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Sehgal D, Oliveira C, Mathioni S, Widdison S, Plumb W, Campos B, Kaundun SS. Genomic characterisation and dissection of the onset of resistance to acetyl CoA carboxylase-inhibiting herbicides in a large collection of Digitaria insularis from Brazil. Front Genet 2024; 15:1340852. [PMID: 38440194 PMCID: PMC10910277 DOI: 10.3389/fgene.2024.1340852] [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: 11/19/2023] [Accepted: 01/19/2024] [Indexed: 03/06/2024] Open
Abstract
An in-depth genotypic characterisation of a diverse collection of Digitaria insularis was undertaken to explore the neutral genetic variation across the natural expansion range of this weed species in Brazil. With the exception of Minas Gerais, populations from all other states showed high estimates of expected heterozygosity (HE > 0.60) and genetic diversity. There was a lack of population structure based on geographic origin and a low population differentiation between populations across the landscape as evidenced by average Fst value of 0.02. On combining haloxyfop [acetyl CoA carboxylase (ACCase)-inhibiting herbicide] efficacy data with neutral genetic variation, we found evidence of presence of two scenarios of resistance evolution in this weed species. Whilst populations originating from north-eastern region demonstrated an active role of gene flow, populations from the mid-western region displayed multiple, independent resistance evolution as the major evolutionary mechanism. A target-site mutation (Trp2027Cys) in the ACCase gene, observed in less than 1% of resistant populations, could not explain the reduced sensitivity of 15% of the populations to haloxyfop. The genetic architecture of resistance to ACCase-inhibiting herbicides was dissected using a genome wide association study (GWAS) approach. GWAS revealed association of three SNPs with reduced sensitivity to haloxyfop and clethodim. In silico analysis of these SNPs revealed important non-target site genes belonging to families involved in herbicide detoxification, including UDPGT91C1 and GT2, and genes involved in vacuolar sequestration-based degradation pathway. Exploration of five genomic prediction models revealed that the highest prediction power (≥0.80) was achieved with the models Bayes A and RKHS, incorporating SNPs with additive effects and epistatic interactions, respectively.
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Affiliation(s)
- Deepmala Sehgal
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Claudia Oliveira
- Syngenta Crop Protection, Holambra Research and Development Center, São Paulo, Brazil
| | - Sandra Mathioni
- Syngenta Crop Protection, Holambra Research and Development Center, São Paulo, Brazil
| | - Stephanie Widdison
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Will Plumb
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Breno Campos
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
| | - Shiv Shankhar Kaundun
- Syngenta Ltd., Jealott’s Hill International Research Centre, Bracknell, United Kingdom
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Patriarcheas D, Momtareen T, Gallagher JEG. Yeast of Eden: microbial resistance to glyphosate from a yeast perspective. Curr Genet 2023; 69:203-212. [PMID: 37269314 PMCID: PMC10716058 DOI: 10.1007/s00294-023-01272-4] [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: 04/07/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/05/2023]
Abstract
First marketed as RoundUp, glyphosate is history's most popular herbicide because of its low acute toxicity to metazoans and broad-spectrum effectiveness across plant species. The development of glyphosate-resistant crops has led to increased glyphosate use and consequences from the use of glyphosate-based herbicides (GBH). Glyphosate has entered the food supply, spurred glyphosate-resistant weeds, and exposed non-target organisms to glyphosate. Glyphosate targets EPSPS/AroA/Aro1 (orthologs across plants, bacteria, and fungi), the rate-limiting step in the production of aromatic amino acids from the shikimate pathway. Metazoans lacking this pathway are spared from acute toxicity and acquire their aromatic amino acids from their diet. However, glyphosate resistance is increasing in non-target organisms. Mutations and natural genetic variation discovered in Saccharomyces cerevisiae illustrate similar types of glyphosate resistance mechanisms in fungi, plants, and bacteria, in addition to known resistance mechanisms such as mutations in Aro1 that block glyphosate binding (target-site resistance (TSR)) and mutations in efflux drug transporters non-target-site resistance (NTSR). Recently, genetic variation and mutations in an amino transporter affecting glyphosate resistance have uncovered potential off-target effects of glyphosate in fungi and bacteria. While glyphosate is a glycine analog, it is transported into cells using an aspartic/glutamic acid (D/E) transporter. The size, shape, and charge distribution of glyphosate closely resembles D/E, and, therefore, glyphosate is a D/E amino acid mimic. The mitochondria use D/E in several pathways and mRNA-encoding mitochondrial proteins are differentially expressed during glyphosate exposure. Mutants downstream of Aro1 are not only sensitive to glyphosate but also a broad range of other chemicals that cannot be rescued by exogenous supplementation of aromatic amino acids. Glyphosate also decreases the pH when unbuffered and many studies do not consider the differences in pH that affect toxicity and resistance mechanisms.
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Affiliation(s)
- Dionysios Patriarcheas
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506, USA
| | - Taizina Momtareen
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506, USA
| | - Jennifer E G Gallagher
- Department of Biology, West Virginia University, 53 Campus Drive, Morgantown, WV, 26506, USA.
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3
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Brunharo CACG, Tranel PJ. Repeated evolution of herbicide resistance in Lolium multiflorum revealed by haplotype-resolved analysis of acetyl-CoA carboxylase. Evol Appl 2023; 16:1969-1981. [PMID: 38143902 PMCID: PMC10739073 DOI: 10.1111/eva.13615] [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: 03/03/2023] [Revised: 06/27/2023] [Accepted: 10/24/2023] [Indexed: 12/26/2023] Open
Abstract
Herbicide resistance in weeds is one of the greatest challenges in modern food production. The grass species Lolium multiflorum is an excellent model species to investigate evolution under similar selection pressure because populations have repeatedly evolved resistance to many herbicides, utilizing a multitude of mechanisms to neutralize herbicide damage. In this work, we investigated the gene that encodes acetyl-CoA carboxylase (ACCase), the target site of the most successful herbicide group available for grass weed control. We sampled L. multiflorum populations from agricultural fields with history of intense herbicide use, and studied their response to three ACCase-inhibiting herbicides. To elucidate the mechanisms of herbicide resistance and the genetic relationship among populations, we resolved the haplotypes of 97 resistant and susceptible individuals by sequencing ACCase amplicons using long-read DNA sequencing technologies. Our dose-response data indicated the existence of many, often unpredictable, resistance patterns to ACCase-inhibiting herbicides, where populations exhibited as much as 37-fold reduction in herbicide response. The majority of the populations exhibited resistance to all three herbicides studied. Phylogenetic and molecular genetic analyses revealed multiple evolutionary origins of resistance-endowing ACCase haplotypes, as well as widespread admixture in the region regardless of cropping system. The amplicons generated were diverse, with haplotypes exhibiting 26-110 polymorphisms. Polymorphisms included insertions and deletions 1-31 bp in length, none of which were associated with the resistance phenotype based on an association analysis. We also found evidence that some populations have multiple mechanisms of resistance. Our results highlight the astounding genetic diversity in L. multiflorum populations, and the potential for repeated evolution of herbicide resistance across the landscape that challenges weed management approaches and jeopardizes sustainable weed control practices. We provide an in-depth discussion of the evolutionary and practical implications of our results.
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Affiliation(s)
- Caio A. C. G. Brunharo
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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Gupta S, Harkess A, Soble A, Van Etten M, Leebens-Mack J, Baucom RS. Interchromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance. THE NEW PHYTOLOGIST 2023; 238:1263-1277. [PMID: 36721257 DOI: 10.1111/nph.18782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance. Here, using herbicide-resistant populations of the common morning glory (Ipomoea purpurea), we perform a multilevel analysis of the genome and transcriptome to uncover putative loci involved in nontarget-site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations. We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate (RoundUp) resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost. Overall, our work suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are potentially maintained through generations via ILD, and that the fitness cost associated with resistance in this species is likely a by-product of genetic hitchhiking.
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Affiliation(s)
- Sonal Gupta
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Alex Harkess
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Anah Soble
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
| | - Megan Van Etten
- Biology Department, Pennsylvania State University, Dunmore, PA, 18512, USA
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Regina S Baucom
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
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5
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Ferreira MF, Torres C, Bracamonte E, Galetto L. Glyphosate affects the susceptibility of non-target native plant species according to their stage of development and degree of exposure in the landscape. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161091. [PMID: 36566866 DOI: 10.1016/j.scitotenv.2022.161091] [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: 10/12/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Unsustainable agriculture is producing a great socio-ecological transformation in Latin America because it has expanded into areas occupied by native forests. Glyphosate is the most widely used herbicide, with severe ecotoxicological effects on non-target organisms. The aim of this study was to determine the effects of glyphosate on seedlings of 24 non-target herbaceous and non-herbaceous plant species present in forest relicts of Argentine Chaco. The effects of a gradient of glyphosate doses (525, 1050, 2100, 4200, and 8400 g ai/ha) were measured in seedlings of each species under greenhouse conditions. Seedlings were grown from seeds collected from native forest fragments of different sizes (assuming three different degrees of historical exposure to glyphosate in the landscape). Doses were applied at different stages of seedling development (five- and ten-weeks after emergence), and phytotoxicity, growth reduction, and sensitivity were measured. Glyphosate produced lethal or sublethal effects in all 24 species, some of which were very sensitive (>60 % of the species presented strong to severe growth reduction with ¼ of the dose used on crops). The greatest toxicological effects were related to early stage of development, herbaceous species, and low historical exposure to glyphosate. According to the species sensitivity distribution, the drift-dose to protect 95 % of the plant species that occur in larger forest fragments should not exceed 5 % of the dose commonly used on crops. These results suggest that the current weed management linked to glyphosate-resistant crops could lead to a gradual loss of biodiversity in the landscape. Concurrently, selection of glyphosate-tolerant biotypes in some non-target species could represent a very problematic cycle for the current model of industrial agriculture. Some alternatives for weed control are proposed.
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Affiliation(s)
- María Florencia Ferreira
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba-Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Vélez Sarsfield 1611, Córdoba, Argentina
| | - Carolina Torres
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba-Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Vélez Sarsfield 1611, Córdoba, Argentina; Cátedra de Diversidad Biológica III, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Avenida Vélez Sarsfield 1611, Córdoba, Argentina
| | - Enzo Bracamonte
- Cátedra de Ecotoxicología, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Ingeniero Agrónomo Félix Aldo Marrone 746, Córdoba, Argentina
| | - Leonardo Galetto
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba-Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida Vélez Sarsfield 1611, Córdoba, Argentina; Cátedra de Diversidad Biológica III, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Avenida Vélez Sarsfield 1611, Córdoba, Argentina.
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6
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Diversity of Herbicide-Resistance Mechanisms of Avena fatua L. to Acetyl-CoA Carboxylase-Inhibiting Herbicides in the Bajio, Mexico. PLANTS 2022; 11:plants11131644. [PMID: 35807596 PMCID: PMC9269088 DOI: 10.3390/plants11131644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022]
Abstract
Herbicide resistance is an evolutionary process that affects entire agricultural regions’ yield and productivity. The high number of farms and the diversity of weed management can generate hot selection spots throughout the regions. Resistant biotypes can present a diversity of mechanisms of resistance and resistance factors depending on selective conditions inside the farm; this situation is similar to predictions by the geographic mosaic theory of coevolution. In Mexico, the agricultural region of the Bajio has been affected by herbicide resistance for 25 years. To date, Avena fatua L. is one of the most abundant and problematic weed species. The objective of this study was to determine the mechanism of resistance of biotypes with failures in weed control in 70 wheat and barley crop fields in the Bajio, Mexico. The results showed that 70% of farms have biotypes with target site resistance (TSR). The most common mutations were Trp–1999–Cys, Asp–2078–Gly, Ile–2041–Asn, and some of such mutations confer cross-resistance to ACCase-inhibiting herbicides. Metabolomic fingerprinting showed four different metabolic expression patterns. The results confirmed that in the Bajio, there exist multiple selection sites for both resistance mechanisms, which proves that this area can be considered as a geographic mosaic of resistance.
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Ravet K, Sparks CD, Dixon AL, Küpper A, Westra EP, Pettinga DJ, Tranel PJ, Felix J, Morishita DW, Jha P, Kniss A, Stahlman PW, Neve P, Patterson EL, Westra P, Gaines TA. Genomic-based epidemiology reveals independent origins and gene flow of glyphosate resistance in Bassia scoparia populations across North America. Mol Ecol 2021; 30:5343-5359. [PMID: 34614274 PMCID: PMC9297870 DOI: 10.1111/mec.16215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 08/26/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022]
Abstract
Genomic-based epidemiology can provide insight into the origins and spread of herbicide resistance mechanisms in weeds. We used kochia (Bassia scoparia) populations resistant to the herbicide glyphosate from across western North America to test the alternative hypotheses that (i) a single EPSPS gene duplication event occurred initially in the Central Great Plains and then subsequently spread to all other geographical areas now exhibiting glyphosate-resistant kochia populations or that (ii) gene duplication occurred multiple times in independent events in a case of parallel evolution. We used qPCR markers previously developed for measuring the structure of the EPSPS tandem duplication to investigate whether all glyphosate-resistant individuals had the same EPSPS repeat structure. We also investigated population structure using simple sequence repeat markers to determine the relatedness of kochia populations from across the Central Great Plains, Northern Plains and the Pacific Northwest. We found that the original EPSPS duplication genotype was predominant in the Central Great Plains where glyphosate resistance was first reported. We identified two additional EPSPS duplication genotypes, one having geographical associations with the Northern Plains and the other with the Pacific Northwest. The EPSPS duplication genotype from the Pacific Northwest seems likely to represent a second, independent evolutionary origin of a resistance allele. We found evidence of gene flow across populations and a general lack of population structure. The results support at least two independent evolutionary origins of glyphosate resistance in kochia, followed by substantial and mostly geographically localized gene flow to spread the resistance alleles into diverse genetic backgrounds.
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Affiliation(s)
- Karl Ravet
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
- Present address:
Department of Soil and Crop SciencesColorado State UniversityFort CollinsColoradoUSA
| | - Crystal D. Sparks
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Andrea L. Dixon
- Rothamsted ResearchWest Common HarpendenHertfordshireUK
- Center for Outcomes Research and EpidemiologyCollege of Veterinary MedicineKansas State UniversityManhattanKansasUSA
| | - Anita Küpper
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
- Crop Science DivisionWeed ControlBayer AGFrankfurt am MainGermany
| | - Eric P. Westra
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Dean J. Pettinga
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
| | | | - Joel Felix
- Oregon State University, Malheur Experiment StationOntarioORUSA
| | - Don W. Morishita
- Kimberly Research and Extension CenterUniversity of IdahoKimberlyIdahoUSA
| | - Prashant Jha
- Department of AgronomyIowa State UniversityAmesIowaUSA
| | - Andrew Kniss
- Department of Plant SciencesUniversity of WyomingLaramieWyomingUSA
| | | | - Paul Neve
- Rothamsted ResearchWest Common HarpendenHertfordshireUK
- Department of Plant & Environmental SciencesUniversity of CopenhagenTaastrupDenmark
| | - Eric L. Patterson
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Philip Westra
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Todd A. Gaines
- Department of Agricultural BiologyColorado State UniversityFort CollinsColoradoUSA
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8
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Josephs EB, Van Etten ML, Harkess A, Platts A, Baucom RS. Adaptive and maladaptive expression plasticity underlying herbicide resistance in an agricultural weed. Evol Lett 2021; 5:432-440. [PMID: 34367667 PMCID: PMC8327940 DOI: 10.1002/evl3.241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/29/2021] [Accepted: 05/20/2021] [Indexed: 11/09/2022] Open
Abstract
Plastic phenotypic responses to environmental change are common, yet we lack a clear understanding of the fitness consequences of these plastic responses. Here, we use the evolution of herbicide resistance in the common morning glory (Ipomoea purpurea) as a model for understanding the relative importance of adaptive and maladaptive gene expression responses to herbicide. Specifically, we compare leaf gene expression changes caused by herbicide to the expression changes that evolve in response to artificial selection for herbicide resistance. We identify a number of genes that show plastic and evolved responses to herbicide and find that for the majority of genes with both plastic and evolved responses, plastic responses appear to be adaptive. We also find that selection for herbicide response increases gene expression plasticity. Overall, these results show the importance of adaptive plasticity for herbicide resistance in a common weed and that expression changes in response to strong environmental change can be adaptive.
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Affiliation(s)
- Emily B. Josephs
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824
- Ecology, Evolution, and Behavior ProgramMichigan State UniversityEast LansingMichigan48824
| | - Megan L. Van Etten
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichigan48109
- Biology DepartmentPennsylvania State UniversityDunmorePennsylvania18512
| | - Alex Harkess
- Department of Crop, Soil, and Environmental SciencesAuburn UniversityAuburnAlabama36849
- HudsonAlpha Institute for BiotechnologyHuntsvilleAlabama35806
| | - Adrian Platts
- Department of Plant BiologyMichigan State UniversityEast LansingMichigan48824
| | - Regina S. Baucom
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichigan48109
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9
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Keshtkar E, Kudsk P, Mesgaran MB. Perspective: common errors in dose-response analysis and how to avoid them. PEST MANAGEMENT SCIENCE 2021; 77:2599-2608. [PMID: 33415846 DOI: 10.1002/ps.6268] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/21/2020] [Accepted: 01/08/2021] [Indexed: 05/12/2023]
Abstract
Dose-response experiments are conducted to determine the toxicity of chemicals on organisms. The relationship between dose and response is described by different statistical models. The four-parameter log-logistic model is widely used in pesticide sciences to derive biologically relevant parameters such as ED50 and resistance index (RI). However, there are some common errors associated with the calculation of ED50 and RI that can lead to erroneous conclusions. Here we discuss five common errors and propose guidance to avoid them. We suggest (i) all response curves must be fitted simultaneously to allow for proper comparison of parameters across curves, (ii) in the case of nonparallel curves absolute ED50 must be used instead of relative ED50 , (iii) standard errors or confidence intervals of the parameters must be reported, (iv) the e parameter in asymmetrical models is not equal to ED50 and hence absolute ED50 must be estimated, and (v) when the four-parameter log-logistic model returns a negative value for the lower asymptote, which is biologically meaningless in most cases, the model should be reduced to its three-parameter version or other types of model should be applied. The mixed-effects model and the meta-analytic approach are suggested as appropriate to average the parameters across repeated dose-response experiments. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Eshagh Keshtkar
- Department of Agronomy, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Per Kudsk
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Mohsen B Mesgaran
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
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10
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Van Etten ML, Soble A, Baucom RS. Variable inbreeding depression may explain associations between the mating system and herbicide resistance in the common morning glory. Mol Ecol 2021; 30:5422-5437. [PMID: 33604956 DOI: 10.1111/mec.15852] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 01/18/2021] [Accepted: 02/10/2021] [Indexed: 12/12/2022]
Abstract
Inbreeding depression is a central parameter underlying mating system variation in nature and one that can be altered by environmental stress. Although a variety of systems show that inbreeding depression tends to increase under stressful conditions, we have very little understanding across most organisms how the level of inbreeding depression may change as a result of adaptation to stressors. In this work we examined the potential that inbreeding depression varied among lineages of Ipomoea purpurea artificially evolved to exhibit divergent levels of herbicide resistance. We examined inbreeding depression in a variety of fitness-related traits in both the growth chamber and in the field, and paired this work with an examination of gene expression changes. We found that, while inbreeding depression was present across many of the traits, lineages artificially selected for increased herbicide resistance often showed no evidence of inbreeding depression in the presence of herbicide, and in fact, showed evidence of outbreeding depression in some traits compared to nonselected control lines and lineages selected for increased herbicide susceptibility. Further, at the transcriptome level, the resistant selection lines had differing patterns of gene expression according to breeding type (inbred vs. outcrossed) compared to the control and susceptible selection lines. Our data together indicate that inbreeding depression may be lessened in populations that are adapting to regimes of strong selection.
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Affiliation(s)
- Megan L Van Etten
- Biology Department, Pennsylvania State University, Dunmore, Pennsylvania, USA
| | - Anah Soble
- Ecology and Evolutionary Biology Department, University of Michigan, Ann Arbor, Michigan, USA
| | - Regina S Baucom
- Ecology and Evolutionary Biology Department, University of Michigan, Ann Arbor, Michigan, USA
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11
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Baek Y, Bobadilla LK, Giacomini DA, Montgomery JS, Murphy BP, Tranel PJ. Evolution of Glyphosate-Resistant Weeds. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 255:93-128. [PMID: 33932185 DOI: 10.1007/398_2020_55] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Widespread adoption of glyphosate-resistant crops and concomitant reliance on glyphosate for weed control set an unprecedented stage for the evolution of herbicide-resistant weeds. There are now 48 weed species that have evolved glyphosate resistance. Diverse glyphosate-resistance mechanisms have evolved, including single, double, and triple amino acid substitutions in the target-site gene, duplication of the gene encoding the target site, and others that are rare or nonexistent for evolved resistance to other herbicides. This review summarizes these resistance mechanisms, discusses what is known about their evolution, and concludes with some of the impacts glyphosate-resistant weeds have had on weed management.
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Affiliation(s)
- Yousoon Baek
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Darci A Giacomini
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | | | - Brent P Murphy
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA.
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12
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Van Etten M, Lee KM, Chang SM, Baucom RS. Parallel and nonparallel genomic responses contribute to herbicide resistance in Ipomoea purpurea, a common agricultural weed. PLoS Genet 2020; 16:e1008593. [PMID: 32012153 PMCID: PMC7018220 DOI: 10.1371/journal.pgen.1008593] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 02/13/2020] [Accepted: 01/03/2020] [Indexed: 12/30/2022] Open
Abstract
The repeated evolution of herbicide resistance has been cited as an example of genetic parallelism, wherein separate species or genetic lineages utilize the same genetic solution in response to selection. However, most studies that investigate the genetic basis of herbicide resistance examine the potential for changes in the protein targeted by the herbicide rather than considering genome-wide changes. We used a population genomics screen and targeted exome re-sequencing to uncover the potential genetic basis of glyphosate resistance in the common morning glory, Ipomoea purpurea, and to determine if genetic parallelism underlies the repeated evolution of resistance across replicate resistant populations. We found no evidence for changes in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), glyphosate's target protein, that were associated with resistance, and instead identified five genomic regions that showed evidence of selection. Within these regions, genes involved in herbicide detoxification-cytochrome P450s, ABC transporters, and glycosyltransferases-are enriched and exhibit signs of selective sweeps. One region under selection shows parallel changes across all assayed resistant populations whereas other regions exhibit signs of divergence. Thus, while it appears that the physiological mechanism of resistance in this species is likely the same among resistant populations, we find patterns of both similar and divergent selection across separate resistant populations at particular loci.
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Affiliation(s)
- Megan Van Etten
- Biology Department, Penn State-Scranton, Dunmore, Pennsylvania, United States of America
| | - Kristin M. Lee
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Shu-Mei Chang
- Plant Biology Department, University of Georgia, Athens, Georgia, United States of America
| | - Regina S. Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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Baucom RS. Evolutionary and ecological insights from herbicide-resistant weeds: what have we learned about plant adaptation, and what is left to uncover? THE NEW PHYTOLOGIST 2019; 223:68-82. [PMID: 30710343 DOI: 10.1111/nph.15723] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
The evolution of herbicide resistance in crop weeds presents one of the greatest challenges to agriculture and the production of food. Herbicide resistance has been studied for more than 60 yr, in the large part by researchers seeking to design effective weed control programs. As an outcome of this work, various unique questions in plant adaptation have been addressed. Here, I collate recent research on the herbicide-resistant problem in light of key questions and themes in evolution and ecology. I highlight discoveries made on herbicide-resistant weeds in three broad areas - the genetic basis of adaptation, evolutionary constraints, experimental evolution - and similarly discuss questions left to be answered. I then develop how one would use herbicide-resistance evolution as a model for studying eco-evolutionary dynamics within a community context. My overall goals are to highlight important findings in the weed science literature that are relevant to themes in plant adaptation and to stimulate the use of herbicide-resistant plants as models for addressing key questions within ecology and evolution.
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Affiliation(s)
- Regina S Baucom
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
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Hawkins NJ, Bass C, Dixon A, Neve P. The evolutionary origins of pesticide resistance. Biol Rev Camb Philos Soc 2019; 94:135-155. [PMID: 29971903 PMCID: PMC6378405 DOI: 10.1111/brv.12440] [Citation(s) in RCA: 259] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 06/01/2018] [Accepted: 06/06/2018] [Indexed: 01/24/2023]
Abstract
Durable crop protection is an essential component of current and future food security. However, the effectiveness of pesticides is threatened by the evolution of resistant pathogens, weeds and insect pests. Pesticides are mostly novel synthetic compounds, and yet target species are often able to evolve resistance soon after a new compound is introduced. Therefore, pesticide resistance provides an interesting case of rapid evolution under strong selective pressures, which can be used to address fundamental questions concerning the evolutionary origins of adaptations to novel conditions. We ask: (i) whether this adaptive potential originates mainly from de novo mutations or from standing variation; (ii) which pre-existing traits could form the basis of resistance adaptations; and (iii) whether recurrence of resistance mechanisms among species results from interbreeding and horizontal gene transfer or from independent parallel evolution. We compare and contrast the three major pesticide groups: insecticides, herbicides and fungicides. Whilst resistance to these three agrochemical classes is to some extent united by the common evolutionary forces at play, there are also important differences. Fungicide resistance appears to evolve, in most cases, by de novo point mutations in the target-site encoding genes; herbicide resistance often evolves through selection of polygenic metabolic resistance from standing variation; and insecticide resistance evolves through a combination of standing variation and de novo mutations in the target site or major metabolic resistance genes. This has practical implications for resistance risk assessment and management, and lessons learnt from pesticide resistance should be applied in the deployment of novel, non-chemical pest-control methods.
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Affiliation(s)
- Nichola J. Hawkins
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenAL5 4SEU.K.
| | - Chris Bass
- Department of BiosciencesUniversity of Exeter, Penryn CampusCornwallTR10 9FEU.K.
| | - Andrea Dixon
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenAL5 4SEU.K.
- Department of Plant BiologyUniversity of GeorgiaAthensGA 30602U.S.A.
| | - Paul Neve
- Department of Biointeractions and Crop ProtectionRothamsted ResearchHarpendenAL5 4SEU.K.
