Log in

Editor's Picks

The oak tree in Skjomendalen © Gerhard Sørensen-Fuglem and Cecilia Piccirilli Bjerkeset
An oak grows north of the Arctic Circle in Norway
Website Editor | Aug 14, 2023
Unusual symptoms linked to phytoplasma infection in Quercus humboldtiii, Colombia © Eric Boa
Symptoms linked to phytoplasma infection found in Quercus...
Website Editor | Aug 06, 2023
Different names are being used for one species.
Website Editor | Jun 20, 2023

Plant Focus

A small but mature Alabama sandstone oak producing acorns © Patrick Thompson
A Critically Endangered dwarf oak 

Population Genetics of Quercus macrocarpa

PDF icon Log in or register to access the full text.

Mira Garner, Kasey Pham, Alan T. Whittemore, Jeannine Cavender-Bares, Paul F. Gugger, Paul S. Manos, Ian S. Pearse, and Andrew L. Hipp

Published May 2019 in International Oaks No. 30: 131–138


The widespread Eastern North American oak, Quercus macrocarpa, is an ideal species for studying hybridization. Like most oaks, it exhibits strong morphological and ecological species coherence, but it hybridizes readily with at least eight currently or historically sympatric oak species throughout its range from Texas north to Manitoba, and from Michigan west across the Great Plains. Its geographic and ecological variation makes it a good candidate to address the question of how hybridization and gene flow might affect adaptation. Our study investigates (1) population genetic structure of Q. macrocarpa and (2) genetic coherence of the species throughout its range, as it comes into contact with five widespread cooccurring White Oak species whose ranges all overlap a subset of the range of Q. macrocarpa.


population genetics, Quercus macrocarpa, hybridization, Hyb-Seq, syngameon, White Oaks, Quercus section Quercus


Bolger, A.M., M. Lohse, and B. Usadel. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120.

Burger, W.C. 1975. The Species Concept in Quercus. Taxon 24: 45-50.

Chechowitz, N., D.M. Chappell, S.I. Guttman, and L.A. Weight. 1990. Morphological, electrophoretic, and ecological analysis of Quercus macrocarpa populations in the Black Hills of South Dakota and Wyoming. Canadian Journal of Botany 68(10): 2185-2194.

Cokus, S.J., P.F. Gugger, and V.L. Sork. 2015. Evolutionary insights from de novo transcriptome assembly and SNP discovery in California white oaks. BMC Genomics 16(1): 552.

Coombes, A.J., and W.N. Coates. 1997. Oglethorpe and the Oglethorpe Oak. Arnoldia 57(7): 25-30.

Craft, K.J., and M.V. Ashley. 2006. Population differentiation among three species of white oak in northeastern Illinois. Canadian Journal of Forest Research 36(1): 206-215.

Dow, B.D., and M.V. Ashley. 1996. Microsatellite analysis of seed dispersal and parentage of saplings in bur oak, Quercus macrocarpa. Molecular Ecology 5(5): 615-627.

Geburek, T., and P. Tripp-Knowles. 1994. Genetic architecture in bur oak, Quercus macrocarpa (Fagaceae), inferred by means of spatial autocorrelation analysis. Plant Systematics and Evolution 189: 63-74.

Gray, A., and W.S. Sullivant. 1848. A manual of the botany of the northern United States, from New England to Wisconsin and south to Ohio and Pennsylvania inclusive (the mosses and liverworts by Wm. S. Sullivant) arranged according to the natural system. Boston and London: J. Munroe, J. Chapman.

Gugger, P.F., S.J. Cokus, M. Pellegrini, and V.L.  Sork VL. Association of transcriptome-wide sequence variation with climate gradients in valley oak (Quercus lobata). Tree genetics & genomes 12(2):15.

Hardin, J.W. 1975. Hybridization and introgression in Quercus alba. Journal of the Arnold Arboretum 56(3): 336-363.

Hipp, A.L., P.S. Manos, A. González-Rodríguez, M. Hahn, M. Kaproth, J.D. McVay, S. Valencia Avalos, and J. Cavender-Bares. 2018. Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity. New Phytologist 217(1): 439-452.

Johnson, M.G., E.M. Gardner, Y. Liu, R. Medina, B. Goffinet, A.J. Shaw, N.J.C.  Zerega, and N.J. Wickett. 2016. HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Applications in Plant Sciences 4(7): 1600016.

Katoh, K., K. Misawa, K. Kuma, and T. Miyata. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30(14): 3059-3066.

Lesur, I., G. Le Provost, P. Bento, C. Da Silva, J.-C. Leplé, F. Murat, S. Ueno, J. Bartholomé,  C. Lalanne, F. Ehrenmann, C. Noirot, C. Burban, V. Léger, J. Amselem, C. Belser, H. Quesneville, M. Stierschneider, S. Fluch, L. Feldhahn, M. Tarkka, S. Herrmann, F. Buscot, C. Klopp, A. Kremer, J. Salse, J.-M. Aury, and C. Plomion. 2015. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics 16(1): 112.

McVay, J.D., A.L. Hipp, and P.S. Manos. 2017a. A genetic legacy of introgression confounds phylogeny and biogeography in oaks. Proceedings of the Royal Society B: Biological Sciences 284: 20170300.

McVay, J.D., D. Hauser, A.L. Hipp, and P.S. Manos. 2017b. Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America. Genome 60: 733-742.

Meireles, J.E., A. Beulke, D.S. Borkowski, J. Romero-Severson, and J. Cavender-Bares. 2017. Balancing selection maintains diversity in a cold tolerance gene in broadly distributed live oaks. Genome 60: 762-769.

Muller, C.H. 1961. The Live Oaks of the Series Virentes. The American Midland Naturalist 65: 17-39.

Oney-Birol, S., S. Fitz-Gibbon, J.-M. Chen, P.F. Gugger, and V.L. Sork. 2018. Assessment of shared alleles in drought-associated candidate genes among southern California white oak species (Quercus sect. Quercus). BMC Genetics 19: 88.

Plomion, C., J.-M. Aury, J.Amselem, T. Alaeitabar, V. Barbe, C. Belser, H. Bergès, C. Bodénès, N. Boudet, C. Boury, A. Canaguier, A. Couloux, C. Da Silva, S. Duplessis, F. Ehrenmann, B. Estrada-Mairey, S. Fouteau, N. Francillonne, C. Gaspin, C. Guichard, C. Klopp, K. Labadie, C. Lalanne, I. Le Clainche, J.-C. Leplé, G. Le Provost, T. Leroy, I. Lesur, F. Martin, J. Mercier, C. Michotey, F. Murat, F. Salin, D. Steinbach, P. Faivre-Rampant, P. Wincker, J. Salse, H. Quesneville, and A. Kremer. 2016. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Molecular Ecology Resources 16: 254-265.

Plomion, C., Aury, J.-M., Amselem, J., Leroy, T., Murat, F., Duplessis, S., Faye, S., Francillonne, N., Labadie, K., Le Provost, G., I. Lesur, J. Bartholomé, P. Faivre-Rampant, A. Kohler, J.-C. Leplé, N. Chantret, J. Chen, A. Diévart, T. Alaeitabar, V. Barbe, C. Belser, H. Bergès, C. Bodénès, M.-B. Bogeat-Triboulot, M.-L. Bouffaud, B. Brachi, E. Chancerel, D. Cohen, A. Couloux, C. Da Silva, C. Dossat, F. Ehrenmann, C. Gaspin, J. Grima-Pettenati, E. Guichoux, A. Hecker, S. Herrmann, P. Hugueney, I. Hummel, C. Klopp, C. Lalanne, M. Lascoux, E. Lasserre, A. Lemainque, M.-L.L Desprez-Loustau, I. Luyten, M.-A. Madoui, S. Mangenot, C. Marchal, F. Maumus, J. Mercier, C. Michotey, O. Panaud, N. Picault, N. Rouhier, O. Rué, C. Rustenholz, F. Salin, M. Soler, M. Tarkka, A. Velt, A.E. Zanne, F. Martin, P. Wincker, H. Quesneville, Antoine Kremer, and J. Salse. 2018. Oak genome reveals facets of long lifespan. Nature Plants 4: 440-452.

Pritchard, J.K., M. Stephens, and P. Donnelly. 2000. Inference of Population Structure Using Multilocus Genotype Data. Genetics 155: 945.

Schnabel, A., and J.L. Hamrick. 1990. Comparative Analysis of Population Genetic Structure in Quercus macrocarpa and Q. gambelii (Fagaceae). Systematic Botany 15: 240-251.

Sork, V.L., K. Squire, P.F. Gugger, S. Steele, E.D. Levy, and A.J. Eckert. 2016. Landscape genomic analysis of candidate genes for climate adaptation in a California endemic oak, Quercus lobata Née (Fagaceae). American Journal of Botany 103: 33-46.

Van Valen, L. 1976. Ecological Species, Multispecies, and Oaks. Taxon 25, 233–239.

Villaverde, T., L. Pokorny, S. Olsson, M. Rincón-Barrado, M.G. Johnson, E.M. Gardner, N.J. Wickett, J. Molero, R. Riina, and I. Sanmartín. 2018. Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above. New Phytologist 220(2): 636-650.

Weitemier, K., S.C.K. Straub, R.C. Cronn, M. Fishbein, R. Schmickl, A. McDonnell, and A. Liston. 2014. Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics. Applications in Plant Sciences 2: 1400042.