1
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Madgwick PG, Tunstall T, Kanitz R. Evolutionary rescue in resistance to pesticides. Proc Biol Sci 2024; 291:20240805. [PMID: 38917864 DOI: 10.1098/rspb.2024.0805] [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: 10/20/2023] [Accepted: 06/03/2024] [Indexed: 06/27/2024] Open
Abstract
Evolutionary rescue occurs when the genetic evolution of adaptation saves a population from decline or extinction after environmental change. The evolution of resistance to pesticides is a special scenario of abrupt environmental change, where rescue occurs under (very) strong selection for one or a few de novo resistance mutations of large effect. Here, a population genetic model of evolutionary rescue with density-dependent population change is developed, with a focus on deriving results that are important to resistance management. Massive stochastic simulations are used to generate observations, which are accurately predicted using analytical approximations. Key results include the probability density function for the time to resistance and the probability of population extinction. The distribution of resistance times shows a lag period, a narrow peak and a long tail. Surprisingly, the mean time to resistance can increase with the strength of selection because, if a mutation does not occur early on, then its emergence is delayed by the pesticide reducing the population size. The probability of population extinction shows a sharp transition, in that when extinction is possible, it is also highly likely. Consequently, population suppression and (local) eradication can be theoretically achievable goals, as novel strategies to delay resistance evolution.
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Affiliation(s)
- Philip G Madgwick
- Syngenta, Jealott's Hill International Research Centre , Bracknell RG42 6EY, UK
| | - Thomas Tunstall
- Living Systems Institute, University of Exeter , Exeter EX4 4PY, UK
| | - Ricardo Kanitz
- Syngenta Crop Protection, Rosentalstrasse 67 , Basel CH-4058, Switzerland
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2
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Pezzini D, Taylor KL, Reisig DD, Fritz ML. Cross-pollination in seed-blended refuge and selection for Vip3A resistance in a lepidopteran pest as detected by genomic monitoring. Proc Natl Acad Sci U S A 2024; 121:e2319838121. [PMID: 38513093 PMCID: PMC10990109 DOI: 10.1073/pnas.2319838121] [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: 11/17/2023] [Accepted: 12/13/2023] [Indexed: 03/23/2024] Open
Abstract
The evolution of pest resistance to management tools reduces productivity and results in economic losses in agricultural systems. To slow its emergence and spread, monitoring and prevention practices are implemented in resistance management programs. Recent work suggests that genomic approaches can identify signs of emerging resistance to aid in resistance management. Here, we empirically examined the sensitivity of genomic monitoring for resistance management in transgenic Bt crops, a globally important agricultural innovation. Whole genome resequencing of wild North American Helicoverpa zea collected from non-expressing refuge and plants expressing Cry1Ab confirmed that resistance-associated signatures of selection were detectable after a single generation of exposure. Upon demonstrating its sensitivity, we applied genomic monitoring to wild H. zea that survived Vip3A exposure resulting from cross-pollination of refuge plants in seed-blended plots. Refuge seed interplanted with transgenic seed exposed H. zea to sublethal doses of Vip3A protein in corn ears and was associated with allele frequency divergence across the genome. Some of the greatest allele frequency divergence occurred in genomic regions adjacent to a previously described candidate gene for Vip3A resistance. Our work highlights the power of genomic monitoring to sensitively detect heritable changes associated with field exposure to Bt toxins and suggests that seed-blended refuge will likely hasten the evolution of resistance to Vip3A in lepidopteran pests.
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Affiliation(s)
- Daniela Pezzini
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC27513
| | - Katherine L. Taylor
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC27513
- Department of Entomology, University of Maryland, College Park, MD20742
| | - Dominic D. Reisig
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC27513
| | - Megan L. Fritz
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC27513
- Department of Entomology, University of Maryland, College Park, MD20742
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3
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Goebl AM, Kane NC, Doak DF, Rieseberg LH, Ostevik KL. Adaptation to distinct habitats is maintained by contrasting selection at different life stages in sunflower ecotypes. Mol Ecol 2024; 33:e16785. [PMID: 36374153 DOI: 10.1111/mec.16785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/20/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
Conspecific populations living in adjacent but contrasting microenvironments represent excellent systems for studying natural selection. These systems are valuable because gene flow is expected to force genetic homogeneity except at loci experiencing divergent selection. A history of reciprocal transplant and common garden studies in such systems, and a growing number of genomic studies, have contributed to understanding how selection operates in natural populations. While selection can vary across different fitness components and life stages, few studies have investigated how this ultimately affects allele frequencies and the maintenance of divergence between populations. Here, we study two sunflower ecotypes in distinct, adjacent habitats by combining demographic models with genome-wide sequence data to estimate fitness and allele frequency change at multiple life stages. This framework allows us to estimate that only local ecotypes are likely to experience positive population growth (λ > 1) and that the maintenance of divergent adaptation appears to be mediated via habitat- and life stage-specific selection. We identify genetic variation, significantly driven by loci in chromosomal inversions, associated with different life history strategies in neighbouring ecotypes that optimize different fitness components and may contribute to the maintenance of distinct ecotypes.
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Affiliation(s)
- April M Goebl
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Daniel F Doak
- Environmental Studies Programme, University of Colorado, Boulder, Colorado, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kate L Ostevik
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, California, USA
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4
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Battlay P, Wilson J, Bieker VC, Lee C, Prapas D, Petersen B, Craig S, van Boheemen L, Scalone R, de Silva NP, Sharma A, Konstantinović B, Nurkowski KA, Rieseberg LH, Connallon T, Martin MD, Hodgins KA. Large haploblocks underlie rapid adaptation in the invasive weed Ambrosia artemisiifolia. Nat Commun 2023; 14:1717. [PMID: 36973251 PMCID: PMC10042993 DOI: 10.1038/s41467-023-37303-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 03/11/2023] [Indexed: 03/29/2023] Open
Abstract
Adaptation is the central feature and leading explanation for the evolutionary diversification of life. Adaptation is also notoriously difficult to study in nature, owing to its complexity and logistically prohibitive timescale. Here, we leverage extensive contemporary and historical collections of Ambrosia artemisiifolia-an aggressively invasive weed and primary cause of pollen-induced hayfever-to track the phenotypic and genetic causes of recent local adaptation across its native and invasive ranges in North America and Europe, respectively. Large haploblocks-indicative of chromosomal inversions-contain a disproportionate share (26%) of genomic regions conferring parallel adaptation to local climates between ranges, are associated with rapidly adapting traits, and exhibit dramatic frequency shifts over space and time. These results highlight the importance of large-effect standing variants in rapid adaptation, which have been critical to A. artemisiifolia's global spread across vast climatic gradients.
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Affiliation(s)
- Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Jonathan Wilson
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Christopher Lee
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Diana Prapas
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Bent Petersen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, 08100, Bedong, Kedah, Malaysia
| | - Sam Craig
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Lotte van Boheemen
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Romain Scalone
- Department of Crop Production Ecology, Uppsala Ecology Center, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany
| | - Nissanka P de Silva
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Amit Sharma
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Bojan Konstantinović
- Department of Environmental and Plant Protection, Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Kristin A Nurkowski
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - Tim Connallon
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.
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5
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Sibly RM, Curnow RN. Allele frequencies and selection coefficients in locally adapted populations. J Theor Biol 2023; 565:111463. [PMID: 36914112 DOI: 10.1016/j.jtbi.2023.111463] [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: 07/19/2022] [Revised: 12/22/2022] [Accepted: 03/08/2023] [Indexed: 03/15/2023]
Abstract
Understanding the role of natural selection in driving evolutionary change requires accurate estimates of the strength of selection acting at the genetic level in the wild. This is challenging to achieve but may be easier in the case of populations in migration-selection balance. When two populations are at equilibrium under migration-selection balance, there exist loci whose alleles are selected different ways in the two populations. Such loci can be identified from genome sequencing by their high values of FST. This raises the question of what is the strength of selection on locally-adaptive alleles. To answer this question we analyse a 1-locus 2-allele model of a population distributed between two niches. We show by simulation of selected cases that the outputs from finite-population models are essentially the same as those from deterministic infinite-population models. We then derive theory for the infinite-population model showing the dependence of selection coefficients on equilibrium allele frequencies, migration rates, dominance and relative population sizes in the two niches. An Excel spreadsheet is provided for the calculation of selection coefficients and their approximate standard errors from observed values of population parameters. We illustrate our results with a worked example, with graphs showing the dependence of selection coefficients on equilibrium allele frequencies, and graphs showing how FST depends on the selection coefficients acting on the alleles at a locus. Given the extent of recent progress in ecological genomics, we hope our methods may help those studying migration-selection balance to quantify the advantages conferred by adaptive genes.
