Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics

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

Deep phylogenetic incongruence in the angiosperm clade Rosidae

(2015) Miao Sun et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications

(2015) David C. Tank et al.   NEW PHYTOLOGIST

Large-scale phylogenetic analyses reveal multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms associated with climate change

(2015) Hong-Lei Li et al.   Scientific Reports

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

(2015) Marina Marcet-Houben et al.   PLOS BIOLOGY

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

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

A precise chloroplast genome of Nelumbo nucifera (Nelumbonaceae) evaluated with Sanger, Illumina MiSeq, and PacBio RS II sequencing platforms: insight into the plastid evolution of basal eudicots

(2014) Zhihua Wu et al.   BMC PLANT BIOLOGY

Causes, consequences and solutions of phylogenetic incongruence

(2014) A. Som   BRIEFINGS IN BIOINFORMATICS

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

Sibbaldia: a molecular phylogenetic study of a remarkably polyphyletic genus in Rosaceae

(2014) Torsten Eriksson et al.   PLANT SYSTEMATICS 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

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

(2013) Craig F. Barrett et al.   ANNALS OF BOTANY

Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.)

(2013) Lidan Sun et al.   BMC GENETICS

Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species

(2013) H. Hirakawa et al.   DNA RESEARCH

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

Plastid Genome Sequence of a Wild Woody Oil Species, Prinsepia utilis, Provides Insights into Evolutionary and Mutational Patterns of Rosaceae Chloroplast Genomes

(2013) Shuo Wang et al.   PLoS One

treePL: divergence time estimation using penalized likelihood for large phylogenies

(2012) Stephen A. Smith et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

(2012) Matthew Parks et al.   BMC EVOLUTIONARY BIOLOGY

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

Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

(2012) Z. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Pipid Root

(2012) Adam J. Bewick et al.   SYSTEMATIC BIOLOGY

Nelumbonaceae: Systematic position and species diversification revealed by the complete chloroplast genome

(2012) Jian-Hua XUE et al.   Journal of Systematics and Evolution

Angiosperm phylogeny: 17 genes, 640 taxa

(2011) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection

(2011) Riaz Ahmad et al.   BMC GENOMICS

Systematic Error in Seed Plant Phylogenomics

(2011) Bojian Zhong 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

Multi-gene analysis provides a well-supported phylogeny of Rosales

(2011) Shu-dong Zhang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda

(2011) L. I. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mammalian phylogeny reveals recent diversification rate shifts

(2011) T. Stadler   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic Analysis Resolves the Interordinal Relationships and Rapid Diversification of the Laurasiatherian Mammals

(2011) Xuming Zhou et al.   SYSTEMATIC BIOLOGY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

The age and diversification of the angiosperms re-revisited

(2010) Charles D. Bell et al.   AMERICAN JOURNAL OF BOTANY

Early evolutionary history of the flowering plant family Annonaceae: steady diversification and boreotropical geodispersal

(2010) Thomas L. P. Couvreur et al.   JOURNAL OF BIOGEOGRAPHY

Automated Removal of Noisy Data in Phylogenomic Analyses

(2010) Vadim V. Goremykin et al.   JOURNAL OF MOLECULAR EVOLUTION

The Position of Gnetales among Seed Plants: Overcoming Pitfalls of Chloroplast Phylogenomics

(2010) B. Zhong et al.   MOLECULAR BIOLOGY AND EVOLUTION

Complete Plastid Genome Sequences of Three Rosids (Castanea, Prunus, Theobroma): Evidence for At Least Two Independent Transfers of rpl22 to the Nucleus

(2010) R. K. Jansen et al.   MOLECULAR BIOLOGY AND 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

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

(2010) M. J. Moore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Increased seasonality through the Eocene to Oligocene transition in northern high latitudes

(2009) James S. Eldrett et al.   NATURE

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

Angiosperm diversification through time

(2008) Susana Magallón et al.   AMERICAN JOURNAL OF BOTANY

A Phylogenomic Study of Birds Reveals Their Evolutionary History

(2008) S. J. Hackett et al.   SCIENCE

Resolving an Ancient, Rapid Radiation in Saxifragales

(2008) Shuguang Jian et al.   SYSTEMATIC BIOLOGY