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15
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Alvarado-Serrano DF, Van Etten ML, Chang SM, Baucom RS. The relative contribution of natural landscapes and human-mediated factors on the connectivity of a noxious invasive weed. Heredity (Edinb) 2018; 122:29-40. [PMID: 29967398 DOI: 10.1038/s41437-018-0106-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 01/20/2023] Open
Abstract
Examining how the landscape may influence gene flow is at the forefront of understanding population differentiation and adaptation. Such understanding is crucial in light of ongoing environmental changes and the elevated risk of ecosystems alteration. In particular, knowledge of how humans may influence population structure is imperative to allow for informed decisions in management and conservation as well as to gain a better understanding of anthropogenic impacts on the interplay between gene flow, genetic drift, and selection. Here, we use genome-wide molecular markers to characterize the population genetic structure and connectivity of Ipomoea purpurea (Convolvulaceae), a noxious invasive weed. We, likewise, assess the interaction between natural and human-driven influences on genetic differentiation among populations. Our analyses find that human population density is an important predictor of pairwise population differentiation, suggesting that the agricultural and/or horticultural trade may be involved in maintaining some level of connectivity across distant agricultural fields. Climatic variation appears as an additional predictor of genetic connectivity in this species. We discuss the implications of these results and highlight future research needed to disentangle the mechanistic processes underlying population connectivity of weeds.
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Affiliation(s)
- Diego F Alvarado-Serrano
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University, 2020E Biological Science Building, Ann Arbor, MI, 48109-1085, USA.
| | - Megan L Van Etten
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University, 2020E Biological Science Building, Ann Arbor, MI, 48109-1085, USA
| | - Shu-Mei Chang
- Department of Plant Biology, University of Georgia, Rm 3613; 2502 Miller Plant Sciences, Athens, GA, 30602-7271, USA
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University, 2020E Biological Science Building, Ann Arbor, MI, 48109-1085, USA
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Cousens RD, Fournier-Level A. Herbicide resistance costs: what are we actually measuring and why? PEST MANAGEMENT SCIENCE 2018; 74:1539-1546. [PMID: 29205805 DOI: 10.1002/ps.4819] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 05/12/2023]
Abstract
Despite the considerable research efforts invested over the years to measure the fitness costs of herbicide resistance, these have rarely been used to inform a predictive theory about the fate of resistance once the herbicide is discontinued. One reason for this may be the reductive focus on relative fitness of two genotypes as a single measure of differential performance. Although the extent of variation in relative fitness between resistant and susceptible plants has not been assessed consistently, we know enough about plant physiology and ecology not to reduce it to a single fixed value. Research must therefore consider carefully the relevance of the experimental environment, the life stage and the choice of metric when measuring fitness-related traits. The reason most often given for measuring the cost of resistance, prediction of the impacts of management options on population dynamics, cannot be addressed using arbitrary components of fitness or a fixed value of relative fitness. To inform management options, the measurement of traits that capture the relevant processes and the main causes of their variation are required. With an emphasis on the benefit of field experiments measured over multiple time points and seasons, we highlight examples of studies that have made significant advances in this direction. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Roger D Cousens
- School of BioSciences, The University of Melbourne, Victoria, Australia
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Kreiner JM, Stinchcombe JR, Wright SI. Population Genomics of Herbicide Resistance: Adaptation via Evolutionary Rescue. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:611-635. [PMID: 29140727 DOI: 10.1146/annurev-arplant-042817-040038] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The evolution of herbicide resistance in weed populations is a highly replicated example of adaptation surmounting the race against extinction, but the factors determining its rate and nature remain poorly understood. Here, we explore theory and empirical evidence for the importance of population genetic parameters-including effective population size, dominance, mutational target size, and gene flow-in influencing the probability and mode of herbicide resistance adaptation and its variation across species. We compiled data on the number of resistance mutations across populations for 79 herbicide-resistant species. Our findings are consistent with theoretical predictions that self-fertilization reduces resistance adaptation from standing variation within populations, but increases independent adaptation across populations. Furthermore, we provide evidence for a ploidy-mating system interaction that may reflect trade-offs in polyploids between increased effective population size and greater masking of beneficial mutations. We highlight the power of population genomic approaches to provide insights into the evolutionary dynamics of herbicide resistance with important implications for understanding the limits of adaptation.
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Affiliation(s)
- Julia M Kreiner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada; , ,
| | | | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada; , ,
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Küpper A, Manmathan HK, Giacomini D, Patterson EL, McCloskey WB, Gaines TA. Population Genetic Structure in Glyphosate-Resistant and -Susceptible Palmer Amaranth ( Amaranthus palmeri) Populations Using Genotyping-by-sequencing (GBS). FRONTIERS IN PLANT SCIENCE 2018; 9:29. [PMID: 29422910 PMCID: PMC5788914 DOI: 10.3389/fpls.2018.00029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/09/2018] [Indexed: 05/25/2023]
Abstract
Palmer amaranth (Amaranthus palmeri) is a major weed in United States cotton and soybean production systems. Originally native to the Southwest, the species has spread throughout the country. In 2004 a population of A. palmeri was identified with resistance to glyphosate, a herbicide heavily relied on in modern no-tillage and transgenic glyphosate-resistant (GR) crop systems. This project aims to determine the degree of genetic relatedness among eight different populations of GR and glyphosate-susceptible (GS) A. palmeri from various geographic regions in the United States by analyzing patterns of phylogeography and diversity to ascertain whether resistance evolved independently or spread from outside to an Arizona locality (AZ-R). Shikimic acid accumulation and EPSPS genomic copy assays confirmed resistance or susceptibility. With a set of 1,351 single nucleotide polymorphisms (SNPs), discovered by genotyping-by-sequencing (GBS), UPGMA phylogenetic analysis, principal component analysis, Bayesian model-based clustering, and pairwise comparisons of genetic distances were conducted. A GR population from Tennessee and two GS populations from Georgia and Arizona were identified as genetically distinct while the remaining GS populations from Kansas, Arizona, and Nebraska clustered together with two GR populations from Arizona and Georgia. Within the latter group, AZ-R was most closely related to the GS populations from Kansas and Arizona followed by the GR population from Georgia. GR populations from Georgia and Tennessee were genetically distinct from each other. No isolation by distance was detected and A. palmeri was revealed to be a species with high genetic diversity. The data suggest the following two possible scenarios: either glyphosate resistance was introduced to the Arizona locality from the east, or resistance evolved independently in Arizona. Glyphosate resistance in the Georgia and Tennessee localities most likely evolved separately. Thus, modern farmers need to continue to diversify weed management practices and prevent seed dispersal to mitigate herbicide resistance evolution in A. palmeri.
