Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes

Dynamic evolution ofGeraniummitochondrial genomes through multiple horizontal and intracellular gene transfers

(2015) Seongjun Park et al.   NEW PHYTOLOGIST

Miniaturized mitogenome of the parasitic plantViscum scurruloideumis extremely divergent and dynamic and has lost allnadgenes

(2015) Elizabeth Skippington et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread mitovirus sequences in plant genomes

(2015) Jeremy A. Bruenn et al.   PeerJ

Cophylogenetic interactions between marine viruses and eukaryotic picophytoplankton

(2014) Laure Bellec et al.   BMC EVOLUTIONARY BIOLOGY

Genes and Junk in Plant Mitochondria—Repair Mechanisms and Selection

(2014) Alan C. Christensen   Genome Biology and Evolution

Minireview: DNA replication in plant mitochondria

(2014) John D. Cupp et al.   MITOCHONDRION

Unprecedented Heterogeneity in the Synonymous Substitution Rate within a Plant Genome

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

Nucleotide substitution analyses of the glaucophyte Cyanophora suggest an ancestrally lower mutation rate in plastid vs mitochondrial DNA for the Archaeplastida

(2014) David Roy Smith et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Dubious resolution and support from published sparse supermatrices: The importance of thorough tree searches

(2014) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Disparate parametric branch-support values from ambiguous characters

(2014) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The “fossilized” mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate

(2013) Aaron O Richardson et al.   BMC BIOLOGY

Plant Mitochondrial Genome Evolution Can Be Explained by DNA Repair Mechanisms

(2013) Alan C. Christensen   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

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quantification and relative severity of inflated branch-support values generated by alternative methods: An empirical example

(2013) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution

(2013) D. M. de Vienne et al.   NEW PHYTOLOGIST

Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm Amborella

(2013) D. W. Rice et al.   SCIENCE

De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome

(2012) Massimo Iorizzo et al.   BMC PLANT BIOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Intraspecific variation in mitochondrial genome sequence, structure, and gene content inSilene vulgaris, an angiosperm with pervasive cytoplasmic male sterility

(2012) Daniel B. Sloan et al.   NEW PHYTOLOGIST

Phylogenetic Relationships of Silene multinervia and Silene Section Conoimorpha (Caryophyllaceae)

(2012) Anja. Rautenberg et al.   SYSTEMATIC BOTANY

Rapid Evolution of Enormous, Multichromosomal Genomes in Flowering Plant Mitochondria with Exceptionally High Mutation Rates

(2012) Daniel B. Sloan et al.   PLOS BIOLOGY

The Oxytricha trifallax Mitochondrial Genome

(2011) Estienne C. Swart et al.   Genome Biology and Evolution

Spurious 99% bootstrap and jackknife support for unsupported clades

(2011) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins

(2011)   NEW PHYTOLOGIST

Jane: a new tool for the cophylogeny reconstruction problem

(2010) Chris Conow et al.   Algorithms for Molecular Biology

TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

(2010) Ben C Stöver et al.   BMC BIOINFORMATICS

Testing for Selection on Synonymous Sites in Plant Mitochondrial DNA: The Role of Codon Bias and RNA Editing

(2010) Daniel B. Sloan et al.   JOURNAL OF MOLECULAR EVOLUTION

Biased gene transfer mimics patterns created through shared ancestry

(2010) C. P. Andam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae

(2009) Daniel B Sloan et al.   BMC EVOLUTIONARY BIOLOGY

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS

Frequent, Phylogenetically Local Horizontal Transfer of the cox1 Group I Intron in Flowering Plant Mitochondria

(2008) M. V. Sanchez-Puerta et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

(2008) G DROUIN et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A genome-wide view of the spectrum of spontaneous mutations in yeast

(2008) M. Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The mitochondrial genome of a cytoplasmic male sterile line of perennial ryegrass (Lolium perenne L.) contains an integrated linear plasmid-like element

(2008) Paul McDermott et al.   THEORETICAL AND APPLIED GENETICS

Linear plasmids in plant mitochondria: Peaceful coexistences or malicious invasions?

(2007) Hirokazu Handa   MITOCHONDRION