Phylogenetic relationships in Chinese oaks (Fagaceae, Quercus): Evidence from plastid genome using low-coverage whole genome sequencing

Uncovering the genomic signature of ancient introgression between white oak lineages ( Quercus )

(2019) Andrew A. Crowl et al.   NEW PHYTOLOGIST

East Asian origins of European holly oaks ( Quercus section Ilex Loudon) via the Tibet‐Himalaya

(2019) Xiao‐Long Jiang et al.   JOURNAL OF BIOGEOGRAPHY

Genomic landscape of the global oak phylogeny

(2019) Andrew L. Hipp et al.   NEW PHYTOLOGIST

Phylogeny and biogeography of East Asian evergreen oaks ( Quercus section Cyclobalanopsis ; Fagaceae): Insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia

(2018) Min Deng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

RADseq data reveal ancient, but not pervasive, introgression between Californian tree and scrub oak species (Quercus sect. Quercus : Fagaceae)

(2018) Bernard Y. Kim et al.   MOLECULAR ECOLOGY

Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)

(2017) Alexis R. Sullivan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Warm-cold colonization: response of oaks to uplift of the Himalaya-Hengduan Mountains

(2017) Hong-Hu Meng et al.   MOLECULAR ECOLOGY

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics

(2017) Shu-Dong Zhang et al.   NEW PHYTOLOGIST

Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot

(2017) Yaowu Xing et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Landscape genomic analysis of candidate genes for climate adaptation in a California endemic oak, Quercus lobata

(2016) V. L. Sork et al.   AMERICAN JOURNAL OF BOTANY

Phylogeography of Quercus aquifolioides provides novel insights into the Neogene history of a major global hotspot of plant diversity in south-west China

(2016) Fang K. Du et al.   JOURNAL OF BIOGEOGRAPHY

Signatures of local adaptation in candidate genes of oaks (Quercusspp.) with respect to present and future climatic conditions

(2016) Christian Rellstab et al.   MOLECULAR ECOLOGY

Phylogeographic structuring of plastome diversity in Mediterranean oaks (Quercus Group Ilex, Fagaceae)

(2016) Martina Vitelli et al.   Tree Genetics & Genomes

Genetic Structure and Evolutionary History of Three Alpine Sclerophyllous Oaks in East Himalaya-Hengduan Mountains and Adjacent Regions

(2016) Li Feng et al.   Frontiers in Plant Science

Comparative Analysis of the Complete Chloroplast Genomes of Five Quercus Species

(2016) Yanci Yang et al.   Frontiers in Plant Science

Plastome data reveal multiple geographic origins ofQuercusGroup Ilex

(2016) Marco Cosimo Simeone et al.   PeerJ

Historical introgression among the American live oaks and the comparative nature of tests for introgression

(2015) Deren A. R. Eaton et al.   EVOLUTION

Combining molecular and fossil data to infer demographic history ofQuercus cerris: insights on European eastern glacial refugia

(2015) F. Bagnoli et al.   JOURNAL OF BIOGEOGRAPHY

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 and biogeography of the American live oaks (QuercussubsectionVirentes): a genomic and population genetics approach

(2015) Jeannine Cavender-Bares et al.   MOLECULAR ECOLOGY

Multiple glacial refugia for cool-temperate deciduous trees in northern East Asia: the Mongolian oak as a case study

(2015) Yan-Fei Zeng et al.   MOLECULAR ECOLOGY

Chloroplast capture and intra- and inter-continental biogeographic diversification in the Asian – New World disjunct plant genus Osmorhiza (Apiaceae)

(2015) Ting-Shuang Yi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates

(2015) Andan Zhu et al.   NEW PHYTOLOGIST

Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots

(2015) Craig F. Barrett et al.   NEW PHYTOLOGIST

Leaf epidermal features ofQuercussubgenusCyclobalanopsis(Fagaceae) and their systematic significance

(2015) Min Deng et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

The Chloroplast Genome of Elaeagnus macrophylla and trnH Duplication Event in Elaeagnaceae

(2015) Kyoung Su Choi et al.   PLoS One

Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships

(2014) Hui Huang et al.   BMC EVOLUTIONARY BIOLOGY

Sky islands of southwest China. I: an overview of phylogeographic patterns

(2014) Kai He et al.   CHINESE SCIENCE BULLETIN

Pollen morphology and ultrastructure ofQuercuswith focus on Group Ilex (=QuercussubgenusHeterobalanus(Oerst.) Menitsky): implications for oak systematics and evolution

(2014) Thomas Denk et al.   GRANA

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

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

Complete Chloroplast Genome Sequence of Omani Lime (Citrus aurantiifolia) and Comparative Analysis within the Rosids

(2014) Huei-Jiun Su et al.   PLoS One

Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)

(2014) Peng-Fei Ma et al.   SYSTEMATIC BIOLOGY

Multiple nuclear genes stabilize the phylogenetic backbone of the genusQuercus

(2014) François Hubert et al.   SYSTEMATICS AND BIODIVERSITY

Phylogeography of Quercus glauca (Fagaceae), a dominant tree of East Asian subtropical evergreen forests, based on three chloroplast DNA interspace sequences

(2014) Jin Xu et al.   Tree Genetics & Genomes

Pyrosequencing of the northern red oak (Quercus rubra L.) chloroplast genome reveals high quality polymorphisms for population management

(2014) Lisa W. Alexander et al.   Tree Genetics & Genomes

Application of plastid and nuclear markers to DNA barcoding of Euro-Mediterranean oaks (Quercus, Fagaceae): problems, prospects and phylogenetic implications

(2013) Marco C. Simeone et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Phylogenetic Analysis of 47 Chloroplast Genomes Clarifies the Contribution of Wild Species to the Domesticated Apple Maternal Line

(2013) Svetlana V. Nikiforova et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Influence of late Quaternary climate change on present patterns of genetic variation in valley oak,Quercus lobataNée

(2013) Paul F. Gugger et al.   MOLECULAR ECOLOGY

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

Plastid genomes and deep relationships among the commelinid monocot angiosperms

(2012) Craig F. Barrett et al.   CLADISTICS

The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps

(2012) E. Mosca et al.   MOLECULAR ECOLOGY

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Horizontal transfer of chloroplast genomes between plant species

(2012) S. Stegemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular and morphological support for a Florida origin of the Cuban oak

(2011) Paul F. Gugger et al.   JOURNAL OF BIOGEOGRAPHY

Geographic variation in the structure of oak hybrid zones provides insights into the dynamics of speciation

(2011) YAN-FEI ZENG et al.   MOLECULAR ECOLOGY

Quercus macrantheraFisch. & Mey. ex Hohen. andQuercus ibericaM. Bieb.: Taxonomic definition and systematic relationships with European oaks inferred from nuclear internal transcribed spacer (ITS) data

(2011) A. Papini et al.   PLANT BIOSYSTEMS

Migration of endpoints of two genes relative to boundaries between regions of the plastid genome in the grass family (Poaceae)

(2010) Jerrold I. Davis et al.   AMERICAN JOURNAL OF BOTANY

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

Exploring Species Limits in Two Closely Related Chinese Oaks

(2010) Yan-Fei Zeng et al.   PLoS One

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

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

Evidence of chloroplast capture in South American Nothofagus (subgenus Nothofagus, Nothofagaceae)

(2009) M. Cristina Acosta et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots

(2008) Rui-Jiang Wang et al.   BMC EVOLUTIONARY BIOLOGY