in gene regulatory regions. Sayal, Dresch et al. show that the regulatory properties of specific control proteins are accessible by employing quantitative experiments and mathematical models. Similar studies will be required to learn how mutations found across the genome may alter gene expression, leading to better diagnosis and treatment of disease. DOI:http://dx.doi.org/10.7554/eLife.08445.002
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Affiliation(s)
- Rupinder Sayal
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Biochemistry, DAV University, Jalandhar, India
| | - Jacqueline M Dresch
- Department of Mathematics, Michigan State University, East Lansing, United States.,Department of Mathematics and Computer Science, Clark University, Worcester, United States
| | - Irina Pushel
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Stowers Institute for Medical Research, Kansas City, United States
| | - Benjamin R Taylor
- Department of Computer Science and Engineering, Michigan State University, East Lansing, United States.,School of Computer Science, Georgia Institute of Technology, Atlanta, United States
| | - David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
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27
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Affiliation(s)
- Justin Fear
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Brian Oliver
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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28
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He X, Zhou S, St. Armour GE, Mackay TFC, Anholt RRH. Epistatic partners of neurogenic genes modulate Drosophila olfactory behavior. GENES, BRAIN, AND BEHAVIOR 2016; 15:280-90. [PMID: 26678546 PMCID: PMC4841442 DOI: 10.1111/gbb.12279] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/02/2015] [Accepted: 12/04/2015] [Indexed: 02/04/2023]
Abstract
The extent to which epistasis affects the genetic architecture of complex traits is difficult to quantify, and identifying variants in natural populations with epistatic interactions is challenging. Previous studies in Drosophila implicated extensive epistasis between variants in genes that affect neural connectivity and contribute to natural variation in olfactory response to benzaldehyde. In this study, we implemented a powerful screen to quantify the extent of epistasis as well as identify candidate interacting variants using 203 inbred wild-derived lines with sequenced genomes of the Drosophila melanogaster Genetic Reference Panel (DGRP). We crossed the DGRP lines to P[GT1]-element insertion mutants in Sema-5c and neuralized (neur), two neurodevelopmental loci which affect olfactory behavior, and to their coisogenic wild-type control. We observed significant variation in olfactory responses to benzaldehyde among F1 genotypes and for the DGRP line by mutant genotype interactions for both loci, showing extensive nonadditive genetic variation. We performed genome-wide association analyses to identify the candidate modifier loci. None of these polymorphisms were in or near the focal genes; therefore, epistasis is the cause of the nonadditive genetic variance. Candidate genes could be placed in interaction networks. Several candidate modifiers are associated with neural development. Analyses of mutants of candidate epistatic partners with neur (merry-go-round (mgr), prospero (pros), CG10098, Alhambra (Alh) and CG12535) and Sema-5c (CG42540 and bruchpilot (brp)) showed aberrant olfactory responses compared with coisogenic controls. Thus, integrating genome-wide analyses of natural variants with mutations at defined genomic locations in a common coisogenic background can unmask specific epistatic modifiers of behavioral phenotypes.
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Affiliation(s)
- X. He
- Department of EntomologySouth China Agricultural UniversityGuangzhouChina
| | - S. Zhou
- Department of Biological SciencesProgram in Genetics and W. M. Keck Center for Behavioral BiologyRaleighNCUSA
| | - G. E. St. Armour
- Department of Biological SciencesProgram in Genetics and W. M. Keck Center for Behavioral BiologyRaleighNCUSA
| | - T. F. C. Mackay
- Department of Biological SciencesProgram in Genetics and W. M. Keck Center for Behavioral BiologyRaleighNCUSA
| | - R. R. H. Anholt
- Department of Biological SciencesProgram in Genetics and W. M. Keck Center for Behavioral BiologyRaleighNCUSA
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29
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Garlapow ME, Huang W, Yarboro MT, Peterson KR, Mackay TFC. Quantitative Genetics of Food Intake in Drosophila melanogaster. PLoS One 2015; 10:e0138129. [PMID: 26375667 PMCID: PMC4574202 DOI: 10.1371/journal.pone.0138129] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/25/2015] [Indexed: 12/16/2022] Open
Abstract
Food intake is an essential animal activity, regulated by neural circuits that motivate food localization, evaluate nutritional content and acceptance or rejection responses through the gustatory system, and regulate neuroendocrine feedback loops that maintain energy homeostasis. Excess food consumption in people is associated with obesity and metabolic and cardiovascular disorders. However, little is known about the genetic basis of natural variation in food consumption. To gain insights in evolutionarily conserved genetic principles that regulate food intake, we took advantage of a model system, Drosophila melanogaster, in which food intake, environmental conditions and genetic background can be controlled precisely. We quantified variation in food intake among 182 inbred, sequenced lines of the Drosophila melanogaster Genetic Reference Panel (DGRP). We found significant genetic variation in the mean and within-line environmental variance of food consumption and observed sexual dimorphism and genetic variation in sexual dimorphism for both food intake traits (mean and variance). We performed genome wide association (GWA) analyses for mean food intake and environmental variance of food intake (using the coefficient of environmental variation, CVE, as the metric for environmental variance) and identified molecular polymorphisms associated with both traits. Validation experiments using RNAi-knockdown confirmed 24 of 31 (77%) candidate genes affecting food intake and/or variance of food intake, and a test cross between selected DGRP lines confirmed a SNP affecting mean food intake identified in the GWA analysis. The majority of the validated candidate genes were novel with respect to feeding behavior, and many had mammalian orthologs implicated in metabolic diseases.
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Affiliation(s)
- Megan E. Garlapow
- Program in Genetics, North Carolina State University, Raleigh, NC, 27695–7614, United States of America
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, United States of America
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, 27695, United States of America
| | - Wen Huang
- Program in Genetics, North Carolina State University, Raleigh, NC, 27695–7614, United States of America
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, United States of America
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, 27695, United States of America
| | - Michael T. Yarboro
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, United States of America
| | - Kara R. Peterson
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, United States of America
| | - Trudy F. C. Mackay
- Program in Genetics, North Carolina State University, Raleigh, NC, 27695–7614, United States of America
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, United States of America
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, 27695, United States of America
- * E-mail:
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30
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Storz JF, Bridgham JT, Kelly SA, Garland T. Genetic approaches in comparative and evolutionary physiology. Am J Physiol Regul Integr Comp Physiol 2015; 309:R197-214. [PMID: 26041111 PMCID: PMC4525326 DOI: 10.1152/ajpregu.00100.2015] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/23/2015] [Indexed: 01/04/2023]
Abstract
Whole animal physiological performance is highly polygenic and highly plastic, and the same is generally true for the many subordinate traits that underlie performance capacities. Quantitative genetics, therefore, provides an appropriate framework for the analysis of physiological phenotypes and can be used to infer the microevolutionary processes that have shaped patterns of trait variation within and among species. In cases where specific genes are known to contribute to variation in physiological traits, analyses of intraspecific polymorphism and interspecific divergence can reveal molecular mechanisms of functional evolution and can provide insights into the possible adaptive significance of observed sequence changes. In this review, we explain how the tools and theory of quantitative genetics, population genetics, and molecular evolution can inform our understanding of mechanism and process in physiological evolution. For example, lab-based studies of polygenic inheritance can be integrated with field-based studies of trait variation and survivorship to measure selection in the wild, thereby providing direct insights into the adaptive significance of physiological variation. Analyses of quantitative genetic variation in selection experiments can be used to probe interrelationships among traits and the genetic basis of physiological trade-offs and constraints. We review approaches for characterizing the genetic architecture of physiological traits, including linkage mapping and association mapping, and systems approaches for dissecting intermediary steps in the chain of causation between genotype and phenotype. We also discuss the promise and limitations of population genomic approaches for inferring adaptation at specific loci. We end by highlighting the role of organismal physiology in the functional synthesis of evolutionary biology.
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Affiliation(s)
- Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska;
| | - Jamie T Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon
| | - Scott A Kelly
- Department of Zoology, Ohio Wesleyan University, Delaware, Ohio; and
| | - Theodore Garland
- Department of Biology, University of California, Riverside, Riverside, California
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31
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Ullastres A, Petit N, González J. Exploring the Phenotypic Space and the Evolutionary History of a Natural Mutation in Drosophila melanogaster. Mol Biol Evol 2015; 32:1800-14. [PMID: 25862139 PMCID: PMC4476160 DOI: 10.1093/molbev/msv061] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A major challenge of modern Biology is elucidating the functional consequences of natural mutations. Although we have a good understanding of the effects of laboratory-induced mutations on the molecular- and organismal-level phenotypes, the study of natural mutations has lagged behind. In this work, we explore the phenotypic space and the evolutionary history of a previously identified adaptive transposable element insertion. We first combined several tests that capture different signatures of selection to show that there is evidence of positive selection in the regions flanking FBti0019386 insertion. We then explored several phenotypes related to known phenotypic effects of nearby genes, and having plausible connections to fitness variation in nature. We found that flies with FBti0019386 insertion had a shorter developmental time and were more sensitive to stress, which are likely to be the adaptive effect and the cost of selection of this mutation, respectively. Interestingly, these phenotypic effects are not consistent with a role of FBti0019386 in temperate adaptation as has been previously suggested. Indeed, a global analysis of the population frequency of FBti0019386 showed that climatic variables explain well the FBti0019386 frequency patterns only in Australia. Finally, although FBti0019386 insertion could be inducing the formation of heterochromatin by recruiting HP1a (Heterochromatin Protein 1a) protein, the insertion is associated with upregulation of sra in adult females. Overall, our integrative approach allowed us to shed light on the evolutionary history, the relevant fitness effects, and the likely molecular mechanisms of an adaptive mutation and highlights the complexity of natural genetic variants.
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Affiliation(s)
- Anna Ullastres
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Natalia Petit
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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32
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Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits. Genetics 2015; 199:991-1005. [PMID: 25672748 PMCID: PMC4391575 DOI: 10.1534/genetics.115.175075] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/05/2015] [Indexed: 11/18/2022] Open
Abstract
Evolve and resequence studies combine artificial selection experiments with massively parallel sequencing technology to study the genetic basis for complex traits. In these experiments, individuals are selected for extreme values of a trait, causing alleles at quantitative trait loci (QTL) to increase or decrease in frequency in the experimental population. We present a new analysis of the power of artificial selection experiments to detect and localize quantitative trait loci. This analysis uses a simulation framework that explicitly models whole genomes of individuals, quantitative traits, and selection based on individual trait values. We find that explicitly modeling QTL provides qualitatively different insights than considering independent loci with constant selection coefficients. Specifically, we observe how interference between QTL under selection affects the trajectories and lengthens the fixation times of selected alleles. We also show that a substantial portion of the genetic variance of the trait (50–100%) can be explained by detected QTL in as little as 20 generations of selection, depending on the trait architecture and experimental design. Furthermore, we show that power depends crucially on the opportunity for recombination during the experiment. Finally, we show that an increase in power is obtained by leveraging founder haplotype information to obtain allele frequency estimates.
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33
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Ajjuri RR, Hall M, Reiter LT, O’Donnell JM. Drosophila. Mov Disord 2015. [DOI: 10.1016/b978-0-12-405195-9.00005-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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34
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Dmitriew C, Blanckenhorn WU. Condition dependence and the maintenance of genetic variance in a sexually dimorphic black scavenger fly. J Evol Biol 2014; 27:2408-19. [DOI: 10.1111/jeb.12488] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 08/25/2014] [Indexed: 11/29/2022]
Affiliation(s)
- C. Dmitriew
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
| | - W. U. Blanckenhorn
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
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35
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Gene expression variation in Drosophila melanogaster due to rare transposable element insertion alleles of large effect. Genetics 2014; 199:85-93. [PMID: 25335504 PMCID: PMC4286695 DOI: 10.1534/genetics.114.170837] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Transposable elements are a common source of genetic variation that may play a substantial role in contributing to gene expression variation. However, the contribution of transposable elements to expression variation thus far consists of a handful of examples. We used previously published gene expression data from 37 inbred Drosophila melanogaster lines from the Drosophila Genetic Reference Panel to perform a genome-wide assessment of the effects of transposable elements on gene expression. We found thousands of transcripts with transposable element insertions in or near the transcript and that the presence of a transposable element in or near a transcript is significantly associated with reductions in expression. We estimate that within this example population, ∼2.2% of transcripts have a transposable element insertion, which significantly reduces expression in the line containing the transposable element. We also find that transcripts with insertions within 500 bp of the transcript show on average a 0.67 standard deviation decrease in expression level. These large decreases in expression level are most pronounced for transposable element insertions close to transcripts and the effect diminishes for more distant insertions. This work represents the first genome-wide analysis of gene expression variation due to transposable elements and suggests that transposable elements are an important class of mutation underlying expression variation in Drosophila and likely in other systems, given the ubiquity of these mobile elements in eukaryotic genomes.
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36
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Ho WC, Zhang J. The genotype-phenotype map of yeast complex traits: basic parameters and the role of natural selection. Mol Biol Evol 2014; 31:1568-80. [PMID: 24723420 PMCID: PMC4032135 DOI: 10.1093/molbev/msu131] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Most phenotypic traits are controlled by many genes, but a global picture of the genotype-phenotype map (GPM) is lacking. For example, in no species do we know generally how many genes affect a trait and how large these effects are. It is also unclear to what extent GPMs are shaped by natural selection. Here we address these fundamental questions using the reverse genetic data of 220 morphological traits in 4,718 budding yeast strains, each of which lacks a nonessential gene. We show that 1) the proportion of genes affecting a trait varies from <1% to >30%, averaging 6%, 2) most traits are impacted by many more small-effect genes than large-effect genes, and 3) the mean effect of all nonessential genes on a trait decreases precipitously as the estimated importance of the trait to fitness increases. An analysis of 3,116 yeast gene expression traits in 754 gene-deletion strains reveals a similar pattern. These findings illustrate the power of genome-wide reverse genetics in genotype-phenotype mapping, uncover an enormous range of genetic complexity of phenotypic traits, and suggest that the GPM of cellular organisms has been shaped by natural selection for mutational robustness.
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Affiliation(s)
- Wei-Chin Ho
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor
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37
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Avila V, Pérez-Figueroa A, Caballero A, Hill WG, García-Dorado A, López-Fanjul C. The action of stabilizing selection, mutation, and drift on epistatic quantitative traits. Evolution 2014; 68:1974-87. [PMID: 24689841 DOI: 10.1111/evo.12413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 03/05/2014] [Indexed: 01/14/2023]
Abstract
For a quantitative trait under stabilizing selection, the effect of epistasis on its genetic architecture and on the changes of genetic variance caused by bottlenecking were investigated using theory and simulation. Assuming empirical estimates of the rate and effects of mutations and the intensity of selection, we assessed the impact of two-locus epistasis (synergistic/antagonistic) among linked or unlinked loci on the distribution of effects and frequencies of segregating loci in populations at the mutation-selection-drift balance. Strong pervasive epistasis did not modify substantially the genetic properties of the trait and, therefore, the most likely explanation for the low amount of variation usually accounted by the loci detected in genome-wide association analyses is that many causal loci will pass undetected. We investigated the impact of epistasis on the changes in genetic variance components when large populations were subjected to successive bottlenecks of different sizes, considering the action of genetic drift, operating singly (D), or jointly with mutation (MD) and selection (MSD). An initial increase of the different components of the genetic variance, as well as a dramatic acceleration of the between-line divergence, were always associated with synergistic epistasis but were strongly constrained by selection.
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Affiliation(s)
- Victoria Avila
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain; Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, United Kingdom.
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38
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Abstract
When polygenic traits are under stabilizing selection, many different combinations of alleles allow close adaptation to the optimum. If alleles have equal effects, all combinations that result in the same deviation from the optimum are equivalent. Furthermore, the genetic variance that is maintained by mutation-selection balance is [Formula: see text] per locus, where μ is the mutation rate and S the strength of stabilizing selection. In reality, alleles vary in their effects, making the fitness landscape asymmetric and complicating analysis of the equilibria. We show that that the resulting genetic variance depends on the fraction of alleles near fixation, which contribute by [Formula: see text], and on the total mutational effects of alleles that are at intermediate frequency. The interplay between stabilizing selection and mutation leads to a sharp transition: alleles with effects smaller than a threshold value of [Formula: see text] remain polymorphic, whereas those with larger effects are fixed. The genetic load in equilibrium is less than for traits of equal effects, and the fitness equilibria are more similar. We find that if the optimum is displaced, alleles with effects close to the threshold value sweep first, and their rate of increase is bounded by [Formula: see text] Long-term response leads in general to well-adapted traits, unlike the case of equal effects that often end up at a suboptimal fitness peak. However, the particular peaks to which the populations converge are extremely sensitive to the initial states and to the speed of the shift of the optimum trait value.
