Allopatric divergence and hybridization within Cupressus chengiana (Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China

Genomic Patterns of Local Adaptation under Gene Flow in Arabidopsis lyrata

(2019) Tuomas Hämälä et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut

(2019) Bo-Wen Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide Dissection of Co-selected UV-B Responsive Pathways in the UV-B Adaptation of Qingke

(2019) Xingquan Zeng et al.   Molecular Plant

Genomic architecture and introgression shape a butterfly radiation

(2019) Nathaniel B. Edelman et al.   SCIENCE

Mapping footprints of past genetic exchange

(2019) Loren H. Rieseberg   SCIENCE

Interspecific introgression mediates adaptation to whole genome duplication

(2019) Sarah Marburger et al.   Nature Communications

Population genetic analyses of the endangered alpine Sinadoxa corydalifolia (Adoxaceae) provide insights into future conservation

(2018) Yaling Wang et al.   BIODIVERSITY AND CONSERVATION

Selection and environmental adaptation along a path to speciation in the Tibetan frogNanorana parkeri

(2018) Guo-Dong Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The complete chloroplast genome of Cupressus jiangeensis (cupressaceae), a critically endangered conifer species in China

(2018) Jialiang Li et al.   Conservation Genetics Resources

Genetic diversity and demographic analysis of an endangered tree species Diplopanax stachyanthus in subtropical China: implications for conservation and management

(2018) Li Feng et al.   CONSERVATION GENETICS

Genome-Wide Evolutionary Analysis of Natural History and Adaptation in the World’s Tigers

(2018) Yue-Chen Liu et al.   CURRENT BIOLOGY

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

Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq

(2018) Carolina Osuna-Mascaró et al.   Scientific Reports

Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants

(2017) Amanda R. De La Torre et al.   MOLECULAR BIOLOGY AND EVOLUTION

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

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

Hybrid speciation leads to novel male secondary sexual ornamentation of an Amazonian bird

(2017) Alfredo O. Barrera-Guzmán et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid hybrid speciation in Darwin’s finches

(2017) Sangeet Lamichhaney et al.   SCIENCE

Allopatric divergence, demographic history, and conservation implications of an endangered conifer Cupressus chengiana in the eastern Qinghai-Tibet Plateau

(2017) Ting-Ting Xu et al.   Tree Genetics & Genomes

Redefining the Role of Admixture and Genomics in Species Conservation

(2017) Bridgett M. vonHoldt et al.   Conservation Letters

RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis

(2017) Lei Zhang et al.   Nature Communications

Species Delimitation and Lineage Separation History of a Species Complex of Aspens in China

(2017) Honglei Zheng et al.   Frontiers in Plant Science

Effects of Mountain Uplift and Climatic Oscillations on Phylogeography and Species Divergence in Four Endangered Notopterygium Herbs

(2017) Khurram Shahzad et al.   Frontiers in Plant Science

The genomic mosaicism of hybrid speciation

(2017) Tore O. Elgvin et al.   Science Advances

Multi-locus Analyses Reveal Four Giraffe Species Instead of One

(2016) Julian Fennessy et al.   CURRENT BIOLOGY

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

Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing

(2016) Guangpeng Ren et al.   NEW PHYTOLOGIST

Hybridization in Plants: Old Ideas, New Techniques

(2016) Benjamin E. Goulet et al.   PLANT PHYSIOLOGY

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Exploring population size changes using SNP frequency spectra

(2015) Xiaoming Liu et al.   NATURE GENETICS

Species delimitation and relationships: The dance of the seven veils

(2015) Yamama Naciri et al.   TAXON

Evolutionary origin and demographic history of an ancient conifer (Juniperus microsperma) in the Qinghai-Tibetan Plateau

(2015) Hui-Ying Shang et al.   Scientific Reports

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan biotas

(2014) Adrien Favre et al.   BIOLOGICAL REVIEWS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Diploid hybrid origin ofOstryopsis intermedia(Betulaceae) in the Qinghai-Tibet Plateau triggered by Quaternary climate change

(2014) Bingbing Liu et al.   MOLECULAR ECOLOGY

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

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

Evolutionary diversifications of plants on the Qinghai-Tibetan Plateau

(2014) Jun Wen et al.   Frontiers in Genetics

Genetic Diversity and Conservation Implications of Four Cupressus Species in China as Revealed by Microsatellite Markers

(2013) Xu Lu et al.   BIOCHEMICAL GENETICS

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

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

Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai-Tibet Plateau: homoploid hybrid origin and Pleistocene expansion

(2013) Yongshuai Sun et al.   MOLECULAR ECOLOGY

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

Geological and ecological factors drive cryptic speciation of yews in a biodiversity hotspot

(2013) Jie Liu et al.   NEW PHYTOLOGIST

Strong Purifying Selection at Synonymous Sites in D. melanogaster

(2013) David S. Lawrie et al.   PLoS Genetics

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Collinearity: a review of methods to deal with it and a simulation study evaluating their performance

(2012) Carsten F. Dormann et al.   ECOGRAPHY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Harnessing genomics for delineating conservation units

(2012) W. Chris Funk et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

POPULATION GENETIC EVIDENCE FOR COMPLEX EVOLUTIONARY HISTORIES OF FOUR HIGH ALTITUDE JUNIPER SPECIES IN THE QINGHAI-TIBETAN PLATEAU

(2011) Zhonghu Li et al.   EVOLUTION

Testing for Ancient Admixture between Closely Related Populations

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

Plant molecular phylogeography in China and adjacent regions: Tracing the genetic imprints of Quaternary climate and environmental change in the world’s most diverse temperate flora

(2011) Ying-Xiong Qiu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Phylogeography and allopatric divergence of cypress species (Cupressus L.) in the Qinghai-Tibetan Plateau and adjacent regions

(2010) Tingting Xu et al.   BMC EVOLUTIONARY BIOLOGY

Identifying Populations for Conservation on the Basis of Genetic Markers

(2010) Rémy J. Petit et al.   CONSERVATION BIOLOGY

ENMTools: a toolbox for comparative studies of environmental niche models

(2010) Dan L. Warren et al.   ECOGRAPHY

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Reconstructing Neogene vegetation and climates to infer tectonic uplift in western Yunnan, China

(2010) Bai-Nian Sun et al.   PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

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

Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci

(2009) Yuan Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity

(2009) Ikuo Uchiyama et al.   NUCLEIC ACIDS RESEARCH

Metabolism and roles of stilbenes in plants

(2009) Julie Chong et al.   PLANT SCIENCE

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

(2008) Cuong Than et al.   BMC BIOINFORMATICS

Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation

(2008) Steven J. Phillips et al.   ECOGRAPHY

ENVIRONMENTAL NICHE EQUIVALENCY VERSUS CONSERVATISM: QUANTITATIVE APPROACHES TO NICHE EVOLUTION

(2008) Dan L. Warren et al.   EVOLUTION

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

Stilbene Oligomers fromParthenocissus laetevirens: Isolation, Biomimetic Synthesis, Absolute Configuration, and Implication of Antioxidative Defense System in the Plant

(2008) Shan He et al.   JOURNAL OF ORGANIC CHEMISTRY

Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage

(2008) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION