| Year |
Citation |
Score |
| 2024 |
Zuntini AR, Carruthers T, Maurin O, Bailey PC, Leempoel K, Brewer GE, Epitawalage N, Françoso E, Gallego-Paramo B, McGinnie C, Negrão R, Roy SR, Simpson L, Toledo Romero E, Barber VMA, ... ... Simmons MP, et al. Phylogenomics and the rise of the angiosperms. Nature. PMID 38658746 DOI: 10.1038/s41586-024-07324-0 |
0.329 |
|
| 2023 |
Simmons MP, Goloboff PA, Stöver BC, Springer MS, Gatesy J. Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses. Cladistics : the International Journal of the Willi Hennig Society. PMID 37096985 DOI: 10.1111/cla.12540 |
0.322 |
|
| 2021 |
Simmons MP, Freudenstein JV. Artifacts of Coding Amino Acids and Other Composite Characters for Phylogenetic Analysis. Cladistics : the International Journal of the Willi Hennig Society. 18: 354-365. PMID 34911253 DOI: 10.1111/j.1096-0031.2002.tb00156.x |
0.757 |
|
| 2021 |
Simmons MP, Ochoterena H, Freudenstein JV. Conflict between Amino Acid and Nucleotide Characters. Cladistics : the International Journal of the Willi Hennig Society. 18: 200-206. PMID 34911223 DOI: 10.1111/j.1096-0031.2002.tb00148.x |
0.761 |
|
| 2021 |
Simmons MP. A Fundamental Problem with Amino-Acid-Sequence Characters for Phylogenetic Analyses. Cladistics : the International Journal of the Willi Hennig Society. 16: 274-282. PMID 34902932 DOI: 10.1111/j.1096-0031.2000.tb00283.x |
0.304 |
|
| 2021 |
Simmons MP, Reeves A, Davis JI. Character-state space versus rate of evolution in phylogenetic inference. Cladistics : the International Journal of the Willi Hennig Society. 20: 191-204. PMID 34892933 DOI: 10.1111/j.1096-0031.2004.00014.x |
0.643 |
|
| 2021 |
Simmons MP, Springer MS, Gatesy J. Gene-tree misrooting drives conflicts in phylogenomic coalescent analyses of palaeognath birds. Molecular Phylogenetics and Evolution. 107344. PMID 34748873 DOI: 10.1016/j.ympev.2021.107344 |
0.391 |
|
| 2021 |
Simmons MP, Gatesy J. Collapsing dubiously resolved gene-tree branches in phylogenomic coalescent analyses. Molecular Phylogenetics and Evolution. 107092. PMID 33545272 DOI: 10.1016/j.ympev.2021.107092 |
0.383 |
|
| 2020 |
Simmons MP, Kessenich J. Divergence and support among slightly suboptimal likelihood gene trees. Cladistics : the International Journal of the Willi Hennig Society. 36: 322-340. PMID 34618962 DOI: 10.1111/cla.12404 |
0.318 |
|
| 2020 |
Cámara-Leret R, Frodin DG, Adema F, Anderson C, Appelhans MS, Argent G, Arias Guerrero S, Ashton P, Baker WJ, Barfod AS, Barrington D, Borosova R, Bramley GLC, Briggs M, Buerki S, ... ... Simmons MP, et al. New Guinea has the world's richest island flora. Nature. PMID 32760001 DOI: 10.1038/S41586-020-2549-5 |
0.405 |
|
| 2020 |
Jallet D, Xing D, Hughes A, Moosburner M, Simmons MP, Allen AE, Peers G. Mitochondrial fatty acid β-oxidation is required for storage lipid catabolism in a marine diatom. The New Phytologist. PMID 32535932 DOI: 10.1111/Nph.16744 |
0.302 |
|
| 2019 |
Springer MS, Molloy EK, Sloan DB, Simmons MP, Gatesy J. ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets. The Journal of Heredity. PMID 31837265 DOI: 10.1093/Jhered/Esz076 |
0.425 |
|
| 2019 |
Gatesy J, Sloan DB, Warren JM, Baker RH, Simmons MP, Springer MS. Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts. Molecular Phylogenetics and Evolution. 106539. PMID 31226465 DOI: 10.1016/J.Ympev.2019.106539 |
0.474 |
|
| 2019 |
Li M, Zhao H, Zhao F, Jiang L, Peng H, Zhang W, Simmons MP. Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae). Annals of Botany. PMID 31152554 DOI: 10.1093/Aob/Mcz062 |
0.335 |
|
| 2019 |
Simmons MP, Kessenich J. Divergence and support among slightly suboptimal likelihood gene trees Cladistics. 36: 322-340. DOI: 10.1111/Cla.12404 |
0.392 |
|
| 2018 |
Polato NR, Gill BA, Shah AA, Gray MM, Casner KL, Barthelet A, Messer PW, Simmons MP, Guayasamin JM, Encalada AC, Kondratieff BC, Flecker AS, Thomas SA, Ghalambor CK, Poff NL, et al. Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains. Proceedings of the National Academy of Sciences of the United States of America. PMID 30397141 DOI: 10.1073/Pnas.1809326115 |
0.374 |
|
| 2018 |
Simmons MP, Sloan DB, Springer MS, Gatesy J. Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses. Molecular Phylogenetics and Evolution. PMID 30391518 DOI: 10.1016/J.Ympev.2018.10.001 |
0.398 |
|
| 2018 |
Wang J, Cappa JJ, Harris JP, Edger PP, Zhou W, Pires JC, Adair M, Unruh SA, Simmons MP, Schiavon M, Pilon-Smits EAH. Transcriptome-wide comparison of selenium hyperaccumulator and non-accumulator Stanleya species provides new insight into key processes mediating the hyperaccumulation syndrome. Plant Biotechnology Journal. PMID 29412503 DOI: 10.1111/Pbi.12897 |
0.745 |
|
| 2017 |
Gatesy J, Meredith RW, Janecka JE, Simmons MP, Murphy WJ, Springer MS. Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family-level tree for Mammalia. Cladistics : the International Journal of the Willi Hennig Society. 33: 295-332. PMID 34715726 DOI: 10.1111/cla.12170 |
0.339 |
|
| 2017 |
Tembrock LR, Simmons MP, Richards CM, Reeves PA, Reilley A, Curto MA, Meimberg H, Ngugi G, Demissew S, Al Khulaidi AW, Al-Thobhani M, Simpson S, Varisco DM. Phylogeography of the wild and cultivated stimulant plant qat (Catha edulis, Celastraceae) in areas of historical cultivation. American Journal of Botany. PMID 28411209 DOI: 10.3732/Ajb.1600437 |
0.358 |
|
| 2017 |
Tembrock LR, Broeckling CD, Heuberger AL, Simmons MP, Stermitz FR, Uvarov JM. Employing Two-stage Derivatisation and GC-MS to Assay for Cathine and Related Stimulant Alkaloids across the Celastraceae. Phytochemical Analysis : Pca. PMID 28124803 DOI: 10.1002/Pca.2671 |
0.356 |
|
| 2017 |
Biral L, Simmons MP, Smidt EC, Tembrock LR, Bolson M, Archer RH, Lombardi JA. Systematics of New World Maytenus (Celastraceae) and a New Delimitation of the Genus Systematic Botany. 42: 1-14. DOI: 10.1600/036364417X696456 |
0.466 |
|
| 2017 |
Simmons MP. 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. DOI: 10.1111/Jse.12233 |
0.385 |
|
| 2016 |
Gill BA, Kondratieff BC, Casner KL, Encalada AC, Flecker AS, Gannon DG, Ghalambor CK, Guayasamin JM, Poff NL, Simmons MP, Thomas SA, Zamudio KR, Funk WC. Cryptic species diversity reveals biogeographic support for the 'mountain passes are higher in the tropics' hypothesis. Proceedings. Biological Sciences / the Royal Society. 283. PMID 27306051 DOI: 10.1098/Rspb.2016.0553 |
0.428 |
|
| 2016 |
Simmons MP, Gatesy J. Biases of tree-independent-character-subsampling methods. Molecular Phylogenetics and Evolution. PMID 27103257 DOI: 10.1016/J.Ympev.2016.04.022 |
0.443 |
|
| 2016 |
Gu C, Tembrock LR, Johnson NG, Simmons MP, Wu Z. The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae). Plos One. 11: e0150752. PMID 26950701 DOI: 10.1371/Journal.Pone.0150752 |
0.382 |
|
| 2016 |
Simmons MP, Sloan DB, Gatesy J. The effects of subsampling gene trees on coalescent methods applied to ancient divergences. Molecular Phylogenetics and Evolution. PMID 26768112 DOI: 10.1016/J.Ympev.2015.12.013 |
0.402 |
|
| 2016 |
Warren JM, Simmons MP, Wu Z, Sloan DB. Linear plasmids and the rate of sequence evolution in plant mitochondrial genomes. Genome Biology and Evolution. PMID 26759362 DOI: 10.1093/Gbe/Evw003 |
0.399 |
|
| 2016 |
Darbyshire I, Simmons MP, Cappa JJ, Breteler FJ, Buerki S. Pleurostylia serrulata and Two Allied New Species from Africa are Actually Members of the New World Crossopetalum (Celastraceae) Systematic Botany. 41: 851-864. DOI: 10.1600/036364416X693955 |
0.788 |
|
| 2016 |
Simmons MP. Mutually exclusive phylogenomic inferences at the root of the angiosperms: Amborella
is supported as sister and Observed Variability is biased Cladistics. 33: 488-512. DOI: 10.1111/Cla.12177 |
0.333 |
|
| 2016 |
Gatesy J, Meredith RW, Janecka JE, Simmons MP, Murphy WJ, Springer MS. Resolution of a concatenation/coalescence kerfuffle: Partitioned coalescence support and a robust family-level tree for Mammalia Cladistics. DOI: 10.1111/Cla.12170 |
0.448 |
|
| 2015 |
Bacon CD, Simmons MP, Archer RH, Zhao LC, Andriantiana J. Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar. Molecular Phylogenetics and Evolution. PMID 26432393 DOI: 10.1016/J.Ympev.2015.09.013 |
0.452 |
|
| 2015 |
Simmons MP, Gatesy J. Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms. Molecular Phylogenetics and Evolution. 91: 98-122. PMID 26002829 DOI: 10.1016/J.Ympev.2015.05.011 |
0.433 |
|
| 2015 |
Cappa JJ, Yetter C, Fakra S, Cappa PJ, DeTar R, Landes C, Pilon-Smits EA, Simmons MP. Evolution of selenium hyperaccumulation in Stanleya (Brassicaceae) as inferred from phylogeny, physiology and X-ray microprobe analysis. The New Phytologist. 205: 583-95. PMID 25262627 DOI: 10.1111/Nph.13071 |
0.752 |
|
| 2014 |
Simmons MP. A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses. Molecular Phylogenetics and Evolution. 80: 267-80. PMID 25173567 DOI: 10.1016/J.Ympev.2014.08.021 |
0.422 |
|
| 2014 |
Goloboff PA, Simmons MP. Bias in tree searches and its consequences for measuring group supports. Systematic Biology. 63: 851-61. PMID 25074580 DOI: 10.1093/Sysbio/Syu051 |
0.407 |
|
| 2014 |
Simmons MP, Goloboff PA. Dubious resolution and support from published sparse supermatrices: the importance of thorough tree searches. Molecular Phylogenetics and Evolution. 78: 334-48. PMID 24929246 DOI: 10.1016/J.Ympev.2014.06.002 |
0.406 |
|
| 2014 |
Simmons MP, Randle CP. Disparate parametric branch-support values from ambiguous characters. Molecular Phylogenetics and Evolution. 78: 66-86. PMID 24821621 DOI: 10.1016/J.Ympev.2014.04.029 |
0.38 |
|
| 2014 |
Cappa JJ, Cappa PJ, El Mehdawi AF, McAleer JM, Simmons MP, Pilon-Smits EA. Characterization of selenium and sulfur accumulation across the genus Stanleya (Brassicaceae): A field survey and common-garden experiment. American Journal of Botany. 101: 830-839. PMID 24752889 DOI: 10.3732/Ajb.1400041 |
0.71 |
|
| 2014 |
Simmons MP. Limitations of locally sampled characters in phylogenetic analyses of sparse supermatrices. Molecular Phylogenetics and Evolution. 74: 1-14. PMID 24530637 DOI: 10.1016/J.Ympev.2014.01.030 |
0.378 |
|
| 2014 |
Simmons MP, Norton AP. Divergent maximum-likelihood-branch-support values for polytomies. Molecular Phylogenetics and Evolution. 73: 87-96. PMID 24503481 DOI: 10.1016/J.Ympev.2014.01.018 |
0.346 |
|
| 2014 |
Groppo M, Simmons MP, Cappa JJ, Biral L, Lombardi JA. A new species of maytenus (Celastraceae) with fleshy fruits from eastern brazil, with notes on the delimitation of maytenus Systematic Botany. 39: 478-484. DOI: 10.1600/036364414X680726 |
0.788 |
|
| 2013 |
Bacon CD, Michonneau F, Henderson AJ, McKenna MJ, Milroy AM, Simmons MP. Geographic and taxonomic disparities in species diversity: dispersal and diversification rates across Wallace's line. Evolution; International Journal of Organic Evolution. 67: 2058-71. PMID 23815659 DOI: 10.1111/Evo.12084 |
0.392 |
|
| 2013 |
Simmons MP, Goloboff PA. An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters. Molecular Phylogenetics and Evolution. 69: 265-75. PMID 23764338 DOI: 10.1016/J.Ympev.2013.06.001 |
0.382 |
|
| 2013 |
Simmons MP, Norton AP. Quantification and relative severity of inflated branch-support values generated by alternative methods: an empirical example. Molecular Phylogenetics and Evolution. 67: 277-96. PMID 23403225 DOI: 10.1016/J.Ympev.2013.01.020 |
0.378 |
|
| 2013 |
Guo X, Wang RJ, Simmons MP, But PP, Yu J. Phylogeny of the Asian Hedyotis-Oldenlandia complex (Spermacoceae, Rubiaceae): evidence for high levels of polyphyly and the parallel evolution of diplophragmous capsules. Molecular Phylogenetics and Evolution. 67: 110-22. PMID 23333437 DOI: 10.1016/J.Ympev.2013.01.006 |
0.431 |
|
| 2013 |
Simmons MP, Cappa JJ. Wilczekra, a new genus of celastraceae for a disjunct lineage of euonymus Systematic Botany. 38: 148-153. DOI: 10.1600/036364413X661881 |
0.77 |
|
| 2013 |
Curto MA, Tembrock LR, Puppo P, Nogueira M, Simmons MP, Meimberg H. Evaluation of microsatellites of Catha edulis (qat; Celastraceae) identified using pyrosequencing Biochemical Systematics and Ecology. 49: 1-9. DOI: 10.1016/J.Bse.2013.02.002 |
0.35 |
|
| 2012 |
Bacon CD, McKenna MJ, Simmons MP, Wagner WL. Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia). Bmc Evolutionary Biology. 12: 23. PMID 22353848 DOI: 10.1186/1471-2148-12-23 |
0.426 |
|
| 2012 |
Bacon CD, Baker WJ, Simmons MP. Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae). Systematic Biology. 61: 426-42. PMID 22223444 DOI: 10.1093/Sysbio/Syr123 |
0.424 |
|
| 2012 |
Simmons MP. Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data. Molecular Phylogenetics and Evolution. 62: 472-84. PMID 22067131 DOI: 10.1016/J.Ympev.2011.10.017 |
0.366 |
|
| 2012 |
Simmons MP, McKenna MJ, Bacon CD, Yakobson K, Cappa JJ, Archer RH, Ford AJ. Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes. Molecular Phylogenetics and Evolution. 62: 9-20. PMID 22001302 DOI: 10.1016/J.Ympev.2011.08.022 |