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39
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Caballero A, García-Dorado A. Allelic diversity and its implications for the rate of adaptation. Genetics 2013; 195:1373-84. [PMID: 24121776 PMCID: PMC3832279 DOI: 10.1534/genetics.113.158410] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 10/08/2013] [Indexed: 11/18/2022] Open
Abstract
Genetic variation is usually estimated empirically from statistics based on population gene frequencies, but alternative statistics based on allelic diversity (number of allelic types) can provide complementary information. There is a lack of knowledge, however, on the evolutionary implications attached to allelic-diversity measures, particularly in structured populations. In this article we simulated multiple scenarios of single and structured populations in which a quantitative trait subject to stabilizing selection is adapted to different fitness optima. By forcing a global change in the optima we evaluated which diversity variables are more strongly correlated with both short- and long-term adaptation to the new optima. We found that quantitative genetic variance components for the trait and gene-frequency-diversity measures are generally more strongly correlated with short-term response to selection, whereas allelic-diversity measures are more correlated with long-term and total response to selection. Thus, allelic-diversity variables are better predictors of long-term adaptation than gene-frequency variables. This observation is also extended to unlinked neutral markers as a result of the information they convey on the demographic population history. Diffusion approximations for the allelic-diversity measures in a finite island model under the infinite-allele neutral mutation model are also provided.
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Affiliation(s)
- Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain
| | - Aurora García-Dorado
- Departamento de Genética, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28080 Madrid, Spain
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40
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Caballero A, García-Dorado A. Allelic diversity and its implications for the rate of adaptation. Genetics 2013; 195:1373-1384. [PMID: 24121776 DOI: 10.1534/genetics.113.158410/-/dc1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Genetic variation is usually estimated empirically from statistics based on population gene frequencies, but alternative statistics based on allelic diversity (number of allelic types) can provide complementary information. There is a lack of knowledge, however, on the evolutionary implications attached to allelic-diversity measures, particularly in structured populations. In this article we simulated multiple scenarios of single and structured populations in which a quantitative trait subject to stabilizing selection is adapted to different fitness optima. By forcing a global change in the optima we evaluated which diversity variables are more strongly correlated with both short- and long-term adaptation to the new optima. We found that quantitative genetic variance components for the trait and gene-frequency-diversity measures are generally more strongly correlated with short-term response to selection, whereas allelic-diversity measures are more correlated with long-term and total response to selection. Thus, allelic-diversity variables are better predictors of long-term adaptation than gene-frequency variables. This observation is also extended to unlinked neutral markers as a result of the information they convey on the demographic population history. Diffusion approximations for the allelic-diversity measures in a finite island model under the infinite-allele neutral mutation model are also provided.
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Affiliation(s)
- Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain
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41
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Nuzhdin SV, Turner TL. Promises and limitations of hitchhiking mapping. Curr Opin Genet Dev 2013; 23:694-9. [PMID: 24239053 PMCID: PMC3872824 DOI: 10.1016/j.gde.2013.10.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 08/20/2013] [Accepted: 10/03/2013] [Indexed: 12/18/2022]
Abstract
Building the connection between genetic and phenotypic variation is an important 'work in progress', and one that will enable proactive diagnosis and treatment in medicine, promote development of environment-targeted varieties in agriculture, and clarify the limits of species adaptation to changing environments in conservation. Quantitative trait loci (QTL) mapping and genome wide association (GWA) studies have recently been allied to an additional focus on 'hitchhiking' (HH) mapping--using changes in allele frequency due to artificial or natural selection. This older technique has been popularized by the falling costs of high throughput sequencing. Initial HH-resequensing experiments seem to have found many thousands of polymorphisms responding to selection. We argue that this interpretation appears too optimistic, and that the data might in fact be more consistent with dozens, rather than thousands, of loci under selection. We propose several developments required for sensible data analyses that will fully realize the great power of the HH technique, and outline ways of moving forward.
