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Mark P. Simmons · SciRah

Researcher profile · Semantic Scholar

Mark P. Simmons

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Mark P. Simmons — researcher profile on SciRah

h-index: 46
Works: 125
Citations: 10K

Most-cited papers

Functional trait niches of North American lotic insects: traits-based ecological applications in light of phylogenetic relationships
N. Poff, J. Olden, Nicole K. M. Vieira, D. Finn +2 more
2006Journal of The North American Benthological Society851 citations Open access
Semantic Scholar
Phylogenomics and the rise of the angiosperms
A. Zuntini, Tom Carruthers, Olivier Maurin, P. Bailey +275 more
2024Nature349 citations Open access
Semantic Scholar
Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains
N. Polato, Brian A. Gill, Alisha A. Shah, Miranda M. Gray +13 more
2018Proceedings of the National Academy of Sciences of the United States of America228 citations Open access
Semantic Scholar
New Guinea has the world’s richest island flora
R. Cámara‐Leret, D. Frodin, F. Adema, C. Anderson +95 more
2020Nature181 citations Open access
Semantic Scholar
Phylogeny of the Cucurbitales based on DNA sequences of nine loci from three genomes: implications for morphological and sexual system evolution.
Li-Bing Zhang, Mark P. Simmons, A. Kocyan, S. Renner
2006Molecular Phylogenetics and Evolution133 citations
Semantic Scholar
Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes
Dale N. Richardson, Mark P. Simmons, A. Reddy
2006BMC Genomics125 citations Open access
Semantic Scholar
Misleading results of likelihood‐based phylogenetic analyses in the presence of missing data
Mark P. Simmons
2012Cladistics117 citations Open access
Semantic Scholar
The relative performance of indel-coding methods in simulations.
Mark P. Simmons, K. Müller, A. Norton
2007Molecular Phylogenetics and Evolution106 citations
Semantic Scholar
Phylogeny and Delimitation of the Celastrales Inferred from Nuclear and Plastid Genes
Li-Bing Zhang, Mark P. Simmons
200697 citations
Semantic Scholar
Cryptic species diversity reveals biogeographic support for the ‘mountain passes are higher in the tropics’ hypothesis
Brian A. Gill, B. Kondratieff, K. L. Casner, A. Encalada +9 more
2016Proceedings of the Royal Society of London. Biological Sciences91 citations Open access
Semantic Scholar
Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms.
Mark P. Simmons, J. Gatesy
2015Molecular Phylogenetics and Evolution90 citations
Semantic Scholar
Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae).
C. Bacon, W. Baker, Mark P. Simmons
2012Systematic Biology86 citations Open access
Semantic Scholar
Transcriptome‐wide comparison of selenium hyperaccumulator and nonaccumulator Stanleya species provides new insight into key processes mediating the hyperaccumulation syndrome
Jiameng Wang, J. Cappa, Jonathan P Harris, P. Edger +7 more
2018Plant Biotechnology Journal84 citations Open access
Semantic Scholar
Phylogeny of the Celastreae (Celastraceae) and the relationships of Catha edulis (qat) inferred from morphological characters and nuclear and plastid genes.
Mark P. Simmons, J. Cappa, R. Archer, A. Ford +2 more
2008Molecular Phylogenetics and Evolution81 citations
Semantic Scholar
Molecular analyses of the Chinese herb Leigongteng (Tripterygium wilfordii Hook.f.).
Sue Ka-Yee Law, Mark P. Simmons, N. Techen, I. Khan +3 more
2011Phytochemistry79 citations
Semantic Scholar
Anchored Phylogenomics of Angiosperms I: Assessing the Robustness of Phylogenetic Estimates
Christopher E. Buddenhagen, A. Lemmon, E. Lemmon, J. Bruhl +14 more
2016bioRxiv78 citations Open access
Semantic Scholar
Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data.
Mark P. Simmons
2012Molecular Phylogenetics and Evolution78 citations
Semantic Scholar
Spurious 99% bootstrap and jackknife support for unsupported clades.
Mark P. Simmons, J. Freudenstein
2011Molecular Phylogenetics and Evolution78 citations
Semantic Scholar
Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family‐level tree for Mammalia
J. Gatesy, Robert W. Meredith, J. Janecka, Mark P. Simmons +2 more
2017Cladistics76 citations
Semantic Scholar
A Thorny Dilemma: Testing Alternative Intrageneric Classifications within Ziziphus (Rhamnaceae)
Melissa B. Islam, Mark P. Simmons
200671 citations
Semantic Scholar
A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference.
Mark P. Simmons, Li-Bing Zhang, C. Webb, K. Müller
2007Molecular Phylogenetics and Evolution68 citations
Semantic Scholar
Rapid Intraspecific Evolution of miRNA and siRNA Genes in the Mosquito Aedes aegypti
S. A. Bernhardt, Mark P. Simmons, K. Olson, B. Beaty +2 more
2012PLoS ONE60 citations Open access
Semantic Scholar
Divergent maximum-likelihood-branch-support values for polytomies.
Mark P. Simmons, A. Norton
2014Molecular Phylogenetics and Evolution59 citations
Semantic Scholar
Characterization of selenium and sulfur accumulation across the genus Stanleya (Brassicaceae): A field survey and common-garden experiment.
J. Cappa, P. Cappa, A. F. El-Mehdawi, Jenna M. McAleer +2 more
2014American-Eurasian journal of botany58 citations Open access
Semantic Scholar
Congruence of Molecular, Morphological, and Biochemical Profiles in Rutaceae: a Cladistic Analysis of the Subfamilies Rutoideae and Toddalioideae
Wing-Sem Poon, P. Shaw, Mark P. Simmons, P. But
200755 citations
Semantic Scholar
A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses.
Mark P. Simmons
2014Molecular Phylogenetics and Evolution50 citations
Semantic Scholar
Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia)
C. Bacon, M. McKenna, Mark P. Simmons, W. Wagner
2012BMC Evolutionary Biology49 citations Open access
Semantic Scholar
The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae)
Cui-Hua Gu, L. R. Tembrock, Nels G. Johnson, Mark P. Simmons +1 more
2016PLoS ONE47 citations Open access
Semantic Scholar
GEOGRAPHIC AND TAXONOMIC DISPARITIES IN SPECIES DIVERSITY: DISPERSAL AND DIVERSIFICATION RATES ACROSS WALLACE'S LINE
C. Bacon, François Michonneau, A. Henderson, M. McKenna +2 more
2013Evolution; international journal of organic evolution47 citations
Semantic Scholar
Phylogeny of the Asian Hedyotis-Oldenlandia complex (Spermacoceae, Rubiaceae): evidence for high levels of polyphyly and the parallel evolution of diplophragmous capsules.
Xing Guo, Rui-Jiang Wang, Mark P. Simmons, P. But +1 more
2013Molecular Phylogenetics and Evolution47 citations
Semantic Scholar
Collapsing dubiously resolved gene-tree branches in phylogenomic coalescent analyses.
Mark P. Simmons, J. Gatesy
2021Molecular Phylogenetics and Evolution46 citations
Semantic Scholar
The effects of subsampling gene trees on coalescent methods applied to ancient divergences.
Mark P. Simmons, Daniel B. Sloan, J. Gatesy
2016Molecular Phylogenetics and Evolution46 citations Open access
Semantic Scholar
Evolution of selenium hyperaccumulation in Stanleya (Brassicaceae) as inferred from phylogeny, physiology and X-ray microprobe analysis.
J. Cappa, Crystal Yetter, S. Fakra, P. Cappa +4 more
2015New Phytologist44 citations Open access
Semantic Scholar
Delimitation of the Segregate Genera of Maytenus s. l. (Celastraceae) Based on Morphological and Molecular Characters
M. McKenna, Mark P. Simmons, C. Bacon, J. A. Lombardi
201144 citations
Semantic Scholar
Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes.
Mark P. Simmons, M. McKenna, C. Bacon, K. Yakobson +3 more
2012Molecular Phylogenetics and Evolution43 citations
Semantic Scholar
Application of DNA barcodes in Hedyotis L. (Spermacoceae, Rubiaceae)
Xing Guo, Mark P. Simmons, Paul Pui-Hay But, P. Shaw +1 more
201139 citations Open access
Semantic Scholar
Are mitochondrial genes useful for the analysis of monocot relationships
Jerrold I. Davis, G. Petersen, O. Seberg, D. Stevenson +7 more
200639 citations
Semantic Scholar
How can third codon positions outperform first and second codon positions in phylogenetic inference? An empirical example from the seed plants.
Mark P. Simmons, Li-Bing Zhang, C. Webb, Aaron Reeves
2006Systematic Biology38 citations
Semantic Scholar
Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts
J. Gatesy, Daniel B. Sloan, J. Warren, R. Baker +2 more
2018bioRxiv36 citations Open access
Semantic Scholar
Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses.
Mark P. Simmons, Daniel B. Sloan, M. Springer, J. Gatesy
2019Molecular Phylogenetics and Evolution35 citations Open access
Semantic Scholar
ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets.
M. Springer, E. Molloy, Daniel B. Sloan, Mark P. Simmons +1 more
2019Journal of Heredity35 citations Open access
Semantic Scholar
Phylogeny of Celastraceae Subfamily Salacioideae and Tribe Lophopetaleae Inferred from Morphological Characters and Nuclear and Plastid Genes
Jennifer M. Coughenour, Mark P. Simmons, J. A. Lombardi, J. Cappa
201034 citations
Semantic Scholar
Co-variation in methanotroph community composition and activity in three temperate grassland soils
C. Judd, A. Koyama, Mark P. Simmons, Paul E. Brewer +1 more
201632 citations
Semantic Scholar
Systematics of New World Maytenus (Celastraceae) and a New Delimitation of the Genus
L. Biral, Mark P. Simmons, E. Smidt, L. R. Tembrock +3 more
2017Systematic Botany31 citations
Semantic Scholar
Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar.
C. Bacon, Mark P. Simmons, R. Archer, Liang-Cheng Zhao +1 more
2016Molecular Phylogenetics and Evolution31 citations Open access
Semantic Scholar
Quantification of the success of phylogenetic inference in simulations
Mark P. Simmons, C. Webb
200631 citations Open access
Semantic Scholar
Phylogeny of Celastraceae Subfamilies Cassinoideae and Tripterygioideae Inferred from Morphological Characters and Nuclear and Plastid Loci
Mark P. Simmons, C. Bacon, J. Cappa, M. McKenna
201230 citations
Semantic Scholar
Mitochondrial fatty acid β-oxidation is required for storage lipid catabolism in a marine diatom.
Denis Jallet, Deng-Hui Xing, Alexander Hughes, Mark Moosburner +3 more
2020New Phytologist29 citations
Semantic Scholar
Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes
J. Warren, Mark P. Simmons, Zhi-Qiang Wu, Daniel B. Sloan
2016Genome Biology and Evolution29 citations Open access
Semantic Scholar
Dubious resolution and support from published sparse supermatrices: the importance of thorough tree searches.
Mark P. Simmons, P. Goloboff
2014Molecular Phylogenetics and Evolution29 citations Open access
Semantic Scholar

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