0.79 |
|
| 2012 |
Simmons MP, Bacon CD, Cappa JJ, McKenna MJ. Phylogeny of celastraceae subfamilies cassinoideae and tripterygioideae inferred from morphological characters and nuclear and plastid loci Systematic Botany. 37: 456-467. DOI: 10.1600/036364412X635502 |
0.785 |
|
| 2012 |
Simmons MP. Misleading results of likelihood-based phylogenetic analyses in the presence of missing data Cladistics. 28: 208-222. DOI: 10.1111/J.1096-0031.2011.00375.X |
0.367 |
|
| 2011 |
Simmons MP, Freudenstein JV. Spurious 99% bootstrap and jackknife support for unsupported clades. Molecular Phylogenetics and Evolution. 61: 177-91. PMID 21703355 DOI: 10.1016/J.Ympev.2011.06.003 |
0.745 |
|
| 2011 |
Bacon CD, Johnson GP, Meimberg H, Puppo P, Simmons MP, Wagner WL. Development of microsatellites in the Hawaiian endemic palm Pritchardia martii (Arecaceae) and their utility in congeners. American Journal of Botany. 98: e139-40. PMID 21653501 DOI: 10.3732/Ajb.1100073 |
0.393 |
|
| 2011 |
Coughenour JM, Simmons MP, Lombardi JA, Yakobson K, Archer RH. Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid loci. Molecular Phylogenetics and Evolution. 59: 320-30. PMID 21338700 DOI: 10.1016/J.Ympev.2011.02.017 |
0.463 |
|
| 2011 |
Law SK, Simmons MP, Techen N, Khan IA, He MF, Shaw PC, But PP. Molecular analyses of the Chinese herb Leigongteng (Tripterygium wilfordii Hook.f.). Phytochemistry. 72: 21-6. PMID 21094504 DOI: 10.1016/J.Phytochem.2010.10.015 |
0.307 |
|
| 2011 |
McKenna MJ, Simmons MP, Bacon CD, Lombardi JA. Delimitation of the segregate genera of Maytenus s. l. (Celastraceae) based on morphological and molecular characters Systematic Botany. 36: 922-932. DOI: 10.1600/036364411X604930 |
0.39 |
|
| 2011 |
Guo X, Simmons MP, But PPH, Shaw PC, Wang RJ. Application of DNA barcodes in Hedyotis L. (Spermacoceae, Rubiaceae) Journal of Systematics and Evolution. 49: 203-212. DOI: 10.1111/J.1759-6831.2011.00130.X |
0.422 |
|
| 2011 |
Simmons MP, Müller KF, Webb CT. The deterministic effects of alignment bias in phylogenetic inference Cladistics. 27: 402-416. DOI: 10.1111/J.1096-0031.2010.00333.X |
0.407 |
|
| 2011 |
Simmons MP, Zhang LB, Müller KF. Phylogenetic inference using non-redundant coding of dependent characters versus alternative approaches for protein-coding genes Cladistics. 27: 186-196. DOI: 10.1111/J.1096-0031.2010.00327.X |
0.405 |
|
| 2010 |
Simmons MP, Müller KF, Norton AP. 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: 1004-16. PMID 20849963 DOI: 10.1016/J.Ympev.2010.09.004 |
0.392 |
|
| 2010 |
Coughenour JM, Simmons MP, Lombardi JA, Cappa JJ. Phylogeny of celastraceae subfamily salacioideae and tribe lophopetaleae inferred from morphological characters and nuclear and plastid genes Systematic Botany. 35: 358-367. DOI: 10.1600/036364410791638289 |
0.783 |
|
| 2009 |
BUT PP, POON AW, SHAW P, SIMMONS MP, GREGER H. Contribution of molecular cladistics to the taxonomy of Rutaceae in China Journal of Systematics and Evolution. 47: 144-150. DOI: 10.1111/J.1759-6831.2009.00013.X |
0.355 |
|
| 2008 |
Simmons MP. Potential use of host-derived genome signatures to root virus phylogenies. Molecular Phylogenetics and Evolution. 49: 969-78. PMID 18793737 DOI: 10.1016/J.Ympev.2008.08.014 |
0.304 |
|
| 2008 |
Simmons MP, Cappa JJ, Archer RH, Ford AJ, Eichstedt D, Clevinger CC. 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: 745-57. PMID 18550389 DOI: 10.1016/J.Ympev.2008.04.039 |
0.794 |
|
| 2008 |
Simmons MP, Müller KF, Webb CT. The relative sensitivity of different alignment methods and character codings in sensitivity analysis Cladistics. 24: 1039-1050. DOI: 10.1111/J.1096-0031.2008.00230.X |
0.352 |
|
| 2008 |
Simmons MP, Richardson D, Reddy ASN. 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. DOI: 10.1111/J.1096-0031.2007.00183.X |
0.461 |
|
| 2007 |
Simmons MP, Müller K, Norton AP. The relative performance of indel-coding methods in simulations. Molecular Phylogenetics and Evolution. 44: 724-40. PMID 17512758 DOI: 10.1016/J.Ympev.2007.04.001 |
0.324 |
|
| 2007 |
Zhang LB, Simmons MP, Renner SS. A phylogeny of Anisophylleaceae based on six nuclear and plastid loci: ancient disjunctions and recent dispersal between South America, Africa, and Asia. Molecular Phylogenetics and Evolution. 44: 1057-67. PMID 17433719 DOI: 10.1016/J.Ympev.2007.03.002 |
0.453 |
|
| 2007 |
Simmons MP, Zhang LB, Webb CT, Müller K. A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference. Molecular Phylogenetics and Evolution. 42: 528-42. PMID 16997581 DOI: 10.1016/J.Ympev.2006.08.008 |
0.442 |
|
| 2007 |
Poon W, Shaw P, Simmons MP, But PP. Congruence of Molecular, Morphological, and Biochemical Profiles in Rutaceae: a Cladistic Analysis of the Subfamilies Rutoideae and Toddalioideae Systematic Botany. 32: 837-846. DOI: 10.1043/06-48.1 |
0.408 |
|
| 2006 |
Simmons MP, Zhang LB, Webb CT, Reeves A. How can third codon positions outperform first and second codon positions in phylogenetic inference? An empirical example from the seed plants. Systematic Biology. 55: 245-58. PMID 16551581 DOI: 10.1080/10635150500481473 |
0.392 |
|
| 2006 |
Richardson DN, Simmons MP, Reddy AS. Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes. Bmc Genomics. 7: 18. PMID 16448571 DOI: 10.1186/1471-2164-7-18 |
0.362 |
|
| 2006 |
Zhang LB, Simmons MP, Kocyan A, Renner SS. 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: 305-22. PMID 16293423 DOI: 10.1016/J.Ympev.2005.10.002 |
0.478 |
|
| 2006 |
Peterson G, Seberg O, Davis J, Goldman D, Stevenson D, Campbell L, Michaelangeli F, Specht C, Chase M, Fay M, Pires C, Freudenstein J, Hardy C, Simmons M. Mitochondrial Data in Monocot Phylologenetics Aliso. 22: 52-62. DOI: 10.5642/Aliso.20062201.05 |
0.79 |
|
| 2006 |
Davis JI, Petersen G, Seberg O, Stevenson DW, Hardy CR, Simmons MP, Michelangeli FA, Goldman DH, Campbell LM, Specht CD, Cohen JI. Are mitochondrial genes useful for the analysis of monocot relationships? Taxon. 55: 857-870. DOI: 10.2307/25065681 |
0.685 |
|
| 2006 |
Poff NL, Olden JD, Vieira NKM, Finn DS, Simmons MP, Kondratieff BC. Functional trait niches of North American lotic insects: Traits-based ecological applications in light of phylogenetic relationships Journal of the North American Benthological Society. 25: 730-755. DOI: 10.1899/0887-3593(2006)025[0730:Ftnona]2.0.Co;2 |
0.348 |
|
| 2006 |
Islam MB, Simmons MP. A thorny dilemma: Testing alternative intrageneric classifications within Ziziphus (Rhamnaceae) Systematic Botany. 31: 826-842. DOI: 10.1600/036364406779695997 |
0.452 |
|
| 2006 |
Zhang LB, Simmons MP. Phylogeny and delimitation of the celastrales inferred from nuclear and plastid genes Systematic Botany. 31: 122-137. DOI: 10.1600/036364406775971778 |
0.422 |
|
| 2006 |
Simmons MP, Webb CT. Quantification of the success of phylogenetic inference in simulations Cladistics. 22: 249-255. DOI: 10.1111/J.1096-0031.2006.00105.X |
0.4 |
|
| 2006 |
Simmons MP, Zhang LB, Webb CT, Reeves A, Miller JA. The relative performance of Bayesian and parsimony approaches when sampling characters evolving under homogeneous and heterogeneous sets of parameters Cladistics. 22: 171-185. DOI: 10.1111/J.1096-0031.2006.00098.X |
0.342 |
|
| 2006 |
Islam MB, Simmons MP, Archer RH. Phylogeny of the Elaeodendron group (Celastraceae) inferred from morphological characters and nuclear and plastid genes Systematic Botany. 31: 512-524. DOI: 10.1043/05-68.1 |
0.402 |
|
| 2004 |
Simmons MP, Carr TG, O'Neill K. Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters. Molecular Phylogenetics and Evolution. 32: 913-26. PMID 15288066 DOI: 10.1016/J.Ympev.2004.04.011 |
0.4 |
|
| 2004 |
Simmons MP. Independence of alignment and tree search. Molecular Phylogenetics and Evolution. 31: 874-9. PMID 15120385 DOI: 10.1016/J.Ympev.2003.10.008 |
0.389 |
|
| 2004 |
Simmons MP, Miya M. Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes. Molecular Phylogenetics and Evolution. 31: 351-62. PMID 15019630 DOI: 10.1016/J.Ympev.2003.08.004 |
0.435 |
|
| 2004 |
Simmons MP, Pickett KM, Miya M. How meaningful are Bayesian support values? Molecular Biology and Evolution. 21: 188-99. PMID 14595090 DOI: 10.1093/Molbev/Msh014 |
0.374 |
|
| 2004 |
Davis JI, Stevenson DW, Petersen G, Seberg O, Campbell LM, Freudenstein JV, Goldman DH, Hardy CR, Michelangeli FA, Simmons MP, Specht CD, Vergara-Silva F, Gandolfo M. 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. DOI: 10.1600/0363644041744365 |
0.794 |
|
| 2004 |
Simmons MP, Reeves A, Davis JI. Character-state space versus rate of evolution in phylogenetic inference Cladistics. 20: 191-204. DOI: 10.1111/J.1096-0031.2004.00014.X |
0.67 |
|
| 2003 |
Baumberger N, Doesseger B, Guyot R, Diet A, Parsons RL, Clark MA, Simmons MP, Bedinger P, Goff SA, Ringli C, Keller B. Whole-genome comparison of leucine-rich repeat extensins in Arabidopsis and rice. A conserved family of cell wall proteins form a vegetative and a reproductive clade. Plant Physiology. 131: 1313-26. PMID 12644681 DOI: 10.1104/Pp.102.014928 |
0.39 |
|
| 2003 |
Simmons MP, Freudenstein JV. The effects of increasing genetic distance on alignment of, and tree construction from, rDNA internal transcribed spacer sequences. Molecular Phylogenetics and Evolution. 26: 444-51. PMID 12644403 DOI: 10.1016/S1055-7903(02)00366-4 |
0.752 |
|
| 2003 |
Freudenstein JV, Pickett KM, Simmons MP, Wenzel JW. From basepairs to birdsongs: Phylogenetic data in the age of genomics Cladistics. 19: 333-347. DOI: 10.1111/J.1096-0031.2003.Tb00377.X |
0.753 |
|
| 2002 |
Simmons MP, Ochoterena H, Freudenstein JV. Amino acid vs. nucleotide characters: challenging preconceived notions. Molecular Phylogenetics and Evolution. 24: 78-90. PMID 12128030 DOI: 10.1016/S1055-7903(02)00202-6 |
0.759 |
|
| 2002 |
Simmons MP, Freudenstein JV. Uninode coding vs gene tree parsimony for phylogenetic reconstruction using duplicate genes. Molecular Phylogenetics and Evolution. 23: 481-98. PMID 12099800 DOI: 10.1016/S1055-7903(02)00033-7 |
0.76 |
|
| 2002 |
Simmons MP, Randle CP, Freudenstein JV, Wenzel JW. Limitations of relative apparent synapomorphy analysis (RASA) for measuring phylogenetic signal. Molecular Biology and Evolution. 19: 14-23. PMID 11752186 DOI: 10.1093/Oxfordjournals.Molbev.A003978 |
0.752 |
|
| 2002 |
Simmons MP, Ochoterena H, Freudenstein JV. Conflict between amino acid and nucleotide characters Cladistics. 18: 200-206. DOI: 10.1111/J.1096-0031.2002.Tb00148.X |
0.772 |
|
| 2002 |
Simmons MP, Freudenstein JV. Artifacts of coding amino acids and other composite characters for phylogenetic analysis Cladistics. 18: 354-365. DOI: 10.1006/Clad.2002.0201 |
0.768 |
|
| 2002 |
Simmons MP, Ochoterena H, Freudenstein JV. Regular ArticleConflict between Amino Acid and Nucleotide Characters Cladistics. 18. DOI: 10.1006/Clad.2001.0189 |
0.771 |
|
| 2001 |
Simmons MP, Ochoterena H, Carr TG. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses Systematic Biology. 50: 454-462. PMID 12116587 DOI: 10.1080/10635150120427 |
0.401 |
|
| 2001 |
Simmons MP, Savolainen V, Clevinger CC, Archer RH, Davis JI. Phylogeny of the Celastraceae inferred from 26S nuclear ribosomal DNA, phytochrome B, rbcL, atpB, and morphology. Molecular Phylogenetics and Evolution. 19: 353-66. PMID 11399146 DOI: 10.1006/Mpev.2001.0937 |
0.708 |
|
| 2001 |
Barker NP, Clark LG, Davis JI, Duvall MR, Guala GF, Hsiao C, Kellogg EA, Linder P, Mason-Garner RJ, Mathews SY, Simmons MP, Soreng RJ, Spangler RE. Phylogeny and subfamilial classification of the grasses (Poaceae) Annals of the Missouri Botanical Garden. 88: 373-457. DOI: 10.2307/3298585 |
0.639 |
|
| 2001 |
Simmons MP, Clevinger CC, Savolainen V, Archer RH, Mathews S, Doyle JJ. Phylogeny of the celastraceae inferred from phytochrome B gene sequence and morphology American Journal of Botany. 88: 313-325. DOI: 10.2307/2657021 |
0.439 |
|
| 2000 |
Simmons MP, Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses Systematic Biology. 49: 369-381. PMID 12118412 DOI: 10.1093/Sysbio/49.2.369 |
0.382 |
|
| 2000 |
Simmons MP, Donovan Bailey C, Nixon KC. Phylogeny reconstruction using duplicate genes. Molecular Biology and Evolution. 17: 469-73. PMID 10742039 DOI: 10.1093/Oxfordjournals.Molbev.A026327 |
0.613 |
|
| 2000 |
Simmons MP. A fundamental problem with amino-acid-sequence characters for phylogenetic analyses Cladistics. 16: 274-282. DOI: 10.1006/Clad.2000.0134 |
0.418 |
|
| 1999 |
Simmons MP, Hedin JP. Relationships and morphological character change among genera of Celastraceae sensu lato (including Hippocrateaceae) Annals of the Missouri Botanical Garden. 86: 723-757. DOI: 10.2307/2666152 |
0.368 |
|
| 1998 |
Davis JI, Simmons MP, Stevenson DW, Wendel JF. Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences. Systematic Biology. 47: 282-310. PMID 12064229 DOI: 10.1080/106351598260923 |
0.677 |
|
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