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Affiliation(s)
- Sergey V Nuzhdin
- Program in Molecular and Computation Biology, University of Southern California, Los Angeles 90089, United States.
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Abstract
Drosophila melanogaster has been widely used as a model of human Mendelian disease, but its value in modeling complex disease has received little attention. Fly models of complex disease would enable high-resolution mapping of disease-modifying loci and the identification of novel targets for therapeutic intervention. Here, we describe a fly model of permanent neonatal diabetes mellitus and explore the complexity of this model. The approach involves the transgenic expression of a misfolded mutant of human preproinsulin, hINSC96Y, which is a cause of permanent neonatal diabetes. When expressed in fly imaginal discs, hINSC96Y causes a reduction of adult structures, including the eye, wing, and notum. Eye imaginal discs exhibit defects in both the structure and the arrangement of ommatidia. In the wing, expression of hINSC96Y leads to ectopic expression of veins and mechano-sensory organs, indicating disruption of wild-type signaling processes regulating cell fates. These readily measurable “disease” phenotypes are sensitive to temperature, gene dose, and sex. Mutant (but not wild-type) proinsulin expression in the eye imaginal disc induces IRE1-mediated XBP1 alternative splicing, a signal for endoplasmic reticulum stress response activation, and produces global change in gene expression. Mutant hINS transgene tester strains, when crossed to stocks from the Drosophila Genetic Reference Panel, produce F1 adults with a continuous range of disease phenotypes and large broad-sense heritability. Surprisingly, the severity of mutant hINS-induced disease in the eye is not correlated with that in the notum in these crosses, nor with eye reduction phenotypes caused by the expression of two dominant eye mutants acting in two different eye development pathways, Drop (Dr) or Lobe (L), when crossed into the same genetic backgrounds. The tissue specificity of genetic variability for mutant hINS-induced disease has, therefore, its own distinct signature. The genetic dominance of disease-specific phenotypic variability in our model of misfolded human proinsulin makes this approach amenable to genome-wide association study in a simple F1 screen of natural variation.
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43
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Wray GA. Genomics and the Evolution of Phenotypic Traits. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135828] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Evolutionary genetics has entered an unprecedented era of discovery, catalyzed in large part by the development of technologies that provide information about genome sequence and function. An important benefit is the ability to move beyond a handful of model organisms in lab settings to identify the genetic basis for evolutionarily interesting traits in many organisms in natural settings. Other benefits are the abilities to identify causal mutations and validate their phenotypic consequences more readily and in many more species. Genomic technologies have reinvigorated interest in some of the most fundamental and persistent questions in evolutionary genetics, revealed previously unsuspected evolutionary phenomena, and opened the door to a wide range of new questions.
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Affiliation(s)
- Gregory A. Wray
- Department of Biology and Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27701
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44
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Boell L. Lines of least resistance and genetic architecture of house mouse (Mus musculus) mandible shape. Evol Dev 2013; 15:197-204. [PMID: 23607303 DOI: 10.1111/ede.12033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Evolution along "lines of least resistance (LLR)" is a well-established phenomenon, which is ultimately based on variational properties of the developmental system. However, it has remained unclear which aspects of development are responsible for observed distributions of variation. This article suggests that house mouse mandible shape may present an opportunity for future research in this field. The genetic architecture of mouse mandible shape has been investigated in the laboratory, and its evolution has been surveyed in studies on natural variation. Here, I ask whether evolutionary diversification of mandible shape follows "LLR" by comparing principal directions of genetic and evolutionary variation, and I assess the potential contribution of specific genomic regions to evolutionary divergence along these directions. The role of two aspects of development, QTL number (presumably reflecting mutational target size) and canalization, is comparatively assessed. Overall, our results demonstrate a strong tendency of genetic and evolutionary systems to vary along similar directions, suggesting that mandible shape evolves along LLR at the level of populations, subspecies and species. At the level of genetic factors, effects bearing similarity to directions of evolution are significantly overrepresented, providing support for the mutational target size hypothesis. A role for canalization is not supported by a clear correlation between directions of evolution and size of genetic effects; however, the evidence for canalization remains ambiguous. These results provide some insights into how the developmental system may shape the variational properties of genetic systems and thus influence the direction of evolution.
