Population transcriptomic sequencing reveals allopatric divergence and local adaptation in Pseudotaxus chienii (Taxaceae)

Genetic Variation Related to High Elevation Adaptation Revealed by Common Garden Experiments in Pinus yunnanensis

(2020) Yan-Qiang Sun et al.   Frontiers in Genetics

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

(2020) Jialiang Li et al.   MOLECULAR ECOLOGY

Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species

(2020) Matthew J.S. Gibson et al.   MOLECULAR ECOLOGY

The climatic association of population divergence and future extinction risk of Solanum pimpinellifolium

(2020) Ya-Ping Lin et al.   AoB Plants

Characterization and Analysis of the Full-Length Transcriptomes of Multiple Organs in Pseudotaxus chienii (W.C.Cheng) W.C.Cheng

(2020) Li Liu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

New insights into the population genetics of partially clonal organisms: when seagrass data meet theoretical expectations

(2020) Sophie Arnaud‐Haond et al.   MOLECULAR ECOLOGY

LFMM 2: Fast and accurate inference of gene-environment associations in genome-wide studies

(2019) Kevin Caye et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude

(2019) Ticao Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting the genetic basis of local adaptation in loblolly pine ( Pinus taeda L.) using whole exome‐wide genotyping and an integrative landscape genomics analysis approach

(2019) Mengmeng Lu et al.   Ecology and Evolution

Identification of putative key genes for coastal environments and cold adaptation in mangrove Kandelia obovata through transcriptome analysis

(2019) Wenyue Su et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Evolutionary history of a relict conifer, Pseudotaxus chienii (Taxaceae), in south-east China during the late Neogene: old lineage, young populations

(2019) Yixuan Kou et al.   ANNALS OF BOTANY

Landscape genomics predicts climate change‐related genetic offset for the widespread Platycladus orientalis (Cupressaceae)

(2019) Kai‐Hua Jia et al.   Evolutionary Applications

Colourful cones: how did flower colour first evolve?

(2019) Paula J Rudall   JOURNAL OF EXPERIMENTAL BOTANY

OUP accepted manuscript

(2018)   ANNALS OF BOTANY

Transcriptome sequencing dissection of the mechanisms underlying differential cold sensitivity in young and mature leaves of the tea plant ( Camellia sinensis )

(2018) Na-na Li et al.   JOURNAL OF PLANT PHYSIOLOGY

Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations

(2018) Brenna R. Forester et al.   MOLECULAR ECOLOGY

Coexpression network revealing the plasticity and robustness of population transcriptome during the initial stage of domesticating energy crop Miscanthus lutarioriparius

(2018) Shilai Xing et al.   PLANT MOLECULAR BIOLOGY

The genomics of local adaptation in trees: are we out of the woods yet?

(2018) Brandon M. Lind et al.   Tree Genetics & Genomes

The Transcriptomic Responses of Pinus massoniana to Drought Stress

(2018) Mingfeng Du et al.   Forests

SMS: Smart Model Selection in PhyML

(2017) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population transcriptomic characterization of the genetic and expression variation of a candidate progenitor of Miscanthus energy crops

(2017) Juan Yan et al.   MOLECULAR ECOLOGY

Gene-based SNP identification and validation in soybean using next-generation transcriptome sequencing

(2017) Yong Guo et al.   MOLECULAR GENETICS AND GENOMICS

Transcriptomic Response of Chinese Yew (Taxus chinensis) to Cold Stress

(2017) Delong Meng et al.   Frontiers in Plant Science

Directional genetic differentiation and relative migration

(2016) Lisa Sundqvist et al.   Ecology and Evolution

Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?

(2015) Mariano Alvarez et al.   MOLECULAR ECOLOGY

Genetic relationships and ecological divergence in Salix species and populations in Taiwan

(2015) Chun-Lin Huang et al.   Tree Genetics & Genomes

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Population transcriptomics reveals a potentially positive role of expression diversity in adaptation

(2014) Qin Xu et al.   Journal of Integrative Plant Biology

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation

(2014) Mbaye Tine et al.   Nature Communications

Genetic diversity and population structure of the endangered conifer Taxus wallichiana var. mairei (Taxaceae) revealed by Simple Sequence Repeat (SSR) markers

(2013) De-Quan Zhang et al.   BIOCHEMICAL SYSTEMATICS AND ECOLOGY

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets

(2013) Xiao Xu et al.   BMC BIOINFORMATICS

Where is positional uncertainty a problem for species distribution modelling?

(2013) Babak Naimi et al.   ECOGRAPHY

Potential for evolutionary responses to climate change - evidence from tree populations

(2013) Florian J. Alberto et al.   GLOBAL CHANGE BIOLOGY

Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models

(2013) Eric Frichot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations

(2013) Stéphane De Mita et al.   MOLECULAR ECOLOGY

SNP development from RNA-seq data in a nonmodel fish: how many individuals are needed for accurate allele frequency prediction?

(2013) C. Schunter et al.   Molecular Ecology Resources

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

Phylogeography and genetic effects of habitat fragmentation on endangeredTaxus yunnanensisin southwest China as revealed by microsatellite data

(2013) Y. C. Miao et al.   PLANT BIOLOGY

Enhancements to the ADMIXTURE algorithm for individual ancestry estimation

(2011) David H Alexander et al.   BMC BIOINFORMATICS

Abiotic stress tolerance mediated by protein ubiquitination

(2011) W. J. Lyzenga et al.   JOURNAL OF EXPERIMENTAL BOTANY

Signal transduction during cold, salt, and drought stresses in plants

(2011) Guo-Tao Huang et al.   MOLECULAR BIOLOGY REPORTS

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

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

ENMTools: a toolbox for comparative studies of environmental niche models

(2010) Dan L. Warren et al.   ECOGRAPHY

Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae)

(2010) A. J. Eckert et al.   GENETICS

The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing

(2010) JULIE JEUKENS et al.   MOLECULAR ECOLOGY

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

Genomics and the future of conservation genetics

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

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Adaptation genomics: the next generation

(2010) Jessica Stapley et al.   TRENDS IN ECOLOGY & EVOLUTION

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

High genetic differentiation and variation as revealed by ISSR marker in Pseudotaxus chienii (Taxaceae), an old rare conifer endemic to China

(2009) Yingjuan Su et al.   BIOCHEMICAL SYSTEMATICS AND ECOLOGY

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A global overview of drought and heat-induced tree mortality reveals emerging climate change risks for forests

(2009) Craig D. Allen et al.   FOREST ECOLOGY AND MANAGEMENT

Changes in plasma membrane lipids, aquaporins and proton pump of broccoli roots, as an adaptation mechanism to salinity

(2009) Luis López-Pérez et al.   PHYTOCHEMISTRY

A nuclear-localized HSP70 confers thermoprotective activity and drought-stress tolerance on plants

(2008) Eun Kyung Cho et al.   BIOTECHNOLOGY LETTERS

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

(2008) Steven J. Phillips et al.   ECOGRAPHY

Slope, aspect and climate: Spatially explicit and implicit models of topographic microclimate in chalk grassland

(2008) Jonathan Bennie et al.   ECOLOGICAL MODELLING

Genetic and bioclimatic variation in Solanum pimpinellifolium

(2008) Elena Zuriaga et al.   GENETIC RESOURCES AND CROP 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

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE