Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal tree of life

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

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

Plastomes of the green algae Hydrodictyon reticulatum and Pediastrum duplex (Sphaeropleales, Chlorophyceae)

(2017) Hilary A. McManus et al.   PeerJ

Hiding in plain sight: Koshicola spirodelophila gen. et sp. nov. (Chaetopeltidales, Chlorophyceae), a novel green alga associated with the aquatic angiosperm Spirodela polyrhiza

(2016) Shin Watanabe et al.   AMERICAN JOURNAL OF BOTANY

Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution

(2016) Karolina Fučíková et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Testing the boundaries of the green algal speciesPediastrum alternans(Chlorophyceae) using conventional, geometric morphometric and phylogenetic methods

(2016) Joanna Lenarczyk et al.   PHYCOLOGIA

Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae)

(2015) Claude Lemieux et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic patterns of gene rearrangements in four mitochondrial genomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae)

(2015) Audrey A. Farwagi et al.   BMC GENOMICS

Dynamic Evolution of the Chloroplast Genome in the Green Algal Classes Pedinophyceae and Trebouxiophyceae

(2015) Monique Turmel et al.   Genome Biology and Evolution

Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

(2015) Julia Chifman et al.   JOURNAL OF THEORETICAL BIOLOGY

Phycas: Software for Bayesian Phylogenetic Analysis

(2015) Paul O. Lewis et al.   SYSTEMATIC BIOLOGY

RECG Maintains Plastid and Mitochondrial Genome Stability by Suppressing Extensive Recombination between Short Dispersed Repeats

(2015) Masaki Odahara et al.   PLoS Genetics

Strain survey on three continents confirms the polyphyly of the genus Pediastrum (Hydrodictyaceae, Chlorophyceae).

(2015) Mrutyunjay Jena et al.   Fottea

Why are most organelle genomes transmitted maternally?

(2014) Stephan Greiner et al.   BIOESSAYS

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

Gene Arrangement Convergence, Diverse Intron Content, and Genetic Code Modifications in Mitochondrial Genomes of Sphaeropleales (Chlorophyta)

(2014) Karolina Fučíková et al.   Genome Biology and Evolution

Response of Pediastrum in German floodplain lakes to Late Glacial climate changes

(2014) Falko Turner et al.   JOURNAL OF PALEOLIMNOLOGY

Phylogenomics of the plant family Araceae

(2014) Claudia L. Henriquez et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inclusion of chloroplast genes that have undergone expansion misleads phylogenetic reconstruction in the Chlorophyta

(2013) Phil M. Novis et al.   AMERICAN JOURNAL OF BOTANY

Puttingincertae sedistaxa in their place: a proposal for ten new families and three new genera in Sphaeropleales (Chlorophyceae, Chlorophyta)

(2013) Karolina Fučíková et al.   JOURNAL OF PHYCOLOGY

Reconstruction of the Ancestral Plastid Genome in Geraniaceae Reveals a Correlation between Genome Rearrangements, Repeats, and Nucleotide Substitution Rates

(2013) Mao-Lun Weng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Organelle Genome Complexity Scales Positively with Organism Size in Volvocine Green Algae

(2013) David Roy Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets

(2013) Marc Lohse et al.   NUCLEIC ACIDS RESEARCH

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

(2013) D. W. Rice et al.   SCIENCE

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Gene transfer: anything goes in plant mitochondria

(2011) John M Archibald et al.   BMC BIOLOGY

MOLECULAR PHYLOGENETIC RELATIONSHIPS IN THE FRESHWATER FAMILY HYDRODICTYACEAE (SPHAEROPLEALES, CHLOROPHYCEAE), WITH AN EMPHASIS ON PEDIASTRUM DUPLEX1

(2011) Hilary A. McManus et al.   JOURNAL OF PHYCOLOGY

Invasion of protein coding genes by green algal ribosomal group I introns

(2011) Hilary A. McManus et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

The Exceptionally Large Chloroplast Genome of the Green Alga Floydiella terrestris Illuminates the Evolutionary History of the Chlorophyceae

(2010) J. S. Brouard et al.   Genome Biology and Evolution

Choosing among Partition Models in Bayesian Phylogenetics

(2010) Y. Fan et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

The ecology of Pediastrum (Chlorophyceae) in subarctic lakes and their potential as paleobioindicators

(2009) Kaarina Weckström et al.   JOURNAL OF PALEOLIMNOLOGY

Domain-Based and Family-Specific Sequence Identity Thresholds Increase the Levels of Reliable Protein Function Transfer

(2008) Sarah Addou et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Systematics and the Diatom Species

(2008) Andrew J. Alverson   PROTIST