Low Copy Nuclear Genes Used in Species-Level Studies of Plants adh (Sang et al. 1997) argenine carboxylase (Galloway et al. 1998) CRABS CLAW (CRC) (Oh and Manos 2008) GBSSI (granule bound starch synthase) or waxy (Harbaugh 2008, Mason-Gamer et al. 1998, Winkworth and Donoghue 2004) glutamine synthetase (Emshwiller and Doyle 1999) glycerol 3-phosphate acyltransferase (Tank and Sang 2001) Hf1 (Chen et al. 2007) histone H3 intron (Doyle et al. 1996) LEAFY (Oh and Potter 2003) malate synthase (Lewis and Doyle 2001) NADP-dependent isocitrate dehydrogenase (IDH) (Weese and Johnson 2005) nitrate reductase (Howarth and Baum 2002) PEP carboxylase (Gaskin and Schaal 2002, Helfgott and Mason-Gamer 2004) pgiC (Gottlieb and Ford 1996) Phytochromes (Mathews et al. 1995) pistillata (Bailey and Doyle 1999) RNA polymerase II (RPB2) (Goetsch et al. 2005, Oxelman et al. 2004, Popp and Oxelman 2007, Thomas et al. 2006) sorbitol 6-phosphate dehydrogenase (Bortiri et al. 2002) Reviews of the topic by (Sang 2002, Sang and Zhang 1999, Whittall et al. 2006) Literature Cited Bailey, C., and J. Doyle. 1999. Potential phylogenetic utility of the low-copy nuclear gene pistillata in dicotyledonous plants: comparison to nrDNA ITS and trnL intron in Sphaerocardamum and other Brassicaceae. Mol Phylogenet Evol 13: 20-30. Bortiri, E., S. Oh, F. Gao, and D. Potter. 2002. The phylogenetic utility of nucleotide sequences of sorbitol 6-phosphate dehydrogenase in Prunus (Rosaceae). Amer. J. Bot. 89: 16971708. Chen, S. M., K. Matsubara, T. Omori, H. Kokubun, H. Kodama, H. Watanabe, G. Hashimoto, E. Marchesi, L. Bullrich, and T. Ando. 2007. Phylogenetic analysis of the genus Petunia (Solanaceae) based on the sequence of the Hf1 gene. Journal of Plant Research 120: 385397. Doyle, J., V. Kanazin, and R. Shoemaker. 1996. Phylogenetic utility of histone H3 intron sequences in the perennial relatives of soybean (Glycine: Leguminosae). Mol Phylogenet Evol 6: 438-447. Emshwiller, E., and J. Doyle. 1999. Chloroplast-expressed glutamine synthetase (ncpGS): potential utility for phylogenetic studies with an example from Oxalis (Oxalidaceae). Mol Phylogenet Evol 12(3): 310-319. Galloway, G., R. Malmberg, and R. Price. 1998. Phylogenetic utility of the nuclear gene arginine decarboxylase: An example from Brassicaceae. Mol. Biol. Evol. 15: 1312-1320. Gaskin, J. F., and B. A. Schaal. 2002. Hybrid Tamarix widespread in U.S. invasion and undetected in native Asian range. Proc. Natl. Acad. Sci. USA 99: 11256-11259. Goetsch, L., A. J. Eckert, and B. D. Hall. 2005. The molecular systematics of Rhododendron (Ericaceae): A phylogeny based upon RPB2 gene sequences. Systematic Botany 30: 616626. Gottlieb, L., and V. Ford. 1996. Phylogenetic relationships among the sections of Clarkia (Onagraceae) inferred from the nucleotide sequences of PgiC. Systematic Botany 21: 4562. Harbaugh, D. T. 2008. Polyploid and hybrid origins of pacific island sandalwoods (Santalum, Santalaceae) inferred from low-copy nuclear and flow cytometry data. International Journal of Plant Sciences 169: 677-685. Helfgott, D. M., and R. J. Mason-Gamer. 2004. The evolution of North American Elymus (Triticeae, Poaceae) allotetraploids: Evidence from phosphoenolpyruvate carboxylase gene sequences. Systematic Botany 29: 850-861. Howarth, D. G., and B. A. Baum. 2002. Phylogenetic utility of a nuclear intron from nitrate reductase for the study of closely related plant species. Mol Phylogenet Evol 23: 525-528. Lewis, C., and J. Doyle. 2001. Phylogenetic utility of the nuclear gene malate synthase in the palm family (Arecaceae). Mol. Phylogenet. Evol. 19: 409-420. Mason-Gamer, R., C. Weil, and E. Kellogg. 1998. Granule-bound starch synthase: structure, function, and phylogenetic utility. Mol Biol Evol 15: 1658-1673. Mathews, S., M. Lavin, and R. A. Sharrock. 1995. Evolution of the phytochrome gene family and Its utility for phylogenetic analyses of angiosperms. Annals of the Missouri Botanical Garden 82: 296-321. 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. Oh, S. H., and D. Potter. 2003. Phylogenetic utility of the second intron of LEAFY in Neillia and Stephanandra (Rosaceae) and implications for the origin of Stephanandra. Molecular Phylogenetics and Evolution 29: 203-215. Oxelman, B., N. Yoshikawa, B. McConaughy, J. Lou, A. Denton, and B. D. Hall. 2004. Rpb2 gene phylogeny in flowering plants, with particular emphasis on asterids. Mol Phylogenet Evol. 32: 462-479. Popp, M., and B. Oxelman. 2007. Origin and evolution of North American polyploid Silene (Caryophyllaceae). American Journal of Botany 94: 330-349. Sang, T. 2002. Utility of low-copy nuclear gene sequences in plant phylogenetics. Critical Reviews in Biochemistry and Molecular Biology 37: 121-147. Sang, T., M. J. Donoghue, and D. Zhang. 1997. Evolution of alcohol dehdrogenase genes in peonies (Paeonia): phylogenetic relationships of putative nonhybrid species. Mol. Phylog. Evol. 14: 994-1007. Sang, T., and D. Zhang. 1999. Reconstructing hybrid speciation using sequences of low copy nuclear genes: Hybrid origins of five Paeonia species based on Adh gene phylogenies. Syst. Bot. 24: 148-163. Tank, D., and T. Sang. 2001. Phylogenetic utility of the glycerol-3-phosphate acyltransferase gene: evolution and implications in Paeonia (Paeoniaceae). Molecular Phylogenetics And Evolution 19: 421-429. Thomas, M. M., N. C. Garwood, W. J. Baker, S. A. Henderson, S. J. Russell, D. R. Hodel, and R. M. Bateman. 2006. Molecular phylogeny of the palm genus Chamaedorea, based on the low-copy nuclear genes PRK and RPB2. Molecular Phylogenetics and Evolution 38: 398-415. Weese, T. L., and L. A. Johnson. 2005. Utility of NADP-dependent isocitrate dehydrogenase for species-level evolutionary inference in angiosperm phylogeny: a case study in Saltugilia. Mol Phylogenet Evol. 36: 24--41. Whittall, J. B., A. Medina-Marino, E. A. Zimmer, and S. A. Hodges. 2006. Generating singlecopy nuclear gene data for a recent adaptive radiation. Molecular Phylogenetics and Evolution 39: 124-134. Winkworth, R. C., and M. J. Donoghue. 2004. Viburnum phylogeny: evidence from the duplicated nuclear gene GBSSI. Molecular Phylogenetics and Evolution 33: 109-126.