Mark Simmons

Publications

• Benefits of alignment quality-control processing steps and an Angiosperms353 phylogenomics pipeline applied to the Celastrales
• The relative performance of indel-coding methods in simulations
• Ten Rules for Associate Editors
• Employing Two-stage Derivatisation and GC-MS to Assay for Cathine and Related Stimulant Alkaloids across the Celastraceae
• Mutually exclusive phylogenomic inferences at the root of the angiosperms: Amborella is supported as sister and Observed Variability is biased
• Cryptic species diversity reveals biogeographic support for the 'mountain passes are higher in the tropics' hypothesis
• Gene-tree misrooting drives conflicts in phylogenomic coalescent analyses of palaeognath birds
• ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets
• Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains
• Adenine center dot cytosine substitutions are an alternative pathway of compensatory mutation in angiosperm ITS2
• Co-variation in methanotroph community composition and activity in three temperate grassland soils
• Thistle be a mess: Untangling the taxonomy of Cirsium (Cardueae: Compositae) in North America
• Divergence and support among slightly suboptimal likelihood gene trees
• Transcriptome-wide comparison of selenium hyperaccumulator and nonaccumulator Stanleya species provides new insight into key processes mediating the hyperaccumulation syndrome
• Clonal Diversity, Cultivar Traits, Geographic Dispersal, and the Ethnotaxonomy of Cultivated Qat (Catha edulis, Celastraceae)
• Systematics of New World Maytenus (Celastraceae) and a New Delimitation of the Genus
• Ten Simple Rules for Writing a Reply Paper
• Collapsing dubiously resolved gene-tree branches in phylogenomic coalescent analyses
• Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes
• Resolution of a concatenation/coalescence kerfuffle: partitioned coalescence support and a robust family-level tree for Mammalia
• Pleurostylia serrulata and Two Allied New Species from Africa are Actually Members of the New World Crossopetalum (Celastraceae)
• The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae)
• Mitochondrial fatty acid beta-oxidation is required for storage-lipid catabolism in a marine diatom
• New Guinea has the world's richest island flora
• Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses
• Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms
• Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts
• Relative benefits of amino-acid, codon, degeneracy, DNA, and purine-pyrimidine character coding for phylogenetic analyses of exons
• Biases of tree-independent-character-subsampling methods
• Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae)
• Biogeography of the Malagasy Celastraceae: Multiple independent origins followed by widespread dispersal of genera from Madagascar
• Phylogeography of the wild and cultivated stimulant plant qat (Catha edulis, Celastraceae ) in areas of historical cultivation
• The effects of subsampling gene trees on coalescent methods applied to ancient divergences
• Transcriptome-wide comparison of selenium hyperaccumulator and nonaccumulator Stanleya species provides new insight into key processes mediating the hyperaccumulation syndrome
• The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae)
• Thistle be a mess: Untangling the taxonomy of Cirsium (Cardueae: Compositae) in North America
• Adenine•cytosine substitutions are an alternative pathway of compensatory mutation in angiosperm ITS2
• Phylogenomics and the rise of the angiosperms.
• Divergent maximum-likelihood-branch-support values for polytomies.
• Disparate parametric branch-support values from ambiguous characters.
• Origin and evolution of Kinesin-like calmodulin-binding protein.
• The deterministic effects of alignment bias in phylogenetic inference.
• Rapid intraspecific evolution of miRNA and siRNA genes in the mosquito Aedes aegypti.
• The relative performance of Bayesian and parsimony approaches when sampling characters evolving under homogeneous and heterogeneous sets of parameters.
• Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae).
• The relative sensitivity of different alignment methods and character codings in sensitivity analysis.
• The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae)
• Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses.
• Development of microsatellites in the Hawaiian endemic palm Pritchardia martii (Arecaceae) and their utility in congeners.
• Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes.
• How meaningful are Bayesian support values?
• Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia).
• Molecular analyses of the Chinese herb Leigongteng (Tripterygium wilfordii Hook.f.).
• Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes.
• Character-state space versus rate of evolution in phylogenetic inference.
• Dubious resolution and support from published sparse supermatrices: the importance of thorough tree searches.
• Spurious 99% bootstrap and jackknife support for unsupported clades.
• A phylogeny of Anisophylleaceae based on six nuclear and plastid loci: ancient disjunctions and recent dispersal between South America, Africa, and Asia.
• Artifacts of Coding Amino Acids and Other Composite Characters for Phylogenetic Analysis.
• Phylogenetic inference using non-redundant coding of dependent characters versus alternative approaches for protein-coding genes.
• Conflict between Amino Acid and Nucleotide Characters.
• Geographic and taxonomic disparities in species diversity: dispersal and diversification rates across Wallace's line.
• A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses.
• Phylogeny of the Cucurbitales based on DNA sequences of nine loci from three genomes: implications for morphological and sexual system evolution.
• Amino acid vs. nucleotide characters: challenging preconceived notions.
• Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae)