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John Thomson Lovell

TitleAsst Professor Adjunct
InstitutionUniversity of Colorado Boulder
DepartmentEcology & Evolutionary Biology

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Lei L, Gordon SP, Liu L, Sade N, Lovell JT, Rubio Wilhelmi MDM, Singan V, Sreedasyam A, Hestrin R, Phillips J, Hernandez BT, Barry K, Shu S, Jenkins J, Schmutz J, Goodstein DM, Thilmony R, Blumwald E, Vogel JP. The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum. G3 (Bethesda). 2023 Dec 29; 14(1). PMID: 37883711.
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    2. Sreedasyam A, Plott C, Hossain MS, Lovell JT, Grimwood J, Jenkins JW, Daum C, Barry K, Carlson J, Shu S, Phillips J, Amirebrahimi M, Zane M, Wang M, Goodstein D, Haas FB, Hiss M, Perroud PF, Jawdy SS, Yang Y, Hu R, Johnson J, Kropat J, Gallaher SD, Lipzen A, Shakirov EV, Weng X, Torres-Jerez I, Weers B, Conde D, Pappas MR, Liu L, Muchlinski A, Jiang H, Shyu C, Huang P, Sebastian J, Laiben C, Medlin A, Carey S, Carrell AA, Chen JG, Perales M, Swaminathan K, Allona I, Grattapaglia D, Cooper EA, Tholl D, Vogel JP, Weston DJ, Yang X, Brutnell TP, Kellogg EA, Baxter I, Udvardi M, Tang Y, Mockler TC, Juenger TE, Mullet J, Rensing SA, Tuskan GA, Merchant SS, Stacey G, Schmutz J. JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom. Nucleic Acids Res. 2023 09 08; 51(16):8383-8401. PMID: 37526283.
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    3. Devos KM, Qi P, Bahri BA, Gimode DM, Jenike K, Manthi SJ, Lule D, Lux T, Martinez-Bello L, Pendergast TH, Plott C, Saha D, Sidhu GS, Sreedasyam A, Wang X, Wang H, Wright H, Zhao J, Deshpande S, de Villiers S, Dida MM, Grimwood J, Jenkins J, Lovell J, Mayer KFX, Mneney EE, Ojulong HF, Schatz MC, Schmutz J, Song B, Tesfaye K, Odeny DA. Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet. Nat Commun. 2023 06 21; 14(1):3694. PMID: 37344528.
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    4. Tilhou NW, Poudel HP, Lovell J, Mamidi S, Schmutz J, Daum C, Zane M, Yoshinaga Y, Lipzen A, Casler MD. Genomic prediction of switchgrass winter survivorship across diverse lowland populations. G3 (Bethesda). 2023 03 09; 13(3). PMID: 36648238.
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    5. Scarlett VT, Lovell JT, Shao M, Phillips J, Shu S, Lusinska J, Goodstein DM, Jenkins J, Grimwood J, Barry K, Chalhoub B, Schmutz J, Hasterok R, Catal?n P, Vogel JP. Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium. Genetics. 2023 02 09; 223(2). PMID: 36218464.
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    6. Healey AL, Piatkowski B, Lovell JT, Sreedasyam A, Carey SB, Mamidi S, Shu S, Plott C, Jenkins J, Lawrence T, Aguero B, Carrell AA, Nieto-Lugilde M, Talag J, Duffy A, Jawdy S, Carter KR, Boston LB, Jones T, Jaramillo-Chico J, Harkess A, Barry K, Keymanesh K, Bauer D, Grimwood J, Gunter L, Schmutz J, Weston DJ, Shaw AJ. Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics. Nat Plants. 2023 02; 9(2):238-254. PMID: 36747050.
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    7. Paczesniak D, Pellino M, Goertzen R, Guenter D, Jahnke S, Fischbach A, Lovell JT, Sharbel TF. Seed size, endosperm and germination variation in sexual and apomictic Boechera. Front Plant Sci. 2022; 13:991531. PMID: 36466233.
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    8. Weng X, Haque T, Zhang L, Razzaque S, Lovell JT, Palacio-Mej?a JD, Duberney P, Lloyd-Reilley J, Bonnette J, Juenger TE. A Pleiotropic Flowering Time QTL Exhibits Gene-by-Environment Interaction for Fitness in a Perennial Grass. Mol Biol Evol. 2022 Oct 07; 39(10). PMID: 36149808.
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    9. Lovell JT, Sreedasyam A, Schranz ME, Wilson M, Carlson JW, Harkess A, Emms D, Goodstein DM, Schmutz J. GENESPACE tracks regions of interest and gene copy number variation across multiple genomes. Elife. 2022 09 09; 11. PMID: 36083267.
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    10. Marchant DB, Chen G, Cai S, Chen F, Schafran P, Jenkins J, Shu S, Plott C, Webber J, Lovell JT, He G, Sandor L, Williams M, Rajasekar S, Healey A, Barry K, Zhang Y, Sessa E, Dhakal RR, Wolf PG, Harkess A, Li FW, R?ssner C, Becker A, Gramzow L, Xue D, Wu Y, Tong T, Wang Y, Dai F, Hua S, Wang H, Xu S, Xu F, Duan H, Thei?en G, McKain MR, Li Z, McKibben MTW, Barker MS, Schmitz RJ, Stevenson DW, Zumajo-Cardona C, Ambrose BA, Leebens-Mack JH, Grimwood J, Schmutz J, Soltis PS, Soltis DE, Chen ZH. Dynamic genome evolution in a model fern. Nat Plants. 2022 09; 8(9):1038-1051. PMID: 36050461.
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    11. VanWallendael A, Benucci GMN, da Costa PB, Fraser L, Sreedasyam A, Fritschi F, Juenger TE, Lovell JT, Bonito G, Lowry DB. Host genotype controls ecological change in the leaf fungal microbiome. PLoS Biol. 2022 08; 20(8):e3001681. PMID: 35951523.
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    12. Lovell JT, Grimwood J. The first complete human genome. Nature. 2022 06; 606(7914):468-469. PMID: 35606432.
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    13. Carey SB, Lovell JT, Jenkins J, Leebens-Mack J, Schmutz J, Wilson MA, Harkess A. Representing sex chromosomes in genome assemblies. Cell Genom. 2022 May 11; 2(5). PMID: 35720975.
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    14. Napier JD, Grabowski PP, Lovell JT, Bonnette J, Mamidi S, Gomez-Hughes MJ, VanWallendael A, Weng X, Handley LH, Kim MK, Boe AR, Fay PA, Fritschi FB, Jastrow JD, Lloyd-Reilley J, Lowry DB, Matamala R, Mitchell RB, Rouquette FM, Wu Y, Webber J, Jones T, Barry K, Grimwood J, Schmutz J, Juenger TE. A generalist-specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range. Proc Natl Acad Sci U S A. 2022 04 12; 119(15):e2118879119. PMID: 35377798.
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    15. Muchlinski A, Jia M, Tiedge K, Fell JS, Pelot KA, Chew L, Davisson D, Chen Y, Siegel J, Lovell JT, Zerbe P. Cytochrome P450-catalyzed biosynthesis of furanoditerpenoids in the bioenergy crop switchgrass (Panicum virgatum L.). Plant J. 2021 11; 108(4):1053-1068. PMID: 34514645.
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    16. Lovell JT, Bentley NB, Bhattarai G, Jenkins JW, Sreedasyam A, Alarcon Y, Bock C, Boston LB, Carlson J, Cervantes K, Clermont K, Duke S, Krom N, Kubenka K, Mamidi S, Mattison CP, Monteros MJ, Pisani C, Plott C, Rajasekar S, Rhein HS, Rohla C, Song M, Hilaire RS, Shu S, Wells L, Webber J, Heerema RJ, Klein PE, Conner P, Wang X, Grauke LJ, Grimwood J, Schmutz J, Randall JJ. Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding. Nat Commun. 2021 07 05; 12(1):4125. PMID: 34226565.
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    17. Carey SB, Jenkins J, Lovell JT, Maumus F, Sreedasyam A, Payton AC, Shu S, Tiley GP, Fernandez-Pozo N, Healey A, Barry K, Chen C, Wang M, Lipzen A, Daum C, Saski CA, McBreen JC, Conrad RE, Kollar LM, Olsson S, Huttunen S, Landis JB, Burleigh JG, Wickett NJ, Johnson MG, Rensing SA, Grimwood J, Schmutz J, McDaniel SF. Gene-rich UV sex chromosomes harbor conserved regulators of sexual development. Sci Adv. 2021 06; 7(27). PMID: 34193417.
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    18. Li H, Hu X, Lovell JT, Grabowski PP, Mamidi S, Chen C, Amirebrahimi M, Kahanda I, Mumey B, Barry K, Kudrna D, Schmutz J, Lachowiec J, Lu C. Genetic dissection of natural variation in oilseed traits of camelina by whole-genome resequencing and QTL mapping. Plant Genome. 2021 07; 14(2):e20110. PMID: 34106529.
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    19. Choi JY, Abdulkina LR, Yin J, Chastukhina IB, Lovell JT, Agabekian IA, Young PG, Razzaque S, Shippen DE, Juenger TE, Shakirov EV, Purugganan MD. Natural variation in plant telomere length is associated with flowering time. Plant Cell. 2021 05 31; 33(4):1118-1134. PMID: 33580702.
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    20. Healey AL, Shepherd M, King GJ, Butler JB, Freeman JS, Lee DJ, Potts BM, Silva-Junior OB, Baten A, Jenkins J, Shu S, Lovell JT, Sreedasyam A, Grimwood J, Furtado A, Grattapaglia D, Barry KW, Hundley H, Simmons BA, Schmutz J, Vaillancourt RE, Henry RJ. Pests, diseases, and aridity have shaped the genome of Corymbia citriodora. Commun Biol. 2021 05 10; 4(1):537. PMID: 33972666.
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    21. Lovell JT, MacQueen AH, Mamidi S, Bonnette J, Jenkins J, Napier JD, Sreedasyam A, Healey A, Session A, Shu S, Barry K, Bonos S, Boston L, Daum C, Deshpande S, Ewing A, Grabowski PP, Haque T, Harrison M, Jiang J, Kudrna D, Lipzen A, Pendergast TH, Plott C, Qi P, Saski CA, Shakirov EV, Sims D, Sharma M, Sharma R, Stewart A, Singan VR, Tang Y, Thibivillier S, Webber J, Weng X, Williams M, Wu GA, Yoshinaga Y, Zane M, Zhang L, Zhang J, Behrman KD, Boe AR, Fay PA, Fritschi FB, Jastrow JD, Lloyd-Reilley J, Mart?nez-Reyna JM, Matamala R, Mitchell RB, Rouquette FM, Ronald P, Saha M, Tobias CM, Udvardi M, Wing RA, Wu Y, Bartley LE, Casler M, Devos KM, Lowry DB, Rokhsar DS, Grimwood J, Juenger TE, Schmutz J. Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature. 2021 02; 590(7846):438-444. PMID: 33505029.
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    22. Mamidi S, Healey A, Huang P, Grimwood J, Jenkins J, Barry K, Sreedasyam A, Shu S, Lovell JT, Feldman M, Wu J, Yu Y, Chen C, Johnson J, Sakakibara H, Kiba T, Sakurai T, Tavares R, Nusinow DA, Baxter I, Schmutz J, Brutnell TP, Kellogg EA. A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci. Nat Biotechnol. 2020 10; 38(10):1203-1210. PMID: 33020633.
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    23. Bragg J, Tomasi P, Zhang L, Williams T, Wood D, Lovell JT, Healey A, Schmutz J, Bonnette JE, Cheng P, Chanbusarakum L, Juenger T, Tobias CM. Environmentally responsive QTL controlling surface wax load in switchgrass. Theor Appl Genet. 2020 Nov; 133(11):3119-3137. PMID: 32803378.
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    24. Chen ZJ, Sreedasyam A, Ando A, Song Q, De Santiago LM, Hulse-Kemp AM, Ding M, Ye W, Kirkbride RC, Jenkins J, Plott C, Lovell J, Lin YM, Vaughn R, Liu B, Simpson S, Scheffler BE, Wen L, Saski CA, Grover CE, Hu G, Conover JL, Carlson JW, Shu S, Boston LB, Williams M, Peterson DG, McGee K, Jones DC, Wendel JF, Stelly DM, Grimwood J, Schmutz J. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nat Genet. 2020 05; 52(5):525-533. PMID: 32313247.
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    25. Abdulkina LR, Kobayashi C, Lovell JT, Chastukhina IB, Aklilu BB, Agabekian IA, Suesc?n AV, Valeeva LR, Nyamsuren C, Aglyamova GV, Sharipova MR, Shippen DE, Juenger TE, Shakirov EV. Components of the ribosome biogenesis pathway underlie establishment of telomere length set point in Arabidopsis. Nat Commun. 2019 12 02; 10(1):5479. PMID: 31792215.
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    26. Muchlinski A, Chen X, Lovell JT, K?llner TG, Pelot KA, Zerbe P, Ruggiero M, Callaway L, Laliberte S, Chen F, Tholl D. Biosynthesis and Emission of Stress-Induced Volatile Terpenes in Roots and Leaves of Switchgrass (Panicum virgatum L.). Front Plant Sci. 2019; 10:1144. PMID: 31608090.
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    27. Wang B, Mojica JP, Perera N, Lee CR, Lovell JT, Sharma A, Adam C, Lipzen A, Barry K, Rokhsar DS, Schmutz J, Mitchell-Olds T. Correction to: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta. Genome Biol. 2019 08 09; 20(1):161. PMID: 31399118.
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    28. Wang B, Mojica JP, Perera N, Lee CR, Lovell JT, Sharma A, Adam C, Lipzen A, Barry K, Rokhsar DS, Schmutz J, Mitchell-Olds T. Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta. Genome Biol. 2019 06 21; 20(1):126. PMID: 31227026.
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    29. Lowry DB, Lovell JT, Zhang L, Bonnette J, Fay PA, Mitchell RB, Lloyd-Reilley J, Boe AR, Wu Y, Rouquette FM, Wynia RL, Weng X, Behrman KD, Healey A, Barry K, Lipzen A, Bauer D, Sharma A, Jenkins J, Schmutz J, Fritschi FB, Juenger TE. QTL ? environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient. Proc Natl Acad Sci U S A. 2019 06 25; 116(26):12933-12941. PMID: 31182579.
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    30. Khasanova A, Lovell JT, Bonnette J, Weng X, Jenkins J, Yoshinaga Y, Schmutz J, Juenger TE. The Genetic Architecture of Shoot and Root Trait Divergence Between Mesic and Xeric Ecotypes of a Perennial Grass. Front Plant Sci. 2019; 10:366. PMID: 31019518.
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    31. Weng X, Lovell JT, Schwartz SL, Cheng C, Haque T, Zhang L, Razzaque S, Juenger TE. Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C4 grass. Plant Cell Environ. 2019 07; 42(7):2165-2182. PMID: 30847928.
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    32. Monroe JG, Powell T, Price N, Mullen JL, Howard A, Evans K, Lovell JT, McKay JK. Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. Elife. 2018 12 06; 7. PMID: 30520727.
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    33. Lovell JT, Jenkins J, Lowry DB, Mamidi S, Sreedasyam A, Weng X, Barry K, Bonnette J, Campitelli B, Daum C, Gordon SP, Gould BA, Khasanova A, Lipzen A, MacQueen A, Palacio-Mej?a JD, Plott C, Shakirov EV, Shu S, Yoshinaga Y, Zane M, Kudrna D, Talag JD, Rokhsar D, Grimwood J, Schmutz J, Juenger TE. The genomic landscape of molecular responses to natural drought stress in Panicum hallii. Nat Commun. 2018 12 06; 9(1):5213. PMID: 30523281.
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    34. Campitelli BE, Kenney AM, Hopkins R, Soule J, Lovell JT, Juenger TE. Genetic Mapping Reveals an Anthocyanin Biosynthesis Pathway Gene Potentially Influencing Evolutionary Divergence between Two Subspecies of Scarlet Gilia (Ipomopsis aggregata). Mol Biol Evol. 2018 04 01; 35(4):807-822. PMID: 29253197.
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    35. Milano ER, Payne CE, Wolfrum E, Lovell J, Jenkins J, Schmutz J, Juenger TE. Quantitative trait loci for cell wall composition traits measured using near-infrared spectroscopy in the model C4 perennial grass Panicum hallii. Biotechnol Biofuels. 2018; 11:25. PMID: 29434668.
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    36. Monroe JG, Allen ZA, Tanger P, Mullen JL, Lovell JT, Moyers BT, Whitley D, McKay JK. TSPmap, a tool making use of traveling salesperson problem solvers in the efficient and accurate construction of high-density genetic linkage maps. BioData Min. 2017; 10:38. PMID: 29270228.
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    37. Tanger P, Klassen S, Mojica JP, Lovell JT, Moyers BT, Baraoidan M, Naredo ME, McNally KL, Poland J, Bush DR, Leung H, Leach JE, McKay JK. Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice. Sci Rep. 2017 02 21; 7:42839. PMID: 28220807.
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    38. Lovell JT, Williamson RJ, Wright SI, McKay JK, Sharbel TF. Mutation Accumulation in an Asexual Relative of Arabidopsis. PLoS Genet. 2017 01; 13(1):e1006550. PMID: 28068346.
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    39. Lovell JT, Shakirov EV, Schwartz S, Lowry DB, Aspinwall MJ, Taylor SH, Bonnette J, Palacio-Mejia JD, Hawkes CV, Fay PA, Juenger TE. Promises and Challenges of Eco-Physiological Genomics in the Field: Tests of Drought Responses in Switchgrass. Plant Physiol. 2016 10; 172(2):734-748. PMID: 27246097.
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    40. Mojica JP, Mullen J, Lovell JT, Monroe JG, Paul JR, Oakley CG, McKay JK. Genetics of water use physiology in locally adapted Arabidopsis thaliana. Plant Sci. 2016 Oct; 251:12-22. PMID: 27593459.
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    41. Lovell JT, Schwartz S, Lowry DB, Shakirov EV, Bonnette JE, Weng X, Wang M, Johnson J, Sreedasyam A, Plott C, Jenkins J, Schmutz J, Juenger TE. Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4 grass. Genome Res. 2016 Apr; 26(4):510-8. PMID: 26953271.
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    42. Lovell JT, McKay JK. Ecological genetics of range size variation in Boechera spp. (Brassicaceae). Ecol Evol. 2015 Nov; 5(21):4962-75. PMID: 26640674.
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    43. Mau M, Lovell JT, Corral JM, Kiefer C, Koch MA, Aliyu OM, Sharbel TF. Hybrid apomicts trapped in the ecological niches of their sexual ancestors. Proc Natl Acad Sci U S A. 2015 May 05; 112(18):E2357-65. PMID: 25902513.
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    44. Lovell JT, Mullen JL, Lowry DB, Awole K, Richards JH, Sen S, Verslues PE, Juenger TE, McKay JK. Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana. Plant Cell. 2015 Apr; 27(4):969-83. PMID: 25873386.
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    45. Lovell JT, Grogan K, Sharbel TF, McKay JK. Mating system and environmental variation drive patterns of adaptation in Boechera spatifolia (Brassicaceae). Mol Ecol. 2014 09; 23(18):4486-97. PMID: 25112786.
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    46. ?grena J, Oakley CG, McKay JK, Lovell JT, Schemske DW. Genetic mapping of adaptation reveals fitness tradeoffs in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2013 Dec 24; 110(52):21077-82. PMID: 24324156.
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    47. Lovell JT, Aliyu OM, Mau M, Schranz ME, Koch M, Kiefer C, Song BH, Mitchell-Olds T, Sharbel TF. On the origin and evolution of apomixis in Boechera. Plant Reprod. 2013 Dec; 26(4):309-15. PMID: 23783772.
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    48. Lovell JT, Juenger TE, Michaels SD, Lasky JR, Platt A, Richards JH, Yu X, Easlon HM, Sen S, McKay JK. Pleiotropy of FRIGIDA enhances the potential for multivariate adaptation. Proc Biol Sci. 2013 Jul 22; 280(1763):20131043. PMID: 23698015.
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    49. Lovell JT. Boechera Summit 2011. Mol Ecol. 2011 Dec; 20(23):4840-2. PMID: 22059516.
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