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Plant Focus

A guest post by Matt Candeias, host of the In Defense of Plants podcast and blog

Genetic Distinctions Among Oaks in the University of California , Davis Arboretum: Contributions to Oak Phylogeny

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Terence M. Murphy and Daniel Potter

Published May 2017 in International Oaks No. 28: 59–72


DNA samples of oaks from the collection at the University of California, Davis Arboretum have been isolated, and partial sequences determined for genes of ribulosebisphosphate carboxylase large subunit and for internal transcribed sequences of ribosomal RNA genes. A comparison of these sequences contributes to an elucidation of the phylogeny of this important plant genus. The agreement between the patterns with rbcL and ITS sequences strengthens considerably the conclusion that these molecular data can reveal the actual pattern of evolutionary relationships among the Quercus species.


phylogenetic analysis, gene sequencing,  ribulosebisphosphate carboxylase (rbcL), internal transcribed sequence (ITS), transfer RNA (trnL/trnF)


Darriba, D., G.L. Taboada, R. Doallo, and D. Posada. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9: 772.

Guindon, S., and O. Gascuel. 2003. A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Systematic Biology 52: 696-704.

Jackson, R.B., L.A. Moore, W.A. Hoffmann, W.T. Pockman, and C.R. Linder. 1999. 

Ecosystem rooting depth determined with caves and DNA.  Proc. Natl. Acad. Sci. 96: 11387-11392.

Manos, P.S., J.J. Doyle, and K.C. Nixon. 1999. Phylogeny, biogeography, and processes of molecular differentiation in Quercus subgenus Quercus (Fagaceae). Mol. Phylogenet. Evol. 12: 333-349.

Manos, P.S., and A.M. Stanford. 2001. The historical biogeography of Fagaceae: tracking the Tertiary history of temperate and subtropical forests of the northern hemisphere. Int. J. Plant Sci. 162 (6 Suppl.): s77-s93.

Manos, P.S., Z.-K. Zhou, and C.H. Cannon. 2001. Systematics of Fagaceae: phylogenetic tests of reproductive trait evolution. Int. J. Plant Sci. 162: 1361-1379.

Nixon, K.C. 2002. The Oak (Quercus) Biodiversity of California and Adjacent Regions. USDA Forest Service Gen. Tech. Rep. PSW-GTR-184. 2002. http://www.fs.fed.us/psw/publications/documents/gtr-184/001_Nixon.pdf

Oh, S.H., and P.S. Manos. 2008. Molecular phylogenetics and cupule evolution in Fagaceae as inferred from nuclear CRABS CLAW sequences. Taxon 57: 434-451.

Pearse, I.S., and A.L. Hipp. 2009. Phylogenetic and trait similarity to a native species predict herbivory on non-native oaks. Proc. Natl. Acad. Sci. 106: 18097-18102.

Quercus Portal, https://w3.pierroton.inra.fr/QuercusPortal/index.php?p=PHYLOGENY (accessed 7/23/13)

Ronquist, F., and J.P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.

Samuel, R., A. Bachmair, J. Jobst, J., and F. Ehrendorfer. 1998. ITS sequences from nuclear rDNA suggest unexpected phylogenetic relationships between Euro-Mediterrannean, East Asiatic and North American taxa of Quercus (Fagaceae). Plant Syst. Evol. 
211: 129-139.

Thompson, J.D., T.J. Gibson,T.J., F. Plewniak, F. Jeanmougin, and D.G. Higgins. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25:4876-4882. 

Xu, L.A. 2004. Diversité de l’ADN chloroplastique et relations phylogénétiques au sein des Fagacées et du genre Quercus. Thèse Université Henri Poincaré, Nancy, 129 pages.