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Filatov DA, Kirkpatrick M. How does evolution work in superabundant microbes? Trends Microbiol 2024; 32:836-846. [PMID: 38360431 DOI: 10.1016/j.tim.2024.01.009] [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: 10/13/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024]
Abstract
Marine phytoplankton play crucial roles in the Earth's ecological, chemical, and geological processes. They are responsible for about half of global primary production and drive the ocean biological carbon pump. Understanding how plankton species may adapt to the Earth's rapidly changing environments is evidently an urgent priority. This problem requires evolutionary genetic approaches as evolution occurs at the level of allele frequency change within populations driven by genetic drift and natural selection (microevolution). Plankters such as the coccolithophore Gephyrocapsa huxleyi and the cyanobacterium Prochlorococcus 'marinus' are among Earth's most abundant organisms. In this opinion paper we discuss how evolution in astronomically large populations of superabundant microbes (SAMs) may act fundamentally differently than it does in the populations of more modest size found in well-studied organisms. This offers exciting opportunities to study evolution in the conditions that have yet to be explored and also leads to unique challenges. Exploring these opportunities and challenges is the goal of this article.
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Affiliation(s)
- Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
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2
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Wang Y, Allen SL, Reddiex AJ, Chenoweth SF. The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach. Mol Ecol 2024:e17499. [PMID: 39188068 DOI: 10.1111/mec.17499] [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: 03/20/2024] [Revised: 07/22/2024] [Accepted: 08/07/2024] [Indexed: 08/28/2024]
Abstract
This study explores the impact of positive selection on the genetic composition of a Drosophila serrata population in eastern Australia through a comprehensive analysis of 110 whole genome sequences. Utilizing an advanced deep learning algorithm (partialS/HIC) and a range of inferred demographic histories, we identified that approximately 14% of the genome is directly affected by sweeps, with soft sweeps being more prevalent (10.6%) than hard sweeps (2.1%), and partial sweeps being uncommon (1.3%). The algorithm demonstrated robustness to demographic assumptions in classifying complete sweeps but faced challenges in distinguishing neutral regions from partial sweeps and linked regions under demographic misspecification. The findings reveal the indirect influence of sweeps on nearly two-thirds of the genome through linkage, with an over-representation of putatively deleterious variants suggesting that positive selection drags deleterious variants to higher frequency due to hitchhiking with beneficial loci. Gene ontology enrichment analysis further supported our confidence in the accuracy of sweep detection as several traits expected to be under positive selection due to evolutionary arms races (e.g. immunity) were detected in hard sweeps. This study provides valuable insights into the direct and indirect contributions of positive selection in shaping genomic variation in natural populations.
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Affiliation(s)
- Yiguan Wang
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Scott L Allen
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Adam J Reddiex
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Biological Data Science Institute, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Stephen F Chenoweth
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
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3
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Whitehouse LS, Ray D, Schrider DR. Tree sequences as a general-purpose tool for population genetic inference. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.20.581288. [PMID: 39185244 PMCID: PMC11343121 DOI: 10.1101/2024.02.20.581288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
As population genetics data increases in size new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures are computationally and storage efficient, but are not interchangeable with existing data structures used for many population genetic inference methodologies such as the use of convolutional neural networks (CNNs) applied to population genetic alignments. To better utilize these new data structures we propose and implement a graph convolutional network (GCN) to directly learn from tree sequence topology and node data, allowing for the use of neural network applications without an intermediate step of converting tree sequences to population genetic alignment format. We then compare our approach to standard CNN approaches on a set of previously defined benchmarking tasks including recombination rate estimation, positive selection detection, introgression detection, and demographic model parameter inference. We show that tree sequences can be directly learned from using a GCN approach and can be used to perform well on these common population genetics inference tasks with accuracies roughly matching or even exceeding that of a CNN-based method. As tree sequences become more widely used in population genetics research we foresee developments and optimizations of this work to provide a foundation for population genetics inference moving forward.
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Affiliation(s)
- Logan S. Whitehouse
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Dylan Ray
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Daniel R. Schrider
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
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4
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Longan ER, Fay JC. The distribution of beneficial mutational effects between two sister yeast species poorly explains natural outcomes of vineyard adaptation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.597243. [PMID: 38895255 PMCID: PMC11185594 DOI: 10.1101/2024.06.03.597243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Domesticated strains of Saccharomyces cerevisiae have adapted to resist copper and sulfite, two chemical stressors commonly used in winemaking. S. paradoxus, has not adapted to these chemicals despite being consistently present in sympatry with S. cerevisiae in vineyards. This contrast represents a case of apparent evolutionary constraints favoring greater adaptive capacity in S. cerevisiae. In this study, we used a comparative mutagenesis approach to test whether S. paradoxus is mutationally constrained with respect to acquiring greater copper and sulfite resistance. For both species, we assayed the rate, effect size, and pleiotropic costs of resistance mutations and sequenced a subset of 150 mutants isolated from our screen. We found that the distributions of mutational effects displayed by the two species were very similar and poorly explained the natural pattern. We also found that chromosome VIII aneuploidy and loss of function mutations in PMA1 confer copper resistance in both species, whereas loss of function mutations in REG1 were only a viable route to copper resistance in S. cerevisiae. We also observed a single de novo duplication of the CUP1 gene in S. paradoxus but none in S. cerevisiae. For sulfite, loss of function mutations in RTS1 and KSP1 confer resistance in both species, but mutations in RTS1 have larger average effects in S. paradoxus. Our results show that even when the distributions of mutational effects are largely similar, species can differ in the adaptive paths available to them. They also demonstrate that assays of the distribution of mutational effects may lack predictive insight concerning adaptive outcomes.
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Affiliation(s)
- Emery R. Longan
- University of Rochester, Department of Biology, Rochester, NY, 14620 USA
| | - Justin C. Fay
- University of Rochester, Department of Biology, Rochester, NY, 14620 USA
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5
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Hernandes N, Qi XM, Bhide S, Brown C, Camm BJ, Baxter SW, Robin C. Acetylcholine esterase of Drosophila melanogaster: a laboratory model to explore insecticide susceptibility gene drives. PEST MANAGEMENT SCIENCE 2024; 80:2950-2964. [PMID: 38344908 DOI: 10.1002/ps.8003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/28/2024] [Accepted: 02/12/2024] [Indexed: 03/01/2024]
Abstract
BACKGROUND One of the proposed applications of gene drives has been to revert pesticide resistant mutations back to the ancestral susceptible state. Insecticides that have become ineffective because of the rise of resistance could have reinvigorated utility and be used to suppress pest populations again, perhaps at lower application doses. RESULTS We have created a laboratory model for susceptibility gene drives that replaces field-selected resistant variants of the acetylcholine esterase (Ace) locus of Drosophila melanogaster with ancestral susceptible variants. We constructed a CRISPR/Cas9 homing drive and found that homing occurred in many genetic backgrounds with varying efficiencies. While the drive itself could not be homozygous, it converted resistant alleles into susceptible ones and produced recessive lethal alleles that could suppress populations. Our studies provided evidence for two distinct classes of gene drive resistance (GDR): rather than being mediated by the conventional non-homologous end-joining (NHEJ) pathway, one seemed to involve short homologous repair and the other was defined by genetic background. Additionally, we used simulations to explore a distinct application of susceptibility drives; the use of chemicals to prevent the spread of synthetic gene drives into protected areas. CONCLUSIONS Insecticide susceptibility gene drives could be useful tools to control pest insects however problems with particularities of target loci and GDR will need to be overcome for them to be effective. Furthermore, realistic patterns of pest dispersal and high insecticide exposure rates would be required if susceptibility were to be useful as a 'safety-switch' to prevent the unwanted spread of gene drives. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Natalia Hernandes
- The School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Xiaomeng Mollyann Qi
- The School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Soumitra Bhide
- The School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Courtney Brown
- The School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin J Camm
- The School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Simon W Baxter
- The School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Charles Robin
- The School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
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Martin NS, Schaper S, Camargo CQ, Louis AA. Non-Poissonian Bursts in the Arrival of Phenotypic Variation Can Strongly Affect the Dynamics of Adaptation. Mol Biol Evol 2024; 41:msae085. [PMID: 38693911 PMCID: PMC11156200 DOI: 10.1093/molbev/msae085] [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: 11/08/2023] [Revised: 03/01/2024] [Accepted: 04/17/2024] [Indexed: 05/03/2024] Open
Abstract
Modeling the rate at which adaptive phenotypes appear in a population is a key to predicting evolutionary processes. Given random mutations, should this rate be modeled by a simple Poisson process, or is a more complex dynamics needed? Here we use analytic calculations and simulations of evolving populations on explicit genotype-phenotype maps to show that the introduction of novel phenotypes can be "bursty" or overdispersed. In other words, a novel phenotype either appears multiple times in quick succession or not at all for many generations. These bursts are fundamentally caused by statistical fluctuations and other structure in the map from genotypes to phenotypes. Their strength depends on population parameters, being highest for "monomorphic" populations with low mutation rates. They can also be enhanced by additional inhomogeneities in the mapping from genotypes to phenotypes. We mainly investigate the effect of bursts using the well-studied genotype-phenotype map for RNA secondary structure, but find similar behavior in a lattice protein model and in Richard Dawkins's biomorphs model of morphological development. Bursts can profoundly affect adaptive dynamics. Most notably, they imply that fitness differences play a smaller role in determining which phenotype fixes than would be the case for a Poisson process without bursts.
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Affiliation(s)
- Nora S Martin
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Steffen Schaper
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Chico Q Camargo
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, UK
- Faculty of Environment, Science and Economy, University of Exeter, Exeter EX4 4QF, UK
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, UK
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7
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Chen J, Liu C, Li W, Zhang W, Wang Y, Clark AG, Lu J. From sub-Saharan Africa to China: Evolutionary history and adaptation of Drosophila melanogaster revealed by population genomics. SCIENCE ADVANCES 2024; 10:eadh3425. [PMID: 38630810 PMCID: PMC11023512 DOI: 10.1126/sciadv.adh3425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
Drosophila melanogaster is a widely used model organism for studying environmental adaptation. However, the genetic diversity of populations in Asia is poorly understood, leaving a notable gap in our knowledge of the global evolution and adaptation of this species. We sequenced genomes of 292 D. melanogaster strains from various ecological settings in China and analyzed them along with previously published genome sequences. We have identified six global genetic ancestry groups, despite the presence of widespread genetic admixture. The strains from China represent a unique ancestry group, although detectable differentiation exists among populations within China. We deciphered the global migration and demography of D. melanogaster, and identified widespread signals of adaptation, including genetic changes in response to insecticides. We validated the effects of insecticide resistance variants using population cage trials and deep sequencing. This work highlights the importance of population genomics in understanding the genetic underpinnings of adaptation, an effort that is particularly relevant given the deterioration of ecosystems.
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Affiliation(s)
- Junhao Chen
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chenlu Liu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Weixuan Li
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenxia Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yirong Wang
- College of Biology, Hunan University, Changsha 410082, China
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
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Nunez JCB, Lenhart BA, Bangerter A, Murray CS, Mazzeo GR, Yu Y, Nystrom TL, Tern C, Erickson PA, Bergland AO. A cosmopolitan inversion facilitates seasonal adaptation in overwintering Drosophila. Genetics 2024; 226:iyad207. [PMID: 38051996 PMCID: PMC10847723 DOI: 10.1093/genetics/iyad207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
Fluctuations in the strength and direction of natural selection through time are a ubiquitous feature of life on Earth. One evolutionary outcome of such fluctuations is adaptive tracking, wherein populations rapidly adapt from standing genetic variation. In certain circumstances, adaptive tracking can lead to the long-term maintenance of functional polymorphism despite allele frequency change due to selection. Although adaptive tracking is likely a common process, we still have a limited understanding of aspects of its genetic architecture and its strength relative to other evolutionary forces such as drift. Drosophila melanogaster living in temperate regions evolve to track seasonal fluctuations and are an excellent system to tackle these gaps in knowledge. By sequencing orchard populations collected across multiple years, we characterized the genomic signal of seasonal demography and identified that the cosmopolitan inversion In(2L)t facilitates seasonal adaptive tracking and shows molecular footprints of selection. A meta-analysis of phenotypic studies shows that seasonal loci within In(2L)t are associated with behavior, life history, physiology, and morphological traits. We identify candidate loci and experimentally link them to phenotype. Our work contributes to our general understanding of fluctuating selection and highlights the evolutionary outcome and dynamics of contemporary selection on inversions.
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Affiliation(s)
- Joaquin C B Nunez
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
- Department of Biology, University of Vermont, 109 Carrigan Drive, Burlington, VT 05405, USA
| | - Benedict A Lenhart
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Alyssa Bangerter
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Connor S Murray
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Giovanni R Mazzeo
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Yang Yu
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Taylor L Nystrom
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Courtney Tern
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
| | - Priscilla A Erickson
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
- Department of Biology, University of Richmond, 138 UR Drive, Richmond, VA 23173, USA
| | - Alan O Bergland
- Department of Biology, University of Virginia, 90 Geldard Drive, Charlottesville, VA 22901, USA
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9
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Schrider DR. Allelic gene conversion softens selective sweeps. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570141. [PMID: 38106127 PMCID: PMC10723294 DOI: 10.1101/2023.12.05.570141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The prominence of positive selection, in which beneficial mutations are favored by natural selection and rapidly increase in frequency, is a subject of intense debate. Positive selection can result in selective sweeps, in which the haplotype(s) bearing the adaptive allele "sweep" through the population, thereby removing much of the genetic diversity from the region surrounding the target of selection. Two models of selective sweeps have been proposed: classical sweeps, or "hard sweeps", in which a single copy of the adaptive allele sweeps to fixation, and "soft sweeps", in which multiple distinct copies of the adaptive allele leave descendants after the sweep. Soft sweeps can be the outcome of recurrent mutation to the adaptive allele, or the presence of standing genetic variation consisting of multiple copies of the adaptive allele prior to the onset of selection. Importantly, soft sweeps will be common when populations can rapidly adapt to novel selective pressures, either because of a high mutation rate or because adaptive alleles are already present. The prevalence of soft sweeps is especially controversial, and it has been noted that selection on standing variation or recurrent mutations may not always produce soft sweeps. Here, we show that the inverse is true: selection on single-origin de novo mutations may often result in an outcome that is indistinguishable from a soft sweep. This is made possible by allelic gene conversion, which "softens" hard sweeps by copying the adaptive allele onto multiple genetic backgrounds, a process we refer to as a "pseudo-soft" sweep. We carried out a simulation study examining the impact of gene conversion on sweeps from a single de novo variant in models of human, Drosophila, and Arabidopsis populations. The fraction of simulations in which gene conversion had produced multiple haplotypes with the adaptive allele upon fixation was appreciable. Indeed, under realistic demographic histories and gene conversion rates, even if selection always acts on a single-origin mutation, sweeps involving multiple haplotypes are more likely than hard sweeps in large populations, especially when selection is not extremely strong. Thus, even when the mutation rate is low or there is no standing variation, hard sweeps are expected to be the exception rather than the rule in large populations. These results also imply that the presence of signatures of soft sweeps does not necessarily mean that adaptation has been especially rapid or is not mutation limited.
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Affiliation(s)
- Daniel R Schrider
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
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10
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Courtier-Orgogozo V. The loci of insect phenotypic evolution. CURRENT OPINION IN INSECT SCIENCE 2023; 60:101134. [PMID: 37858791 DOI: 10.1016/j.cois.2023.101134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/21/2023]
Abstract
Insects are important elements of terrestrial ecosystems because they pollinate plants, destroy crops, transmit diseases to livestock and humans, and are important components of food chains. Here, I used Gephebase, a manually curated database of genetic variants associated with natural and domesticated trait variation, to explore current knowledge about the genes and the mutations known to contribute to natural phenotypic variation in insects. Analysis of over 600 mutations reveals that data are concentrated toward certain species and traits and that experimental approaches have changed over time. The distribution of coding and cis-regulatory changes varies with traits, experimental approaches, and identified gene loci. Recent studies highlight the important role of standing variation, repeated mutations in hotspot genes, recombination, inversions, and introgression.
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11
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Haberkorn C, David J, Henri H, Delpuech J, Lasseur R, Vavre F, Varaldi J. A major 6 Mb superlocus is involved in pyrethroid resistance in the common bed bug Cimex lectularius. Evol Appl 2023; 16:1012-1028. [PMID: 37216030 PMCID: PMC10197226 DOI: 10.1111/eva.13550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/23/2023] [Accepted: 04/04/2023] [Indexed: 05/24/2023] Open
Abstract
In the last few years, the bed bug Cimex lectularius has been an increasing problem worldwide, mainly due to the development of insecticide resistance to pyrethroids. The characterization of resistance alleles is a prerequisite to improve surveillance and resistance management. To identify genomic variants associated with pyrethroid resistance in Cimex lectularius, we compared the genetic composition of two recent and resistant populations with that of two ancient-susceptible strains using a genome-wide pool-seq design. We identified a large 6 Mb "superlocus" showing particularly high genetic differentiation and association with the resistance phenotype. This superlocus contained several clustered resistance genes and was also characterized by a high density of structural variants (inversions, duplications). The possibility that this superlocus constitutes a resistance "supergene" that evolved after the clustering of alleles adapted to insecticide and after reduction in recombination is discussed.
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Affiliation(s)
- Chloé Haberkorn
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
- IZInovationLyonFrance
| | - Jean‐Philippe David
- Laboratoire d'Écologie AlpineUMR UGA‐USMB‐CNRS 5553 Université Grenoble Alpes CS 40700Grenoble cedex 9France
| | - Hélène Henri
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | - Jean‐Marie Delpuech
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | | | - Fabrice Vavre
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
| | - Julien Varaldi
- CNRS, VetAgro Sup, UMR 5558, Laboratoire de Biométrie et Biologie ÉvolutiveUniversité de Lyon, Université Lyon 1VilleurbanneFrance
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12
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Renault D, Elfiky A, Mohamed A. Predicting the insecticide-driven mutations in a crop pest insect: Evidence for multiple polymorphisms of acetylcholinesterase gene with potential relevance for resistance to chemicals. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:18937-18955. [PMID: 36219281 DOI: 10.1007/s11356-022-23309-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
The silverleaf whitefly Bemisia tabaci (Gennadius, 1889) (Homoptera: Aleyrodidae) is a serious invasive herbivorous insect pest worldwide. The excessive use of pesticides has progressively selected B. tabaci specimens, reducing the effectiveness of the treatments, and ultimately ending in the selection of pesticide-resistant strains. The management of this crop pest has thus become challenging owing to the level of resistance to all major classes of recommended insecticides. Here, we used in silico techniques for detecting sequence polymorphisms in ace1 gene from naturally occurring B. tabaci variants, and monitor the presence and frequency of the detected putative mutations from 30 populations of the silverleaf whitefly from Egypt and Pakistan. We found several point mutations in ace1-type acetylcholinesterase (ace1) in the studied B. tabaci variants naturally occurring in the field. By comparing ace1 sequence data from an organophosphate-susceptible and an organophosphate-resistant strains of B. tabaci to ace1 sequence data retrieved from GenBank for that species and to nucleotide polymorphisms from other arthropods, we identified novel mutations that could potentially influence insecticide resistance. Homology modeling and molecular docking analyses were performed to determine if the mutation-induced changes in form 1 acetylcholinesterase (AChE1) structure could confer resistance to carbamate and organophosphate insecticides. Mutations had small effects on binding energy (ΔGb) interactions between mutant AChE1 and insecticides; they altered the conformation of the peripheral anionic site of AChE1, and modified the enzyme surface, and these changes have potential effects on the target-site sensitivity. Altogether, the results from this study provide information on genic variants of B. tabaci ace1 for future monitoring insecticide resistance development and report a potential case of environmentally driven gene variations.
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Affiliation(s)
- David Renault
- University of Rennes, CNRS, ECOBIO (Ecosystèmes, Biodiversité, Evolution), UMR, 6553, Rennes, France.
- Institut Universitaire de France, 1 rue Descartes, 75231, Paris Cedex 05, France.
| | - Abdo Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Amr Mohamed
- Department of Entomology, Faculty of Science, Cairo University, Giza, 12613, Egypt
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13
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Harris M, Garud NR. Enrichment of Hard Sweeps on the X Chromosome in Drosophila melanogaster. Mol Biol Evol 2022; 40:6955808. [PMID: 36546413 PMCID: PMC9825254 DOI: 10.1093/molbev/msac268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/11/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
The characteristic properties of the X chromosome, such as male hemizygosity and its unique inheritance pattern, expose it to natural selection in a way that can be different from the autosomes. Here, we investigate the differences in the tempo and mode of adaptation on the X chromosome and autosomes in a population of Drosophila melanogaster. Specifically, we test the hypothesis that due to hemizygosity and a lower effective population size on the X, the relative proportion of hard sweeps, which are expected when adaptation is gradual, compared with soft sweeps, which are expected when adaptation is rapid, is greater on the X than on the autosomes. We quantify the incidence of hard versus soft sweeps in North American D. melanogaster population genomic data with haplotype homozygosity statistics and find an enrichment of the proportion of hard versus soft sweeps on the X chromosome compared with the autosomes, confirming predictions we make from simulations. Understanding these differences may enable a deeper understanding of how important phenotypes arise as well as the impact of fundamental evolutionary parameters on adaptation, such as dominance, sex-specific selection, and sex-biased demography.
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Affiliation(s)
- Mariana Harris
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA
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14
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Macdonald SJ, Long AD. Discovery of malathion resistance QTL in Drosophila melanogaster using a bulked phenotyping approach. G3 (BETHESDA, MD.) 2022; 12:jkac279. [PMID: 36250804 PMCID: PMC9713458 DOI: 10.1093/g3journal/jkac279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/09/2022] [Indexed: 12/03/2022]
Abstract
Drosophila melanogaster has proved an effective system with which to understand the evolutionary genetics and molecular mechanisms of insecticide resistance. Insecticide use has left signatures of selection in the fly genome, and both functional and quantitative genetic studies in the system have identified genes and variants associated with resistance. Here, we use D. melanogaster and leverage a bulk phenotyping and pooled sequencing "extreme quantitative trait loci" approach to genetically dissect variation in resistance to malathion, an organophosphate insecticide. We resolve 2 quantitative trait loci, one of which implicates allelic variation at the cytochrome P450 gene Cyp6g1, a strong candidate based on previous work. The second shows no overlap with hits from a previous genome-wide association study for malathion resistance, recapitulating other studies showing that different strategies for complex trait dissection in flies can yield apparently different architectures. Notably, we see no genetic signal at the Ace gene. Ace encodes the target of organophosphate insecticide inhibition, and genome-wide association studies have identified strong Ace-linked associations with resistance in flies. The absence of quantitative trait locus implicating Ace here is most likely because our mapping population does not segregate for several of the known functional polymorphisms impacting resistance at Ace, perhaps because our population is derived from flies collected prior to the widespread use of organophosphate insecticides. Our fundamental approach can be an efficient, powerful strategy to dissect genetic variation in resistance traits. Nonetheless, studies seeking to interrogate contemporary insecticide resistance variation may benefit from deriving mapping populations from more recently collected strains.
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Affiliation(s)
- Stuart J Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66046, USA
- Center for Computational Biology, University of Kansas, Lawrence, KS 66047, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California at Irvine, Irvine, CA 92697, USA
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15
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Min J, Gupta M, Desai MM, Weissman DB. Spatial structure alters the site frequency spectrum produced by hitchhiking. Genetics 2022; 222:iyac139. [PMID: 36094352 PMCID: PMC9630975 DOI: 10.1093/genetics/iyac139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
The reduction of genetic diversity due to genetic hitchhiking is widely used to find past selective sweeps from sequencing data, but very little is known about how spatial structure affects hitchhiking. We use mathematical modeling and simulations to find the unfolded site frequency spectrum left by hitchhiking in the genomic region of a sweep in a population occupying a 1D range. For such populations, sweeps spread as Fisher waves, rather than logistically. We find that this leaves a characteristic 3-part site frequency spectrum at loci very close to the swept locus. Very low frequencies are dominated by recent mutations that occurred after the sweep and are unaffected by hitchhiking. At moderately low frequencies, there is a transition zone primarily composed of alleles that briefly "surfed" on the wave of the sweep before falling out of the wavefront, leaving a spectrum close to that expected in well-mixed populations. However, for moderate-to-high frequencies, there is a distinctive scaling regime of the site frequency spectrum produced by alleles that drifted to fixation in the wavefront and then were carried throughout the population. For loci slightly farther away from the swept locus on the genome, recombination is much more effective at restoring diversity in 1D populations than it is in well-mixed ones. We find that these signatures of space can be strong even in apparently well-mixed populations with negligible spatial genetic differentiation, suggesting that spatial structure may frequently distort the signatures of hitchhiking in natural populations.
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Affiliation(s)
- Jiseon Min
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA
- Quantitative Biology Initiative, Harvard University, Cambridge, MA 02138, USA
| | - Misha Gupta
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael M Desai
- NSF-Simons Center for Mathematical and Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA
- Quantitative Biology Initiative, Harvard University, Cambridge, MA 02138, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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16
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Khatri BS, Burt A. A theory of resistance to multiplexed gene drive demonstrates the significant role of weakly deleterious natural genetic variation. Proc Natl Acad Sci U S A 2022; 119:e2200567119. [PMID: 35914131 PMCID: PMC9371675 DOI: 10.1073/pnas.2200567119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/28/2022] [Indexed: 11/18/2022] Open
Abstract
Evolution of resistance is a major barrier to successful deployment of gene-drive systems to suppress natural populations, which could greatly reduce the burden of many vector-borne diseases. Multiplexed guide RNAs (gRNAs) that require resistance mutations in all target cut sites are a promising antiresistance strategy since, in principle, resistance would only arise in unrealistically large populations. Using stochastic simulations that accurately model evolution at very large population sizes, we explore the probability of resistance due to three important mechanisms: 1) nonhomologous end-joining mutations, 2) single-nucleotide mutants arising de novo, or 3) single-nucleotide polymorphisms preexisting as standing variation. Our results explore the relative importance of these mechanisms and highlight a complexity of the mutation-selection-drift balance between haplotypes with complete resistance and those with an incomplete number of resistant alleles. We find that this leads to a phenomenon where weakly deleterious naturally occurring variants greatly amplify the probability of multisite resistance compared to de novo mutation. This key result provides design criterion for antiresistance multiplexed systems, which, in general, will need a larger number of gRNAs compared to de novo expectations. This theory may have wider application to the evolution of resistance or evolutionary rescue when multiple changes are required before selection can act.
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Affiliation(s)
- Bhavin S. Khatri
- Department of Life Sciences, Imperial College London, Ascot SL5 7PY, United Kingdom
- Chromosome Segregation Laboratory, and Mechanobiology and Biophysics Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Austin Burt
- Department of Life Sciences, Imperial College London, Ascot SL5 7PY, United Kingdom
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17
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Abstract
We discuss the genetic, demographic, and selective forces that are likely to be at play in restricting observed levels of DNA sequence variation in natural populations to a much smaller range of values than would be expected from the distribution of census population sizes alone-Lewontin's Paradox. While several processes that have previously been strongly emphasized must be involved, including the effects of direct selection and genetic hitchhiking, it seems unlikely that they are sufficient to explain this observation without contributions from other factors. We highlight a potentially important role for the less-appreciated contribution of population size change; specifically, the likelihood that many species and populations may be quite far from reaching the relatively high equilibrium diversity values that would be expected given their current census sizes.
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Affiliation(s)
- Brian Charlesworth
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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18
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Tergemina E, Elfarargi AF, Flis P, Fulgione A, Göktay M, Neto C, Scholle M, Flood PJ, Xerri SA, Zicola J, Döring N, Dinis H, Krämer U, Salt DE, Hancock AM. A two-step adaptive walk rewires nutrient transport in a challenging edaphic environment. SCIENCE ADVANCES 2022; 8:eabm9385. [PMID: 35584228 PMCID: PMC9116884 DOI: 10.1126/sciadv.abm9385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Most well-characterized cases of adaptation involve single genetic loci. Theory suggests that multilocus adaptive walks should be common, but these are challenging to identify in natural populations. Here, we combine trait mapping with population genetic modeling to show that a two-step process rewired nutrient homeostasis in a population of Arabidopsis as it colonized the base of an active stratovolcano characterized by extremely low soil manganese (Mn). First, a variant that disrupted the primary iron (Fe) uptake transporter gene (IRT1) swept quickly to fixation in a hard selective sweep, increasing Mn but limiting Fe in the leaves. Second, multiple independent tandem duplications occurred at NRAMP1 and together rose to near fixation in the island population, compensating the loss of IRT1 by improving Fe homeostasis. This study provides a clear case of a multilocus adaptive walk and reveals how genetic variants reshaped a phenotype and spread over space and time.
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Affiliation(s)
- Emmanuel Tergemina
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ahmed F. Elfarargi
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Paulina Flis
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nr Loughborough, LE12 5RD Nottingham, UK
| | - Andrea Fulgione
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Mehmet Göktay
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Célia Neto
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Marleen Scholle
- Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Pádraic J. Flood
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Sophie-Asako Xerri
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Johan Zicola
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Nina Döring
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Herculano Dinis
- Parque Natural do Fogo, Direção Nacional do Ambiente, 115 Chã d’Areia, Praia, Santiago, Cabo Verde, Africa
- Associação Projecto Vitó, 8234, Xaguate, Cidade de São Filipe, Fogo, Cabo Verde, Africa
| | - Ute Krämer
- Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - David E. Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nr Loughborough, LE12 5RD Nottingham, UK
| | - Angela M. Hancock
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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19
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Muralidhar P, Veller C. Dominance shifts increase the likelihood of soft selective sweeps. Evolution 2022; 76:966-984. [PMID: 35213740 PMCID: PMC9928167 DOI: 10.1111/evo.14459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/04/2022] [Indexed: 01/21/2023]
Abstract
Genetic models of adaptation to a new environment have typically assumed that the alleles involved maintain a constant fitness dominance across the old and new environments. However, theories of dominance suggest that this should often not be the case. Instead, the alleles involved should frequently shift from recessive deleterious in the old environment to dominant beneficial in the new environment. Here, we study the consequences of these expected dominance shifts for the genetics of adaptation to a new environment. We find that dominance shifts increase the likelihood that adaptation occurs from standing variation, and that multiple alleles from the standing variation are involved (a soft selective sweep). Furthermore, we find that expected dominance shifts increase the haplotypic diversity of selective sweeps, rendering soft sweeps more detectable in small genomic samples. In cases where an environmental change threatens the viability of the population, we show that expected dominance shifts of newly beneficial alleles increase the likelihood of evolutionary rescue and the number of alleles involved. Finally, we apply our results to a well-studied case of adaptation to a new environment: the evolution of pesticide resistance at the Ace locus in Drosophila melanogaster. We show that, under reasonable demographic assumptions, the expected dominance shift of resistant alleles causes soft sweeps to be the most frequent outcome in this case, with the primary source of these soft sweeps being the standing variation at the onset of pesticide use, rather than recurrent mutation thereafter.
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Affiliation(s)
- Pavitra Muralidhar
- Center for Population Biology, University of California,
Davis, CA 95616,Department of Evolution and Ecology, University of
California, Davis, CA 95616,corresponding author:
| | - Carl Veller
- Center for Population Biology, University of California,
Davis, CA 95616,Department of Evolution and Ecology, University of
California, Davis, CA 95616
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20
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Porretta D, Mastrantonio V, Lucchesi V, Bellini R, Vontas J, Urbanelli S. Historical samples reveal a combined role of agriculture and public-health applications in vector resistance to insecticides. PEST MANAGEMENT SCIENCE 2022; 78:1567-1572. [PMID: 34984788 PMCID: PMC9303699 DOI: 10.1002/ps.6775] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/28/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Insecticide resistance is the major threat to vector control and for the prevention of vector-borne diseases. Because almost all insecticides used against insect vectors are or have been used in agriculture, a connection between agricultural insecticide use and resistance in insect vectors has been hypothesized. However, it is challenging to find a causal link between past agricultural use of insecticides and current resistance in vector populations without historical data series. Here we investigated the relative contribution across time of agricultural and public-health insecticide applications in selecting for diflubenzuron (DFB) resistance in Culex pipiens populations. Using DNA sequencing, we looked for DFB resistant mutations in current and historical mosquito samples, dating back to the 1980s-1990s, when DFB was used in agriculture but not yet in mosquito control. RESULTS In the samples collected before the introduction of DFB in vector control, we found the resistant mutation I1043M in rural regions but not any of the neighboring urban and natural areas, indicating that the selection pressure was derived by agriculture. However, after the introduction of DFB for vector control, the resistant mutations were found across all study areas showing that the initial selection from agriculture was further boosted by the selection pressure imposed by the mosquito control applications in the 2000s. CONCLUSIONS Our findings support a combined role of agricultural and public-health use of insecticides in vector resistance across time and call for specific actions in integrated resistance management, including increased communication between agriculture and health practitioners. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Daniele Porretta
- Department of Environmental BiologySapienza University of RomeRomeItaly
| | | | | | - Romeo Bellini
- Medical and Veterinary Entomology DepartmentCentro Agricoltura Ambiente ‘G. Nicoli’BolognaItaly
| | - John Vontas
- Department of Crop Science, Pesticide Science LabAgricultural University of AthensAthensGreece
- Institute of Molecular Biology and BiotechnologyFoundation for Research and Technology HellasHeraklion, CreteGreece
| | - Sandra Urbanelli
- Department of Environmental BiologySapienza University of RomeRomeItaly
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21
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Pélissié B, Chen YH, Cohen ZP, Crossley MS, Hawthorne DJ, Izzo V, Schoville SD. Genome resequencing reveals rapid, repeated evolution in the Colorado potato beetle. Mol Biol Evol 2022; 39:6511499. [PMID: 35044459 PMCID: PMC8826761 DOI: 10.1093/molbev/msac016] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Insecticide resistance and rapid pest evolution threatens food security and the development of sustainable agricultural practices, yet the evolutionary mechanisms that allow pests to rapidly adapt to control tactics remains unclear. Here we examine how a global super-pest, the Colorado potato beetle (CPB), Leptinotarsa decemlineata, rapidly evolves resistance to insecticides. Using whole genome resequencing and transcriptomic data focused on its ancestral and pest range in North America, we assess evidence for three, non-mutually exclusive models of rapid evolution: pervasive selection on novel mutations, rapid regulatory evolution, and repeated selection on standing genetic variation. Population genomic analysis demonstrates that CPB is geographically structured, even among recently established pest populations. Pest populations exhibit similar levels of nucleotide diversity, relative to non-pest populations, and show evidence of recent expansion. Genome scans provide clear signatures of repeated adaptation across CPB populations, with especially strong evidence of selection on insecticide resistance genes in different populations. Analyses of gene expression show that constitutive upregulation of candidate insecticide resistance genes drives distinctive population patterns. CPB evolves insecticide resistance repeatedly across agricultural regions, leveraging similar genetic pathways but different genes, demonstrating a polygenic trait architecture for insecticide resistance that can evolve from standing genetic variation. Despite expectations, we do not find support for strong selection on novel mutations, or rapid evolution from selection on regulatory genes. These results suggest that integrated pest management practices must mitigate the evolution of polygenic resistance phenotypes among local pest populations, in order to maintain the efficacy and sustainability of novel control techniques.
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Affiliation(s)
- Benjamin Pélissié
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yolanda H Chen
- Department of Plant and Soil Science, University of Vermont, Burlington, VT 05405, USA
| | - Zachary P Cohen
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael S Crossley
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David J Hawthorne
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Victor Izzo
- Department of Plant and Soil Science, University of Vermont, Burlington, VT 05405, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
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22
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Kreiner JM, Sandler G, Stern AJ, Tranel PJ, Weigel D, Stinchcombe J, Wright SI. Repeated origins, widespread gene flow, and allelic interactions of target-site herbicide resistance mutations. eLife 2022; 11:70242. [PMID: 35037853 PMCID: PMC8798060 DOI: 10.7554/elife.70242] [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: 05/11/2021] [Accepted: 01/16/2022] [Indexed: 11/13/2022] Open
Abstract
Causal mutations and their frequency in agricultural fields are well-characterized for herbicide resistance. However, we still lack understanding of their evolutionary history: the extent of parallelism in the origins of target-site resistance (TSR), how long these mutations persist, how quickly they spread, and allelic interactions that mediate their selective advantage. We addressed these questions with genomic data from 19 agricultural populations of common waterhemp (Amaranthus tuberculatus), which we show to have undergone a massive expansion over the past century, with a contemporary effective population size estimate of 8 x 107. We found variation at seven characterized TSR loci, two of which had multiple amino acid substitutions, and three of which were common. These three common resistance variants show extreme parallelism in their mutational origins, with gene flow having shaped their distribution across the landscape. Allele age estimates supported a strong role of adaptation from de novo mutations, with a median age of 30 suggesting that most resistance alleles arose soon after the onset of herbicide use. However, resistant lineages varied in both their age and evidence for selection over two different timescales, implying considerable heterogeneity in the forces that govern their persistence. Two such forces are intra- and inter-locus allelic interactions; we report a signal of extended haplotype competition between two common TSR alleles, and extreme linkage with genome-wide alleles with known functions in resistance adaptation. Together, this work reveals a remarkable example of spatial parallel evolution in a metapopulation, with important implications for the management of herbicide resistance.
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Affiliation(s)
- Julia M Kreiner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - George Sandler
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Aaron J Stern
- Graduate Group in Computational Biology, University of California, Berkeley, Berkeley, United States
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, United States
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - John Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Stephen Isaac Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
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23
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Lange JD, Bastide H, Lack JB, Pool JE. A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population. Mol Biol Evol 2021; 39:6491261. [PMID: 34971382 PMCID: PMC8826484 DOI: 10.1093/molbev/msab368] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Population genetics seeks to illuminate the forces shaping genetic variation, often based on a single snapshot of genomic variation. However, utilizing multiple sampling times to study changes in allele frequencies can help clarify the relative roles of neutral and non-neutral forces on short time scales. This study compares whole-genome sequence variation of recently collected natural population samples of Drosophila melanogaster against a collection made approximately 35 years prior from the same locality—encompassing roughly 500 generations of evolution. The allele frequency changes between these time points would suggest a relatively small local effective population size on the order of 10,000, significantly smaller than the global effective population size of the species. Some loci display stronger allele frequency changes than would be expected anywhere in the genome under neutrality—most notably the tandem paralogs Cyp6a17 and Cyp6a23, which are impacted by structural variation associated with resistance to pyrethroid insecticides. We find a genome-wide excess of outliers for high genetic differentiation between old and new samples, but a larger number of adaptation targets may have affected SNP-level differentiation versus window differentiation. We also find evidence for strengthening latitudinal allele frequency clines: northern-associated alleles have increased in frequency by an average of nearly 2.5% at SNPs previously identified as clinal outliers, but no such pattern is observed at random SNPs. This project underscores the scientific potential of using multiple sampling time points to investigate how evolution operates in natural populations, by quantifying how genetic variation has changed over ecologically relevant timescales.
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Affiliation(s)
- Jeremy D Lange
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Héloïse Bastide
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Justin B Lack
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706
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24
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Nunez JCB, Rong S, Ferranti DA, Damian‐Serrano A, Neil KB, Glenner H, Elyanow RG, Brown BRP, Alm Rosenblad M, Blomberg A, Johannesson K, Rand DM. From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles. Mol Ecol 2021; 30:6417-6433. [PMID: 33960035 PMCID: PMC9292448 DOI: 10.1111/mec.15949] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/25/2022]
Abstract
The northern acorn barnacle (Semibalanus balanoides) is a robust system to study the genetic basis of adaptations to highly heterogeneous environments. Adult barnacles may be exposed to highly dissimilar levels of thermal stress depending on where they settle in the intertidal (i.e., closer to the upper or lower tidal boundary). For instance, barnacles near the upper tidal limit experience episodic summer temperatures above recorded heat coma levels. This differential stress at the microhabitat level is also dependent on the aspect of sun exposure. In the present study, we used pool-seq approaches to conduct a genome wide screen for loci responding to intertidal zonation across the North Atlantic basin (Maine, Rhode Island, and Norway). Our analysis discovered 382 genomic regions containing SNPs which are consistently zonated (i.e., SNPs whose frequencies vary depending on their position in the rocky intertidal) across all surveyed habitats. Notably, most zonated SNPs are young and private to the North Atlantic. These regions show high levels of genetic differentiation across ecologically extreme microhabitats concomitant with elevated levels of genetic variation and Tajima's D, suggesting the action of non-neutral processes. Overall, these findings support the hypothesis that spatially heterogeneous selection is a general and repeatable feature for this species, and that natural selection can maintain functional genetic variation in heterogeneous environments.
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Affiliation(s)
- Joaquin C. B. Nunez
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
- Present address:
Department of BiologyUniversity of VirginiaCharlottesvilleVAUSA
| | - Stephen Rong
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
- Center for Computational Molecular BiologyBrown UniversityProvidenceRIUSA
| | - David A. Ferranti
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
| | | | - Kimberly B. Neil
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
| | - Henrik Glenner
- Department of Biological SciencesUniversity of BergenBergenNorway
- Center of Macroecology and Climate, GLOBEUniversity of CopenhagenCopenhagenDenmark
| | - Rebecca G. Elyanow
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
- Center for Computational Molecular BiologyBrown UniversityProvidenceRIUSA
| | - Bianca R. P. Brown
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
| | - Magnus Alm Rosenblad
- Department of Chemistry and Molecular BiologyUniversity of GothenburgLundberg LaboratoryGöteborgSweden
| | - Anders Blomberg
- Department of Chemistry and Molecular BiologyUniversity of GothenburgLundberg LaboratoryGöteborgSweden
| | - Kerstin Johannesson
- Department of Marine SciencesUniversity of GothenburgTjärnö Marine LaboratoryStrömstadSweden
| | - David M. Rand
- Department of Ecology and Evolutionary BiologyBrown UniversityProvidenceRIUSA
- Center for Computational Molecular BiologyBrown UniversityProvidenceRIUSA
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25
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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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26
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Buffalo V. Quantifying the relationship between genetic diversity and population size suggests natural selection cannot explain Lewontin's Paradox. eLife 2021; 10:e67509. [PMID: 34409937 PMCID: PMC8486380 DOI: 10.7554/elife.67509] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/16/2021] [Indexed: 12/21/2022] Open
Abstract
Neutral theory predicts that genetic diversity increases with population size, yet observed levels of diversity across metazoans vary only two orders of magnitude while population sizes vary over several. This unexpectedly narrow range of diversity is known as Lewontin's Paradox of Variation (1974). While some have suggested selection constrains diversity, tests of this hypothesis seem to fall short. Here, I revisit Lewontin's Paradox to assess whether current models of linked selection are capable of reducing diversity to this extent. To quantify the discrepancy between pairwise diversity and census population sizes across species, I combine previously-published estimates of pairwise diversity from 172 metazoan taxa with newly derived estimates of census sizes. Using phylogenetic comparative methods, I show this relationship is significant accounting for phylogeny, but with high phylogenetic signal and evidence that some lineages experience shifts in the evolutionary rate of diversity deep in the past. Additionally, I find a negative relationship between recombination map length and census size, suggesting abundant species have less recombination and experience greater reductions in diversity due to linked selection. However, I show that even assuming strong and abundant selection, models of linked selection are unlikely to explain the observed relationship between diversity and census sizes across species.
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Affiliation(s)
- Vince Buffalo
- Institute for Ecology and Evolution, University of OregonEugeneUnited States
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27
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Mastrantonio V, Porretta D, Lucchesi V, Güz N, Çağatay NS, Bellini R, Vontas J, Urbanelli S. Evolution of Adaptive Variation in the Mosquito Culex pipiens: Multiple Independent Origins of Insecticide Resistance Mutations. INSECTS 2021; 12:insects12080676. [PMID: 34442242 PMCID: PMC8396673 DOI: 10.3390/insects12080676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary The application of insecticides to control insect pests can result in the evolution of resistance. Within a population, the individuals carrying the resistant mutation survive after insecticide application while the others die, leading to the spread of resistance. The finding that the same mutations confer insecticide resistance in different species or populations raises the question how often these mutations arise in natural populations. Resistant mutations can originate once within a population and then spread. Alternatively, multiple origins can occur within the same population or in different geographic areas. Here, we used a phylogenetic approach to investigate the origin of three mutations conferring resistance to diflubenzuron insecticide in Italian and Turkish populations of the mosquito Culex pipiens. Our results support a scenario of multiple origins of the mutations. Resistance is a major threat to mosquito control, and these findings help inform resistance management. At the same time, insecticide resistance is an informative model for studying the origin of adaptive variation. In the words of Rachel Carson, “If Darwin were alive today, he would be astounded and delighted by the impressive verification that his theories of the survival of the fittest are receiving from the insect world” (Silent Spring, 1962) Abstract Insecticide resistance is an informative model for studying the appearance of adaptive traits. Simultaneously, understanding how many times resistance mutations originate is essential to design effective resistance management. In the mosquito Culex pipiens, target–site resistance to the insecticide diflubenzuron (DFB) has been recently found in Italian and Turkish populations. Three point mutations confer it at the codon 1043 of the chitin synthase 1 gene (chs-1): I1043L, I1043M, and I1043F. Whether the resistant mutations originated independently from different susceptible alleles or sequentially from resistant alleles and whether resistant alleles from Italy and Turkey have originated once or multiple times remain unresolved. Here, we sequenced a fragment of the chs-1 gene carrying the resistant mutations and inferred the phylogenetic relationships among susceptible and resistant alleles. Confirming previous findings, we found the three mutations in Italy and the I1043M in Turkey. Notably, the I1043F was also found for the first time in Turkish samples, highlighting the need for extensive monitoring activities. Phylogenetic analyses are consistent with an independent origin of the I1043F, I1043M, and I1043L mutations from different susceptible alleles and with multiple independent origins of the Italian and Turkish I1043M and I1043F alleles.
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Affiliation(s)
- Valentina Mastrantonio
- Department of Environmental Biology, Faculty of Mathematical, Physical and Natural Sciences, Sapienza University of Rome, 00185 Rome, Italy; (V.M.); (V.L.); (S.U.)
| | - Daniele Porretta
- Department of Environmental Biology, Faculty of Mathematical, Physical and Natural Sciences, Sapienza University of Rome, 00185 Rome, Italy; (V.M.); (V.L.); (S.U.)
- Correspondence:
| | - Valentina Lucchesi
- Department of Environmental Biology, Faculty of Mathematical, Physical and Natural Sciences, Sapienza University of Rome, 00185 Rome, Italy; (V.M.); (V.L.); (S.U.)
| | - Nurper Güz
- Molecular Entomology Laboratory, Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara 06100, Turkey; (N.G.); (N.S.Ç.)
| | - Naciye Sena Çağatay
- Molecular Entomology Laboratory, Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara 06100, Turkey; (N.G.); (N.S.Ç.)
| | - Romeo Bellini
- Medical and Veterinary Entomology Department, Centro Agricoltura Ambiente “G. Nicoli”, 40014 Bologna, Italy;
| | - John Vontas
- Department of Crop Science, Pesticide Science Lab, Faculty of Crop Science, Agricultural University of Athens, 11855 Athens, Greece;
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, 70013 Heraklion, Crete, Greece
| | - Sandra Urbanelli
- Department of Environmental Biology, Faculty of Mathematical, Physical and Natural Sciences, Sapienza University of Rome, 00185 Rome, Italy; (V.M.); (V.L.); (S.U.)
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28
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Rodrigues MF, Cogni R. Genomic Responses to Climate Change: Making the Most of the Drosophila Model. Front Genet 2021; 12:676218. [PMID: 34326859 PMCID: PMC8314211 DOI: 10.3389/fgene.2021.676218] [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: 03/04/2021] [Accepted: 06/15/2021] [Indexed: 11/18/2022] Open
Abstract
It is pressing to understand how animal populations evolve in response to climate change. We argue that new sequencing technologies and the use of historical samples are opening unprecedented opportunities to investigate genome-wide responses to changing environments. However, there are important challenges in interpreting the emerging findings. First, it is essential to differentiate genetic adaptation from phenotypic plasticity. Second, it is extremely difficult to map genotype, phenotype, and fitness. Third, neutral demographic processes and natural selection affect genetic variation in similar ways. We argue that Drosophila melanogaster, a classical model organism with decades of climate adaptation research, is uniquely suited to overcome most of these challenges. In the near future, long-term time series genome-wide datasets of D. melanogaster natural populations will provide exciting opportunities to study adaptation to recent climate change and will lay the groundwork for related research in non-model systems.
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Affiliation(s)
- Murillo F. Rodrigues
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Rodrigo Cogni
- Department of Ecology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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29
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Lynch M, Ho WC. The Limits to Estimating Population-Genetic Parameters with Temporal Data. Genome Biol Evol 2021; 12:443-455. [PMID: 32181820 PMCID: PMC7197491 DOI: 10.1093/gbe/evaa056] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2020] [Indexed: 11/14/2022] Open
Abstract
The ability to obtain genome-wide sequences of very large numbers of individuals from natural populations raises questions about optimal sampling designs and the limits to extracting information on key population-genetic parameters from temporal-survey data. Methods are introduced for evaluating whether observed temporal fluctuations in allele frequencies are consistent with the hypothesis of random genetic drift, and expressions for the expected sampling variances for the relevant statistics are given in terms of sample sizes and numbers. Estimation methods and aspects of statistical reliability are also presented for the mean and temporal variance of selection coefficients. For nucleotide sites that pass the test of neutrality, the current effective population size can be estimated by a method of moments, and expressions for its sampling variance provide insight into the degree to which such methodology can yield meaningful results under alternative sampling schemes. Finally, some caveats are raised regarding the use of the temporal covariance of allele-frequency change to infer selection. Taken together, these results provide a statistical view of the limits to population-genetic inference in even the simplest case of a closed population.
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Affiliation(s)
- Michael Lynch
- Biodesign Center for Mechanisms of Evolution, Arizona State University
| | - Wei-Chin Ho
- Biodesign Center for Mechanisms of Evolution, Arizona State University
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30
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Machado HE, Bergland AO, Taylor R, Tilk S, Behrman E, Dyer K, Fabian DK, Flatt T, González J, Karasov TL, Kim B, Kozeretska I, Lazzaro BP, Merritt TJS, Pool JE, O'Brien K, Rajpurohit S, Roy PR, Schaeffer SW, Serga S, Schmidt P, Petrov DA. Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila. eLife 2021; 10:e67577. [PMID: 34155971 PMCID: PMC8248982 DOI: 10.7554/elife.67577] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022] Open
Abstract
To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched in large chromosomal inversions, and we find a broad concordance between seasonal and spatial allele frequency change. The direction of allele frequency change at seasonally variable polymorphisms can be predicted by weather conditions in the weeks prior to sampling, linking the environment and the genomic response to selection. Our results suggest that fluctuating selection is an important evolutionary force affecting patterns of genetic variation in Drosophila.
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Affiliation(s)
- Heather E Machado
- Department of Biology, Stanford UniversityStanfordUnited States
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | - Alan O Bergland
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Biology, University of VirginiaCharlottesvilleUnited States
| | - Ryan Taylor
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Susanne Tilk
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Emily Behrman
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Kelly Dyer
- Department of Genetics, University of GeorgiaAthensUnited States
| | - Daniel K Fabian
- Institute of Population Genetics, Vetmeduni ViennaViennaAustria
- Centre for Pathogen Evolution, Department of Zoology, University of CambridgeCambridgeUnited Kingdom
| | - Thomas Flatt
- Institute of Population Genetics, Vetmeduni ViennaViennaAustria
- Department of Biology, University of FribourgFribourgSwitzerland
| | - Josefa González
- Institute of Evolutionary Biology, CSIC- Universitat Pompeu FabraBarcelonaSpain
| | - Talia L Karasov
- Department of Biology, University of UtahSalt Lake CityUnited States
| | - Bernard Kim
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Iryna Kozeretska
- Taras Shevchenko National University of KyivKyivUkraine
- National Antarctic Scientific Centre of Ukraine, Taras Shevchenko Blvd.KyivUkraine
| | - Brian P Lazzaro
- Department of Entomology, Cornell UniversityIthacaUnited States
| | - Thomas JS Merritt
- Department of Chemistry & Biochemistry, Laurentian UniversitySudburyCanada
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-MadisonMadisonUnited States
| | - Katherine O'Brien
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Subhash Rajpurohit
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Paula R Roy
- Department of Ecology and Evolutionary Biology, University of KansasLawrenceUnited States
| | - Stephen W Schaeffer
- Department of Biology, The Pennsylvania State UniversityUniversity ParkUnited States
| | - Svitlana Serga
- Taras Shevchenko National University of KyivKyivUkraine
- National Antarctic Scientific Centre of Ukraine, Taras Shevchenko Blvd.KyivUkraine
| | - Paul Schmidt
- Department of Biology, University of PennsylvaniaPhiladelphiaUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
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31
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Svedberg J, Shchur V, Reinman S, Nielsen R, Corbett-Detig R. Inferring Adaptive Introgression Using Hidden Markov Models. Mol Biol Evol 2021; 38:2152-2165. [PMID: 33502512 PMCID: PMC8097282 DOI: 10.1093/molbev/msab014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Adaptive introgression-the flow of adaptive genetic variation between species or populations-has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a hidden Markov model-based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized data sets for realistic population and selection parameters. We apply Ancestry_HMM-S to a data set of an admixed Drosophila melanogaster population from South Africa and we identify 17 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in data sets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.
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Affiliation(s)
- Jesper Svedberg
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Vladimir Shchur
- National Research University Higher School of Economics, Moscow, Russian Federation
| | - Solomon Reinman
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
| | - Rasmus Nielsen
- National Research University Higher School of Economics, Moscow, Russian Federation
- Department of Integrative Biology and Department of Statistics, UC Berkeley, Berkeley, CA, USA
- Center for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, Genomics Institute, UC Santa Cruz, Santa Cruz, CA, USA
- National Research University Higher School of Economics, Moscow, Russian Federation
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32
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Harris AM, DeGiorgio M. A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data. Mol Biol Evol 2021; 37:3023-3046. [PMID: 32392293 PMCID: PMC7530616 DOI: 10.1093/molbev/msaa115] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Selective sweeps are frequent and varied signatures in the genomes of natural populations, and detecting them is consequently important in understanding mechanisms of adaptation by natural selection. Following a selective sweep, haplotypic diversity surrounding the site under selection decreases, and this deviation from the background pattern of variation can be applied to identify sweeps. Multiple methods exist to locate selective sweeps in the genome from haplotype data, but none leverages the power of a model-based approach to make their inference. Here, we propose a likelihood ratio test statistic T to probe whole-genome polymorphism data sets for selective sweep signatures. Our framework uses a simple but powerful model of haplotype frequency spectrum distortion to find sweeps and additionally make an inference on the number of presently sweeping haplotypes in a population. We found that the T statistic is suitable for detecting both hard and soft sweeps across a variety of demographic models, selection strengths, and ages of the beneficial allele. Accordingly, we applied the T statistic to variant calls from European and sub-Saharan African human populations, yielding primarily literature-supported candidates, including LCT, RSPH3, and ZNF211 in CEU, SYT1, RGS18, and NNT in YRI, and HLA genes in both populations. We also searched for sweep signatures in Drosophila melanogaster, finding expected candidates at Ace, Uhg1, and Pimet. Finally, we provide open-source software to compute the T statistic and the inferred number of presently sweeping haplotypes from whole-genome data.
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Affiliation(s)
- Alexandre M Harris
- Department of Biology, Pennsylvania State University, University Park, PA.,Molecular, Cellular, and Integrative Biosciences, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL
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33
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Pelizzola M, Behr M, Li H, Munk A, Futschik A. Multiple haplotype reconstruction from allele frequency data. NATURE COMPUTATIONAL SCIENCE 2021; 1:262-271. [PMID: 38217170 DOI: 10.1038/s43588-021-00056-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 03/12/2021] [Indexed: 01/15/2024]
Abstract
Because haplotype information is of widespread interest in biomedical applications, effort has been put into their reconstruction. Here, we propose an efficient method, called haploSep, that is able to accurately infer major haplotypes and their frequencies just from multiple samples of allele frequency data. Even the accuracy of experimentally obtained allele frequencies can be improved by re-estimating them from our reconstructed haplotypes. From a methodological point of view, we model our problem as a multivariate regression problem where both the design matrix and the coefficient matrix are unknown. Compared to other methods, haploSep is very fast, with linear computational complexity in the haplotype length. We illustrate our method on simulated and real data focusing on experimental evolution and microbial data.
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Affiliation(s)
- Marta Pelizzola
- Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Merle Behr
- University of California, Berkeley, CA, USA
| | - Housen Li
- University of Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Axel Munk
- University of Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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34
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Brevik K, Bueno EM, McKay S, Schoville SD, Chen YH. Insecticide exposure affects intergenerational patterns of DNA methylation in the Colorado potato beetle, Leptinotarsa decemlineata. Evol Appl 2021; 14:746-757. [PMID: 33767749 PMCID: PMC7980262 DOI: 10.1111/eva.13153] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/23/2022] Open
Abstract
Insecticide use is pervasive as a selective force in modern agroecosystems. Insect herbivores exposed to these insecticides have been able to rapidly evolve resistance to them, but how they are able to do so is poorly understood. One possible but largely unexplored explanation is that exposure to sublethal doses of insecticides may alter epigenetic patterns that are heritable. For instance, epigenetic mechanisms, such as DNA methylation that modifies gene expression without changing the underlying genetic code, may facilitate the emergence of resistant phenotypes in complex ways. We assessed the effects of sublethal insecticide exposure, with the neonicotinoid imidacloprid, on DNA methylation in the Colorado potato beetle, Leptinotarsa decemlineata, examining both global changes in DNA methylation and specific changes found within genes and transposable elements. We found that exposure to insecticide led to decreases in global DNA methylation for parent and F2 generations and that many of the sites of changes in methylation are found within genes associated with insecticide resistance, such as cytochrome P450s, or within transposable elements. Exposure to sublethal doses of insecticide caused heritable changes in DNA methylation in an agricultural insect herbivore. Therefore, epigenetics may play a role in insecticide resistance, highlighting a fundamental mechanism of evolution while informing how we might better coexist with insect species in agroecosystems.
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Affiliation(s)
- Kristian Brevik
- Department of Plant and Soil ScienceUniversity of VermontBurlingtonVTUSA
| | - Erika M. Bueno
- Department of Plant and Soil ScienceUniversity of VermontBurlingtonVTUSA
| | - Stephanie McKay
- Department of Animal and Veterinary SciencesUniversity of VermontBurlingtonVTUSA
| | | | - Yolanda H. Chen
- Department of Plant and Soil ScienceUniversity of VermontBurlingtonVTUSA
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35
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Rogers RL, Grizzard SL, Titus-McQuillan JE, Bockrath K, Patel S, Wares JP, Garner JT, Moore CC. Gene family amplification facilitates adaptation in freshwater unionid bivalve Megalonaias nervosa. Mol Ecol 2021; 30:1155-1173. [PMID: 33382161 DOI: 10.1111/mec.15786] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/01/2020] [Accepted: 12/14/2020] [Indexed: 01/05/2023]
Abstract
Freshwater unionid bivalves currently face severe anthropogenic challenges. Over 70% of species in the United States are threatened, endangered or extinct due to pollution, damming of waterways and overfishing. These species are notable for their unusual life history strategy, parasite-host co-evolution and biparental mitochondrial inheritance. Among this clade, the washboard mussel Megalonaias nervosa is one species that remains prevalent across the Southeastern United States, with robust population sizes. We have created a reference genome for M. nervosa to determine how genome content has evolved in the face of these widespread environmental challenges. We observe dynamic changes in genome content, with a burst of recent transposable element proliferation causing a 382 Mb expansion in genome content. Birth-death models suggest rapid expansions among gene families, with a mutation rate of 1.16 × 10-8 duplications per gene per generation. Cytochrome P450 gene families have experienced exceptional recent amplification beyond expectations based on genome-wide birth-death processes. These genes are associated with increased rates of amino acid changes, a signature of selection driving evolution of detox genes. Fitting evolutionary models of adaptation from standing genetic variation, we can compare adaptive potential across species and mutation types. The large population size in M. nervosa suggests a 4.7-fold advantage in the ability to adapt from standing genetic variation compared with a low diversity endemic E. hopetonensis. Estimates suggest that gene family evolution may offer an exceptional substrate of genetic variation in M. nervosa, with Psgv = 0.185 compared with Psgv = 0.067 for single nucleotide changes. Hence, we suggest that gene family evolution is a source of 'hopeful monsters' within the genome that may facilitate adaptation when selective pressures shift. These results suggest that gene family expansion is a key driver of adaptive evolution in this key species of freshwater Unionidae that is currently facing widespread environmental challenges. This work has clear implications for conservation genomics on freshwater bivalves as well as evolutionary theory. This genome represents a first step to facilitate reverse ecological genomics in Unionidae and identify the genetic underpinnings of phenotypic diversity.
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Affiliation(s)
- Rebekah L Rogers
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
| | - Stephanie L Grizzard
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA.,Department of Biological Sciences, Old Dominion University, Norfolk, VA, USA
| | | | - Katherine Bockrath
- Department of Genetics, University of Georgia, Athens, GA, USA.,U.S. Fish and Wildlife Service, Midwest Fisheries Center Whitney Genetics Lab, Onalaska, WI, USA
| | - Sagar Patel
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA.,Department of Biology, Saint Louis University, St. Louis, MO, USA.,Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - John P Wares
- Department of Genetics, University of Georgia, Athens, GA, USA.,Odum School of Ecology, University of Georgia, Athens, GA, USA
| | - Jeffrey T Garner
- Division of Wildlife and Freshwater Fisheries, Alabama Department of Conservation and Natural Resources, Florence, AL, USA
| | - Cathy C Moore
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
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36
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Garud NR, Messer PW, Petrov DA. Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data. PLoS Genet 2021; 17:e1009373. [PMID: 33635910 PMCID: PMC7946363 DOI: 10.1371/journal.pgen.1009373] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 03/10/2021] [Accepted: 01/17/2021] [Indexed: 12/12/2022] Open
Abstract
Whether hard sweeps or soft sweeps dominate adaptation has been a matter of much debate. Recently, we developed haplotype homozygosity statistics that (i) can detect both hard and soft sweeps with similar power and (ii) can classify the detected sweeps as hard or soft. The application of our method to population genomic data from a natural population of Drosophila melanogaster (DGRP) allowed us to rediscover three known cases of adaptation at the loci Ace, Cyp6g1, and CHKov1 known to be driven by soft sweeps, and detected additional candidate loci for recent and strong sweeps. Surprisingly, all of the top 50 candidates showed patterns much more consistent with soft rather than hard sweeps. Recently, Harris et al. 2018 criticized this work, suggesting that all the candidate loci detected by our haplotype statistics, including the positive controls, are unlikely to be sweeps at all and that instead these haplotype patterns can be more easily explained by complex neutral demographic models. They also claim that these neutral non-sweeps are likely to be hard instead of soft sweeps. Here, we reanalyze the DGRP data using a range of complex admixture demographic models and reconfirm our original published results suggesting that the majority of recent and strong sweeps in D. melanogaster are first likely to be true sweeps, and second, that they do appear to be soft. Furthermore, we discuss ways to take this work forward given that most demographic models employed in such analyses are necessarily too simple to capture the full demographic complexity, while more realistic models are unlikely to be inferred correctly because they require a large number of free parameters.
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Affiliation(s)
- Nandita R. Garud
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, United States of America
- Department of Human Genetics, University of California, Los Angeles, California, United States of America
| | - Philipp W. Messer
- Department of Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, California, United States of America
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37
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Abstract
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its worldwide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this book chapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of noncoding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field.
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38
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Abstract
HIV can evolve remarkably quickly in response to antiretroviral therapies and the immune system. This evolution stymies treatment effectiveness and prevents the development of an HIV vaccine. Consequently, there has been a great interest in using population genetics to disentangle the forces that govern the HIV adaptive landscape (selection, drift, mutation, and recombination). Traditional population genetics approaches look at the current state of genetic variation and infer the processes that can generate it. However, because HIV evolves rapidly, we can also sample populations repeatedly over time and watch evolution in action. In this paper, we demonstrate how time series data can bound evolutionary parameters in a way that complements and informs traditional population genetic approaches. Specifically, we focus on our recent paper (Feder et al., 2016, eLife), in which we show that, as improved HIV drugs have led to fewer patients failing therapy due to resistance evolution, less genetic diversity has been maintained following the fixation of drug resistance mutations. Because soft sweeps of multiple drug resistance mutations spreading simultaneously have been previously documented in response to the less effective HIV therapies used early in the epidemic, we interpret the maintenance of post-sweep diversity in response to poor therapies as further evidence of soft sweeps and therefore a high population mutation rate (θ) in these intra-patient HIV populations. Because improved drugs resulted in rarer resistance evolution accompanied by lower post-sweep diversity, we suggest that both observations can be explained by decreased population mutation rates and a resultant transition to hard selective sweeps. A recent paper (Harris et al., 2018, PLOS Genetics) proposed an alternative interpretation: Diversity maintenance following drug resistance evolution in response to poor therapies may have been driven by recombination during slow, hard selective sweeps of single mutations. Then, if better drugs have led to faster hard selective sweeps of resistance, recombination will have less time to rescue diversity during the sweep, recapitulating the decrease in post-sweep diversity as drugs have improved. In this paper, we use time series data to show that drug resistance evolution during ineffective treatment is very fast, providing new evidence that soft sweeps drove early HIV treatment failure.
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Affiliation(s)
- Alison F. Feder
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Pleuni S. Pennings
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, California, United States of America
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39
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Achary VMM, Sheri V, Manna M, Panditi V, Borphukan B, Ram B, Agarwal A, Fartyal D, Teotia D, Masakapalli SK, Agrawal PK, Reddy MK. Overexpression of improved EPSPS gene results in field level glyphosate tolerance and higher grain yield in rice. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2504-2519. [PMID: 32516520 PMCID: PMC7680544 DOI: 10.1111/pbi.13428] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/29/2020] [Accepted: 04/18/2020] [Indexed: 05/15/2023]
Abstract
Glyphosate is a popular, systemic, broad-spectrum herbicide used in modern agriculture. Being a structural analog of phosphoenolpyruvate (PEP), it inhibits 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) which is responsible for the biosynthesis of aromatic amino acids and various aromatic secondary metabolites. Taking a lead from glyphosate-resistant weeds, two mutant variants of the rice EPSPS gene were developed by amino acid substitution (T173I + P177S; TIPS-OsEPSPS and G172A + T173I + P177S; GATIPS-OsEPSPS). These mutated EPSPS genes were overexpressed in rice under the control of either native EPSPS or constitutive promoters (maize ubiquitin [ZmUbi] promoter). The overexpression of TIPS-OsEPSPS under the control of the ZmUbi promoter resulted in higher tolerance to glyphosate (up to threefold of the recommended dose) without affecting the fitness and related agronomic traits of plants in both controlled and field conditions. Furthermore, such rice lines produced 17%-19% more grains compared to the wild type (WT) in the absence of glyphosate application and the phenylalanine and tryptophan contents in the transgenic seeds were found to be significantly higher in comparison with WT seeds. Our results also revealed that the native promoter guided expression of modified EPSPS genes did not significantly improve the glyphosate tolerance. The present study describing the introduction of a crop-specific TIPS mutation in class I aroA gene of rice and its overexpression have potential to substantially improve the yield and field level glyphosate tolerance in rice. This is the first report to observe that the EPSPS has role to play in improving grain yield of rice.
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Affiliation(s)
- V. Mohan Murali Achary
- Crop Improvement GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Vijay Sheri
- Crop Improvement GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Mrinalini Manna
- Crop Improvement GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Varakumar Panditi
- Crop Improvement GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Bhabesh Borphukan
- Crop Improvement GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Babu Ram
- Crop Improvement GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Aakrati Agarwal
- Crop Improvement GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Dhirendra Fartyal
- Crop Improvement GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Deepa Teotia
- Crop Improvement GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | | | | | - Malireddy K. Reddy
- Crop Improvement GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
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40
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Galtier N, Rousselle M. How Much Does Ne Vary Among Species? Genetics 2020; 216:559-572. [PMID: 32839240 PMCID: PMC7536855 DOI: 10.1534/genetics.120.303622] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/20/2020] [Indexed: 11/18/2022] Open
Abstract
Genetic drift is an important evolutionary force of strength inversely proportional to Ne , the effective population size. The impact of drift on genome diversity and evolution is known to vary among species, but quantifying this effect is a difficult task. Here we assess the magnitude of variation in drift power among species of animals via its effect on the mutation load - which implies also inferring the distribution of fitness effects of deleterious mutations. To this aim, we analyze the nonsynonymous (amino-acid changing) and synonymous (amino-acid conservative) allele frequency spectra in a large sample of metazoan species, with a focus on the primates vs. fruit flies contrast. We show that a Gamma model of the distribution of fitness effects is not suitable due to strong differences in estimated shape parameters among taxa, while adding a class of lethal mutations essentially solves the problem. Using the Gamma + lethal model and assuming that the mean deleterious effects of nonsynonymous mutations is shared among species, we estimate that the power of drift varies by a factor of at least 500 between large-Ne and small-Ne species of animals, i.e., an order of magnitude more than the among-species variation in genetic diversity. Our results are relevant to Lewontin's paradox while further questioning the meaning of the Ne parameter in population genomics.
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Affiliation(s)
- Nicolas Galtier
- Institute of Evolution Sciences of Montpellier (ISEM), CNRS, University of Montpellier, IRD, EPHE, 34095 Montpellier, France
| | - Marjolaine Rousselle
- Institute of Evolution Sciences of Montpellier (ISEM), CNRS, University of Montpellier, IRD, EPHE, 34095 Montpellier, France
- Bioinformatics Research Centre, Aarhus University, DK Aarhus, Denmark
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41
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Jakobson CM, Jarosz DF. What Has a Century of Quantitative Genetics Taught Us About Nature's Genetic Tool Kit? Annu Rev Genet 2020; 54:439-464. [PMID: 32897739 DOI: 10.1146/annurev-genet-021920-102037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The complexity of heredity has been appreciated for decades: Many traits are controlled not by a single genetic locus but instead by polymorphisms throughout the genome. The importance of complex traits in biology and medicine has motivated diverse approaches to understanding their detailed genetic bases. Here, we focus on recent systematic studies, many in budding yeast, which have revealed that large numbers of all kinds of molecular variation, from noncoding to synonymous variants, can make significant contributions to phenotype. Variants can affect different traits in opposing directions, and their contributions can be modified by both the environment and the epigenetic state of the cell. The integration of prospective (synthesizing and analyzing variants) and retrospective (examining standing variation) approaches promises to reveal how natural selection shapes quantitative traits. Only by comprehensively understanding nature's genetic tool kit can we predict how phenotypes arise from the complex ensembles of genetic variants in living organisms.
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Affiliation(s)
- Christopher M Jakobson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA;
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA; .,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
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42
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Burskaia V, Naumenko S, Schelkunov M, Bedulina D, Neretina T, Kondrashov A, Yampolsky L, Bazykin GA. Excessive Parallelism in Protein Evolution of Lake Baikal Amphipod Species Flock. Genome Biol Evol 2020; 12:1493-1503. [PMID: 32653919 DOI: 10.1093/gbe/evaa138] [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] [Accepted: 07/03/2020] [Indexed: 11/12/2022] Open
Abstract
Repeated emergence of similar adaptations is often explained by parallel evolution of underlying genes. However, evidence of parallel evolution at amino acid level is limited. When the analyzed species are highly divergent, this can be due to epistatic interactions underlying the dynamic nature of the amino acid preferences: The same amino acid substitution may have different phenotypic effects on different genetic backgrounds. Distantly related species also often inhabit radically different environments, which makes the emergence of parallel adaptations less likely. Here, we hypothesize that parallel molecular adaptations are more prevalent between closely related species. We analyze the rate of parallel evolution in genome-size sets of orthologous genes in three groups of species with widely ranging levels of divergence: 46 species of the relatively recent lake Baikal amphipod radiation, a species flock of very closely related cichlids, and a set of significantly more divergent vertebrates. Strikingly, in genes of amphipods, the rate of parallel substitutions at nonsynonymous sites exceeded that at synonymous sites, suggesting rampant selection driving parallel adaptation. At sites of parallel substitutions, the intraspecies polymorphism is low, suggesting that parallelism has been driven by positive selection and is therefore adaptive. By contrast, in cichlids, the rate of nonsynonymous parallel evolution was similar to that at synonymous sites, whereas in vertebrates, this rate was lower than that at synonymous sites, indicating that in these groups of species, parallel substitutions are mainly fixed by drift.
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Affiliation(s)
- Valentina Burskaia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Moscow Oblast, Russia
| | - Sergey Naumenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Mikhail Schelkunov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Moscow Oblast, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
| | - Daria Bedulina
- Institute of Biology, Irkutsk State University, Russia
- Baikal Research Centre, Irkutsk, Russia
| | - Tatyana Neretina
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
- N.A. Pertsov White Sea Biological Station, Lomonosov Moscow State University, Primorskiy, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
| | - Alexey Kondrashov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Russia
- Department of Ecology and Evolutionary Biology, University of Michigan
| | - Lev Yampolsky
- Department of Biological Sciences, East Tennessee State University
| | - Georgii A Bazykin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Moscow Oblast, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
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43
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Rousselle M, Simion P, Tilak MK, Figuet E, Nabholz B, Galtier N. Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals. PLoS Genet 2020; 16:e1008668. [PMID: 32251427 PMCID: PMC7162527 DOI: 10.1371/journal.pgen.1008668] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/16/2020] [Accepted: 02/14/2020] [Indexed: 12/16/2022] Open
Abstract
Whether adaptation is limited by the beneficial mutation supply is a long-standing question of evolutionary genetics, which is more generally related to the determination of the adaptive substitution rate and its relationship with species effective population size (Ne) and genetic diversity. Empirical evidence reported so far is equivocal, with some but not all studies supporting a higher adaptive substitution rate in large-Ne than in small-Ne species. We gathered coding sequence polymorphism data and estimated the adaptive amino-acid substitution rate ωa, in 50 species from ten distant groups of animals with markedly different population mutation rate θ. We reveal the existence of a complex, timescale dependent relationship between species adaptive substitution rate and genetic diversity. We find a positive relationship between ωa and θ among closely related species, indicating that adaptation is indeed limited by the mutation supply, but this was only true in relatively low-θ taxa. In contrast, we uncover no significant correlation between ωa and θ at a larger taxonomic scale, suggesting that the proportion of beneficial mutations scales negatively with species' long-term Ne.
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Affiliation(s)
| | - Paul Simion
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
- LEGE, Department of Biology, University of Namur, Namur, Belgium
| | - Marie-Ka Tilak
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Emeric Figuet
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Benoit Nabholz
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Nicolas Galtier
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
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44
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Terekhanova NV, Barmintseva AE, Kondrashov AS, Bazykin GA, Mugue NS. Architecture of Parallel Adaptation in Ten Lacustrine Threespine Stickleback Populations from the White Sea Area. Genome Biol Evol 2020; 11:2605-2618. [PMID: 31406984 PMCID: PMC6761963 DOI: 10.1093/gbe/evz175] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2019] [Indexed: 12/20/2022] Open
Abstract
Adaptation of threespine stickleback to freshwater involves parallel recruitment of freshwater alleles in clusters of closely linked sites, or divergence islands (DIs). However, it remains unclear to what extent the DIs and the alleles that constitute them coincide between populations that underwent adaptation to freshwater independently. We examine threespine sticklebacks from ten freshwater lakes that emerged 500–1500 years ago in the White Sea basin, with the emphasis on repeatability of genomic patterns of adaptation among the lake populations and the role of local recombination rate in the distribution and structure of DIs. The 65 detected DIs are clustered in the genome, forming 12 aggregations, and this clustering cannot be explained by the variation of the recombination rate. Only 21 of the DIs are present in all the freshwater populations, likely being indispensable for successful colonization of freshwater environment by the ancestral marine population. Within most DIs, the same set of single nucleotide polymorphisms (SNPs) distinguish marine and freshwater haplotypes in all the lake populations; however, in some DIs, freshwater alleles differ between populations, suggesting that they could have been established by recruitment of different haplotypes in different populations.
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Affiliation(s)
- Nadezhda V Terekhanova
- Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Sector for Molecular Evolution, Institute for Information Transmission Problems of the RAS (Kharkevich Institute), Moscow, Russia
| | - Anna E Barmintseva
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, Moscow, Russia
| | - Alexey S Kondrashov
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan.,M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Sector for Molecular Evolution, Institute for Information Transmission Problems of the RAS (Kharkevich Institute), Moscow, Russia
| | - Nikolai S Mugue
- Laboratory of Molecular Genetics, Russian Federal Research Institute of Fisheries and Oceanography, Moscow, Russia.,N. K. Koltzov Institute of Developmental Biology RAS, Moscow, Russia
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45
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Hartfield M, Bataillon T. Selective Sweeps Under Dominance and Inbreeding. G3 (BETHESDA, MD.) 2020; 10:1063-1075. [PMID: 31974096 PMCID: PMC7056974 DOI: 10.1534/g3.119.400919] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/18/2020] [Indexed: 12/26/2022]
Abstract
A major research goal in evolutionary genetics is to uncover loci experiencing positive selection. One approach involves finding 'selective sweeps' patterns, which can either be 'hard sweeps' formed by de novo mutation, or 'soft sweeps' arising from recurrent mutation or existing standing variation. Existing theory generally assumes outcrossing populations, and it is unclear how dominance affects soft sweeps. We consider how arbitrary dominance and inbreeding via self-fertilization affect hard and soft sweep signatures. With increased self-fertilization, they are maintained over longer map distances due to reduced effective recombination and faster beneficial allele fixation times. Dominance can affect sweep patterns in outcrossers if the derived variant originates from either a single novel allele, or from recurrent mutation. These models highlight the challenges in distinguishing hard and soft sweeps, and propose methods to differentiate between scenarios.
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Affiliation(s)
- Matthew Hartfield
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario M5S 3B2, Canada,
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark, and
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark, and
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46
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Sprengelmeyer QD, Mansourian S, Lange JD, Matute DR, Cooper BS, Jirle EV, Stensmyr MC, Pool JE. Recurrent Collection of Drosophila melanogaster from Wild African Environments and Genomic Insights into Species History. Mol Biol Evol 2020; 37:627-638. [PMID: 31730190 PMCID: PMC7038662 DOI: 10.1093/molbev/msz271] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster. This globally distributed human commensal is thought to originate from sub-Saharan Africa, yet until recently, it had never been reported from undisturbed wilderness environments that could reflect its precommensal niche. Here, we document the collection of 288 D. melanogaster individuals from multiple African wilderness areas in Zambia, Zimbabwe, and Namibia. The presence of D. melanogaster in these remote woodland environments is consistent with an ancestral range in southern-central Africa, as opposed to equatorial regions. After sequencing the genomes of 17 wilderness-collected flies collected from Kafue National Park in Zambia, we found reduced genetic diversity relative to town populations, elevated chromosomal inversion frequencies, and strong differences at specific genes including known insecticide targets. Combining these genomes with existing data, we probed the history of this species' geographic expansion. Demographic estimates indicated that expansion from southern-central Africa began ∼10,000 years ago, with a Saharan crossing soon after, but expansion from the Middle East into Europe did not begin until roughly 1,400 years ago. This improved model of demographic history will provide an important resource for future evolutionary and genomic studies of this key model organism. Our findings add context to the history of D. melanogaster, while opening the door for future studies on the biological basis of adaptation to human environments.
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Affiliation(s)
| | | | - Jeremy D Lange
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI
| | - Daniel R Matute
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Brandon S Cooper
- Division of Biological Sciences, University of Montana, Missoula, MT
| | | | | | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI
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47
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Khatri BS, Burt A. Robust Estimation of Recent Effective Population Size from Number of Independent Origins in Soft Sweeps. Mol Biol Evol 2020; 36:2040-2052. [PMID: 30968124 PMCID: PMC6736332 DOI: 10.1093/molbev/msz081] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Estimating recent effective population size is of great importance in characterizing and predicting the evolution of natural populations. Methods based on nucleotide diversity may underestimate current day effective population sizes due to historical bottlenecks, whereas methods that reconstruct demographic history typically only detect long-term variations. However, soft selective sweeps, which leave a fingerprint of mutational history by recurrent mutations on independent haplotype backgrounds, holds promise of an estimate more representative of recent population history. Here, we present a simple and robust method of estimation based only on knowledge of the number of independent recurrent origins and the current frequency of the beneficial allele in a population sample, independent of the strength of selection and age of the mutation. Using a forward-time theoretical framework, we show the mean number of origins is a function of θ=2Nμ and current allele frequency, through a simple equation, and the distribution is approximately Poisson. This estimate is robust to whether mutants preexisted before selection arose and is equally accurate for diploid populations with incomplete dominance. For fast (e.g., seasonal) demographic changes compared with time scale for fixation of the mutant allele, and for moderate peak-to-trough ratios, we show our constant population size estimate can be used to bound the maximum and minimum population size. Applied to the Vgsc gene of Anopheles gambiae, we estimate an effective population size of roughly 6×107, and including seasonal demographic oscillations, a minimum effective population size >3×107, and a maximum <6×109, suggesting a mean ∼109.
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Affiliation(s)
- Bhavin S Khatri
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, United Kingdom.,The Francis Crick Institute, London, United Kingdom
| | - Austin Burt
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, United Kingdom
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48
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Stewart NB, Rogers RL. Chromosomal rearrangements as a source of new gene formation in Drosophila yakuba. PLoS Genet 2019; 15:e1008314. [PMID: 31545792 PMCID: PMC6776367 DOI: 10.1371/journal.pgen.1008314] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 10/03/2019] [Accepted: 07/17/2019] [Indexed: 11/19/2022] Open
Abstract
The origins of new genes are among the most fundamental questions in evolutionary biology. Our understanding of the ways that new genetic material appears and how that genetic material shapes population variation remains incomplete. De novo genes and duplicate genes are a key source of new genetic material on which selection acts. To better understand the origins of these new gene sequences, we explored the ways that structural variation might alter expression patterns and form novel transcripts. We provide evidence that chromosomal rearrangements are a source of novel genetic variation that facilitates the formation of de novo exons in Drosophila. We identify 51 cases of de novo exon formation created by chromosomal rearrangements in 14 strains of D. yakuba. These new genes inherit transcription start signals and open reading frames when the 5' end of existing genes are combined with previously untranscribed regions. Such new genes would appear with novel peptide sequences, without the necessity for secondary transitions from non-coding RNA to protein. This mechanism of new peptide formations contrasts with canonical theory of de novo gene progression requiring non-coding intermediaries that must acquire new mutations prior to loss via pseudogenization. Hence, these mutations offer a means to de novo gene creation and protein sequence formation in a single mutational step, answering a long standing open question concerning new gene formation. We further identify gene expression changes to 134 existing genes, indicating that these mutations can alter gene regulation. Population variability for chromosomal rearrangements is considerable, with 2368 rearrangements observed across 14 inbred lines. More rearrangements were identified on the X chromosome than any of the autosomes, suggesting the X is more susceptible to chromosome alterations. Together, these results suggest that chromosomal rearrangements are a source of variation in populations that is likely to be important to explain genetic and therefore phenotypic diversity.
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Affiliation(s)
- Nicholas B. Stewart
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
- Department of Biological Sciences, Ft Hays State University, Ft Hays, Kansas, United States of America
| | - Rebekah L. Rogers
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
- * E-mail:
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49
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Hill T, Koseva BS, Unckless RL. The Genome of Drosophila innubila Reveals Lineage-Specific Patterns of Selection in Immune Genes. Mol Biol Evol 2019; 36:1405-1417. [PMID: 30865231 PMCID: PMC6573480 DOI: 10.1093/molbev/msz059] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pathogenic microbes can exert extraordinary evolutionary pressure on their hosts. They can spread rapidly and sicken or even kill their host to promote their own proliferation. Because of this strong selective pressure, immune genes are some of the fastest evolving genes across metazoans, as highlighted in mammals and insects. Drosophila melanogaster serves as a powerful model for studying host/pathogen evolution. While Drosophila melanogaster are frequently exposed to various pathogens, little is known about D. melanogaster's ecology, or if they are representative of other Drosophila species in terms of pathogen pressure. Here, we characterize the genome of Drosophila innubila, a mushroom-feeding species highly diverged from D. melanogaster and investigate the evolution of the immune system. We find substantial differences in the rates of evolution of immune pathways between D. innubila and D. melanogaster. Contrasting what was previously found for D. melanogaster, we find little evidence of rapid evolution of the antiviral RNAi genes and high rates of evolution in the Toll pathway. This suggests that, while immune genes tend to be rapidly evolving in most species, the specific genes that are fastest evolving may depend either on the pathogens faced by the host and/or divergence in the basic architecture of the host's immune system.
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Affiliation(s)
- Tom Hill
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS
| | | | - Robert L Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS
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50
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Filatov DA. Extreme Lewontin's Paradox in Ubiquitous Marine Phytoplankton Species. Mol Biol Evol 2019; 36:4-14. [PMID: 30351418 DOI: 10.1093/molbev/msy195] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Larger populations are expected to have larger genetic diversity. However, as pointed out by Lewontin in 1974, the range of population sizes exceeds the range of genetic diversity by many orders of magnitude (a.k.a. "Lewontin's paradox," LP). The reasons for LP remain obscure. Here, This paper reports an extreme case of LP in astronomically large populations of the ubiquitous unicellular marine phytoplankton species Emiliania huxleyi (Haptophyta)-the species that accounts for 10-20% of primary productivity in the oceans and its blooms are so extensive that they are visible from space. This study demonstrates that despite the wide distribution and enormous population size, the world-wide sample of E. huxleyi strains with sequenced genomes represents a single cohesive species and contains surprisingly limited genetic diversity (π ∼ 0.006 per silent site). The patterns of polymorphism reveal even larger populations in the past, and frequent recombination (ρ ∼ 0.006) throughout the genome, ruling out demographic history and asexual reproduction as possible causes of low polymorphism in E. huxleyi. Natural selection wiping out genetic diversity at linked sites (a.k.a. "genetic draft") must be strong and frequent to account for low polymorphism in E. huxleyi. This study sheds the first light on poorly understood evolutionary genetic processes in astronomically large populations of marine microplankton.
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Affiliation(s)
- Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
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