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Keller AG, Dahlhoff EP, Bracewell R, Chatla K, Bachtrog D, Rank NE, Williams CM. Multi-locus genomic signatures of local adaptation to snow across the landscape in California populations of a willow leaf beetle. Proc Biol Sci 2023; 290:20230630. [PMID: 37583321 PMCID: PMC10427825 DOI: 10.1098/rspb.2023.0630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/14/2023] [Indexed: 08/17/2023] Open
Abstract
Organisms living in mountains contend with extreme climatic conditions, including short growing seasons and long winters with extensive snow cover. Anthropogenic climate change is driving unprecedented, rapid warming of montane regions across the globe, resulting in reduced winter snowpack. Loss of snow as a thermal buffer may have serious consequences for animals overwintering in soil, yet little is known about how variability in snowpack acts as a selective agent in montane ecosystems. Here, we examine genomic variation in California populations of the leaf beetle Chrysomela aeneicollis, an emerging natural model system for understanding how organisms respond to climate change. We used a genotype-environment association approach to identify genomic signatures of local adaptation to microclimate in populations from three montane regions with variable snowpack and a coastal region with no snow. We found that both winter-associated environmental variation and geographical distance contribute to overall genomic variation across the landscape. We identified non-synonymous variation in novel candidate loci associated with cytoskeletal function, ion transport and membrane stability, cellular processes associated with cold tolerance in other insects. These findings provide intriguing evidence that variation in snowpack imposes selective gradients in montane ecosystems.
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Affiliation(s)
- Abigail G. Keller
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | | | - Ryan Bracewell
- Department of Biology, Indiana University Bloomington, Bloomington, IN, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Nathan E. Rank
- Department of Biology, Sonoma State University, Rohnert Park, CA, USA
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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: 1] [Impact Index Per Article: 0.5] [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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3
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Önder BŞ, Aksoy CF. Seasonal variation in wing size and shape of Drosophila melanogaster reveals rapid adaptation to environmental changes. Sci Rep 2022; 12:14622. [PMID: 36028640 PMCID: PMC9418266 DOI: 10.1038/s41598-022-18891-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
Populations in seasonal fluctuating environments receive multiple environmental cues and must deal with this heterogenic environment to survive and reproduce. An enlarged literature shows that this situation can be resolved through rapid adaptation in Drosophila melanogaster populations. Long-term monitoring of a population in its natural habitat and quantitative measurement of its responses to seasonal environmental changes are important for understanding the adaptive response of D. melanogaster to temporal variable selection. Here, we use inbred lines of a D. melanogaster population collected at monthly intervals between May to October over a temporal scale spanning three consecutive years to understand the variation in wing size and wing shape over these timepoints. The wing size and shape of this population changed significantly between months and a seasonal cycle of this traits is repeated for three years. Our results suggest that the effects of environmental variables that generated variation in body size between populations such as latitudinal clines, are a selective pressure in a different manner in terms of seasonal variation. Temperature related variable have a significant nonlinear relation to this fluctuating pattern in size and shape, whereas precipitation and humidity have a sex-specific effect which is more significant in males.
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Affiliation(s)
- Banu Şebnem Önder
- Genetic Variation and Adaptation Laboratory, Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey.
| | - Cansu Fidan Aksoy
- Genetic Variation and Adaptation Laboratory, Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
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4
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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: 5] [Impact Index Per Article: 1.7] [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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5
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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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Williams CM, Ragland GJ, Betini G, Buckley LB, Cheviron ZA, Donohue K, Hereford J, Humphries MM, Lisovski S, Marshall KE, Schmidt PS, Sheldon KS, Varpe Ø, Visser ME. Understanding Evolutionary Impacts of Seasonality: An Introduction to the Symposium. Integr Comp Biol 2018; 57:921-933. [PMID: 29045649 DOI: 10.1093/icb/icx122] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Seasonality is a critically important aspect of environmental variability, and strongly shapes all aspects of life for organisms living in highly seasonal environments. Seasonality has played a key role in generating biodiversity, and has driven the evolution of extreme physiological adaptations and behaviors such as migration and hibernation. Fluctuating selection pressures on survival and fecundity between summer and winter provide a complex selective landscape, which can be met by a combination of three outcomes of adaptive evolution: genetic polymorphism, phenotypic plasticity, and bet-hedging. Here, we have identified four important research questions with the goal of advancing our understanding of evolutionary impacts of seasonality. First, we ask how characteristics of environments and species will determine which adaptive response occurs. Relevant characteristics include costs and limits of plasticity, predictability, and reliability of cues, and grain of environmental variation relative to generation time. A second important question is how phenological shifts will amplify or ameliorate selection on physiological hardiness. Shifts in phenology can preserve the thermal niche despite shifts in climate, but may fail to completely conserve the niche or may even expose life stages to conditions that cause mortality. Considering distinct environmental sensitivities of life history stages will be key to refining models that forecast susceptibility to climate change. Third, we must identify critical physiological phenotypes that underlie seasonal adaptation and work toward understanding the genetic architectures of these responses. These architectures are key for predicting evolutionary responses. Pleiotropic genes that regulate multiple responses to changing seasons may facilitate coordination among functionally related traits, or conversely may constrain the expression of optimal phenotypes. Finally, we must advance our understanding of how changes in seasonal fluctuations are impacting ecological interaction networks. We should move beyond simple dyadic interactions, such as predator prey dynamics, and understand how these interactions scale up to affect ecological interaction networks. As global climate change alters many aspects of seasonal variability, including extreme events and changes in mean conditions, organisms must respond appropriately or go extinct. The outcome of adaptation to seasonality will determine responses to climate change.
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Affiliation(s)
- Caroline M Williams
- Department of Integrative Biology, University of California, 3040 Valley Life Sciences Building, Berkeley, CA 94705, USA
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado, Denver, CO, USA
| | - Gustavo Betini
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Lauren B Buckley
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | | | - Joe Hereford
- Department of Ecology and Evolution, University of California, Davis, CA, USA
| | - Murray M Humphries
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
| | - Simeon Lisovski
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA, USA
| | | | - Paul S Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Kimberly S Sheldon
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
| | - Øystein Varpe
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, Norway.,Akvaplan-niva, Fram Centre, Tromsø, Norway
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands
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7
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Kapun M, Fabian DK, Goudet J, Flatt T. Genomic Evidence for Adaptive Inversion Clines in Drosophila melanogaster. Mol Biol Evol 2016; 33:1317-36. [PMID: 26796550 DOI: 10.1093/molbev/msw016] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Clines in chromosomal inversion polymorphisms-presumably driven by climatic gradients-are common but there is surprisingly little evidence for selection acting on them. Here we address this long-standing issue in Drosophila melanogaster by using diagnostic single nucleotide polymorphism (SNP) markers to estimate inversion frequencies from 28 whole-genome Pool-seq samples collected from 10 populations along the North American east coast. Inversions In(3L)P, In(3R)Mo, and In(3R)Payne showed clear latitudinal clines, and for In(2L)t, In(2R)NS, and In(3R)Payne the steepness of the clinal slopes changed between summer and fall. Consistent with an effect of seasonality on inversion frequencies, we detected small but stable seasonal fluctuations of In(2R)NS and In(3R)Payne in a temperate Pennsylvanian population over 4 years. In support of spatially varying selection, we observed that the cline in In(3R)Payne has remained stable for >40 years and that the frequencies of In(2L)t and In(3R)Payne are strongly correlated with climatic factors that vary latitudinally, independent of population structure. To test whether these patterns are adaptive, we compared the amount of genetic differentiation of inversions versus neutral SNPs and found that the clines in In(2L)t and In(3R)Payne are maintained nonneutrally and independent of admixture. We also identified numerous clinal inversion-associated SNPs, many of which exhibit parallel differentiation along the Australian cline and reside in genes known to affect fitness-related traits. Together, our results provide strong evidence that inversion clines are maintained by spatially-and perhaps also temporally-varying selection. We interpret our data in light of current hypotheses about how inversions are established and maintained.
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Affiliation(s)
- Martin Kapun
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Daniel K Fabian
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Thomas Flatt
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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Behrman EL, Watson SS, O'Brien KR, Heschel MS, Schmidt PS. Seasonal variation in life history traits in two Drosophila species. J Evol Biol 2015; 28:1691-704. [PMID: 26174167 DOI: 10.1111/jeb.12690] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/30/2015] [Accepted: 07/01/2015] [Indexed: 01/16/2023]
Abstract
Seasonal environmental heterogeneity is cyclic, persistent and geographically widespread. In species that reproduce multiple times annually, environmental changes across seasonal time may create different selection regimes that may shape the population ecology and life history adaptation in these species. Here, we investigate how two closely related species of Drosophila in a temperate orchard respond to environmental changes across seasonal time. Natural populations of Drosophila melanogaster and Drosophila simulans were sampled at four timepoints from June through November to assess seasonal change in fundamental aspects of population dynamics as well as life history traits. D. melanogaster exhibit pronounced change across seasonal time: early in the season, the population is inferred to be uniformly young and potentially represents the early generation following overwintering survivorship. D. melanogaster isofemale lines derived from the early population and reared in a common garden are characterized by high tolerance to a variety of stressors as well as a fast rate of development in the laboratory environment that declines across seasonal time. In contrast, wild D. simulans populations were inferred to be consistently heterogeneous in age distribution across seasonal collections; only starvation tolerance changed predictably over seasonal time in a parallel manner as in D. melanogaster. These results suggest fundamental differences in population and evolutionary dynamics between these two taxa associated with seasonal heterogeneity in environmental parameters and associated selection pressures.
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Affiliation(s)
- E L Behrman
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - S S Watson
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - K R O'Brien
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - M S Heschel
- Department of Organismal Biology & Ecology, Colorado College, Colorado Springs, CO, USA
| | - P S Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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The Monopolization Hypothesis and the dispersal–gene flow paradox in aquatic organisms. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2002. [DOI: 10.1016/s1146-609x(02)01145-1] [Citation(s) in RCA: 538] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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