Link to publications on Google Scholar

McNeal, J., J. R. Bennett, A. D. Wolfe, and S. Mathews. 2013. Phylogeny of Orobanchaceae inferred from five genes resolves the earliest split between hemi- and holoparasites American Journal of Botany 100: 971-983.

Mathews, S., and E. M. Kramer. 2012. Genetic perspectives on a Russian doll, or taking the ovule from naked to nested. New Phytologist 194: 910-933.

Xi, Z., B. R. Ruhfel, H. Schaefer, A. Amorim, M. Sugumaran, K. J. Wurdack. P. F. Stevens, S. Mathews*, and C. C. Davis*. 2012. Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales. Proceedings of the National Academy of Sciences, USA 109: 17519-17524. * Co-corresponding authors.

Mathews, S., D. Tremonte. 2012. Tests of the link between functional innovation and positive selection at phytochrome A. The phylogenetic distribution of far-red high irradiance responses in seedling development. International Journal of Plant Sciences 173(6): 662-672.

Leslie, A. B., J. M. Beaulieu, P. R. Crane, M. J. Donoghue, and S. Mathews. Divergent evolutionary dynamics among Northern and Southern Hemisphere conifers. Proceedings of the National Academy of Sciences, USA 109: 16217-16221.

Nagalingum N. S., C. R. Marshall, T. B. Quental, H. S. Rai, D. P. Little, S. Mathews. 2011. Recent synchronous radiation of a living fossil. Science 334(6057): 796-799.

Beilstein, M. A., N. S. Nagalingum, M. D. Clements, S. R. Manchester, and S. Mathews. 2010. Dated molecular phylogenies indicate a Miocene for Arabidopsis thaliana. Proceedings of the National Academy of Sciences, USA 107 (43): 18724-18727 [pdf].

Mathews, S. 2010. Evolutionary studies illuminate the structural-functional model of plant phytochromes. The Plant Cell 22: 4-16. [pdf]

Mathews, S., M. D. Clements, and M. A. Beilstein. 2010. A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants. Phil. Trans. R. Soc. B 365: 383-395.

Mathews, S. 2009. Phylogenetic relationships among seed plants: persistent questions and the limits of molecular data. Am. J. Bot. 96: 228-236.

Kolmos, E., M. Nowak, M. Werner, K. Fischer, G. Schwarz, S. Mathews, H. Schoof, F. Nagy, J. M. Bujnicki, and S. J. Davis. 2009. Integrating ELF4 into the circadian system through combined structural and functional studies. HFSP Journal http://hfspj.aip.org/doi/10.2976/1.3218766.

Beilstein, M. A., I. A. Al-Shehbaz, S. Mathews, and E. A. Kellogg. 2008. Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited. Amer. J. Bot. 95: 1307-1327.

Mathews, S., and K. McBreen. 2008. Phylogenetic relationships of B-related phytochromes in the Brassicaceae: Redundancy and the persistence of phytochrome D. Molec. Phylogenet. Evol. 49: 411-433.

Saarela, J. M., H. S. Rai, J. A. Doyle, P. K. Endress, S. Mathews, A. D. Marchant, B. G. Briggs, S. W. Graham.  2007. Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree. Nature 446: 312-315. [pdf]

Burleigh, J. G., and S. Mathews.  2007.  Assessing systematic error in the inference of seed plant phylogeny. Int. J. Pl. Sci. 168: 125-135. [pdf]

Burleigh, J. G., and S. Mathews.  2007. Assessing Among-locus variation in the inference of seed plant phylogeny.  Int. J. Pl. Sci. 168: 111-124.  [pdf]

Mathews, S. 2006. Phytochrome-mediated development in land plants: red light sensing evolves to meet the challenges of changing light environments. Invited review article. Molec. Ecol. 15(12): 3483–3503. [pdf]

Bennett, J. R., and Mathews, S. 2006. Phylogeny of the parasitic plant family Orobanchaceae inferred from phytochrome A. Amer. J. Bot. 93: 1039-1051. [pdf]

Sharrock, R. A., Mathews, S. 2006. Phytochrome genes in higher plants: structure, expression, and evolution. Pp 99-129 in: Photomorphogenesis in Plants and Bacteria (Eds. E. Schafer and F. Nagy), Kluwer, Dordrect, The Netherlands.

Duvall, M., S. Mathews, N. A. Mohammad, and T. Russell.  2006.  Placing the monocots; conflicting signal from trigenomic analyses. In Monocots: comparative biology and evolution, vol. 1, 77-88. (Eds. J. T. Columbus, E. A. Friar, C. W. Hamilton, J. M. Porter, L. M. Prince, and M. G. Simpson), Rancho Santa Ana Botanic Garden, Claremont, California.

Theuri, J., Phelps-Durr, T., Mathews, S., Birchler, J. 2005. A comparative study of retrotransposons in the centromeric regions of A and B chromosomes of maize. Cytogenet. Genome Res. 110: 203-208. [pdf]

Mathews, S. 2005. Phytochrome evolution in green and nongreen plants. J. Heredity. 96(3): 1-8. [pdf]

Mathews, S. 2005. Analytical methods for studying the evolution of paralogs using duplicate gene data sets. Method. Enzymol. 395: 724-745. [pdf]

Burleigh, J. G., and S. Mathews. 2004. Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life. Amer. J. Bot. 91: 1599-1613. [pdf]

Davis, C. C., P. W. Fritsch, C. D. Bell, S.Mathews. 2004. High latitude Tertiary migrations of an exclusively tropical clade: evidence from Malpighiaceae. Int. J. Plant Sci. 165 (4): S107-S121. [pdf]

Provan, J., P. M Biss, D. McMeel, and S. Mathews. 2004. Universal primers for the amplification of chloroplast microsatellites in grasses (Poaceae). Molec. Ecol. Notes 4 (2): 262-264. [pdf]

Mathews, S. 2004. The study of ancient adaptation: A case study of a phytochrome gene pair from early-diverging angiosperms. In: The Molecular Genetics and Ecology of Plant Adaptation, (Eds. Q. Cronk and I. E. P. Taylor) National Research Council of Canada Research Press.

Mathews, S., J. G. Burleigh, and M. J. Donoghue. 2003. Adaptive evolution in the photosensory domain of phytochrome A in early angiosperms. Mol. Biol. Evol. 20: 1087-1097. [pdf]

Davis, C. C., C. D. Bell, P. W. Fritsch, and S. Mathews. 2002. Phylogeny of Acridocarpus-Brachylophon (Malpighiaceae): implications for tertiary tropical floras and Afroasian biogeography. Evolution. 56: 2395-2405. [pdf]

Davis, C. C., C. D. Bell, S. Mathews, and M. J. Donoghue. 2002. Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae. Proc. Natl. Acad. Sci. USA 99: 6833-6837. [pdf]

Zanis, M. J., D. E. Soltis, P. S. Soltis, S. Mathews, and M. J. Donoghue. 2002. The root of the angiosperms revisited. Proc. Natl. Acad. Sci. USA 99: 6848-6853. [pdf]

Mathews, S., R. E. Spangler, R. J. Mason-Gamer, E. A. Kellogg. 2002. Phylogeny of Andropogoneae inferred from phytochrome B, GBSSI, and ndhF. Int. J. Plant Sci. 163: 441-450. [pdf]

Grass Phylogeny Working Group. 2001. Phylogeny and subfamilial classification of the Poaceae. Ann. Missouri Bot. Gard. 88: 313-457.

Simmons, M. P., C. C. Clevenger, V. Savolainen, R. H. Archer, S. Mathews, and J. J. Doyle. 2001. Phylogeny of the Celastraceae inferred from phytochrome B and morphology. Am. J. Bot. 88: 313-325. [pdf]

Mathews, S., and M. J. Donoghue. 2000. Basal angiosperm phylogeny inferred from duplicate phytochromes A and C. Int. J. Plant Sci. 161(6 Suppl.): S41-S55. [pdf]

Clark, L.G., M. Kobayashi, S. Mathews, R. Spangler and E. A. Kellogg. 2000. The Puelioideae, A New Subfamily of Poaceae. Syst. Bot. 25(2): 181-187. [pdf]

Mathews, S., R. C. Tsai, and E. A. Kellogg. 2000. Phylogenetic structure in the grass family (Poaceae): evidence from the nuclear gene phytochrome B. Am. J. Bot. 87: 96-107. [pdf]

Mathews, S., and M. J. Donoghue. 1999. The root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science 286: 947-950. [pdf]

Mathews, S., and M. Lavin. 1998. A biosystematic study of Castilleja crista-galli: an allopolyploid origin reexamined. Syst. Bot. 23: 213-230. [pdf]

Donoghue, M. J., and S. Mathews. 1998. Duplicate genes and the root of the angiosperms, with a preliminary analysis of phytochrome genes. Mol. Phyl. Evol. 9: 489-500. [pdf]

Lavin, M., E. Eshbaugh, J.-M. Hu, S. Mathews, and R. A. Sharrock. 1998. Monophyletic subgroups of the tribe Millettieae (Leguminosae) as revealed by phytochrome nucleotide sequence data. Am. J. Bot. 85: 412-433. [pdf]

Mathews, S., and R. A. Sharrock. 1997. Phytochrome gene diversity. Pl. Cell Environm. 20: 666-671. [pdf]

Mathews, S., and R. A. Sharrock. 1996. The phytochrome gene family in grasses (Poaceae): a phylogeny and evidence that grasses have a subset of the loci found in dicot angiosperms. Mol. Biol. Evol. 13: 1141-1150. [pdf]

Mathews, S., M. Lavin, and R. A. Sharrock. 1995. Evolution of the phytochrome gene family and its utility for phylogenetic analyses of angiosperms. Ann. Missouri Bot. Gard. 82: 296-321. [pdf]

Clack, T. S., S. Mathews, and R. A. Sharrock. 1994. The phytochrome apoprotein family in Arabidopsis is encoded by five genes: the sequences and expression of PHYD and PHYE. Plant Mol. Biol. 25: 413-427.

Lavin, M., S. Mathews, and C. Hughes. 1991. Intraspecific chloroplast variation in Gliricidia (Leguminosae): intraspecific phylogeny and tokogeny. Am. J. Bot. 78: 1576-1585. [pdf]