Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae)

Phylotranscriptomics of Theaceae: generic-level relationships, reticulation and whole-genome duplication

(2022) Qiong Zhang et al.   ANNALS OF BOTANY

Phylogenetics based on three nuclear regions and its implications for systematics and evolutionary history of global Camellia (Theaceae)

(2022) Dongwei Zhao et al.   Journal of Systematics and Evolution

Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants

(2022) Qiong Wu et al.   PLANT JOURNAL

Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia

(2021) Li Li et al.   BMC GENOMICS

Nuclear Phylotranscriptomics/Phylogenomics Support Numerous Polyploidization Events and Hypotheses for the Evolution of Rhizobial Nitrogen-Fixing Symbiosis in Fabaceae

(2021) Yiyong Zhao et al.   Molecular Plant

Phylogenomic approach reveals strong signatures of introgression in the rapid diversification of Neotropical true fruit flies (Anastrepha: Tephritidae)

(2021) Carlos Congrains et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily

(2021) Hong‐Xin Wang et al.   Journal of Systematics and Evolution

Development of genic SSR marker resources from RNA-seq data in Camellia japonica and their application in the genus Camellia

(2021) Qingyuan Li et al.   Scientific Reports

Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene

(2021) Hanghui Kong et al.   SYSTEMATIC BIOLOGY

Phytogeographic History of the Tea Family Inferred Through High-Resolution Phylogeny and Fossils

(2021) Yujing Yan et al.   SYSTEMATIC BIOLOGY

Rapid Radiation and Rampant Reticulation: Phylogenomics of South American Liolaemus Lizards

(2021) Damien Esquerré et al.   SYSTEMATIC BIOLOGY

Speciation along the elevation gradient: Divergence of Roscoea species within the south slope of the Himalayas

(2021) Jian-Li Zhao et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales

(2020) Drew A. Larson et al.   AMERICAN JOURNAL OF BOTANY

Phylotranscriptomics in Cucurbitaceae Reveal Multiple Whole Genome Duplications and Key Morphological and Molecular Innovations

(2020) Jing Guo et al.   Molecular Plant

Genomic data reveals two distinct species from the widespread alpine ginger Roscoea tibetica Batalin (Zingiberaceae)

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

Asterid phylogenomics/phylotranscriptomics uncover morphological evolutionary histories and support phylogenetic placement for numerous whole genome duplications

(2020) Caifei Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

A phylogeny for the Drosophila montium species group: a model clade for comparative analyses

(2020) William R. Conner et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome sequences provide insights into the reticulate origin and unique traits of woody bamboos

(2019) Zhen-Hua Guo et al.   Molecular Plant

Outgroup sampling in phylogenetics: Severity of test and successive outgroup expansion

(2019) Taran Grant   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Phylogenomic conflict resulting from ancient introgression following species diversification in Stewartia s.l. (Theaceae)

(2019) Han-Yang Lin et al.   MOLECULAR PHYLOGENETICS 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

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

Assessing the Impacts of Positive Selection on Coalescent-Based Species Tree Estimation and Species Delimitation

(2018) Richard H Adams et al.   SYSTEMATIC BIOLOGY

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

(2018) et al.   Genes

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)

(2017) Nicolás García et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae)

(2017) Hong-Juan Wang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Insights into the historical assembly of East Asian subtropical evergreen broadleaved forests revealed by the temporal history of the tea family

(2017) Xiang-Qin Yu et al.   NEW PHYTOLOGIST

Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets

(2017) Liping Zeng et al.   NEW PHYTOLOGIST

Reticulation, divergence, and the phylogeography–phylogenetics continuum

(2016) Scott V. Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inconsistency of Species Tree Methods under Gene Flow

(2016) Claudia Solís-Lemus et al.   SYSTEMATIC BIOLOGY

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

(2016) Claudia Solís-Lemus et al.   PLoS Genetics

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

(2015) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

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

What's in an Outgroup? The Impact of Outgroup Choice on the Phylogenetic Position of Thalattosuchia (Crocodylomorpha) and the Origin of Crocodyliformes

(2015) Eric W. Wilberg   SYSTEMATIC BIOLOGY

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

(2014) Hui Huang et al.   BMC EVOLUTIONARY BIOLOGY

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Evaluating the Effects of Non-Neutral Molecular Markers on Phylogeny Inference

(2014) Dawn M. Roje   PLoS One

Molecular Phylogeny of Tribe Theeae (Theaceae s.s.) and Its Implications for Generic Delimitation

(2014) Wei Zhang et al.   PLoS One

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

(2014) Liping Zeng et al.   Nature Communications

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

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

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae

(2013) Lei Zhao et al.   PLoS One

Comparative Chloroplast Genomes of Camellia Species

(2013) Jun-Bo Yang et al.   PLoS One

The potential of genomics in plant systematics

(2013) Douglas E. Soltis et al.   TAXON

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

(2012) M. Kearse et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dispersion of rDNA loci and its implications on intragenomic variability and phylogenetic studies in Camellia

(2012) Kunjupillai Vijayan et al.   SCIENTIA HORTICULTURAE

Purifying Selection Can Obscure the Ancient Age of Viral Lineages

(2011) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

Molecular taxonomy of Camellia (Theaceae) inferred from nrITS sequences

(2009) K. Vijayan et al.   AMERICAN JOURNAL OF BOTANY

The causes of mitochondrial DNA gene tree paraphyly in birds

(2009) Bailey D. McKay et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION