Phylogenomic evidence for ancient recombination between plastid genomes of the Cupressus-Juniperus-Xanthocyparis complex (Cupressaceae)

Insights into the Existence of Isomeric Plastomes in Cupressoideae (Cupressaceae)

(2017) Xiao-Jian Qu et al.   Genome Biology and Evolution

DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution

(2017) Xuhua Xia   JOURNAL OF HEREDITY

Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae)

(2017) Alexis R. Sullivan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiple measures could alleviate long-branch attraction in phylogenomic reconstruction of Cupressoideae (Cupressaceae)

(2017) Xiao-Jian Qu et al.   Scientific Reports

Importance of incomplete lineage sorting and introgression in the origin of shared genetic variation between two closely related pines with overlapping distributions

(2016) Y Zhou et al.   HEREDITY

A new classification and linear sequence of extant gymnosperms

(2016) M. J. M. Christenhusz et al.   Phytotaxa

A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the GenusCitrus

(2015) Jose Carbonell-Caballero et al.   MOLECULAR BIOLOGY AND EVOLUTION

ycf1, the most promising plastid DNA barcode of land plants

(2015) Wenpan Dong et al.   Scientific Reports

Predominant and Substoichiometric Isomers of the Plastid Genome Coexist within Juniperus Plants and Have Shifted Multiple Times during Cupressophyte Evolution

(2014) Wenhu Guo et al.   Genome Biology and Evolution

Unprecedented Heterogeneity in the Synonymous Substitution Rate within a Plant Genome

(2014) Andan Zhu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes

(2013) Felix Grewe et al.   BMC EVOLUTIONARY BIOLOGY

The Complete Chloroplast Genome Sequence of Cephalotaxus oliveri (Cephalotaxaceae): Evolutionary Comparison of Cephalotaxus Chloroplast DNAs and Insights into the Loss of Inverted Repeat Copies in Gymnosperms

(2013) Xuan Yi et al.   Genome Biology and Evolution

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

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

Three genome-based phylogeny of Cupressaceae s.l.: Further evidence for the evolution of gymnosperms and Southern Hemisphere biogeography

(2012) Zu-Yu Yang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic relationships among the New World cypresses (Hesperocyparis; Cupressaceae): evidence from noncoding chloroplast DNA sequences

(2012) Randall G. Terry et al.   PLANT SYSTEMATICS AND EVOLUTION

Distribution of living Cupressaceae reflects the breakup of Pangea

(2012) K. Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Diversification and biogeography of Juniperus (Cupressaceae): variable diversification rates and multiple intercontinental dispersals

(2010) Kangshan Mao et al.   NEW PHYTOLOGIST

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

Biparental inheritance of plastidial and mitochondrial DNA and hybrid variegation in Pelargonium

(2009) Andreas Weihe et al.   MOLECULAR GENETICS AND GENOMICS

Reticulate evolution and incomplete lineage sorting among the ponderosa pines

(2009) Ann Willyard et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species

(2008) Tomonori Hirao et al.   BMC PLANT BIOLOGY

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

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

Reticulate evolution in Thuja inferred from multiple gene sequences: Implications for the study of biogeographical disjunction between eastern Asia and North America

(2008) Dan Peng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reticulate or tree-like chloroplast DNA evolution in Sileneae (Caryophyllaceae)?

(2008) Per Erixon et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION