Evolutionary origin of a tetraploid Allium species on the Qinghai–Tibet Plateau

Extant timetrees are consistent with a myriad of diversification histories

(2020) Stilianos Louca et al.   NATURE

A chromosome-level genome assembly of garlic (Allium sativum L.) provides insights into genome evolution and allicin biosynthesis

(2020) Xiudong Sun et al.   Molecular Plant

Hybrid speciation via inheritance of alternate alleles of parental isolating genes

(2020) Zefu Wang et al.   Molecular Plant

A Phytogeographic Divide Along the 500 mm Isohyet in the Qinghai-Tibet Plateau: Insights From the Phylogeographic Evidence of Chinese Alliums (Amaryllidaceae)

(2019) MinJie Li et al.   Frontiers in Plant Science

WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations

(2019) Yongzhi Yang et al.   BMC BIOINFORMATICS

Insights from genomes into the evolutionary importance and prevalence of hybridization in nature

(2019) Scott A. Taylor et al.   Nature Ecology & Evolution

Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros

(2019) Changfei Guan et al.   BMC PLANT BIOLOGY

Phylogenomics of the genus Populus reveals extensive interspecific gene flow and balancing selection

(2019) Mingcheng Wang et al.   NEW PHYTOLOGIST

Taxonomic revision of Allium cyathophorum (Amaryllidaceae)

(2019) MIN JIE LI et al.   Phytotaxa

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

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

What do we mean when we talk about hybrid speciation?

(2018) Molly Schumer et al.   HEREDITY

Shifts in plant distributions in response to climate warming in a biodiversity hotspot, the Hengduan Mountains

(2018) Qianlong Liang et al.   JOURNAL OF BIOGEOGRAPHY

Meiotic chromosome stability of a newly formed allohexaploid wheat is facilitated by selection under abiotic stress as a spandrel

(2018) Yao Bian et al.   NEW PHYTOLOGIST

Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor

(2017) Xin Luo et al.   MOLECULAR ECOLOGY

The evolutionary significance of polyploidy

(2017) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Rapid hybrid speciation in Darwin’s finches

(2017) Sangeet Lamichhaney et al.   SCIENCE

Cytotaxonomy of Allium (Amaryllidaceae) subgenera Cyathophora and Amerallium sect. Bromatorrhiza

(2017) MIN-JIE LI et al.   Phytotaxa

Polyploidy: Pitfalls and paths to a paradigm

(2016) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Meiosis in autopolyploid and allopolyploid Arabidopsis

(2016) Andrew Lloyd et al.   CURRENT OPINION IN PLANT BIOLOGY

Genomics of hybridization and its evolutionary consequences

(2016) Richard J. Abbott et al.   MOLECULAR ECOLOGY

Revisiting the evolutionary events in Allium subgenus Cyathophora (Amaryllidaceae): Insights into the effect of the Hengduan Mountains Region (HMR) uplift and Quaternary climatic fluctuations to the environmental changes in the Qinghai-Tibet Plateau

(2016) Min-Jie Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Plann: A Command-Line Application for Annotating Plastome Sequences

(2015) Daisie I. Huang et al.   Applications in Plant Sciences

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

The role of homoploid hybridization in evolution: A century of studies synthesizing genetics and ecology

(2014) S. B. Yakimowski et al.   AMERICAN JOURNAL OF BOTANY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

Natural hybrids between Tragopogon mirus and T. miscellus (Asteraceae): A new perspective on karyotypic changes following hybridization at the polyploid level

(2013) Malorie J. Lipman et al.   AMERICAN JOURNAL OF BOTANY

Hybridization and speciation

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

Phylogenetic reappraisal of Allium subgenus Cyathophora (Amaryllidaceae) and related taxa, with a proposal of two new sections

(2013) De-Qing Huang et al.   JOURNAL OF PLANT RESEARCH

Detecting and Locating Whole Genome Duplications on a Phylogeny: A Probabilistic Approach

(2013) Charles-Elie Rabier 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

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

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

(2012) Limin Fu 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

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

Chromosome pairing affinities in interspecific hybrids reflect phylogenetic distances among lady's slipper orchids (Paphiopedilum)

(2011) Yung-I Lee et al.   ANNALS OF BOTANY

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

The crucial role of the accessible area in ecological niche modeling and species distribution modeling

(2011) Narayani Barve et al.   ECOLOGICAL MODELLING

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Diversity dynamics: molecular phylogenies need the fossil record

(2010) Tiago B. Quental et al.   TRENDS IN ECOLOGY & EVOLUTION

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Two extinct diploid progenitors were involved in allopolyploid formation in the Hordeum murinum (Poaceae: Triticeae) taxon complex

(2009) Sabine S. Jakob et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

(2009) J. A. Fawcett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS

ENVIRONMENTAL NICHE EQUIVALENCY VERSUS CONSERVATISM: QUANTITATIVE APPROACHES TO NICHE EVOLUTION

(2008) Dan L. Warren et al.   EVOLUTION