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Research Articles

Multiple nuclear genes stabilize the phylogenetic backbone of the genus Quercus

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Pages 405-423 | Received 26 Nov 2013, Accepted 13 Jun 2014, Published online: 06 Aug 2014

References

  • Acosta, M.C. & Premoli, A.C. 2010. Evidence of chloroplast capture in South American Nothofagus (subgenus Nothofagus, Nothofagaceae). Molecular Phylogenetics and Evolution 54, 235–242.
  • Axelrod, D.I. 1983. Biogeography of oaks in the Arcto-Tertiary province. Annals of the Missouri Botanical Garden 70, 629–657.
  • Bellarosa, R., Simeone, M.C., Papini, A. & Schirone, B. 2005. Utility of ITS sequence data for phylogenetic reconstruction of Italian Quercus spp. Molecular Phylogenetics and Evolution 34, 355–370.
  • Berger, S.A., Krompass, D. & Stamatakis, A. 2011. Accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Systematic Biology 60, 291–302.
  • Bergsten, J. 2005. A review of long-branch attraction. Cladistics 21, 163–193.
  • Boavida, L.C., Silva, J.P. & Feijo, J.A. 2001. Sexual reproduction in the cork oak (Quercus suber L). – II. Crossing intra- and interspecific barriers. Sexual Plant Reproduction 14, 143–152.
  • Bouchal, J. 2013. The microflora of the latest Eocene (Priabonian) Florissant Formation, a combined method approach. Masters thesis, University of Vienna, Vienna, Austria.
  • Burgarella, C., Lorenzo, Z., Jabbour-Zahab, R., Lumaret, R., Guichoux, E., Petit, R.J., Soto, A. & Gil, L. 2009. Detection of hybrids in nature: application to oaks (Quercus suber and Q. ilex). Heredity 102, 442–452.
  • Camus, A. 1936–1938. Les Chênes. Monographie du genre Quercus. Tome I. Genre Quercus, sous-genre Cyclobalanopsis, sous-genre Euquercus (sections Cerris et Mesobalanus). Paul Lechevalier Edition, Paris, France.
  • Camus, A. 1936–1954. Les Chênes. Monographie du genre Quercus et Monographie du genre Lithocarpus. Paul Lechevalier Edition, Paris, France.
  • Cohen, K., Finney, S. & Gibbard, P. 2012. International chronostratigraphic chart, IUGS.
  • Cottam, W.P., Tucker, J.M. & Santamour, F.S. 1982. Oak hybridization at the University of Utah. State Arboretum of Utah, Salt Lake City, UT, USA.
  • Crepet, W.L. & Nixon, K.C. 1989. Earliest megafossil evidence of Fagaceae: phylogenetic and biogeographic implications. American Journal of Botany 76, 842–855.
  • Daghlian, C.P. & Crepet, W.L. 1983. Oak catkins, leaves and fruits from the Oligocene Catahoula Formation and their evolutionary significance. American Journal of Botany 70, 639–649.
  • Denk, T. & Grimm, G.W. 2009. Significance of pollen characteristics for infrageneric classification and phylogeny in Quercus (Fagaceae). International Journal of Plant Sciences 170, 926–940.
  • Denk, T. & Grimm, G.W. 2010. The oaks of western Eurasia: traditional classifications and evidence from two nuclear markers. Taxon 59, 351–366.
  • Denk, T., GrĹmsson, F. & Zetter, R. 2010. Episodic migration of oaks to Iceland: evidence for a North Atlantic ‘land bridge’ in the latest Miocene. American Journal of Botany 97, 276–287.
  • Denk, T., GrÍmsson, F. & Zetter, R. 2012. Fagaceae from the early Oligocene of Central Europe: persisting new world and emerging old world biogeographic links. Review of Palaeobotany and Palynology 169, 7–20.
  • Denk, T. & Tekleva, M.V. In press. Pollen morphology and ultrastructure of Quercus with focus on Group Ilex (=Quercus Subgenus Heterobalanus (Oerst.) Menitsky): implications for oak systematics and evolution. Grana (in press).
  • Drummond, A.J., Suchard, M.A., Xie, D. & Rambaut, A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29, 1969–1973.
  • Edgar, R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32, 1792–1797.
  • Gouy, M., Guindon, S. & Gascuel, O. 2010. SeaView Version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27, 221–224.
  • Govaerts, R. & Frodin, D.G. 1998. World Checklist and Bibliography of Fagales (Betulaceae, Corylaceae, Fagaceae and Ticodendraceae). Royal Botanic Gardens, Kew, UK.
  • Grimm, G.W., Renner, S.S., Stanamakis, A. & Hemleben, V. 2006. A nuclear ribosomal DNA phylogeny of acer inferred with maximum likelihood, splits graphs, and motif analysis of 606 sequences. Evolutionary Bioinformatics 2, 7–22.
  • Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41, 95–98.
  • Huelsenbeck, J.P. & Ronquist, F. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754–755.
  • Huson, D.H. & Bryant, D. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23, 254–267.
  • Jahren, A. 2007. The Arctic forest of the middle Eocene. Annual Review of Earth and Planetary Sciences 35, 509–540.
  • Kmenta, M.2011. Die Mikroflora der untermiozänen Fundstelle Altmittweida. Master thesis, University of Vienna, Vienna, Austria.
  • Kremer, A. & Petit, R. 1993. Gene diversity in natural populations of oak species. Annals of Forest Science 50, 186–202.
  • Kremer, A., Abbott, A.G., Carlson, J.E., Manos, P.S., Plomion, C., Sisco, P., Staton, M.E., Ueno, S. & Vendramin, G.G. 2012. Genomics of Fagaceae. Tree Genetics and Genomes 8, 583–610.
  • KvaČek, Z. & Walther, H. 1989. Palaeobotanical studies in Fagaceae of the European Tertiary. Plant Systematics and Evolution 162, 213–229.
  • Lumaret, R. & Jabbour-zahab, R. 2009. Ancient and current gene flow between two distantly related Mediterranean oak species, Quercus suber and Q. ilex. Annals of Botany 104, 725–736.
  • Manchester, S. 1994. Fruits and seeds of the Middle Eocene nut beds flora, Clarno Formation, Oregon. Palaeontographica Americana 58, 1–205.
  • Manos, P.S. & Stanford, A.M. 2001. The historical biogeography of Fagaceae: tracking the tertiary history of temperate and subtropical forests of the northern hemisphere. International Journal of Plant Sciences 162, 77–93.
  • Manos, P.S., Doyle, J.J. & Nixon, K.C. 1999. Phylogeny, biogeography, and processes of molecular differentiation in Quercus subgenus Quercus (Fagaceae). Molecular Phylogenetics and Evolution 12, 333–349.
  • Manos, P.S., Zhou, Z.K. & Cannon, C.H. 2001. Systematics of Fagaceae: phylogenetic tests of reproductive trait evolution. International Journal of Plant Sciences 162, 1361–1379.
  • Manos, P.S., Cannon, C.H. & Oh, S.-H. 2008. Phylogenetic relationships and taxonomic status of the paleoendemic Fagaceae of Western North America: recognition of a new genus, Notholithocarpus. Madroño 55, 181–190.
  • Mcintyre, D. 1991. Pollen and spore flora of an Eocene forest, eastern Axel Heiberg Island. In: Christie, R. & McMillan, N., Eds., Tertiary Fossil Forest of the Geodetic Hills, Axel Heiberg Island, Arctic Archipelago. Geological Survey of Canada Bulletin 403, 83–97.
  • Mciver, E. & Basinger, J. 1999. Early Tertiary floral evolution in the Canadian high arctic. Annals of the Missouri Botanical Garden 86, 523–545.
  • Menitsky, Y.L. 1984. Duby Asii. Nauka, Leningrad, Soviet Union.
  • Menitsky, Y.L. 2005. Oaks of Asia. Science Publishers, Enfield, NH, USA.
  • Mir, C., Toumi, L., Jarne, P., Sarda, V., DI Giusto, F. & Lumaret, R. 2006. Endemic North African Quercus afares Pomel originates from hybridisation between two genetically very distant oak species (Q. suber L. and Q. canariensis Willd.): evidence from nuclear and cytoplasmic markers. Heredity (Edinburgh) 96, 175–184.
  • Moran, E.V., Willis, J. & Clark, J.S. 2012. Genetic evidence for hybridization in red oaks (Quercus sect. Lobatae, Fagaceae). American Journal of Botany 99, 92–100.
  • Nixon, K. 1993. Infrageneric classification of Quercus (Fagaceae) and typification of sectional names. Annals of Forest Science 50, 25–34.
  • Oh, S.H. & Manos, P.S. 2008. Molecular phylogenetics and cupule evolution in Fagaceae as inferred from nuclear CRABS CLAW sequences. Taxon 57, 434–451.
  • Ørsted, A.S. 1867. Bidrag til Egeslægtens Systematik. Bianco Luno, Kjøbenhavn, Denmark.
  • Premoli, A.C., Mathiasen, P., Cristina Acosta, M. & Ramos, V.A. 2012. Phylogeographically concordant chloroplast DNA divergence in sympatric Nothofagus s.s. How deep can it be? New Phytologist 193, 261–275.
  • Rambaut, A. & Drummond, A. 2007. Tracer v1.4. http://beast.bio.ed.ac.uk/Tracer (accessed 13 June 2014).
  • Rokas, A., Kruger, D. & Carroll, S.B. 2005. Animal evolution and the molecular signature of radiations compressed in time. Science 310, 1933–1938.
  • Rushton, B. 1993. Natural hybridization within the genus Quercus L. Annals of Forest Science 50, 73–90.
  • Samuel, R., Bachmair, A., Jobst, J. & Ehrendorfer, F. 1998. ITS sequences from nuclear rDNA suggest unexpected phylogenetic relationships between Euro-Mediterranean, East Asiatic and North American taxa of Quercus (Fagaceae). Plant Systematics and Evolution 211, 129–139.
  • Schnitzler, J.P., Steinbrecher, R., Zimmer, I., Steigner, D. & Fladung, M. 2004. Hybridization of European oaks (Quercus ilex x Q-robur) results in a mixed isoprenoid emitter type. Plant Cell and Environment 27, 585–593.
  • Schwarz, O. 1936. Entwurf zu einem natürlichen System der Cupuliferen und der Gattung Quercus L. Notizblätter des Botanischen Garten zu Berlin-Dahlem 13, 1–22.
  • Schwarz, O. 1936–39. Monographie der Eichen Europas und des Mittelmeergebietes. Series: Repertorium specierum nov. regni vegetabilis, Sonderbeihefte, Selbstverlag Friedrich Fedde, Dahlem-Berlin, Germany.
  • Schwarz, O. 1993. Quercus L. In: Tutin, T.G., Heywood, V.H., Burges, N.A., Valentine, D.H., Walters, S.M. & Webb, D.A., Eds., Flora Europaea. Cambridge University Press, Cambridge, UK.
  • Scornavacca, C., Berry, V., Lefort, V., Douzery, E.J.P. & Ranwez, V. 2008. PhySIC_IST: cleaning source trees to infer more informative supertrees. BioMed Central Bioinformatics 9, 413.
  • Simeone, M.C., Piredda, R., Papini, A., Vessella, F. & Schirone, B. 2013. Application of plastid and nuclear markers to DNA barcoding of Euro–Mediterranean oaks (Quercus, Fagaceae): problems, prospects and phylogenetic implications. Botanical Journal of the Linnean Society 172, 478–499.
  • Smiley, C.J. & Huggins, L.M. 1981. Pseudofagus idahoensis, n. gen. et sp. (Fagaceae) from the Miocene Clarkia Flora of Idaho. American Journal of Botany 58, 741–761.
  • Solomon, A. 1983a. Pollen morphology and plant taxonomy of white oaks in eastern North America. American Journal of Botany 70, 481–494.
  • Solomon, A. 1983b. Pollen morphology and plant taxonomy of red oaks in eastern North America. American Journal of Botany 70, 495–507.
  • Stamatakis, A. 2006. raxml-vi-hpc: Maximum-Likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688–2690.
  • Stamatakis, A., Hoover, P. & Rougemont, J. 2008. A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology 57, 758–771.
  • Tamura, K., Dudley, J., Nei, M. & Kumar, S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24, 1596–1599.
  • Ueno, S., Le Provost, G., Leger, V., Klopp, C., Noirot, C., Frigerio, J.M., Salin, F., Salse, J., Abrouk, M., Murat, F., Brendel, O., Derory, J., Abadie, P., Leger, P., Cabane, C., Barre, A., DE Daruvar, A., Couloux, A., Wincker, P., Reviron, M.P., Kremer, A. & Plomion, C. 2010. Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BioMed Central Genomics 11, 650.
  • Valencia, S.A. 2004. Diversidad del genero Quercus (Fagaceae) en Mexico. Boletin de la Sociedad Boanica de Mexico 75, 33–54.
  • Velitzelos, D., Bouchal, J.M. & Denk, T. 2014. Review of the Cenozoic floras and vegetation of Greece. Review of Palaeobotany and Palynology 204, 56–117.
  • Whitfield, J.B. & Kjer, K.M. 2008. Ancient rapid radiations of insects: challenges for phylogenetic analysis. Annual Review of Entomology 53, 449–472.
  • Xu, L., 2004. Diversité de l'ADN chloroplastique et relations phylogénétiques au sein des Fagacées et du genre Quercus. PhD thesis, University of Henri Poincaré, Nancy, France.
  • Xu, L., Kremer, A., BodÉnÈs, C. & Huang, M.R. 2005. Chloroplast DNA diversity and phylogenetic relationships in botanical sections of the genus Quercus L In: Rogers, R., Ducousso, A. & Kanazashi, A., Eds., Integration of silviculture and genetics in creating and sustaining of oak forests. Proceedings of the Joint Meeting of IUFRO Working Groups Genetics of Quercus and Improvement and Silviculture of Oaks. FFPRI (Forestry and Forest Products Research Institute), pp. 113–121.
  • Zhang, D.X. & Hewitt, G.M. 1996. Nuclear integrations: challenges for mitochondrial DNA markers. Trends in Ecology and Evolution 11, 247–251.

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