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. Simmons, M.P. and J. Gatesy. 2016. Biases of tree-independent-character-subsampling methods. Molecular Phylogenetics and Evolution 100: 424-443. 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. 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. 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. 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. 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. Simmons, M.P. 2015. Ten simple rules for writing a reply paper. PLoS Computational Biology 11: e1004536. 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. 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. Goloboff, P.A. and M.P. Simmons. 2014. Bias in tree searches, and its consequences for measuring group supports. Systematic Biology 63: 851-861. 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. 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. Simmons, M.P. and C.P. Randle. 2014. Disparate parametric branch-support values from ambiguous characters. Molecular Phylogenetics and Evolution 78: 66-86. 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. 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. Simmons, M.P. 2014. Limitations of locally sampled characters in phylogenetic analyses of sparse supermatrices. Molecular Phylogenetics and Evolution 74: 1-14. Simmons, M.P. and A.P. Norton. 2014. Divergent maximum-likelihood-branch-support values for polytomies. Molecular Phylogenetics and Evolution 73: 87-96. 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. 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. 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. 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. 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. 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. 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.