Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data

Restriction‐site associated DNA sequencing data reveal a radiation of willow species ( Salix L., Salicaceae) in the Hengduan Mountains and adjacent areas

(2020) Li He et al.   Journal of Systematics and Evolution

Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae)

(2019) Marie K Brandrud et al.   SYSTEMATIC BIOLOGY

Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut

(2019) Bo-Wen Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)

(2018) Jonna S. Eriksson et al.   BMC EVOLUTIONARY BIOLOGY

The Analysis of Polyploid Genetic Data

(2018) Patrick G Meirmans et al.   JOURNAL OF HEREDITY

HyDe: A Python Package for Genome-Scale Hybridization Detection

(2018) Paul D Blischak et al.   SYSTEMATIC BIOLOGY

Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

(2018) Tobias Andermann et al.   SYSTEMATIC BIOLOGY

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

(2018) Andrew Rambaut et al.   SYSTEMATIC BIOLOGY

Haplotype-Based Genotyping in Polyploids

(2018) Josh P. Clevenger et al.   Frontiers in Plant Science

Analysis of evolution and genetic diversity of sweetpotato and its related different polyploidy wild species I. trifida using RAD-seq

(2018) J. Y. Feng et al.   BMC PLANT BIOLOGY

RAD sequencing resolved phylogenetic relationships in European shrub willows (Salix L. subg. Chamaetia and subg. Vetrix ) and revealed multiple evolution of dwarf shrubs

(2018) Natascha Dorothea Wagner et al.   Ecology and Evolution

RAD-seq reveals genetic structure of the F2-generation of natural willow hybrids (Salix L.) and a great potential for interspecific introgression

(2018) Susanne Gramlich et al.   BMC PLANT BIOLOGY

RADseq provides evidence for parallel ecotypic divergence in the autotetraploid Cochlearia officinalis in Northern Norway

(2017) Marie K. Brandrud et al.   Scientific Reports

Phylogenetic analysis of RAD-seq data: examining the influence of gene genealogy conflict on analysis of concatenated data

(2016) David M. Rivers et al.   CLADISTICS

Evolution in situ: hybrid origin and establishment of willows (Salix L.) on alpine glacier forefields

(2016) S Gramlich et al.   HEREDITY

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Karyotype evolution supports the molecular phylogeny in the genus Ranunculus (Ranunculaceae)

(2016) Matthias Baltisberger et al.   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants

(2016) Deren A. R. Eaton et al.   SYSTEMATIC BIOLOGY

An analytical toolkit for polyploid willow discrimination

(2016) Wei Guo et al.   Scientific Reports

Fitness of natural willow hybrids in a pioneer mosaic hybrid zone

(2016) Susanne Gramlich et al.   Ecology and Evolution

Phylogeny of Salix subgenus Salix s.l. (Salicaceae): delimitation, biogeography, and reticulate evolution

(2015) Jie Wu et al.   BMC EVOLUTIONARY BIOLOGY

Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations

(2015) Josh Clevenger et al.   Molecular Plant

On the relative abundance of autopolyploids and allopolyploids

(2015) Michael S. Barker et al.   NEW PHYTOLOGIST

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

(2015) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

The geography of hybrid speciation in plants

(2015) Joachim W. Kadereit   TAXON

Genetic relationships and ecological divergence in Salix species and populations in Taiwan

(2015) Chun-Lin Huang et al.   Tree Genetics & Genomes

Phylogenomics of polyploidFothergilla(Hamamelidaceae) by RAD-tag based GBS-insights into species origin and effects of software pipelines

(2015) Zhe-Chen Qi et al.   Journal of Systematics and Evolution

Phylogenetic Relationships of American Willows (Salix L., Salicaceae)

(2015) Aurélien Lauron-Moreau et al.   PLoS One

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Gene Duplication, Population Genomics, and Species-Level Differentiation within a Tropical Mountain Shrub

(2014) Alicia Mastretta-Yanes et al.   Genome Biology and Evolution

Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep?

(2014) Diana M. Percy et al.   MOLECULAR ECOLOGY

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data

(2014) Andrew L. Hipp et al.   PLoS One

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Tapping the Promise of Genomics in Species with Complex, Nonmodel Genomes

(2013) Candice N. Hirsch et al.   Annual Review of Plant Biology

Detection and genotyping of restriction fragment associated polymorphisms in polyploid crops with a pseudo-reference sequence: a case study in allotetraploid Brassica napus

(2013) Xun Chen et al.   BMC GENOMICS

Hybridization and speciation

(2013) R. Abbott et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools

(2013) France Dufresne et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

A population genetic model to infer allotetraploid speciation and long-term evolution applied to two yarrow species

(2013) Yan-Ping Guo et al.   NEW PHYTOLOGIST

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

(2013) Marie Cariou et al.   Ecology and Evolution

Habitat specialization and the role of trait lability in structuring diverse willow (genusSalix) communities

(2012) Jessica A. Savage et al.   ECOLOGY

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quaternary phylogeography: the roots of hybrid zones

(2011) Godfrey M. Hewitt   GENETICA

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Recently Formed Polyploid Plants Diversify at Lower Rates

(2011) I. Mayrose et al.   SCIENCE

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The Role of Hybridization in Plant Speciation

(2009) Pamela S. Soltis et al.   Annual Review of Plant 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 frequency of polyploid speciation in vascular plants

(2009) T. E. Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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