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Cheng J, Li J, Zhang Z, Lu H, Chen G, Yao B, Dong Y, Ma L, Yuan X, Xu J, Zhang Y, Dai W, Yang X, Xue L, Zhang Y, Zhang C, Mauricio R, Peng G, Hu S, Valverde BE, Song X, Li Y, Stift M, Qiang S. Autopolyploidy‐driven range expansion of a temperate‐originated plant to pan‐tropic under global change. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1445] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jiliang Cheng
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Jun Li
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Zheng Zhang
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Huan Lu
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Guoqi Chen
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Beibei Yao
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Yingxue Dong
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Ling Ma
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Xiaoxiao Yuan
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Jingxuan Xu
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Ying Zhang
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Weimin Dai
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Xianghong Yang
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Lifang Xue
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Yu Zhang
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Chaobin Zhang
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Rodney Mauricio
- Department of Genetics University of Georgia Athens Georgia30602USA
| | - Gary Peng
- Agriculture and Agri‐Food Canada 107 Science Place Saskatoon SaskatchewanS7N 0X2Canada
| | - Shuijin Hu
- Department of Entomology and Plant Pathology North Carolina State University Raleigh North Carolina27695USA
- College of Resources and Environmental Sciences Nanjing Agricultural University Nanjing210095China
| | - Bernal E. Valverde
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
- College of Life Sciences University of Copenhagen Taastrup Denmark
| | - Xiaoling Song
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
| | - Yi Li
- Department of Plant Science and Landscape Architecture College of Agriculture and Natural Resources University of Connecticut Storrs Connecticut06269USA
| | - Marc Stift
- Ecology Department of Biology University of Konstanz Konstanz78457Germany
| | - Sheng Qiang
- Weed Research Laboratory Nanjing Agricultural University Nanjing210095China
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Bayona-Vásquez NJ, Glenn TC, Kieran TJ, Pierson TW, Hoffberg SL, Scott PA, Bentley KE, Finger JW, Louha S, Troendle N, Diaz-Jaimes P, Mauricio R, Faircloth BC. Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD). PeerJ 2019; 7:e7724. [PMID: 31616583 PMCID: PMC6791345 DOI: 10.7717/peerj.7724] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/22/2019] [Indexed: 11/24/2022] Open
Abstract
Molecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions of the genome from many individuals (e.g., RADseq, GBS). However, researchers often find the existing methods expensive to initiate and/or difficult to implement consistently, especially because it is difficult to multiplex sufficient numbers of samples to fill entire sequencing lanes. Here, we introduce a low-cost and highly robust approach for the construction of dual-digest RADseq libraries that build on adapters and primers designed in Adapterama I. Major features of our method include: (1) minimizing the number of processing steps; (2) focusing on a single strand of sample DNA for library construction, allowing the use of a non-phosphorylated adapter on one end; (3) ligating adapters in the presence of active restriction enzymes, thereby reducing chimeras; (4) including an optional third restriction enzyme to cut apart adapter-dimers formed by the phosphorylated adapter, thus increasing the efficiency of adapter ligation to sample DNA, which is particularly effective when only low quantity/quality DNA samples are available; (5) interchangeable adapter designs; (6) incorporating variable-length internal indexes within the adapters to increase the scope of sample indexing, facilitate pooling, and increase sequence diversity; (7) maintaining compatibility with universal dual-indexed primers and thus, Illumina sequencing reagents and libraries; and, (8) easy modification for the identification of PCR duplicates. We present eight adapter designs that work with 72 restriction enzyme combinations. We demonstrate the efficiency of our approach by comparing it with existing methods, and we validate its utility through the discovery of many variable loci in a variety of non-model organisms. Our 2RAD/3RAD method is easy to perform, has low startup costs, has increased utility with low-concentration input DNA, and produces libraries that can be highly-multiplexed and pooled with other Illumina libraries.
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Affiliation(s)
- Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
| | - Todd W. Pierson
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Sandra L. Hoffberg
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States of America
| | - Peter A. Scott
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States of America
| | - Kerin E. Bentley
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: LeafWorks Inc., Sebastopol, CA, United States of America
| | - John W. Finger
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Nicholas Troendle
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Natural, Health, and Mathematical Sciences, MidAmerica Nazarene University, Olathe, KS, United States of America
| | - Pindaro Diaz-Jaimes
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodney Mauricio
- Department of Genetics, University of Georgia, Athens, GA, United States of America
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, United States of America
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3
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Glenn TC, Pierson TW, Bayona-Vásquez NJ, Kieran TJ, Hoffberg SL, Thomas IV JC, Lefever DE, Finger JW, Gao B, Bian X, Louha S, Kolli RT, Bentley KE, Rushmore J, Wong K, Shaw TI, Rothrock Jr MJ, McKee AM, Guo TL, Mauricio R, Molina M, Cummings BS, Lash LH, Lu K, Gilbert GS, Hubbell SP, Faircloth BC. Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix). PeerJ 2019; 7:e7786. [PMID: 31616589 PMCID: PMC6791344 DOI: 10.7717/peerj.7786] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/29/2019] [Indexed: 12/26/2022] Open
Abstract
Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. In many cases, NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR products. In Adapterama I, we presented universal stubs and primers to produce thousands of unique index combinations and a modifiable system for incorporating them into Illumina libraries. Here, we describe multiple ways to use the Adapterama system and other approaches for amplicon sequencing on Illumina instruments. In the variant we use most frequently for large-scale projects, we fuse partial adapter sequences (TruSeq or Nextera) onto the 5' end of locus-specific PCR primers with variable-length tag sequences between the adapter and locus-specific sequences. These fusion primers can be used combinatorially to amplify samples within a 96-well plate (8 forward primers + 12 reverse primers yield 8 × 12 = 96 combinations), and the resulting amplicons can be pooled. The initial PCR products then serve as template for a second round of PCR with dual-indexed iTru or iNext primers (also used combinatorially) to make full-length libraries. The resulting quadruple-indexed amplicons have diversity at most base positions and can be pooled with any standard Illumina library for sequencing. The number of sequencing reads from the amplicon pools can be adjusted, facilitating deep sequencing when required or reducing sequencing costs per sample to an economically trivial amount when deep coverage is not needed. We demonstrate the utility and versatility of our approaches with results from six projects using different implementations of our protocols. Thus, we show that these methods facilitate amplicon library construction for Illumina instruments at reduced cost with increased flexibility. A simple web page to design fusion primers compatible with iTru primers is available at: http://baddna.uga.edu/tools-taggi.html. A fast and easy to use program to demultiplex amplicon pools with internal indexes is available at: https://github.com/lefeverde/Mr_Demuxy.
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Affiliation(s)
- Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Todd W. Pierson
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
| | - Sandra L. Hoffberg
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, United States of America
| | - Jesse C. Thomas IV
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Daniel E. Lefever
- Department of Veterinary Biosciences and Diagnostic Imaging, University of Georgia, Athens, GA, United States of America
- Current affiliation: Integrative Systems Biology and Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - John W. Finger
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Bei Gao
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Medicine, University of California, San Diego, CA, United States of America
| | - Xiaoming Bian
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Complex Carbohydrate Research Center and Department of Microbiology, University of Georgia, Athens, GA, United States of America
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Ramya T. Kolli
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, United States of America
- Current affiliation: Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States of America
| | - Kerin E. Bentley
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: LeafWorks Inc., Sebastopol, CA, United States of America
| | - Julie Rushmore
- School of Ecology & College of Veterinary Medicine, University of Georgia, Athens, GA, United States of America
- Current affiliation: Epicenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Kelvin Wong
- US Environmental Protection Agency, Athens, GA, United States of America
- Current affiliation: California Water Service, 1720 N First St, San Jose, CA, United States of America
| | - Timothy I. Shaw
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- US Environmental Protection Agency, Athens, GA, United States of America
- Current affiliation: Department of Computational Biology, St. Jude Childrens Research Hospital, Memphis, TN, United States of America
| | | | - Anna M. McKee
- South Atlantic Water Science Center, U.S. Geological Survey, Norcross, GA, United States of America
| | - Tai L. Guo
- Department of Veterinary Biosciences and Diagnostic Imaging, University of Georgia, Athens, GA, United States of America
| | - Rodney Mauricio
- Department of Genetics, University of Georgia, Athens, GA, United States of America
| | - Marirosa Molina
- US Environmental Protection Agency, Athens, GA, United States of America
- Current affiliation: National Exposure Research Laboratory, US Environmental Protection Agency, Research Triangle Park, NC, United States of America
| | - Brian S. Cummings
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, United States of America
| | - Lawrence H. Lash
- Department of Pharmacology, Wayne State University, Detroit, MI, United States of America
| | - Kun Lu
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC, United States of America
| | - Gregory S. Gilbert
- Environmental Studies Department, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Stephen P. Hubbell
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, United States of America
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Herrmann E, Ermiş E, Meier R, Blatti-Moreno M, Knecht U, Aebersold D, Manser P, Mauricio R. Fully Automated Segmentation of the Brain Resection Cavity for Radiation Target Volume Definition in Glioblastoma Patients. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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5
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Hoffberg SL, Troendle NJ, Glenn TC, Mahmud O, Louha S, Chalopin D, Bennetzen JL, Mauricio R. A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library. G3 (Bethesda) 2018; 8:1855-1861. [PMID: 29703783 PMCID: PMC5982815 DOI: 10.1534/g3.118.200101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/19/2018] [Indexed: 11/18/2022]
Abstract
The western mosquitofish, Gambusia affinis, is a freshwater poecilid fish native to the southeastern United States but with a global distribution due to widespread human introduction. Gambusia affinis has been used as a model species for a broad range of evolutionary and ecological studies. We sequenced the genome of a male G. affinis to facilitate genetic studies in diverse fields including invasion biology and comparative genetics. We generated Illumina short read data from paired-end libraries and in vitro proximity-ligation libraries. We obtained 54.9× coverage, N50 contig length of 17.6 kb, and N50 scaffold length of 6.65 Mb. Compared to two other species in the Poeciliidae family, G. affinis has slightly fewer genes that have shorter total, exon, and intron length on average. Using a set of universal single-copy orthologs in fish genomes, we found 95.5% of these genes were complete in the G. affinis assembly. The number of transposable elements in the G. affinis assembly is similar to those of closely related species. The high-quality genome sequence and annotations we report will be valuable resources for scientists to map the genetic architecture of traits of interest in this species.
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Affiliation(s)
| | | | - Travis C Glenn
- Department of Genetics
- Department of Environmental Health Science
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602
| | - Ousman Mahmud
- Department of Genetics
- Department of Computational Biology
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602
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6
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Hoffberg SL, Mauricio R, Hall RJ. Control or re-treat? Model-based guidelines for managing established plant invasions. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1632-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Mauricio R, Rausher MD. EXPERIMENTAL MANIPULATION OF PUTATIVE SELECTIVE AGENTS PROVIDES EVIDENCE FOR THE ROLE OF NATURAL ENEMIES IN THE EVOLUTION OF PLANT DEFENSE. Evolution 2017; 51:1435-1444. [PMID: 28568624 DOI: 10.1111/j.1558-5646.1997.tb01467.x] [Citation(s) in RCA: 266] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/1996] [Accepted: 05/30/1997] [Indexed: 11/29/2022]
Abstract
Although biologists have long assumed that plant resistance characters evolved under selection exerted by such natural enemies as herbivores and pathogens, experimental evidence for this assumption is sparse. We present evidence that natural enemies exert selection on particular plant resistance characters. Specifically, we demonstrate that elimination of natural enemies from an experimental field population of Arabidopsis thaliana alters the pattern of selection on genetic variation in two characters that have been shown to reduce herbivore damage in the field: total glucosinolate concentration and trichome density. The change in pattern of selection reveals that natural enemies imposed selection favoring increased glucosinolate concentration and increased trichome density, and thus, supports one of the major assumptions of the coevolution hypothesis. We also demonstrate that a pattern of stabilizing selection on glucosinolate concentration results from a balance between the costs and benefits associated with increasing levels of this resistance character. This result provides direct confirmation of the appropriateness of cost-benefit models for characterizing the evolution of plant defenses.
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Affiliation(s)
- Rodney Mauricio
- Department of Zoology, Duke University, Durham, North Carolina, 27708-0325
| | - Mark D Rausher
- Department of Zoology, Duke University, Durham, North Carolina, 27708-0325
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Guo C, Du J, Wang L, Yang S, Mauricio R, Tian D, Gu T. Insertions/Deletions-Associated Nucleotide Polymorphism in Arabidopsis thaliana. Front Plant Sci 2016; 7:1792. [PMID: 27965694 PMCID: PMC5127803 DOI: 10.3389/fpls.2016.01792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/15/2016] [Indexed: 06/06/2023]
Abstract
Although high levels of within-species variation are commonly observed, a general mechanism for the origin of such variation is still lacking. Insertions and deletions (indels) are a widespread feature of genomes and we hypothesize that there might be an association between indels and patterns of nucleotide polymorphism. Here, we investigate flanking sequences around 18 indels (>100 bp) among a large number of accessions of the plant, Arabidopsis thaliana. We found two distinct haplotypes, i.e., a nucleotide dimorphism, present around each of these indels and dimorphic haplotypes always corresponded to the indel-present/-absent patterns. In addition, the peaks of nucleotide diversity between the two divergent alleles were closely associated with these indels. Thus, there exists a close association between indels and dimorphisms. Further analysis suggests that indel-associated substitutions could be an important component of genetic variation shaping nucleotide polymorphism in Arabidopsis. Finally, we suggest a mechanism by which indels might generate these highly divergent haplotypes. This study provides evidence that nucleotide dimorphisms, which are frequently regarded as evidence of frequency-dependent selection, could be explained simply by structural variation in the genome.
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Affiliation(s)
- Changjiang Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjing, China
| | - Jianchang Du
- Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjing, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjing, China
| | - Rodney Mauricio
- Department of Genetics, University of GeorgiaAthens, GA, USA
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing UniversityNanjing, China
| | - Tingting Gu
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural UniversityNanjing, China
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9
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Hoffberg SL, Kieran TJ, Catchen JM, Devault A, Faircloth BC, Mauricio R, Glenn TC. RAD
cap: sequence capture of dual‐digest
RAD
seq libraries with identifiable duplicates and reduced missing data. Mol Ecol Resour 2016; 16:1264-78. [DOI: 10.1111/1755-0998.12566] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/06/2016] [Accepted: 07/11/2016] [Indexed: 12/21/2022]
Affiliation(s)
| | - Troy J. Kieran
- Department of Environmental Health Science University of Georgia Athens GA 30602 USA
| | - Julian M. Catchen
- Department of Animal Biology University of Illinois Urbana IL 61801 USA
| | | | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA 70803 USA
| | - Rodney Mauricio
- Department of Genetics University of Georgia Athens GA 30602 USA
| | - Travis C. Glenn
- Department of Genetics University of Georgia Athens GA 30602 USA
- Department of Environmental Health Science University of Georgia Athens GA 30602 USA
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Bentley KE, Mauricio R. High degree of clonal reproduction and lack of large-scale geographic patterning mark the introduced range of the invasive vine, kudzu (Pueraria montana var. lobata), in North America. Am J Bot 2016; 103:1499-1507. [PMID: 27555435 DOI: 10.3732/ajb.1500434] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 06/20/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Pueraria montana var. lobata, or kudzu, is an invasive species whose invasion in North America is not genetically well characterized. The clonality of kudzu introduces challenges to population genetic analyses that can bias the assessment of spatial patterns of genotypes. Assessing patterns of genetic diversity while considering clonality is necessary to understand the invasion and spread of kudzu in its invasive range. METHODS We screened 1747 individuals from 87 populations across the invasive range with 15 microsatellite markers and a 789 bp chloroplast region. We performed detailed clonal analyses and tested levels of genetic diversity, population structure, and phylogeographic relationships. KEY RESULTS Kudzu exhibited a clonal rate of 80%, and was more heterozygous than other long-lived perennials. We detected only 353 distinct clonal lineages, with over 60% sharing a maternal haplotype. Populations were established with few genotypes, many consisting of only a single clone. We found no isolation by distance. Despite high genetic diversity, we found little geographic patterning. CONCLUSIONS Kudzu is highly clonal with few genetically distinct lineages and haplotypes existing in the introduced range. Our data are consistent with a large single introduction, or a few at most. Introduced lineages are geographically randomly distributed but isolated, suggesting that genotypes rarely expand into already established populations. No route of expansion was detectable from an original introduction. The invasion of kudzu does not seem to have been dominated by a single genotype, thus standing genetic variation and phenotypic plasticity are more likely mechanisms explaining kudzu's invasion success.
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Affiliation(s)
- Kerin E Bentley
- Department of Genetics, Davison Life Sciences Building, University of Georgia, Athens, Georgia 30602 USA
| | - Rodney Mauricio
- Department of Genetics, Davison Life Sciences Building, University of Georgia, Athens, Georgia 30602 USA
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Bayer A, Goldman K, Mauricio R, Nachtigall M, Naftolin F, Nachtigall L. Long term hormone replacement therapy (HT) does not affect post-menopausal total body composition. Fertil Steril 2015. [DOI: 10.1016/j.fertnstert.2015.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Bentley KE, Berryman KR, Hopper M, Hoffberg SL, Myhre KE, Iwao K, Lee JB, Glenn TC, Mauricio R. Eleven microsatellites in an emerging invader, Phytolacca americana (Phytolaccaceae), from its native and introduced ranges. Appl Plant Sci 2015; 3:apps1500002. [PMID: 25798346 PMCID: PMC4356323 DOI: 10.3732/apps.1500002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 01/30/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY To facilitate population genetic analyses, microsatellite markers were developed for pokeweed (Phytolacca americana), a large, weedy, perennial herb native to eastern North America that is emerging as a significant invasive species in China. METHODS AND RESULTS We mined 1,100,538 Illumina MiSeq reads from genomic DNA for microsatellites and identified 58 primer pairs. We screened these primers for polymorphism in two native and two invasive populations. We identified 11 loci that amplified consistently. The number of alleles per locus ranged from two to six, and observed heterozygosity ranged from 0.00 to 1.00. All loci were largely monomorphic within populations but different among populations. The primers were of very limited use in the congener P. acinosa. CONCLUSIONS These loci will provide a valuable resource to study the population genetics and invasion history of P. americana.
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Affiliation(s)
- Kerin E. Bentley
- Department of Genetics, University of Georgia, Athens, Georgia 30602 USA
| | - Kaelyn R. Berryman
- Department of Genetics, University of Georgia, Athens, Georgia 30602 USA
| | - McGee Hopper
- Department of Genetics, University of Georgia, Athens, Georgia 30602 USA
| | - Sandra L. Hoffberg
- Department of Genetics, University of Georgia, Athens, Georgia 30602 USA
| | - Karin E. Myhre
- Department of Comparative Literature, University of Georgia, Athens, Georgia 30602 USA
| | - Keisuke Iwao
- Department of Sociology, Momoyama Gakuin University, Izumi, Osaka, 594-1198, Japan
| | - Jared B. Lee
- Department of Genetics, University of Georgia, Athens, Georgia 30602 USA
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, Georgia 30602 USA
| | - Rodney Mauricio
- Department of Genetics, University of Georgia, Athens, Georgia 30602 USA
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Dahn HA, Lee JB, Bentley KE, Glenn TC, Mauricio R. Development of 12 novel microsatellite loci for invasive Chinese privet (Ligustrum sinense) from its introduced range. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0397-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Koelling VA, Mauricio R. Genetic factors associated with mating system cause a partial reproductive barrier between two parapatric species of leavenworthia (brassicaceae). Am J Bot 2010; 97:412-22. [PMID: 20526457 PMCID: PMC2879664 DOI: 10.3732/ajb.0900184] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Reproductive barriers play a major role in the origin and maintenance of biodiversity by restricting gene flow between species. Although both pre- and postzygotic barriers often isolate species, prezygotic barriers are thought to contribute more to reproductive isolation. We investigated possible reproductive barriers between Leavenworthia alabamica and L. crassa, parapatric species with high morphological and ecological similarity and the ability to hybridize. Using greenhouse and field experiments, we tested for habitat isolation and genetic incompatibilities. From controlled crosses, we identified unilateral incompatibility (a partial prezygotic barrier associated with the self-incompatibility system), but no evidence of other genetic incompatibilities. We found a small reduction in pollen viability of F(1) hybrids and early germination of F(1), F(2), and BC hybrids relative to L. alabamica and L. crassa in a common garden experiment, but the effect on fitness was not tested. Field studies of hybrid pollen viability and germination are needed to determine if they contribute to reproductive isolation. In a reciprocal transplant, we found no evidence of habitat isolation or reduced hybrid survival (from seedling to adult stage) or reproduction. These data suggest unilateral incompatibility partially reproductively isolates L. alabamica and L. crassa, but no other reproductive barriers could be detected.
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Affiliation(s)
- Vanessa A. Koelling
- Department of Genetics, University of Georgia, Athens, Georgia 30602-7223 USA
| | - Rodney Mauricio
- Department of Genetics, University of Georgia, Athens, Georgia 30602-7223 USA
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Abstract
Evolutionary biologists explain the maintenance of intermediate levels of defense in plant populations as being due to trade-offs, or negative genetic covariances among ecologically important traits. Attempts at detecting trade-offs as constraints on the evolution of defense have not always been successful, leading some to conclude that such trade-offs rarely explain current levels of defense in the population. Using the agricultural pest Ipomoea purpurea, we measured correlations between traits involved in defense to glyphosate, the active ingredient in Roundup, a widely used herbicide. We found significant allocation costs of tolerance, as well as trade-offs between resistance and two measures of tolerance to glyphosate. Selection on resistance and tolerance exhibited differing patterns: tolerance to leaf damage was under negative directional selection, whereas resistance was under positive directional selection. The joint pattern of selection on resistance and tolerance to leaf damage indicated the presence of alternate peaks in the fitness landscape such that a combination of either high tolerance and low resistance, or high resistance and low tolerance was favored. The widespread use of this herbicide suggests that it is likely an important selective agent on weed populations. Understanding the evolutionary dynamics of herbicide defense traits is thus of increasing importance in the context of human-mediated evolution.
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Affiliation(s)
- Regina S Baucom
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.
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Abstract
The extent to which epistasis contributes to adaptation and speciation has been a controversial topic in evolutionary genetics. One experimental approach to study epistasis is based on quantitative trait locus (QTL) mapping using molecular markers. Comparisons can be made among all possible pair-wise combinations of the markers, irrespective of whether an additive QTL is associated with a marker; several software packages have been developed that facilitate this. We review several examples of using this approach to identify epistatic QTLs for traits of evolutionary or ecological interest. While there is variability in the results, the number of epistatic QTL interactions is often greater than or equal to the number of additive QTLs. The magnitude of epistatic effects can be larger than the additive effects. Thus, epistatic interactions seem to be an important part of natural genetic variation. Future studies of epistatic QTLs could lead to descriptions of the genetic networks underlying variation for fitness-related traits.
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Affiliation(s)
- Russell L Malmberg
- Department of Plant Biology, University of Georgia, Athens, 30602-7271, USA.
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Stansfield W, Mauricio R, Tang R, Selzman C. Proteasome inhibition promotes regression of left ventricular hypertrophy. J Surg Res 2006. [DOI: 10.1016/j.jss.2005.11.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Malmberg RL, Held S, Waits A, Mauricio R. Epistasis for fitness-related quantitative traits in Arabidopsis thaliana grown in the field and in the greenhouse. Genetics 2005; 171:2013-27. [PMID: 16157670 PMCID: PMC1456117 DOI: 10.1534/genetics.105.046078] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 08/29/2005] [Indexed: 11/18/2022] Open
Abstract
The extent to which epistasis contributes to adaptation, population differentiation, and speciation is a long-standing and important problem in evolutionary genetics. Using recombinant inbred (RI) lines of Arabidopsis thaliana grown under natural field conditions, we have examined the genetic architecture of fitness-correlated traits with respect to epistasis; we identified both single-locus additive and two-locus epistatic QTL for natural variation in fruit number, germination, and seed length and width. For fruit number, we found seven significant epistatic interactions, but only two additive QTL. For seed germination, length, and width, there were from two to four additive QTL and from five to eight epistatic interactions. The epistatic interactions were both positive and negative. In each case, the magnitude of the epistatic effects was roughly double that of the effects of the additive QTL, varying from -41% to +29% for fruit number and from -5% to +4% for seed germination, length, and width. A number of the QTL that we describe participate in more than one epistatic interaction, and some loci identified as additive also may participate in an epistatic interaction; the genetic architecture for fitness traits may be a network of additive and epistatic effects. We compared the map positions of the additive and epistatic QTL for germination, seed width, and seed length from plants grown in both the field and the greenhouse. While the total number of significant additive and epistatic QTL was similar under the two growth conditions, the map locations were largely different. We found a small number of significant epistatic QTL x environment effects when we tested directly for them. Our results support the idea that epistatic interactions are an important part of natural genetic variation and reinforce the need for caution in comparing results from greenhouse-grown and field-grown plants.
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Affiliation(s)
- Russell L Malmberg
- Department of Plant Biology, 2502 Plant Sciences Building, University of Georgia, Athens, GA 30602, USA.
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Abstract
Ecologists study the rules that govern processes influencing the distribution and abundance of organisms, particularly with respect to the interactions of organisms with their biotic and abiotic environments. Over the past decades, using a combination of sophisticated mathematical models and rigorous experiments, ecologists have made considerable progress in understanding the complex web of interactions that constitute an ecosystem. The field of genomics runs on a path parallel to ecology. Like ecology, genomicists seek to understand how each gene in the genome interacts with every other gene and how each gene interacts with multiple, environmental factors. Gene networks connect genes as complex as the 'webs' that connect the species in an ecosystem. In fact, genes exist in an ecosystem we call the genome. The genome as ecosystem is more than a metaphor--it serves as the conceptual foundation for an interdisciplinary approach to the study of complex systems characteristic of both genomics and ecology. Through the infusion of genomics into ecology and ecology into genomics both fields will gain fresh insight into the outstanding major questions of their disciplines.
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Affiliation(s)
- Rodney Mauricio
- Department of Genetics, Davison Life sciences complex, University of Georgia, Athens, GA 30602-7223, USA.
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Abstract
Although much is known about the molecular genetic basis of trichome development in Arabidopsis thaliana, less is known about the underlying genetic basis of continuous variation in a trait known to be of adaptive importance: trichome density. The density of leaf trichomes is known to be a major determinant of herbivore damage in natural populations of A. thaliana and herbivores are a significant selective force on genetic variation for trichome density. A number of developmental changes occur during ontogeny in A. thaliana, including changes in trichome density. I used multiple interval mapping (MIM) analysis to identify QTL responsible for trichome density on both juvenile leaves and adult leaves in replicate, independent trials and asked whether those QTL changed with ontogeny. In both juvenile and adult leaves, I detected a single major QTL on chromosome 2 that explained much of the genetic variance. Although additional QTL were detected, there were no consistent differences in the genetic architecture of trichome density measured on juvenile and adult leaves. The finding of a single QTL of major effect for a trait of known adaptive importance suggests that genes of major effect may play an important role in adaptation.
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Affiliation(s)
- Rodney Mauricio
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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Abstract
Hybridization is increasingly recognized as a significant creative force in evolution. Interbreeding among species can lead to the creation of novel genotypes and morphologies that lead to adaptation. On the Hawaiian island of O'ahu, populations of two species of plants in the endemic genus Lipochaeta grow at similar elevations in the northern Wai'anae Mountains. These two species represent extremes of the phenotypic distribution of leaf shape: the leaves of Lipochaeta tenuifolia individuals are compound and highly dissected while leaves of L. tenuis are simple. Based primarily on leaf shape morphology, a putative hybrid population of Lipochaeta located at Pu'u Kawiwi was identified. Individuals in this population exhibit a range of leaf shapes intermediate in varying degrees between the leaf shapes of the putative parental species. We analyzed individuals from pure populations of L. tenuifolia, L. tenuis and the putative hybrids using 133 AFLP markers. Genetic analysis of these neutral markers provided support for the hybrid origin of this population. The correlation between genetic background and leaf morphology in the hybrids suggested that the genome of the parental species with simple leaves might have significantly contributed to the evolution of a novel, compound leaf morphology.
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Affiliation(s)
- Stacy Jørgensen
- Department of Geography, University of Georgia, Athens, GA 30602, USA.
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Richards CL, Hamrick JL, Donovan LA, Mauricio R. Unexpectedly high clonal diversity of two salt marsh perennials across a severe environmental gradient. Ecol Lett 2004. [DOI: 10.1111/j.1461-0248.2004.00674.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Jørgensen S, Mauricio R. Neutral genetic variation among wild North American populations of the weedy plant Arabidopsis thaliana is not geographically structured. Mol Ecol 2004; 13:3403-13. [PMID: 15487999 DOI: 10.1111/j.1365-294x.2004.02329.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We investigated neutral genetic variation within and among 53 wild-collected populations of the weedy annual plant, Arabidopsis thaliana, in North America, using amplified fragment length polymorphism (AFLP) markers. A. thaliana is thought to have been introduced to North America from Eurasia by humans; such an introduction might be expected to leave a clear geographical signal in the genetic data. To detect such patterns, we sampled populations at several hierarchical geographical levels. We collected individuals from populations in two areas of the Southeast and one in the Midwest, as well as individuals from populations in the Pacific Northwest and Northeast. To estimate within-population variation, we sampled eight individuals from each of six populations in the Southeast and Midwest. Among all 95 individuals analysed, we detected 131 polymorphic AFLP fragments. We found no evidence for continental or regional diversification. Individuals sampled from Midwestern and Southeastern populations intermingled in a neighbour-joining tree, and Mantel tests conducted within the Midwestern and Southeastern regions as well as the full data set failed to detect any significant relationship between geographical and genetic distance. These results mirror those found for most global surveys of neutral genetic variability in A. thaliana. Surprisingly, we detected substantial amounts of neutral genetic variability within populations. The levels of genetic variation within populations, coupled with the nongeographical nature of divergence among populations, are consistent with contemporary gene flow and point to a complex and dynamic population history of A. thaliana in North America.