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Affiliation(s)
| | - Robert N Curnow
- Department of Mathematics and Statistics, University of Reading, UK.
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6
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Waselkov K, Olsen KM. Herbaria reveal cost of the Green Revolution. Science 2022; 378:1053-1054. [PMID: 36480609 DOI: 10.1126/science.ade4615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rapid weed evolution is exposed by genome sequencing of natural history collections.
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Affiliation(s)
- Katherine Waselkov
- Department of Biology, California State University, Fresno, Fresno, CA 93740, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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7
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Fritz ML. Utility and challenges of using whole‐genome resequencing to detect emerging insect and mite resistance in agroecosystems. Evol Appl 2022; 15:1505-1520. [PMID: 36330307 PMCID: PMC9624086 DOI: 10.1111/eva.13484] [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: 12/02/2021] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022] Open
Abstract
Arthropods that invade agricultural ecosystems systematically evolve resistance to the control measures used against them, and this remains a significant and ongoing challenge for sustainable food production systems. Early detection of resistance evolution could prompt remedial action to slow the spread of resistance alleles in the landscape. Historical approaches used to detect emerging resistance included phenotypic monitoring of agricultural pest populations, as well as monitoring of allele frequency changes at one or a few candidate pesticide resistance genes. In this article, I discuss the successes and limitations of these traditional monitoring approaches and then consider whether whole‐genome scanning could be applied to samples collected from agroecosystems over time for resistance monitoring. I examine the qualities of agroecosystems that could impact application of this approach to pesticide resistance monitoring and describe a recent retrospective analysis where genome scanning successfully detected an oligogenic response to selection by pesticides years prior to pest management failure. I conclude by considering areas of further study that will shed light on the feasibility of applying whole‐genome scanning for resistance risk monitoring in agricultural pest species.
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Affiliation(s)
- Megan L. Fritz
- Department of Entomology University of Maryland College Park Maryland USA
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8
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Gompert Z, Feder JL, Nosil P. The short-term, genome-wide effects of indirect selection deserve study: A response to Charlesworth and Jensen (2022). Mol Ecol 2022; 31:4444-4450. [PMID: 35909250 DOI: 10.1111/mec.16614] [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: 01/31/2022] [Revised: 06/21/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022]
Abstract
We recently published a paper quantifying the genome-wide consequences of natural selection, including the effects of indirect selection due to the correlation of genetic regions (neutral or selected) with directly selected regions (Gompert et al., 2022). In their critique of our paper, Charlesworth and Jensen (2022) make two main points: (i) indirect selection is equivalent to hitchhiking and thus well documented (i.e., our results are not novel) and (ii) that we do not demonstrate the source of linkage disequilibrium (LD) between SNPs and the Mel-Stripe locus in the Timema cristinae experiment we analyse. As we discuss in detail below, neither of these are substantial criticisms of our work.
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Affiliation(s)
- Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah, USA.,Ecology Center, Utah State University, Logan, Utah, USA
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Patrik Nosil
- CEFE, University Montpellier, CNRS, EPHE, IRD, University Paul Valéry Montpellier 3, Montpellier, France
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9
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Pérez‐Pereira N, López‐Cortegano E, García‐Dorado A, Caballero A. Prediction of fitness under different breeding designs in conservation programs. Anim Conserv 2022. [DOI: 10.1111/acv.12804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- N. Pérez‐Pereira
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
| | - E. López‐Cortegano
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
| | - A. García‐Dorado
- Departamento de Genética, Facultad de Ciencias Biológicas Universidad Complutense Madrid Spain
| | - A. Caballero
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
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10
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Aguirre WE, Reid K, Rivera J, Heins DC, Veeramah KR, Bell MA. Freshwater Colonization, Adaptation, and Genomic Divergence in Threespine Stickleback. Integr Comp Biol 2022; 62:388-405. [PMID: 35660873 PMCID: PMC9405723 DOI: 10.1093/icb/icac071] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/25/2022] [Accepted: 05/24/2022] [Indexed: 11/14/2022] Open
Abstract
The Threespine Stickleback is ancestrally a marine fish, but many marine populations breed in fresh water (i.e., are anadromous), facilitating their colonization of isolated freshwater habitats a few years after they form. Repeated adaptation to fresh water during at least 10 My and continuing today has led to Threespine Stickleback becoming a premier system to study rapid adaptation. Anadromous and freshwater stickleback breed in sympatry and may hybridize, resulting in introgression of freshwater-adaptive alleles into anadromous populations, where they are maintained at low frequencies as ancient standing genetic variation. Anadromous stickleback have accumulated hundreds of freshwater-adaptive alleles that are disbursed as few loci per marine individual and provide the basis for adaptation when they colonize fresh water. Recent whole-lake experiments in lakes around Cook Inlet, Alaska have revealed how astonishingly rapid and repeatable this process is, with the frequency of 40% of the identified freshwater-adaptive alleles increasing from negligible (∼1%) in the marine founder to ≥50% within ten generations in fresh water, and freshwater phenotypes evolving accordingly. These high rates of genomic and phenotypic evolution imply very intense directional selection on phenotypes of heterozygotes. Sexual recombination rapidly assembles freshwater-adaptive alleles that originated in different founders into multilocus freshwater haplotypes, and regions important for adaptation to freshwater have suppressed recombination that keeps advantageous alleles linked within large haploblocks. These large haploblocks are also older and appear to have accumulated linked advantageous mutations. The contemporary evolution of Threespine Stickleback has provided broadly applicable insights into the mechanisms that facilitate rapid adaptation.
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Affiliation(s)
- Windsor E Aguirre
- Department of Biological Sciences, DePaul University, Chicago, IL 60614, USA
| | - Kerry Reid
- School of Biological Sciences, Area of Ecology and Biodiversity, University of Hong Kong, Hong Kong, SAR, China.,Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jessica Rivera
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - David C Heins
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans 70118, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, CA 94720, USA
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11
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Bendall EE, Bagley RK, Sousa VC, Linnen CR. Faster-haplodiploid evolution under divergence-with-gene-flow: simulations and empirical data from pine-feeding hymenopterans. Mol Ecol 2022; 31:2348-2366. [PMID: 35231148 DOI: 10.1111/mec.16410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 11/28/2022]
Abstract
Although haplodiploidy is widespread in nature, the evolutionary consequences of this mode of reproduction are not well characterized. Here, we examine how genome-wide hemizygosity and a lack of recombination in haploid males affects genomic differentiation in populations that diverge via natural selection while experiencing gene flow. First, we simulated diploid and haplodiploid "genomes" (500-kb loci) evolving under an isolation-with-migration model with mutation, drift, selection, migration, and recombination; and examined differentiation at neutral sites both tightly and loosely linked to a divergently selected site. So long as there is divergent selection and migration, sex-limited hemizygosity and recombination cause elevated differentiation (i.e., produce a "faster-haplodiploid effect") in haplodiploid populations relative to otherwise equivalent diploid populations, for both recessive and codominant mutations. Second, we used genome-wide SNP data to model divergence history and describe patterns of genomic differentiation between sympatric populations of Neodiprion lecontei and N. pinetum, a pair of pine sawfly species (order: Hymenoptera; family: Diprionidae) that are specialized on different pine hosts. These analyses support a history of continuous gene exchange throughout divergence and reveal a pattern of heterogeneous genomic differentiation that is consistent with divergent selection on many unlinked loci. Third, using simulations of haplodiploid and diploid populations evolving according to the estimated divergence history of N. lecontei and N. pinetum, we found that divergent selection would lead to higher differentiation in haplodiploids. Based on these results, we hypothesize that haplodiploids undergo divergence-with-gene-flow and sympatric speciation more readily than diploids.
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Affiliation(s)
- Emily E Bendall
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Robin K Bagley
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA.,Department of Evolution, Ecology, and Organismal Biology, The Ohio State University at Lima, Lima, OH, 45804, USA
| | - Vitor C Sousa
- CE3C - Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculdade de Ciências da Universidade de Lisboa, University of Lisbon, Campo Grande 1749-016, Lisboa, Portugal
| | - Catherine R Linnen
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA
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12
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Sakai S. Why are deleterious mutations maintained in selfing populations? An analysis of the effects of early- and late-acting mutations by a two-locus two-allele model. J Theor Biol 2022; 533:110956. [PMID: 34736949 DOI: 10.1016/j.jtbi.2021.110956] [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: 02/01/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 10/19/2022]
Abstract
Frequencies of deleterious mutations are higher than expected in many plants. Here, by developing a two-locus two-allele model, I examine the effects of differential timing of the expression of deleterious mutations (two-stage effects) on the maintenance of mutations. I assume early- and late-acting loci to distinguish whether maintenance of mutations in populations with high selfing rates is explained better by two-stage effects of single mutations, or by separate mutations in both early- and late-acting loci. I found that, when ovules are overproduced, the stable frequency of early-acting mutations is higher if mutations also occur in a late-acting locus than if a late-acting mutation is lacking. The stable frequency of late-acting mutations is higher if mutations also occur in an early-acting locus than if an early-acting mutation is lacking. Selective interference does not account for these results because analyses in which the number of loci subject to mutations is equalized are included. Overproduction of ovules has little effect on maintenance if either early- or late-acting mutations are lacking, whereas when ovules are not overproduced, the two-stage effect does not enhance the maintenance of mutations. Hence, mutations occurring in both loci coupled with overproduction of ovules enhances the maintenance of mutations in populations with high selfing rates. The detailed mechanisms underlying the two-stage effect were also analyzed.
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Affiliation(s)
- Satoki Sakai
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan.
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13
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Gompert Z, Feder JL, Nosil P. Natural selection drives genome-wide evolution via chance genetic associations. Mol Ecol 2021; 31:467-481. [PMID: 34704650 DOI: 10.1111/mec.16247] [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: 07/07/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 11/29/2022]
Abstract
Understanding selection's impact on the genome is a major theme in biology. Functionally neutral genetic regions can be affected indirectly by natural selection, via their statistical association with genes under direct selection. The genomic extent of such indirect selection, particularly across loci not physically linked to those under direct selection, remains poorly understood, as does the time scale at which indirect selection occurs. Here, we use field experiments and genomic data in stick insects, deer mice and stickleback fish to show that widespread statistical associations with genes known to affect fitness cause many genetic loci across the genome to be impacted indirectly by selection. This includes regions physically distant from those directly under selection. Then, focusing on the stick insect system, we show that statistical associations between SNPs and other unknown, causal variants result in additional indirect selection in general and specifically within genomic regions of physically linked loci. This widespread indirect selection necessarily makes aspects of evolution more predictable. Thus, natural selection combines with chance genetic associations to affect genome-wide evolution across linked and unlinked loci and even in modest-sized populations. This process has implications for the application of evolutionary principles in basic and applied science.
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Affiliation(s)
- Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah, USA.,Ecology Center, Utah State University, Logan, Utah, USA
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
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14
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Abstract
AbstractGenetic rescue is increasingly considered a promising and underused conservation strategy to reduce inbreeding depression and restore genetic diversity in endangered populations, but the empirical evidence supporting its application is limited to a few generations. Here we discuss on the light of theory the role of inbreeding depression arising from partially recessive deleterious mutations and of genetic purging as main determinants of the medium to long-term success of rescue programs. This role depends on two main predictions: (1) The inbreeding load hidden in populations with a long stable demography increases with the effective population size; and (2) After a population shrinks, purging tends to remove its (partially) recessive deleterious alleles, a process that is slower but more efficient for large populations than for small ones. We also carry out computer simulations to investigate the impact of genetic purging on the medium to long term success of genetic rescue programs. For some scenarios, it is found that hybrid vigor followed by purging will lead to sustained successful rescue. However, there may be specific situations where the recipient population is so small that it cannot purge the inbreeding load introduced by migrants, which would lead to increased fitness inbreeding depression and extinction risk in the medium to long term. In such cases, the risk is expected to be higher if migrants came from a large non-purged population with high inbreeding load, particularly after the accumulation of the stochastic effects ascribed to repeated occasional migration events. Therefore, under the specific deleterious recessive mutation model considered, we conclude that additional caution should be taken in rescue programs. Unless the endangered population harbors some distinctive genetic singularity whose conservation is a main concern, restoration by continuous stable gene flow should be considered, whenever feasible, as it reduces the extinction risk compared to repeated occasional migration and can also allow recolonization events.
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15
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Pérez-Pereira N, Pouso R, Rus A, Vilas A, López-Cortegano E, García-Dorado A, Quesada H, Caballero A. Long-term exhaustion of the inbreeding load in Drosophila melanogaster. Heredity (Edinb) 2021; 127:373-383. [PMID: 34400819 PMCID: PMC8478893 DOI: 10.1038/s41437-021-00464-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 07/29/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
Inbreeding depression, the decline in fitness of inbred individuals, is a ubiquitous phenomenon of great relevance in evolutionary biology and in the fields of animal and plant breeding and conservation. Inbreeding depression is due to the expression of recessive deleterious alleles that are concealed in heterozygous state in noninbred individuals, the so-called inbreeding load. Genetic purging reduces inbreeding depression by removing these alleles when expressed in homozygosis due to inbreeding. It is generally thought that fast inbreeding (such as that generated by full-sib mating lines) removes only highly deleterious recessive alleles, while slow inbreeding can also remove mildly deleterious ones. However, a question remains regarding which proportion of the inbreeding load can be removed by purging under slow inbreeding in moderately large populations. We report results of two long-term slow inbreeding Drosophila experiments (125-234 generations), each using a large population and a number of derived lines with effective sizes about 1000 and 50, respectively. The inbreeding load was virtually exhausted after more than one hundred generations in large populations and between a few tens and over one hundred generations in the lines. This result is not expected from genetic drift alone, and is in agreement with the theoretical purging predictions. Computer simulations suggest that these results are consistent with a model of relatively few deleterious mutations of large homozygous effects and partially recessive gene action.
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Affiliation(s)
- Noelia Pérez-Pereira
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Ramón Pouso
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Ana Rus
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Ana Vilas
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Eugenio López-Cortegano
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain ,grid.4305.20000 0004 1936 7988Present Address: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Aurora García-Dorado
- grid.4795.f0000 0001 2157 7667Facultad de Ciencias Biológicas, Departamento de Genética, Universidad Complutense, Madrid, Spain
| | - Humberto Quesada
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Armando Caballero
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
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16
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Madgwick PG, Kanitz R. Evolution of resistance under alternative models of selective interference. J Evol Biol 2021; 34:1608-1623. [PMID: 34449949 PMCID: PMC9293239 DOI: 10.1111/jeb.13919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/28/2021] [Accepted: 08/19/2021] [Indexed: 01/19/2023]
Abstract
The use of multiple pesticides or drugs can lead to a simultaneous selection pressure for resistance alleles at different loci. Models of resistance evolution focus on how this can delay the spread of resistance through a population, but often neglect how this can also reduce the probability that a resistance allele spreads. This neglected factor has been studied in a parallel literature as selective interference. Models of interference use alternative constructions of fitness, where selection coefficients from different loci either add or multiply. Although these are equivalent under weak selection, the two constructions make alternative predictions under the strong selection that characterizes resistance evolution. Here, simulations are used to examine the effects of interference on the probability of fixation and time to fixation of a new and strongly beneficial mutation in the presence of another strongly beneficial allele with variable starting frequency. The results from simulations show a complicated pattern of effects. The key result is that, under multiplicativity, the presence of the strongly beneficial allele leads to a small reduction in the probability of fixation for the new beneficial mutation up to ~10%, and a negligible increase in the average time to fixation up to ~2%, whereas under additivity, the effect is more substantial at up to ~50% for the probability of fixation and ~100% for the average time to fixation. Consequently, the effect of interference is only an important feature of resistance evolution under additivity. Current evidence from studies of experimental evolution provides widespread support for the basic features of additivity, which suggests that interference may afford resistance a different pattern of evolution than other adaptations: rather than the gradual and simultaneous selection of many alleles with small effects, the rapid evolution of resistance may involve the sequential selection of alleles with large effects.
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Affiliation(s)
- Philip G Madgwick
- Syngenta, Jealott's Hill International Research Centre, Bracknell, UK
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17
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Michael CA, Gillings MR, Blaskovich MAT, Franks AE. The Antimicrobial Resistance Crisis: An Inadvertent, Unfortunate but Nevertheless Informative Experiment in Evolutionary Biology. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.692674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The global rise of antimicrobial resistance (AMR) phenotypes is an exemplar for rapid evolutionary response. Resistance arises as a consequence of humanity’s widespread and largely indiscriminate use of antimicrobial compounds. However, some features of this crisis remain perplexing. The remarkably widespread and rapid rise of diverse, novel and effective resistance phenotypes is in stark contrast to the apparent paucity of antimicrobial producers in the global microbiota. From the viewpoint of evolutionary theory, it should be possible to use selection coefficients to examine these phenomena. In this work we introduce an elaboration on the selection coefficient s termed selective efficiency, considering the genetic, metabolic, ecological and evolutionary impacts that accompany selective phenotypes. We then demonstrate the utility of the selective efficiency concept using AMR and antimicrobial production phenotypes as ‘worked examples’ of the concept. In accomplishing this objective, we also put forward cogent hypotheses to explain currently puzzling aspects of the AMR crisis. Finally, we extend the selective efficiency concept into a consideration of the ongoing management of the AMR crisis.
