Tackling Rapid Radiations With Targeted Sequencing

Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes

(2019) Thomas L. P. Couvreur et al.   Frontiers in Plant Science

A broader circumscription of Bulbostylis including Nemum (Abildgaardieae: Cyperaceae)

(2019) ERIC H. ROALSON et al.   Phytotaxa

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

(2019) Yang Liu et al.   Nature Communications

Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms

(2019) Grace E. Brewer et al.   Frontiers in Plant Science

Hyb-Seq for Flowering Plant Systematics

(2019) Steven Dodsworth et al.   TRENDS IN PLANT SCIENCE

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Phylogeny and Systematics of Cyperaceae, the Evolution and Importance of Embryo Morphology

(2018) Ilias Semmouri et al.   BOTANICAL REVIEW

Bridging the micro- and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above

(2018) Tamara Villaverde et al.   NEW PHYTOLOGIST

Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics

(2018) John H. Chau et al.   Applications in Plant Sciences

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

Allopatric speciation despite historical gene flow: Divergence and hybridization in Carex furva and C. lucennoiberica (Cyperaceae) inferred from plastid and nuclear RAD-seq data

(2017) Enrique Maguilla et al.   MOLECULAR ECOLOGY

Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics

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

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV

(2016)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Biogeography of the cosmopolitan sedges (Cyperaceae) and the area-richness correlation in plants

(2016) Daniel Spalink et al.   JOURNAL OF BIOGEOGRAPHY

A dated phylogeny of the papilionoid legume genus Canavalia reveals recent diversification by a pantropical liana lineage

(2016) Cristiane Snak et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Retrieval of hundreds of nuclear loci from herbarium specimens

(2016) Michelle L. Hart et al.   TAXON

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

Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern AfricanOxalis(Oxalidaceae)

(2015) Roswitha Schmickl et al.   Molecular Ecology Resources

Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment

(2015) Jessica D. Stephens et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

TOPO6: a nuclear single-copy gene for plant phylogenetic inference

(2015) Frank R. Blattner   PLANT SYSTEMATICS AND EVOLUTION

Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

(2015) James A. Nicholls et al.   Frontiers in Plant Science

MarkerMiner 1.0: A New Application for Phylogenetic Marker Development Using Angiosperm Transcriptomes

(2015) Srikar Chamala et al.   Applications in Plant Sciences

tqDist: a library for computing the quartet and triplet distances between binary or general trees

(2014) Andreas Sand et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: A case study in Carex (Cyperaceae)

(2014) Marcial Escudero 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

Taxonomic changes in C4 Cyperus (Cypereae, Cyperoideae, Cyperaceae): combining the sedge genera Ascolepis, Kyllinga and Pycreus into Cyperus s.l.

(2014) ISABEL LARRIDON et al.   Phytotaxa

A new classification for Lipocarpha and Volkiella as infrageneric taxa of Cyperus s.l. (Cypereae, Cyperoideae, Cyperaceae): insights from species tree reconstruction supplemented with morphological and floral developmental data

(2014) KENNETH BAUTERS et al.   Phytotaxa

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

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

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

(2014) Naim Matasci et al.   GigaScience

Shifts in diversification rates and clade ages explain species richness in higher-level sedge taxa (Cyperaceae)

(2013) Marcial Escudero et al.   AMERICAN JOURNAL OF BOTANY

Towards a new classification of the giant paraphyletic genusCyperus(Cyperaceae): phylogenetic relationships and generic delimitation in C4Cyperus

(2013) Isabel Larridon et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recognition of two major clades and early diverged groups within the subfamily Cyperoideae (Cyperaceae) including Korean sedges

(2012) Jongduk Jung et al.   JOURNAL OF PLANT RESEARCH

Using Supermatrices for Phylogenetic Inquiry: An Example Using the Sedges

(2012) Cody E. Hinchliff et al.   SYSTEMATIC BIOLOGY

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

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

Affinities in C3Cyperus lineages (Cyperaceae) revealed using molecular phylogenetic data and carbon isotope analysis

(2011) ISABEL LARRIDON et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy

(2011) A. R. Nabhan et al.   BRIEFINGS IN BIOINFORMATICS

DOES HYBRIDIZATION DRIVE THE TRANSITION TO ASEXUALITY IN DIPLOID BOECHERA?

(2011) James B. Beck et al.   EVOLUTION

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

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

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

(2010) Jill M Duarte et al.   BMC EVOLUTIONARY BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The pentatricopeptide repeat (PPR) gene family, a tremendous resource for plant phylogenetic studies

(2009) Yao-Wu Yuan et al.   NEW PHYTOLOGIST

Phylogeny of Cyperaceae Based on DNA Sequence Data: Current Progress and Future Prospects

(2008) A. Muthama Muasya et al.   BOTANICAL REVIEW

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One