相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Regional occupancy increases for widespread species but decreases for narrowly distributed species in metacommunity time series
Wu-Bing Xu et al.
NATURE COMMUNICATIONS (2023)
Distinct hybridization modes in wide- and narrow-ranged lineages of Causonis (Vitaceae)
Jinren Yu et al.
BMC BIOLOGY (2023)
Directional turnover towards larger-ranged plants over time and across habitats
Ingmar R. Staude et al.
ECOLOGY LETTERS (2022)
Expansion of the rare Eucalyptus risdonii under climate change through hybridization with a closely related species despite hybrid inferiority
T. R. Pfeilsticker et al.
ANNALS OF BOTANY (2022)
Tree2GD: a phylogenomic method to detect large-scale gene duplication events
Duoyuan Chen et al.
BIOINFORMATICS (2022)
Dsuite - Fast D-statistics and related admixture evidence from VCF files
Milan Malinsky et al.
MOLECULAR ECOLOGY RESOURCES (2021)
Causonis sessilifolia (Vitaceae), a new species from Thailand
Anna Trias-Blasi et al.
PHYTOKEYS (2021)
Phylogeny, character evolution and taxonomic revision of Causonis, a segregate genus from Cayratia (Vitaceae)
Gaurav Parmar et al.
TAXON (2021)
The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales
Liming Cai et al.
SYSTEMATIC BIOLOGY (2021)
Rapid Evolution of Invasive Weeds Under Climate Change: Present Evidence and Future Research Needs
David R. Clements et al.
FRONTIERS IN AGRONOMY (2021)
Polyploidy: an evolutionary and ecological force in stressful times
Yves Van de Peer et al.
PLANT CELL (2021)
Reticulate Evolution Helps Explain Apparent Homoplasy in Floral Biology and Pollination in Baobabs (Adansonia; Bombacoideae; Malvaceae)
Nisa Karimi et al.
SYSTEMATIC BIOLOGY (2020)
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Bui Quang Minh et al.
MOLECULAR BIOLOGY AND EVOLUTION (2020)
Generalist plants are more competitive and more functionally similar to each other than specialist plants: insights from network analyses
Pierre Denelle et al.
JOURNAL OF BIOGEOGRAPHY (2020)
Replacements of small- by large-ranged species scale up to diversity loss in Europe's temperate forest biome
Ingmar R. Staude et al.
NATURE ECOLOGY & EVOLUTION (2020)
The evolutionary conundrum of whole-genome duplication
Lorenzo Carretero-Paulet et al.
AMERICAN JOURNAL OF BOTANY (2020)
Asterid Phylogenomics/Phylotranscriptomics Uncover Morphological Evolutionary Histories and Support Phylogenetic Placement for Numerous Whole-Genome Duplications
Caifei Zhang et al.
MOLECULAR BIOLOGY AND EVOLUTION (2020)
An astronomically dated record of Earth's climate and its predictability over the last 66 million years
Thomas Westerhold et al.
SCIENCE (2020)
GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
Jian-Jun Jin et al.
GENOME BIOLOGY (2020)
The global biogeography of polyploid plants
Anna Rice et al.
NATURE ECOLOGY & EVOLUTION (2019)
PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes
Xiao-Jian Qu et al.
PLANT METHODS (2019)
Origins and Assembly of Malesian Rainforests
Robert M. Kooyman et al.
Annual Review of Ecology Evolution and Systematics (2019)
More is less: net gain in species richness, but biotic homogenization over 140 years
Tora Finderup Nielsen et al.
ECOLOGY LETTERS (2019)
wgd-simple command line tools for the analysis of ancient whole-genome duplications
Arthur Zwaenepoel et al.
BIOINFORMATICS (2019)
The causes of evolvability and their evolution
Joshua L. Payne et al.
NATURE REVIEWS GENETICS (2019)
UFBoot2: Improving the Ultrafast Bootstrap Approximation
Diep Thi Hoang et al.
MOLECULAR BIOLOGY AND EVOLUTION (2018)
Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life
James B. Pease et al.
AMERICAN JOURNAL OF BOTANY (2018)
Gene flow analysis method, the D-statistic, is robust in a wide parameter space
Yichen Zheng et al.
BMC BIOINFORMATICS (2018)
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
Chao Zhang et al.
BMC BIOINFORMATICS (2018)
Significance of whole-genome duplications on the emergence of evolutionary novelties
Yuuta Moriyama et al.
BRIEFINGS IN FUNCTIONAL GENOMICS (2018)
So many genes, so little time: A practical approach to divergence-time estimation in the genomic era
Stephen A. Smith et al.
PLOS ONE (2018)
Genome size variation and evolution in the grape family Vitaceae
Zhao-Fu Chu et al.
JOURNAL OF SYSTEMATICS AND EVOLUTION (2018)
Widespread winners and narrow-ranged losers: Land use homogenizes biodiversity in local assemblages worldwide
Tim Newbold et al.
PLOS BIOLOGY (2018)
Hybridization can promote adaptive radiation by means of transgressive segregation
Kotaro Kagawa et al.
ECOLOGY LETTERS (2018)
WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas
Stephen E. Fick et al.
INTERNATIONAL JOURNAL OF CLIMATOLOGY (2017)
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
Jaime Huerta-Cepas et al.
MOLECULAR BIOLOGY AND EVOLUTION (2017)
PhyloNetworks: A Package for Phylogenetic Networks
Claudia Solis-Lemus et al.
MOLECULAR BIOLOGY AND EVOLUTION (2017)
ModelFinder: fast model selection for accurate phylogenetic estimates
Subha Kalyaanamoorthy et al.
NATURE METHODS (2017)
The evolutionary significance of polyploidy
Yves Van de Peer et al.
NATURE REVIEWS GENETICS (2017)
Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events
Gregg W. C. Thomas et al.
SYSTEMATIC BIOLOGY (2017)
Contentious relationships in phylogenomic studies can be driven by a handful of genes
Xing-Xing Shen et al.
NATURE ECOLOGY & EVOLUTION (2017)
Adaptive introgression as a resource for management and genetic conservation in a changing climate
Jill A. Hamilton et al.
CONSERVATION BIOLOGY (2016)
Direct Estimate of the Spontaneous Mutation Rate Uncovers the Effects of Drift and Recombination in the Chlamydomonas reinhardtii Plastid Genome
Rob W. Ness et al.
MOLECULAR BIOLOGY AND EVOLUTION (2016)
Hybridization and extinction
Marco Todesco et al.
EVOLUTIONARY APPLICATIONS (2016)
TransRate: reference-free quality assessment of de novo transcriptome assemblies
Richard Smith-Unna et al.
GENOME RESEARCH (2016)
Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
Olga Chernomor et al.
SYSTEMATIC BIOLOGY (2016)
Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation
James B. Pease et al.
PLOS BIOLOGY (2016)
HYBPIPER: EXTRACTING CODING SEQUENCE AND INTRONS FOR PHYLOGENETICS FROM HIGH-THROUGHP UT SEQUENCING READS USING TARGET ENRICHMENT
Matthew G. Johnson et al.
APPLICATIONS IN PLANT SCIENCES (2016)
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Felipe A. Simao et al.
BIOINFORMATICS (2015)
Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
Stephen A. Smith et al.
BMC EVOLUTIONARY BIOLOGY (2015)
RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography
Yan Yu et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2015)
Exploring Tree-Like and Non-Tree-Like Patterns Using Genome Sequences: An Example Using the Inbreeding Plant Species Arabidopsis thaliana (L.) Heynh
Noah W. M. Stenz et al.
SYSTEMATIC BIOLOGY (2015)
Genetic rescue to the rescue
Andrew R. Whiteley et al.
TRENDS IN ECOLOGY & EVOLUTION (2015)
Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes
Steven B. Cannon et al.
MOLECULAR BIOLOGY AND EVOLUTION (2015)
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
David M. Emms et al.
GENOME BIOLOGY (2015)
ASTRAL: genome-scale coalescent-based species tree estimation
S. Mirarab et al.
BIOINFORMATICS (2014)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
InterProScan 5: genome-scale protein function classification
Philip Jones et al.
BIOINFORMATICS (2014)
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Alexandros Stamatakis
BIOINFORMATICS (2014)
Hybridisation is associated with increased fecundity and size in invasive taxa: meta-analytic support for the hybridisation-invasion hypothesis
Stephen M. Hovick et al.
ECOLOGY LETTERS (2014)
TreSpEx-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information
Torsten H. Struck
EVOLUTIONARY BIOINFORMATICS (2014)
Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics
Ya Yang et al.
MOLECULAR BIOLOGY AND EVOLUTION (2014)
Lineage diversification and hybridization in the Cayratia japonica- Cayratia tenuifolia species complex
Naoko Ishikawa et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2014)
The Influence of Gene Flow on Species Tree Estimation: A Simulation Study
Adam D. Leache et al.
SYSTEMATIC BIOLOGY (2014)
Model Selection in Historical Biogeography Reveals that Founder-Event Speciation Is a Crucial Process in Island Clades
Nicholas J. Matzke
SYSTEMATIC BIOLOGY (2014)
How important is intraspecific genetic admixture to the success of colonising populations?
Marc Rius et al.
TRENDS IN ECOLOGY & EVOLUTION (2014)
Niche breadth predicts geographical range size: a general ecological pattern
Rachel A. Slatyer et al.
ECOLOGY LETTERS (2013)
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh et al.
MOLECULAR BIOLOGY AND EVOLUTION (2013)
On the accumulation of deleterious mutations during range expansions
S. Peischl et al.
MOLECULAR ECOLOGY (2013)
Inferring ancient divergences requires genes with strong phylogenetic signals
Leonidas Salichos et al.
NATURE (2013)
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
Brian J. Haas et al.
NATURE PROTOCOLS (2013)
Transcriptome Sequences Resolve Deep Relationships of the Grape Family
Jun Wen et al.
PLOS ONE (2013)
Evolutionary rescue by beneficial mutations in environments that change in space and time
Mark Kirkpatrick et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2013)
Bayesian Analysis of Biogeography when the Number of Areas is Large
Michael J. Landis et al.
SYSTEMATIC BIOLOGY (2013)
Rare Species Support Vulnerable Functions in High-Diversity Ecosystems
David Mouillot et al.
PLOS BIOLOGY (2013)
The more the better? The role of polyploidy in facilitating plant invasions
Mariska te Beest et al.
ANNALS OF BOTANY (2012)
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
Matthew Kearse et al.
BIOINFORMATICS (2012)
Niche breadth, rarity and ecological characteristics within a regional flora spanning large environmental gradients
Isabelle Boulangeat et al.
JOURNAL OF BIOGEOGRAPHY (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
Fredrik Ronquist et al.
SYSTEMATIC BIOLOGY (2012)
A genome triplication associated with early diversification of the core eudicots
Yuannian Jiao et al.
GENOME BIOLOGY (2012)
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G. Grabherr et al.
NATURE BIOTECHNOLOGY (2011)
Bushkiller (Cayratia japonica) Response to Selected Herbicides
Amanda M. West et al.
INVASIVE PLANT SCIENCE AND MANAGEMENT (2011)
Phybase: an R package for species tree analysis
Liang Liu et al.
BIOINFORMATICS (2010)
Genomic admixture increases fitness during a biological invasion
S. R. Keller et al.
JOURNAL OF EVOLUTIONARY BIOLOGY (2010)
Geographic and phylogenetic patterns in Silene section Melandrium (Caryophyllaceae) as inferred from chloroplast and nuclear DNA sequences
Anja Rautenberg et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2010)
FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments
Morgan N. Price et al.
PLOS ONE (2010)
Patterns of hybridization in plants
Kenneth D. Whitney et al.
PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS (2010)
ANGIOSPERM DIVERSIFICATION THROUGH TIME
Susana Magallon et al.
AMERICAN JOURNAL OF BOTANY (2009)
Evolution and Ecology of Species Range Limits
Jason P. Sexton et al.
ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS (2009)
The Role of Hybridization in Plant Speciation
Pamela S. Soltis et al.
ANNUAL REVIEW OF PLANT BIOLOGY (2009)
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Salvador Capella-Gutierrez et al.
BIOINFORMATICS (2009)
OPINION The evolutionary significance of ancient genome duplications
Yves Van de Peer et al.
NATURE REVIEWS GENETICS (2009)
Gene tree discordance, phylogenetic inference and the multispecies coalescent
James H. Degnan et al.
TRENDS IN ECOLOGY & EVOLUTION (2009)
Perspective - Genomic plasticity and the diversity of polyploid plants
A. R. Leitch et al.
SCIENCE (2008)
Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis
Richard H. Ree et al.
SYSTEMATIC BIOLOGY (2008)
A selective sweep in the chloroplast DNA of dioecious Silene (Section Elisanthe)
Graham Muir et al.
GENETICS (2007)
Genetic rescue persists beyond first-generation outbreeding in small populations of a rare plant
Yvonne Willi et al.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2007)
Seed morphology of modern and fossil Ampelocissus (Vitaceae) and implications for phytogeography
Iju Chen et al.
AMERICAN JOURNAL OF BOTANY (2007)
PAML 4: Phylogenetic analysis by maximum likelihood
Ziheng Yang
MOLECULAR BIOLOGY AND EVOLUTION (2007)
Limits to evolution at range margins: when and why does adaptation fail?
Jon R. Bridle et al.
TRENDS IN ECOLOGY & EVOLUTION (2007)
Relative importance for linear regression in R:: The package relaimpo
Ulrike Groemping
JOURNAL OF STATISTICAL SOFTWARE (2006)
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Weizhong Li et al.
BIOINFORMATICS (2006)
Widespread genome duplications throughout the history of flowering plants
Liying Cui et al.
GENOME RESEARCH (2006)
Discordance of species trees with their most likely gene trees
James H. Degnan et al.
PLOS GENETICS (2006)
Application of phylogenetic networks in evolutionary studies
DH Huson et al.
MOLECULAR BIOLOGY AND EVOLUTION (2006)
Maximum entropy modeling of species geographic distributions
SJ Phillips et al.
ECOLOGICAL MODELLING (2006)
Very high resolution interpolated climate surfaces for global land areas
RJ Hijmans et al.
INTERNATIONAL JOURNAL OF CLIMATOLOGY (2005)
Polyploidy in arctic plants
C Brochmann et al.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY (2004)
Predicting the risk of extinction through hybridization
DE Wolf et al.
CONSERVATION BIOLOGY (2001)
The evolutionary fate and consequences of duplicate genes
M Lynch et al.
SCIENCE (2000)
Alternative causes for range limits: a metapopulation perspective
RD Holt et al.
ECOLOGY LETTERS (2000)