Dating the Species Network: Allopolyploidy and Repetitive DNA Evolution in American Daisies (Melampodium sect. Melampodium, Asteraceae)

StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates

(2017) Huw A. Ogilvie et al.   MOLECULAR BIOLOGY AND EVOLUTION

Has the connection between polyploidy and diversification actually been tested?

(2016) Elizabeth A Kellogg   CURRENT OPINION IN PLANT BIOLOGY

Multiple Polyploidization Events across Asteraceae with Two Nested Events in the Early History Revealed by Nuclear Phylogenomics

(2016) Chien-Hsun Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid Nicotiana (Solanaceae)

(2016) Steven Dodsworth et al.   PLANT SYSTEMATICS AND EVOLUTION

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae)

(2016) Jamie McCann et al.   PLoS One

The wondrous cycles of polyploidy in plants

(2015) Jonathan F. Wendel   AMERICAN JOURNAL OF BOTANY

Genome size diversity in angiosperms and its influence on gene space

(2015) Steven Dodsworth et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Formamide-Free Genomic in situ Hybridization Allows Unambiguous Discrimination of Highly Similar Parental Genomes in Diploid Hybrids and Allopolyploids

(2015) Tae-Soo Jang et al.   CYTOGENETIC AND GENOME RESEARCH

Satellite DNA in Plants: More than Just Rubbish

(2015) Manuel A. Garrido-Ramos   CYTOGENETIC AND GENOME RESEARCH

Analysis of the giant genomes ofFritillaria(Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size

(2015) Laura J. Kelly et al.   NEW PHYTOLOGIST

Assignment of Homoeologs to Parental Genomes in Allopolyploids for Species Tree Inference, with an Example from Fumaria (Papaveraceae)

(2015) Yann J. K. Bertrand et al.   SYSTEMATIC BIOLOGY

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

(2015) Jiří Macas et al.   PLoS One

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

Patterns of chromosomal variation in natural populations of the neoallotetraploid Tragopogon mirus (Asteraceae)

(2014) M Chester et al.   HEREDITY

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

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

When fathers are instant losers: homogenization of rDNA loci in recently formedCardamine × schulziitrigenomic allopolyploid

(2014) Judita Zozomová-Lihová et al.   NEW PHYTOLOGIST

Polyploidy: adaptation to the genomic environment

(2014) Jesse D. Hollister   NEW PHYTOLOGIST

From Gene Trees to a Dated Allopolyploid Network: Insights from the Angiosperm Genus Viola (Violaceae)

(2014) Thomas Marcussen et al.   SYSTEMATIC BIOLOGY

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

Evolutionary Consequences, Constraints and Potential of Polyploidy in Plants

(2013) H. Weiss-Schneeweiss et al.   CYTOGENETIC AND GENOME RESEARCH

The widespread crucifer speciesCardamine flexuosais an allotetraploid with a conserved subgenomic structure

(2013) Terezie Mandáková et al.   NEW PHYTOLOGIST

The More the Merrier: Recent Hybridization and Polyploidy in Cardamine

(2013) T. Mandakova et al.   PLANT CELL

Diploidization and genome size change in allopolyploids is associated with differential dynamics of low- and high-copy sequences

(2013) Simon Renny-Byfield et al.   PLANT JOURNAL

Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins

(2013) P. M. Shih et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Statistical Inference of Allopolyploid Species Networks in the Presence of Incomplete Lineage Sorting

(2013) Graham Jones et al.   SYSTEMATIC BIOLOGY

Polyploidy and its effect on evolutionary success: old questions revisited with new tools

(2012) A Madlung   HEREDITY

Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Independent, Rapid and Targeted Loss of Highly Repetitive DNA in Natural and Synthetic Allopolyploids of Nicotiana tabacum

(2012) Simon Renny-Byfield et al.   PLoS One

Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae)

(2012) M. Chester et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

THE PROMISCUOUS AND THE CHASTE: FREQUENT ALLOPOLYPLOID SPECIATION AND ITS GENOMIC CONSEQUENCES IN AMERICAN DAISIES (MELAMPODIUM SECT. MELAMPODIUM; ASTERACEAE)

(2011) Hanna Weiss-Schneeweiss et al.   EVOLUTION

Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana tabacum, Predominantly through the Elimination of Paternally Derived Repetitive DNAs

(2011) S. Renny-Byfield et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Inferring Species Networks from Gene Trees in High-Polyploid North American and Hawaiian Violets (Viola, Violaceae)

(2011) Thomas Marcussen et al.   SYSTEMATIC BIOLOGY

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

(2011) Daniel L. Ayres et al.   SYSTEMATIC BIOLOGY

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae)

(2010) Jin Koh et al.   BMC GENOMICS

Adding time-calibrated branch lengths to the Asteraceae supertree

(2010) Rubén TORICES   Journal of Systematics and Evolution

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular phylogenetic analyses of nuclear and plastid DNA sequences support dysploid and polyploid chromosome number changes and reticulate evolution in the diversification of Melampodium (Millerieae, Asteraceae)

(2009) Cordula Blöch et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Dating the origins of polyploidy events

(2009) Jeff J. Doyle et al.   NEW PHYTOLOGIST

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 DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants

(2009) J. S. Hawkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of rDNA in Nicotiana Allopolyploids: A Potential Link between rDNA Homogenization and Epigenetics

(2008) A. Kovarik et al.   ANNALS OF BOTANY

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS

The Dynamic Ups and Downs of Genome Size Evolution in Brassicaceae

(2008) M. A. Lysak et al.   MOLECULAR BIOLOGY AND EVOLUTION