Works by Simmons, Mark P.

Results: 50

How Meaningful Are Bayesian Support Values?

Published in:

Molecular Biology & Evolution, 2004, v. 21, n. 1, p. 188, doi. 10.1093/molbev/msh014

By:

Simmons, Mark P.;
Pickett, Kurt M.;
Miya, Masaki

Publication type:

Article

Limitations of Relative Apparent Synapomorphy Analysis (RASA) for Measuring Phylogenetic Signal.

Published in:

Molecular Biology & Evolution, 2002, v. 19, n. 1, p. 14, doi. 10.1093/oxfordjournals.molbev.a003978

By:

Simmons, Mark P.;
Randle, Christopher P.;
Freudenstein, John V.;
Wenzel, John W.

Publication type:

Article

Phylogeny Reconstruction Using Duplicate Genes.

Published in:

Molecular Biology & Evolution, 2000, v. 17, n. 4, p. 469, doi. 10.1093/oxfordjournals.molbev.a026327

By:

Simmons, Mark P.;
Donovan Bailey, C.;
Nixon, Kevin C.

Publication type:

Article

Employing Two-stage Derivatisation and GC-MS to Assay for Cathine and Related Stimulant Alkaloids across the Celastraceae.

Published in:

Phytochemical Analysis, 2017, v. 28, n. 4, p. 257, doi. 10.1002/pca.2671

By:

Tembrock, Luke R.;
Broeckling, Corey D.;
Heuberger, Adam L.;
Simmons, Mark P.;
Stermitz, Frank R.;
Uvarov, Jessica M.

Publication type:

Article

CHARACTERIZATION OF SELENIUM AND SULFUR ACCUMULATION ACROSS THE GENUS STANLEYA (BRASSICACEAE): A FIELD SURVEY AND COMMON-GARDEN EXPERIMENT.

Published in:

American Journal of Botany, 2014, v. 101, n. 5, p. 830, doi. 10.3732/ajb.1400041

By:

Cappa, Jennifer J.;
Cappa, Patrick J.;
El Mehdawi, Ali F.;
McAleer, Jenna M.;
Simmons, Mark P.;
Pilon‐Smits, Elizabeth A. H.

Publication type:

Article

DEVELOPMENT OF MICROSATELLITES IN THE HAWAIIAN ENDEMIC PALM PRITCHARDIA MARTII (ARECACEAE) AND THEIR UTILITY IN CONGENERS.

Published in:

American Journal of Botany, 2011, v. 98, n. 6, p. e139, doi. 10.3732/ajb.1100073

By:

BACON, CHRISTINE D.;
JOHNSON, GABRIEL P.;
MEIMBERG, HARALD;
PUPPO, PAMELA;
SIMMONS, MARK P.;
WAGNER, WARREN L.

Publication type:

Article

PHYLOGENY OF THE CELASTRACEAE INFERRED FROM PHYTOCHROME B GENE SEQUENCE AND MORPHOLOGY.

Published in:

American Journal of Botany, 2001, v. 88, n. 2, p. 313, doi. 10.2307/2657021

By:

Simmons, Mark P.;
Clevinger, Curtis C.

Publication type:

Article

Mitochondrial fatty acid β‐oxidation is required for storage‐lipid catabolism in a marine diatom.

Published in:

New Phytologist, 2020, v. 228, n. 3, p. 946, doi. 10.1111/nph.16744

By:

Jallet, Denis;
Xing, Denghui;
Hughes, Alexander;
Moosburner, Mark;
Simmons, Mark P.;
Allen, Andrew E.;
Peers, Graham

Publication type:

Article

Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes.

Published in:

Genome Biology & Evolution, 2016, v. 8, n. 2, p. 364, doi. 10.1093/gbe/evw003

By:

Warren, Jessica M.;
Simmons, Mark P.;
Zhiqiang Wu;
Sloan, Daniel B.

Publication type:

Article

The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae).

Published in:

PLoS ONE, 2016, v. 11, n. 3, p. 1, doi. 10.1371/journal.pone.0150752

By:

Gu, Cuihua;
Tembrock, Luke R.;
Johnson, Nels G.;
Simmons, Mark P.;
Wu, Zhiqiang

Publication type:

Article

Thistle be a mess: Untangling the taxonomy of Cirsium (Cardueae: Compositae) in North America.

Published in:

Journal of Systematics & Evolution, 2020, v. 58, n. 6, p. 881, doi. 10.1111/jse.12692

By:

Ackerfield, Jennifer R.;
Keil, David J.;
Hodgson, Wendy C.;
Simmons, Mark. P.;
Fehlberg, Shannon D.;
Funk, Vicki A.

Publication type:

Article

Relative benefits of amino-acid, codon, degeneracy, DNA, and purine-pyrimidine character coding for phylogenetic analyses of exons.

Published in:

Journal of Systematics & Evolution, 2017, v. 55, n. 2, p. 85, doi. 10.1111/jse.12233

By:

Simmons, Mark P.

Publication type:

Article

Application of DNA barcodes in Hedyotis L. (Spermacoceae, Rubiaceae).

Published in:

Journal of Systematics & Evolution, 2011, v. 49, n. 3, p. 203, doi. 10.1111/j.1759-6831.2011.00130.x

By:

Xing GUO;
SIMMONS, Mark P.;
Paul Pui-Hay BUT;
Pang-Chui SHAW;
Rui-Jiang WANG

Publication type:

Article

Contribution of molecular cladistics to the taxonomy of Rutaceae in China*.

Published in:

Journal of Systematics & Evolution, 2009, v. 47, n. 2, p. 144, doi. 10.1111/j.1759-6831.2009.00013.x

By:

BUT, Paul Pui-Hay;
POON, Alice Wing-Sem;
SHAW, Pang-Chui;
SIMMONS, Mark P.;
GREGER, Harald

Publication type:

Article

Phylogeography of the wild and cultivated stimulant plant qat (Catha edulis, Celastraceae) in areas of historical cultivation.

Published in:

American Journal of Botany, 2017, v. 104, n. 4, p. 538, doi. 10.3732/ajb.1600437

By:

Tembrock, Luke R.;
Simmons, Mark P.;
Richards, Christopher M.;
Reeves, Patrick A.;
Reilley, Ann;
Curto, Manuel A.;
Meimberg, Harald;
Ngugi, Grace;
Demissew, Sebsebe;
Al Khulaidi, Abdul Wali;
Al‐Thobhani, Mansoor;
Simpson, Sheron;
Varisco, Daniel M.

Publication type:

Article

Molecular phylogeny and revised classification of Eucosma Hübner and related genera ( Lepidoptera: Tortricidae: Eucosmini).

Published in:

Systematic Entomology, 2014, v. 39, n. 1, p. 49, doi. 10.1111/syen.12036

By:

GILLIGAN, TODD M.;
WRIGHT, DONALD J.;
MUNZ, JACOB;
YAKOBSON, KENDRA;
SIMMONS, MARK P.

Publication type:

Article

Evolution of selenium hyperaccumulation in Stanleya (Brassicaceae) as inferred from phylogeny, physiology and X-ray microprobe analysis.

Published in:

New Phytologist, 2015, v. 205, n. 2, p. 583, doi. 10.1111/nph.13071

By:

Cappa, Jennifer J.;
Yetter, Crystal;
Fakra, Sirine;
Cappa, Patrick J.;
DeTar, Rachael;
Landes, Corbett;
Pilon‐Smits, Elizabeth A. H.;
Simmons, Mark P.

Publication type:

Article

Ten Rules for Associate Editors.

Published in:

Botanical Review, 2018, v. 84, n. 2, p. 99, doi. 10.1007/s12229-018-9199-4

By:

Simmons, Mark P.

Publication type:

Article

Ten Simple Rules for Writing a Reply Paper.

Published in:

2015

By:

Simmons, Mark P.

Publication type:

Editorial

Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses.

Published in:

Cladistics, 2023, v. 39, n. 5, p. 418, doi. 10.1111/cla.12540

By:

Simmons, Mark P.;
Goloboff, Pablo A.;
Stöver, Ben C.;
Springer, Mark S.;
Gatesy, John

Publication type:

Article

Benefits of alignment quality‐control processing steps and an Angiosperms353 phylogenomics pipeline applied to the Celastrales.

Published in:

Cladistics, 2022, v. 38, n. 5, p. 595, doi. 10.1111/cla.12507

By:

Simmons, Mark P.;
Maurin, Olivier;
Bailey, Paul;
Brewer, Grace E.;
Roy, Shyamali;
Lombardi, Julio A.;
Forest, Félix;
Baker, William J.

Publication type:

Article

Divergence and support among slightly suboptimal likelihood gene trees.

Published in:

Cladistics, 2020, v. 36, n. 3, p. 322, doi. 10.1111/cla.12404

By:

Simmons, Mark P.;
Kessenich, John

Publication type:

Article

Mutually exclusive phylogenomic inferences at the root of the angiosperms: Amborella is supported as sister and Observed Variability is biased.

Published in:

Cladistics, 2017, v. 33, n. 5, p. 488, doi. 10.1111/cla.12177

By:

Simmons, Mark P.

Publication type:

Article

Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family-level tree for Mammalia.

Published in:

Cladistics, 2017, v. 33, n. 3, p. 295, doi. 10.1111/cla.12170

By:

Gatesy, John;
Meredith, Robert W.;
Janecka, Jan E.;
Simmons, Mark P.;
Murphy, William J.;
Springer, Mark S.

Publication type:

Article

Misleading results of likelihood-based phylogenetic analyses in the presence of missing data.

Published in:

Cladistics, 2012, v. 28, n. 2, p. 208, doi. 10.1111/j.1096-0031.2011.00375.x

By:

Simmons, Mark P.

Publication type:

Article

Phylogenetic inference using non-redundant coding of dependent characters versus alternative approaches for protein-coding genes.

Published in:

Cladistics, 2011, v. 27, n. 2, p. 186, doi. 10.1111/j.1096-0031.2010.00327.x

By:

Simmons, Mark P.;
Li-Bing Zhang;
Müller, Kai F.

Publication type:

Article

The deterministic effects of alignment bias in phylogenetic inference.

Published in:

Cladistics, 2011, v. 27, n. 4, p. 402, doi. 10.1111/j.1096-0031.2010.00333.x

By:

Simmons, Mark P.;
Müller, Kai F.;
Webb, Colleen T.

Publication type:

Article

The relative sensitivity of different alignment methods and character codings in sensitivity analysis.

Published in:

2008

By:

Simmons, Mark P.;
Müller, Kai F.;
Webb, Colleen T.

Publication type:

Letter

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.

Published in:

Cladistics, 2008, v. 24, n. 3, p. 372, doi. 10.1111/j.1096-0031.2007.00183.x

By:

Simmons, Mark P.;
Richardson, Dale;
Reddy, Anireddy S. N.

Publication type:

Article

The relative performance of Bayesian and parsimony approaches when sampling characters evolving under homogeneous and heterogeneous sets of parameters.

Published in:

Cladistics, 2006, v. 22, n. 2, p. 171, doi. 10.1111/j.1096-0031.2006.00098.x

By:

Simmons, Mark P.;
Zhang, Li-Bing;
Webb, Colleen T.;
Reeves, Aaron;
Miller, Jeremy A.

Publication type:

Article

Quantification of the success of phylogenetic inference in simulations.

Published in:

Cladistics, 2006, v. 22, n. 3, p. 249, doi. 10.1111/j.1096-0031.2006.00105.x

By:

Simmons, Mark P.;
Webb, Colleen T.

Publication type:

Article

Character-state space versus rate of evolution in phylogenetic inference.

Published in:

Cladistics, 2004, v. 20, n. 2, p. 191, doi. 10.1111/j.1096-0031.2004.00014.x

By:

Simmons, Mark P.;
Reeves, Aaron;
Davis, Jerrold I.

Publication type:

Article

From basepairs to birdsongs: phylogenetic data in the age of genomics

Published in:

Cladistics, 2003, v. 19, n. 4, p. 333, doi. 10.1111/j.1096-0031.2003.tb00377.x

By:

Freudenstein, John V.;
Pickett, Kurt M.;
Simmons, Mark P.;
Wenzel, John W.

Publication type:

Article

Artifacts of Coding Amino Acids and Other Composite Characters for Phylogenetic Analysis

Published in:

Cladistics, 2002, v. 18, n. 3, p. 354, doi. 10.1111/j.1096-0031.2002.tb00156.x

By:

Simmons, Mark P.;
Freudenstein, John V.

Publication type:

Article

Conflict between Amino Acid and Nucleotide Characters

Published in:

Cladistics, 2002, v. 18, n. 2, p. 200, doi. 10.1111/j.1096-0031.2002.tb00148.x

By:

Simmons, Mark P.;
Ochoterena, Helga;
Freudenstein, John V.

Publication type:

Article

A Fundamental Problem with Amino-Acid-Sequence Characters for Phylogenetic Analyses.

Published in:

Cladistics, 2000, v. 16, n. 3, p. 274, doi. 10.1111/j.1096-0031.2000.tb00283.x

By:

Simmons, Mark P.

Publication type:

Article

ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets.

Published in:

Journal of Heredity, 2020, v. 111, n. 2, p. 147, doi. 10.1093/jhered/esz076

By:

Springer, Mark S;
Molloy, Erin K;
Sloan, Daniel B;
Simmons, Mark P;
Gatesy, John

Publication type:

Article

Haydenoxylon, a Replacement Name for Haydenia (Celastraceae).

Published in:

Novon, 2014, v. 23, n. 2, p. 224, doi. 10.3417/2014011

By:

Simmons, Mark P.;
Barrie, Fred R.

Publication type:

Article

Are mitochondrial genes useful for the analysis of monocot relationships?

Published in:

Taxon, 2006, v. 55, n. 4, p. 857, doi. 10.2307/25065681

By:

Davis, Jerrold I.;
Petersen, Gitte;
Seberg, Ole;
Stevenson, Dennis W.;
Hardy, Christopher R.;
Simmons, Mark P.;
Michelangeli, Fabian A.;
Goldman, Douglas H.;
Campbell, Lisa M.;
Specht, Chelsea D.;
Cohen, James I.

Publication type:

Article

Transcriptome‐wide comparison of selenium hyperaccumulator and nonaccumulator Stanleya species provides new insight into key processes mediating the hyperaccumulation syndrome.

Published in:

Plant Biotechnology Journal, 2018, v. 16, n. 9, p. 1582, doi. 10.1111/pbi.12897

By:

Wang, Jiameng;
Cappa, Jennifer J.;
Harris, Jonathan P.;
Edger, Patrick P.;
Zhou, Wen;
Pires, J. Chris;
Adair, Michael;
Unruh, Sarah A.;
Simmons, Mark P.;
Schiavon, Michela;
Pilon‐Smits, Elizabeth A. H.

Publication type:

Article

Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae).

Published in:

Annals of Botany, 2019, v. 124, n. 2, p. 233, doi. 10.1093/aob/mcz062

By:

Li, Meihui;
Zhao, Hong;
Zhao, Fengxi;
Jiang, Lu;
Peng, Huasheng;
Zhang, Wei;
Simmons, Mark P

Publication type:

Article

Rapid Intraspecific Evolution of miRNA and siRNA Genes in the Mosquito Aedes aegypti.

