Phylogeny of oaks

Oaks (the flowering plant genus Quercus) include some of America’s most ecologically and economically important trees. The approximately 255 oaks of the New World oak lineage dominate North American and Mexican woody plant biomass, biodiversity, ecology, and nutrient cycling. Despite the significant ecosystem services provided by oaks, the biodiversity of this genus is poorly understood. In this project, collaborators from The Morton Arboretum (IL), the University of Notre Dame (IN), Duke University (NC), University of Minnesota, and Universidad Nacional Autónoma de México undertook a comprehensive systematic study of the oaks of the New World. The project will integrate next-generation genomic (DNA) sequencing, plant physiology, and direct study of plants in the field and museum collections to gain insights into the oak tree of life and the basic question of how oak traits, distributions, and diversity evolve in response to changes in habitat and climate.

This project has been supported by NSF-DEB Award #1146488, 2012-2016, the Arboretum’s Center for Tree Science, and a Fulbright Award (2014).

Products to date


  • Cavender-Bares J. 2019. Diversification, adaptation, and community assembly of the American oaks (Quercus), a model clade for integrating ecology and evolution. New Phytologist 221: 669–692.
  • Cavender-Bares, J., Gonzalez-Rodriguez, A., Eaton, D.A.R., Hipp, A., Buelke, A., and P. Manos. 2015. Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): A genomic and population genetic approach. Molecular Ecology 24: 3668–3687. doi:10.1111/mec.13269. [LINK]
  • Cavender-Bares J, Kothari S, Meireles JE, Kaproth MA, Manos PS, Hipp AL. 2018. The role of diversification in community assembly of the oaks (Quercus L.) across the continental U.S. American Journal of Botany 105: 565–586.
  • Cavender-Bares J, Kothari S, Meireles JE, Manos PS, Kaproth M, Hipp AL. In press. The role of diversification in the continental scale community assembly of the American oaks (Quercus).
  • Crowl AA, Manos PS, McVay JD, Lemmon AR, Lemmon EM, Hipp AL. 2019. Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus). New Phytologist doi:10.1111/nph.15842.
  • Deng M, Jiang X-L, Hipp AL, Manos PS, Hahn M. 2018. Phylogeny and biogeography of East Asian evergreen oaks (Quercus section Cyclobalanopsis; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia. Molecular Phylogenetics and Evolution 119: 170–181. [LINK].
  • Deng, M, A. L. Hipp, Yi-Gang Song, Qian-Sheng Li, A. Coombes, and A. Cotton. 2014. Leaf epidermal features of Quercus subgenus Cyclobalanopsis (Fagaceae) and their systematic significance. Botanical Journal of the Linnaean Society 176: 224–259. [LINK]
  • Denk T, Grimm GW, Manos PS, Deng M, Hipp AL. 2017. An Updated Infrageneric Classification of the Oaks: Review of Previous Taxonomic Schemes and Synthesis of Evolutionary Patterns. In: Gil-Pelegrín E, Peguero-Pina J-J, Sancho-Knapik D (eds.): Tree Physiology. Oaks Physiological Ecology. Exploring the Functional Diversity of Genus Quercus L. Springer, Cham, 13–38. [LINK]
  • Eaton, D.A.R., A.L. Hipp, A. Gonzalez-Rodriguez, J. Cavender-Bares. 2015. Introgression obscures and reveals historical relationships among the American live oaks. Evolution 69: 2587–2601. [LINK]
  • Fallon, B. and J. Cavender-Bares. in press. Leaf-­level trade­offs between drought avoidance and desiccation recovery drive elevation stratification in arid oaks. Ecosphere.
  • Fitzek E, Delcamp A, Guichoux E, Hahn M, Lobdell M, Hipp AL. 2018. A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting. Ecology and Evolution 8: 5837–5851.
  • Fitz-Gibbon S, Hipp AL, Pham KK, et al. 2017. Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus subgenus Quercus). Genome 60: 743-755. [LINK]
  • Hauser DA, Keuter A, McVay JD, Hipp AL, and Manos PS. 2017. The evolution and diversification of the red oaks of the California Floristic Province (Quercus section Lobatae, series Agrifoliae). American Journal of Botany 104: 1581-1595. [LINK]
  • Hipp A.L., Eaton D.A.R., Cavender-Bares J., Fitzek E., Nipper R. and Manos P.S. 2014. A framework phylogeny of the American oak clade based on sequenced RAD data. PLoS ONE 9: e93975. [LINK – open access]
  • Hipp AL, Manos PS, González-Rodríguez A, Hahn M, Kaproth M, McVay JD, Avalos SV, Cavender-Bares J. 2018. Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity. New Phytologist 217: 439–452.
  • Hipp AL, Manos PS, Hahn M, Avishai M, Bodénès C, Cavender‐Bares J, Crowl AA, Deng M, Denk T, Fitz‐Gibbon S, et al. 2019a. Genomic landscape of the global oak phylogeny. New Phytologist doi:10.1111/nph.16162.
  • Hipp AL, Whittemore AT, Garner M, Hahn M, Fitzek E, Guichoux E, Cavender-Bares J, Gugger PF, Manos PS, Pearse IS, et al. 2019b. Genomic identity of white oak species in an eastern North American syngameon. Annals of the Missouri Botanical Garden 104: xxx–xxx.
  • Jiang X-L, Hipp AL, Deng M, Su T, Zhou Z-K, Yan M-X. 2019. East Asian origins of European holly oaks via the Tibet-Himalayas. Journal of Biogeography doi:10.1111/jbi.13654.
  • Kremer A, Hipp AL. Oaks: an evolutionary success story. New Phytologist n/a.
  • McVay JD, Hauser D, Hipp AL, and Manos PS. 2017. Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in Western North America. Genome 60: 733-742. [LINK]
  • McVay JD, Hipp AL & Manos PS. 2017. A genetic legacy of introgression confounds phylogeny and biogeography in oaks. Proc. R. Soc. B 284: 20170300. [LINK]
  • Pearse, I.S. and A.L. Hipp. 2014. Native plant diversity increases herbivory to non-natives. Proceedings of the Royal Society B: Biological Sciences 281: 20141841. [LINK]
  • Pham KK, Hipp AL, Manos PS, et al. 2017. A Time and a Place for Everything: Phylogenetic history and geography as joint predictors of oak plastome phylogeny. Genome 60: 720-732.
  • Ramírez-Valiente JA, López R, Hipp AL, Aranda I. 2019. Correlated evolution of morphology, gas exchange, growth rates and hydraulics as a response to precipitation and temperature regimes in oaks ( Quercus ). New Phytologist: nph.16320.
  • Ree, R.H. and A.L. Hipp. 2015. Inferring phylogenetic history from restriction site associated DNA (RADseq). In: Elvira Hoerandl and Marc Appelhans (eds.): Next Generation Sequencing in Plant Systematics, pp 181-204. Koeltz Scientific Books, Koenigstein. doi: 10.14630/000007 [PDF]
  • Song, Y, M. Deng, A. L. Hipp, Q. Li. 2014. Leaf morphological evidence of natural hybridization between two oak species (Quercus austrocochinchinensis and Q. kerrii) and its implications for conservation management. European Journal of Forest Research 134: 139-151. DOI: 10.1007/s10342-014-0839-x. [LINK]
  • Yan M, Liu R, Li Y, Hipp AL, Deng M, Xiong Y. 2019. Ancient events and climate adaptive capacity shaped distinct chloroplast genetic structure in the oak lineages. BMC Evolutionary Biology 19: 202.


  • Cannon CH, Brendel O, Deng M, Hipp AL, Kremer A, Kua C-S, Plomion C, Romero‐Severson J, Sork VL. 2018. Gaining a global perspective on Fagaceae genomic diversification and adaptation. New Phytologist 218: 894–897.
  • Hipp AL, Gonzalez-Martinez SC, Jaramillo-Correa JP. 2017. The Evolution of Tree Diversity: Proceedings of the 2016 IUFRO Genomics and Forest Tree Genetics Conference, Phylogenetics and Genomic Evolution Session, Arcachon, France. Genome 60: v–vi.
  • Hipp AL. 2016. Oak Research in 2015: a Snapshot from the IOS Conference. International Oak Journal 27.


  • Cavender-Bares, J. 2016. Diversity, distribution, and ecosystem services of the North American oaks. International Oak Journal 27.
  • Garner M, Pham KK, Whittemore AT, Cavender-Bares J, Gugger PF, Manos PS, Pearse IS, Hipp AL. 2019. From Manitoba to Texas: A study of the population genetic structure of bur oak (Quercus macrocarpa). International Oaks: The Journal of the International Oak Society 30: 131–138.
  • Hipp AL. 2019. Pharaoh’s Dance: the oak genomic mosaic. International Oaks: The Journal of the International Oak Society 30: 53–62.
  • Hipp, A.L. 2015. Should Hybridization Make Us Skeptical of the Oak Phylogeny? International Oak Journal 26: 9–18. [PDF]
  • Hipp, A.L. 2017. American oaks in an evolutionary context. In: Jerome, D. et al. (eds.) The Red List of US Oaks, pp. 10-11. The Morton Arboretum and USDA Forest Service, Lisle.
  • Hipp, A.L., D.A. Eaton, J. Cavender-Bares, R. Nipper, P.S. Manos. 2013. Using phylogenomics to infer the evolutionary history of oaks. International Oak Journal 24: 61–71. [PDF]
  • Hipp, A.L., S.C. Gonzalez-Martinez, and J.P. Jaramillo-Correa. 2017. The Evolution of Tree Diversity: Proceedings of the 2016 IUFRO Genomics and Forest Tree Genetics Conference, Phylogenetics and Genomic Evolution Session, Arcachon, France. Genome 60: v-vi.
  • Kaproth, M. and J. Cavender-Bares. 2016. Drought tolerance and climatic distributions of the American oaks. International Oak Journal.
  • Keuter A, Manos PS. 2019. Agrifoliae: the California Red Oaks. International Oaks: The Journal of the International Oak Society 30: 191–202.
  • Manos, P.S. 2016. Systematics and biogeography of the American oaks.  International Oak Journal 27: 23-36.