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Affiliation(s)
- Louis Boell
- Max-Planck-Institut für Evolutionsbiologie, August-Thienemann-str. 2, Plön 24306, Germany.
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45
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Stringer S, Derks EM, Kahn RS, Hill WG, Wray NR. Assumptions and properties of limiting pathway models for analysis of epistasis in complex traits. PLoS One 2013; 8:e68913. [PMID: 23935903 PMCID: PMC3728313 DOI: 10.1371/journal.pone.0068913] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 06/03/2013] [Indexed: 11/19/2022] Open
Abstract
For most complex traits, results from genome-wide association studies show that the proportion of the phenotypic variance attributable to the additive effects of individual SNPs, that is, the heritability explained by the SNPs, is substantially less than the estimate of heritability obtained by standard methods using correlations between relatives. This difference has been called the "missing heritability". One explanation is that heritability estimates from family (including twin) studies are biased upwards. Zuk et al. revisited overestimation of narrow sense heritability from twin studies as a result of confounding with non-additive genetic variance. They propose a limiting pathway (LP) model that generates significant epistatic variation and its simple parametrization provides a convenient way to explore implications of epistasis. They conclude that over-estimation of narrow sense heritability from family data ('phantom heritability') may explain an important proportion of missing heritability. We show that for highly heritable quantitative traits large phantom heritability estimates from twin studies are possible only if a large contribution of common environment is assumed. The LP model is underpinned by strong assumptions that are unlikely to hold, including that all contributing pathways have the same mean and variance and are uncorrelated. Here, we relax the assumptions that underlie the LP model to be more biologically plausible. Together with theoretical, empirical, and pragmatic arguments we conclude that in outbred populations the contribution of additive genetic variance is likely to be much more important than the contribution of non-additive variance.
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Affiliation(s)
- Sven Stringer
- Department of Psychiatry, Amsterdam Medical Center, Amsterdam, The Netherlands.
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46
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Cridland JM, Macdonald SJ, Long AD, Thornton KR. Abundance and distribution of transposable elements in two Drosophila QTL mapping resources. Mol Biol Evol 2013; 30:2311-27. [PMID: 23883524 PMCID: PMC3773372 DOI: 10.1093/molbev/mst129] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Here we present computational machinery to efficiently and accurately identify transposable element (TE) insertions in 146 next-generation sequenced inbred strains of Drosophila melanogaster. The panel of lines we use in our study is composed of strains from a pair of genetic mapping resources: the Drosophila Genetic Reference Panel (DGRP) and the Drosophila Synthetic Population Resource (DSPR). We identified 23,087 TE insertions in these lines, of which 83.3% are found in only one line. There are marked differences in the distribution of elements over the genome, with TEs found at higher densities on the X chromosome, and in regions of low recombination. We also identified many more TEs per base pair of intronic sequence and fewer TEs per base pair of exonic sequence than expected if TEs are located at random locations in the euchromatic genome. There was substantial variation in TE load across genes. For example, the paralogs derailed and derailed-2 show a significant difference in the number of TE insertions, potentially reflecting differences in the selection acting on these loci. When considering TE families, we find a very weak effect of gene family size on TE insertions per gene, indicating that as gene family size increases the number of TE insertions in a given gene within that family also increases. TEs are known to be associated with certain phenotypes, and our data will allow investigators using the DGRP and DSPR to assess the functional role of TE insertions in complex trait variation more generally. Notably, because most TEs are very rare and often private to a single line, causative TEs resulting in phenotypic differences among individuals may typically fail to replicate across mapping panels since individual elements are unlikely to segregate in both panels. Our data suggest that “burden tests” that test for the effect of TEs as a class may be more fruitful.
