Mark P. Simmons

发表

The deterministic effects of alignment bias in phylogenetic inference

Kai F. Müller, Mark P. Simmons, Colleen T. Webb, 2011, Cladistics : the international journal of the Willi Hennig Society.

Ten Simple Rules for Writing a Reply Paper

Mark P. Simmons, M. Simmons, 2015, PLoS Comput. Biol..

Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts

Richard H. Baker, Mark P. Simmons, John Gatesy, 2018, bioRxiv.

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

Mark P. Simmons, M. Simmons, 2012, Cladistics : the international journal of the Willi Hennig Society.

Functional trait niches of North American lotic insects: traits-based ecological applications in light of phylogenetic relationships

N. LeRoy Poff, Julian D. Olden, Mark P. Simmons, 2006, Journal of the North American Benthological Society.

Phylogeny and Delimitation of the Celastrales Inferred from Nuclear and Plastid Genes

Mark P. Simmons, M. Simmons, Li‐Bing Zhang, 2006 .

Mitochondrial Data in Monocot Phylologenetics

Jerrold I. Davis, Mark P. Simmons, M. Chase, 2006 .

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

Mark P. Simmons, A. Henderson, M. Simmons, 2013, Evolution; international journal of organic evolution.

Phylogeny and subfamilial classification of the grasses (Poaceae)

Jerrold I. Davis, Mark P. Simmons, M. Simmons, 2001 .

Evaluation of microsatellites of Catha edulis (qat; Celastraceae) identified using pyrosequencing

Mark P. Simmons, M. Simmons, M. Curto, 2013 .

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

Mark P. Simmons, Daniel B. Sloan, M. Simmons, 2016, Genome biology and evolution.

Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses.

Mark P. Simmons, Daniel B. Sloan, M. Springer, 2019, Molecular phylogenetics and evolution.

Anchored Phylogenomics of Angiosperms I: Assessing the Robustness of Phylogenetic Estimates

Mark P. Simmons, M. Donoghue, P. Soltis, 2016, bioRxiv.

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

Mark P. Simmons, M. Simmons, Zhiqiang Wu, 2016, PloS one.

Phylogeny of the Celastreae (Celastraceae) and the relationships of Catha edulis (qat) inferred from morphological characters and nuclear and plastid genes.

Mark P. Simmons, M. Simmons, R. Archer, 2008, Molecular phylogenetics and evolution.

Co-variation in methanotroph community composition and activity in three temperate grassland soils

Mark P. Simmons, M. Simmons, A. Koyama, 2016 .

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

Mark P. Simmons, M. Simmons, W. Black, 2012, PloS one.

A phylogeny of Anisophylleaceae based on six nuclear and plastid loci: ancient disjunctions and recent dispersal between South America, Africa, and Asia.

Mark P. Simmons, M. Simmons, S. Renner, 2007, Molecular phylogenetics and evolution.

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

Mark P. Simmons, W. Murphy, M. Springer, 2017, Cladistics : the international journal of the Willi Hennig Society.

How can third codon positions outperform first and second codon positions in phylogenetic inference? An empirical example from the seed plants.

Mark P. Simmons, C. Webb, M. Simmons, 2006, Systematic biology.

Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters.

Mark P. Simmons, M. Simmons, T. Carr, 2004, Molecular phylogenetics and evolution.

Character‐state space versus rate of evolution in phylogenetic inference

Jerrold I. Davis, Mark P. Simmons, M. Simmons, 2004, Cladistics : the international journal of the Willi Hennig Society.

Amino acid vs. nucleotide characters: challenging preconceived notions.

Mark P. Simmons, M. Simmons, H. Ochoterena, 2002, Molecular phylogenetics and evolution.

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

Mark P. Simmons, M. Simmons, J. Freudenstein, 2002, Cladistics : the international journal of the Willi Hennig Society.

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

Erin K. Molloy, Mark P. Simmons, Daniel B. Sloan, 2019, The Journal of heredity.

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

Mark P. Simmons, M. Simmons, J. Wenzel, 2003 .

Gaps as characters in sequence-based phylogenetic analyses.

Mark P. Simmons, M. Simmons, H. Ochoterena, 2000, Systematic biology.

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

Mark P. Simmons, M. Simmons, 2017, Cladistics : the international journal of the Willi Hennig Society.

Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia)

Mark P. Simmons, M. Simmons, M. McKenna, 2012, BMC Evolutionary Biology.

A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference.

Mark P. Simmons, C. Webb, M. Simmons, 2007, Molecular phylogenetics and evolution.

A Thorny Dilemma: Testing Alternative Intrageneric Classifications within Ziziphus (Rhamnaceae)

Mark P. Simmons, M. Simmons, Melissa B. Islam, 2006 .

Uninode coding vs gene tree parsimony for phylogenetic reconstruction using duplicate genes.

Mark P. Simmons, M. Simmons, J. Freudenstein, 2002, Molecular phylogenetics and evolution.

Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes

Dale N. Richardson, Mark P. Simmons, M. Simmons, 2006, BMC Genomics.