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Nosil P, de Carvalho CF, Villoutreix R, Zamorano LS, Sinclair-Waters M, Planidin NP, Parchman TL, Feder J, Gompert Z. Evolution repeats itself in replicate long-term studies in the wild. SCIENCE ADVANCES 2024; 10:eadl3149. [PMID: 38787954 PMCID: PMC11122682 DOI: 10.1126/sciadv.adl3149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/22/2024] [Indexed: 05/26/2024]
Abstract
The extent to which evolution is repeatable remains debated. Here, we study changes over time in the frequency of cryptic color-pattern morphs in 10 replicate long-term field studies of a stick insect, each spanning at least a decade (across 30 years of total data). We find predictable "up-and-down" fluctuations in stripe frequency in all populations, representing repeatable evolutionary dynamics based on standing genetic variation. A field experiment demonstrates that these fluctuations involve negative frequency-dependent natural selection (NFDS). These fluctuations rely on demographic and selective variability that pushes populations away from equilibrium, such that they can reliably move back toward it via NFDS. Last, we show that the origin of new cryptic forms is associated with multiple structural genomic variants such that which mutations arise affects evolution at larger temporal scales. Thus, evolution from existing variation is predictable and repeatable, but mutation adds complexity even for traits evolving deterministically under natural selection.
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Affiliation(s)
- Patrik Nosil
- Theoretical and Experimental Ecology (SETE), CNRS, 2 route du CNRS, 09200 Moulis, France
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | | | - Laura S. Zamorano
- Theoretical and Experimental Ecology (SETE), CNRS, 2 route du CNRS, 09200 Moulis, France
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | | | | | - Jeffrey Feder
- Department of Biology, Notre Dame University, South Bend, IN 11111, USA
| | - Zach Gompert
- Department of Biology, Utah State University, Logan, UT 84322, USA
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2
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Goldberg JK, Allan CW, Copetti D, Matzkin LM, Bronstein J. A pooled-sample draft genome assembly provides insights into host plant-specific transcriptional responses of a Solanaceae-specializing pest, Tupiocoris notatus (Hemiptera: Miridae). Ecol Evol 2024; 14:e10979. [PMID: 38476697 PMCID: PMC10928254 DOI: 10.1002/ece3.10979] [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: 09/25/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 03/14/2024] Open
Abstract
The assembly of genomes from pooled samples of genetically heterogenous samples of conspecifics remains challenging. In this study, we show that high-quality genome assemblies can be produced from samples of multiple wild-caught individuals. We sequenced DNA extracted from a pooled sample of conspecific herbivorous insects (Hemiptera: Miridae: Tupiocoris notatus) acquired from a greenhouse infestation in Tucson, Arizona (in the range of 30-100 individuals; 0.5 mL tissue by volume) using PacBio highly accurate long reads (HiFi). The initial assembly contained multiple haplotigs (>85% BUSCOs duplicated), but duplicate contigs could be easily purged to reveal a highly complete assembly (95.6% BUSCO, 4.4% duplicated) that is highly contiguous by short-read assembly standards (N 50 = 675 kb; Largest contig = 4.3 Mb). We then used our assembly as the basis for a genome-guided differential expression study of host plant-specific transcriptional responses. We found thousands of genes (N = 4982) to be differentially expressed between our new data from individuals feeding on Datura wrightii (Solanaceae) and existing RNA-seq data from Nicotiana attenuata (Solanaceae)-fed individuals. We identified many of these genes as previously documented detoxification genes such as glutathione-S-transferases, cytochrome P450s, and UDP-glucosyltransferases. Together our results show that long-read sequencing of pooled samples can provide a cost-effective genome assembly option for small insects and can provide insights into the genetic mechanisms underlying interactions between plants and herbivorous pests.
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Affiliation(s)
- Jay K. Goldberg
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
- Department of Cellular and Developmental BiologyJohn Innes CentreNorwichNorfolkUK
| | - Carson W. Allan
- Department of EntomologyUniversity of ArizonaTucsonArizonaUSA
| | - Dario Copetti
- Arizona Genomics InstituteUniversity of ArizonaTucsonArizonaUSA
- BIO5 InstituteUniversity of ArizonaTucsonArizonaUSA
| | - Luciano M. Matzkin
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
- Department of EntomologyUniversity of ArizonaTucsonArizonaUSA
- BIO5 InstituteUniversity of ArizonaTucsonArizonaUSA
| | - Judith Bronstein
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
- Department of EntomologyUniversity of ArizonaTucsonArizonaUSA
- BIO5 InstituteUniversity of ArizonaTucsonArizonaUSA
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3
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Ali HAA, Coulson T, Clegg SM, Quilodrán CS. The effect of divergent and parallel selection on the genomic landscape of divergence. Mol Ecol 2024; 33:e17225. [PMID: 38063473 DOI: 10.1111/mec.17225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/25/2023] [Accepted: 11/16/2023] [Indexed: 01/25/2024]
Abstract
While the role of selection in divergence along the speciation continuum is theoretically well understood, defining specific signatures of selection in the genomic landscape of divergence is empirically challenging. Modelling approaches can provide insight into the potential role of selection on the emergence of a heterogenous genomic landscape of divergence. Here, we extend and apply an individual-based approach that simulates the phenotypic and genotypic distributions of two populations under a variety of selection regimes, genotype-phenotype maps, modes of migration, and genotype-environment interactions. We show that genomic islands of high differentiation and genomic valleys of similarity may respectively form under divergent and parallel selection between populations. For both types of between-population selection, negative and positive frequency-dependent selection within populations generated genomic islands of higher magnitude and genomic valleys of similarity, respectively. Divergence rates decreased under strong dominance with divergent selection, as well as in models including genotype-environment interactions under parallel selection. For both divergent and parallel selection models, divergence rate was higher under an intermittent migration regime between populations, in contrast to a constant level of migration across generations, despite an equal number of total migrants. We highlight that interpreting a particular evolutionary history from an observed genomic pattern must be done cautiously, as similar patterns may be obtained from different combinations of evolutionary processes. Modelling approaches such as ours provide an opportunity to narrow the potential routes that generate the genomic patterns of specific evolutionary histories.
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Affiliation(s)
- Hisham A A Ali
- Department of Biology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, UK
| | - Tim Coulson
- Department of Biology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, UK
| | - Sonya M Clegg
- Department of Biology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, UK
| | - Claudio S Quilodrán
- Department of Biology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, UK
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
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Goldberg JK, Olcerst A, McKibben M, Hare JD, Barker MS, Bronstein JL. A de novo long-read genome assembly of the sacred datura plant (Datura wrightii) reveals a role of tandem gene duplications in the evolution of herbivore-defense response. BMC Genomics 2024; 25:15. [PMID: 38166627 PMCID: PMC10759348 DOI: 10.1186/s12864-023-09894-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
The sacred datura plant (Solanales: Solanaceae: Datura wrightii) has been used to study plant-herbivore interactions for decades. The wealth of information that has resulted leads it to have potential as a model system for studying the ecological and evolutionary genomics of these interactions. We present a de novo Datura wrightii genome assembled using PacBio HiFi long-reads. Our assembly is highly complete and contiguous (N50 = 179Mb, BUSCO Complete = 97.6%). We successfully detected a previously documented ancient whole genome duplication using our assembly and have classified the gene duplication history that generated its coding sequence content. We use it as the basis for a genome-guided differential expression analysis to identify the induced responses of this plant to one of its specialized herbivores (Coleoptera: Chrysomelidae: Lema daturaphila). We find over 3000 differentially expressed genes associated with herbivory and that elevated expression levels of over 200 genes last for several days. We also combined our analyses to determine the role that different gene duplication categories have played in the evolution of Datura-herbivore interactions. We find that tandem duplications have expanded multiple functional groups of herbivore responsive genes with defensive functions, including UGT-glycosyltranserases, oxidoreductase enzymes, and peptidase inhibitors. Overall, our results expand our knowledge of herbivore-induced plant transcriptional responses and the evolutionary history of the underlying herbivore-response genes.
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Affiliation(s)
- Jay K Goldberg
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
| | - Aaron Olcerst
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - Michael McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - J Daniel Hare
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Judith L Bronstein
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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Christie MR, McNickle GG. Negative frequency dependent selection unites ecology and evolution. Ecol Evol 2023; 13:e10327. [PMID: 37484931 PMCID: PMC10361363 DOI: 10.1002/ece3.10327] [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: 06/02/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023] Open
Abstract
From genes to communities, understanding how diversity is maintained remains a fundamental question in biology. One challenging to identify, yet potentially ubiquitous, mechanism for the maintenance of diversity is negative frequency dependent selection (NFDS), which occurs when entities (e.g., genotypes, life history strategies, species) experience a per capita reduction in fitness with increases in relative abundance. Because NFDS allows rare entities to increase in frequency while preventing abundant entities from excluding others, we posit that negative frequency dependent selection plays a central role in the maintenance of diversity. In this review, we relate NFDS to coexistence, identify mechanisms of NFDS (e.g., mutualism, predation, parasitism), review strategies for identifying NFDS, and distinguish NFDS from other mechanisms of coexistence (e.g., storage effects, fluctuating selection). We also emphasize that NFDS is a key place where ecology and evolution intersect. Specifically, there are many examples of frequency dependent processes in ecology, but fewer cases that link this process to selection. Similarly, there are many examples of selection in evolution, but fewer cases that link changes in trait values to negative frequency dependence. Bridging these two well-developed fields of ecology and evolution will allow for mechanistic insights into the maintenance of diversity at multiple levels.
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Affiliation(s)
- Mark R. Christie
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteIndianaUSA
| | - Gordon G. McNickle
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
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De-la-Cruz IM, Kariñho-Betancourt E, Núñez-Farfán J, Oyama K. Gene family evolution and natural selection signatures in Datura spp. (Solanaceae). Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.916762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Elucidating the diversification process of congeneric species makes it necessary to identify the factors promoting species variation and diversification. Comparative gene family analysis allows us to elucidate the evolutionary history of species by identifying common genetic/genomic mechanisms underlying species responses to biotic and abiotic environments at the genomic level. In this study, we analyzed the high-quality transcriptomes of four Datura species, D. inoxia, D. pruinosa, D. stramonium, and D. wrightii. We performed a thorough comparative gene family analysis to infer the role of selection in molecular variation, changes in protein physicochemical properties, and gain/loss of genes during their diversification processes. The results revealed common and species-specific signals of positive selection, physicochemical divergence and/or expansion of metabolic genes (e.g., transferases and oxidoreductases) associated with terpene and tropane metabolism and some resistance genes (R genes). The gene family analysis presented here is a valuable tool for understanding the genome evolution of economically and ecologically significant taxa such as the Solanaceae family.
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Madsen T, Stille B, Ujvari B, Bauwens D, Endler JA. Negative frequency-dependent selection on polymorphic color morphs in adders. Curr Biol 2022; 32:3385-3388.e3. [PMID: 35714607 DOI: 10.1016/j.cub.2022.05.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/02/2022] [Accepted: 05/26/2022] [Indexed: 11/28/2022]
Abstract
Color pattern polymorphism occurs when more than one form is found within the same population. It is widespread in a variety of taxa, leading us to ask what maintains this variation. One stabilizing mechanism is negative frequency-dependent selection, also known as apostatic selection, in which the fitness of a phenotype decreases with its frequency.1-6 Negative frequency-dependent selection has been proposed as one of the most powerful selective forces in maintaining phenotypic and genetic diversity in both plant and animal populations.1,5 Despite its importance and experimental evidence,1,2,6 no study has documented that natural selection due to predation may result in negative frequency-dependent selection in a wild undisturbed vertebrate population. Here, we report the results of a long-term study, spanning 37 years from 1984 to 2020, of two distinct color morphs, zigzag and melanistic, within a population of adult adders (Vipera berus) on the island of Hallands Väderö in southern Sweden (Figure 1). Our results strongly suggest that the color pattern polymorphism is maintained by negative frequency-dependent natural selection in both males and females.
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Affiliation(s)
- Thomas Madsen
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3217, Australia.
| | - Bo Stille
- Kokkini Kefalovrysso 1410, 49100 Corfu, Greece
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3217, Australia
| | - Dirk Bauwens
- Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - John A Endler
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC 3217, Australia; Terrestrial Ecology, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia.
