Population genomic evidence for radiative divergence of four Orychophragmus (Brassicaceae) species in eastern Asia

Interspecific Divergence of Two Sinalliaria (Brassicaceae) Species in Eastern China

(2018) Lei Zhang et al.   Frontiers in Plant Science

Analyses of genome-scale variation reveal divergence of two Sinalliaria species (Brassicaceae) with continuous but limited gene flow

(2018) Tian-Jing Wang et al.   Journal of Systematics and Evolution

Reticulate evolution within a spruce ( Picea ) species complex revealed by population genomic analysis

(2018) Yongshuai Sun et al.   EVOLUTION

Population genomic analysis reveals that homoploid hybrid speciation can be a lengthy process

(2018) Dafu Ru et al.   MOLECULAR ECOLOGY

Trans‐lineage polymorphism and nonbifurcating diversification of the genus Picea

(2018) Shuo Feng et al.   NEW PHYTOLOGIST

Ancient hybridization and strong adaptation to viruses across African vervet monkey populations

(2017) Hannes Svardal et al.   NATURE GENETICS

Genomic evidence for polyphyletic origins and interlineage gene flow within complex taxa: a case study ofPicea brachytylain the Qinghai-Tibet Plateau

(2016) Dafu Ru et al.   MOLECULAR ECOLOGY

Genomic variation at the tips of the adaptive radiation of Darwin's finches

(2016) Jaime A. Chaves et al.   MOLECULAR ECOLOGY

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

(2016) Polina Yu Novikova et al.   NATURE GENETICS

The Evolving Theory of Evolutionary Radiations

(2016) M. Simões et al.   TRENDS IN ECOLOGY & EVOLUTION

Species Delimitation and Interspecific Relationships of the Genus Orychophragmus (Brassicaceae) Inferred from Whole Chloroplast Genomes

(2016) Huan Hu et al.   Frontiers in Plant Science

Adaptive radiation versus ‘radiation’ and ‘explosive diversification’: why conceptual distinctions are fundamental to understanding evolution

(2015) Thomas J. Givnish   NEW PHYTOLOGIST

Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploidCapsella bursa-pastoris

(2015) Gavin M. Douglas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species delimitation in Orychophragmus (Brassicaceae) based on chloroplast and nuclear DNA barcodes

(2015) Huan Hu et al.   TAXON

The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

(2015) Alexander Suh et al.   PLOS BIOLOGY

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)

(2015) Nicolas Delhomme et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coalescent Methods Are Robust to the Simultaneous Effects of Long Branches and Incomplete Lineage Sorting

(2014) L. Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rapid radiation and dispersal out of the Qinghai-Tibetan Plateau of an alpine plant lineage Rhodiola (Crassulaceae)

(2014) Jian-Qiang Zhang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolutionary history and underlying adaptation of alpine plants on the Qinghai-Tibet Plateau

(2014) Jian-Quan LIU et al.   Journal of Systematics and Evolution

Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data

(2013) B. L. Browning et al.   GENETICS

Hybridization and speciation

(2013) R. Abbott et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Adaptive radiation, correlated and contingent evolution, and net species diversification in Bromeliaceae

(2013) Thomas J. Givnish et al.   MOLECULAR PHYLOGENETICS 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

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes

(2013) Huan Qiu et al.   Frontiers in Plant Science

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Molecular phylogenetics: principles and practice

(2012) Ziheng Yang et al.   NATURE REVIEWS GENETICS

Phylogeographic studies of plants in China: Advances in the past and directions in the future

(2012) Jian-Quan LIU et al.   Journal of Systematics and Evolution

fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios

(2011) Laurent Excoffier et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Enhancements to the ADMIXTURE algorithm for individual ancestry estimation

(2011) David H Alexander et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

Contemporaneous and recent radiations of the world's major succulent plant lineages

(2011) M. Arakaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic Insights on Adaptive Radiation

(2010) Richard E. Glor   Annual Review of Ecology Evolution and Systematics

Phybase: an R package for species tree analysis

(2010) L. Liu et al.   BIOINFORMATICS

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

msABC: a modification of Hudson’s ms to facilitate multi-locus ABC analysis

(2010) P. PAVLIDIS et al.   Molecular Ecology Resources

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Adaptive radiation, nonadaptive radiation, ecological speciation and nonecological speciation

(2009) Rebecca J. Rundell et al.   TRENDS IN ECOLOGY & EVOLUTION

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH