1
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Bitter MC, Berardi S, Oken H, Huynh A, Lappo E, Schmidt P, Petrov DA. Continuously fluctuating selection reveals fine granularity of adaptation. Nature 2024:10.1038/s41586-024-07834-x. [PMID: 39143223 DOI: 10.1038/s41586-024-07834-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 07/16/2024] [Indexed: 08/16/2024]
Abstract
Temporally fluctuating environmental conditions are a ubiquitous feature of natural habitats. Yet, how finely natural populations adaptively track fluctuating selection pressures via shifts in standing genetic variation is unknown1,2. Here we generated genome-wide allele frequency data every 1-2 generations from a genetically diverse population of Drosophila melanogaster in extensively replicated field mesocosms from late June to mid-December (a period of approximately 12 total generations). Adaptation throughout the fundamental ecological phases of population expansion, peak density and collapse was underpinned by extremely rapid, parallel changes in genomic variation across replicates. Yet, the dominant direction of selection fluctuated repeatedly, even within each of these ecological phases. Comparing patterns of change in allele frequency to an independent dataset procured from the same experimental system demonstrated that the targets of selection are predictable across years. In concert, our results reveal a fitness relevance of standing variation that is likely to be masked by inference approaches based on static population sampling or insufficiently resolved time-series data. We propose that such fine-scaled, temporally fluctuating selection may be an important force contributing to the maintenance of functional genetic variation in natural populations and an important stochastic force impacting genome-wide patterns of diversity at linked neutral sites, akin to genetic draft.
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Affiliation(s)
- M C Bitter
- Department of Biology, Stanford University, Stanford, CA, USA.
| | - S Berardi
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - H Oken
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - A Huynh
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Egor Lappo
- Department of Biology, Stanford University, Stanford, CA, USA
| | - P Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - D A Petrov
- Department of Biology, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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2
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Brud E. Season-specific dominance broadly stabilizes polymorphism under symmetric and asymmetric multivoltinism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.20.567918. [PMID: 38045349 PMCID: PMC10690222 DOI: 10.1101/2023.11.20.567918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Seasonality causes intraannual fitness changes in multivoltine populations (defined as having multiple generations per year). While it is well-known that seasonally balanced polymorphism is established by overdominance in geometric mean fitness, an unsettled aspect of the deterministic theory is the relative contribution of various season-specific dominance mechanisms to the potential for polymorphism. In particular, the relative importance of seasonally-reversing and non-reversing schemes remains unclear. Here I analyze the parameter space for the discrete generation two-season multivoltine model and conclude that, in general, a substantial fraction of stabilizing schemes are non-reversing with the season (~25-50%). In addition, I derive the approximate equilibrium allele frequency cycle under bivoltinism, and find that the amplitude of allelic oscillation is maximized by non-reversing dominance if the selection coefficients are roughly symmetric. Lastly, I derive conditions for the intralocus evolution of dominance. These predict a long-term trend toward maximally beneficial reversal. Overall, the results counter the disproportionate emphasis placed on dominance reversal as a stabilizing mechanism and clarify that non-reversing dominance is expected to frequently characterize seasonally fluctuating alleles under both weak and strong selection, especially in their early history. I conclude that seasonally alternating selection regimes are easily able to maintain allelic variation without restrictive assumptions on either selection coefficients or dominance parameters.
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Affiliation(s)
- Evgeny Brud
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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3
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Grieshop K, Ho EKH, Kasimatis KR. Dominance reversals: the resolution of genetic conflict and maintenance of genetic variation. Proc Biol Sci 2024; 291:20232816. [PMID: 38471544 DOI: 10.1098/rspb.2023.2816] [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: 06/02/2023] [Accepted: 02/05/2024] [Indexed: 03/14/2024] Open
Abstract
Beneficial reversals of dominance reduce the costs of genetic trade-offs and can enable selection to maintain genetic variation for fitness. Beneficial dominance reversals are characterized by the beneficial allele for a given context (e.g. habitat, developmental stage, trait or sex) being dominant in that context but recessive where deleterious. This context dependence at least partially mitigates the fitness consequence of heterozygotes carrying one non-beneficial allele for their context and can result in balancing selection that maintains alternative alleles. Dominance reversals are theoretically plausible and are supported by mounting empirical evidence. Here, we highlight the importance of beneficial dominance reversals as a mechanism for the mitigation of genetic conflict and review the theory and empirical evidence for them. We identify some areas in need of further research and development and outline three methods that could facilitate the identification of antagonistic genetic variation (dominance ordination, allele-specific expression and allele-specific ATAC-Seq (assay for transposase-accessible chromatin with sequencing)). There is ample scope for the development of new empirical methods as well as reanalysis of existing data through the lens of dominance reversals. A greater focus on this topic will expand our understanding of the mechanisms that resolve genetic conflict and whether they maintain genetic variation.
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Affiliation(s)
- Karl Grieshop
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada M5S 1A1
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Eddie K H Ho
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202, USA
| | - Katja R Kasimatis
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada M5S 1A1
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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4
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Rybnikov SR, Hübner S, Korol AB. A Numerical Model Supports the Evolutionary Advantage of Recombination Plasticity in Shifting Environments. Am Nat 2024; 203:E78-E91. [PMID: 38358806 DOI: 10.1086/728405] [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] [Indexed: 02/17/2024]
Abstract
AbstractNumerous empirical studies have witnessed an increase in meiotic recombination rate in response to physiological stress imposed by unfavorable environmental conditions. Thus, inherited plasticity in recombination rate is hypothesized to be evolutionarily advantageous in changing environments. Previous theoretical models proceeded from the assumption that organisms increase their recombination rate when the environment becomes more stressful and demonstrated the evolutionary advantage of such a form of plasticity. Here, we numerically explore a complementary scenario-when the plastic increase in recombination rate is triggered by the environmental shifts. Specifically, we assume increased recombination in individuals developing in a different environment than their parents and, optionally, also in offspring of such individuals. We show that such shift-inducible recombination is always superior when the optimal constant recombination implies an intermediate rate. Moreover, under certain conditions, plastic recombination may also appear beneficial when the optimal constant recombination is either zero or free. The advantage of plastic recombination was better predicted by the range of the population's mean fitness over the period of environmental fluctuations, compared with the geometric mean fitness. These results hold for both panmixia and partial selfing, with faster dynamics of recombination modifier alleles under selfing. We think that recombination plasticity can be acquired under the control of environmentally responsive mechanisms, such as chromatin epigenetics remodeling.
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5
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Bitter MC, Berardi S, Oken H, Huynh A, Schmidt P, Petrov DA. Continuously fluctuating selection reveals extreme granularity and parallelism of adaptive tracking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.562586. [PMID: 37904939 PMCID: PMC10614893 DOI: 10.1101/2023.10.16.562586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Temporally fluctuating environmental conditions are a ubiquitous feature of natural habitats. Yet, how finely natural populations adaptively track fluctuating selection pressures via shifts in standing genetic variation is unknown. We generated high-frequency, genome-wide allele frequency data from a genetically diverse population of Drosophila melanogaster in extensively replicated field mesocosms from late June to mid-December, a period of ∼12 generations. Adaptation throughout the fundamental ecological phases of population expansion, peak density, and collapse was underpinned by extremely rapid, parallel changes in genomic variation across replicates. Yet, the dominant direction of selection fluctuated repeatedly, even within each of these ecological phases. Comparing patterns of allele frequency change to an independent dataset procured from the same experimental system demonstrated that the targets of selection are predictable across years. In concert, our results reveal fitness-relevance of standing variation that is likely to be masked by inference approaches based on static population sampling, or insufficiently resolved time-series data. We propose such fine-scaled temporally fluctuating selection may be an important force maintaining functional genetic variation in natural populations and an important stochastic force affecting levels of standing genetic variation genome-wide.
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6
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Nunez JCB, Lenhart BA, Bangerter A, Murray CS, Mazzeo GR, Yu Y, Nystrom TL, Tern C, Erickson PA, Bergland AO. A cosmopolitan inversion facilitates seasonal adaptation in overwintering Drosophila. Genetics 2024; 226:iyad207. [PMID: 38051996 PMCID: PMC10847723 DOI: 10.1093/genetics/iyad207] [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: 10/08/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
Fluctuations in the strength and direction of natural selection through time are a ubiquitous feature of life on Earth. One evolutionary outcome of such fluctuations is adaptive tracking, wherein populations rapidly adapt from standing genetic variation. In certain circumstances, adaptive tracking can lead to the long-term maintenance of functional polymorphism despite allele frequency change due to selection. Although adaptive tracking is likely a common process, we still have a limited understanding of aspects of its genetic architecture and its strength relative to other evolutionary forces such as drift. Drosophila melanogaster living in temperate regions evolve to track seasonal fluctuations and are an excellent system to tackle these gaps in knowledge. By sequencing orchard populations collected across multiple years, we characterized the genomic signal of seasonal demography and identified that the cosmopolitan inversion In(2L)t facilitates seasonal adaptive tracking and shows molecular footprints of selection. A meta-analysis of phenotypic studies shows that seasonal loci within In(2L)t are associated with behavior, life history, physiology, and morphological traits. We identify candidate loci and experimentally link them to phenotype. Our work contributes to our general understanding of fluctuating selection and highlights the evolutionary outcome and dynamics of contemporary selection on inversions.
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Affiliation(s)
- Joaquin C B Nunez
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
- Department of Biology, University of Vermont, 109 Carrigan Drive, Burlington, VT 05405, USA
| | - Benedict A Lenhart
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Alyssa Bangerter
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Connor S Murray
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Giovanni R Mazzeo
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Yang Yu
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Taylor L Nystrom
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Courtney Tern
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Priscilla A Erickson
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
- Department of Biology, University of Richmond, 138 UR Drive, Richmond, VA 23173, USA
| | - Alan O Bergland
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
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7
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Yamamichi M, Letten AD, Schreiber SJ. Eco-evolutionary maintenance of diversity in fluctuating environments. Ecol Lett 2023; 26 Suppl 1:S152-S167. [PMID: 37840028 DOI: 10.1111/ele.14286] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/23/2023] [Accepted: 06/24/2023] [Indexed: 10/17/2023]
Abstract
Growing evidence suggests that temporally fluctuating environments are important in maintaining variation both within and between species. To date, however, studies of genetic variation within a population have been largely conducted by evolutionary biologists (particularly population geneticists), while population and community ecologists have concentrated more on diversity at the species level. Despite considerable conceptual overlap, the commonalities and differences of these two alternative paradigms have yet to come under close scrutiny. Here, we review theoretical and empirical studies in population genetics and community ecology focusing on the 'temporal storage effect' and synthesise theories of diversity maintenance across different levels of biological organisation. Drawing on Chesson's coexistence theory, we explain how temporally fluctuating environments promote the maintenance of genetic variation and species diversity. We propose a further synthesis of the two disciplines by comparing models employing traditional frequency-dependent dynamics and those adopting density-dependent dynamics. We then address how temporal fluctuations promote genetic and species diversity simultaneously via rapid evolution and eco-evolutionary dynamics. Comparing and synthesising ecological and evolutionary approaches will accelerate our understanding of diversity maintenance in nature.
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Affiliation(s)
- Masato Yamamichi
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Andrew D Letten
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Sebastian J Schreiber
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California, USA
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8
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Kim Y. Partial protection from fluctuating selection leads to evolution towards wider population size fluctuation and a novel mechanism of balancing selection. Proc Biol Sci 2023; 290:20230822. [PMID: 37339748 PMCID: PMC10281806 DOI: 10.1098/rspb.2023.0822] [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: 12/20/2022] [Accepted: 05/26/2023] [Indexed: 06/22/2023] Open
Abstract
When a population is partially protected from fluctuating selection, as when a seed bank is present, variance in fitness will be reduced and reproductive success of the population will be promoted. This study further investigates the effect of such a 'refuge' from fluctuating selection using a mathematical model that couples demographic and evolutionary dynamics. While alleles that cause smaller fluctuations in population density should be positively selected according to classical theoretic predictions, this study finds the opposite: alleles that increase the amplitude of population size fluctuation are positively selected if population density is weakly regulated. Under strong density regulation with a constant carrying capacity, long-term maintenance of polymorphism caused by the storage effect emerges. However, if the carrying capacity of the population is oscillating, mutant alleles whose fitness fluctuates in the same direction as population size are positively selected, eventually reaching fixation or intermediate frequencies that oscillate over time. This oscillatory polymorphism, which requires fitness fluctuations that can arise with simple trade-offs in life-history traits, is a novel form of balancing selection. These results highlight the importance of allowing joint demographic and population genetic changes in models, the failure of which prevents the discovery of novel eco-evolutionary dynamics.
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Affiliation(s)
- Yuseob Kim
- Division of EcoScience and Department of Life Science, Ewha Womans University, Ewhayeodae-gil 52, Seodaemun-gu, Seoul 03760, Korea
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9
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Fluctuating selection and the determinants of genetic variation. Trends Genet 2023; 39:491-504. [PMID: 36890036 DOI: 10.1016/j.tig.2023.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 03/08/2023]
Abstract
Recent studies of cosmopolitan Drosophila populations have found hundreds to thousands of genetic loci with seasonally fluctuating allele frequencies, bringing temporally fluctuating selection to the forefront of the historical debate surrounding the maintenance of genetic variation in natural populations. Numerous mechanisms have been explored in this longstanding area of research, but these exciting empirical findings have prompted several recent theoretical and experimental studies that seek to better understand the drivers, dynamics, and genome-wide influence of fluctuating selection. In this review, we evaluate the latest evidence for multilocus fluctuating selection in Drosophila and other taxa, highlighting the role of potential genetic and ecological mechanisms in maintaining these loci and their impacts on neutral genetic variation.
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10
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Pfenninger M, Foucault Q. Population Genomic Time Series Data of a Natural Population Suggests Adaptive Tracking of Fluctuating Environmental Changes. Integr Comp Biol 2022; 62:1812-1826. [PMID: 35762661 DOI: 10.1093/icb/icac098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 01/05/2023] Open
Abstract
Natural populations are constantly exposed to fluctuating environmental changes that negatively affect their fitness in unpredictable ways. While theoretical models show the possibility of counteracting these environmental changes through rapid evolutionary adaptations, there have been few empirical studies demonstrating such adaptive tracking in natural populations. Here, we analyzed environmental data, fitness-related phenotyping and genomic time-series data sampled over 3 years from a natural Chironomus riparius (Diptera, Insecta) population to address this question. We show that the population's environment varied significantly on the time scale of the sampling in many selectively relevant dimensions, independently of each other. Similarly, phenotypic fitness components evolved significantly on the same temporal scale (mean 0.32 Haldanes), likewise independent from each other. The allele frequencies of 367,446 SNPs across the genome showed evidence of positive selection. Using temporal correlation of spatially coherent allele frequency changes revealed 35,574 haplotypes with more than one selected SNP. The mean selection coefficient for these haplotypes was 0.30 (s.d. = 0.68). The frequency changes of these haplotypes clustered in 46 different temporal patterns, indicating concerted, independent evolution of many polygenic traits. Nine of these patterns were strongly correlated with measured environmental variables. Enrichment analysis of affected genes suggested the implication of a wide variety of biological processes. Thus, our results suggest overall that the natural population of C. riparius tracks environmental change through rapid polygenic adaptation in many independent dimensions. This is further evidence that natural selection is pervasive at the genomic level and that evolutionary and ecological time scales may not differ at all, at least in some organisms.
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Affiliation(s)
- Markus Pfenninger
- Department Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128 Mainz, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Quentin Foucault
- Department Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,Institute for Molecular and Organismic Evolution, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 7, 55128 Mainz, Germany
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11
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Steinmetz B, Meyer I, Shnerb NM. Evolution in fluctuating environments: A generic modular approach. Evolution 2022; 76:2739-2757. [PMID: 36097355 PMCID: PMC9828023 DOI: 10.1111/evo.14616] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 07/23/2022] [Indexed: 01/22/2023]
Abstract
Evolutionary processes take place in fluctuating environments, where carrying capacities and selective forces vary over time. The fate of a mutant type and the persistence time of polymorphic states were studied in some specific cases of varying environments, but a generic methodology is still lacking. Here, we present such a general analytic framework. We first identify a set of elementary building blocks, a few basic demographic processes like logistic or exponential growth, competition at equilibrium, sudden decline, and so on. For each of these elementary blocks, we evaluate the mean and the variance of the changes in the frequency of the mutant population. Finally, we show how to find the relevant terms of the diffusion equation for each arbitrary combination of these blocks. Armed with this technique one may calculate easily the quantities that govern the evolutionary dynamics, like the chance of ultimate fixation, the time to absorption, and the time to fixation.
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Affiliation(s)
- Bnaya Steinmetz
- Department of PhysicsBar‐Ilan UniversityRamat‐GanIL52900Israel
| | - Immanuel Meyer
- Department of PhysicsBar‐Ilan UniversityRamat‐GanIL52900Israel
| | - Nadav M. Shnerb
- Department of PhysicsBar‐Ilan UniversityRamat‐GanIL52900Israel
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12
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Kozlov MV, Oudendijk Z, Forsman A, Lanta V, Barclay MVL, Gusarov VI, Gustafsson B, Huang ZZ, Kruglova OY, Marusik YM, Mikhailov YE, Mutanen M, Schneider A, Sekerka L, Sergeev ME, Zverev V, Zvereva EL. Climate shapes the spatiotemporal variation in color morph diversity and composition across the distribution range of Chrysomela lapponica leaf beetle. INSECT SCIENCE 2022; 29:942-955. [PMID: 34432950 DOI: 10.1111/1744-7917.12966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/19/2021] [Accepted: 08/22/2021] [Indexed: 06/13/2023]
Abstract
Color polymorphism offers rich opportunities for studying the eco-evolutionary mechanisms that drive the adaptations of local populations to heterogeneous and changing environments. We explored the color morph diversity and composition in a Chrysomela lapponica leaf beetle across its entire distribution range to test the hypothesis that environmental and climatic variables shape spatiotemporal variation in the phenotypic structure of a polymorphic species. We obtained information on 13 617 specimens of this beetle from museums, private collections, and websites. These specimens (collected from 1830-2020) originated from 959 localities spanning 33° latitude, 178° longitude, and 4200 m altitude. We classified the beetles into five color morphs and searched for environmental factors that could explain the variation in the level of polymorphism (quantified by the Shannon diversity index) and in the relative frequencies of individual color morphs. The highest level of polymorphism was found at high latitudes and altitudes. The color morphs differed in their climatic requirements; composition of colour morphs was independent of the geographic distance that separated populations but changed with collection year, longitude, mean July temperature and between-year temperature fluctuations. The proportion of melanic beetles, in line with the thermal melanism hypothesis, increased with increasing latitude and altitude and decreased with increasing climate seasonality. Melanic morph frequencies also declined during the past century, but only at high latitudes and altitudes where recent climate warming was especially strong. The observed patterns suggest that color polymorphism is especially advantageous for populations inhabiting unpredictable environments, presumably due to the different climatic requirements of coexisting color morphs.
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Affiliation(s)
| | - Zowi Oudendijk
- Department of Biology, University of Turku, Turku, Finland
- Department of Animal Ecology and Physiology, Radboud University, Nijmegen, The Netherlands
| | - Anders Forsman
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Vojtěch Lanta
- Institute of Botany, The Czech Academy of Sciences, Dukelská, Třeboň, Czech Republic
| | | | | | - Bert Gustafsson
- Departmant of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | | | | | - Yuri M Marusik
- Department of Biocenology, Institute for Biological Problems of the North, Far East Branch of the Russian Academy of Sciences, Magadan, Russia
- Department of Zoology & Entomology, University of the Free State, Bloemfontein, South Africa
| | - Yuri E Mikhailov
- Department of Ecology & Nature Management, Ural State Forest Engineering University, Yekaterinburg, Russia
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Alexander Schneider
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany
| | - Lukáš Sekerka
- Department of Entomology, National Museum, Prague 9, Cirkusová, Czech Republic
| | - Maksim E Sergeev
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Vitali Zverev
- Department of Biology, University of Turku, Turku, Finland
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13
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Yamamichi M. How does genetic architecture affect eco-evolutionary dynamics? A theoretical perspective. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200504. [PMID: 35634922 PMCID: PMC9149794 DOI: 10.1098/rstb.2020.0504] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Recent studies have revealed the importance of feedbacks between contemporary rapid evolution (i.e. evolution that occurs through changes in allele frequencies) and ecological dynamics. Despite its inherent interdisciplinary nature, however, studies on eco-evolutionary feedbacks have been mostly ecological and tended to focus on adaptation at the phenotypic level without considering the genetic architecture of evolutionary processes. In empirical studies, researchers have often compared ecological dynamics when the focal species under selection has a single genotype with dynamics when it has multiple genotypes. In theoretical studies, common approaches are models of quantitative traits where mean trait values change adaptively along the fitness gradient and Mendelian traits with two alleles at a single locus. On the other hand, it is well known that genetic architecture can affect short-term evolutionary dynamics in population genetics. Indeed, recent theoretical studies have demonstrated that genetic architecture (e.g. the number of loci, linkage disequilibrium and ploidy) matters in eco-evolutionary dynamics (e.g. evolutionary rescue where rapid evolution prevents extinction and population cycles driven by (co)evolution). I propose that theoretical approaches will promote the synthesis of functional genomics and eco-evolutionary dynamics through models that combine population genetics and ecology as well as nonlinear time-series analyses using emerging big data.
This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
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Affiliation(s)
- Masato Yamamichi
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
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14
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Mancilla-Morales MD, Velarde E, Contreras-Rodríguez A, Gómez-Lunar Z, Rosas-Rodríguez JA, Heras J, Soñanez-Organis JG, Ruiz EA. Characterization, Selection, and Trans-Species Polymorphism in the MHC Class II of Heermann’s Gull (Charadriiformes). Genes (Basel) 2022; 13:genes13050917. [PMID: 35627302 PMCID: PMC9140796 DOI: 10.3390/genes13050917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 11/16/2022] Open
Abstract
The major histocompatibility complex (MHC) enables vertebrates to cope with pathogens and maintain healthy populations, thus making it a unique set of loci for addressing ecology and evolutionary biology questions. The aim of our study was to examine the variability of Heermann’s Gull MHC class II (MHCIIB) and compare these loci with other Charadriiformes. Fifty-nine MHCIIB haplotypes were recovered from sixty-eight Heermann’s Gulls by cloning, of them, twelve were identified as putative true alleles, forty-five as unique alleles, and two as pseudogenes. Intra and interspecific relationships indicated at least two loci in Heermann’s Gull MHCIIB and trans-species polymorphism among Charadriiformes (coinciding with the documented evidence of two ancient avian MHCIIB lineages, except in the Charadriidae family). Additionally, sites under diversifying selection revealed a better match with peptide-binding sites inferred in birds than those described in humans. Despite the negative anthropogenic activity reported on Isla Rasa, Heermann’s Gull showed MHCIIB variability consistent with population expansion, possibly due to a sudden growth following conservation efforts. Duplication must play an essential role in shaping Charadriiformes MHCIIB variability, buffering selective pressures through balancing selection. These findings suggest that MHC copy number and protected islands can contribute to seabird conservation.
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Affiliation(s)
- Misael Daniel Mancilla-Morales
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico
- Correspondence: (M.D.M.-M.); (J.G.S.-O.); (E.A.R.)
| | - Enriqueta Velarde
- Instituto de Ciencias Marinas y Pesquerías, Universidad Veracruzana, Hidalgo 617, Colonia Río Jamapa, Boca del Rio, Veracruz CP 94290, Mexico;
| | - Araceli Contreras-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico; (A.C.-R.); (Z.G.-L.)
| | - Zulema Gómez-Lunar
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico; (A.C.-R.); (Z.G.-L.)
| | - Jesús A. Rosas-Rodríguez
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Lázaro Cárdenas del Río No. 100, Francisco Villa, Navojoa CP 85880, Mexico;
| | - Joseph Heras
- Departament of Biology, California State University, San Bernardino, 5500 University Parkway, San Bernardino, CA 92407, USA;
| | - José G. Soñanez-Organis
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Lázaro Cárdenas del Río No. 100, Francisco Villa, Navojoa CP 85880, Mexico;
- Correspondence: (M.D.M.-M.); (J.G.S.-O.); (E.A.R.)
| | - Enrico A. Ruiz
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Ciudad de Mexico CP 11340, Mexico
- Correspondence: (M.D.M.-M.); (J.G.S.-O.); (E.A.R.)
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15
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Rudman SM, Greenblum SI, Rajpurohit S, Betancourt NJ, Hanna J, Tilk S, Yokoyama T, Petrov DA, Schmidt P. Direct observation of adaptive tracking on ecological time scales in Drosophila. Science 2022; 375:eabj7484. [PMID: 35298245 PMCID: PMC10684103 DOI: 10.1126/science.abj7484] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Direct observation of evolution in response to natural environmental change can resolve fundamental questions about adaptation, including its pace, temporal dynamics, and underlying phenotypic and genomic architecture. We tracked the evolution of fitness-associated phenotypes and allele frequencies genome-wide in 10 replicate field populations of Drosophila melanogaster over 10 generations from summer to late fall. Adaptation was evident over each sampling interval (one to four generations), with exceptionally rapid phenotypic adaptation and large allele frequency shifts at many independent loci. The direction and basis of the adaptive response shifted repeatedly over time, consistent with the action of strong and rapidly fluctuating selection. Overall, we found clear phenotypic and genomic evidence of adaptive tracking occurring contemporaneously with environmental change, thus demonstrating the temporally dynamic nature of adaptation.
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Affiliation(s)
- Seth M. Rudman
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- School of Biological Sciences, Washington State University, Vancouver, WA 98686, USA
| | - Sharon I. Greenblum
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Subhash Rajpurohit
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biological and Life Sciences, Ahmedabad University, Ahmedabad 380009, GJ, India
| | | | - Jinjoo Hanna
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susanne Tilk
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Tuya Yokoyama
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Paul Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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16
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Pande J, Shnerb NM. How temporal environmental stochasticity affects species richness: destabilization, neutralization and the storage effect. J Theor Biol 2022; 539:111053. [DOI: 10.1016/j.jtbi.2022.111053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 01/16/2022] [Accepted: 02/02/2022] [Indexed: 10/19/2022]
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17
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Ebel ER, Uricchio LH, Petrov DA, Egan ES. Revisiting the malaria hypothesis: accounting for polygenicity and pleiotropy. Trends Parasitol 2022; 38:290-301. [PMID: 35065882 PMCID: PMC8916997 DOI: 10.1016/j.pt.2021.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 10/19/2022]
Abstract
The malaria hypothesis predicts local, balancing selection of deleterious alleles that confer strong protection from malaria. Three protective variants, recently discovered in red cell genes, are indeed more common in African than European populations. Still, up to 89% of the heritability of severe malaria is attributed to many genome-wide loci with individually small effects. Recent analyses of hundreds of genome-wide association studies (GWAS) in humans suggest that most functional, polygenic variation is pleiotropic for multiple traits. Interestingly, GWAS alleles and red cell traits associated with small reductions in malaria risk are not enriched in African populations. We propose that other selective and neutral forces, in addition to malaria prevalence, explain the global distribution of most genetic variation impacting malaria risk.
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18
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Abdul-Rahman F, Tranchina D, Gresham D. Fluctuating Environments Maintain Genetic Diversity through Neutral Fitness Effects and Balancing Selection. Mol Biol Evol 2021; 38:4362-4375. [PMID: 34132791 PMCID: PMC8476146 DOI: 10.1093/molbev/msab173] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Genetic variation is the raw material upon which selection acts. The majority of environmental conditions change over time and therefore may result in variable selective effects. How temporally fluctuating environments impact the distribution of fitness effects and in turn population diversity is an unresolved question in evolutionary biology. Here, we employed continuous culturing using chemostats to establish environments that switch periodically between different nutrient limitations and compared the dynamics of selection to static conditions. We used the pooled Saccharomyces cerevisiae haploid gene deletion collection as a synthetic model for populations comprising thousands of unique genotypes. Using barcode sequencing, we find that static environments are uniquely characterized by a small number of high-fitness genotypes that rapidly dominate the population leading to dramatic decreases in genetic diversity. By contrast, fluctuating environments are enriched in genotypes with neutral fitness effects and an absence of extreme fitness genotypes contributing to the maintenance of genetic diversity. We also identified a unique class of genotypes whose frequencies oscillate sinusoidally with a period matching the environmental fluctuation. Oscillatory behavior corresponds to large differences in short-term fitness that are not observed across long timescales pointing to the importance of balancing selection in maintaining genetic diversity in fluctuating environments. Our results are consistent with a high degree of environmental specificity in the distribution of fitness effects and the combined effects of reduced and balancing selection in maintaining genetic diversity in the presence of variable selection.
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Affiliation(s)
- Farah Abdul-Rahman
- Department of Biology, New York University, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Daniel Tranchina
- Department of Biology, New York University, New York, NY, USA
- Courant Math Institute, New York University, New York, NY, USA
| | - David Gresham
- Department of Biology, New York University, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
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19
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Martin-Roy R, Nygård E, Nouhaud P, Kulmuni J. Differences in Thermal Tolerance between Parental Species Could Fuel Thermal Adaptation in Hybrid Wood Ants. Am Nat 2021; 198:278-294. [PMID: 34260873 DOI: 10.1086/715012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractGenetic variability is essential for adaptation and could be acquired via hybridization with a closely related lineage. We use ants to investigate thermal adaptation and the link between temperature and genetic variation arising from hybridization. We test for differences in cold and heat tolerance between Finnish Formica polyctena and Formica aquilonia wood ants and their naturally occurring hybrids. Using workers, we find that the parental individuals differ in both cold and heat tolerances and express thermal limits that reflect their global distributions. Hybrids, however, cannot combine thermal tolerance of parental species as they have the same heat tolerance as F. polyctena but not the same cold tolerance as F. aquilonia. We then focus on a single hybrid population to investigate the relationship between temperature variation and genetic variation across 16 years using reproductive individuals. On the basis of the thermal tolerance results, we expected the frequency of putative F. polyctena alleles to increase in warm years and F. aquilonia alleles to increase in cold years. We find support for this in hybrid males but not in hybrid females. These results contribute to understanding the outcomes of hybridization, which may be sex specific or depend on the environment. Furthermore, genetic variability resulting from hybridization could help hybrid wood ants cope with changing thermal conditions.
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20
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Machado HE, Bergland AO, Taylor R, Tilk S, Behrman E, Dyer K, Fabian DK, Flatt T, González J, Karasov TL, Kim B, Kozeretska I, Lazzaro BP, Merritt TJS, Pool JE, O'Brien K, Rajpurohit S, Roy PR, Schaeffer SW, Serga S, Schmidt P, Petrov DA. Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila. eLife 2021; 10:e67577. [PMID: 34155971 PMCID: PMC8248982 DOI: 10.7554/elife.67577] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022] Open
Abstract
To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched in large chromosomal inversions, and we find a broad concordance between seasonal and spatial allele frequency change. The direction of allele frequency change at seasonally variable polymorphisms can be predicted by weather conditions in the weeks prior to sampling, linking the environment and the genomic response to selection. Our results suggest that fluctuating selection is an important evolutionary force affecting patterns of genetic variation in Drosophila.
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Affiliation(s)
- Heather E Machado
- Department of Biology, Stanford UniversityStanfordUnited States
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | - Alan O Bergland
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Biology, University of VirginiaCharlottesvilleUnited States
| | - Ryan Taylor
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Susanne Tilk
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Emily Behrman
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Kelly Dyer
- Department of Genetics, University of GeorgiaAthensUnited States
| | - Daniel K Fabian
- Institute of Population Genetics, Vetmeduni ViennaViennaAustria
- Centre for Pathogen Evolution, Department of Zoology, University of CambridgeCambridgeUnited Kingdom
| | - Thomas Flatt
- Institute of Population Genetics, Vetmeduni ViennaViennaAustria
- Department of Biology, University of FribourgFribourgSwitzerland
| | - Josefa González
- Institute of Evolutionary Biology, CSIC- Universitat Pompeu FabraBarcelonaSpain
| | - Talia L Karasov
- Department of Biology, University of UtahSalt Lake CityUnited States
| | - Bernard Kim
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Iryna Kozeretska
- Taras Shevchenko National University of KyivKyivUkraine
- National Antarctic Scientific Centre of Ukraine, Taras Shevchenko Blvd.KyivUkraine
| | - Brian P Lazzaro
- Department of Entomology, Cornell UniversityIthacaUnited States
| | - Thomas JS Merritt
- Department of Chemistry & Biochemistry, Laurentian UniversitySudburyCanada
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-MadisonMadisonUnited States
| | - Katherine O'Brien
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Subhash Rajpurohit
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Paula R Roy
- Department of Ecology and Evolutionary Biology, University of KansasLawrenceUnited States
| | - Stephen W Schaeffer
- Department of Biology, The Pennsylvania State UniversityUniversity ParkUnited States
| | - Svitlana Serga
- Taras Shevchenko National University of KyivKyivUkraine
- National Antarctic Scientific Centre of Ukraine, Taras Shevchenko Blvd.KyivUkraine
| | - Paul Schmidt
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
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21
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Ehrlich MA, Wagner DN, Oleksiak MF, Crawford DL. Polygenic Selection within a Single Generation Leads to Subtle Divergence among Ecological NichesINc. Genome Biol Evol 2021; 13:evaa257. [PMID: 33313716 PMCID: PMC7875003 DOI: 10.1093/gbe/evaa257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 09/09/2020] [Accepted: 12/09/2020] [Indexed: 11/23/2022] Open
Abstract
Selection on standing genetic variation may be effective enough to allow for adaptation to distinct niche environments within a single generation. Minor allele frequency changes at multiple, redundant loci of small effect can produce remarkable phenotypic shifts. Yet, demonstrating rapid adaptation via polygenic selection in the wild remains challenging. Here we harness natural replicate populations that experience similar selection pressures and harbor high within-, yet negligible among-population genetic variation. Such populations can be found among the teleost Fundulus heteroclitus that inhabits marine estuaries characterized by high environmental heterogeneity. We identify 10,861 single nucleotide polymorphisms in F. heteroclitus that belong to a single, panmictic population yet reside in environmentally distinct niches (one coastal basin and three replicate tidal ponds). By sampling at two time points within a single generation, we quantify both allele frequency change within as well as spatial divergence among niche subpopulations. We observe few individually significant allele frequency changes yet find that the "number" of moderate changes exceeds the neutral expectation by 10-100%. We find allele frequency changes to be significantly concordant in both direction and magnitude among all niche subpopulations, suggestive of parallel selection. In addition, within-generation allele frequency changes generate subtle but significant divergence among niches, indicative of local adaptation. Although we cannot distinguish between selection and genotype-dependent migration as drivers of within-generation allele frequency changes, the trait/s determining fitness and/or migration likelihood appear to be polygenic. In heterogeneous environments, polygenic selection and polygenic, genotype-dependent migration offer conceivable mechanisms for within-generation, local adaptation to distinct niches.
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Affiliation(s)
- Moritz A Ehrlich
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, FL, USA
| | - Dominique N Wagner
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, FL, USA
| | - Marjorie F Oleksiak
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, FL, USA
| | - Douglas L Crawford
- Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, FL, USA
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22
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Nabutanyi P, Wittmann MJ. Models for Eco-Evolutionary Extinction Vortices under Balancing Selection. Am Nat 2021; 197:336-350. [PMID: 33625964 DOI: 10.1086/712805] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractThe smaller a population is, the faster it loses genetic diversity as a result of genetic drift. Loss of genetic diversity can reduce population growth rate, making populations even smaller and more vulnerable to loss of genetic diversity. Ultimately, the population can be driven to extinction by this "eco-evolutionary extinction vortex." While there are already quantitative models for extinction vortices resulting from inbreeding depression and mutation accumulation, to date extinction vortices resulting from loss of genetic diversity at loci under various forms of balancing selection have been mainly described verbally. To understand better when such extinction vortices arise and to develop methods for detecting them, we propose quantitative eco-evolutionary models, both stochastic individual-based simulations and deterministic approximations, linking loss of genetic diversity and population decline. Using mathematical analysis and simulations, we identify parameter combinations that exhibit strong interactions between population size and genetic diversity and match our definition of an eco-evolutionary vortex (i.e., per capita population decline rates and per-locus fixation rates increase with decreasing population size and number of polymorphic loci). We further highlight cues that may be exhibited by such populations but find that classical early-warning signals are of limited use in detecting populations undergoing an eco-evolutionary extinction vortex.
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23
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Zhdanova OL, Frisman EY. Genetic polymorphism under cyclical selection in long-lived species: The complex effect of age structure and maternal selection. J Theor Biol 2021; 512:110564. [PMID: 33359207 DOI: 10.1016/j.jtbi.2020.110564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 11/30/2022]
Abstract
Maternal selection and overlapping generations can facilitate the stable coexistence of alleles under temporally fluctuating environment. Using mathematical models, we considered the complex effect of both factors on the maintenance of genetic polymorphism in cyclically changing environments. We concentrated on asymmetric cyclic selection, which allows describing fluctuations of environments by analogy of food resources cycles with rare peaks and prolonged decline of prey abundance. The complex effect of maternal selection and overlapping generations turned out to work as follows: although overlapping generations always tend to dilate the polymorphism region, odd and even external cycles produce different types of polymorphism regions. Maternal selection under external odd cycles extends the coexistence region comparing with classic selection. Even cycles produce a part of parameter region, where the picture changes radically, and classic selection becomes more effective in maintaining polymorphism. Our models have clear biological interpretation, because we tried to model a situation demonstrated by natural populations of arctic foxes. The litter size being a major life history trait is a sex-limited female trait. It is influenced by maternal selection with cyclical fluctuations because of oscillations in food abundance. Arctic fox is a long-lived species having an age structure. The obtained results showed that compared with the simple Mendelian inheritance in the classic model, this trait inheritance allows polymorphism to be maintained in a wider range of the parameter that characterizes the advantage of survival in a small litter. Besides, adding overlapping generations to the model further broadens the parameter space for the protected polymorphism. Thus, this study shows that maternal selection and overlapping generations increases the chances of maintaining polymorphism in populations of arctic foxes.
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Affiliation(s)
- Oksana L Zhdanova
- Insititute for Automation and Control Processes, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, Russia.
| | - Efim Ya Frisman
- Institute for Complex Analysis of Regional Problem, Far Eastern Branch, Russian Academy of Sciences, Birobidzhan 679016, Russia.
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24
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25
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Evolutionary origins of genomic adaptations in an invasive copepod. Nat Ecol Evol 2020; 4:1084-1094. [DOI: 10.1038/s41559-020-1201-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 04/14/2020] [Indexed: 12/18/2022]
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26
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Pettersen AK, Hall MD, White CR, Marshall DJ. Metabolic rate, context-dependent selection, and the competition-colonization trade-off. Evol Lett 2020; 4:333-344. [PMID: 32774882 PMCID: PMC7403701 DOI: 10.1002/evl3.174] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/08/2020] [Accepted: 04/20/2020] [Indexed: 01/24/2023] Open
Abstract
Metabolism is linked with the pace‐of‐life, co‐varying with survival, growth, and reproduction. Metabolic rates should therefore be under strong selection and, if heritable, become less variable over time. Yet intraspecific variation in metabolic rates is ubiquitous, even after accounting for body mass and temperature. Theory predicts variable selection maintains trait variation, but field estimates of how selection on metabolism varies are rare. We use a model marine invertebrate to estimate selection on metabolic rates in the wild under different competitive environments. Fitness landscapes varied among environments separated by a few centimeters: interspecific competition selected for higher metabolism, and a faster pace‐of‐life, relative to competition‐free environments. Populations experience a mosaic of competitive regimes; we find metabolism mediates a competition‐colonization trade‐off across these regimes. Although high metabolic phenotypes possess greater competitive ability, in the absence of competitors, low metabolic phenotypes are better colonizers. Spatial heterogeneity and the variable selection on metabolic rates that it generates is likely to maintain variation in metabolic rate, despite strong selection in any single environment.
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Affiliation(s)
- Amanda K Pettersen
- School of Biological Sciences/Centre for Geometric Biology Monash University Melbourne VIC 3800 Australia.,Department of Biology Lund University Lund 221 00 Sweden
| | - Matthew D Hall
- School of Biological Sciences/Centre for Geometric Biology Monash University Melbourne VIC 3800 Australia
| | - Craig R White
- School of Biological Sciences/Centre for Geometric Biology Monash University Melbourne VIC 3800 Australia
| | - Dustin J Marshall
- School of Biological Sciences/Centre for Geometric Biology Monash University Melbourne VIC 3800 Australia
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27
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Bürger R. Multilocus population-genetic theory. Theor Popul Biol 2020; 133:40-48. [DOI: 10.1016/j.tpb.2019.09.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/01/2019] [Accepted: 09/09/2019] [Indexed: 01/03/2023]
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