Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication

The influence of habitat on the evolution of plants: a case study across Saxifragales

(2016) Rafael Rubio de Casas et al.   ANNALS OF BOTANY

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

Has the connection between polyploidy and diversification actually been tested?

(2016) Elizabeth A Kellogg   CURRENT OPINION IN PLANT BIOLOGY

Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia

(2016) Federico Plazzi et al.   Genome Biology and Evolution

Lineage-Specific Reductions of Plastid Genomes in an Orchid Tribe with Partially and Fully Mycoheterotrophic Species

(2016) Yan-Lei Feng et al.   Genome Biology and Evolution

Species delimitations in plants: lessons learned from potato taxonomy by a practicing taxonomist

(2016) David M. Spooner   Journal of Systematics and Evolution

Multiple Events of Allopolyploidy in the Evolution of the Racemose Lineages in Prunus (Rosaceae) Based on Integrated Evidence from Nuclear and Plastid Data

(2016) Liang Zhao et al.   PLoS One

Resolution of Brassicaceae Phylogeny Using Nuclear Genes Uncovers Nested Radiations and Supports Convergent Morphological Evolution

(2015) Chien-Hsun Huang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

(2015) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the GenusCitrus

(2015) Jose Carbonell-Caballero et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogeny of Rosa sections Chinenses and Synstylae (Rosaceae) based on chloroplast and nuclear markers

(2015) Zhang-Ming Zhu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Early genome duplications in conifers and other seed plants

(2015) Z. Li et al.   Science Advances

Effects of apomixis and polyploidy on diversification and geographic distribution in Amelanchier (Rosaceae)

(2014) Michael B. Burgess et al.   AMERICAN JOURNAL OF BOTANY

Phylogeny and biogeography of wild roses with specific attention to polyploids

(2014) Marie Fougère-Danezan et al.   ANNALS OF BOTANY

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes

(2014) Steven B. Cannon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diversification of almonds, peaches, plums and cherries – Molecular systematics and biogeographic history of Prunus (Rosaceae)

(2014) Siew-Wai Chin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2014) Liping Zeng et al.   Nature Communications

Fruit Development and Ripening

(2013) Graham B. Seymour et al.   Annual Review of Plant Biology

Phylogenetic analysis of PISTILLATA sequences in Neillia (Rosaceae)

(2013) Sang-Hun Oh   JOURNAL OF PLANT BIOLOGY

Reprint of: Using nuclear gene data for plant phylogenetics: Progress and prospects

(2013) Elizabeth A. Zimmer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

The genome of the pear (Pyrus bretschneideri Rehd.)

(2012) J. Wu et al.   GENOME RESEARCH

Expanded phylogenetic and dating analyses of the apples and their relatives (Pyreae, Rosaceae)

(2012) Eugenia Y.Y. Lo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms

(2012) Ning Zhang et al.   NEW PHYTOLOGIST

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Molecular Genetic Features of Polyploidization and Aneuploidization Reveal Unique Patterns for Genome Duplication in Diploid Malus

(2012) Michael J. Considine et al.   PLoS One

Past Climate Change and Plant Evolution in Western North America: A Case Study in Rosaceae

(2012) Mats Töpel et al.   PLoS One

The genome of Prunus mume

(2012) Qixiang Zhang et al.   Nature Communications

A genome triplication associated with early diversification of the core eudicots

(2012) Yuannian Jiao et al.   GENOME BIOLOGY

A brief history of fruits and frugivores

(2011) Theodore H. Fleming et al.   ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY

Selection for Higher Gene Copy Number after Different Types of Plant Gene Duplications

(2011) Corey M. Hudson et al.   Genome Biology and Evolution

Prunus and Oemleria (Rosaceae) Flowers from the Late Early Eocene Republic Flora of Northeastern Washington State, U.S.A.

(2011) John C. Benedict et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

Two-Phase Resolution of Polyploidy in theArabidopsisMetabolic Network Gives Rise to Relative and Absolute Dosage Constraints

(2011) Michaël Bekaert et al.   PLANT CELL

RECONSTRUCTING RETICULATION HISTORY IN A PHYLOGENETIC FRAMEWORK AND THE POTENTIAL OF ALLOPATRIC SPECIATION DRIVEN BY POLYPLOIDY IN AN AGAMIC COMPLEX IN CRATAEGUS (ROSACEAE)

(2010) Eugenia Y. Y. Lo et al.   EVOLUTION

A comprehensive chloroplast DNA-based phylogeny of the genus Potentilla (Rosaceae): Implications for its geographic origin, phylogeography and generic circumscription

(2010) Christoph Dobeš et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

An Andean radiation: polyploidy in the tree genus Polylepis (Rosaceae, Sanguisorbeae)

(2010) A. N. Schmidt-Lebuhn et al.   PLANT BIOLOGY

Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition

(2009) Michael Freeling   Annual Review of Plant Biology

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

Allopolyploidy in Fragariinae (Rosaceae): Comparing four DNA sequence regions, with comments on classification

(2009) Magnus Lundberg et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): New insights from phylogenetic analyses of low-copy nuclear genes

(2009) M. Rousseau-Gueutin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Rosid radiation and the rapid rise of angiosperm-dominated forests

(2009) H. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Morphotype Catalogue, Floristic Analysis and Stratigraphic Description of the Aspen Shale Flora(Cretaceous–Albian) of Southwestern Wyoming

(2008) Daniel J. Peppe et al.   Bulletin of the Peabody Museum of Natural History

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION

Molecular phylogenetics of Alchemilla, Aphanes and Lachemilla (Rosaceae) inferred from plastid and nuclear intron and spacer DNA sequences, with comments on generic classification

(2008) B. Gehrke et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics

(2008) James C. Zachos et al.   NATURE

Hemiplasy: A New Term in the Lexicon of Phylogenetics

(2008) John C. Avise et al.   SYSTEMATIC BIOLOGY