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Items: 1 to 50 of 70

1.

Complex reproductive secretions occur in all extant gymnosperm lineages: a proteomic survey of gymnosperm pollination drops.

Prior N, Little SA, Boyes I, Griffith P, Husby C, Pirone-Davies C, Stevenson DW, Tomlinson PB, von Aderkas P.

Plant Reprod. 2018 Nov 14. doi: 10.1007/s00497-018-0348-z. [Epub ahead of print]

PMID:
30430247
2.

Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots.

Givnish TJ, Zuluaga A, Spalink D, Soto Gomez M, Lam VKY, Saarela JM, Sass C, Iles WJD, de Sousa DJL, Leebens-Mack J, Chris Pires J, Zomlefer WB, Gandolfo MA, Davis JI, Stevenson DW, dePamphilis C, Specht CD, Graham SW, Barrett CF, Ané C.

Am J Bot. 2018 Nov;105(11):1888-1910. doi: 10.1002/ajb2.1178. Epub 2018 Oct 24.

PMID:
30368769
3.

Taxonomic review of Ceratozamia (Zamiaceae) in the Sierra Madre Oriental, Mexico.

Martínez-Domínguez L, Nicolalde-Morejón F, Vergara-Silva F, Stevenson DW.

PhytoKeys. 2018 Jun 21;(100):91-124. doi: 10.3897/phytokeys.100.23152. eCollection 2018.

4.

Gymnosperms on the EDGE.

Forest F, Moat J, Baloch E, Brummitt NA, Bachman SP, Ickert-Bond S, Hollingsworth PM, Liston A, Little DP, Mathews S, Rai H, Rydin C, Stevenson DW, Thomas P, Buerki S.

Sci Rep. 2018 Apr 16;8(1):6053. doi: 10.1038/s41598-018-24365-4.

5.

Crowds Replicate Performance of Scientific Experts Scoring Phylogenetic Matrices of Phenotypes.

O'Leary MA, Alphonse K, Mariangeles AH, Cavaliere D, Cirranello A, Dietterich TG, Julius M, Kaufman S, Law E, Passarotti M, Reft A, Robalino J, Simmons NB, Smith SY, Stevenson DW, Theriot E, Velazco PM, Walls RL, Yu M, Daly M.

Syst Biol. 2018 Jan 1;67(1):49-60. doi: 10.1093/sysbio/syx052.

PMID:
29253296
6.

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution.

Lang D, Ullrich KK, Murat F, Fuchs J, Jenkins J, Haas FB, Piednoel M, Gundlach H, Van Bel M, Meyberg R, Vives C, Morata J, Symeonidi A, Hiss M, Muchero W, Kamisugi Y, Saleh O, Blanc G, Decker EL, van Gessel N, Grimwood J, Hayes RD, Graham SW, Gunter LE, McDaniel SF, Hoernstein SNW, Larsson A, Li FW, Perroud PF, Phillips J, Ranjan P, Rokshar DS, Rothfels CJ, Schneider L, Shu S, Stevenson DW, Thümmler F, Tillich M, Villarreal Aguilar JC, Widiez T, Wong GK, Wymore A, Zhang Y, Zimmer AD, Quatrano RS, Mayer KFX, Goodstein D, Casacuberta JM, Vandepoele K, Reski R, Cuming AC, Tuskan GA, Maumus F, Salse J, Schmutz J, Rensing SA.

Plant J. 2018 Feb;93(3):515-533. doi: 10.1111/tpj.13801.

7.

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.

Cooper L, Meier A, Laporte MA, Elser JL, Mungall C, Sinn BT, Cavaliere D, Carbon S, Dunn NA, Smith B, Qu B, Preece J, Zhang E, Todorovic S, Gkoutos G, Doonan JH, Stevenson DW, Arnaud E, Jaiswal P.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1168-D1180. doi: 10.1093/nar/gkx1152.

8.

Evolution of strigolactone receptors by gradual neo-functionalization of KAI2 paralogues.

Bythell-Douglas R, Rothfels CJ, Stevenson DWD, Graham SW, Wong GK, Nelson DC, Bennett T.