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Affiliation(s)
- Julie M Cridland
- Department of Ecology, Evolution and Physiology, University of California, Irvine
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47
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Kulikov AM, Mel’nikov AI, Gornostaev NG, Lazebny OE. Dominance status of shape of male genitalia in interspecific crosses of some Drosophila virilis group species. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413060069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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48
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Idaghdour Y, Awadalla P. Exploiting gene expression variation to capture gene-environment interactions for disease. Front Genet 2013; 3:228. [PMID: 23755064 PMCID: PMC3668192 DOI: 10.3389/fgene.2012.00228] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/10/2012] [Indexed: 12/18/2022] Open
Abstract
Gene-environment interactions have long been recognized as a fundamental concept in evolutionary, quantitative, and medical genetics. In the genomics era, study of how environment and genome interact to shape gene expression variation is relevant to understanding the genetic architecture of complex phenotypes. While genetic analysis of gene expression variation focused on main effects, little is known about the extent of interaction effects implicating regulatory variants and their consequences on transcriptional variation. Here we survey the current state of the concept of transcriptional gene-environment interactions and discuss its utility for mapping disease phenotypes in light of the insights gained from genome-wide association studies of gene expression.
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Affiliation(s)
- Youssef Idaghdour
- Sainte-Justine Research Center, University of Montreal Montreal, QC, Canada
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49
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Vermeulen CJ, Pedersen KS, Beck HC, Petersen J, Gagalova KK, Loeschcke V. Proteomic characterization of inbreeding-related cold sensitivity in Drosophila melanogaster. PLoS One 2013; 8:e62680. [PMID: 23658762 PMCID: PMC3642220 DOI: 10.1371/journal.pone.0062680] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 03/23/2013] [Indexed: 11/30/2022] Open
Abstract
Inbreeding depression is a widespread phenomenon of central importance to agriculture, medicine, conservation biology and evolutionary biology. Although the population genetic principles of inbreeding depression are well understood, we know little about its functional genomic causes. To provide insight into the molecular interplay between intrinsic stress responses, inbreeding depression and temperature tolerance, we performed a proteomic characterization of a well-defined conditional inbreeding effect in a single line of Drosophila melanogaster, which suffers from extreme cold sensitivity and lethality. We identified 48 differentially expressed proteins in a conditional lethal line as compared to two control lines. These proteins were enriched for proteins involved in hexose metabolism, in particular pyruvate metabolism, and many were found to be associated with lipid particles. These processes can be linked to known cold tolerance mechanisms, such as the production of cryoprotectants, membrane remodeling and the build-up of energy reserves. We checked mRNA-expression of seven genes with large differential protein expression. Although protein expression poorly correlated with gene expression, we found a single gene (CG18067) that, after cold shock, was upregulated in the conditional lethal line both at the mRNA and protein level. Expression of CG18067 also increased in control flies after cold shock, and has previously been linked to cold exposure and chill coma recovery time. Many differentially expressed proteins in our study appear to be involved in cold tolerance in non-inbred individuals. This suggest the conditional inbreeding effect to be caused by misregulation of physiological cold tolerance mechanisms.
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Affiliation(s)
- Cornelis J Vermeulen
- Ecology and Genetics, Department of Biological Sciences, Aarhus University, Aarhus, Denmark.
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50
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Albertson R, Tan V, Leads RR, Reyes M, Sullivan W, Casper-Lindley C. Mapping Wolbachia distributions in the adult Drosophila brain. Cell Microbiol 2013; 15:1527-44. [PMID: 23490256 DOI: 10.1111/cmi.12136] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 02/22/2013] [Accepted: 03/02/2013] [Indexed: 01/03/2023]
Abstract
The maternally inherited bacterium Wolbachia infects the germline of most arthropod species. Using Drosophila simulans and D. melanogaster, we demonstrate that localization of Wolbachia to the fat bodies and adult brain is likely also a conserved feature of Wolbachia infection. Examination of three Wolbachia strains (WMel , WRiv , WPop ) revealed that the bacteria preferentially concentrate in the central brain with low titres in the optic lobes. Distribution within regions of the central brain is largely determined by the Wolbachia strain, while the titre is influenced by both, the host species and the bacteria strain. In neurons of the central brain and ventral nerve cord, Wolbachia preferentially localizes to the neuronal cell bodies but not to axons. All examined Wolbachia strains are present intracellularly or in extracellular clusters, with the pathogenic WPop strain exhibiting the largest and most abundant clusters. We also discovered that 16 of 40 lines from the Drosophila Genetic Reference Panel are Wolbachia infected. Direct comparison of Wolbachia infected and cured lines from this panel reveals that differences in physiological traits (chill coma recovery, starvation, longevity) are partially due to host line influences. In addition, a tetracycline-induced increase in Drosophila longevity was detected many generations after treatment.
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