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Affiliation(s)
- Anita Küpper
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
| | - Harish K. Manmathan
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Darci Giacomini
- Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - Eric L. Patterson
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
| | | | - Todd A. Gaines
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
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19
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Kissane Z, Shephard JM. The rise of glyphosate and new opportunities for biosentinel early-warning studies. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2017; 31:1293-1300. [PMID: 28474816 DOI: 10.1111/cobi.12955] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 04/04/2017] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
Glyphosate has become the most commonly used herbicide worldwide and is reputedly environmentally benign, nontoxic, and safe for use near wildlife and humans. However, studies indicate its toxicity is underestimated and its persistence in the environment is greater than once thought. Its actions as a neurotoxin and endocrine disruptor indicate its potential to act in similar ways to persistent organic pollutants such as the organochlorines dichlorodiphenyltrichloroethane (DDT) and dioxin. Exposure to glyphosate and glyphosate-based herbicides for both wildlife and people is likely to be chronic and at sublethal levels, with multiple and ongoing exposure events occurring in urban and agricultural landscapes. Despite this, there has been little research on the impact of glyphosate on wildlife populations, and existing studies appear in the agricultural, toxicology, and water-chemistry literature that may have limited visibility among wildlife biologists. These studies clearly demonstrate a link between chronic exposure and neurotoxicity, endocrine disruption, cell damage, and immune suppression. There is a strong case for the recognition of glyphosate as an emerging organic contaminant and substantial potential exists for collaborative research among ecologists, toxicologists, and chemists to quantify the impact of glyphosate on wildlife and to evaluate the role of biosentinel species in a preemptive move to mitigate downstream impacts on people. There is scope to develop a decision framework to aid the choice of species to biomonitor and analysis methods based on the target contaminant, spatial and temporal extent of contamination, and perceived risk. Birds in particular offer considerable potential in this role because they span agricultural and urban environments, coastal, inland, and wetland ecosystems where glyphosate residues are known to be present.
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Affiliation(s)
- Zoe Kissane
- School of Veterinary and Life Sciences, Murdoch University, 90 South St Murdoch, Western Australia, Australia
| | - Jill M Shephard
- School of Veterinary and Life Sciences, Murdoch University, 90 South St Murdoch, Western Australia, Australia
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20
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Alvarado-Serrano DF, Chang SM, Baucom RS. Natural and Anthropogenic Influences on the Mating System of the Common Morning Glory. J Hered 2017; 109:126-137. [DOI: 10.1093/jhered/esx104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 11/13/2017] [Indexed: 11/13/2022] Open
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Weis AE. Detecting the "invisible fraction" bias in resurrection experiments. Evol Appl 2017; 11:88-95. [PMID: 29302274 PMCID: PMC5748523 DOI: 10.1111/eva.12533] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/24/2017] [Indexed: 01/04/2023] Open
Abstract
The resurrection approach is a powerful tool for estimating phenotypic evolution in response to global change. Ancestral generations, revived from dormant propagules, are grown side by side with descendent generations in the same environment. Phenotypic differences between the generations can be attributed to genetic change over time. Project Baseline was established to capitalize on this potential in flowering plants. Project participants collected, froze, and stored seed from 10 or more natural populations of 61 North American plant species. These will be made available in the future for resurrection experiments. One problem with this approach can arise if nonrandom mortality during storage biases the estimate of ancestral mean phenotype, which in turn would bias the estimate of evolutionary change. This bias—known as the “invisible fraction” problem—can arise if seed traits that affect survival during storage and revival are genetically correlated to postemergence traits of interest. The bias is trivial if seed survival is high. Here, I show that with low seed survival, bias can be either trivial or catastrophic. Serious bias arises when (i) most seeds deaths are selective with regard to the seed traits, and (ii) the genetic correlations between the seed and postemergence traits are strong. An invisible fraction bias can be diagnosed in seed collections that are family structured. A correlation between the family mean survival rate and the family mean of a focal postemergence trait indicates that seed mortality was not random with respect to genes affecting the focal trait, biasing the sample mean. Fortunately, family structure was incorporated into the sampling scheme for the Project Baseline collection, which will allow bias detection. New and developing statistical procedures that can incorporate genealogical information into the analysis of resurrection experiments may enable bias correction.
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Affiliation(s)
- Arthur E Weis
- Department of Ecology and Evolutionary Biology University of Toronto Toronto ON Canada.,Koffler Scientific Reserve at Jokers Hill University of Toronto King City ON Canada
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22
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Franks SJ, Hamann E, Weis AE. Using the resurrection approach to understand contemporary evolution in changing environments. Evol Appl 2017; 11:17-28. [PMID: 29302269 PMCID: PMC5748528 DOI: 10.1111/eva.12528] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/27/2017] [Indexed: 12/23/2022] Open
Abstract
The resurrection approach of reviving ancestors from stored propagules and comparing them with descendants under common conditions has emerged as a powerful method of detecting and characterizing contemporary evolution. As climatic and other environmental conditions continue to change at a rapid pace, this approach is becoming particularly useful for predicting and monitoring evolutionary responses. We evaluate this approach, explain the advantages and limitations, suggest best practices for implementation, review studies in which this approach has been used, and explore how it can be incorporated into conservation and management efforts. We find that although the approach has thus far been used in a limited number of cases, these studies have provided strong evidence for rapid contemporary adaptive evolution in a variety of systems, particularly in response to anthropogenic environmental change, although it is far from clear that evolution will be able to rescue many populations from extinction given current rates of global changes. We also highlight one effort, known as Project Baseline, to create a collection of stored seeds that can take advantage of the resurrection approach to examine evolutionary responses to environmental change over the coming decades. We conclude that the resurrection approach is a useful tool that could be more widely employed to examine basic questions about evolution in natural populations and to assist in the conservation and management of these populations as they face continued environmental change.
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Affiliation(s)
| | - Elena Hamann
- Department of Biology Fordham University Bronx NY USA
| | - Arthur E Weis
- Department of Ecology and Evolutionary Biology Koffler Scientific Reserve at Jokers Hill University of Toronto Toronto ON Canada
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Karn E, Jasieniuk M. Genetic diversity and structure of Lolium perenne ssp. multiflorum in California vineyards and orchards indicate potential for spread of herbicide resistance via gene flow. Evol Appl 2017; 10:616-629. [PMID: 28616068 PMCID: PMC5469165 DOI: 10.1111/eva.12478] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/05/2017] [Indexed: 11/28/2022] Open
Abstract
Management of agroecosystems with herbicides imposes strong selection pressures on weedy plants leading to the evolution of resistance against those herbicides. Resistance to glyphosate in populations of Lolium perenne L. ssp. multiflorum is increasingly common in California, USA, causing economic losses and the loss of effective management tools. To gain insights into the recent evolution of glyphosate resistance in L. perenne in perennial cropping systems of northwest California and to inform management, we investigated the frequency of glyphosate resistance and the genetic diversity and structure of 14 populations. The sampled populations contained frequencies of resistant plants ranging from 10% to 89%. Analyses of neutral genetic variation using microsatellite markers indicated very high genetic diversity within all populations regardless of resistance frequency. Genetic variation was distributed predominantly among individuals within populations rather than among populations or sampled counties, as would be expected for a wide-ranging outcrossing weed species. Bayesian clustering analysis provided evidence of population structuring with extensive admixture between two genetic clusters or gene pools. High genetic diversity and admixture, and low differentiation between populations, strongly suggest the potential for spread of resistance through gene flow and the need for management that limits seed and pollen dispersal in L. perenne.
