Target enrichment improves phylogenetic resolution in the genus Zanthoxylum (Rutaceae) and indicates both incomplete lineage sorting and hybridization events

Zanthoxylum nitidum (Roxb.) DC: Traditional uses, phytochemistry, pharmacological activities and toxicology

(2020) Qiang Lu et al.   JOURNAL OF ETHNOPHARMACOLOGY

Phylogenomics unravels Quaternary vicariance and allopatric speciation patterns in temperate‐montane plant species: A case study on the Ranunculus auricomus species complex

(2020) Salvatore Tomasello et al.   MOLECULAR ECOLOGY

The importance of historical ecology for interpreting evolutionary processes in plants of oceanic islands

(2020) Tod F. Stuessy   Journal of Systematics and Evolution

Phylogenomic relationships and character evolution of the grape family (Vitaceae)

(2020) Zhi-Yao Ma et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Rise of Apomixis in Natural Plant Populations

(2019) Diego Hojsgaard et al.   Frontiers in Plant Science

Chloroplast phylogenomic data support Paleocene - Eocene amphi-Pacific early radiation for the Asian Palmate core Araliaceae

(2019) Virginia Valcárcel et al.   Journal of Systematics and Evolution

A customized nuclear target enrichment approach for developing a phylogenomic baseline for Dioscorea yams (Dioscoreaceae)

(2019) Marybel Soto Gomez et al.   Applications in Plant Sciences

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

(2018) James B. Pease et al.   AMERICAN JOURNAL OF BOTANY

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Reconstructing geographical parthenogenesis: effects of niche differentiation and reproductive mode on Holocene range expansion of an alpine plant

(2018) Bernhard Kirchheimer et al.   ECOLOGY LETTERS

HybPhyloMaker: Target Enrichment Data Analysis From Raw Reads to Species Trees

(2018) Tomáš Fér et al.   Evolutionary Bioinformatics

Phylogeny and biogeography of the pantropical genus Zanthoxylum and its closest relatives in the proto-Rutaceae group (Rutaceae)

(2018) Marc S. Appelhans et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

The odd one out or a hidden generalist: Hawaiian Melicope (Rutaceae) do not share traits associated with successful island colonization

(2018) Claudia Paetzold et al.   Journal of Systematics and Evolution

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors

(2017) Donald M. Bryant et al.   Cell Reports

Targeted NGS for species level phylogenomics: “made to measure” or “one size fits all”?

(2017) Malvina Kadlec et al.   PeerJ

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

(2016) Andreanna J. Welch et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

AMAS: a fast tool for alignment manipulation and computing of summary statistics

(2016) Marek L. Borowiec   PeerJ

ExaML version 3: a tool for phylogenomic analyses on supercomputers

(2015) Alexey M. Kozlov et al.   BIOINFORMATICS

Evolution of the mating system in colonizing plants

(2015) John R. Pannell   MOLECULAR ECOLOGY

Using nuclear gene data for plant phylogenetics: Progress and prospects II. Next-gen approaches

(2015) Elizabeth A. Zimmer et al.   Journal of Systematics and Evolution

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

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

Does polyploidy facilitate long-distance dispersal?

(2014) H. Peter Linder et al.   ANNALS OF BOTANY

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab 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

Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

(2014) Liping Zeng et al.   Nature Communications

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

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

Molecular phylogenetic analysis of Hawaiian Rutaceae (Melicope,PlatydesmaandZanthoxylum) and their different colonization patterns

(2013) Marc S. Appelhans et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

A melissopalynological study of artisanal honey produced in Catamarca (Argentina)

(2013) María Cristina Costa et al.   GRANA

Geographical parthenogenesis and population genetic structure in the alpine species Ranunculus kuepferi (Ranunculaceae)

(2013) A-C Cosendai et al.   HEREDITY

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

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

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon 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

Next-generation hybridization and introgression

(2011) A D Twyford et al.   HEREDITY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Darwin's Finches as Seed Predators and Dispersers

(2009) Ana Mireya Guerrero et al.   Wilson Journal of Ornithology

Frugivory by the fish Brycon hilarii (Characidae) in western Brazil

(2008) Paula Reys et al.   ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY

Interspecific variation in primary seed dispersal in a tropical forest

(2008) Helene C. Muller-Landau et al.   JOURNAL OF ECOLOGY

High population differentiation and unusual haplotype structure in a shade-intolerant pioneer tree species, Zanthoxylum ailanthoides (Rutaceae) revealed by analysis of DNA polymorphism at four nuclear loci

(2008) K. KAMIYA et al.   MOLECULAR ECOLOGY