Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity

Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content

(2016) Fay-Wei Li et al.   Genome Biology and Evolution

Another look at the phylogenetic position of the grape order Vitales: Chloroplast phylogenomics with an expanded sampling of key lineages

(2016) Ning Zhang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Desmophlebiaceae and Desmophlebium: A new family and genus of Eupolypod II ferns

(2016) Claudine M. Mynssen et al.   TAXON

A community-derived classification for extant lycophytes and ferns

(2016)   Journal of Systematics and Evolution

Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots

(2015) Craig F. Barrett et al.   NEW PHYTOLOGIST

Molecular Phylogeny of the Cliff Ferns (Woodsiaceae: Polypodiales) with a Proposed Infrageneric Classification

(2015) Yizhen Shao et al.   PLoS One

Chloroplast phylogenomics resolves key relationships in ferns

(2015) Jin-Mei Lu et al.   Journal of Systematics and Evolution

Two New Fern Chloroplasts and Decelerated Evolution Linked to the Long Generation Time in Tree Ferns

(2014) B. Zhong et al.   Genome Biology and Evolution

Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

(2014) Liping Zeng et al.   Nature Communications

Stasis and convergence characterize morphological evolution in eupolypod II ferns

(2013) Michael A. Sundue et al.   ANNALS OF BOTANY

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

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

Toward a new circumscription of the twinsorus-fern genus Diplazium (Athyriaceae): A molecular phylogeny with morphological implications and infrageneric taxonomy

(2013) Ran Wei et al.   TAXON

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates

(2012) Julien Soubrier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Exploring generic delimitation within the fern family Thelypteridaceae

(2012) Li-Juan He et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms

(2012) Ning Zhang et al.   NEW PHYTOLOGIST

Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

(2012) Z. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Overcoming Deep Roots, Fast Rates, and Short Internodes to Resolve the Ancient Rapid Radiation of Eupolypod II Ferns

(2012) Carl J. Rothfels et al.   SYSTEMATIC BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Phylogenetic Positions of the Enigmatic Asiatic Fern Genera Diplaziopsis and Rhachidosorus from Analyses of Four Plastid Genes

(2011) Li Chunxiang et al.   AMERICAN FERN JOURNAL

Systematic Error in Seed Plant Phylogenomics

(2011) Bojian Zhong et al.   Genome Biology and Evolution

First insights into fern matK phylogeny

(2011) Li-Yaung Kuo et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The phylogeny of the BEP clade in grasses revisited: Evidence from the whole-genome sequences of chloroplasts

(2011) Zhi-Qiang Wu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Bayesian random local clocks, or one rate to rule them all

(2010) Alexei J Drummond et al.   BMC BIOLOGY

Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages

(2010) Kenneth G Karol et al.   BMC EVOLUTIONARY BIOLOGY

Bayesian analysis of elapsed times in continuous-time Markov chains

(2010) Marco A. R. Ferreira et al.   CANADIAN JOURNAL OF STATISTICS-REVUE CANADIENNE DE STATISTIQUE

The evolution of chloroplast genes and genomes in ferns

(2010) Paul G. Wolf et al.   PLANT MOLECULAR BIOLOGY

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Complete chloroplast genome sequence of a tree fern Alsophila spinulosa: insights into evolutionary changes in fern chloroplast genomes

(2009) Lei Gao et al.   BMC EVOLUTIONARY BIOLOGY

Evidence for a Cenozoic radiation of ferns in an angiosperm-dominated canopy

(2009) E. Schuettpelz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Resolving an Ancient, Rapid Radiation in Saxifragales

(2008) Shuguang Jian et al.   SYSTEMATIC BIOLOGY