Google Scholar Profile

# Indicates UofM graduate student; § UofM undergraduate student; † Fulbright Fellow


🌻+ 🍄 Brown, S.P., J.R. Mandel. Rapid restructuring of rhizosphere and endospheric fungal communities with drought in multiple lines of domesticated sunflower. Phytobiomes,

🌼 Moore-Pollard, E.R., D.S. Jones, J.R. Mandel. Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems. Applications in Plant Sciences,

🌼 Roeble, L, K. J. van Benthem, P. Weigelt, H. Kreft, M.L. Knope, J.R. Mandel, P. Vargas, R.S. Etienne, L. Valente. Asteraceae in isolation: diversity and island biogeography ofthe largest plant family, EcoEvoRxiv,


🍄 Weaver, M.A., C. Bowen, L.C. Park, A. Bastidas, S.G. Drewry#, J.R. Mandel. Genetic diversity of Aspergillus flavus on maize in Guatemala and identification of potential biocontrol isolates. Foods,

🌻 Herrando-Moraira, S., Roquet, C., Calleja, J.A., Chen, Y.S., Fujikawa, K., Galbany-Casals, M., Garcia-Jacas, N., Liu, J.Q., López-Alvarado, J., López-Pujol, J. Mandel, I. Mehregan, L. Sáez, A. Sennikov, A. Susanna, R. Vilatersana, L-S. Xu. (2023) Impact of the climatic changes in the Pliocene-Pleistocene transition on Irano-Turanian species. The radiation of genus Jurinea (Compositae). Molecular Phylogenetics and Evolution,

🌻 Moore-Pollard, E.R.#, J.R. Mandel. From paralogy to hybridization: Investigating causes of underlying phylogenomic discordance using the complex genus Packera (Senecioneae; Asteraceae). bioRxiv 2023.08.14.553290

🌻 Moore-Pollard, E.R.#, D.S. Jones, J.R. Mandel.Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems. bioRxiv, 2023.07. 19.54908

🌻 Moore-Pollard, E.R. #, J.R. Mandel. Resolving evolutionary relationships in the groundsels: phylogenomics, divergence time estimates, and biogeography of Packera (Asteraceae: Senecioneae). bioRxiv, 2023.07. 18.549592

🌻 Mandel, J.R., E.R. Moore-Pollard#, J.M. Bonifacino. The Reinvention of Compositae: Vicki Funk’s legacy in the systematics of the largest plant family on Earth. International Journal of Plant Sciences; Guest Editors of Special Issue.

🌻 Moore-Pollard, E.R.#, J.R. Mandel. Packed with Packera Á. Löve & D. Löve: Brief history of the “aureoid Senecio” subgroup in Senecioneae. Capitulum 2(2): 51-58.

🌻 Ballou, S.M.#, K.A. Omand, J. Karberg, J.M. Bonifacino, J.R. Mandel. A harried past for a glabrous lettuce: Resurrection of Lactuca sanguinea Bigelow (Cichorieae), the wood lettuce from Nantucket Island, Massachusetts, USA. Capitulum 2(2): 57-62.


🍄 Weaver M., K.A. Callicott, H.L. Mehl, J. Opoku, L.C. Park, K.S. Fields§, J.R. Mandel. Characterization of the Aspergillus flavus population from highly aflatoxin-contaminated corn in the United States. Toxins, 14(11):755.

🌻 Palazzesi L., J. Pellicer, V.D. Barreda, B. Loeuille, J.R. Mandel, L. Pokorny, C.M. Siniscalchi, M.C. Tellería, O. Hidalgo. Asteraceae as a model system for evolutionary studies: from fossils to genomes. Botanical Journal of the Linnean Society, 200(2):143-164.

🌱 Molofsky, J., B. Beckage, S. Boatwright, C. Hui, S. Keller, J.R. Mandel, D. Park, D.M. Richardson. Optimal differentiation to the edge of trait space (EoTS). Evolutionary Ecology, 36(5):743-752.

🌻 Lee, J.S, M. Jahani, K. Huang, J.R. Mandel, L.F. Marek, J.M. Burke, N.B. Langlade, G.L. Owens, L.H. Rieseberg. Expression complementation of gene presence/absence polymorphisms in hybrids contributes importantly to heterosis in sunflower, Journal of Advanced Research.

🌻 Hernández F.†, R.B. Vercellino, C. Pandolfo, J.R. Mandel, A. Presotto. Rapid evolution of seed dormancy during sunflower de-domestication. Journal of Heredity, 113(3):288-297.

🍄 Weaver MA, N Mirza N#, JR Mandel, CD Boyette, SP Brown. Whole-genome sequence and draft assembly of the biocontrol fungal pathogen Albifimbria verrucaria CABI-IMI 368023. Microbiology Resource Announcements 11: e00909-21.

🌻 Moore, E.R#. C.M. Siniscalchi, J.R. Mandel. Reevaluating genetic diversity and structure of Helianthus verticillatus (Asteraceae) after the discovery of new populations. Castanea, 86(2):196-213.


🌱 Morris, A.B., C.J Baskauf, J.T. Diggs, A.N. Egan, D. Lincicome, J.R. Mandel, C.J. Visger. Conserving the flora of limestone cedar glade communities of the southeastern United States. In Imperiled: The Encyclopedia of Conservation, Elsevier.

🌼 Bonifacino, J.M., J.R. Mandel, A. Moore, E.R. Moore#, B. Loeuille, L. Roeble. CAPITULUM: The Compositae Newsletter Reloaded. Taxon. doi.org10.1002/tax.12571

🌻 Mandel, J.R. What’s all the hype about HybSeq? A brief history and introduction to target enrichment in Compositae. Capitulum 1(1): 44-47. Download here: Mandel2021Capitulum.pdf

🌻 Moore, E.R.# What in the whorled: The rediscovery of Helianthus verticillatus Small (Heliantheae) over 100 years later. Capitulum 1(1): 61-64.

🌻 Hernández, F†., R.B. Vercellino, C. Pandolfo, J.R. Mandel, A. Presotto. Rapid evolution of weedy traits during sunflower de-domestication: the importance of hybridization and standing genetic variation. bioRxiv,

🌻 Siniscalchi, C.M., O. Hildago, L. Palazzesi, J. Pellicer, L. Pokorny, O. Maurin, I.J. Leitch, F. Forest, W.J. Baker, J.R. Mandel. Lineage-specific vs universal: comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family. Applications in Plant Sciences,

🌻 Siniscalchi, C.M., R.D. Edwards, J.L. Gomez§, E.R.Moore#, J.R. Mandel. Photosynthesis metabolism in the Compositae: current knowledge and future directions. Taxon.

🌼 Thapa, R., R.J. Bayer, J.R. Mandel. Genetic diversity, population structure, and ancestry estimation in the Antennaria rosea (Asteraceae: Gnaphalieae) polyploid agamic complex. Taxon.


🌼 Lichter-Marck, I, W. Freyman, G. Johnson, C.M. Siniscalchi, J.R. Mandel, A. Castro Castro, B. Baldwin. Phylogenomics of the rock daisy tribe (Perityleae; Asteraceae) provides new insights into morphological and chromosomal evolution. Journal of Systematics and Evolution.

🌻 Watson, L.E., C.M., Siniscalchi, J.R. Mandel. Phylogenomics of the Hyperdiverse Daisy Tribes: Anthemideae, Astereae, Calenduleae, Gnaphalieae, and Senecioneae (Asteraceae). Journal of Systematics and Evolution, doi: 10.1111/jse.12698.

🥕 Mandel, J.R., A.J. Ramsey, J.M. Holley, V.A. Scott, D. Mody, P. Abbot. Disentangling complex inheritance patterns of plant organellar genomes: an example from carrot. Journal of Heredity.

🌻 Herrando-Moraira S., J.A. Calleja, M. Galbany-Casals, N. Garcia-Jacas, J-Q. Liu, J. López-Alvarado, J. López-Pujol, J.R. Mandel, N. Montes-Moreno, C. Roquet, L. Sáez, A. Sennikov, A. Susanna, R. Vilatersana. Generic boundaries in subtribe Saussureinae (Compositae-Cardueae): insights from Hyb-Seq data. Taxon. doi: 10.1002/tax.12314.

🌻 Goncalves, D.P., R.K. Jansen, T.A. Ruhlman, J.R. Mandel. Under the rug: Abandoning persistent misconceptions that obfuscate organelle evolution. Molecular Phylogenetics and Evolution.

🌻 Susanna, A., B.G. Baldwin, R.J. Bayer, J.M. Bonifacino, N. Garcia-Jacas, S.C. Keeley, J.R. Mandel, S. Ortiz, H. Robinson, T.F. Stuessy. The classification of the Compositae: A tribute to Vicki Ann Funk (1947–2019). Taxon. doi:10.1002/tax.12235.

🌻 Thapa, R., R.J. Bayer, J.R. Mandel. Phylogenomics Resolves the Relationships within Antennaria (Asteraceae, Gnaphalieae) and Yields New Insights into its Morphological Character Evolution and Biogeography. Systematic Botany. 45(2):387-402.

🐍 Carrasco-Harris#, M.F., J.R. Mandel, C.M. Siniscalchi, S. Reichling, J.A. Cole. Population genetics of copperheads (Agkistrodon contortrix) within an urban forest. Herpetological Conservation & Biology, 51(1), 1–7.


🌻 Jones, K.E., T. Fér, R.E. Schmickl, R.B. Dikow, V.A. Funk, S. Herrando-Moraira, C.M. Siniscalchi, A. Susanna, M. Slovák, R. Thapa#, L.E. Watson, J.R. Mandel. An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. Applications in Plant Sciences. doi:10.1002/aps3.11295

🌻Mandel, J.R., R.B. Dikow, C.M. Siniscalchi, R. Thapa#, L.E. Watson, V.A. Funk. A fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae. Proceedings of the National Academy of Sciences, 10.1073/pnas.1903871116

🌻 Siniscalchi, C.M., B. Loeuille, J.R. Mandel, J.R. Pirani. Using genomic data to develop SSR markers for species of Chresta (Vernonieae, Asteraceae) from the Caatinga. Brazilian Journal of Botany.

🌷 Mandel, J.R., C.K Major§, R.J. Bayer, J.E. Moore. Combining studies of genetic diversity and demography in a long-lived clonal herb. PLoS ONE. 14(10): e0224123.

🌻 Siniscalchi, C.M., B. Loeuille, V.A. Funk, J.R. Mandel, J.R. Pirani. Phylogenomics yields new insight into relationships within Vernonieae (Asteraceae). Frontiers in Plant Sciences. doi: 10.3389/fpls.2019.01224.

🥕 Ramsey A.J.#, S.M. Ballou#, J.R. Mandel. Altered pollination ecology of a native plant species in the presence of an attractive non-native plant species. Rhodora. 121: 987, 159–173.

🌻 Hernandez, F. † Poverene, M., J.R. Mandel. Genetic diversity and population structure of wild sunflower (Helianthus annuus L.) in Argentina: reconstructing its invasion history. Journal of Heredity. 110: 6, 746–759.

🥕 Ramsey, A. J.#, D.E. McCauley, Mandel, J.R. Heteroplasmy and patterns of cytonuclear linkage disequilibrium in wild carrot. Integrative and Comparative Biology,

🥕 Mandel, J.R., J. Brunet. Gene Flow in Carrot. In: The Carrot Genome, Ed. P. Simon, M. Iorizzo, D. Grzebelus, R. Baranski. Springer-Verlag: Heidelberg, Dordrecht, London, New York, Tokyo.

🥕 Ramsey A.J. #, J.R. Mandel. When one genome is not enough: Organellar heteroplasmy in plants. Annual Plants Review online. doi:10.1002/9781119312994.apr0616

🌻 Thapa, R. #, R.J. Bayer, J.R. Mandel. Development and characterization of microsatellite markers for Antennaria corymbosa (Asteraceae) and close relatives. Applications in Plant Sciences. doi:10.1002/aps3.11268.

🌻 Herrando-Moraira S., J.A. Calleja, M. Galbany-Casals, N. Garcia-Jacas, J-Q. Liu, J. López-Alvarado, J. López-Pujol, J.R. Mandel, N. Montes-Moreno, C. Roquet, L. Sáez, A. Sennikov, A. Susanna, R. Vilatersana. Nuclear and plastid DNA phylogeny of the tribe Cardueae (Compositae) with Hyb-Seq data: A new subtribal classification and a temporal framework for the origin of the tribe and the subtribes. Molecular Phylogenetics and Evolution. 137: 313-332.

🌼 Mandel J.R. A Jurassic leap for flowering plants. Nature Plants 5: 455–456.

🥕 Phan V., D-T. Pham#, C. Melton#, A.J Ramsey#, B.J Daigle Jr., J.R. Mandel. icHET: Interactive Visualization of Cytoplasmic Heteroplasmy. Bioinformatics,

🌻 Dowell, J., E. Clark, T. Pliakas, J.R. Mandel, J.M Burke, L.A. Donovan, C. Mason. Genome wide association mapping of floral traits in cultivated sunflower (Helianthus annuus). Journal of Heredity. 10.1093/jhered/esz013 Cover Image.


🌻 Hubner S., N. Bercovich, M. Todesco, J.R. Mandel, et al. Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance. Nature Plants, 5:54–62.

🌻 Herrando-Moraira S., J.A. Calleja, P. Carnicero-Campmany, K.Fujikawa, M. Galbany-Casals, N. Garcia-Jacas, H-T. Im, S-C. Kim, J. Liu, J. López-Alvarado, J. López-Pujol, J.R. Mandel, S. Massó, I. Mehregan, N. Montes-Moreno, E. Pyak, C. Roquet, L. Sáez, A. Sennikov, A. Susanna, V. Roser. Exploring data processing strategies in NGS target enrichment to disentangle radiations in the tribe Cardueae (Compositae). Molecular Phylogenetics and Evolution, 128:69-87. 10.1016/j.ympev.2018.07.012.


🌻 Mandel, J.R., M.S. Barker, R.J. Bayer, R.B. Dikow, K. Jones, S. Keeley, C.M. Siniscalchi, R. Thapa, L.E. Watson, V.A. Funk. The Compositae Tree of Life in the age of phylogenomics. Journal of Systematics and Evolution, Special Issue on Frontiers in Plant Systematics and Evolution. doi: 10.1111/jse.12265.

🌻 Badouin, H., J. Gouzy, C.J. Grassa, F. Murat, S.E. Staton, L. Cottret, C. Lelandais-Brière, G. Owens, S. Carrrère, B. Mayjonade, L. Legrand, N. Gill, N.C. Kane, J.E. Bowers, S. Hubner, A. Bellec, A. Berard, H. Bergès, N. Blanchet, M.-C. Boniface, B. Dominique, O. Catrice, N. Chaidir, C. Claudel, C. Donnadieu, T. Faraut, G. Fievet, N. Helmstetter, M. King, S.J. Knapp, Z. Lai, M.-C. Le Paslier, Y. Lippi, L. Lorenzon, J.R. Mandel, G. Marage, G. Marchand, E. Marquand, E. Bret-Mestries, E. Morien, S. Nambeesan, T. Nguyen, P. Pegot-Espagnet, N. Pouilly, F. Raftis, E. Sallet, T. Schiex, J. Thomas, C. Vandecasteele, D. Varès, F. Vear, S. Vautrin, M. Crespi, B. Mangin, J.M. Burke, J. Salse, S. Muños, P. Vincourt, L.H. Rieseberg, N.B. Langlade. 2017. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Nature,


🌱 Folk, R.A, J.R. Mandel, J.V. Freudenstein. Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms. Systematic Biology, doi: 10.1093/sysbio/syw083.

🥕 Mandel, J.R., A.J. Ramsey, M. Iorizzo, P.W. Simon. Patterns of gene flow between crop and wild carrot, Daucus carota (Apiaceae) in the United States. PLoS ONE, e0161971. doi:10.1371/journal.pone.0161971.


🌻 Mandel, J.R., R.B. Dikow, V.A. Funk. Using phylogenomics to resolve mega-families: an example from Compositae. Journal of Systematics and Evolution, in press.

🥕 Mandel, J.R., D. E. McCauley. Pervasive mitochondrial sequence heteroplasmy in natural populations of wild carrot, Daucus carota spp. carota L. PLoS ONE, 10(8): e0136303. doi:10.1371/journal.pone.0136303.

🌱 Folk, R.A, J.R. Mandel, J.V. Freudenstein. A Protocol for Targeted Enrichment of Intron-Containing Sequence Markers for Recent Radiations: A Phylogenomic Example from Heuchera (Saxifragaceae). Applications in Plant Sciences, 3(8): 1500039. doi:10.3732/apps.1500039.

🌻 Mason, C.M., C.D.A. Ishibashi, A.M. Rea, J.R. Mandel, J.M. Burke, L.A Donovan. Environmental requirements trump genetic factors in explaining narrow endemism in two imperiled Florida sunflowers. Conservation Genetics, doi:10.1007/s10592-015-0739-8.

🌻 Nambeesan, S.U., J.R. Mandel, J.E. Bowers, L.F. Marek, D. Ebert, J. Corbi, L.H. Rieseberg, S.J. Knapp, and J.M. Burke. Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching. BMC Plant Biology, 15:84. doi:10.1186/s12870-015-0458-9.


🌻 Mandel, J. R., E. V McAssey, S. Nambeesan, E. Garcia-Navarro, J. M. Burke. Molecular evolution of candidate genes for crop-related traits in sunflower (Helianthus annuus L.). PLoS ONE, 10.1371/journal.pone.0099620.

🌻 Mandel, J. R., R. B. Dikow, V. A. Funk, R. R. Masalia, S. E. Staton, A. Kozik, R. W. Michelmore, L. H. Rieseberg, J. M. Burke. A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae. Applications in Plant Sciences, 2(2):1300085. Link to paper.

🌱 Baskauf, C. J., J. R. Mandel, D. E. McCauley. Population genetics of Braun’s rockcress (Boechera perstellata, Brassicaceae), an endangered plant with a disjunct distribution. Journal of Heredity, 105(2):265–275.


🌻 Chapman, M. A., J. R. Mandel, J. M. Burke. Sequence validation of candidates for selectively important genes in sunflower. PLoS ONE, 8(8): e71941.

🌻 Mandel, J. R., S. Nambeesan, J. E. Bowers, L. F. Marek, D. P. Ebert, L. H. Rieseberg, S. J. Knapp, J. M. Burke. Association mapping and the genomic consequences of selection in sunflower. PLoS Genetics, 9: e1003378.

🌻 Gevaert, S. D., J. R. Mandel, J. M. Burke, L. A. Donovan. High genetic diversity and low population structure in Porter’s sunflower (Helianthus porteri). Journal of Heredity, 104(3): 407-415.

🌻 Mandel, J. R., E. F. Milton, L. A. Donovan, S. J. Knapp, J. M. Burke. Genetic diversity and population structure in the rare Algodones sunflower (Helianthus niveus ssp. tephrodes) and comparison to related sunflowers. Conservation Genetics, 14(1): 31-40.


🥕 Mandel, J. R., E. A. McAssey, D. E. McCauley. Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota). Journal of Heredity, 103(3): 418-425.

🌻 Bachlava, E., C. A. Taylor, S. Tang, J. E. Bowers, J. R. Mandel, J. M. Burke, S. J. Knapp. SNP Discovery and Development of a High-Density Genotyping Array for Sunflower. PLoS One, 7(1): e29814. doi:10.1371/journal.pone.0029814.


🌻 Mandel, J. R., J. M. Dechaine, L. F. Marek, J.M. Burke. Genetic diversity and population structure in cultivated sunflower and a comparison to its wild progenitor, Helianthus annuus L. Theoretical and Applied Genetics, 123(5): 693-704.


🌻 Mandel, J. R. Clonal diversity, spatial dynamics, and small genetic population size in the rare sunflower, Helianthus verticillatus. Conservation Genetics, 11(5): 2055-2059.

🌱 Bentley, K. E., J. R. Mandel, D. E. McCauley. Paternal leakage and heteroplasmy of mitochondrial genomes in Silene vulgaris: evidence from experimental crosses. Genetics, 185(3): 961-968.


🌻 Ellis, J. R., D. E. McCauley. Phenotypic differentiation in fitness related traits between populations of an extremely rare sunflower: conservation management of isolated populations. Biological Conservation, 142(8): 1836-1843.


🌻 Ellis, J. R., K. E. Bentley, D. E. McCauley. Detection of rare paternal leakage in controlled crosses of the endangered sunflower Helianthus verticillatus. Heredity, 100(6): 574-580.

🌱 McCauley, D. E., J. R. Ellis. Recombination and linkage disequilibrium among mitochondrial genes in structured populations of the gynodioecious plant Silene vulgaris. Evolution, 62(4): 823-832. Faculty of 1000 article.


🌱 Ellis, J. R., J. M. Burke. EST-SSRs as a resource for population genetic analyses. Heredity 99(2): 125-132. Cited 200+ times, 9/2013.


🌻 Ellis, J. R., C. H. Pashley, J. M. Burke, D. E. McCauley. High genetic diversity in a rare and endangered sunflower as compared to a common congener. Molecular Ecology 15(9): 2345-2355.

🌻 Pashley C. H., J. R. Ellis, D. E. McCauley, J. M. Burke. EST Databases as a source for molecular markers: lessons from Helianthus. Journal of Heredity 97(4): 381-388.

Note: Prior to 2010, JR Mandel published under JR Ellis.


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