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Affiliation(s)
- Elizabeth Karn
- University of California DavisDepartment of Plant SciencesDavisCAUSA
| | - Marie Jasieniuk
- University of California DavisDepartment of Plant SciencesDavisCAUSA
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Barker BS, Andonian K, Swope SM, Luster DG, Dlugosch KM. Population genomic analyses reveal a history of range expansion and trait evolution across the native and invaded range of yellow starthistle (Centaurea solstitialis). Mol Ecol 2017; 26:1131-1147. [PMID: 28029713 DOI: 10.1111/mec.13998] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/11/2016] [Accepted: 12/19/2016] [Indexed: 12/25/2022]
Abstract
Identifying sources of genetic variation and reconstructing invasion routes for non-native introduced species is central to understanding the circumstances under which they may evolve increased invasiveness. In this study, we used genome-wide single nucleotide polymorphisms to study the colonization history of Centaurea solstitialis in its native range in Eurasia and invasions into the Americas. We leveraged this information to pinpoint key evolutionary shifts in plant size, a focal trait associated with invasiveness in this species. Our analyses revealed clear population genomic structure of potential source populations in Eurasia, including deep differentiation of a lineage found in the southern Apennine and Balkan Peninsulas and divergence among populations in Asia, eastern Europe and western Europe. We found strongest support for an evolutionary scenario in which western European populations were derived from an ancient admixture event between populations from eastern Europe and Asia, and subsequently served as the main genetic 'bridgehead' for introductions to the Americas. Introductions to California appear to be from a single source region, and multiple, independent introductions of divergent genotypes likely occurred into the Pacific Northwest. Plant size has evolved significantly at three points during range expansion, including a large size increase in the lineage responsible for the aggressive invasion of the California interior. These results reveal a long history of colonization, admixture and trait evolution in C. solstitialis, and suggest routes for improving evidence-based management decisions for one of the most ecologically and economically damaging invasive species in the western United States.
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Affiliation(s)
- Brittany S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Krikor Andonian
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Sarah M Swope
- Department of Biology, Mills College, Oakland, CA, 94613, USA
| | - Douglas G Luster
- USDA-ARS Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD, 21702, USA
| | - Katrina M Dlugosch
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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Tafoya-Razo JA, Núñez-Farfán J, Torres-García JR. Migration by seed dispersal of ACCase-inhibitor-resistant Avena fatua in north-western Mexico. PEST MANAGEMENT SCIENCE 2017; 73:167-173. [PMID: 27038305 DOI: 10.1002/ps.4282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND Biotypes of Avena fatua resistant to ACCase-inhibiting herbicides have been reported in the States of Baja California (BC) and Sonora (SON), Mexico. We hypothesised that resistant biotypes present in SON (Valle de Hermosillo and Valle del Yaqui) are derived from a resistant population from BC (Valle de Mexicali) via gene flow through the transport and exchange of contaminated wheat seed. This study aimed to determine (1) the resistance of A. fatua to ACCase-inhibiting herbicides in populations from BC and SON, (2) the mutation at the site of action and (3) the genetic structure and gene flow among populations. RESULTS DNA sequencing showed that all biotypes shared the same mutation (Leu × Ile at codon 1781). Microsatellites showed evidence of a genetic bottleneck in SON, and spatial analysis of molecular variance grouped one biotype from the Valle de Mexicali with two biotypes from the Valle de Hermosillo. Migration analysis suggested gene flow from the Valle de Mexicali to the Valle de Hermosillo, but not to the Valle del Yaqui. CONCLUSIONS The presence of resistant biotypes of A. fatua in the Valle de Hermosillo, SON, are likely derived from seeds from BC, possibly through the transport of contaminated wheat seeds. © 2016 Society of Chemical Industry.
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Affiliation(s)
- J Antonio Tafoya-Razo
- Departamento de Parasitología Agrícola, Universidad Autónoma Chapingo, Texcoco, State of Mexico, Mexico
| | - Juan Núñez-Farfán
- Laboratorio de Genética Ecológica y Evolución, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jesús R Torres-García
- Laboratorio de Genética Ecológica y Evolución, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Karn E, Jasieniuk M. Nucleotide Diversity at Site 106 of EPSPS in Lolium perenne L. ssp. multiflorum from California Indicates Multiple Evolutionary Origins of Herbicide Resistance. FRONTIERS IN PLANT SCIENCE 2017; 8:777. [PMID: 28536598 PMCID: PMC5423406 DOI: 10.3389/fpls.2017.00777] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/25/2017] [Indexed: 05/15/2023]
Abstract
The repeated evolution of herbicide resistance in weeds is an ongoing problem in agricultural regions across the world, and presents a unique system in which to study the origins and spread of adaptive traits across heterogeneous landscapes. Lolium perenne ssp. multiflorum (Lam.) (Italian ryegrass) is a widespread grass weed of agricultural crops that has repeatedly evolved resistance to herbicides across the world. In California, resistance to glyphosate has become increasingly common. To identify the mechanisms conferring glyphosate resistance in California populations of L. perenne and to gain insights into the evolutionary origins and spread of resistance in the region, we investigated the frequency of target-site mutations conferring resistance to glyphosate combined with the frequency of resistant individuals in 14 populations. A region of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) was sequenced in 401 individuals to assay for target site mutations. Seven unique alleles were detected at codon site 106, four of which have been previously shown to confer target-site-based resistance to glyphosate. Four different resistance alleles were detected, indicating that resistance to glyphosate has evolved multiple times in the region. In two populations, no EPSPS mutations were detected despite the presence of resistant plants, strongly suggesting that non-target-site-based mechanisms confer resistance to glyphosate in these populations. It is likely that resistance to glyphosate in these 14 California populations of L. perenne derives from at least five evolutionary origins, indicating that adaptive traits can evolve repeatedly over agricultural landscapes.
