Publications

2019

・ 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. (2019) An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. Applications in Plant Sciences.

・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. (2019) PLoS ONE. 14(10): e0224123.

・Siniscalchi, C.M., B. Loeuille, V.A. Funk, J.R. Mandel, J.R. Pirani. (2019) 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. (2019) Altered pollination ecology of a native plant species in the presence of an attractive non-native plant species. Rhodora.

・Hernandez, F. † Poverene, M., J.R. Mandel. (2019) Genetic diversity and population structure of wild sunflower (Helianthus annuus L.) in Argentina: reconstructing its invasion history. Journal of Heredity.

・Ramsey, A. J.#, D.E. McCauley, Mandel, J.R. (2019) Heteroplasmy and patterns of cytonuclear linkage disequilibrium in wild carrot. Integrative and Comparative Biology, https://doi.org/10.1093/icb/icz102.

・Mandel, J.R., J. Brunet. (2019) 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.

・Mandel, J.R., R.B. Dikow, C.M. Siniscalchi, R. Thapa#, L.E. Watson, V.A. Funk. (2019) A fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae. PNAS. 10.1073/pnas.1903871116

・Ramsey A.J. #, J.R. Mandel. (2019) 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. (2019) Development and characterization of microsatellite markers for Antennaria corymbosa (Asteraceae) and close relatives. Applications in Plant Sciences.

・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. (2019) 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.

・J.R. Mandel. (2019) 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. (2019) icHET: Interactive Visualization of Cytoplasmic Heteroplasmy. Bioinformatics, doi.org/10.1093/bioinformatics/btz300.

・Dowell, J., E. Clark, T. Pliakas, J.R. Mandel, J.M Burke, L.A. Donovan, C. Mason. (2019) Genome wide association mapping of floral traits in cultivated sunflower (Helianthus annuus). Journal of Heredity. 10.1093/jhered/esz013 Cover Image.

2018

・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.

2017

・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, http://dx.doi.org/10.1038/nature22380.

2016

・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.

2015

・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.

2014

・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.

2013

・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.

2012

・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.

2011

・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.

2010

・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.

2009

・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.

2008

・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.

2007

・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.

2006

・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.

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

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