BMC Biol. 2017 Jun 29;15(1):52. doi: 10.1186/s12915-017-0397-z.

9.

Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes.

Johnson KL, Cassin AM, Lonsdale A, Wong GK, Soltis DE, Miles NW, Melkonian M, Melkonian B, Deyholos MK, Leebens-Mack J, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Carpenter EJ, Bacic A, Doblin MS, Schultz CJ.

Plant Physiol. 2017 Jun;174(2):904-921. doi: 10.1104/pp.17.00295. Epub 2017 Apr 26.

10.

Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants.

Jia Q, Li G, Köllner TG, Fu J, Chen X, Xiong W, Crandall-Stotler BJ, Bowman JL, Weston DJ, Zhang Y, Chen L, Xie Y, Li FW, Rothfels CJ, Larsson A, Graham SW, Stevenson DW, Wong GK, Gershenzon J, Chen F.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12328-12333. Epub 2016 Oct 10.

11.

The Evolution of HD2 Proteins in Green Plants.

Bourque S, Jeandroz S, Grandperret V, Lehotai N, Aimé S, Soltis DE, Miles NW, Melkonian M, Deyholos MK, Leebens-Mack JH, Chase MW, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Yan Z, Xie Y, Carpenter EJ, Wong GKS, Wendehenne D, Nicolas-Francès V.

Trends Plant Sci. 2016 Dec;21(12):1008-1016. doi: 10.1016/j.tplants.2016.10.001. Epub 2016 Oct 24. Review.

PMID:
27789157
12.

Challenging the paradigms of leaf evolution: Class III HD-Zips in ferns and lycophytes.

Vasco A, Smalls TL, Graham SW, Cooper ED, Wong GK, Stevenson DW, Moran RC, Ambrose BA.

New Phytol. 2016 Nov;212(3):745-758. doi: 10.1111/nph.14075. Epub 2016 Jul 7.

13.

Molecular phylogenetics of the Ronnbergia Alliance (Bromeliaceae, Bromelioideae) and insights into their morphological evolution.

Aguirre-Santoro J, Michelangeli FA, Stevenson DW.

Mol Phylogenet Evol. 2016 Jul;100:1-20. doi: 10.1016/j.ympev.2016.04.007. Epub 2016 Apr 6.

PMID:
27060423
14.

Data supporting the nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae).

Comer JR, Zomlefer WB, Barrett CF, Stevenson DW, Heyduk K, Leebens-Mack JH.

Data Brief. 2016 Mar 2;7:532-6. doi: 10.1016/j.dib.2016.02.063. eCollection 2016 Jun.

15.

A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales.

McKain MR, Tang H, McNeal JR, Ayyampalayam S, Davis JI, dePamphilis CW, Givnish TJ, Pires JC, Stevenson DW, Leebens-Mack JH.

Genome Biol Evol. 2016 Apr 21;8(4):1150-64. doi: 10.1093/gbe/evw060.

16.

Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae).

Comer JR, Zomlefer WB, Barrett CF, Stevenson DW, Heyduk K, Leebens-Mack JH.

Mol Phylogenet Evol. 2016 Apr;97:32-42. doi: 10.1016/j.ympev.2015.12.015. Epub 2015 Dec 31.

PMID:
26748268
17.

Anatomy of fleshy fruits in the monocots.

Thadeo M, Hampilos KE, Stevenson DW.

Am J Bot. 2015 Nov;102(11):1757-79. doi: 10.3732/ajb.1500204. Epub 2015 Oct 27.

18.

Algal ancestor of land plants was preadapted for symbiosis.

Delaux PM, Radhakrishnan GV, Jayaraman D, Cheema J, Malbreil M, Volkening JD, Sekimoto H, Nishiyama T, Melkonian M, Pokorny L, Rothfels CJ, Sederoff HW, Stevenson DW, Surek B, Zhang Y, Sussman MR, Dunand C, Morris RJ, Roux C, Wong GK, Oldroyd GE, Ané JM.

Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13390-5. doi: 10.1073/pnas.1515426112. Epub 2015 Oct 5.

19.

The origin and evolution of phototropins.

Li FW, Rothfels CJ, Melkonian M, Villarreal JC, Stevenson DW, Graham SW, Wong GK, Mathews S, Pryer KM.

Front Plant Sci. 2015 Aug 12;6:637. doi: 10.3389/fpls.2015.00637. eCollection 2015.

20.

Phytochrome diversity in green plants and the origin of canonical plant phytochromes.

Li FW, Melkonian M, Rothfels CJ, Villarreal JC, Stevenson DW, Graham SW, Wong GK, Pryer KM, Mathews S.

Nat Commun. 2015 Jul 28;6:7852. doi: 10.1038/ncomms8852.

21.

The evolutionary history of ferns inferred from 25 low-copy nuclear genes.

Rothfels CJ, Li FW, Sigel EM, Huiet L, Larsson A, Burge DO, Ruhsam M, Deyholos M, Soltis DE, Stewart CN Jr, Shaw SW, Pokorny L, Chen T, dePamphilis C, DeGironimo L, Chen L, Wei X, Sun X, Korall P, Stevenson DW, Graham SW, Wong GK, Pryer KM.

Am J Bot. 2015 Jul;102(7):1089-107. doi: 10.3732/ajb.1500089. Epub 2015 Jul 16.

22.

Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using plastid sequences derived from next-generation sequencing.

Comer JR, Zomlefer WB, Barrett CF, Davis JI, Stevenson DW, Heyduk K, Leebens-Mack JH.

Am J Bot. 2015 Jun;102(6):888-99. doi: 10.3732/ajb.1500057. Epub 2015 May 29.

23.

Data access for the 1,000 Plants (1KP) project.

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, Soltis PS, Rothfels C, Pokorny L, Shaw JA, DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, Leebens-Mack J, Wong GK.

Gigascience. 2014 Oct 27;3:17. doi: 10.1186/2047-217X-3-17. eCollection 2014. Review.

24.

Phylotranscriptomic analysis of the origin and early diversification of land plants.

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 Z, Yan Z, Wu X, Sun X, Wong GK, Leebens-Mack J.

Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):E4859-68. doi: 10.1073/pnas.1323926111. Epub 2014 Oct 29.

25.

Between two fern genomes.

Sessa EB, Banks JA, Barker MS, Der JP, Duffy AM, Graham SW, Hasebe M, Langdale J, Li FW, Marchant DB, Pryer KM, Rothfels CJ, Roux SJ, Salmi ML, Sigel EM, Soltis DE, Soltis PS, Stevenson DW, Wolf PG.

Gigascience. 2014 Sep 25;3:15. doi: 10.1186/2047-217X-3-15. eCollection 2014. Review.

26.

Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor.

Floyd SK, Ryan JG, Conway SJ, Brenner E, Burris KP, Burris JN, Chen T, Edger PP, Graham SW, Leebens-Mack JH, Pires JC, Rothfels CJ, Sigel EM, Stevenson DW, Neal Stewart C Jr, Wong GK, Bowman JL.

Mol Phylogenet Evol. 2014 Dec;81:159-73. doi: 10.1016/j.ympev.2014.06.017. Epub 2014 Sep 27.

27.

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns.

Li FW, Villarreal JC, Kelly S, Rothfels CJ, Melkonian M, Frangedakis E, Ruhsam M, Sigel EM, Der JP, Pittermann J, Burge DO, Pokorny L, Larsson A, Chen T, Weststrand S, Thomas P, Carpenter E, Zhang Y, Tian Z, Chen L, Yan Z, Zhu Y, Sun X, Wang J, Stevenson DW, Crandall-Stotler BJ, Shaw AJ, Deyholos MK, Soltis DE, Graham SW, Windham MD, Langdale JA, Wong GK, Mathews S, Pryer KM.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):6672-7. doi: 10.1073/pnas.1319929111. Epub 2014 Apr 14.

28.

Conserved genetic regions across angiosperms as tools to develop single-copy nuclear markers in gymnosperms: an example using cycads.

Salas-Leiva DE, Meerow AW, Francisco-Ortega J, Calonje M, Griffith MP, Stevenson DW, Nakamura K.

Mol Ecol Resour. 2014 Jul;14(4):831-45. doi: 10.1111/1755-0998.12228. Epub 2014 Mar 5.

PMID:
24444413
29.

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

Barrett CF, Specht CD, Leebens-Mack J, Stevenson DW, Zomlefer WB, Davis JI.

Ann Bot. 2014 Jan;113(1):119-33. doi: 10.1093/aob/mct264. Epub 2013 Nov 25.

30.

Transcriptome-mining for single-copy nuclear markers in ferns.

Rothfels CJ, Larsson A, Li FW, Sigel EM, Huiet L, Burge DO, Ruhsam M, Graham SW, Stevenson DW, Wong GK, Korall P, Pryer KM.

PLoS One. 2013 Oct 8;8(10):e76957. doi: 10.1371/journal.pone.0076957. eCollection 2013.

31.

Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony, likelihood and species tree inference methods.

Salas-Leiva DE, Meerow AW, Calonje M, Griffith MP, Francisco-Ortega J, Nakamura K, Stevenson DW, Lewis CE, Namoff S.

Ann Bot. 2013 Nov;112(7):1263-78. doi: 10.1093/aob/mct192. Epub 2013 Aug 29.

32.

Evolution of the class IV HD-zip gene family in streptophytes.

Zalewski CS, Floyd SK, Furumizu C, Sakakibara K, Stevenson DW, Bowman JL.

Mol Biol Evol. 2013 Oct;30(10):2347-65. doi: 10.1093/molbev/mst132. Epub 2013 Jul 27.

33.

Next-generation phenomics for the Tree of Life.

Burleigh JG, Alphonse K, Alverson AJ, Bik HM, Blank C, Cirranello AL, Cui H, Daly M, Dietterich TG, Gasparich G, Irvine J, Julius M, Kaufman S, Law E, Liu J, Moore L, O'Leary MA, Passarotti M, Ranade S, Simmons NB, Stevenson DW, Thacker RW, Theriot EC, Todorovic S, Velazco PM, Walls RL, Wolfe JM, Yu M.

PLoS Curr. 2013 Jun 26;5. pii: ecurrents.tol.085c713acafc8711b2ff7010a4b03733. doi: 10.1371/currents.tol.085c713acafc8711b2ff7010a4b03733.

34.

The plant ontology as a tool for comparative plant anatomy and genomic analyses.

Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall CJ, Rensing S, Hiss M, Lang D, Reski R, Berardini TZ, Li D, Huala E, Schaeffer M, Menda N, Arnaud E, Shrestha R, Yamazaki Y, Jaiswal P.

Plant Cell Physiol. 2013 Feb;54(2):e1. doi: 10.1093/pcp/pcs163. Epub 2012 Dec 5.

35.

Zamia (Cycadales: Zamiaceae) on Puerto Rico: asymmetric genetic differentiation and the hypothesis of multiple introductions.

Meerow AW, Francisco-Ortega J, Calonje M, Griffith MP, Ayala-Silva T, Stevenson DW, Nakamura K.

Am J Bot. 2012 Nov;99(11):1828-39. doi: 10.3732/ajb.1200494. Epub 2012 Nov 1.

36.

DNA barcode identification of black cohosh herbal dietary supplements.

Baker DA, Stevenson DW, Little DP.

J AOAC Int. 2012 Jul-Aug;95(4):1023-34.

PMID:
22970567
37.

Ontologies as integrative tools for plant science.

Walls RL, Athreya B, Cooper L, Elser J, Gandolfo MA, Jaiswal P, Mungall CJ, Preece J, Rensing S, Smith B, Stevenson DW.

Am J Bot. 2012 Aug;99(8):1263-75. doi: 10.3732/ajb.1200222. Epub 2012 Jul 30.

38.

Phylogeny of the Asparagales based on three plastid and two mitochondrial genes.

Seberg O, Petersen G, Davis JI, Pires JC, Stevenson DW, Chase MW, Fay MF, Devey DS, Jørgensen T, Sytsma KJ, Pillon Y.

Am J Bot. 2012 May;99(5):875-89. doi: 10.3732/ajb.1100468. Epub 2012 Apr 26.

39.

Homologies of the flower and inflorescence in the early-divergent grass Anomochloa (Poaceae).

Sajo MG, Pabón-Mora N, Jardim J, Stevenson DW, Rudall PJ.

Am J Bot. 2012 Apr;99(4):614-28. doi: 10.3732/ajb.1100290. Epub 2012 Mar 20.

40.

A genome triplication associated with early diversification of the core eudicots.

Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR, McNeal J, Rolf M, Ruzicka DR, Wafula E, Wickett NJ, Wu X, Zhang Y, Wang J, Zhang Y, Carpenter EJ, Deyholos MK, Kutchan TM, Chanderbali AS, Soltis PS, Stevenson DW, McCombie R, Pires JC, Wong GK, Soltis DE, Depamphilis CW.

Genome Biol. 2012 Jan 26;13(1):R3. doi: 10.1186/gb-2012-13-1-r3.

41.

A functional phylogenomic view of the seed plants.

Lee EK, Cibrian-Jaramillo A, Kolokotronis SO, Katari MS, Stamatakis A, Ott M, Chiu JC, Little DP, Stevenson DW, McCombie WR, Martienssen RA, Coruzzi G, Desalle R.

PLoS Genet. 2011 Dec;7(12):e1002411. doi: 10.1371/journal.pgen.1002411. Epub 2011 Dec 15.

42.

Character-based, population-level DNA barcoding in Mexican species of Zamia L. (Zamiaceae: Cycadales).

Nicolalde-Morejón F, Vergara-Silva F, González-Astorga J, Stevenson DW.

Mitochondrial DNA. 2010 Dec;21 Suppl 1:51-9. doi: 10.3109/19401736.2010.539215.

PMID:
21271859
43.

Are substitution rates and RNA editing correlated?

Cuenca A, Petersen G, Seberg O, Davis JI, Stevenson DW.

BMC Evol Biol. 2010 Nov 11;10:349. doi: 10.1186/1471-2148-10-349.

44.

Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution.

Cibrián-Jaramillo A, De la Torre-Bárcena JE, Lee EK, Katari MS, Little DP, Stevenson DW, Martienssen R, Coruzzi GM, DeSalle R.

Genome Biol Evol. 2010 Jul 12;2:225-39. doi: 10.1093/gbe/evq012.

45.

Plant science research in botanic gardens.

Crane PR, Hopper SD, Raven PH, Stevenson DW.

Trends Plant Sci. 2009 Nov;14(11):575-7. doi: 10.1016/j.tplants.2009.09.007. Epub 2009 Oct 1. No abstract available.

PMID:
19800836
46.

The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data.

de la Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R.

PLoS One. 2009 Jun 2;4(6):e5764. doi: 10.1371/journal.pone.0005764.

47.

Comparative ovule and megagametophyte development in Hydatellaceae and water lilies reveal a mosaic of features among the earliest angiosperms.

Rudall PJ, Remizowa MV, Beer AS, Bradshaw E, Stevenson DW, Macfarlane TD, Tuckett RE, Yadav SR, Sokoloff DD.

Ann Bot. 2008 May;101(7):941-56. doi: 10.1093/aob/mcn032. Epub 2008 Mar 30.

48.
49.

Morphology of Hydatellaceae, an anomalous aquatic family recently recognized as an early-divergent angiosperm lineage.

Rudall PJ, Sokoloff DD, Remizowa MV, Conran JG, Davis JI, Macfarlane TD, Stevenson DW.

Am J Bot. 2007 Jul;94(7):1073-92. doi: 10.3732/ajb.94.7.1073.

50.

Nuclear genome size in Selaginella.

Little DP, Moran RC, Brenner ED, Stevenson DW.

Genome. 2007 Apr;50(4):351-6.

PMID:
17546093

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