publications

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1. Hayden, W.J., M.P. Simmons, and L.J. Swanson. 1993. Wood anatomy of Amanoa (Euphorbiaceae). IAWA Journal 14: 205-213.

2. Simmons, M.P., W.J. Hayden, and D.M.E. Ware. 1995. The vascular flora of the Potomac River watershed of King George County, Virginia. Castanea 60: 179-209.

3. Simmons, M.P. and W.J. Hayden. 1997. Revision of the cerrado hemicryptophytic Chamaesyce of Boissier's Pleiadeniae (Euphorbiaceae). Brittonia 49: 155-180.

4. Davis, J.I., M.P. Simmons, D.W. Stevenson, and J.F. Wendel. 1998. Data decisiveness and data quality in phylogenetic analysis: an example from the monocots using mitochondrial atpA sequences. Systematic Biology 47: 282-310.

5. Simmons, M.P. and J.P. Hedin. 1999. Relationships and morphological character change among genera of the Celastraceae sensu lato (including Hippocrateaceae). Annals of the Missouri Botanical Garden 86: 723-757.

6. Stevenson, D.W., J.I. Davis, J.V. Freudenstein, C.R. Hardy, M.P. Simmons, and C.D. Specht. 2000. A phylogenetic analysis of the monocotyledons based on morphological and molecular character sets, with comments on the placement of Acorus and Hydatellaceae. Pages 17-24 in Monocots systematics and evolution (K. L. Wilson and D. A. Morrison, eds.). CSIRO Publishing, Sydney.

7. Simmons, M.P. 2000. A fundamental problem with amino-acid-sequence characters for phylogenetic analyses. Cladistics 16: 274-282.

8. Simmons, M.P. and H. Ochoterena. 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369-381.

9. Simmons, M.P., C.D. Bailey, and K.C. Nixon. 2000. Phylogeny reconstruction using duplicate genes. Molecular Biology and Evolution 17: 469-473.

10. Barker, N.P., L.G. Clark, J.I. Davis, M.R. Duvall, G.F. Guala, C. Hsiao, E.A. Kellogg, H.P. Linder, R. Mason-Gamer, S.Y. Mathews, M.P. Simmons, R.J. Soreng, and R.E. Spangler. 2001. Phylogeny and subfamilial classification of the grasses (Poaceae). Annals of the Missouri Botanical Garden 88: 373-457.

11. Simmons, M.P., C.C. Clevinger, V. Savolainen, R.H. Archer, S. Mathews, and J.J. Doyle. 2001. Phylogeny of the Celastraceae inferred from phytochrome B gene sequence and morphology. American Journal of Botany 88: 313-325.

12. Simmons, M.P., V. Savolainen, C.C. Clevinger, R.H. Archer, and J.I. Davis. 2001. Phylogeny of the Celastraceae inferred from 26S nuclear ribosomal DNA, phytochrome B, rbcL, atpB, and morphology. Molecular Phylogenetics and Evolution 19: 353-366.

13. Simmons, M.P., H. Ochoterena, and T. Carr. 2001. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Systematic Biology 50: 454-462.

14. Simmons, M.P. and J.V. Freudenstein. 2002. Uninode coding vs. gene-tree parsimony for phylogenetic reconstruction using duplicate genes. Molecular Phylogenetics and Evolution 23: 481-498.

15. Simmons, M.P. and J.V. Freudenstein. 2002. Artifacts of coding amino acids and other composite characters for phylogenetic analysis. Cladistics 18: 354-365.

16. Simmons, M.P., C. Randle, J.V. Freudenstein, and J.W. Wenzel. 2002. Limitations of Relative Apparent Synapomorphy Analysis (RASA) for measuring phylogenetic signal. Molecular Biology and Evolution 19: 14-23.

17. Simmons, M.P., H. Ochoterena and J.V. Freudenstein. 2002. Conflict between amino acid and nucleotide characters. Cladistics 18: 200-206.

18. Simmons, M.P., H. Ochoterena and J.V. Freudenstein. 2002. Amino acid vs. nucleotide characters: challenging preconceived notions. Molecular Phylogenetics and Evolution 24: 78-90.

19. Simmons, M.P. and J.V. Freudenstein. 2003. The effects of increasing genetic distance on alignment of, and tree construction from, rDNA internal transcribed spacer sequences. Molecular Phylogenetics and Evolution 26: 444-451.

20. Baumberger, N., B. Doesseger, R. Guyot, A. Diet, R.L. Parsons, M.A. Clark, M.P. Simmons, P.A Bedinger, S.A. Goff, C. Ringli, and B. Keller. 2003. Whole-genome comparison of LRR-extensins (LRXs) in Arabidopsis thaliana and Oryza sativa: a conserved family of cell wall proteins form a vegetative and a reproductive clade. Plant Physiology 131: 1313-1326.

21. Freudenstein, J.V., K.M. Pickett, M.P. Simmons, and J.W. Wenzel. 2003. From basepairs to bird songs: phylogenetic data in the age of genomics. Cladistics 19: 333-347.

22. Simmons, M.P. 2004. Celastraceae. Pages 29-64 in The families and genera of vascular plants, volume 6 (K. Kubitzki, ed.). Springer, Berlin.

23. Simmons, M.P. 2004. Parnassiaceae. Pages 291-296 in The families and genera of vascular plants, volume 6 (K. Kubitzki, ed.). Springer, Berlin.

24. Simmons, M.P. 2004. Independence of alignment and tree search. Molecular Phylogenetics and Evolution 31: 874-879.

25. Simmons, M.P. 2004. Hippocrateaceae. Pages 3-19 in Flore de la Nouvelle-Calédonie, volume 25 (P. Morat, ed.). Muséum National d’Histoire Naturelle, Laboratoire de Phanérogramie, Paris.

26. Simmons, M.P. and M. Miya. 2004. Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches. Molecular Phylogenetics and Evolution 31: 351-362.

27. Simmons, M.P., K.M. Pickett and M. Miya. 2004. How meaningful are Bayesian posterior probabilities? Molecular Biology and Evolution 21: 188-199.

28. Simmons, M.P., A. Reeves and J.I. Davis. 2004. Character-state space versus rate of evolution for phylogenetic inference. Cladistics 20: 191-204.

29. Simmons, M.P., T.G. Carr and K. O’Neill. 2004. Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters. Molecular Phylogenetics and Evolution 32: 913-926.

30. Davis, J.I., D.W. Stevenson, G. Petersen, O. Seberg, L.M. Campbell, J.V. Freudenstein, D.H. Goldman, C.R. Hardy, F.A. Michelangeli, M.P. Simmons, C.D. Specht, F. Vergara-Silva, and M.A. Gandolfo. 2004. A phylogeny of the monocots, as inferred from rbcL and atpA sequence variation, and a comparison of methods for calculating jackknife and bootstrap values. Systematic Botany 29: 467-510.

31. Simmons, M.P. 2005. Amino acid versus nucleotide characters for phylogenetic inference of the "basal" angiosperms. Pages 1-27 in Plant genome biodiversity and evolution, volume 1B: phanerogams (A.K. Sharma and A. Sharma, eds.). Science Publishers, Inc., Enfield, New Hampshire.

32. Abdel-Ghany, S.E., I.S. Day, M.P. Simmons, P. Kugrens and A.S.N. Reddy. 2005. Origin and evolution of kinesin-like calmodulin-binding proteins. Plant Physiology 138: 1711-1722.

33. Simmons, M.P. and C.T. Webb. 2006. Quantification of the success of phylogenetic inference in simulations. Cladistics 22: 249-255.

34. Simmons, M.P., L.-B. Zhang, C.T. Webb and A. Reeves. 2006. How can third codon positions outperform first and second codon positions in phylogenetic inference? An empirical example from the seed plants. Systematic Biology 55: 245-258.

35. Simmons, M.P., L.-B. Zhang, C.T. Webb, A. Reeves and J.A. Miller. 2006. The relative performance of Bayesian and parsimony approaches when sampling characters evolving under homogeneous and heterogeneous sets of parameters. Cladistics 22: 171-185.

36. Davis, J.I., G. Petersen, O. Seberg, D.W. Stevenson, C.R. Hardy, M.P. Simmons, F.A. Michelangeli, D.H. Goldman, L.M. Campbell, C.D. Specht and J.I. Cohen. 2006. Are mitochondrial genes useful for the analysis of monocot relationships? Taxon 55: 857-870.

37. Islam, M.B. and M.P. Simmons. 2006. A thorny dilemma: testing alternative intrageneric classifications within Ziziphus (Rhamnaceae). Systematic Botany 31: 826-842.

38. Islam, M.B., M.P. Simmons and R.H. Archer. 2006. Phylogeny of the Elaeodendron group (Celastraceae) inferred from morphological characters and nuclear and plastid genes. Systematic Botany 31: 512-524.

39. Petersen, G., O. Seberg, J.I. Davis, D.H. Goldman, D.W. Stevenson, L.M. Campbell, F.A. Michelangeli, C.D. Specht, M.W. Chase, M.F. Fay, J.C. Pires, J.V. Freudenstein, C.R. Hardy and M.P. Simmons. 2006. Mitochondrial DNA in monocot phylogenetics. Aliso 22: 52-62.

40. Poff, N.L., J.D. Olden, N.K.M. Vieira, D.S. Finn, M.P. Simmons and B.C. Kondratieff. 2006. Functional trait niches of North American lotic insects: evolutionary constraints on trait-based ecological applications. Journal of the North American Benthological Society 25: 730-755.

41. Richardson, D., M.P. Simmons and A.S.N. Reddy. 2006. Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes. BMC Genomics 7: 18.

42. Zhang, L.-B. and M.P. Simmons. 2006. Phylogeny and delimitation of the Celastrales inferred from nuclear and plastid genes. Systematic Botany 31: 122-137.

43. Zhang, L.-B., M.P. Simmons, A. Kocyan, and S.S. Renner. 2006. Phylogeny of the Cucurbitales based on DNA sequences of nine loci from three genomes: implications for morphological and sexual system evolution. Molecular Phylogenetics and Evolution 39: 305-322.

44. Simmons, M.P., K. Müller and A.P. Norton. 2007. The relative performance of indel-coding methods in simulations. Molecular Phylogenetics and Evolution 44: 724-740.

45. Simmons, M.P., L.-B. Zhang, C.T. Webb and K. Müller. 2007. A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference. Molecular Phylogenetics and Evolution 42: 528-542.

46. Zhang, L.-B., M.P. Simmons and S.S. Renner. 2007. A phylogeny of Anisophyllaceae based on six nuclear and plastid loci: ancient disjunctions and recent dispersal between South America, Africa, and Asia. Molecular Phylogenetics and Evolution 44: 1057-1067.

47. Poon, W.-S., P.-C. Shaw, M.P. Simmons and P.P.-H. But. 2007. Congruence of molecular, morphological, and biochemical profiles in Rutaceae: a cladistic analysis of the subfamilies Rutoideae and Toddalioideae. Systematic Botany 32: 837-846.

48. Simmons, M.P. 2008. Celastraceae. Pages 321-322 in Nuevo Catálogo de la Flora de Venezuela (O. Hokche, P.E. Berry, O. Huber, eds.). Fundación Instituto Botánico de Venezuela, Caracas.

49. Simmons, M.P. 2008. Potential use of host-derived genome signatures to root virus phylogenies. Molecular Phylogenetics and Evolution 49: 969-978.

50. Simmons, M.P., J.J. Cappa, R.H. Archer, A.J. Ford, D. Eichstedt and C.C. Clevinger. 2008. Phylogeny of the Celastreae (Celastraceae) and the relationships of Catha edulis (qat) inferred from morphological characters and nuclear and plastid genes. Molecular Phylogenetics and Evolution 48: 745-757.

51. Simmons, M.P., K.F. Müller and C.T. Webb. 2008. The relative sensitivity of different alignment methods and character codings in sensitivity analysis. Cladistics 24: 1039-1050.

52. Simmons, M.P., D. Richardson and A.S.N. Reddy. 2008. Incorporation of gap characters and lineage-specific regions into phylogenetic analyses of gene families from divergent clades: an example from the kinesin superfamily across eukaryotes. Cladistics 24: 372-384.

53. But, P.P.-H., A.W.-S. Poon, P.-C. Shaw, M.P. Simmons and H. Greger. 2009. Contribution of molecular cladistics to the taxonomy of Rutaceae in China. Journal of Systematics and Evolution 47: 144-150.

54. Coughenour, J.M., M.P. Simmons, J.A. Lombardi and J.J. Cappa. 2010. Phylogeny of Celastraceae subfamily Salacioideae and tribe Lophopetaleae inferred from morphological characters and nuclear and plastid genes. Systematic Botany 35: 358-366.

55. Simmons, M.P., K.F. Müller and A.P. Norton. 2010. Alignment of, and phylogenetic inference from, random sequences: the susceptibility of alternative alignment methods to creating artifactual resolution and support. Molecular Phylogenetics and Evolution 57: 1004-1016.

56. Law, S.K.-Y., M.P. Simmons, N. Techen, I.A. Khan, M.-F. He, P.-C. Shaw, and P.P.-H. But. 2011. Molecular analyses of the Chinese herb leigongteng (Tripterygium wilfordii Hook.f.). Phytochemistry 72: 21-26.

57. Simmons, M.P., L.-B. Zhang and K.F. Müller. 2011. Phylogenetic inference using non-redundant coding of dependent characters vs. alternative approaches when applied to protein-coding genes. Cladistics 27: 186-196.

58. Coughenour, J.M., M.P. Simmons, J.A. Lombardi, K. Yakobson and R.H. Archer. 2011. Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid loci. Molecular Phylogenetics and Evolution 59: 320-330.

59. Guo, X., M.P. Simmons, P.P.-H. But, P.-C. Shaw and R.-J Wang. 2011. Application of DNA barcodes in Hedyotis L. (Spermacoceae, Rubiaceae). Journal of Systematics and Evolution 49: 203-212.

60. Simmons, M.P., K.F. Müller and C.T. Webb. 2011. The deterministic effects of alignment bias in phylogenetic inference. Cladistics 27: 402-416.

61. Bacon, C.D., G.P. Johnson, H. Meimberg, P. Puppo, M.P. Simmons, and W.L. Wagner. 2011. Development of microsatellites in the Hawaiian endemic palm Pritchardia martii (Arecaceae) and their utility in congeners. American Journal of Botany Primer Notes & Protocols in the Plant Sciences 98: E139-140.

62. Simmons, M.P. and J.V. Freudenstein. 2011. Spurious 99% bootstrap and jackknife support for unsupported clades. Molecular Phylogenetics and Evolution 61: 177-191.

63. McKenna, M.J., M.P. Simmons, C.D. Bacon and J.A. Lombardi. 2011. Delimitation of the segregate genera of Maytenus sensu lato (Celastraceae) based on morphological and molecular characters. Systematic Botany 36: 922-932.

64. Simmons, M.P. 2012. Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data. Molecular Phylogenetics and Evolution 62: 472-484.

65. Simmons, M.P. 2012. Misleading results of likelihood-based phylogenetic analyses in the presence of missing data. Cladistics 28: 208-222.

66. Simmons, M.P., M.J. McKenna, C.D. Bacon, J.J. Cappa, R.H. Archer and A.J. Ford. 2012. Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid loci.  Molecular Phylogenetics and Evolution 62: 9-20.

67. Simmons, M.P., C.D. Bacon, J.J. Cappa and M.J. McKenna. 2012. Phylogeny of Celastraceae subfamilies Cassinoideae and Tripterygioideae inferred from morphological characters and nuclear and plastid loci. Systematic Botany 37: 456-467.

68. Bacon, C.D., W.J. Baker and M.P. Simmons. 2012. Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae). Systematic Biology 61: 426-442.

69. Bacon, C.D., M.J. McKenna, M.P. Simmons and W.L. Wagner. 2012. Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia). BMC Evolutionary Biology 12: 23.

70. Bernhardt, S.A., M.P. Simmons, K.E. Olson, B.J. Beaty, C.D. Blair, and W.C. Black. 2012. Intraspecific evolution of miRNA and siRNA genes in the mosquito Aedes aegypti. PLoS One 7: e44198.

71. Guo, X., R.-J. Wang, M.P. Simmons, P.P.-H. But and J. Yu. 2013. Phylogeny of the Asian Hedyotis-Oldenlandia complex (Spermacoceae, Rubiaceae): Evidence for high levels of polyphyly and parallel evolution of diplophragmous capsules. Molecular Phylogenetics and Evolution 67: 110-122.

72. Simmons, M.P. and J.J. Cappa. 2013. Wilczekra, a new genus of Celastraceae for a disjunct lineage of Euonymus. Systematic Botany 38: 148-153.

73. Simmons, M.P. and A.P. Norton. 2013. Quantification and relative severity of inflated branch-support values generated by alternative methods: an empirical example. Molecular Phylogenetics and Evolution 67: 277-296.

74. Curto, M.A., L. Tembrock, P. Puppo, M. Nogueira, M.P. Simmons and H. Meimberg. 2013. Evaluation of microsatellites of Catha edulis (qat; Celastraceae) identified using pyrosequencing. Biochemical Systematics and Ecology 49: 1-9.

75. Simmons, M.P. and P.A. Goloboff. 2013. An artifact of undersampling optimal trees in supermatrix analyses of locally sampled characters. Molecular Phylogenetics and Evolution 69: 265-275.

76. Bacon, C.D., F. Michonneau, A.J. Henderson, M.J. McKenna, A.M. Milroy, and M.P. Simmons. 2013. Geographic and taxonomic disparities in species diversity: dispersal and diversification across Wallace's Line. Evolution 67: 2058-2071.

77. Gilligan, T.M., D.J. Wright, J. Munz, K. Yakobson, and M.P. Simmons. 2014. Molecular phylogeny and revised classification of Eucosma Hübner and related genera (Lepidoptera: Tortricidae: Eucosmini). Systematic Entomology 39: 49-67.

78. Simmons, M.P. and A.P. Norton. 2014. Divergent maximum-likelihood-branch-support values for polytomies. Molecular Phylogenetics and Evolution 73: 87-96.

79. Simmons, M.P. 2014. Limitations of locally sampled characters in phylogenetic analyses of sparse supermatrices. Molecular Phylogenetics and Evolution 74: 1-14.

80. Cappa, J.J., P.J. Cappa, A.F. El Mehdawi, J.M. McAleer, M.P. Simmons and E.A.H. Pilon-Smits. 2014. Characterization of selenium and sulfur accumulation in Stanleya (Brassicaceae): a field survey and common-garden experiment. American Journal of Botany 101: 830-839.

81. Groppo, M., M.P. Simmons, J.J. Cappa, L. Biral, and J.A. Lombardi. 2014. A new species of Maytenus (Celastraceae) with fleshy fruits from eastern Brazil with notes on the delimitation of Maytenus. Systematic Botany 39: 478-484.

82. Simmons, M.P. and C.P. Randle. 2014. Disparate parametric branch-support values from ambiguous characters. Molecular Phylogenetics and Evolution 78: 66-86.

83. Simmons, M.P. and P.A. Goloboff. 2014. Dubious resolution and support from published sparse supermatrices: The importance of thorough tree searches. Molecular Phylogenetics and Evolution 78: 334-348.

84. Simmons, M.P. 2014. A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses. Molecular Phylogenetics and Evolution 80: 267-280.

85. Goloboff, P.A. and M.P. Simmons. 2014. Bias in tree searches, and its consequences for measuring group supports. Systematic Biology 63: 851-861.

86. Cappa, J.J., C. Yetter, S. Fakra, P.J. Cappa, R. DeTar, C. Landes, E.A.H. Pilon-Smits, and M.P. Simmons. 2015. Evolution of selenium hyperaccumulation in Stanleya (Brassicaceae) as inferred from phylogeny, physiology and X-ray microprobe analysis. New Phytologist 205: 583-595.

87. Simmons, M.P. and J. Gatesy. 2015. Coalescence vs. concatenation: sophisticated analyses vs. first principles applied to rooting the angiosperms. Molecular Phylogenetics and Evolution 91: 98-122.

88. Simmons, M.P. 2015. Ten simple rules for writing a reply paper. PLoS Computational Biology 11: e1004536.

89. Bacon, C.D., M.P. Simmons, R.H. Archer, L. Zhao, and J. Andriantiana. 2016. Biogeography of the Malagasy Celastraceae: multiple independent origins followed by widespread dispersal of genera from Madagascar. Molecular Phylogenetics and Evolution 94: 365-382.

90. Judd, C.R., A. Koyama, M.P. Simmons, P. Brewer, J.C. von Fischer. 2016. Co-variation in methanotroph community composition and activity in three temperate grassland soils. Soil Biology & Biochemistry 95: 78-86.

91. Simmons, M.P., D.B. Sloan, and J. Gatesy. 2016. The effects of subsampling gene trees on coalescent methods applied to ancient divergences. Molecular Phylogenetics and Evolution 97: 76-89.

92. Warren, J.M., M.P. Simmons, Z. Wu, and D.B. Sloan. 2016. Linear plasmids and the rate of sequence evolution in plant mitochondrial genomes. Genome Biology and Evolution 8: 364-374.

93. Gu, C., L.R. Tembrock, N.G. Johnson, M.P. Simmons, and Z. Wu. 2016. The complete plastid genome of Lagerstroemia fauriei and loss of an rpl2 intron from Lagerstroemia (Lythraceae). PLOS One 11: e0150752.

94. Simmons, M.P. and J. Gatesy. 2016. Biases of tree-independent-character-subsampling methods. Molecular Phylogenetics and Evolution 100: 424-443.

95. Gill, B.A., B.C. Kondratieff, K.L. Casner, A.C. Encalada, A.S. Flecker, D.G. Gannon, C.K. Ghalambor, J.M. Guayasamin, N.L. Poff, M.P. Simmons, S.A. Thomas, K.R. Zamudio, and W.C. Funk. 2016. Cryptic species diversity reveals biogeographic support for the ‘mountain passes are higher in the tropics’ hypothesis. Proceedings of the Royal Society B: Biological Sciences 283: 20160553.

96. Darbyshire, I., M.P. Simmons, J.J. Cappa, F.J. Breteler, and S. Buerki. 2016. A questionable African species of Pleurostylia is actually a member of the New World Crossopetalum (Celastraceae). Systematic Botany 41: 851-864.

97. Buddenhagen, C., A.R. Lemmon, E.M. Lemmon, J. Bruhl, J.J. Cappa, M.J. Donoghue, E.J. Edwards, A. Hipp, M. Kortyna, N. Mitchell, C. Prychid, M.P. Simmons, P. Soltis, S. Wanke, and A. Mast. 2016. Anchored phylogenomics of angiosperms I: assessing the robustness of phylogenetic estimates. bioRxiv.

98. Simmons, M.P. 2017. Relative benefits of amino-acid, codon, degeneracy, DNA, and purine-pyrimidine character coding for phylogenetic analyses of exons. Journal of Systematics and Evolution 55: 85-109.

99. Tembrock, L.R., M.P. Simmons, C.M. Richards, P.A. Reeves, A. Reilley, M.A. Curto, H. Meimberg, G. Ngugi, S. Demissew, A.W. Al Khulaidi, M. Althobhani, S. Simpson, and D.M. Varisco. 2017. Phylogeography of the wild and cultivated stimulant plant qat (Catha edulis, Celastraceae) in areas of historic cultivation. American Journal of Botany 104: 538-549.

100. Gatesy, J., R.W. Meredith, J.E. Janecka, M.P. Simmons, W.J. Murphy, and M.S. Springer. 2017. Resolution of a concatenation/coalescence kerfuffle: partititioned coalescence support and a robust family-level tree for Mammalia. Cladistics 33: 295-332.

101. Tembrock, L.R., C.D. Broeckling, A.L. Heuberger, M.P. Simmons, F.R. Stermitz, and J. Uvarov. 2017. Employing GC-MS and two-stage derivatization to assay for cathine and related stimulant alkaloids across the Celastraceae. Phytochemical Analysis 28: 257-266.

102. Simmons, M.P. 2017. Mutually exclusive phylogenetic inferences from both nuclear and plastid genomic datasets at the root of the angiosperms: Amborella is supported as sister and Observed Variability is biased. Cladistics 33: 488-512.

103. Biral, L., M.P. Simmons, E.C. Smidt, M. Bolson, L.R. Tembrock, R.H. Archer, and J.A. Lombardi. 2017. Systematics of New World Maytenus (Celastraceae) and a new delimitation of the genus. Systematic Botany 42: 680-693.

104. Simmons, M.P. 2018.  Ten rules for associate editors. Botanical Review 84: 99-107.

105. Wang, J., J.J. Cappa, J. Harris, P.P. Edger, W. Zhou, J.C. Pires, M. Adair, S.A. Unruh, M.P. Simmons, M. Schiavon, and E.A.H. Pilon-Smits. 2018. Transcriptome-wide comparison of selenium hyperaccumulator and non-accumulator Stanleya species provides new insight into key processes mediating the hyperaccumulation syndrome. Plant Biotechnology Journal 16: 1582-1594.

106. Polato, N.R., B.A Gill, A.A. Shah, M.M. Gray, KL. Casner, A. Barthelet, P.W. Messer, M.P. Simmons, J.M. Guayasamin, A.C. Encalada, B.C. Kondratieff, A.S. Flecker, S.A. Thomas, C.K. Ghalambor, N.L. Poff, W.C. Funk, and K.R. Zamudio. 2018. Narrow thermal tolerance and low dispersal drive diversification in tropical mountains. Proceedings of the National Academy of Sciences of the U.S.A. 115: 12471-12476.

107. Simmons, M.P., D.B. Sloan, M.S. Springer, and J. Gatesy. 2019. Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses. Molecular Phylogenetics and Evolution 131: 80-92.

108. Gatesy, J., D.B. Sloan, J.M. Warren, R.H. Baker, M.P. Simmons, and M.S. Springer. 2019. Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts. Molecular Phylogenetics and Evolution 139: 106539.

109. Li, M., H. Zhao, F. Zhao, L. Jiang, H. Peng, W. Zhang, and M.P. Simmons. 2019. Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae). Annals of Botany 124: 233-243.

110. Zhang, X., Y. Cao, W. Zhang, and M.P. Simmons. 2020. Adenine•cytosine substitutions are an alternative pathway of compensatory mutation in angiosperm ITS2. RNA 26: 209-217.

111. Springer, M.S., E.K. Molloy, D.B. Sloan, M.P. Simmons, and J. Gatesy. 2020.  ILS-aware analysis of low-homoplasy retroelement insertions: inference of species trees and introgression using quartets. Journal of Heredity 111: 147-168.

112. Simmons, M.P. and J. Kessenich. 2020. Divergence and support among slightly suboptimal likelihood gene trees. Cladistics 36: 322-340.

113. Cámara-Leret, R., [97 co-authors including M.P. Simmons]. 2020. New Guinea has the world’s richest island flora. Nature 584: 579-583.

114. Jallet, D., D. Xing, A. Hughes, M. Moosburner, M.P. Simmons, A.E. Allen, and G. Peers. 2020. The marine diatom Phaeodactylum tricornutum utilizes a mitochondria-located β-oxidation cycle for the catabolism of fatty acids released from storage lipids. New Phytologist 228: 946-958.

115. Tembrock, L.R. M.P. Simmons, C.M. Richards, P.A. Reeves, A. Reilley, M.A. Curto, H. Meimberg, G. Ngugi, Sebsebe Demissew, A.W. Al Khulaidi, M. Al-Thobhani, S. Simpson, and D.M. Varisco. 2020. Clonal diversity, cultivar traits, geographic dispersal, and the ethnotaxonomy of cultivated qat (Catha edulis, Celastraceae). Economic Botany 74: 273-291.

116. Ackerfield, J.R., D.J. Keil, W.C. Hodgson, M.P. Simmons, S.D. Fehlberg, and V.A. Funk. 2020. Thistle be a mess: untangeling the taxonomy of Cirsium (Cardueae: Compositae) in North America. Journal of Systematics and Evolution 58: 881-912.  

117. Simmons, M.P. and J. Gatesy. 2021. Collapsing dubiously resolved gene-tree branches in phylogenomic coalescent analyses. Molecular Phylogenetics and Evolution 158: 107092.

118. Simmons, M.P., M.S. Springer, and J. Gatesy. 2022. Gene-tree misrooting drives conflict in phylogenomic coalescent analyses of palaeognath birds. Molecular Phylogenetics and Evolution 167: 107344.

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