Published in:

PLoS ONE, 2012, v. 7, n. 9, p. 1, doi. 10.1371/journal.pone.0044198

By:

Bernhardt, Scott A.;
Simmons, Mark P.;
Olson, Ken E.;
Beaty, Barry J.;
Blair, Carol D.;
Black, William C.;
Brooke, Basil

Publication type:

Article

Clonal Diversity, Cultivar Traits, Geographic Dispersal, and the Ethnotaxonomy of Cultivated Qat (Catha edulis, Celastraceae).

Published in:

Economic Botany, 2020, v. 74, n. 3, p. 273, doi. 10.1007/s12231-020-09501-4

By:

Tembrock, Luke R.;
Simmons, Mark P.;
Richards, Christopher M.;
Reeves, Patrick A.;
Reilley, Ann;
Curto, Manuel A.;
Meimberg, Harald;
Ngugi, Grace;
Demissew, Sebsebe;
Al-Khulaidi, Abdul Wali;
Al-Thobhani, Mansoor;
Simpson, Sheron;
Varisco, Daniel M.

Publication type:

Article

Bias in Tree Searches and its Consequences for Measuring Group Supports.

Published in:

Systematic Biology, 2014, v. 63, n. 6, p. 851, doi. 10.1093/sysbio/syu051

By:

Goloboff, Pablo A.;
Simmons, Mark P.

Publication type:

Article

Miocene Dispersal Drives Island Radiations in the Palm Tribe Trachycarpeae (Arecaceae).

Published in:

Systematic Biology, 2012, v. 61, n. 3, p. 426, doi. 10.1093/sysbio/syr123

By:

Bacon, Christine D.;
Baker, William J.;
Simmons, Mark P.

Publication type:

Article

How Can Third Codon Positions Outperform First and Second Codon Positions in Phylogenetic Inference? An Empirical Example from the Seed Plants.

Published in:

Systematic Biology, 2006, v. 55, n. 2, p. 245, doi. 10.1080/10635150500481473

By:

Simmons, Mark P.;
Li-Bing Zhang;
Webb, Colleen T.;
Reeves, Aaron

Publication type:

Article

Incorporation, Relative Homoplasy, and Effect of Gap Characters in Sequence-Based Phylogenetic Analyses.

Published in:

Systematic Biology, 2001, v. 50, n. 3, p. 454, doi. 10.1080/106351501300318049

By:

Simmons, Mark P.;
Ochoterena, Helga;
Carr, Timothy G.

Publication type:

Article

Gaps as Characters in Sequence-Based Phylogenetic Analyses.

Published in:

Systematic Biology, 2000, v. 49, n. 2, p. 369, doi. 10.1093/sysbio/49.2.369

By:

Simmons, Mark P.;
Ochoterena, Helga

Publication type:

Article

Data Decisiveness, Data Quality, and Incongruence in Phylogenetic Analysis: An Example From the Monocotyledons Using Mitochondrial atp A Sequences.

Published in:

Systematic Biology, 1998, v. 47, n. 2, p. 282, doi. 10.1080/106351598260923

By:

Davis, Jerrold I.;
Simmons, Mark P.;
Stevenson, Dennis W.;
Wendel, Jonathan F.

Publication type:

Article

GEOGRAPHIC AND TAXONOMIC DISPARITIES IN SPECIES DIVERSITY: DISPERSAL AND DIVERSIFICATION RATES ACROSS WALLACE'S LINE.

Published in:

Evolution, 2013, v. 67, n. 7, p. 2058, doi. 10.1111/evo.12084

By:

Bacon, Christine D.;
Michonneau, François;
Henderson, Andrew J.;
McKenna, Miles J.;
Milroy, Arwen M.;
Simmons, Mark P.

Publication type:

Article