PUBLICATIONS
2021-2023
Harms KE, Watson DM, Santiago-Rosario LY, Mathews S Exposing the error hidden in plain sight: A Critique of Calder's (1983) group selectionist seed-dispersal hypothesis for mistletoe "mimicry" of host plants. Accepted at Ecology and Evolution.
Gueidan C, Mead OL, Nazeem-Bokaree H, Mathews S (2023) First draft of an annotated genome for a lichenised strain of the green alga Diplosphaera chodatii (Prasiolales, Trebouxiophyceae). European Journal of Phycology February 21, 2023. https://doi.org/10.1080/09670262.2023.2165711.
McLay TGB, Murphy DJ, Holmes G, Mathews S, Brown GK, Cantrill DJ, Udovicic F, Allnutt TR, Jackson CJ (2022) A genome resource for Acacia, Australia’s largest plant genus. PLOS ONE October 14, 2022. https://doi.org/10.1371/journal.pone.0274267.
Nazem-Bokaee H, Hom EFY, Warden AC, Mathews S, Gueidan C (2021) Towards a systems biology approach to understanding the lichen symbiosis: opportunities and challenges of implementing network modelling. Frontiers in Microbiology 12: 28
Cai L, Arnold BJ, Xi Z, Khost DE, Patel N, Hartmann CB, Manickam S, Sasirat S, Nikolov LA, Mathews S, Sackton TB, Davis CC (2021) Deeply altered genome architecture in the endoparasitic flowering plant Sapria himalayana Griff. (Rafflesiaceae). Current Biology 31: 1-10. doi.org/10.1016/j.cub.2020.12.045
2011-2020
Povilus R, DaCosta JM, Grassa C, Satyaki PRV, Moeglein M, Jaenisch J, Mathews S, Gehring M, Friedman WE, Davis CC (2020) Water lily (Nymphaea thermarum) genome reveals variable genomic signatures of ancient vascular cambium losses. Proceedings of the National Academy of Sciences, USA. 117(15):8649-8656. doi: 10.1073/pnas.1922873117
Sundaram M, Donoghue MJ, Beaulieu JM, Farjon A, Filer D, Mathews S, Jetz W, Leslie AS (2019) Accumulation over evolutionary time as a major cause of conifer biodiversity hotspots. Proceedings of the Royal Society B 286: 20191887. https://doi.org/10.1098/rspb.2019.1887.
Leslie AS, Beaulieu J, Holman G, Campbell CS, Mei W, Raubeson LA, Mathews S (2018) An overview of extant conifer evolution from the perspective of the fossil record. American Journal of Botany 105(9): 1531-1544. https://doi.org/10.1002/ajb2.1143. 29 August.
Dean GH, Asmarayani R, Ardiyani M, Santika Y, Triono T, Mathews S, Webb CO (2018) Recommendations for generating DNA sequence data in labs with limited molecular biology resources: lessons from a barcoding project in Indonesia. Applications in Plant Sciences https://doi.org/10.1002/aps3.1167. 13 July.
Forest F, Baloch E, Brummitt NA, Bachman S, Moat J, Ickert-Bond S, Hollingsworth PM, Liston A, Little DP, Mathews S, Rai H, Rydin C, Stevenson DW, Thomas P, Buerki S (2018) Gymnosperms on the EDGE. Scientific Reports 8: 6053. doi:10.1038/s41598-018-24365-4
Lu L, Mao L, Yang T, Ye J, Liu B, Li H, Sun M, Miller JT, Mathews S, Hu H, Niu Y, Peng D, Chen Y, Smith SA, Chen M, Xiang K, Le CT, Dang VC, Lu A, Soltis PS, Soltis DE, Li J, Chen Z (2018) Evolutionary history of the angiosperm flora of China. Nature 554: 234-238. doi:10.1038/nature25485
Lu L, Cox CJ, Mathews S, Wang W, Wen J, Chen Z (2018) Optimal data partitioning, multispecies coalescent and Bayesian concordance resolve early divergences of the grape family (Vitaceae) Cladistics 34: 57-77, doi: 10.1111/cla.12191. 6 February.
Holman GH, Del Tredici P, Havill N, Lee NS, Cronn R, Mathews S, Raubeson LA, Campbell CS (2017) A new species and introgression in eastern Asian hemlocks (Pinaceae: Tsuga). Systematic Botany 42(4):733-746. 18 December.
Godfree RC, Marshall DM, Young AG, Miller CH, Mathews S (2017) Empirical evidence of fixed and homeostatic patterns of polyploid advantage in a keystone grass exposed to drought and heat stress. Royal Society Open Science 4(11): 170934. 22 November.
Leslie AB, Beaulieu JM, Mathews S (2017) Variation in seed size is structured by dispersal syndrome and cone morphology in conifers and other non-flowering seed plants. New Phytologist 216: 429-437, doi: 10.1111/nph.14456.
Latvis M, Jacobs SJ, Mortimer SME, Richards M, Blischak PD, Mathews S, Tank DC (2017) Primers for Castilleja and their utility across Orobanchaceae: II. Single-copy nuclear loci. Applications in Plant Sciences 5(9): 1700038.
Latvis M, Mortimer SME, Morales-Briones DF, Torpey S, Uribe-Convers S, Jacobs SJ, Mathews S, Tank DC (2017) Primers for Castilleja and their utility across Orobanchaceae: I. Chloroplast primers. Applications in Plant Sciences 5(9): 1700020.
Rockwell NC, Martin SS, Li F-W, Mathews S, Lagarias JC (2017) The phycocyanobilin chromophore of streptophyte algal phytochromes is synthesized by HY2. New Phytologist 214: 1145-1157. doi: 10.1111/nph.14422.
Gernandt DS, Holman G, Campbell CS, Parks M, Cronn R, Mathews S, Liston A, Stockey RA, Rothwell GW (2016) Phylogenetics of extant and fossil Pinaceae using implied character weighting and model-based methods. Canadian Journal of Botany 884: 863-884.
Pirone-Davies C, Prior N, von Aderkas P, Smith D, Hardie D, Freidman WE, Mathews S (2016) Insights from the pollination drop proteome and the ovule transcriptome of Cephalotaxus at the time of pollination drop production. Annals of Botany 117(6): 973-984.
Li FW, Mathews S (2016) Evolutionary aspects of plant photoreceptors. Journal of Plant Research 129 (2): 115-122. Invited review.
Ruhsam M, Rai HS, Mathews S, Ross GT, Graham SW, Raubeson LA, Mei W, Thomas P, Gardner M, Ennos RA, Hollingsworth PM (2015) Does complete plastid genome sequencing improve species discrimination and phylogenetic resolution in Araucaria? Molecular Ecology Resources 15: 1067-1078. doi: 10.1111/1755-0998.12375.
Hertweck KL, Kinney MS, Stuart SA, Maurin O, Mathews S, Chase MW, Gandolfo MA, Pires JC (2015) Phylogenetics, divergence times, and diversification from three genomic partitions in monocots. Botanical Journal of the Linnean Society 178: 375-393.
Li FW, Rothfels CJ, Melkonian M, Villarreal JC, Stevenson DW, Graham SW, Wong GKS, Mathews S, Pryer KM (2015) The origin and evolution of phototropins. Frontiers in Plant Science 6: 637
Li FW, Melkonian M, Rothfels CJ, Villarreal JC, Stevenson DW, Graham SW, Wong GKS, Pryer KP, Mathews S (2015) Phytochrome diversity in green plants and the origin of canonical phytochromes. Nature Communications 6: 7852 Highlighted by Faculty of 1000.
Lagomarsino LP, Antonelli A, Muchhala N, Timmermann A, Mathews S, & Davis CC (2014) Phylogeny, classification, and fruit evolution of the species-rich neotropical bellflowers (Campanulaceae: Lobelioideae). American Journal of Botany 101 (12): 2097-2112.
Li FW, Villarreal JC, Kelly S, Rothfels CJ, Melkonian M, Frangedakis E, Ruhsam M, Sigel EM, Der JP, Pittermann J, Burge DO, Pokornyk L, Larsson A, Chen T, Weststrand S, Thomas P, Carpenter E, Zhang Y, Tian ZJ, Chen L, Yan ZX, Zhu Y, Sun X, Wang J, Stevenson DW, Crandall-Stotler BJ, Shaw AJ, Deyholos MK, Soltis DE, Graham SW, Windham MD, Langdale JA, Wong GKS, Mathews S, & Pryer KM (2014) Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proceedings of the National Academy of Sciences, USA 111 (18): 6672-6677.
Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian ZJ, Yan ZX, Wu XL, Sun X, Wong GKS, & Leebens-Mack J (2014) Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences, USA 111 (45): E4859-E4868.
Matasci N, Hung LH, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, DePamphilis CW, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, Surek B, Melkonian M, & Soltis DE (2014) Data access for the 1,000 plants (1KP) project. GigaScience 3: 17.
McNeal J, Bennett JR, JR Wolfe JR, and Mathews S (2013) Phylogeny of Orobanchaceae inferred from five genes resolves the earliest split between hemi- and holoparasites. American Journal of Botany 100: 971-983.
Xi Z, Ruhfel BR, Schaefer H, Amorim A, Sugumaran M, Wurdack KJ, Stevens PF, Mathews S*, and Davis CC* (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.
Leslie, A. B, J. M. Beaulieu, P. R. Crane, Donoghue MJ, and Mathews S (2012) Divergent evolutionary dynamics among Northern and Southern Hemisphere conifers. Proceedings of the National Academy of Sciences, USA, 109: 16217-16221.
Mathews S, Tremonte D (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.
Mathews S, Kramer EM (2012) Genetic perspectives on a Russian doll, or taking the ovule from naked to nested. Invited Tansley Review for New Phytologist 194: 910-923.
Nagalingum NS, Marshall CR, Quental TB, Rai HS, Little DP, and Mathews S (2011) Recent synchronous radiation of a living fossil. Science 334(6057): 796-799.
2001-2010
Beilstein MA, Nagalingum NS, Clements MD, Manchester SR, and Mathews S (2010) Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proceedings of the National Academy of Sciences, USA 107 (43): 18724-18727. This paper was highlighted by Faculty of 1000 and identified in November 2011 by Thomson Reuters Essential Science IndicatorsSM as a featured New Hot Paper in the field of Plant & Animal Science, as one of the most-cited papers in this discipline published in the previous two years.
Mathews S (2010) Evolutionary studies illuminate the structural-functional model of plant phytochromes. Invited review. Plant Cell 22: 4-16.
Mathews S, Clements MD, and Beilstein MA (2010) A duplicate gene rooting of seed plants and the phylogenetic position of flowering plants. Philosophical Transactions of the Royal Society Series B 365: 383-395.
Mathews S (2009) Phylogenetic relationships among seed plants: persistent questions and the limits of molecular data. American Journal of Botany 96: 228-236.
Kolmos EM, Nowak M, Werner M, Fischer K, Schwarz G, Mathews S, Schoof H, Nagy F, Bujnicki JM, and Davis SJ (2009) Integrating ELF4 into the circadian system through combined structural and functional studies. HFSP Journal 3(5): 350-366.
Mathews S, and McBreen K (2008) Phylogenetic relationships of B-related phytochromes in the Brassicaceae: Redundancy and the persistence of phytochrome D. Molecular Phylogenetics and Evolution 49: 411-433.
Beilstein MA, Al-Shehbaz IA, Mathews S, and Kellogg EA (2008) Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited. American Journal of Botany 95: 1307-1327.
Saarela JM, Rai HS, Doyle JA, Endress PK, Mathews S, Marchant AD, Briggs BG, and Graham SW (2007) Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree. Nature 446: 312-315.
Burleigh JG, and Mathews S (2007a) Among-locus variation in the inference of seed plant phylogeny. International Journal of Plant Sciences 168: 111-124.
Burleigh JG, and Mathews S (2007b) Assessing systematic error in the inference of seed plant phylogeny. International Journal of Plant Sciences 168: 125-135.
Mathews S (2006) Phytochrome-mediated development in land plants: red light sensing evolves to meet the challenges of changing light environments. Invited review. Molecular Ecology 15: 3483-3503.
Bennett, JR, and Mathews S (2006) Phylogeny of the parasitic plant family Orobanchaceae inferred from phytochrome A. American Journal of Botany 93: 1039-1051.
Duvall M, Mathews S, Mohammad NA, and Russell T (2006) Placing the monocots; conflicting signal from trigenomic analyses. Aliso 22: 77-88
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. Cytogenetic and Genome Research 110: 203-208.
Mathews S (2005) Phytochrome evolution in green and nongreen plants. Journal of Heredity 96: 1-8.
Burleigh JG, and Mathews S (2004) Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life. American Journal of Botany 91: 1599-1613.
Davis CC, Fritsch PW, Bell CD, Mathews S (2004) High latitude Tertiary migrations of an exclusively tropical clade: evidence from Malpighiaceae. International Journal of Plant Sciences 165 (4): S107-S121.
Provan J, Biss PM, McMeel D, and Mathews S (2004) Universal primers for the amplification of chloroplast microsatellites in grasses (Poaceae). Molecular Ecology Notes 4: 262-264.
Mathews S, Burleigh JG, and Donoghue MJ (2003) Adaptive evolution in the photosensory domain of phytochrome A in early angiosperms. Molecular Biology and Evolution 20: 1087-1097.
Davis CC, Bell CD, Fritsch PW, and Mathews S (2002a) Phylogeny of Acridocarpus-Brachylophon (Malpighiaceae): implications for tertiary tropical floras and Afroasian biogeography. Evolution. 56: 2395-2405.
Zanis MJ, Soltis DE, Soltis PS, Mathews S, and Donoghue MJ (2002) The root of the angiosperms revisited. Proceedings of the National Academy of Sciences USA 99: 6848-6853.
Mathews S, Spangler RE, Mason-Gamer RJ, Kellogg EA (2002) Phylogeny of Andropogoneae inferred from phytochrome B, GBSSI, and ndhF. International Journal of Plant Sciences 163: 441-450.
Davis CC, Bell CD, Mathews S, and Donoghue MJ (2002b) Laurasian migration explains Gondwanan disjunctions: evidence from Malpighiaceae. Proceedings of the National Academy of Sciences USA 99: 6833-6837.
Simmons MP, Clevenger CC, Savolainen V, Archer RH, Mathews S, and Doyle JJ (2001) Phylogeny of the Celastraceae inferred from phytochrome B and morphology. American Journal of Botany 88: 313-325.
Grass Phylogeny Working Group (2001) Phylogeny and subfamilial classification of the Poaceae. Annals of the Missouri Botanical Garden 88: 373-457.
1991-2000
Mathews S, Donoghue MJ (2000) Basal angiosperm phylogeny inferred from duplicate phytochromes A and C. International Journal of Plant Sciences 161(6 Suppl.): S41-S55.
Clark LG, Kobayashi M, Mathews S, Spangler R, and Kellogg EA (2000) The Puelioideae, A new subfamily of Poaceae. Systematic Botany 25(2): 181-187.
Mathews S, Tsai RC, and Kellogg EA (2000) Phylogenetic structure in the grass family (Poaceae): evidence from the nuclear gene phytochrome B. American Journal of Botany 87: 96-107.
Mathews S, Donoghue MJ (1999) The root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science 286: 947-950.
Donoghue MJ, Mathews S (1998) Duplicate genes and the root of the angiosperms, with a preliminary analysis of phytochrome genes. Molecular Phylogenetics and Evolution 9: 489-500.
Mathews S, Lavin M (1998) A biosystematic study of Castilleja crista-galli: an allopolyploid origin reexamined. Systematic Botany 23: 213-230.
Lavin M, Eshbaugh E, Hu J-M, Mathews S, and Sharrock RA (1998) Monophyletic subgroups of the tribe Millettieae (Leguminosae) as revealed by phytochrome nucleotide sequence data. American Journal of Botany 85: 412-433.
Mathews S, and Sharrock RA (1997) Phytochrome gene diversity. Invited Review. Plant, Cell & Environment 20: 666-671.
Mathews S, and Sharrock RA (1996) The phytochrome gene family in grasses (Poaceae): a phylogeny and evidence that grasses have a subset of the loci found in dicot angiosperms. Molecular Biology and Evolution 13: 1141-1150.
Mathews S, Lavin M, and Sharrock RA (1995) Evolution of the phytochrome gene family and its utility for phylogenetic analyses of angiosperms. Annals of the Missouri Botanical Garden 82: 296-321.
Clack TS, Mathews S, and Sharrock RA (1994) The phytochrome apoprotein family in Arabidopsis is encoded by five genes: the sequences and expression of PHYD and PHYE. Plant Molecular Biology 25: 413-427.
Lavin M, Mathews S, and Hughes C (1991) Chloroplast variation in Gliricidia (Leguminosae): intraspecific phylogeny and tokogeny. American Journal of Botany 78: 1576-1585.