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Kuester A, Fall E, Chang SM, Baucom RS. Shifts in outcrossing rates and changes to floral traits are associated with the evolution of herbicide resistance in the common morning glory. Ecol Lett 2017; 20:41-49. [PMID: 27905176 DOI: 10.1111/ele.12703] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/27/2016] [Accepted: 10/18/2016] [Indexed: 01/19/2023]
Abstract
Human-mediated selection can strongly influence the evolutionary response of natural organisms within ecological timescales. But what traits allow for, or even facilitate, adaptation to the strong selection humans impose on natural systems? Using a combination of laboratory and greenhouse studies of 32 natural populations of the common agricultural weed, Ipomoea purpurea, we show that herbicide-resistant populations self-fertilise more than susceptible populations. We likewise show that anther-stigma distance, a floral trait associated with self-fertilisation in this species, exhibits a nonlinear relationship with resistance such that the most and least resistant populations exhibit lower anther-stigma separation compared to populations with moderate levels of resistance. Overall, our results extend the general finding that plant mating can be impacted by human-mediated agents of selection to that of the extreme selection of the agricultural system. This work highlights the influence of human-mediated selection on rapid responses of natural populations that can lead to unexpected long-term evolutionary consequences.
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Affiliation(s)
- Adam Kuester
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Eva Fall
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Shu-Mei Chang
- Plant Biology Department, University of Georgia, Athens, GA, 30602, USA
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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Van Etten ML, Kuester A, Chang SM, Baucom RS. Fitness costs of herbicide resistance across natural populations of the common morning glory, Ipomoea purpurea. Evolution 2016; 70:2199-2210. [PMID: 27470166 DOI: 10.1111/evo.13016] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 06/23/2016] [Accepted: 07/06/2016] [Indexed: 11/26/2022]
Abstract
Although fitness costs associated with plant defensive traits are widely expected, they are not universally detected, calling into question their generality. Here, we examine the potential for life-history trade-offs associated with herbicide resistance by examining seed germination, root growth, and above-ground growth across 43 naturally occurring populations of Ipomoea purpurea that vary in their resistance to RoundUp®, the most commonly used herbicide worldwide. We find evidence for life-history trade-offs associated with all three traits; highly resistant populations had lower germination, shorter roots, and smaller above-ground size. A visual exploration of the data indicated that the type of trade-off may differ among populations. Our results demonstrate that costs of adaptation may be present at stages other than simply the production of progeny in this agricultural weed. Additionally, the cumulative effect of costs at multiple life cycle stages can result in severe consequences to fitness when adapting to novel environments.
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Affiliation(s)
- Megan L Van Etten
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48103.
| | - Adam Kuester
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48103
| | - Shu-Mei Chang
- Plant Biology Department, University of Georgia, Athens, Georgia, 30602
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48103
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Kuester A, Wilson A, Chang SM, Baucom RS. A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weed Ipomoea purpurea. Mol Ecol 2016; 25:4508-20. [PMID: 27357067 DOI: 10.1111/mec.13737] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 05/30/2016] [Accepted: 06/22/2016] [Indexed: 01/18/2023]
Abstract
Despite the negative economic and ecological impact of weeds, relatively little is known about the evolutionary mechanisms that influence their persistence in agricultural fields. Here, we use a resurrection approach to examine the potential for genotypic and phenotypic evolution in Ipomoea purpurea, an agricultural weed that is resistant to glyphosate, the most widely used herbicide in current-day agriculture. We found striking reductions in allelic diversity between cohorts sampled nine years apart (2003 vs. 2012), suggesting that populations of this species sampled from agricultural fields have experienced genetic bottleneck events that have led to lower neutral genetic diversity. Heterozygosity excess tests indicate that these bottlenecks may have occurred prior to 2003. A greenhouse assay of individuals sampled from the field as seed found that populations of this species, on average, exhibited modest increases in herbicide resistance over time. However, populations differed significantly between sampling years for resistance: some populations maintained high resistance between the sampling years whereas others exhibited increased or decreased resistance. Our results show that populations of this noxious weed, capable of adapting to strong selection imparted by herbicide application, may lose genetic variation as a result of this or other environmental factors. We probably uncovered only modest increases in resistance on average between sampling cohorts due to a strong and previously identified fitness cost of resistance in this species, along with the potential that nonresistant migrants germinate from the seed bank.
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Affiliation(s)
- Adam Kuester
- Department of Ecology and Evolutionary Biology, University of Michigan, 2059 Kraus Natural Science Building, 830 North University, Ann Arbor, MI, 48109, USA
| | - Ariana Wilson
- Department of Ecology and Evolutionary Biology, University of Michigan, 2059 Kraus Natural Science Building, 830 North University, Ann Arbor, MI, 48109, USA
| | - Shu-Mei Chang
- Plant Biology Department, University of Georgia, 2502 Plant Sciences Building, 120 Carlton Street, Athens, GA, 30602, USA
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, 2059 Kraus Natural Science Building, 830 North University, Ann Arbor, MI, 48109, USA.
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Debban CL, Okum S, Pieper KE, Wilson A, Baucom RS. An examination of fitness costs of glyphosate resistance in the common morning glory, Ipomoea purpurea. Ecol Evol 2015; 5:5284-5294. [PMID: 30151131 PMCID: PMC6102511 DOI: 10.1002/ece3.1776] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 09/05/2015] [Accepted: 09/17/2015] [Indexed: 11/09/2022] Open
Abstract
Fitness costs are frequently invoked to explain the presence of genetic variation underlying plant defense across many types of damaging agents. Despite the expectation that costs of resistance are prevalent, however, they have been difficult to detect in nature. To examine the potential that resistance confers a fitness cost, we examined the survival and fitness of genetic lines of the common morning glory, Ipomoea purpurea, that diverged in the level of resistance to the herbicide glyphosate. We planted a large field experiment and assessed survival following herbicide application as well as fitness of the divergent selection lines in the absence of the herbicide. We found that genetic lines selected for increased resistance exhibited lower death compared to control and susceptible lines in the presence of the herbicide, but no evidence that resistant lines produced fewer seeds in the absence of herbicide. However, susceptible lines produced more viable seeds than resistant or control lines, providing some evidence of a fitness cost in terms of seed germination, and thus potential empirical support for the expectation of trait trade-offs as a consequence of adaptation to novel environments.
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Affiliation(s)
- Catherine L Debban
- Department of Biology University of Virginia 229 Gilmer Hall Charlottesville Virginia 22904
| | - Sara Okum
- Biological Sciences Department University of Cincinnati Cincinnati OH 45221
| | - Kathleen E Pieper
- Davison Life Sciences Building University of Georgia 120 East Green Street Athens Georgia 30602-7223
| | - Ariana Wilson
- Department of Ecology and Evolutionary Biology University of Michigan 2059 Kraus Natural Science Building Ann Arbor Michigan 48103
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology University of Michigan 2059 Kraus Natural Science Building Ann Arbor Michigan 48103
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