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18
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Roberts Kingman GA, Vyas DN, Jones FC, Brady SD, Chen HI, Reid K, Milhaven M, Bertino TS, Aguirre WE, Heins DC, von Hippel FA, Park PJ, Kirch M, Absher DM, Myers RM, Di Palma F, Bell MA, Kingsley DM, Veeramah KR. Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution. SCIENCE ADVANCES 2021; 7:7/25/eabg5285. [PMID: 34144992 PMCID: PMC8213234 DOI: 10.1126/sciadv.abg5285] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/05/2021] [Indexed: 05/30/2023]
Abstract
Similar forms often evolve repeatedly in nature, raising long-standing questions about the underlying mechanisms. Here, we use repeated evolution in stickleback to identify a large set of genomic loci that change recurrently during colonization of freshwater habitats by marine fish. The same loci used repeatedly in extant populations also show rapid allele frequency changes when new freshwater populations are experimentally established from marine ancestors. Marked genotypic and phenotypic changes arise within 5 years, facilitated by standing genetic variation and linkage between adaptive regions. Both the speed and location of changes can be predicted using empirical observations of recurrence in natural populations or fundamental genomic features like allelic age, recombination rates, density of divergent loci, and overlap with mapped traits. A composite model trained on these stickleback features can also predict the location of key evolutionary loci in Darwin's finches, suggesting that similar features are important for evolution across diverse taxa.
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Affiliation(s)
- Garrett A Roberts Kingman
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Deven N Vyas
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Felicity C Jones
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany
| | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
| | - Kerry Reid
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Mark Milhaven
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Thomas S Bertino
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA
| | - Windsor E Aguirre
- Department of Biological Sciences, DePaul University, Chicago, IL 60614-3207, USA
| | - David C Heins
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Frank A von Hippel
- Department of Community, Environment and Policy, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ 85724, USA
| | - Peter J Park
- Department of Biology, Farmingdale State College, Farmingdale, NY 11735-1021, USA
| | - Melanie Kirch
- Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring, Tübingen, Germany
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
| | - Federica Di Palma
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Michael A Bell
- University of California Museum of Paleontology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA.
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19
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O'Dea RE, Lagisz M, Jennions MD, Koricheva J, Noble DWA, Parker TH, Gurevitch J, Page MJ, Stewart G, Moher D, Nakagawa S. Preferred reporting items for systematic reviews and meta-analyses in ecology and evolutionary biology: a PRISMA extension. Biol Rev Camb Philos Soc 2021; 96:1695-1722. [PMID: 33960637 PMCID: PMC8518748 DOI: 10.1111/brv.12721] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 12/29/2022]
Abstract
Since the early 1990s, ecologists and evolutionary biologists have aggregated primary research using meta-analytic methods to understand ecological and evolutionary phenomena. Meta-analyses can resolve long-standing disputes, dispel spurious claims, and generate new research questions. At their worst, however, meta-analysis publications are wolves in sheep's clothing: subjective with biased conclusions, hidden under coats of objective authority. Conclusions can be rendered unreliable by inappropriate statistical methods, problems with the methods used to select primary research, or problems within the primary research itself. Because of these risks, meta-analyses are increasingly conducted as part of systematic reviews, which use structured, transparent, and reproducible methods to collate and summarise evidence. For readers to determine whether the conclusions from a systematic review or meta-analysis should be trusted - and to be able to build upon the review - authors need to report what they did, why they did it, and what they found. Complete, transparent, and reproducible reporting is measured by 'reporting quality'. To assess perceptions and standards of reporting quality of systematic reviews and meta-analyses published in ecology and evolutionary biology, we surveyed 208 researchers with relevant experience (as authors, reviewers, or editors), and conducted detailed evaluations of 102 systematic review and meta-analysis papers published between 2010 and 2019. Reporting quality was far below optimal and approximately normally distributed. Measured reporting quality was lower than what the community perceived, particularly for the systematic review methods required to measure trustworthiness. The minority of assessed papers that referenced a guideline (~16%) showed substantially higher reporting quality than average, and surveyed researchers showed interest in using a reporting guideline to improve reporting quality. The leading guideline for improving reporting quality of systematic reviews is the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) statement. Here we unveil an extension of PRISMA to serve the meta-analysis community in ecology and evolutionary biology: PRISMA-EcoEvo (version 1.0). PRISMA-EcoEvo is a checklist of 27 main items that, when applicable, should be reported in systematic review and meta-analysis publications summarising primary research in ecology and evolutionary biology. In this explanation and elaboration document, we provide guidance for authors, reviewers, and editors, with explanations for each item on the checklist, including supplementary examples from published papers. Authors can consult this PRISMA-EcoEvo guideline both in the planning and writing stages of a systematic review and meta-analysis, to increase reporting quality of submitted manuscripts. Reviewers and editors can use the checklist to assess reporting quality in the manuscripts they review. Overall, PRISMA-EcoEvo is a resource for the ecology and evolutionary biology community to facilitate transparent and comprehensively reported systematic reviews and meta-analyses.
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Affiliation(s)
- Rose E O'Dea
- Evolution & Ecology Research Centre and School of Biological and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Malgorzata Lagisz
- Evolution & Ecology Research Centre and School of Biological and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Michael D Jennions
- Research School of Biology, Australian National University, 46 Sullivans Creek Road, Canberra, 2600, Australia
| | - Julia Koricheva
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, U.K
| | - Daniel W A Noble
- Evolution & Ecology Research Centre and School of Biological and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.,Research School of Biology, Australian National University, 46 Sullivans Creek Road, Canberra, 2600, Australia
| | - Timothy H Parker
- Department of Biology, Whitman College, Walla Walla, WA, 99362, U.S.A
| | - Jessica Gurevitch
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794-5245, U.S.A
| | - Matthew J Page
- School of Public Health and Preventative Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Gavin Stewart
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K
| | - David Moher
- Centre for Journalology, Clinical Epidemiology Program, Ottawa Hospital Research Institute, General Campus, 501 Smyth Road, Room L1288, Ottawa, ON, K1H 8L6, Canada
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre and School of Biological and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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20
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Schluter D, Marchinko KB, Arnegard ME, Zhang H, Brady SD, Jones FC, Bell MA, Kingsley DM. Fitness maps to a large-effect locus in introduced stickleback populations. Proc Natl Acad Sci U S A 2021; 118:e1914889118. [PMID: 33414274 PMCID: PMC7826376 DOI: 10.1073/pnas.1914889118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mutations of small effect underlie most adaptation to new environments, but beneficial variants with large fitness effects are expected to contribute under certain conditions. Genes and genomic regions having large effects on phenotypic differences between populations are known from numerous taxa, but fitness effect sizes have rarely been estimated. We mapped fitness over a generation in an F2 intercross between a marine and a lake stickleback population introduced to a freshwater pond. A quantitative trait locus map of the number of surviving offspring per F2 female detected a single, large-effect locus near Ectodysplasin (Eda), a gene having an ancient freshwater allele causing reduced bony armor and other changes. F2 females homozygous for the freshwater allele had twice the number of surviving offspring as homozygotes for the marine allele, producing a large selection coefficient, s = 0.50 ± 0.09 SE. Correspondingly, the frequency of the freshwater allele increased from 0.50 in F2 mothers to 0.58 in surviving offspring. We compare these results to allele frequency changes at the Eda gene in an Alaskan lake population colonized by marine stickleback in the 1980s. The frequency of the freshwater Eda allele rose steadily over multiple generations and reached 95% within 20 y, yielding a similar estimate of selection, s = 0.49 ± 0.05, but a different degree of dominance. These findings are consistent with other studies suggesting strong selection on this gene (and/or linked genes) in fresh water. Selection on ancient genetic variants carried by colonizing ancestors is likely to increase the prevalence of large-effect fitness variants in adaptive evolution.
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Affiliation(s)
- Dolph Schluter
- Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4;
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Kerry B Marchinko
- Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Matthew E Arnegard
- Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Haili Zhang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Shannon D Brady
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Felicity C Jones
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305
| | - Michael A Bell
- University of California Museum of Paleontology, Berkeley, CA 94720
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305;
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
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21
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DiVittorio CT, Singhal S, Roddy AB, Zapata F, Ackerly DD, Baldwin BG, Brodersen CR, Búrquez A, Fine PVA, Padilla Flores M, Solis E, Morales-Villavicencio J, Morales-Arce D, Kyhos DW. Natural selection maintains species despite frequent hybridization in the desert shrub Encelia. Proc Natl Acad Sci U S A 2020; 117:33373-33383. [PMID: 33318178 PMCID: PMC7776959 DOI: 10.1073/pnas.2001337117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 11/03/2020] [Indexed: 01/01/2023] Open
Abstract
Natural selection is an important driver of genetic and phenotypic differentiation between species. For species in which potential gene flow is high but realized gene flow is low, adaptation via natural selection may be a particularly important force maintaining species. For a recent radiation of New World desert shrubs (Encelia: Asteraceae), we use fine-scale geographic sampling and population genomics to determine patterns of gene flow across two hybrid zones formed between two independent pairs of species with parapatric distributions. After finding evidence for extremely strong selection at both hybrid zones, we use a combination of field experiments, high-resolution imaging, and physiological measurements to determine the ecological basis for selection at one of the hybrid zones. Our results identify multiple ecological mechanisms of selection (drought, salinity, herbivory, and burial) that together are sufficient to maintain species boundaries despite high rates of hybridization. Given that multiple pairs of Encelia species hybridize at ecologically divergent parapatric boundaries, such mechanisms may maintain species boundaries throughout Encelia.
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Affiliation(s)
- Christopher T DiVittorio
- Department of Integrative Biology, University of California, Berkeley, CA 94720;
- TruBreed Technologies, Oakland, CA 94609
| | - Sonal Singhal
- Department of Biology, California State University - Dominguez Hills, Carson, CA 90747;
| | - Adam B Roddy
- School of the Environment, Yale University, New Haven, CT 06511
- Institute of Environment, Department of Biological Sciences, Florida International University, Miami, FL 33199
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095
| | - David D Ackerly
- Department of Integrative Biology, University of California, Berkeley, CA 94720
- Jepson Herbarium, University of California, Berkeley, CA 94720
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
| | - Bruce G Baldwin
- Department of Integrative Biology, University of California, Berkeley, CA 94720
- Jepson Herbarium, University of California, Berkeley, CA 94720
| | | | - Alberto Búrquez
- Instituto de Ecología, Universidad Autónoma de México, Sonora, 83000 Hermosillo, México
| | - Paul V A Fine
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Mayra Padilla Flores
- Department of Biology, California State University - Dominguez Hills, Carson, CA 90747
| | - Elizabeth Solis
- Department of Biology, California State University - Dominguez Hills, Carson, CA 90747
| | | | - David Morales-Arce
- Benito Juárez s/n, Colonia Barrio La Punta, Bahia Asunción, 23960 Baja California Sur, México
| | - Donald W Kyhos
- Department of Plant Biology, University of California, Davis, CA 95616
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22
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Schneider K, White TJ, Mitchell S, Adams CE, Reeve R, Elmer KR. The pitfalls and virtues of population genetic summary statistics: Detecting selective sweeps in recent divergences. J Evol Biol 2020; 34:893-909. [DOI: 10.1111/jeb.13738] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Kevin Schneider
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Tom J. White
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Sonia Mitchell
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Colin E. Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
- Scottish Centre for Ecology and the Natural Environment Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Richard Reeve
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
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23
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Ochoa A, Broe M, Moriarty Lemmon E, Lemmon AR, Rokyta DR, Gibbs HL. Drift, selection and adaptive variation in small populations of a threatened rattlesnake. Mol Ecol 2020; 29:2612-2625. [PMID: 32557885 DOI: 10.1111/mec.15517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/09/2020] [Accepted: 05/21/2020] [Indexed: 01/22/2023]
Abstract
An important goal of conservation genetics is to determine if the viability of small populations is reduced by a loss of adaptive variation due to genetic drift. Here, we assessed the impact of drift and selection on direct measures of adaptive variation (toxin loci encoding venom proteins) in the eastern massasauga rattlesnake (Sistrurus catenatus), a threatened reptile that exists in small isolated populations. We estimated levels of individual polymorphism in 46 toxin loci and 1,467 control loci across 12 populations of this species, and compared the results with patterns of selection on the same loci following speciation of S. catenatus and its closest relative, the western massasauga (S. tergeminus). Multiple lines of evidence suggest that both drift and selection have had observable impacts on standing adaptive variation. In support of drift effects, we found little evidence for selection on toxin variation within populations and a significant positive relationship between current levels of adaptive variation and long- and short-term estimates of effective population size. However, we also observed levels of directional selection on toxin loci among populations that are broadly similar to patterns predicted from interspecific selection analyses that pre-date the effects of recent drift, and that functional variation in these loci persists despite small short-term effective sizes. This suggests that much of the adaptive variation present in populations may represent an example of "drift debt," a nonequilibrium state where present-day levels of variation overestimate the amount of functional genetic diversity present in future populations.
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Affiliation(s)
- Alexander Ochoa
- Ohio Biodiversity Conservation Partnership and Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
| | - Michael Broe
- Ohio Biodiversity Conservation Partnership and Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
| | | | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - H Lisle Gibbs
- Ohio Biodiversity Conservation Partnership and Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, USA
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24
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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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25
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Berny Mier y Teran JC, Konzen ER, Medina V, Palkovic A, Ariani A, Tsai SM, Gilbert ME, Gepts P. Root and shoot variation in relation to potential intermittent drought adaptation of Mesoamerican wild common bean (Phaseolus vulgaris L.). ANNALS OF BOTANY 2019; 124:917-932. [PMID: 30596881 PMCID: PMC6881220 DOI: 10.1093/aob/mcy221] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 11/14/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Wild crop relatives have been potentially subjected to stresses on an evolutionary time scale prior to domestication. Among these stresses, drought is one of the main factors limiting crop productivity and its impact is likely to increase under current scenarios of global climate change. We sought to determine to what extent wild common bean (Phaseolus vulgaris) exhibited adaptation to drought stress, whether this potential adaptation is dependent on the climatic conditions of the location of origin of individual populations, and to what extent domesticated common bean reflects potential drought adaptation. METHODS An extensive and diverse set of wild beans from across Mesoamerica, along with a set of reference Mesoamerican domesticated cultivars, were evaluated for root and shoot traits related to drought adaptation. A water deficit experiment was conducted by growing each genotype in a long transparent tube in greenhouse conditions so that root growth, in addition to shoot growth, could be monitored. RESULTS Phenotypic and landscape genomic analyses, based on single-nucleotide polymorphisms, suggested that beans originating from central and north-west Mexico and Oaxaca, in the driest parts of their distribution, produced more biomass and were deeper-rooted. Nevertheless, deeper rooting was correlated with less root biomass production relative to total biomass. Compared with wild types, domesticated types showed a stronger reduction and delay in growth and development in response to drought stress. Specific genomic regions were associated with root depth, biomass productivity and drought response, some of which showed signals of selection and were previously related to productivity and drought tolerance. CONCLUSIONS The drought tolerance of wild beans consists in its stronger ability, compared with domesticated types, to continue growth in spite of water-limited conditions. This study is the first to relate bean response to drought to environment of origin for a diverse selection of wild beans. It provides information that needs to be corroborated in crosses between wild and domesticated beans to make it applicable to breeding programmes.
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Affiliation(s)
- Jorge C Berny Mier y Teran
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - Enéas R Konzen
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
- Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, Piracicaba, SP, Brasil
| | - Viviana Medina
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - Antonia Palkovic
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - Andrea Ariani
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - Siu M Tsai
- Centro de Energia Nuclear na Agricultura (CENA), Universidade de São Paulo, Piracicaba, SP, Brasil
| | - Matthew E Gilbert
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
| | - P Gepts
- University of California, Department of Plant Sciences/Mail Stop 1, Section of Crop & Ecosystem Sciences, Davis, CA, USA
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26
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Exposito-Alonso M, Burbano HA, Bossdorf O, Nielsen R, Weigel D. Natural selection on the Arabidopsis thaliana genome in present and future climates. Nature 2019; 573:126-129. [PMID: 31462776 DOI: 10.1038/s41586-019-1520-9] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/04/2019] [Indexed: 11/09/2022]
Abstract
Through the lens of evolution, climate change is an agent of natural selection that forces populations to change and adapt, or face extinction. However, current assessments of the risk of biodiversity associated with climate change1 do not typically take into account how natural selection influences populations differently depending on their genetic makeup2. Here we make use of the extensive genome information that is available for Arabidopsis thaliana and measure how manipulation of the amount of rainfall affected the fitness of 517 natural Arabidopsis lines that were grown in Spain and Germany. This allowed us to directly infer selection along the genome3. Natural selection was particularly strong in the hot-dry location in Spain, where 63% of lines were killed and where natural selection substantially changed the frequency of approximately 5% of all genome-wide variants. A significant portion of this climate-driven natural selection of variants was predictable from signatures of local adaptation (R2 = 29-52%), as genetic variants that were found in geographical areas with climates more similar to the experimental sites were positively selected. Field-validated predictions across the species range indicated that Mediterranean and western Siberian populations-at the edges of the environmental limits of this species-currently experience the strongest climate-driven selection. With more frequent droughts and rising temperatures in Europe4, we forecast an increase in directional natural selection moving northwards from the southern end of Europe, putting many native A. thaliana populations at evolutionary risk.
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Affiliation(s)
- Moises Exposito-Alonso
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA.,Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | | | - Hernán A Burbano
- Research Group of Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, London, UK
| | - Oliver Bossdorf
- Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA.,Department of Statistics, University of California Berkeley, Berkeley, CA, USA.,Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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27
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Brady SP, Bolnick DI, Barrett RDH, Chapman L, Crispo E, Derry AM, Eckert CG, Fraser DJ, Fussmann GF, Gonzalez A, Guichard F, Lamy T, Lane J, McAdam AG, Newman AEM, Paccard A, Robertson B, Rolshausen G, Schulte PM, Simons AM, Vellend M, Hendry A. Understanding Maladaptation by Uniting Ecological and Evolutionary Perspectives. Am Nat 2019; 194:495-515. [PMID: 31490718 DOI: 10.1086/705020] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Evolutionary biologists have long trained their sights on adaptation, focusing on the power of natural selection to produce relative fitness advantages while often ignoring changes in absolute fitness. Ecologists generally have taken a different tack, focusing on changes in abundance and ranges that reflect absolute fitness while often ignoring relative fitness. Uniting these perspectives, we articulate various causes of relative and absolute maladaptation and review numerous examples of their occurrence. This review indicates that maladaptation is reasonably common from both perspectives, yet often in contrasting ways. That is, maladaptation can appear strong from a relative fitness perspective, yet populations can be growing in abundance. Conversely, resident individuals can appear locally adapted (relative to nonresident individuals) yet be declining in abundance. Understanding and interpreting these disconnects between relative and absolute maladaptation, as well as the cases of agreement, is increasingly critical in the face of accelerating human-mediated environmental change. We therefore present a framework for studying maladaptation, focusing in particular on the relationship between absolute and relative fitness, thereby drawing together evolutionary and ecological perspectives. The unification of these ecological and evolutionary perspectives has the potential to bring together previously disjunct research areas while addressing key conceptual issues and specific practical problems.
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28
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Backes A, Mäder G, Turchetto C, Segatto AL, Fregonezi JN, Bonatto SL, Freitas LB. How diverse can rare species be on the margins of genera distribution? AOB PLANTS 2019; 11:plz037. [PMID: 31391895 PMCID: PMC6677564 DOI: 10.1093/aobpla/plz037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
Different genetic patterns have been demonstrated for narrowly distributed taxa, many of them linking rarity to evolutionary history. Quite a few species in young genera are endemics and have several populations that present low variability, sometimes attributed to geographical isolation or dispersion processes. Assessing the genetic diversity and structure of such species may be important for protecting them and understanding their diversification history. In this study, we used microsatellite markers and plastid sequences to characterize the levels of genetic variation and population structure of two endemic and restricted species that grow in isolated areas on the margin of the distribution of their respective genera. Plastid and nuclear diversities were very low and weakly structured in their populations. Evolutionary scenarios for both species are compatible with open-field expansions during the Pleistocene interglacial periods and genetic variability supports founder effects to explain diversification. At present, both species are suffering from habitat loss and changes in the environment can lead these species towards extinction.
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Affiliation(s)
- Alice Backes
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Geraldo Mäder
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Caroline Turchetto
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Lúcia Segatto
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Jeferson N Fregonezi
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Sandro L Bonatto
- Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Loreta B Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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29
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Sylvester EVA, Wringe BF, Duffy SJ, Hamilton LC, Fleming IA, Castellani M, Bentzen P, Bradbury IR. Estimating the relative fitness of escaped farmed salmon offspring in the wild and modelling the consequences of invasion for wild populations. Evol Appl 2019; 12:705-717. [PMID: 30976304 PMCID: PMC6439497 DOI: 10.1111/eva.12746] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 12/25/2022] Open
Abstract
Throughout their native range, wild Atlantic salmon populations are threatened by hybridization and introgression with escapees from net-pen salmon aquaculture. Although domestic-wild hybrid offspring have shown reduced fitness in laboratory and field experiments, consequential impacts on population abundance and genetic integrity remain difficult to predict in the field, in part because the strength of selection against domestic offspring is often unknown and context-dependent. Here, we follow a single large escape event of farmed Atlantic salmon in southern Newfoundland and monitor changes in the in-river proportions of hybrids and feral individuals over time using genetically based hybrid identification. Over a three-year period following the escape, the overall proportion of wild parr increased consistently (total wild proportion of 71.6%, 75.1% and 87.5% each year, respectively), with subsequent declines in feral (genetically pure farmed individuals originating from escaped, farmed adults) and hybrid parr. We quantify the strength of selection against parr of aquaculture ancestry and explore the genetic and demographic consequences for populations in the region. Within-cohort changes in the relative proportions of feral and F1 parr suggest reduced relative survival compared to wild individuals over the first (0.15 and 0.81 for feral and F1, respectively) and second years of life (0.26, 0.83). These relative survivorship estimates were used to inform an individual-based salmon eco-genetic model to project changes in adult abundance and overall allele frequency across three invasion scenarios ranging from short-term to long-term invasion and three relative survival scenarios. Modelling results indicate that total population abundance and time to recovery were greatly affected by relative survivorship and predict significant declines in wild population abundance under continued large escape events and calculated survivorship. Overall, this work demonstrates the importance of estimating the strength of selection against domestic offspring in the wild to predict the long-term impact of farmed salmon escape events on wild populations.
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Affiliation(s)
- Emma V. A. Sylvester
- Science Branch, Fisheries and Oceans CanadaSt. John’sNewfoundland and LabradorCanada
| | - Brendan F. Wringe
- Science Branch, Department of Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Steven J. Duffy
- Science Branch, Fisheries and Oceans CanadaSt. John’sNewfoundland and LabradorCanada
| | - Lorraine C. Hamilton
- Aquatic Biotechnology Laboratory, Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Ian A. Fleming
- Memorial University of NewfoundlandDepartment of Ocean SciencesSt. John’sNewfoundland and LabradorCanada
| | - Marco Castellani
- Department of Mechanical EngineeringUniversity of BirminghamBirminghamUK
| | - Paul Bentzen
- Marine Gene Probe Laboratory, Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Ian R. Bradbury
- Science Branch, Fisheries and Oceans CanadaSt. John’sNewfoundland and LabradorCanada
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30
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Barrett RDH, Laurent S, Mallarino R, Pfeifer SP, Xu CCY, Foll M, Wakamatsu K, Duke-Cohan JS, Jensen JD, Hoekstra HE. Linking a mutation to survival in wild mice. Science 2019; 363:499-504. [DOI: 10.1126/science.aav3824] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/06/2018] [Indexed: 12/19/2022]
Abstract
Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments in wild mice. We first directly estimate natural selection on pigmentation traits and an underlying pigment locus, Agouti, by using experimental enclosures of mice on different soil colors. Next, we show how a mutation in Agouti associated with survival causes lighter coat color through changes in its protein binding properties. Together, our findings demonstrate how a sequence variant alters phenotype and then reveal the ensuing ecological consequences that drive changes in population allele frequency, thereby illuminating the process of evolution by natural selection.
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31
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Feder JL, Nosil P, Gompert Z, Flaxman SM, Schilling MP. Barnacles, barrier loci and the systematic building of species. J Evol Biol 2018; 30:1494-1497. [PMID: 28786183 DOI: 10.1111/jeb.13105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 12/20/2022]
Affiliation(s)
- J L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - P Nosil
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Z Gompert
- Department of Biology, Utah State University, Logan, UT, USA
| | - S M Flaxman
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - M P Schilling
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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32
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Matthews B, Best RJ, Feulner PGD, Narwani A, Limberger R. Evolution as an ecosystem process: insights from genomics. Genome 2017; 61:298-309. [PMID: 29241022 DOI: 10.1139/gen-2017-0044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Evolution is a fundamental ecosystem process. The study of genomic variation of organisms can not only improve our understanding of evolutionary processes, but also of contemporary and future ecosystem dynamics. We argue that integrative research between the fields of genomics and ecosystem ecology could generate new insights. Specifically, studies of biodiversity and ecosystem functioning, evolutionary rescue, and eco-evolutionary dynamics could all benefit from information about variation in genome structure and the genetic architecture of traits, whereas genomic studies could benefit from information about the ecological context of evolutionary dynamics. We propose new ways to help link research on functional genomic diversity with (reciprocal) interactions between phenotypic evolution and ecosystem change. Despite numerous challenges, we anticipate that the wealth of genomic data being collected on natural populations will improve our understanding of ecosystems.
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Affiliation(s)
- Blake Matthews
- a Eawag, Department of Aquatic Ecology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Rebecca J Best
- a Eawag, Department of Aquatic Ecology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,b School of Earth Sciences and Environmental Sustainability, Northern Arizona University, 525 S. Beaver Street, Flagstaff, AZ 86011, USA
| | - Philine G D Feulner
- c Eawag, Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,d University of Bern, Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, Bern, Switzerland
| | - Anita Narwani
- a Eawag, Department of Aquatic Ecology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Romana Limberger
- a Eawag, Department of Aquatic Ecology, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland.,e Research Institute for Limnology, University of Innsbruck, Mondsee, Austria
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33
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Rudman SM, Barbour MA, Csilléry K, Gienapp P, Guillaume F, Hairston Jr NG, Hendry AP, Lasky JR, Rafajlović M, Räsänen K, Schmidt PS, Seehausen O, Therkildsen NO, Turcotte MM, Levine JM. What genomic data can reveal about eco-evolutionary dynamics. Nat Ecol Evol 2017; 2:9-15. [DOI: 10.1038/s41559-017-0385-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 10/16/2017] [Indexed: 01/17/2023]
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Seasonally fluctuating selection can maintain polymorphism at many loci via segregation lift. Proc Natl Acad Sci U S A 2017; 114:E9932-E9941. [PMID: 29087300 PMCID: PMC5699028 DOI: 10.1073/pnas.1702994114] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Most natural populations are affected by seasonal changes in temperature, rainfall, or resource availability. Seasonally fluctuating selection could potentially make a large contribution to maintaining genetic polymorphism in populations. However, previous theory suggests that the conditions for multilocus polymorphism are restrictive. Here, we explore a more general class of models with multilocus seasonally fluctuating selection in diploids. In these models, the multilocus genotype is mapped to fitness in two steps. The first mapping is additive across loci and accounts for the relative contributions of heterozygous and homozygous loci-that is, dominance. The second step uses a nonlinear fitness function to account for the strength of selection and epistasis. Using mathematical analysis and individual-based simulations, we show that stable polymorphism at many loci is possible if currently favored alleles are sufficiently dominant. This general mechanism, which we call "segregation lift," requires seasonal changes in dominance, a phenomenon that may arise naturally in situations with antagonistic pleiotropy and seasonal changes in the relative importance of traits for fitness. Segregation lift works best under diminishing-returns epistasis, is not affected by problems of genetic load, and is robust to differences in parameters across loci and seasons. Under segregation lift, loci can exhibit conspicuous seasonal allele-frequency fluctuations, but often fluctuations may be small and hard to detect. An important direction for future work is to formally test for segregation lift in empirical data and to quantify its contribution to maintaining genetic variation in natural populations.
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35
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Abstract
Population geneticists have long sought to understand the contribution of natural selection to molecular evolution. A variety of approaches have been proposed that use population genetics theory to quantify the rate and strength of positive selection acting in a species’ genome. In this review we discuss methods that use patterns of between-species nucleotide divergence and within-species diversity to estimate positive selection parameters from population genomic data. We also discuss recently proposed methods to detect positive selection from a population’s haplotype structure. The application of these tests has resulted in the detection of pervasive adaptive molecular evolution in multiple species.
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36
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Hu J, Barrett RDH. Epigenetics in natural animal populations. J Evol Biol 2017; 30:1612-1632. [PMID: 28597938 DOI: 10.1111/jeb.13130] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 06/01/2017] [Accepted: 06/03/2017] [Indexed: 12/22/2022]
Abstract
Phenotypic plasticity is an important mechanism for populations to buffer themselves from environmental change. While it has long been appreciated that natural populations possess genetic variation in the extent of plasticity, a surge of recent evidence suggests that epigenetic variation could also play an important role in shaping phenotypic responses. Compared with genetic variation, epigenetic variation is more likely to have higher spontaneous rates of mutation and a more sensitive reaction to environmental inputs. In our review, we first provide an overview of recent studies on epigenetically encoded thermal plasticity in animals to illustrate environmentally-mediated epigenetic effects within and across generations. Second, we discuss the role of epigenetic effects during adaptation by exploring population epigenetics in natural animal populations. Finally, we evaluate the evolutionary potential of epigenetic variation depending on its autonomy from genetic variation and its transgenerational stability. Although many of the causal links between epigenetic variation and phenotypic plasticity remain elusive, new data has explored the role of epigenetic variation in facilitating evolution in natural populations. This recent progress in ecological epigenetics will be helpful for generating predictive models of the capacity of organisms to adapt to changing climates.
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Affiliation(s)
- J Hu
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
| | - R D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
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37
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Wadgymar SM, Daws SC, Anderson JT. Integrating viability and fecundity selection to illuminate the adaptive nature of genetic clines. Evol Lett 2017; 1:26-39. [PMID: 30283636 PMCID: PMC6121800 DOI: 10.1002/evl3.3] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/15/2017] [Accepted: 03/20/2017] [Indexed: 12/18/2022] Open
Abstract
Genetically based trait variation across environmental gradients can reflect adaptation to local environments. However, natural populations that appear well-adapted often exhibit directional, not stabilizing, selection on ecologically relevant traits. Temporal variation in the direction of selection could lead to stabilizing selection across multiple episodes of selection, which might be overlooked in short-term studies that evaluate relationships of traits and fitness under only one set of conditions. Furthermore, nonrandom mortality prior to trait expression can bias inferences about trait evolution if viability selection opposes fecundity selection. Here, we leveraged fitness and trait data to test whether phenotypic clines are genetically based and adaptive, whether temporal variation in climate imposes stabilizing selection, and whether viability selection acts on adult phenotypes. We monitored transplants of the subalpine perennial forb, Boechera stricta (Brassicaceae), in common gardens at two elevations over 2-3 years that differed in drought intensity. We quantified viability, and fecundity fitness components for four heritable traits: specific leaf area, integrated water-use efficiency, height at first flower, and flowering phenology. Our results indicate that genetic clines are maintained by selection, but their expression is context dependent, as they do not emerge in all environments. Moreover, selection varied spatially and temporally. Stabilizing selection was most pronounced when we integrated data across years. Finally, viability selection prior to trait expression targeted adult phenotypes (age and size at flowering). Indeed, viability selection for delayed flowering opposed fecundity selection for accelerated flowering; this result demonstrates that neglecting to account for viability selection could lead to inaccurate conclusions that populations are maladapted. Our results suggest that reconciling clinal trait variation with selection requires data collected across multiple spatial scales, time frames, and life-history stages.
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Affiliation(s)
- Susana M Wadgymar
- Department of Genetics and Odum School of Ecology University of Georgia Athens Georgia 30602
| | - S Caroline Daws
- Department of Ecology, Evolution and Behavior University of Minnesota St. Paul Minnesota 55108
| | - Jill T Anderson
- Department of Genetics and Odum School of Ecology University of Georgia Athens Georgia 30602
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38
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Bay RA, Rose N, Barrett R, Bernatchez L, Ghalambor CK, Lasky JR, Brem RB, Palumbi SR, Ralph P. Predicting Responses to Contemporary Environmental Change Using Evolutionary Response Architectures. Am Nat 2017; 189:463-473. [DOI: 10.1086/691233] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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39
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Pankey MS, Foxall RL, Ster IM, Perry LA, Schuster BM, Donner RA, Coyle M, Cooper VS, Whistler CA. Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria. eLife 2017; 6:e24414. [PMID: 28447935 PMCID: PMC5466423 DOI: 10.7554/elife.24414] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/23/2017] [Indexed: 01/14/2023] Open
Abstract
Host immune and physical barriers protect against pathogens but also impede the establishment of essential symbiotic partnerships. To reveal mechanisms by which beneficial organisms adapt to circumvent host defenses, we experimentally evolved ecologically distinct bioluminescent Vibrio fischeri by colonization and growth within the light organs of the squid Euprymna scolopes. Serial squid passaging of bacteria produced eight distinct mutations in the binK sensor kinase gene, which conferred an exceptional selective advantage that could be demonstrated through both empirical and theoretical analysis. Squid-adaptive binK alleles promoted colonization and immune evasion that were mediated by cell-associated matrices including symbiotic polysaccharide (Syp) and cellulose. binK variation also altered quorum sensing, raising the threshold for luminescence induction. Preexisting coordinated regulation of symbiosis traits by BinK presented an efficient solution where altered BinK function was the key to unlock multiple colonization barriers. These results identify a genetic basis for microbial adaptability and underscore the importance of hosts as selective agents that shape emergent symbiont populations.
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Affiliation(s)
- M Sabrina Pankey
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
| | - Randi L Foxall
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
| | - Ian M Ster
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
- Graduate Program in Biochemistry, University of New Hampshire, Durham, United States
| | - Lauren A Perry
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Graduate Program in Microbiology, University of New Hampshire, Durham, United States
| | - Brian M Schuster
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Rachel A Donner
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Matthew Coyle
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Graduate Program in Microbiology, University of New Hampshire, Durham, United States
| | - Vaughn S Cooper
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
| | - Cheryl A Whistler
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, United States
- Northeast Center for Vibrio Disease and Ecology, College of Life Science and Agriculture, University of New Hampshire, Durham, United States
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40
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Holliday JA, Aitken SN, Cooke JEK, Fady B, González-Martínez SC, Heuertz M, Jaramillo-Correa JP, Lexer C, Staton M, Whetten RW, Plomion C. Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding. Mol Ecol 2017; 26:706-717. [PMID: 27997049 DOI: 10.1111/mec.13963] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/07/2016] [Accepted: 12/14/2016] [Indexed: 12/25/2022]
Abstract
Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled 'Genomics and Forest Tree Genetics' was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology.
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Affiliation(s)
- Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, 304 Cheatham Hall, Blacksburg, VA 24061, USA
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T1Z4, Canada
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, 5-108 Centennial Centre for Interdisciplinary Science, Edmonton, AB T6G2E9, Canada
| | - Bruno Fady
- Mediterranean Forest Ecology (URFM), Institut National de la Recherche Agronomique (INRA), Domaine St Paul, Site Agroparc, 84914 Avignon, France
| | | | - Myriam Heuertz
- BIOGECO, INRA, Universite de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Juan-Pablo Jaramillo-Correa
- Institute of Ecology, Universidad Nacional Autonoma de Mexico (UNAM) Circuito Exterior s/n, Apartado Postal 70-275, 04510 Ciudad de México, Mexico City, Mexico
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna Faculty of Life SciencesRennweg 14, Room 217, A-1030, Vienna, Austria
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, 370 Plant Biotechnology Building, 2505 EJ Chapman Drive, Knoxville, TN 37996, USA
| | - Ross W Whetten
- Department of Forestry and Environmental Resources, North Carolina State University Jordan Hall Addition 5231, Raleigh, NC 27695, USA
| | - Christophe Plomion
- BIOGECO, INRA, Universite de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
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Bernatchez L. On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes. JOURNAL OF FISH BIOLOGY 2016; 89:2519-2556. [PMID: 27687146 DOI: 10.1111/jfb.13145] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/23/2016] [Indexed: 05/18/2023]
Abstract
The first goal of this paper was to overview modern approaches to local adaptation, with a focus on the use of population genomics data to detect signals of natural selection in fishes. Several mechanisms are discussed that may enhance the maintenance of genetic variation and evolutionary potential, which have been overlooked and should be considered in future theoretical development and predictive models: the prevalence of soft sweeps, polygenic basis of adaptation, balancing selection and transient polymorphisms, parallel evolution, as well as epigenetic variation. Research on fish population genomics has provided ample evidence for local adaptation at the genome level. Pervasive adaptive evolution, however, seems to almost never involve the fixation of beneficial alleles. Instead, adaptation apparently proceeds most commonly by soft sweeps entailing shifts in frequencies of alleles being shared between differentially adapted populations. One obvious factor contributing to the maintenance of standing genetic variation in the face of selective pressures is that adaptive phenotypic traits are most often highly polygenic, and consequently the response to selection should derive mostly from allelic co-variances among causative loci rather than pronounced allele frequency changes. Balancing selection in its various forms may also play an important role in maintaining adaptive genetic variation and the evolutionary potential of species to cope with environmental change. A large body of literature on fishes also shows that repeated evolution of adaptive phenotypes is a ubiquitous evolutionary phenomenon that seems to occur most often via different genetic solutions, further adding to the potential options of species to cope with a changing environment. Moreover, a paradox is emerging from recent fish studies whereby populations of highly reduced effective population sizes and impoverished genetic diversity can apparently retain their adaptive potential in some circumstances. Although more empirical support is needed, several recent studies suggest that epigenetic variation could account for this apparent paradox. Therefore, epigenetic variation should be fully integrated with considerations pertaining to role of soft sweeps, polygenic and balancing selection, as well as repeated adaptation involving different genetic basis towards improving models predicting the evolutionary potential of species to cope with a changing world.
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Affiliation(s)
- L Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1Y 2T8, Canada
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Gompert Z, Egan SP, Barrett RDH, Feder JL, Nosil P. Multilocus approaches for the measurement of selection on correlated genetic loci. Mol Ecol 2016; 26:365-382. [DOI: 10.1111/mec.13867] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 02/02/2023]
Affiliation(s)
| | - Scott P. Egan
- Department of BioSciences Rice University Houston TX 77005 USA
| | | | - Jeffrey L. Feder
- Department of Biological Science University of Notre Dame South Bend IN 46556 USA
| | - Patrik Nosil
- Department of Animal and Plant Sciences University of Sheffield Sheffield S10 2TN UK
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Song Z, Zhang M, Li F, Weng Q, Zhou C, Li M, Li J, Huang H, Mo X, Gan S. Genome scans for divergent selection in natural populations of the widespread hardwood species Eucalyptus grandis (Myrtaceae) using microsatellites. Sci Rep 2016; 6:34941. [PMID: 27748400 PMCID: PMC5066178 DOI: 10.1038/srep34941] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/20/2016] [Indexed: 11/09/2022] Open
Abstract
Identification of loci or genes under natural selection is important for both understanding the genetic basis of local adaptation and practical applications, and genome scans provide a powerful means for such identification purposes. In this study, genome-wide simple sequence repeats markers (SSRs) were used to scan for molecular footprints of divergent selection in Eucalyptus grandis, a hardwood species occurring widely in costal areas from 32° S to 16° S in Australia. High population diversity levels and weak population structure were detected with putatively neutral genomic SSRs. Using three FST outlier detection methods, a total of 58 outlying SSRs were collectively identified as loci under divergent selection against three non-correlated climatic variables, namely, mean annual temperature, isothermality and annual precipitation. Using a spatial analysis method, nine significant associations were revealed between FST outlier allele frequencies and climatic variables, involving seven alleles from five SSR loci. Of the five significant SSRs, two (EUCeSSR1044 and Embra394) contained alleles of putative genes with known functional importance for response to climatic factors. Our study presents critical information on the population diversity and structure of the important woody species E. grandis and provides insight into the adaptive responses of perennial trees to climatic variations.
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Affiliation(s)
- Zhijiao Song
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
- Baoshan University, Yuanzheng Road, Baoshan 678000, China
| | - Miaomiao Zhang
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
- College of Forestry, South China Agricultural University, 284 Block, Wushan Street, Guangzhou 510642, China
| | - Fagen Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Qijie Weng
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Chanpin Zhou
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Mei Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Jie Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Huanhua Huang
- Guangdong Academy of Forestry, Longdong, Guangzhou 510520, China
| | - Xiaoyong Mo
- College of Forestry, South China Agricultural University, 284 Block, Wushan Street, Guangzhou 510642, China
| | - Siming Gan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing 100091, China
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou 510520, China
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45
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Hansen TF. On bias and precision in meta-analysis: the error in the error. J Evol Biol 2016; 29:1919-1921. [DOI: 10.1111/jeb.12947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 04/16/2016] [Indexed: 12/01/2022]
Affiliation(s)
- T. F. Hansen
- Department of Biology; CEES & EVOGENE; University of Oslo; Oslo Norway
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46
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Gompert Z, Messina FJ. Genomic evidence that resource-based trade-offs limit host-range expansion in a seed beetle. Evolution 2016; 70:1249-64. [DOI: 10.1111/evo.12933] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/15/2016] [Indexed: 01/12/2023]
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