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Chevin L, Gompert Z, Nosil P. Frequency dependence and the predictability of evolution in a changing environment. Evol Lett 2021; 6:21-33. [PMID: 35127135 PMCID: PMC8802243 DOI: 10.1002/evl3.266] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/28/2021] [Accepted: 11/22/2021] [Indexed: 11/09/2022] Open
Abstract
Frequency‐dependent (FD) selection, whereby fitness and selection depend on the genetic or phenotypic composition of the population, arises in numerous ecological contexts (competition, mate choice, crypsis, mimicry, etc.) and can strongly impact evolutionary dynamics. In particular, negative frequency‐dependent selection (NFDS) is well known for its ability to potentially maintain stable polymorphisms, but it has also been invoked as a source of persistent, predictable frequency fluctuations. However, the conditions under which such fluctuations persist are not entirely clear. In particular, previous work rarely considered that FD is unlikely to be the sole driver of evolutionary dynamics when it occurs, because most environments are not static but instead change dynamically over time. Here, we investigate how FD interacts with a temporally fluctuating environment to shape the dynamics of population genetic change. We show that a simple metric introduced by Lewontin, the slope of frequency change against frequency near equilibrium, works as a key criterion for distinguishing microevolutionary outcomes, even in a changing environment. When this slope D is between 0 and –2 (consistent with the empirical examples we review), substantial fluctuations would not persist on their own in a large population occupying a constant environment, but they can still be maintained indefinitely as quasi‐cycles fueled by environmental noise or genetic drift. However, such moderate NFDS buffers and temporally shifts evolutionary responses to periodic environments (e.g., seasonality). Stronger FD, with slope D < –2, can produce self‐sustained cycles that may overwhelm responses to a changing environment, or even chaos that fundamentally limits predictability. This diversity of expected outcomes, together with the empirical evidence for both FD and environment‐dependent selection, suggests that the interplay of internal dynamics with external forcing should be investigated more systematically to reach a better understanding and prediction of evolution.
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Affiliation(s)
| | | | - Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD Montpellier 34090 France
- Department of Biology Utah State University Logan Utah 84322 USA
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Goldberg JK, Sternlieb SR, Pintel G, Delph LF. Observational evidence of herbivore-specific associational effects between neighboring conspecifics in natural, dimorphic populations of Datura wrightii. Ecol Evol 2021; 11:5547-5561. [PMID: 34026028 PMCID: PMC8131817 DOI: 10.1002/ece3.7454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 11/06/2022] Open
Abstract
Associational effects-in which the vulnerability of a plant to herbivores is influenced by its neighbors-have been widely implicated in mediating plant-herbivore interactions. Studies of associational effects typically focus on interspecific interactions or pest-crop dynamics. However, associational effects may also be important for species with intraspecific variation in defensive traits. In this study, we observed hundreds of Datura wrightii-which exhibits dimorphism in its trichome phenotype-from over 30 dimorphic populations across California. Our aim was to determine whether a relationship existed between the trichome phenotype of neighboring conspecifics and the likelihood of being damaged by four species of herbivorous insects. We visited plants at three timepoints to assess how these effects vary both within and between growing seasons. We hypothesized that the pattern of associational effects would provide rare morphs (i.e., focal plants that are a different morph than their neighbors) with an advantage in the form of reduced herbivory, thereby contributing to the negative frequency-dependent selection previously documented in this system. We found the best predictor of herbivory/herbivore presence on focal plants was the phenotype of the focal plant. However, we also found some important neighborhood effects. The total number of plants near a focal individual predicted the likelihood and/or magnitude of herbivory by Tupiochoris notatus, Lema daturaphila, and Manduca sexta. We also found that velvety focal plants with primarily sticky neighbors are more susceptible to infestation by Tupiochoris notatus and Lema daturaphila. This does not align with the hypothesis that associational effects at the near-neighbor scale contribute to a rare-morph advantage in this system. Overall, the results of our study show that the number and trichome-morph composition of neighboring conspecifics impact interactions between D. wrightii and insect herbivores.
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Affiliation(s)
- Jay K. Goldberg
- Department of BiologyIndiana UniversityBloomingtonINUSA
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonAZUSA
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