Resolving Relationships in Mentzelia Section Bartonia (Loasaceae) in the Face of Cytonuclear Discordance

What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol

(2023) John J. Schenk et al.   Applications in Plant Sciences

Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum

(2022) Edeline Gagnon et al.   AMERICAN JOURNAL OF BOTANY

Inferring the genetic responses to acute drought stress across an ecological gradient

(2022) Jessica K. Devitt et al.   BMC GENOMICS

Investigating Phylogenetic Placement and Species-Level Relationships in a Recent Radiation of Mentzelia section Bartonia (Loasaceae) from the Mojave Desert

(2022) Dylan H. Cohen et al.   SYSTEMATIC BOTANY

The Phylogeny of Errazurizia (Fabaceae: Amorpheae) and Description of the New Monotypic Genus Pictarena

(2022) L. Ellie Becklund et al.   SYSTEMATIC BOTANY

The Next Generation of Adaptive Radiation Studies in Plants

(2021) John J. Schenk   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in Alchemilla s.l. (Rosaceae)

(2021) Diego F Morales-Briones et al.   SYSTEMATIC BIOLOGY

The species of Mentzelia (Loasaceae) in Mexico, part 2: Mentzelia section Bartonia

(2021) John Schenk et al.   Botanical Sciences

The species of Mentzelia (Loasaceae) in Mexico, part 1: Sectional diversity

(2021) John Schenk et al.   Botanical Sciences

Elucidating the Evolutionary History of Oenothera Sect. Pachylophus (Onagraceae): A Phylogenomic Approach

(2021) Amanda Patsis et al.   SYSTEMATIC BOTANY

Out of Sight, Out of Mind: Widespread Nuclear and Plastid-Nuclear Discordance in the Flowering Plant Genus Polemonium (Polemoniaceae) Suggests Widespread Historical Gene Flow Despite Limited Nuclear Signal

(2020) Jeffrey P Rose et al.   SYSTEMATIC BIOLOGY

Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous

(2019) Chao-Nan Fu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

(2019) Andrew D. Young et al.   SYSTEMATIC ENTOMOLOGY

Allopatric Speciation Drives Diversification of Ecological Specialists on Sandhills

(2018) John J. Schenk et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus )

(2018) Julie A. Lee-Yaw et al.   NEW PHYTOLOGIST

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-Medoids Clustering

(2018) Matthew G Johnson et al.   SYSTEMATIC BIOLOGY

Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)

(2017) Alexis R. Sullivan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome Skimming: A Rapid Approach to Gaining Diverse Biological Insights into Multicellular Pathogens

(2016) Dee R. Denver et al.   PLoS Pathogens

Hybridization, Introgression, and the Nature of Species Boundaries

(2014) Richard G. Harrison et al.   JOURNAL OF HEREDITY

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

(2014) Kevin Weitemier et al.   Applications in Plant Sciences

Paternal leakage, heteroplasmy, and the evolution of plant mitochondrial genomes

(2013) David E. McCauley   NEW PHYTOLOGIST

Biogeographical diversification ofMentzeliasectionBartoniain western North America

(2012) John J. Schenk   JOURNAL OF BIOGEOGRAPHY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2012) S. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Is Recombination a Problem for Species-Tree Analyses?

(2012) Hayley C. Lanier et al.   SYSTEMATIC BIOLOGY

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Phylogeny and Taxonomy of Mentzelia Section Bartonia (Loasaceae)

(2011) John J. Schenk et al.   SYSTEMATIC BOTANY

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Why does biparental plastid inheritance revive in angiosperms?

(2010) Quan Zhang et al.   JOURNAL OF PLANT RESEARCH

Effects of Substitution Models on Divergence Time Estimates: Simulations and an Empirical Study of Model Uncertainty Using Cornales

(2010) John J. Schenk et al.   SYSTEMATIC BOTANY

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION