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Miranda VH, Amaral RV, Cogni R. Clinal variation in natural populations of Drosophila melanogaster: An old debate about natural selection and neutral processes. Genet Mol Biol 2024; 47Suppl 1:e20230348. [PMID: 39037374 PMCID: PMC11262002 DOI: 10.1590/1678-4685-gmb-2023-0348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/23/2024] [Indexed: 07/23/2024] Open
Abstract
Distinguishing between environmental adaptations and neutral processes poses a challenge in population genetics and evolutionary studies, particularly when phenomena can be explained by both processes. Clines are genotypic or phenotypic characters correlated with environmental variables, because of that correlation, they are used as examples of spatially varying selection. At the same time, many genotypic clines can be explained by demographic history, like isolation by distance or secondary contact zones. Clines have been extensively studied in Drosophila melanogaster, especially in North America and Australia, where they are attributed to both differential selection and various demographic processes. This review explores existing literature supporting this conclusion and suggests new approaches to better understand the influence of these processes on clines. These innovative approaches aim to shed light on the longstanding debate regarding the importance of natural selection versus neutral processes in maintaining variation in natural populations.
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Affiliation(s)
- Vitória H. Miranda
- Universidade de São Paulo, Instituto de Biociências,
Departamento de Ecologia, São Paulo, SP, Brazil
| | - Rafael Viana Amaral
- Universidade de São Paulo, Instituto de Biociências,
Departamento de Ecologia, São Paulo, SP, Brazil
| | - Rodrigo Cogni
- Universidade de São Paulo, Instituto de Biociências,
Departamento de Ecologia, São Paulo, SP, Brazil
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2
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Hidalgo S, Chiu JC. Integration of photoperiodic and temperature cues by the circadian clock to regulate insect seasonal adaptations. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2024; 210:585-599. [PMID: 37584703 PMCID: PMC11057393 DOI: 10.1007/s00359-023-01667-1] [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: 04/14/2023] [Revised: 07/27/2023] [Accepted: 08/06/2023] [Indexed: 08/17/2023]
Abstract
Organisms adapt to unfavorable seasonal conditions to survive. These seasonal adaptations rely on the correct interpretation of environmental cues such as photoperiod, and temperature. Genetic studies in several organisms, including the genetic powerhouse Drosophila melanogaster, indicate that circadian clock components, such as period and timeless, are involved in photoperiodic-dependent seasonal adaptations, but our understanding of this process is far from complete. In particular, the role of temperature as a key factor to complement photoperiodic response is not well understood. The development of new sequencing technologies has proven extremely useful in understanding the plastic changes that the clock and other cellular components undergo in different environmental conditions, including changes in gene expression and alternative splicing. This article discusses the integration of photoperiod and temperature for seasonal biology as well as downstream molecular and cellular pathways involved in the regulation of physiological adaptations that occur with changing seasons. We focus our discussion on the current understanding of the involvement of the molecular clock and the circadian clock neuronal circuits in these adaptations in D. melanogaster.
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Affiliation(s)
- Sergio Hidalgo
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, CA, 95616, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, CA, 95616, USA.
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3
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Štětina T, Koštál V. Mortality caused by extracellular freezing is associated with fragmentation of nuclear DNA in larval haemocytes of two drosophilid flies. J Exp Biol 2023; 226:jeb246456. [PMID: 37846596 DOI: 10.1242/jeb.246456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/09/2023] [Indexed: 10/18/2023]
Abstract
The great complexity of extracellular freezing stress, involving mechanical, osmotic, dehydration and chemical perturbations of the cellular milieu, hampers progress in understanding the nature of freezing injury and the mechanisms to cope with it in naturally freeze-tolerant insects. Here, we show that nuclear DNA fragmentation begins to occur in larval haemocytes of two fly species, Chymomyza costata and Drosophila melanogaster, before or at the same time as the sub-zero temperature is reached that causes irreparable freezing injury and mortality in freeze-sensitive larval phenotypes. However, when larvae of the freeze-tolerant phenotype (diapausing-cold acclimated-hyperprolinemic) of C. costata were subjected to severe freezing stress in liquid nitrogen, no DNA damage was observed. Artificially increasing the proline concentration in freeze-sensitive larvae of both species by feeding them a proline-enriched diet resulted in a decrease in the proportion of nuclei with fragmented DNA during freezing stress. Our results suggest that proline accumulated in diapausing C. costata larvae during cold acclimation may contribute to the protection of nuclear DNA against fragmentation associated with freezing stress.
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Affiliation(s)
- Tomáš Štětina
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, Branišovská 1160-31, 370505 České Budějovice, Czech Republic
| | - Vladimír Koštál
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, Branišovská 1160-31, 370505 České Budějovice, Czech Republic
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4
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DiVito Evans A, Fairbanks RA, Schmidt P, Levine MT. Histone methylation regulates reproductive diapause in Drosophila melanogaster. PLoS Genet 2023; 19:e1010906. [PMID: 37703303 PMCID: PMC10499233 DOI: 10.1371/journal.pgen.1010906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023] Open
Abstract
Fluctuating environments threaten fertility and viability. To better match the immediate, local environment, many organisms adopt alternative phenotypic states, a phenomenon called "phenotypic plasticity." Natural populations that predictably encounter fluctuating environments tend to be more plastic than conspecific populations that encounter a constant environment, suggesting that phenotypic plasticity can be adaptive. Despite pervasive evidence of such "adaptive phenotypic plasticity," gene regulatory mechanisms underlying plasticity remains poorly understood. Here we test the hypothesis that environment-dependent phenotypic plasticity is mediated by epigenetic factors. To test this hypothesis, we exploit the adaptive reproductive arrest of Drosophila melanogaster females, called diapause. Using an inbred line from a natural population with high diapause plasticity, we demonstrate that diapause is determined epigenetically: only a subset of genetically identical individuals enter diapause and this diapause plasticity is epigenetically transmitted for at least three generations. Upon screening a suite of epigenetic marks, we discovered that the active histone marks H3K4me3 and H3K36me1 are depleted in diapausing ovaries. Using ovary-specific knockdown of histone mark writers and erasers, we demonstrate that H3K4me3 and H3K36me1 depletion promotes diapause. Given that diapause is highly polygenic, that is, distinct suites of alleles mediate diapause plasticity across distinct genotypes, we also investigated the potential for genetic variation in diapause-determining epigenetic marks. Specifically, we asked if these histone marks were similarly depleted in diapause of a genotypically distinct line. We found evidence of divergence in both the gene expression program and histone mark abundance. This study reveals chromatin determinants of phenotypic plasticity and suggests that these determinants may be genotype-dependent, offering new insight into how organisms may exploit and evolve epigenetic mechanisms to persist in fluctuating environments.
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Affiliation(s)
- Abigail DiVito Evans
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Regina A. Fairbanks
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Paul Schmidt
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mia T. Levine
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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5
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Kárpáti Z, Deutsch F, Kiss B, Schmitt T. Seasonal changes in photoperiod and temperature lead to changes in cuticular hydrocarbon profiles and affect mating success in Drosophila suzukii. Sci Rep 2023; 13:5649. [PMID: 37024537 PMCID: PMC10079849 DOI: 10.1038/s41598-023-32652-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/30/2023] [Indexed: 04/08/2023] Open
Abstract
Seasonal plasticity in insects is often triggered by temperature and photoperiod changes. When climatic conditions become sub-optimal, insects might undergo reproductive diapause, a form of seasonal plasticity delaying the development of reproductive organs and activities. During the reproductive diapause, the cuticular hydrocarbon (CHC) profile, which covers the insect body surface, might also change to protect insects from desiccation and cold temperature. However, CHCs are often important cues and signals for mate recognition and changes in CHC composition might affect mate recognition. In the present study, we investigated the CHC profile composition and the mating success of Drosophila suzukii in 1- and 5-day-old males and females of summer and winter morphs. CHC compositions differed with age and morphs. However, no significant differences were found between the sexes of the same age and morph. The results of the behavioral assays show that summer morph pairs start to mate earlier in their life, have a shorter mating duration, and have more offspring compared to winter morph pairs. We hypothesize that CHC profiles of winter morphs are adapted to survive winter conditions, potentially at the cost of reduced mate recognition cues.
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Affiliation(s)
- Zsolt Kárpáti
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany.
- Zoology Department, Plant Protection Institute, Centre of Agricultural Research, ELKH, Budapest, Hungary.
| | - Ferenc Deutsch
- Zoology Department, Plant Protection Institute, Centre of Agricultural Research, ELKH, Budapest, Hungary
- Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Balázs Kiss
- Zoology Department, Plant Protection Institute, Centre of Agricultural Research, ELKH, Budapest, Hungary
| | - Thomas Schmitt
- Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Würzburg, Germany
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6
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Rakes LM, Delamont M, Cole C, Yates JA, Blevins LJ, Hassan FN, Bergland AO, Erickson PA. Spatial and temporal variation in abundance of introduced African fig fly ( Zaprionus indianus) (Diptera: Drosophilidae) in the eastern United States. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534156. [PMID: 36993771 PMCID: PMC10055318 DOI: 10.1101/2023.03.24.534156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The African fig fly, Zaprionus indianus (Gupta), has spread globally from its native range in tropical Africa, becoming an invasive crop pest in select areas such as Brazil. Z. indianus was first reported in the United States in 2005 and has since been documented as far north as Canada. As a tropical species, Z. indianus is expected to have low cold tolerance, likely limiting its ability to persist at northern latitudes. In North America, the geographic regions where Z. indianus can thrive and seasonal fluctuations in its abundance are not well understood. The purpose of this study was to characterize the temporal and spatial variation in Z. indianus abundance to better understand its invasion of the eastern United States. We sampled drosophilid communities over the growing season at two orchards in Virginia from 2020-2022 and several locations along the East Coast during the fall of 2022. Virginia abundance curves showed similar seasonal dynamics across years with individuals first detected around July and becoming absent around December. Massachusetts was the northernmost population and no Z. indianus were detected in Maine. Variation in Z. indianus relative abundance was high between nearby orchards and across different fruits within orchards but was not correlated with latitude. Fitness of wild-caught females decreased later in the season and at higher latitudes. The patterns of Z. indianus abundance shown here demonstrate an apparent susceptibility to cold and highlight a need for systematic sampling to accurately characterize the range and spread of Z. indianus.
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Affiliation(s)
- Logan M Rakes
- University of Richmond, Gottwald Center for the Sciences, 138 UR Drive, Richmond, VA 23173, USA
| | - Megan Delamont
- University of Virginia, Physical and Life Sciences Building, 90 Geldard Drive, Charlottesville, VA 22903, USA
| | - Christine Cole
- University of Richmond, Gottwald Center for the Sciences, 138 UR Drive, Richmond, VA 23173, USA
| | - Jillian A Yates
- University of Richmond, Gottwald Center for the Sciences, 138 UR Drive, Richmond, VA 23173, USA
| | - Lynsey Jo Blevins
- University of Virginia, Physical and Life Sciences Building, 90 Geldard Drive, Charlottesville, VA 22903, USA
| | - Fatima Naureen Hassan
- University of Virginia, Physical and Life Sciences Building, 90 Geldard Drive, Charlottesville, VA 22903, USA
| | - Alan O Bergland
- University of Virginia, Physical and Life Sciences Building, 90 Geldard Drive, Charlottesville, VA 22903, USA
| | - Priscilla A Erickson
- University of Richmond, Gottwald Center for the Sciences, 138 UR Drive, Richmond, VA 23173, USA
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7
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Andreatta G, Montagnese S, Costa R. Natural alleles of the clock gene timeless differentially affect life-history traits in Drosophila. Front Physiol 2023; 13:1092951. [PMID: 36703932 PMCID: PMC9871817 DOI: 10.3389/fphys.2022.1092951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/30/2022] [Indexed: 01/12/2023] Open
Abstract
Circadian clocks orchestrate a variety of physiological and behavioural functions within the 24-h day. These timekeeping systems have also been implicated in developmental and reproductive processes that span more (or less) than 24 h. Whether natural alleles of cardinal clock genes affect entire sets of life-history traits (i.e., reproductive arrest, developmental time, fecundity), thus providing a wider substrate for seasonal adaptation, remains unclear. Here we show that natural alleles of the timeless (tim) gene of Drosophila melanogaster, previously shown to modulate flies' propensity to enter reproductive dormancy, differentially affect correlated traits such as early-life fecundity and developmental time. Homozygous flies expressing the shorter TIM isoform (encoded by the s-tim allele) not only show a lower dormancy incidence compared to those homozygous for ls-tim (which produce both the short and an N-terminal additional 23-residues longer TIM isoform), but also higher fecundity in the first 12 days of adult life. Moreover, s-tim homozygous flies develop faster than ls-tim homozygous flies at both warm (25°C) and cold (15°C) temperatures, with the gap being larger at 15°C. In summary, this phenotypic analysis shows that natural variants of tim affect a set of life-history traits associated with reproductive dormancy in Drosophila. We speculate that this provides further adaptive advantage in temperate regions (with seasonal changes) and propose that the underlying mechanisms might not be exclusively dependent on photoperiod, as previously suggested.
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Affiliation(s)
- Gabriele Andreatta
- Department of Biology, University of Padua, Padua, Italy,Max Perutz Laboratories, University of Vienna, Vienna, Austria,*Correspondence: Gabriele Andreatta, ; Rodolfo Costa,
| | - Sara Montagnese
- Department of Medicine, University of Padua, Padua, Italy,Chronobiology, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Rodolfo Costa
- Department of Biology, University of Padua, Padua, Italy,Chronobiology, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom,Institute of Neuroscience, National Research Council (CNR), Padua, Italy,*Correspondence: Gabriele Andreatta, ; Rodolfo Costa,
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8
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Henry LP, Ayroles JF. Drosophila melanogaster microbiome is shaped by strict filtering and neutrality along a latitudinal cline. Mol Ecol 2022; 31:5861-5871. [PMID: 36094780 PMCID: PMC9643648 DOI: 10.1111/mec.16692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 01/13/2023]
Abstract
Microbiomes affect many aspects of host biology, but the eco-evolutionary forces that shape their diversity in natural populations remain poorly understood. Geographical gradients, such as latitudinal clines, generate predictable patterns in biodiversity at macroecological scales, but whether these macroscale processes apply to host-microbiome interactions is an open question. To address this question, we sampled the microbiomes of 13 natural populations of Drosophila melanogaster along a latitudinal cline in the eastern United States. The microbiomes were surprisingly consistent across the cline, as latitude did not predict either alpha or beta diversity. Only a narrow taxonomic range of bacteria were present in all microbiomes, indicating that strict taxonomic filtering by the host and neutral ecological dynamics are the primary factors shaping the fly microbiome. Our findings reveal the complexity of eco-evolutionary interactions shaping microbial variation in D. melanogaster and highlight the need for additional sampling of the microbiomes in natural populations along environmental gradients.
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Affiliation(s)
- Lucas P Henry
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Julien F Ayroles
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
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9
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Yu Y, Bergland AO. Distinct signals of clinal and seasonal allele frequency change at eQTLs in Drosophila melanogaster. Evolution 2022; 76:2758-2768. [PMID: 36097359 PMCID: PMC9710195 DOI: 10.1111/evo.14617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/31/2022] [Accepted: 08/17/2022] [Indexed: 01/22/2023]
Abstract
Populations of short-lived organisms can respond to spatial and temporal environmental heterogeneity through local adaptation. Local adaptation can be reflected on both phenotypic and genetic levels, and it has been documented in many organisms. Although complex fitness-related phenotypes have been shown to vary across latitudinal clines and seasons in similar ways in Drosophila melanogaster populations, the comparative signals of local adaptation across space and time remain poorly understood. Here, we examined patterns of allele frequency change across a latitudinal cline and between seasons at previously reported expression quantitative trait loci (eQTLs). We divided eQTLs into groups by using differential expression profiles of fly populations collected across latitudinal clines or exposed to different environmental conditions. In general, we find that eQTLs are enriched for clinally varying polymorphisms, and that these eQTLs change in frequency in concordant ways across the cline and in response to starvation and chill-coma. The enrichment of eQTLs among seasonally varying polymorphisms is more subtle, and the direction of allele frequency change at eQTLs appears to be somewhat idiosyncratic. Taken together, we suggest that clinal adaptation at eQTLs is at least partially distinct from seasonal adaptation.
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Affiliation(s)
- Yang Yu
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia22904
| | - Alan O. Bergland
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia22904
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10
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Hangartner S, Sgrò CM, Connallon T, Booksmythe I. Sexual dimorphism in phenotypic plasticity and persistence under environmental change: An extension of theory and meta-analysis of current data. Ecol Lett 2022; 25:1550-1565. [PMID: 35334155 PMCID: PMC9311083 DOI: 10.1111/ele.14005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/18/2021] [Accepted: 03/03/2022] [Indexed: 11/29/2022]
Abstract
Populations must adapt to environmental changes to remain viable. Both evolution and phenotypic plasticity contribute to adaptation, with plasticity possibly being more important for coping with rapid change. Adaptation is complex in species with separate sexes, as the sexes can differ in the strength or direction of natural selection, the genetic basis of trait variation, and phenotypic plasticity. Many species show sex differences in plasticity, yet how these differences influence extinction susceptibility remains unclear. We first extend theoretical models of population persistence in changing environments and show that persistence is affected by sexual dimorphism for phenotypic plasticity, trait genetic architecture, and sex-specific selection. Our models predict that female-biased adaptive plasticity-particularly in traits with modest-to-low cross-sex genetic correlations-typically promotes persistence, though we also identify conditions where sexually monomorphic or male-biased plasticity promotes persistence. We then perform a meta-analysis of sex-specific plasticity under manipulated thermal conditions. Although examples of sexually dimorphic plasticity are widely observed, systematic sex differences are rare. An exception-cold resistance-is systematically female-biased and represents a trait wherein sexually dimorphic plasticity might elevate population viability in changing environments. We discuss our results in light of debates about the roles of evolution and plasticity in extinction susceptibility.
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Affiliation(s)
- Sandra Hangartner
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Carla M Sgrò
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Tim Connallon
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Isobel Booksmythe
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
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11
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Hoffmann AA, Bridle J. The dangers of irreversibility in an age of increased uncertainty: revisiting plasticity in invertebrates. OIKOS 2021. [DOI: 10.1111/oik.08715] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ary A. Hoffmann
- School of BioSciences, Bio21 Inst., The Univ. of Melbourne Vic Australia
| | - Jon Bridle
- Dept of Genetics, Evolution and Environment, Univ. College London UK
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12
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Karp X. Hormonal Regulation of Diapause and Development in Nematodes, Insects, and Fishes. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.735924] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Diapause is a state of developmental arrest adopted in response to or in anticipation of environmental conditions that are unfavorable for growth. In many cases, diapause is facultative, such that animals may undergo either a diapause or a non-diapause developmental trajectory, depending on environmental cues. Diapause is characterized by enhanced stress resistance, reduced metabolism, and increased longevity. The ability to postpone reproduction until suitable conditions are found is important to the survival of many animals, and both vertebrate and invertebrate species can undergo diapause. The decision to enter diapause occurs at the level of the whole animal, and thus hormonal signaling pathways are common regulators of the diapause decision. Unlike other types of developmental arrest, diapause is programmed, such that the diapause developmental trajectory includes a pre-diapause preparatory phase, diapause itself, recovery from diapause, and post-diapause development. Therefore, developmental pathways are profoundly affected by diapause. Here, I review two conserved hormonal pathways, insulin/IGF signaling (IIS) and nuclear hormone receptor signaling (NHR), and their role in regulating diapause across three animal phyla. Specifically, the species reviewed are Austrofundulus limnaeus and Nothobranchius furzeri annual killifishes, Caenorhabditis elegans nematodes, and insect species including Drosophila melanogaster, Culex pipiens, and Bombyx mori. In addition, the developmental changes that occur as a result of diapause are discussed, with a focus on how IIS and NHR pathways interact with core developmental pathways in C. elegans larvae that undergo diapause.
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13
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Kurogi Y, Mizuno Y, Imura E, Niwa R. Neuroendocrine Regulation of Reproductive Dormancy in the Fruit Fly Drosophila melanogaster: A Review of Juvenile Hormone-Dependent Regulation. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.715029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Animals can adjust their physiology, helping them survive and reproduce under a wide range of environmental conditions. One of the strategies to endure unfavorable environmental conditions such as low temperature and limited food supplies is dormancy. In some insect species, this may manifest as reproductive dormancy, which causes their reproductive organs to be severely depleted under conditions unsuitable for reproduction. Reproductive dormancy in insects is induced by a reduction in juvenile hormones synthesized in the corpus allatum (pl. corpora allata; CA) in response to winter-specific environmental cues, such as low temperatures and short-day length. In recent years, significant progress has been made in the study of dormancy-inducing conditions dependent on CA control mechanisms in Drosophila melanogaster. This review summarizes dormancy control mechanisms in D. melanogaster and discusses the implications for future studies of insect dormancy, particularly focusing on juvenile hormone-dependent regulation.
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14
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Rodrigues MF, Vibranovski MD, Cogni R. Clinal and seasonal changes are correlated in Drosophila melanogaster natural populations. Evolution 2021; 75:2042-2054. [PMID: 34184262 DOI: 10.1111/evo.14300] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 12/22/2022]
Abstract
Spatial and seasonal variations in the environment are ubiquitous. Environmental heterogeneity can affect natural populations and lead to covariation between environment and allele frequencies. Drosophila melanogaster is known to harbor polymorphisms that change both with latitude and seasons. Identifying the role of selection in driving these changes is not trivial, because nonadaptive processes can cause similar patterns. Given the environment changes in similar ways across seasons and along the latitudinal gradient, one promising approach may be to look for parallelism between clinal and seasonal changes. Here, we test whether there is a genome-wide correlation between clinal and seasonal changes, and whether the pattern is consistent with selection. Allele frequency estimates were obtained from pooled samples from seven different locations along the east coast of the United States, and across seasons within Pennsylvania. We show that there is a genome-wide correlation between clinal and seasonal variations, which cannot be explained by linked selection alone. This pattern is stronger in genomic regions with higher functional content, consistent with natural selection. We derive a way to biologically interpret these correlations and show that around 3.7% of the common, autosomal variants could be under parallel seasonal and spatial selection. Our results highlight the contribution of natural selection in driving fluctuations in allele frequencies in natural fly populations and point to a shared genomic basis to climate adaptation that happens over space and time in D. melanogaster.
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Affiliation(s)
- Murillo F Rodrigues
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil.,Current Address: Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, 97403
| | - Maria D Vibranovski
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil
| | - Rodrigo Cogni
- Department of Ecology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, 05508-090, Brazil
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15
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Betancourt NJ, Rajpurohit S, Durmaz E, Fabian DK, Kapun M, Flatt T, Schmidt P. Allelic polymorphism at foxo contributes to local adaptation in Drosophila melanogaster. Mol Ecol 2021; 30:2817-2830. [PMID: 33914989 PMCID: PMC8693798 DOI: 10.1111/mec.15939] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 04/13/2021] [Indexed: 01/09/2023]
Abstract
The insulin/insulin-like growth factor signalling pathway has been hypothesized as a major determinant of life-history profiles that vary adaptively in natural populations. In Drosophila melanogaster, multiple components of this pathway vary predictably with latitude; this includes foxo, a conserved gene that regulates insulin signalling and has pleiotropic effects on a variety of fitness-associated traits. We hypothesized that allelic variation at foxo contributes to genetic variance for size-related traits that vary adaptively with latitude. We first examined patterns of variation among natural populations along a latitudinal transect in the eastern United States and show that thorax length, wing area, wing loading, and starvation tolerance exhibit significant latitudinal clines for both males and females but that development time does not vary predictably with latitude. We then generated recombinant outbred populations and show that naturally occurring allelic variation at foxo, which exhibits stronger clinality than expected, is associated with the same traits that vary with latitude in the natural populations. Our results suggest that allelic variation at foxo contributes to adaptive patterns of life-history variation in natural populations of this genetic model.
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Affiliation(s)
| | - Subhash Rajpurohit
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- Division of Biological and Life Sciences, Ahmedabad University, Ahmedabad, India
| | - Esra Durmaz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Daniel K. Fabian
- Department of Genetics, University of Cambridge, Cambridge, UK
- European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Thomas Flatt
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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16
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Huang Y, Lack JB, Hoppel GT, Pool JE. Parallel and Population-specific Gene Regulatory Evolution in Cold-Adapted Fly Populations. Genetics 2021; 218:6275754. [PMID: 33989401 PMCID: PMC8864734 DOI: 10.1093/genetics/iyab077] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/10/2021] [Indexed: 11/15/2022] Open
Abstract
Changes in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have assayed within- and between-population variation in gene regulatory traits at a transcriptomic scale, and therefore inferences about the characteristics of adaptive regulatory changes have been elusive. Here, we assess quantitative trait differentiation in gene expression levels and alternative splicing (intron usage) between three closely related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. The cold-adapted populations were known to show population genetic evidence for parallel evolution at the SNP level, and here we find evidence for parallel expression evolution between them, with stronger parallelism at larval and adult stages than for pupae. We also implement a flexible method to estimate cis- vs trans-encoded contributions to expression or splicing differences at the adult stage. The apparent contributions of cis- vs trans-regulation to adaptive evolution vary substantially among population pairs. While two of three population pairs show a greater enrichment of cis-regulatory differences among adaptation candidates, trans-regulatory differences are more likely to be implicated in parallel expression changes between population pairs. Genes with significant cis-effects are enriched for signals of elevated genetic differentiation between cold- and warm-adapted populations, suggesting that they are potential targets of local adaptation. These findings expand our knowledge of adaptive gene regulatory evolution and our ability to make inferences about this important and widespread process.
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Affiliation(s)
- Yuheng Huang
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Justin B Lack
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Grant T Hoppel
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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17
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Olazcuaga L, Loiseau A, Parrinello H, Paris M, Fraimout A, Guedot C, Diepenbrock LM, Kenis M, Zhang J, Chen X, Borowiec N, Facon B, Vogt H, Price DK, Vogel H, Prud'homme B, Estoup A, Gautier M. A Whole-Genome Scan for Association with Invasion Success in the Fruit Fly Drosophila suzukii Using Contrasts of Allele Frequencies Corrected for Population Structure. Mol Biol Evol 2021; 37:2369-2385. [PMID: 32302396 PMCID: PMC7403613 DOI: 10.1093/molbev/msaa098] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or suppressed. Here, we characterized the genome response of the spotted wing drosophila Drosophila suzukii during the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we called C2, that contrasts allele frequencies corrected for population structure. We evaluated this new statistical framework using simulated data sets and implemented it in an upgraded version of the program BayPass. We identified a relatively small set of single-nucleotide polymorphisms that show a highly significant association with the invasive status of D. suzukii populations. In particular, two genes, RhoGEF64C and cpo, contained single-nucleotide polymorphisms significantly associated with the invasive status in the two separate main invasion routes of D. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by nonequilibrium demographic conditions for which binary covariables of interest can be defined at the population level.
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Affiliation(s)
- Laure Olazcuaga
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
| | - Anne Loiseau
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
| | - Hugues Parrinello
- MGX, Biocampus Montpellier, CNRS, INSERM, Universite de Montpellier, Montpellier, France
| | | | - Antoine Fraimout
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
| | | | | | | | - Jinping Zhang
- MoA-CABI Joint Laboratory for Bio-Safety, Chinese Academy of Agricultural Sciences, BeiXiaGuan, Haidian Qu, China
| | - Xiao Chen
- College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan Province, China
| | - Nicolas Borowiec
- UMR INRAE-CNRS-Université Côte d'Azur Sophia Agrobiotech Institute, Sophia Antipolis, France
| | - Benoit Facon
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, INRAE, Saint-Pierre, La Réunion, France
| | - Heidrun Vogt
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Dossenheim, Germany
| | - Donald K Price
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Arnaud Estoup
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
| | - Mathieu Gautier
- INRAE, UMR CBGP (INRAE-IRD-Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France
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18
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Ferris KG, Chavez AS, Suzuki TA, Beckman EJ, Phifer-Rixey M, Bi K, Nachman MW. The genomics of rapid climatic adaptation and parallel evolution in North American house mice. PLoS Genet 2021; 17:e1009495. [PMID: 33914747 PMCID: PMC8084166 DOI: 10.1371/journal.pgen.1009495] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 03/17/2021] [Indexed: 12/23/2022] Open
Abstract
Parallel changes in genotype and phenotype in response to similar selection pressures in different populations provide compelling evidence of adaptation. House mice (Mus musculus domesticus) have recently colonized North America and are found in a wide range of environments. Here we measure phenotypic and genotypic differentiation among house mice from five populations sampled across 21° of latitude in western North America, and we compare our results to a parallel latitudinal cline in eastern North America. First, we show that mice are genetically differentiated between transects, indicating that they have independently colonized similar environments in eastern and western North America. Next, we find genetically-based differences in body weight and nest building behavior between mice from the ends of the western transect which mirror differences seen in the eastern transect, demonstrating parallel phenotypic change. We then conduct genome-wide scans for selection and a genome-wide association study to identify targets of selection and candidate genes for body weight. We find some genomic signatures that are unique to each transect, indicating population-specific responses to selection. However, there is significant overlap between genes under selection in eastern and western house mouse transects, providing evidence of parallel genetic evolution in response to similar selection pressures across North America.
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Affiliation(s)
- Kathleen G. Ferris
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Andreas S. Chavez
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Taichi A. Suzuki
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Elizabeth J. Beckman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Megan Phifer-Rixey
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Michael W. Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America
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19
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The seesaw of diet restriction and lifespan: lessons from Drosophila studies. Biogerontology 2021; 22:253-259. [PMID: 33575931 DOI: 10.1007/s10522-021-09912-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 01/27/2021] [Indexed: 01/19/2023]
Abstract
Diet restriction (DR) studies undergo the implementation of reduced single or multiple component/s of the fly food without causing malnutrition. The question of how and why DR modifies the fate of lifespan in fruit flies Drosophila melanogaster has prompted us to emphasize by attending the control food composition first. Certain concentrations of DR food do not always confer an extended lifespan, rather it enables the flies to achieve their normal lifespan, which was probably reduced by the control food per se (having toxic effect caused due to the excess levels of dietary components). However, the current paradigm of DR studies has elicited its benefits and losses via trade-offs in the organismal traits and have highlighted the need for a common diet, but have not claimed the tested diets as balanced. So, the DR effect on lifespan and other fitness traits cannot be justified only based on varying control food across labs and hence, the approach of DR studies has to be revisited and a balanced diet has to be formulated. The current article discusses the need for a balanced diet, the traits to be considered before designing a diet, and certain problems in the existing synthetic medium. Therefore, based on the control food composition, the validity of lifespan extension conferred by these nutrient restricted diets need to be accounted for.
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20
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Grainger TN, Rudman SM, Schmidt P, Levine JM. Competitive history shapes rapid evolution in a seasonal climate. Proc Natl Acad Sci U S A 2021; 118:e2015772118. [PMID: 33536336 PMCID: PMC8017725 DOI: 10.1073/pnas.2015772118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Eco-evolutionary dynamics will play a critical role in determining species' fates as climatic conditions change. Unfortunately, we have little understanding of how rapid evolutionary responses to climate play out when species are embedded in the competitive communities that they inhabit in nature. We tested the effects of rapid evolution in response to interspecific competition on subsequent ecological and evolutionary trajectories in a seasonally changing climate using a field-based evolution experiment with Drosophila melanogaster Populations of D. melanogaster were either exposed, or not exposed, to interspecific competition with an invasive competitor, Zaprionus indianus, over the summer. We then quantified these populations' ecological trajectories (abundances) and evolutionary trajectories (heritable phenotypic change) when exposed to a cooling fall climate. We found that competition with Z. indianus in the summer affected the subsequent evolutionary trajectory of D. melanogaster populations in the fall, after all interspecific competition had ceased. Specifically, flies with a history of interspecific competition evolved under fall conditions to be larger and have lower cold fecundity and faster development than flies without a history of interspecific competition. Surprisingly, this divergent fall evolutionary trajectory occurred in the absence of any detectible effect of the summer competitive environment on phenotypic evolution over the summer or population dynamics in the fall. This study demonstrates that competitive interactions can leave a legacy that shapes evolutionary responses to climate even after competition has ceased, and more broadly, that evolution in response to one selective pressure can fundamentally alter evolution in response to subsequent agents of selection.
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Affiliation(s)
- Tess Nahanni Grainger
- Ecology and Evolutionary Biology Department, Princeton University, Princeton NJ 08544;
| | - Seth M Rudman
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
- School of Biological Sciences, Washington State University, Vancouver, WA 98686
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Jonathan M Levine
- Ecology and Evolutionary Biology Department, Princeton University, Princeton NJ 08544
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21
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Abstract
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its worldwide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this book chapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of noncoding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field.
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22
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Kapun M, Barrón MG, Staubach F, Obbard DJ, Wiberg RAW, Vieira J, Goubert C, Rota-Stabelli O, Kankare M, Bogaerts-Márquez M, Haudry A, Waidele L, Kozeretska I, Pasyukova EG, Loeschcke V, Pascual M, Vieira CP, Serga S, Montchamp-Moreau C, Abbott J, Gibert P, Porcelli D, Posnien N, Sánchez-Gracia A, Grath S, Sucena É, Bergland AO, Guerreiro MPG, Onder BS, Argyridou E, Guio L, Schou MF, Deplancke B, Vieira C, Ritchie MG, Zwaan BJ, Tauber E, Orengo DJ, Puerma E, Aguadé M, Schmidt P, Parsch J, Betancourt AJ, Flatt T, González J. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses. Mol Biol Evol 2020; 37:2661-2678. [PMID: 32413142 PMCID: PMC7475034 DOI: 10.1093/molbev/msaa120] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.
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Affiliation(s)
- Martin Kapun
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland
- Division of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Maite G Barrón
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Fabian Staubach
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Darren J Obbard
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - R Axel W Wiberg
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Jorge Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
| | - Clément Goubert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Omar Rota-Stabelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’ Adige, Italy
| | - Maaria Kankare
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - María Bogaerts-Márquez
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Annabelle Haudry
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Lena Waidele
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Iryna Kozeretska
- The European Drosophila Population Genomics Consortium (DrosEU)
- General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center of Ministry of Education and Science of Ukraine, Kyiv, Ukraine
| | - Elena G Pasyukova
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratory of Genome Variation, Institute of Molecular Genetics of RAS, Moscow, Russia
| | - Volker Loeschcke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
| | - Marta Pascual
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristina P Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
| | - Svitlana Serga
- The European Drosophila Population Genomics Consortium (DrosEU)
- General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Catherine Montchamp-Moreau
- The European Drosophila Population Genomics Consortium (DrosEU)
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Jessica Abbott
- The European Drosophila Population Genomics Consortium (DrosEU)
- Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Patricia Gibert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Damiano Porcelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Animal and Plant Sciences, Sheffield, United Kingdom
| | - Nico Posnien
- The European Drosophila Population Genomics Consortium (DrosEU)
- Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Universität Göttingen, Göttingen, Germany
| | - Alejandro Sánchez-Gracia
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Sonja Grath
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Élio Sucena
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Alan O Bergland
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Maria Pilar Garcia Guerreiro
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Banu Sebnem Onder
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Eliza Argyridou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Lain Guio
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Mads Fristrup Schou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
- Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Bart Deplancke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Bio-engineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Cristina Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Michael G Ritchie
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
| | - Bas J Zwaan
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratory of Genetics, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Eran Tauber
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Dorcas J Orengo
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Eva Puerma
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Aguadé
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Paul Schmidt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - John Parsch
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Andrea J Betancourt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, United Kingdom
| | - Thomas Flatt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Josefa González
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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23
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Batz ZA, Clemento AJ, Fritzenwanker J, Ring TJ, Garza JC, Armbruster PA. Rapid adaptive evolution of the diapause program during range expansion of an invasive mosquito. Evolution 2020; 74:1451-1465. [PMID: 32490563 PMCID: PMC8023039 DOI: 10.1111/evo.14029] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 05/25/2020] [Indexed: 12/25/2022]
Abstract
In temperate climates, the recurring seasonal exigencies of winter represent a fundamental physiological challenge for a wide range of organisms. In response, many temperate insects enter diapause, an alternative developmental program, including developmental arrest, that allows organisms to synchronize their life cycle with seasonal environmental variation. Geographic variation in diapause phenology contributing to local climatic adaptation is well documented. However, few studies have examined how the rapid evolution of a suite of traits expressed across the diapause program may contribute to climatic adaptation on a contemporary timescale. Here, we investigate the evolution of the diapause program over the past 35 years by leveraging a "natural experiment" presented by the recent invasion of the Asian tiger mosquito, Aedes albopictus, across the eastern United States. We sampled populations from two distinct climatic regions separated by 6° of latitude (∼700 km). Using common-garden experiments, we identified regional genetic divergence in diapause-associated cold tolerance, diapause duration, and postdiapause starvation tolerance. We also found regional divergence in nondiapause thermal performance. In contrast, we observed minimal regional divergence in nondiapause larval growth traits and at neutral molecular marker loci. Our results demonstrate rapid evolution of the diapause program and imply strong selection caused by differences in winter conditions.
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Affiliation(s)
- Zachary A. Batz
- Department of BiologyGeorgetown UniversityWashingtonDC20057
- Current Address: Neurobiology‐Neurodegeneration and Repair LaboratoryNational Eye Institute, National Institute of Health6 Center Drive, Room 307BethesdaMaryland20892
| | - Anthony J. Clemento
- Department of Ocean SciencesUniversity of CaliforniaSanta CruzCalifornia95064
| | | | | | - John Carlos Garza
- Institute of Marine SciencesUniversity of CaliforniaSanta CruzCalifornia95064
- Department of Ocean SciencesUniversity of CaliforniaSanta CruzCalifornia95064
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24
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Zarubin M, Yakhnenko A, Kravchenko E. Transcriptome analysis of Drosophila melanogaster laboratory strains of different geographical origin after long-term laboratory maintenance. Ecol Evol 2020; 10:7082-7093. [PMID: 32760513 PMCID: PMC7391317 DOI: 10.1002/ece3.6410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/28/2020] [Accepted: 05/03/2020] [Indexed: 01/18/2023] Open
Abstract
Positive selection may be the main factor of the between-population divergence in gene expression. Expression profiles of two Drosophila melanogaster laboratory strains of different geographical origin and long-term laboratory maintenance were analyzed using microchip arrays encompassing probes for 18,500 transcripts. The Russian strain D18 and the North American strain Canton-S were compared. A set of 223 known or putative genes demonstrated significant changes in expression levels between these strains. Differentially expressed genes (DEG) were enriched in response to DDT (p = .0014), proteolysis (p = 2.285E-5), transmembrane transport (p = 1.03E-4), carbohydrate metabolic process (p = .0317), protein homotetramerization (p = .0444), and antibacterial humoral response (p = 425E-4). The expression in subset of genes from different categories was verified by qRT-PCR. Analysis of transcript abundance between Canton-S and D18 strains allowed to select several genes to estimate their participation in latitude adaptation. Expression of selected genes was analyzed in five D. melanogaster lines of different geographic origins by qRT-PCR, and we found two candidate genes that may be associated with latitude adaptation in adult flies-smp-30 and Cda9. Quite possible that several alleles of these genes may be important for insect survival in the environments of global warming. It is interesting that the number of genes involved in local adaptation demonstrates expression level appropriate to their geographical origin even after decades of laboratory maintenance.
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Affiliation(s)
- Mikhail Zarubin
- Molecular Genetics GroupDzhelepov Laboratory of nuclear problemsJoint Institute for Nuclear ResearchDubnaRussia
| | - Alena Yakhnenko
- Molecular Genetics GroupDzhelepov Laboratory of nuclear problemsJoint Institute for Nuclear ResearchDubnaRussia
- Laboratory of Analytical and Bioorganic ChemistryLimnological InstituteSiberian Branch of the Russian Academy of ScienceIrkutskRussia
| | - Elena Kravchenko
- Molecular Genetics GroupDzhelepov Laboratory of nuclear problemsJoint Institute for Nuclear ResearchDubnaRussia
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25
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Walters AW, Hughes RC, Call TB, Walker CJ, Wilcox H, Petersen SC, Rudman SM, Newell PD, Douglas AE, Schmidt PS, Chaston JM. The microbiota influences the Drosophila melanogaster life history strategy. Mol Ecol 2020; 29:639-653. [PMID: 31863671 DOI: 10.1111/mec.15344] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 12/03/2019] [Accepted: 12/16/2019] [Indexed: 12/17/2022]
Abstract
Organisms are locally adapted when members of a population have a fitness advantage in one location relative to conspecifics in other geographies. For example, across latitudinal gradients, some organisms may trade off between traits that maximize fitness components in one, but not both, of somatic maintenance or reproductive output. Latitudinal gradients in life history strategies are traditionally attributed to environmental selection on an animal's genotype, without any consideration of the possible impact of associated microorganisms ("microbiota") on life history traits. Here, we show in Drosophila melanogaster, a key model for studying local adaptation and life history strategy, that excluding the microbiota from definitions of local adaptation is a major shortfall. First, we reveal that an isogenic fly line reared with different bacteria varies the investment in early reproduction versus somatic maintenance. Next, we show that in wild fruit flies, the abundance of these same bacteria was correlated with the latitude and life history strategy of the flies, suggesting geographic specificity of the microbiota composition. Variation in microbiota composition of locally adapted D. melanogaster could be attributed to both the wild environment and host genetic selection. Finally, by eliminating or manipulating the microbiota of fly lines collected across a latitudinal gradient, we reveal that host genotype contributes to latitude-specific life history traits independent of the microbiota and that variation in the microbiota can suppress or reverse the differences between locally adapted fly lines. Together, these findings establish the microbiota composition of a model animal as an essential consideration in local adaptation.
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Affiliation(s)
- Amber W Walters
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Rachel C Hughes
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Tanner B Call
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Carson J Walker
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Hailey Wilcox
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Samara C Petersen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Seth M Rudman
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter D Newell
- Department of Biological Sciences, SUNY Oswego, Oswego, NY, USA
| | - Angela E Douglas
- Department of Entomology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Paul S Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - John M Chaston
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
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26
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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: 66] [Impact Index Per Article: 16.5] [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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27
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Davis JS, Moyle LC. Desiccation resistance and pigmentation variation reflects bioclimatic differences in the Drosophila americana species complex. BMC Evol Biol 2019; 19:204. [PMID: 31694548 PMCID: PMC6836511 DOI: 10.1186/s12862-019-1536-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/22/2019] [Indexed: 01/26/2023] Open
Abstract
Background Disentangling the selective factors shaping adaptive trait variation is an important but challenging task. Many studies—especially in Drosophila—have documented trait variation along latitudinal or altitudinal clines, but frequently lack resolution about specific environmental gradients that could be causal selective agents, and often do not investigate covariation between traits simultaneously. Here we examined variation in multiple macroecological factors across geographic space and their associations with variation in three physiological traits (desiccation resistance, UV resistance, and pigmentation) at both population and species scales, to address the role of abiotic environment in shaping trait variation. Results Using environmental data from collection locations of three North American Drosophila species—D. americana americana, D. americana texana and D. novamexicana—we identified two primary axes of macroecological variation; these differentiated species habitats and were strongly loaded for precipitation and moisture variables. In nine focal populations (three per species) assayed for each trait, we detected significant species-level variation for both desiccation resistance and pigmentation, but not for UV resistance. Species-level trait variation was consistent with differential natural selection imposed by variation in habitat water availability, although patterns of variation differed between desiccation resistance and pigmentation, and we found little evidence for pleiotropy between traits. Conclusions Our multi-faceted approach enabled us to identify potential agents of natural selection and examine how they might influence the evolution of multiple traits at different evolutionary scales. Our findings highlight that environmental factors influence functional trait variation in ways that can be complex, and point to the importance of studies that examine these relationships at both population- and species-levels.
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Affiliation(s)
- Jeremy S Davis
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
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28
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Rudman SM, Greenblum S, Hughes RC, Rajpurohit S, Kiratli O, Lowder DB, Lemmon SG, Petrov DA, Chaston JM, Schmidt P. Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster. Proc Natl Acad Sci U S A 2019; 116:20025-20032. [PMID: 31527278 PMCID: PMC6778213 DOI: 10.1073/pnas.1907787116] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Population genomic data has revealed patterns of genetic variation associated with adaptation in many taxa. Yet understanding the adaptive process that drives such patterns is challenging; it requires disentangling the ecological agents of selection, determining the relevant timescales over which evolution occurs, and elucidating the genetic architecture of adaptation. Doing so for the adaptation of hosts to their microbiome is of particular interest with growing recognition of the importance and complexity of host-microbe interactions. Here, we track the pace and genomic architecture of adaptation to an experimental microbiome manipulation in replicate populations of Drosophila melanogaster in field mesocosms. Shifts in microbiome composition altered population dynamics and led to divergence between treatments in allele frequencies, with regions showing strong divergence found on all chromosomes. Moreover, at divergent loci previously associated with adaptation across natural populations, we found that the more common allele in fly populations experimentally enriched for a certain microbial group was also more common in natural populations with high relative abundance of that microbial group. These results suggest that microbiomes may be an agent of selection that shapes the pattern and process of adaptation and, more broadly, that variation in a single ecological factor within a complex environment can drive rapid, polygenic adaptation over short timescales.
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Affiliation(s)
- Seth M Rudman
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104;
| | | | - Rachel C Hughes
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
| | - Subhash Rajpurohit
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Ozan Kiratli
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Dallin B Lowder
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
| | - Skyler G Lemmon
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305
| | - John M Chaston
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
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29
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Durmaz E, Rajpurohit S, Betancourt N, Fabian DK, Kapun M, Schmidt P, Flatt T. A clinal polymorphism in the insulin signaling transcription factor foxo contributes to life-history adaptation in Drosophila. Evolution 2019; 73:1774-1792. [PMID: 31111462 PMCID: PMC6771989 DOI: 10.1111/evo.13759] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 05/04/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022]
Abstract
A fundamental aim of adaptation genomics is to identify polymorphisms that underpin variation in fitness traits. In Drosophila melanogaster, latitudinal life-history clines exist on multiple continents and make an excellent system for dissecting the genetics of adaptation. We have previously identified numerous clinal single-nucleotide polymorphism in insulin/insulin-like growth factor signaling (IIS), a pathway known from mutant studies to affect life history. However, the effects of natural variants in this pathway remain poorly understood. Here we investigate how two clinal alternative alleles at foxo, a transcriptional effector of IIS, affect fitness components (viability, size, starvation resistance, fat content). We assessed this polymorphism from the North American cline by reconstituting outbred populations, fixed for either the low- or high-latitude allele, from inbred DGRP lines. Because diet and temperature modulate IIS, we phenotyped alleles across two temperatures (18°C, 25°C) and two diets differing in sugar source and content. Consistent with clinal expectations, the high-latitude allele conferred larger body size and reduced wing loading. Alleles also differed in starvation resistance and expression of insulin-like receptor, a transcriptional target of FOXO. Allelic reaction norms were mostly parallel, with few GxE interactions. Together, our results suggest that variation in IIS makes a major contribution to clinal life-history adaptation.
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Affiliation(s)
- Esra Durmaz
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Subhash Rajpurohit
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19140
- Division of Biological and Life SciencesAhmedabad UniversityAhmedabadIndia
| | - Nicolas Betancourt
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19140
| | - Daniel K. Fabian
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteWellcome Genome Campus, HinxtonCambridgeUnited Kingdom
- Institut für PopulationsgenetikVetmeduni ViennaViennaAustria
- Vienna Graduate School of Population, GeneticsViennaAustria
| | - Martin Kapun
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Paul Schmidt
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPennsylvania19140
| | - Thomas Flatt
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of BiologyUniversity of FribourgFribourgSwitzerland
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30
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Chu VM, Sallum MAM, Moore TE, Lainhart W, Schlichting CD, Conn JE. Regional variation in life history traits and plastic responses to temperature of the major malaria vector Nyssorhynchus darlingi in Brazil. Sci Rep 2019; 9:5356. [PMID: 30926833 PMCID: PMC6441093 DOI: 10.1038/s41598-019-41651-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 03/13/2019] [Indexed: 11/08/2022] Open
Abstract
The primary Brazilian malaria vector, Nyssorhynchus darlingi (formerly Anopheles darlingi), ranges from 0°S-23°S across three biomes (Amazonia, Cerrado, Mata Atlântica). Rising temperatures will increase mosquito developmental rates, and models predict future malaria transmission by Ny. darlingi in Brazil will shift southward. We reared F1 Ny. darlingi (progeny of field-collected females from 4 state populations across Brazil) at three temperatures (20, 24, 28 °C) and measured key life-history traits. Our results reveal geographic variation due to both genetic differences among localities and plastic responses to temperature differences. Temperature significantly altered all traits: faster larval development, shorter adult life and overall lifespan, and smaller body sizes were seen at 28 °C versus 20 °C. Low-latitude Amazonia mosquitoes had the fastest larval development at all temperatures, but at 28 °C, average development rate of high-latitude Mata Atlântica mosquitoes was accelerated and equivalent to low-latitude Amazonia. Body size of adult mosquitoes from the Mata Atlântica remained larger at all temperatures. We detected genetic variation in the plastic responses among mosquitoes from different localities, with implications for malaria transmission under climate change. Faster development combined with larger body size, without a tradeoff in adult longevity, suggests vectorial capacities of some Mata Atlântica populations may significantly increase under warming climates.
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Affiliation(s)
- V M Chu
- Department of Biomedical Sciences, School of Public Health, University at Albany (State University of New York), Albany, NY, USA.
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.
| | - M A M Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brazil
| | - T E Moore
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - W Lainhart
- Department of Biomedical Sciences, School of Public Health, University at Albany (State University of New York), Albany, NY, USA
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
- Department of Pathology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - C D Schlichting
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - J E Conn
- Department of Biomedical Sciences, School of Public Health, University at Albany (State University of New York), Albany, NY, USA.
- Wadsworth Center, New York State Department of Health, Albany, NY, USA.
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31
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Adrion JR, Begun DJ, Hahn MW. Patterns of transposable element variation and clinality in
Drosophila. Mol Ecol 2019; 28:1523-1536. [DOI: 10.1111/mec.14961] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Jeffrey R. Adrion
- Department of Biology University of Oregon Eugene Oregon
- Department of Biology Indiana University Bloomington Indiana
| | - David J. Begun
- Department of Evolution and Ecology University of California Davis, Davis California
| | - Matthew W. Hahn
- Department of Biology Indiana University Bloomington Indiana
- Department of Computer Science Indiana University Bloomington Indiana
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32
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Kapun M, Flatt T. The adaptive significance of chromosomal inversion polymorphisms inDrosophila melanogaster. Mol Ecol 2018; 28:1263-1282. [DOI: 10.1111/mec.14871] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/01/2018] [Accepted: 09/10/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Martin Kapun
- Department of BiologyUniversity of Fribourg Fribourg Switzerland
| | - Thomas Flatt
- Department of BiologyUniversity of Fribourg Fribourg Switzerland
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33
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Signor SA, New FN, Nuzhdin S. A Large Panel of Drosophila simulans Reveals an Abundance of Common Variants. Genome Biol Evol 2018; 10:189-206. [PMID: 29228179 PMCID: PMC5767965 DOI: 10.1093/gbe/evx262] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2017] [Indexed: 01/03/2023] Open
Abstract
The rapidly expanding availability of large NGS data sets provides an opportunity to investigate population genetics at an unprecedented scale. Drosophila simulans is the sister species of the model organism Drosophila melanogaster, and is often presumed to share similar demographic history. However, previous population genetic and ecological work suggests very different signatures of selection and demography. Here, we sequence a new panel of 170 inbred genotypes of a North American population of D. simulans, a valuable complement to the DGRP and other D. melanogaster panels. We find some unexpected signatures of demography, in the form of excess intermediate frequency polymorphisms. Simulations suggest that this is possibly due to a recent population contraction and selection. We examine the outliers in the D. simulans genome determined by a haplotype test to attempt to parse the contribution of demography and selection to the patterns observed in this population. Untangling the relative contribution of demography and selection to genomic patterns of variation is challenging, however, it is clear that although D. melanogaster was thought to share demographic history with D. simulans different forces are at work in shaping genomic variation in this population of D. simulans.
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Affiliation(s)
- Sarah A Signor
- Department of Molecular and Computational Biology, University of Southern California
| | - Felicia N New
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine
| | - Sergey Nuzhdin
- Department of Molecular and Computational Biology, University of Southern California
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34
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Bauerfeind SS, Schäfer MA, Berger D, Blanckenhorn WU, Fox CW. Replicated latitudinal clines in reproductive traits of European and North American yellow dung flies. OIKOS 2018. [DOI: 10.1111/oik.05421] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Martin A. Schäfer
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich; Zurich Switzerland
| | - David Berger
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich; Zurich Switzerland
- Dept of Ecology and Genetics, Univ. of Uppsala; Uppsala Sweden
| | - Wolf U. Blanckenhorn
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich; Zurich Switzerland
| | - Charles W. Fox
- Dept of Entomology, Univ. of Kentucky; S225 Ag Science Center North Lexington KY 40546-0091 USA
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35
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Durmaz E, Benson C, Kapun M, Schmidt P, Flatt T. An inversion supergene in Drosophila underpins latitudinal clines in survival traits. J Evol Biol 2018; 31:1354-1364. [PMID: 29904977 DOI: 10.1111/jeb.13310] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/09/2018] [Accepted: 06/04/2018] [Indexed: 01/18/2023]
Abstract
Chromosomal inversions often contribute to local adaptation across latitudinal clines, but the underlying selective mechanisms remain poorly understood. We and others have previously shown that a clinal inversion polymorphism in Drosophila melanogaster, In(3R)Payne, underpins body size clines along the North American and Australian east coasts. Here, we ask whether this polymorphism also contributes to clinal variation in other fitness-related traits, namely survival traits (lifespan, survival upon starvation and survival upon cold shock). We generated homokaryon lines, either carrying the inverted or standard chromosomal arrangement, isolated from populations approximating the endpoints of the North American cline (Florida, Maine) and phenotyped the flies at two growth temperatures (18 °C, 25 °C). Across both temperatures, high-latitude flies from Maine lived longer and were more stress resistant than low-latitude flies from Florida, as previously observed. Interestingly, we find that this latitudinal pattern is partly explained by the clinal distribution of the In(3R)P polymorphism, which is at ~ 50% frequency in Florida but absent in Maine: inverted karyotypes tended to be shorter-lived and less stress resistant than uninverted karyotypes. We also detected an interaction between karyotype and temperature on survival traits. As In(3R)P influences body size and multiple survival traits, it can be viewed as a 'supergene', a cluster of tightly linked loci affecting multiple complex phenotypes. We conjecture that the inversion cline is maintained by fitness trade-offs and balancing selection across geography; elucidating the mechanisms whereby this inversion affects alternative, locally adapted phenotypes across the cline is an important task for future work.
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Affiliation(s)
- Esra Durmaz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Clare Benson
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,School of Biological Sciences, University of Manchester, Manchester, UK
| | - Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Flatt
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Department of Biology, University of Fribourg, Fribourg, Switzerland
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36
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Abstract
Sleep is nearly ubiquitous throughout the animal kingdom, yet little is known about how ecological factors or perturbations to the environment shape the duration and timing of sleep. In diverse animal taxa, poor sleep negatively impacts development, cognitive abilities and longevity. In addition to mammals, sleep has been characterized in genetic model organisms, ranging from the nematode worm to zebrafish, and, more recently, in emergent models with simplified nervous systems such as Aplysia and jellyfish. In addition, evolutionary models ranging from fruit flies to cavefish have leveraged natural genetic variation to investigate the relationship between ecology and sleep. Here, we describe the contributions of classical and emergent genetic model systems to investigate mechanisms underlying sleep regulation. These studies highlight fundamental interactions between sleep and sensory processing, as well as a remarkable plasticity of sleep in response to environmental changes. Understanding how sleep varies throughout the animal kingdom will provide critical insight into fundamental functions and conserved genetic mechanisms underlying sleep regulation. Furthermore, identification of naturally occurring genetic variation regulating sleep may provide novel drug targets and approaches to treat sleep-related diseases.
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Affiliation(s)
- Alex C Keene
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458, USA
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Erik R Duboue
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458, USA
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
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37
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Lirakis M, Dolezal M, Schlötterer C. Redefining reproductive dormancy in Drosophila as a general stress response to cold temperatures. JOURNAL OF INSECT PHYSIOLOGY 2018; 107:175-185. [PMID: 29649483 DOI: 10.1016/j.jinsphys.2018.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 04/07/2018] [Accepted: 04/08/2018] [Indexed: 06/08/2023]
Abstract
Organisms regularly encounter unfavorable conditions and the genetic adaptations facilitating survival have been of long-standing interest to evolutionary biologists. Winter is one particularly stressful condition for insects, during which they encounter low temperatures and scarcity of food. Despite dormancy being a well-studied adaptation to facilitate overwintering, there is still considerable controversy about the distribution of dormancy among natural populations and between species in Drosophila. The current definition of dormancy as developmental arrest of oogenesis at the previtellogenic stage (stage 7) distinguishes dormancy from general stress related block of oogenesis at early vitellogenic stages (stages 8 - 9). In an attempt to resolve this, we scrutinized reproductive dormancy in D. melanogaster and D. simulans. We show that dormancy shows the same hallmarks of arrest of oogenesis at stage 9, as described for other stressors and propose a new classification for dormancy. Applying this modified classification, we show that both species express dormancy in cosmopolitan and African populations, further supporting that dormancy uses an ancestral pathway induced by environmental stress. While we found significant differences between individuals and the two Drosophila species in their sensitivity to cold temperature stress, we also noted that extreme temperature stress (8 °C) resulted in very strong dormancy incidence, which strongly reduced the differences seen at less extreme temperatures. We conclude that dormancy in Drosophila should not be considered a special trait, but is better understood as a generic stress response occurring at low temperatures.
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Affiliation(s)
- Manolis Lirakis
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria; Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria.
| | - Marlies Dolezal
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210 Wien, Austria
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38
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Kilgour RJ, McAdam AG, Betini GS, Norris DR. Experimental evidence that density mediates negative frequency-dependent selection on aggression. J Anim Ecol 2018; 87:1091-1101. [PMID: 29446094 DOI: 10.1111/1365-2656.12813] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/25/2018] [Indexed: 11/28/2022]
Abstract
Aggression can be beneficial in competitive environments if aggressive individuals are more likely to access resources than non-aggressive individuals. However, variation in aggressive behaviour persists within populations, suggesting that high levels of aggression might not always be favoured. The goal of this study was to experimentally assess the effects of population density and phenotypic frequency on selection on aggression in a competitive environment. We compared survival of two strains of Drosophila melanogaster that differ in aggression across three density treatments and five frequency treatments (single strain groups, equal numbers of each strain and strains mixed at 3:1 and 1:3 ratios) during a period of limited resources. While there was no difference in survival across single-strain treatments, survival was strongly density dependent, with declining survival as density increased. Furthermore, at medium and high densities, there was evidence of negative frequency-dependent selection, where rare strains experienced greater survival than common strains. However, there was no evidence of negative frequency-dependent selection at low density. Our results indicate that the benefits of aggression during periods of limited resources can depend on the interaction between the phenotypic composition of populations and population density, both of which are mechanisms that could maintain variation in aggressive behaviours within natural populations.
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Affiliation(s)
- R Julia Kilgour
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Andrew G McAdam
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Gustavo S Betini
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - D Ryan Norris
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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Anduaga AM, Nagy D, Costa R, Kyriacou CP. Diapause in Drosophila melanogaster - Photoperiodicity, cold tolerance and metabolites. JOURNAL OF INSECT PHYSIOLOGY 2018; 105:46-53. [PMID: 29339232 DOI: 10.1016/j.jinsphys.2018.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/11/2018] [Accepted: 01/11/2018] [Indexed: 06/07/2023]
Abstract
Unlike many insects where photoperiod per se induces diapause, reproductive arrest in Drosophila melanogaster adult females is observed at colder temperatures and can be enhanced by shorter photoperiods. Traditional experimental protocols raise flies at 25 °C from the larval stage and then the adults are placed at 12 °C for between 12 and 28 days. After 12 days diapause levels are usually higher than at 28 days, suggesting that the flies are in a cold induced quiescence, rather than a true diapause. By raising flies at more realistic lower temperatures, we observe quite dramatic and counter-intuitive effects on diapause, whose levels nevertheless correlate with various indices of cryoprotectant metabolites as well as resistance to chill shock. We also observe that photoperiodic effects are minimised when very small temperature oscillations associated with the light-dark incubator cycles are neutralised. Our results suggest that the reported photoperiodic component of fly diapause, at least in these strains, is mostly due to thermoperiodic rather than photoperiodic stimuli. In addition, the metabolite and chill shock analyses reveal that even by 12 days, flies are entering a state that is resistant to environmental stresses.
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Affiliation(s)
- Ane Martin Anduaga
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Dora Nagy
- Department of Biology, University of Padova, Padova 35131, Italy
| | - Rodolfo Costa
- Department of Biology, University of Padova, Padova 35131, Italy
| | - Charalambos P Kyriacou
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
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40
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Kreß A, Oppold AM, Kuch U, Oehlmann J, Müller R. Cold tolerance of the Asian tiger mosquito Aedes albopictus and its response to epigenetic alterations. JOURNAL OF INSECT PHYSIOLOGY 2017; 99:113-121. [PMID: 28396211 DOI: 10.1016/j.jinsphys.2017.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 06/07/2023]
Abstract
Phenotypic plasticity is considered as one of the key traits responsible for the establishment of populations of the invasive mosquito Aedes albopictus, an important vector of viral and parasitic pathogens. The successful spread of this species to higher altitudes and latitudes may be explained by its ability to rapidly induce a heritable low-temperature phenotype (cold hardiness in eggs). As a result of the low genetic diversity of founder populations, an epigenetic short-term mechanism has been suggested as the driver of this diversification. We investigated if random epigenetic alterations promoted the cold hardiness of Ae. albopictus eggs from a transgenerational study of two epigenetic agents (genistein and vinclozolin). To this end, we evaluated changes in lethal time for 50% of pharate larvae (Lt50) from eggs exposed to -2°C in two subsequent generations that used a new dose-response test design. We detected a significant diversification of the cold hardiness of eggs (up to 64.5%) that was associated with the epigenetic change in the two subsequent offspring generations. An effect size of epigenetically modulated cold hardiness of this magnitude is likely to have an impact on the spatial distribution of this species. Our results provide a framework for further research on epigenetic temperature adaptation of invasive species to better explain and predict their rapid range expansions.
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Affiliation(s)
- Aljoscha Kreß
- Senckenberg Biodiversity and Climate Research Centre, Department Adaptation and Climate, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; Goethe University Frankfurt am Main, Department Aquatic Ecotoxicology, Institute for Ecology, Evolution & Diversity, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany.
| | - Ann-Marie Oppold
- Senckenberg Biodiversity and Climate Research Centre, Department Adaptation and Climate, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; Goethe University Frankfurt am Main, Molecular Ecology Group, Institute for Ecology, Evolution & Diversity, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - Ulrich Kuch
- Goethe University Frankfurt am Main, Institute of Occupational Medicine, Social Medicine and Environmental Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Jörg Oehlmann
- Senckenberg Biodiversity and Climate Research Centre, Department Adaptation and Climate, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; Goethe University Frankfurt am Main, Department Aquatic Ecotoxicology, Institute for Ecology, Evolution & Diversity, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - Ruth Müller
- Goethe University Frankfurt am Main, Institute of Occupational Medicine, Social Medicine and Environmental Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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41
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Allen SL, Bonduriansky R, Sgro CM, Chenoweth SF. Sex-biased transcriptome divergence along a latitudinal gradient. Mol Ecol 2017; 26:1256-1272. [PMID: 28100025 DOI: 10.1111/mec.14015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 11/23/2016] [Accepted: 11/28/2016] [Indexed: 12/26/2022]
Abstract
Sex-dependent gene expression is likely an important genomic mechanism that allows sex-specific adaptation to environmental changes. Among Drosophila species, sex-biased genes display remarkably consistent evolutionary patterns; male-biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex-biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex-specific selection and the evolution of sex-biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11 631 genes across eight populations revealed strong sex differences in the frequency, mode and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male-biased genes, there was no overrepresentation of X-linked genes in males. By contrast, X-linked divergence was elevated in females, especially for female-biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in Drosophila simulans and Drosophila melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro- and micro-ecological spatial scales.
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Affiliation(s)
- Scott L Allen
- The School of Biological Sciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
| | - Russell Bonduriansky
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Carla M Sgro
- School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
| | - Stephen F Chenoweth
- The School of Biological Sciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
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42
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Betini GS, McAdam AG, Griswold CK, Norris DR. A fitness trade-off between seasons causes multigenerational cycles in phenotype and population size. eLife 2017; 6:e18770. [PMID: 28164780 PMCID: PMC5340529 DOI: 10.7554/elife.18770] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 02/06/2017] [Indexed: 11/17/2022] Open
Abstract
Although seasonality is widespread and can cause fluctuations in the intensity and direction of natural selection, we have little information about the consequences of seasonal fitness trade-offs for population dynamics. Here we exposed populations of Drosophila melanogaster to repeated seasonal changes in resources across 58 generations and used experimental and mathematical approaches to investigate how viability selection on body size in the non-breeding season could affect demography. We show that opposing seasonal episodes of natural selection on body size interacted with both direct and delayed density dependence to cause populations to undergo predictable multigenerational density cycles. Our results provide evidence that seasonality can set the conditions for life-history trade-offs and density dependence, which can, in turn, interact to cause multigenerational population cycles.
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Affiliation(s)
- Gustavo S Betini
- Department of Integrative Biology, University of Guelph, Guelph, Canada
| | - Andrew G McAdam
- Department of Integrative Biology, University of Guelph, Guelph, Canada
| | | | - D Ryan Norris
- Department of Integrative Biology, University of Guelph, Guelph, Canada
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43
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Akhund-Zade J, Bergland AO, Crowe SO, Unckless RL. The Genetic Basis of Natural Variation in Drosophila (Diptera: Drosophilidae) Virgin Egg Retention. JOURNAL OF INSECT SCIENCE (ONLINE) 2017; 17:iew094. [PMID: 28042107 PMCID: PMC5270406 DOI: 10.1093/jisesa/iew094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Indexed: 06/06/2023]
Abstract
Drosophila melanogaster is able to thrive in harsh northern climates through adaptations in life-history traits and physiological mechanisms that allow for survival through the winter. We examined the genetic basis of natural variation in one such trait, female virgin egg retention, which was previously shown to vary clinally and seasonally. To further our understanding of the genetic basis and evolution of virgin egg retention, we performed a genome-wide association study (GWAS) using the previously sequenced Drosophila Genetic Reference Panel (DGRP) mapping population. We found 29 single nucleotide polymorphisms (SNPs) associated with virgin egg retention and assayed 6 available mutant lines, each harboring a mutation in a candidate gene, for effects on egg retention time. We found that four out of the six mutant lines had defects in egg retention time as compared with the respective controls: mun, T48, Mes-4, and Klp67A Surprisingly, none of these genes has a recognized role in ovulation control, but three of the four genes have known effects on fertility or have high expression in the ovaries. We also found that the SNP set associated with egg retention time was enriched for clinal SNPs. The majority of clinal SNPs had alleles associated with longer egg retention present at higher frequencies in higher latitudes. Our results support previous studies that show higher frequency of long retention times at higher latitude, providing evidence for the adaptive value of virgin egg-retention.
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Affiliation(s)
- Jamilla Akhund-Zade
- Department of Biology, Stanford University, 371 Serra Street, Palo Alto, CA 94305
- Department of Organismal and Evolutionary Biology, Harvard University, Northwest Labs 248, Cambridge, MA 02138
| | - Alan O Bergland
- Department of Biology, Stanford University, 371 Serra Street, Palo Alto, CA 94305
- Department of Biology, University of Virginia, 063A Gilmer Hall, Charlottesville, VA 22903
| | - Sarah O Crowe
- Department of Entomology, Cornell University, 3125 Comstock Hall, Ithaca, 14853 NY
| | - Robert L Unckless
- Department of Entomology, Cornell University, 3125 Comstock Hall, Ithaca, 14853 NY
- Department of Molecular Biosciences, University of Kansas, 4055 Haworth Hall, Lawrence, KS 66045
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44
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Mathur V, Schmidt PS. Adaptive patterns of phenotypic plasticity in laboratory and field environments in Drosophila melanogaster. Evolution 2016; 71:465-474. [PMID: 27925178 DOI: 10.1111/evo.13144] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 11/08/2016] [Accepted: 11/13/2016] [Indexed: 01/19/2023]
Abstract
Identifying mechanisms of adaptation to variable environments is essential in developing a comprehensive understanding of evolutionary dynamics in natural populations. Phenotypic plasticity allows for phenotypic change in response to changes in the environment, and as such may play a major role in adaptation to environmental heterogeneity. Here, the plasticity of stress response in Drosophila melanogaster originating from two distinct geographic regions and ecological habitats was examined. Adults were given a short-term, 5-day exposure to combinations of temperature and photoperiod to elicit a plastic response for three fundamental aspects of stress tolerance that vary adaptively with geography. This was replicated both in the laboratory and in outdoor enclosures in the field. In the laboratory, geographic origin was the primary determinant of the stress response. Temperature and the interaction between temperature and photoperiod also significantly affected stress resistance. In the outdoor enclosures, plasticity was distinct among traits and between geographic regions. These results demonstrate that short-term exposure of adults to ecologically relevant environmental cues results in predictable effects on multiple aspects of fitness. These patterns of plasticity vary among traits and are highly distinct between the two examined geographic regions, consistent with patterns of local adaptation to climate and associated environmental parameters.
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Affiliation(s)
- Vinayak Mathur
- Department of Biology, University of Pennsylvania, 433 S. University Avenue, Philadelphia, Pennsylvania, 19104.,Current Address: Department of Biology, Georgetown University, Washington, District of Columbia, 20057
| | - Paul S Schmidt
- Department of Biology, University of Pennsylvania, 433 S. University Avenue, Philadelphia, Pennsylvania, 19104
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45
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Rajpurohit S, Hanus R, Vrkoslav V, Behrman EL, Bergland AO, Petrov D, Cvačka J, Schmidt PS. Adaptive dynamics of cuticular hydrocarbons in Drosophila. J Evol Biol 2016; 30:66-80. [PMID: 27718537 DOI: 10.1111/jeb.12988] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/04/2016] [Accepted: 10/06/2016] [Indexed: 01/19/2023]
Abstract
Cuticular hydrocarbons (CHCs) are hydrophobic compounds deposited on the arthropod cuticle that are of functional significance with respect to stress tolerance, social interactions and mating dynamics. We characterized CHC profiles in natural populations of Drosophila melanogaster at five levels: across a latitudinal transect in the eastern United States, as a function of developmental temperature during culture, across seasonal time in replicate years, and as a function of rapid evolution in experimental mesocosms in the field. Furthermore, we also characterized spatial and temporal changes in allele frequencies for SNPs in genes that are associated with the production and chemical profile of CHCs. Our data demonstrate a striking degree of parallelism for clinal and seasonal variation in CHCs in this taxon; CHC profiles also demonstrate significant plasticity in response to rearing temperature, and the observed patterns of plasticity parallel the spatiotemporal patterns observed in nature. We find that these congruent shifts in CHC profiles across time and space are also mirrored by predictable shifts in allele frequencies at SNPs associated with CHC chain length. Finally, we observed rapid and predictable evolution of CHC profiles in experimental mesocosms in the field. Together, these data strongly suggest that CHC profiles respond rapidly and adaptively to environmental parameters that covary with latitude and season, and that this response reflects the process of local adaptation in natural populations of D. melanogaster.
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Affiliation(s)
- S Rajpurohit
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - R Hanus
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - V Vrkoslav
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - E L Behrman
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - A O Bergland
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - D Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
| | - J Cvačka
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - P S Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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46
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Altitudinal variation in lifespan of Drosophila melanogaster populations from the Firtina Valley, northeastern Turkey. J Therm Biol 2016; 61:91-97. [DOI: 10.1016/j.jtherbio.2016.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 11/21/2022]
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47
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Schiesari L, Andreatta G, Kyriacou CP, O’Connor MB, Costa R. The Insulin-Like Proteins dILPs-2/5 Determine Diapause Inducibility in Drosophila. PLoS One 2016; 11:e0163680. [PMID: 27689881 PMCID: PMC5045170 DOI: 10.1371/journal.pone.0163680] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 09/12/2016] [Indexed: 01/28/2023] Open
Abstract
Diapause is an actively induced dormancy that has evolved in Metazoa to resist environmental stresses. In temperate regions, many diapausing insects overwinter at low temperatures by blocking embryonic, larval or adult development. Despite its Afro-tropical origin, Drosophila melanogaster migrated to temperate regions of Asia and Europe where females overwinter as adults by arresting gonadal development (reproductive diapause) at temperatures <13°C. Recent work in D. melanogaster has implicated the developmental hormones dILPs-2 and/or dILP3, and dILP5, homologues of vertebrate insulin/insulin-like growth factors (IGFs), in reproductive arrest. However, polymorphisms in timeless (tim) and couch potato (cpo) dramatically affect diapause inducibility and these dILP experiments could not exclude this common genetic variation contributing to the diapause phenotype. Here, we apply an extensive genetic dissection of the insulin signaling pathway which allows us to see both enhancements and reductions in egg development that are independent of tim and cpo variations. We show that a number of manipulations dramatically enhance diapause to ~100%. These include ablating, or reducing the excitability of the insulin-producing cells (IPCs) that express dILPs-2,3,5 employing the dilp2,3,5-/- triple mutant, desensitizing insulin signaling using a chico mutation, or inhibiting dILP2 and 5 in the hemolymph by over-expressing Imaginal Morphogenesis Protein-Late 2 (Imp-L2). In addition, triple mutant dilp2,3,5-/- females maintain high levels of diapause even when temperatures are raised in adulthood to 19°C. However at 22°C, these females all show egg development revealing that the effects are conditional on temperature and not a general female sterility. In contrast, over-expression of dilps-2/5 or enhancing IPC excitability, led to levels of ovarian arrest that approached zero, underscoring dILPs-2 and 5 as key antagonists of diapause.
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Affiliation(s)
- Luca Schiesari
- Department of Biology, University of Padova, Padova, Italy
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States of America
| | | | | | - Michael B. O’Connor
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States of America
| | - Rodolfo Costa
- Department of Biology, University of Padova, Padova, Italy
- * E-mail:
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48
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Porcelli D, Westram AM, Pascual M, Gaston KJ, Butlin RK, Snook RR. Gene expression clines reveal local adaptation and associated trade-offs at a continental scale. Sci Rep 2016; 6:32975. [PMID: 27599812 PMCID: PMC5013434 DOI: 10.1038/srep32975] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/18/2016] [Indexed: 01/03/2023] Open
Abstract
Local adaptation, where fitness in one environment comes at a cost in another, should lead to spatial variation in trade-offs between life history traits and may be critical for population persistence. Recent studies have sought genomic signals of local adaptation, but often have been limited to laboratory populations representing two environmentally different locations of a species’ distribution. We measured gene expression, as a proxy for fitness, in males of Drosophila subobscura, occupying a 20° latitudinal and 11 °C thermal range. Uniquely, we sampled six populations and studied both common garden and semi-natural responses to identify signals of local adaptation. We found contrasting patterns of investment: transcripts with expression positively correlated to latitude were enriched for metabolic processes, expressed across all tissues whereas negatively correlated transcripts were enriched for reproductive processes, expressed primarily in testes. When using only the end populations, to compare our results to previous studies, we found that locally adaptive patterns were obscured. While phenotypic trade-offs between metabolic and reproductive functions across widespread species are well-known, our results identify underlying genetic and tissue responses at a continental scale that may be responsible for this. This may contribute to understanding population persistence under environmental change.
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Affiliation(s)
- Damiano Porcelli
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Anja M Westram
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Marta Pascual
- Departament de Genètica, Microbiologia I Estabdistica and IrBio, Universitat de Barcelona, Barcelona 08028, ES
| | - Kevin J Gaston
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Rhonda R Snook
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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49
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Kankare M, Parker DJ, Merisalo M, Salminen TS, Hoikkala A. Transcriptional Differences between Diapausing and Non-Diapausing D. montana Females Reared under the Same Photoperiod and Temperature. PLoS One 2016; 11:e0161852. [PMID: 27571415 PMCID: PMC5003386 DOI: 10.1371/journal.pone.0161852] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 08/13/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND A wide range of insects living at higher latitudes enter diapause at the end of the warm season, which increases their chances of survival through harsh winter conditions. In this study we used RNA sequencing to identify genes involved in adult reproductive diapause in a northern fly species, Drosophila montana. Both diapausing and non-diapausing flies were reared under a critical day length and temperature, where about half of the emerging females enter diapause enabling us to eliminate the effects of varying environmental conditions on gene expression patterns of the two types of female flies. RESULTS RNA sequencing revealed large differences between gene expression patterns of diapausing and non-diapausing females, especially in genes involved with metabolism, fatty acid biosynthesis, and metal and nucleotide binding. Differently expressed genes included several gene groups, including myosin, actin and cytochromeP450 genes, which have been previously associated with diapause. This study also identified new candidate genes, including some involved in cuticular hydrocarbon synthesis or regulation (desat1 and desat2), and acyl-CoA Δ11-desaturase activity (CG9747), and few odorant-binding protein genes (e.g. Obp44A). Also, several transposable elements (TEs) showed differential expression between the two female groups motivating future research on their roles in diapause. CONCLUSIONS Our results demonstrate that the adult reproductive diapause in D. montana involves changes in the expression level of a variety of genes involved in key processes (e.g. metabolism and fatty acid biosynthesis) which help diapausing females to cope with overwintering. This is consistent with the view that diapause is a complex adaptive phenotype where not only sexual maturation is arrested, but also changes in adult physiology are required in order to survive over the winter.
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Affiliation(s)
- Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä, Finland
| | - Darren J. Parker
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä, Finland
- Centre for Biological Diversity, School of Biology, University of St Andrews, Fife, KY16 9TH, St Andrews, United Kingdom
| | - Mikko Merisalo
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä, Finland
| | - Tiina S. Salminen
- BioMediTech, Biokatu 6, F1-33014, University of Tampere, Tampere, Finland
| | - Anneli Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä, Finland
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50
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Xiao L, He H, Huang L, Geng T, Fu S, Xue F. Variation of life-history traits of the Asian corn borer, Ostrinia furnacalis in relation to temperature and geographical latitude. Ecol Evol 2016; 6:5129-43. [PMID: 27551371 PMCID: PMC4984492 DOI: 10.1002/ece3.2275] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/31/2016] [Accepted: 06/03/2016] [Indexed: 01/04/2023] Open
Abstract
Life-history traits from four geographical populations (tropical Ledong population [LD], subtropical Guangzhou [GZ] and Yongxiu populations, and temperate Langfang population [LF]) of the Asian corn borer, Ostrinia furnacalis were investigated at a wide range of temperatures (20-32°C). The larval and pupal times were significantly decreased with increasing rearing temperature, and growth rate was positively correlated with temperature. The relationship between body weight and rearing temperature in O. furnacalis did not follow the temperature-size rule (TSR); all populations exhibited the highest pupal and adult weights at high temperatures or intermediate temperatures. However, development time, growth rate, and body weight did not show a constant latitudinal gradient. Across all populations at each temperature, female were significantly bigger than males, showing a female-biased sexual size dimorphism (SSD). Contrary to Rensch's rule, the SSD tended to increase with rising temperature. The subtropical GZ population exhibited the largest degree of dimorphism while the temperate LF exhibited the smallest. Male pupae lose significantly more weight at metamorphosis compared to females. The proportionate weight losses of different populations were significantly different. Adult longevity was significantly decreased with increasing temperature. Between sexes, all populations exhibit a rather female-biased adult longevity. Finally, we discuss the adaptive significance of higher temperature-inducing high body weight in the moth's life history and why the moth exhibits the reverse TSR.
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Affiliation(s)
- Liang Xiao
- Institute of EntomologyJiangxi Agricultural UniversityNanchangChina
| | - Hai‐Min He
- Institute of EntomologyJiangxi Agricultural UniversityNanchangChina
| | - Li‐Li Huang
- Jiangxi Entry Exit Inspection and Quarantine BureauNanchangChina
| | - Ting Geng
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Shu Fu
- Institute of EntomologyJiangxi Agricultural UniversityNanchangChina
| | - Fang‐Sen Xue
- Institute of EntomologyJiangxi Agricultural UniversityNanchangChina
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