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Affiliation(s)
- S Jørgensen
- Department of Genetics, Davison Life Sciences Complex, University of Georgia, Athens, GA 30602-7223, USA
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Abstract
Glyphosate, the active ingredient in the herbicide RoundUp, has increased dramatically in use over the past decade and constitutes a potent anthropogenic source of selection. In the southeastern United States, weedy morning glories have begun to develop tolerance to glyphosate, representing a unique opportunity to examine the evolutionary genetics of a novel trait. We found genetic variation for tolerance, indicating the potential for the population to respond to selection by glyphosate. However, the following significant evolutionary constraint exists: in the absence of glyphosate, tolerant genotypes produced fewer seeds than susceptible genotypes. The combination of strong positive directional selection in the presence of glyphosate and strong negative directional selection in its absence may indicate that the selective landscape of land use could drive the evolutionary trajectory of glyphosate tolerance. Understanding these evolutionary forces is imperative for devising comprehensive management strategies to help slow the rate of the evolution of tolerance.
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Affiliation(s)
- Regina S Baucom
- Department of Genetics, University of Georgia, Athens, GA 30602-7223, USA.
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Mauricio R, Stahl EA, Korves T, Tian D, Kreitman M, Bergelson J. Natural selection for polymorphism in the disease resistance gene Rps2 of Arabidopsis thaliana. Genetics 2003; 163:735-46. [PMID: 12618410 PMCID: PMC1462445 DOI: 10.1093/genetics/163.2.735] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pathogen resistance is an ecologically important phenotype increasingly well understood at the molecular genetic level. In this article, we examine levels of avrRpt2-dependent resistance and Rps2 locus DNA sequence variability in a worldwide sample of 27 accessions of Arabidopsis thaliana. The rooted parsimony tree of Rps2 sequences drawn from a diverse set of ecotypes includes a deep bifurcation separating major resistance and susceptibility clades of alleles. We find evidence for selection maintaining these alleles and identify the N-terminal part of the leucine-rich repeat region as a probable target of selection. Additional protein variants are found within the two major clades and correlate well with measurable differences among ecotypes in resistance to the avirulence gene avrRpt2 of the pathogen Pseudomonas syringae. Long-lived polymorphisms have been observed for other resistance genes of A. thaliana; the Rps2 data suggest that the long-term maintenance of phenotypic variation in resistance genes may be a general phenomenon and are consistent with diversifying selection acting in concert with selection to maintain variation.
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Affiliation(s)
- Rodney Mauricio
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
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Stinchcombe J, Rutter M, Burdick D, Tiffin P, Rausher M, Mauricio R. Testing for Environmentally Induced Bias in Phenotypic Estimates of Natural Selection: Theory and Practice. Am Nat 2002; 160:511-23. [DOI: 10.1086/342069] [Citation(s) in RCA: 193] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
Gregor Mendel was either clever or lucky enough to study traits of simple inheritance in his pea plants; however, many plant characters of interest to modern geneticists are decidedly complex. Understanding the genetic basis of such complex, or quantitative, traits requires a combination of modern molecular genetic techniques and powerful statistical methods. These approaches have begun to give us insight into understanding the evolution of complex traits both in crops and in wild plants.
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Affiliation(s)
- R Mauricio
- Department of Genetics, Life Sciences Building, University of Georgia, Athens, Georgia 30602-7223, USA.
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Abstract
The co-evolutionary 'arms race' is a widely accepted model for the evolution of host-pathogen interactions. This model predicts that variation for disease resistance will be transient, and that host populations generally will be monomorphic at disease-resistance (R-gene) loci. However, plant populations show considerable polymorphism at R-gene loci involved in pathogen recognition. Here we have tested the arms-race model in Arabidopsis thaliana by analysing sequences flanking Rpm1, a gene conferring the ability to recognize Pseudomonas pathogens carrying AvrRpm1 or AvrB. We reject the arms-race hypothesis: resistance and susceptibility alleles at this locus have co-existed for millions of years. To account for the age of alleles and the relative levels of polymorphism within allelic classes, we use coalescence theory to model the long-term accumulation of nucleotide polymorphism in the context of the short-term ecological dynamics of disease resistance. This analysis supports a 'trench warfare' hypothesis, in which advances and retreats of resistance-allele frequency maintain variation for disease resistance as a dynamic polymorphism.
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Affiliation(s)
- E A Stahl
- Committee on Genetics, University of Chicago, Illinois 60637, USA
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Mauricio R, Rausher MD. Experimental Manipulation of Putative Selective Agents Provides Evidence for the Role of Natural Enemies in the Evolution of Plant Defense. Evolution 1997. [DOI: 10.2307/2411196] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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