Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

A Comprehensive and Dated Phylogenomic Analysis of Butterflies

(2018) Marianne Espeland et al.   CURRENT BIOLOGY

Anchored Hybrid Enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex

(2018) Diego Bogarín et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)

(2018) Diego F. Morales-Briones et al.   NEW PHYTOLOGIST

Practical considerations for plant phylogenomics

(2018) Michael R. McKain et al.   Applications in Plant Sciences

Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity

(2017) Ran Wei et al.   Genome Biology and Evolution

Signal, Uncertainty, and Conflict in Phylogenomic Data for a Diverse Lineage of Microbial Eukaryotes (Diatoms, Bacillariophyta)

(2017) Matthew B Parks et al.   MOLECULAR BIOLOGY AND EVOLUTION

Functional ecology of cryptogams: scaling from bryophyte, lichen, and soil crust traits to ecosystem processes

(2017) Kirsten K. Deane-Coe et al.   NEW PHYTOLOGIST

Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti

(2017) Dario Copetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics

(2017) Étienne Léveillé-Bourret et al.   SYSTEMATIC BIOLOGY

Phylogenetic inference and peristome evolution in haplolepideous mosses, focusing on Pseudoditrichaceae and Ditrichaceaes. l.

(2016) Vladimir E. Fedosov et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Peat Moss–Like Vegetative Remains from Ordovician Carbonates

(2016) Christopher Cardona-Correa et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria)

(2016) R. Alexander Pyron et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

(2016) Matthew G. Johnson et al.   Applications in Plant Sciences

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Phylogenomic analyses of species relationships in the genusSabal(Arecaceae) using targeted sequence capture

(2015) Karolina Heyduk et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

(2015) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

Why are most organelle genomes transmitted maternally?

(2014) Stephan Greiner et al.   BIOESSAYS

Should genes with missing data be excluded from phylogenetic analyses?

(2014) Wei Jiang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-Usage Bias

(2014) Yang Liu et al.   SYSTEMATIC BIOLOGY

Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions

(2014) Cymon J. Cox et al.   SYSTEMATIC BIOLOGY

Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts

(2014) B. Laenen et al.   Nature Communications

Moss diversity: A molecular phylogenetic analysis of genera

(2014) C. J. Cox et al.   Phytotaxa

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

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

A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae

(2014) Jennifer R. Mandel et al.   Applications in Plant Sciences

Data access for the 1,000 Plants (1KP) project

(2014) Naim Matasci et al.   GigaScience

Patterns of clade support across the major lineages of moss phylogeny

(2013) Ying Chang et al.   CLADISTICS

Selection Is No More Efficient in Haploid than in Diploid Life Stages of an Angiosperm and a Moss

(2013) Péter Szövényi et al.   MOLECULAR BIOLOGY AND EVOLUTION

A 20-state empirical amino-acid substitution model for green plant chloroplasts

(2013) Cymon J. Cox et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Disentangling knots of rapid evolution: origin and diversification of the moss order Hypnales

(2012) Sanna Huttunen et al.   JOURNAL OF BRYOLOGY

Broad Phylogenomic Sampling and the Sister Lineage of Land Plants

(2012) Ruth E. Timme et al.   PLoS One

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Inferring the higher-order phylogeny of mosses (Bryophyta) and relatives using a large, multigene plastid data set

(2011) Y. Chang et al.   AMERICAN JOURNAL OF BOTANY

Resolving the evolutionary relationships of molluscs with phylogenomic tools

(2011) Stephen A. Smith et al.   NATURE

Establishing a time-scale for plant evolution

(2011) John T. Clarke et al.   NEW PHYTOLOGIST

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

Morphology versus molecules in moss phylogeny: new insights (or controversies) from placental and vascular anatomy in Oedipodium griffithianum

(2011) Roberto Ligrone et al.   PLANT SYSTEMATICS AND EVOLUTION

Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

(2011) John J. Wiens et al.   SYSTEMATIC BIOLOGY

Introducing Intron Locus cox1i624 for Phylogenetic Analyses in Bryophytes: On the Issue of Takakia as Sister Genus to All Other Extant Mosses

(2010) Ute Volkmar et al.   JOURNAL OF MOLECULAR EVOLUTION

Peatmoss (Sphagnum) diversification associated with Miocene Northern Hemisphere climatic cooling?

(2010) A. Jonathan Shaw et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny of the moss class Polytrichopsida (BRYOPHYTA): Generic-level structure and incongruent gene trees

(2010) Neil E. Bell et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

The phylogeny of mosses – Addressing open issues with a new mitochondrial locus: Group I intron cobi420

(2009) Ute Wahrmund et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Characteristics and Prediction of RNA Editing Sites in Transcripts of the Moss Takakia lepidozioides Chloroplast

(2008) K. Yura et al.   DNA RESEARCH

Slow molecular evolution in 18S rDNA, rbcL and nad5 genes of mosses compared with higher plants

(2008) H. K. STENØIEN   JOURNAL OF EVOLUTIONARY BIOLOGY

Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

(2008) G DROUIN et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A morpho-molecular classification of the mosses (Bryophyta)

(2008) Michael Stech et al.   NOVA HEDWIGIA

Taxon Sampling Affects Inferences of Macroevolutionary Processes from Phylogenetic Trees

(2008) Tracy A. Heath et al.   SYSTEMATIC BIOLOGY