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。Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny
Kathryn A. Uckele et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2021)
Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l.
Diego F. Morales-Briones et al.
SYSTEMATIC BIOLOGY (2021)
RASP 4: Ancestral State Reconstruction Tool for Multiple Genes and Characters
Yan Yu et al.
MOLECULAR BIOLOGY AND EVOLUTION (2020)
Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies
Erik J. M. Koenen et al.
NEW PHYTOLOGIST (2020)
Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages
Gregory W. Stull et al.
AMERICAN JOURNAL OF BOTANY (2020)
Phylogenomics, biogeography, and evolution of morphology and ecological niche of the eastern Asian-eastern North AmericanNyssa(Nyssaceae)
Wenbin Zhou et al.
JOURNAL OF SYSTEMATICS AND EVOLUTION (2020)
Allopatric divergence and hybridization within Cupressus chengiana (Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China
Jialiang Li et al.
MOLECULAR ECOLOGY (2020)
Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis
Michelle L. Gaynor et al.
JOURNAL OF SYSTEMATICS AND EVOLUTION (2020)
Phylogenomics, biogeography, and evolution of the blue- or white-fruited dogwoods (Cornus)-Insights into morphological and ecological niche divergence following intercontinental geographic isolation
Kira Lindelof et al.
JOURNAL OF SYSTEMATICS AND EVOLUTION (2020)
Repeated intercontinental migrations and recurring hybridizations characterise the evolutionary history of yew (Taxus L.)
Michael Moller et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2020)
The rise of angiosperms pushed conifers to decline during global cooling
Fabien L. Condamine et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
Jian-Jun Jin et al.
GENOME BIOLOGY (2020)
A transcriptome-based resolution for a key taxonomic controversy in Cupressaceae
Kangshan Mao et al.
ANNALS OF BOTANY (2019)
An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers (Helianthus)
Julie A. Lee-Yaw et al.
NEW PHYTOLOGIST (2019)
Asymmetric biotic interchange across the Bering land bridge between Eurasia and North America
Dechun Jiang et al.
NATIONAL SCIENCE REVIEW (2019)
Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes
Yang Liu et al.
NATURE COMMUNICATIONS (2019)
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis
Remco Bouckaert et al.
PLOS COMPUTATIONAL BIOLOGY (2019)
Phylogenomic analyses reveal an exceptionally high number of evolutionary shifts in a florally diverse Glade of African legumes
Dario Ojeda et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2019)
The importance of the North Atlantic land bridges and eastern Asia in the post-Boreotropical biogeography of the Northern Hemisphere as revealed from the poison ivy genus (Toxicodendron, Anacardiaceae)
Ying Jiang et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2019)
Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous
Chao-Nan Fu et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2019)
Thirty clues to the exceptional diversification of flowering plants
Susana Magallon et al.
ANNALS OF BOTANY (2019)
Trans-lineage polymorphism and nonbifurcating diversification of the genus Picea
Shuo Feng et al.
NEW PHYTOLOGIST (2019)
Phylotranscriptomics resolves interspecific relationships and indicates multiple historical out-of-North America dispersals through the Bering Land Bridge for the genus Picea (Pinaceae)
Cheng-Cheng Shao et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2019)
OrthoFinder: phylogenetic orthology inference for comparative genomics
David M. Emms et al.
GENOME BIOLOGY (2019)
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)
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
Chao Zhang et al.
BMC BIOINFORMATICS (2018)
Reconciling Conflicting Phylogenies in the Origin of Sweet Potato and Dispersal to Polynesia
Pablo Munoz-Rodriguez et al.
CURRENT BIOLOGY (2018)
Conceptual and statistical problems with the DEC plus J model of founder-event speciation and its comparison with DEC via model selection
Richard H. Ree et al.
JOURNAL OF BIOGEOGRAPHY (2018)
From America to Eurasia: a multigenomes history of the genus Abies
Svetlana A. Semerikova et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2018)
Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae)
Diego F. Morales-Briones et al.
NEW PHYTOLOGIST (2018)
A new discovery of Chamaecyparis from the Lower Cretaceous of Inner Mongolia, North China and its significance
Xiao-Hui Xu et al.
REVIEW OF PALAEOBOTANY AND PALYNOLOGY (2018)
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
Andrew Rambaut et al.
SYSTEMATIC BIOLOGY (2018)
The role of land bridges, ancient environments, and migrations in the assembly of the North American flora
Alan Graham
JOURNAL OF SYSTEMATICS AND EVOLUTION (2018)
On the universality of target-enrichment baits for phylogenomic research
Silas Bossert et al.
METHODS IN ECOLOGY AND EVOLUTION (2018)
Incomplete lineage sorting rather than hybridization explains the inconsistent phylogeny of the wisent
Kun Wang et al.
COMMUNICATIONS BIOLOGY (2018)
Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)
Nicolas Garcia et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2017)
Conflicting phylogenomic signals reveal a pattern of reticulate evolution in a recent high-Andean diversification (Asteraceae: Astereae: Diplostephium)
Oscar M. Vargas et al.
NEW PHYTOLOGIST (2017)
Winter storms drive rapid phenotypic, regulatory, and genomic shifts in the green anole lizard
Shane C. Campbell-Staton et al.
SCIENCE (2017)
Evolution of biogeographic disjunction between eastern Asia and North America in Chamaecyparis: Insights from ecological niche models
Ping Liu et al.
PLANT DIVERSITY (2017)
Irrational exuberance for resolved species trees
Matthew W. Hahn et al.
EVOLUTION (2016)
Retrieval of hundreds of nuclear loci from herbarium specimens
Michelle L. Hart et al.
TAXON (2016)
Intercontinental disjunctions between eastern Asia and western North America in vascular plants highlight the biogeographic importance of the Bering land bridge from late Cretaceous to Neogene
Jun Wen et al.
JOURNAL OF SYSTEMATICS AND EVOLUTION (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)
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)
Mitochondrial introgression and complex biogeographic history of the genus Picea
Jin-Hua Ran et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2015)
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
Richard O. Prum et al.
NATURE (2015)
On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods
Sebastien Roch et al.
SYSTEMATIC BIOLOGY (2015)
Evolution of the eastern Asian-North American biogeographic disjunctions in ferns and lycophytes
Jian-Ying Xiang et al.
JOURNAL OF SYSTEMATICS AND EVOLUTION (2015)
Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology
Marcelo Rogalski et al.
FRONTIERS IN PLANT SCIENCE (2015)
A new time tree reveals Earth history's imprint on the evolution of modern birds
Santiago Claramunt et al.
SCIENCE ADVANCES (2015)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Alexandros Stamatakis
BIOINFORMATICS (2014)
ANGSD: Analysis of Next Generation Sequencing Data
Thorfinn Sand Korneliussen et al.
BMC BIOINFORMATICS (2014)
Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees
Leonidas Salichos et al.
MOLECULAR BIOLOGY AND EVOLUTION (2014)
Evolution and biogeography of gymnosperms
Xiao-Quan Wang et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2014)
Model Selection in Historical Biogeography Reveals that Founder-Event Speciation Is a Crucial Process in Island Clades
Nicholas J. Matzke
SYSTEMATIC BIOLOGY (2014)
High-Throughput Genomic Data in Systematics and Phylogenetics
Emily Moriarty Lemmon et al.
ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 44 (2013)
Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle
Noah A. Rosenberg
MOLECULAR BIOLOGY AND EVOLUTION (2013)
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh et al.
MOLECULAR BIOLOGY AND EVOLUTION (2013)
The Norway spruce genome sequence and conifer genome evolution
Bjorn Nystedt 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)
The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals
Maureen A. O'Leary et al.
SCIENCE (2013)
Inferring the biogeographic origins of inter-continental disjunct endemics using a Bayes-DIVA approach
A. J. Harris et al.
JOURNAL OF SYSTEMATICS AND EVOLUTION (2013)
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
Matthew Kearse et al.
BIOINFORMATICS (2012)
Statistics and Truth in Phylogenomics
Sudhir Kumar et al.
MOLECULAR BIOLOGY AND EVOLUTION (2012)
Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms
Ning Zhang et al.
NEW PHYTOLOGIST (2012)
Distribution of living Cupressaceae reflects the breakup of Pangea
Kangshan Mao et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Cenozoic climate change shaped the evolutionary ecophysiology of the Cupressaceae conifers
Jarmila Pittermann et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Best Practices for Justifying Fossil Calibrations
James F. Parham et al.
SYSTEMATIC BIOLOGY (2012)
The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection
Yun Yu et al.
PLOS GENETICS (2012)
Plant Evolution: Pulses of Extinction and Speciation in Gymnosperm Diversity
Charles C. Davis et al.
CURRENT BIOLOGY (2011)
Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times
Mario dos Reis et al.
MOLECULAR BIOLOGY AND EVOLUTION (2011)
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G. Grabherr et al.
NATURE BIOTECHNOLOGY (2011)
DendroPy: a Python library for phylogenetic computing
Jeet Sukumaran et al.
BIOINFORMATICS (2010)
DensiTree: making sense of sets of phylogenetic trees
Remco R. Bouckaert
BIOINFORMATICS (2010)
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
Liang Liu et al.
BMC EVOLUTIONARY BIOLOGY (2010)
Diversification and biogeography of Juniperus (Cupressaceae): variable diversification rates and multiple intercontinental dispersals
Kangshan Mao et al.
NEW PHYTOLOGIST (2010)
Incongruence among mitochondrial, chloroplast and nuclear gene trees in Pinus subgenus Strobus (Pinaceae)
Kiyomi Tsutsui et al.
JOURNAL OF PLANT RESEARCH (2009)
Historical biogeography of the genus Chamaecyparis (Cupressaceae, Coniferales) based on its fossil record
(Christopher) Yu-Sheng Liu et al.
Palaeobiodiversity and Palaeoenvironments (2009)
PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
Cuong Than et al.
BMC BIOINFORMATICS (2008)
An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics
James C. Zachos et al.
NATURE (2008)
Phylogeny and biogeography of Tsuga (Pinaceae) inferred from nuclear ribosomal ITS and chloroplast DNA sequence data
Nathan P. Havill et al.
SYSTEMATIC BOTANY (2008)
PAML 4: Phylogenetic analysis by maximum likelihood
Ziheng Yang
MOLECULAR BIOLOGY AND EVOLUTION (2007)
Paleobiogeography of Africa: How distinct from Gondwana and Laurasia?
Emmanuel Gheerbrant et al.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY (2006)
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
Mikita Suyama et al.
NUCLEIC ACIDS RESEARCH (2006)
Evolution and circumscription of the true cypresses (Cupressaceae: Cupressus)
Damon P. Little
SYSTEMATIC BOTANY (2006)
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Weizhong Li et al.
BIOINFORMATICS (2006)
Discordance of species trees with their most likely gene trees
James H. Degnan et al.
PLOS GENETICS (2006)
APE: Analyses of Phylogenetics and Evolution in R language
E Paradis et al.
BIOINFORMATICS (2004)
Historical biogeography and phylogenetic relationships of the genus Chamaecyparis (Cupressaceae) inferred from chloroplast DNA polymorphism
WP Wang et al.
PLANT SYSTEMATICS AND EVOLUTION (2003)
A refined age for the earliest opening of Bering Strait
AY Gladenkov et al.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY (2002)
Accommodating phylogenetic uncertainty in evolutionary studies
JP Huelsenbeck et al.
SCIENCE (2000)