Phylogenomic inference in extremis : A case study with mycoheterotroph plastomes

Evolution at the tips: Asclepias phylogenomics and new perspectives on leaf surfaces

(2018) Mark Fishbein et al.   AMERICAN JOURNAL OF BOTANY

Plastid phylogenomic analysis of green plants: A billion years of evolutionary history

(2018) Matthew A. Gitzendanner et al.   AMERICAN JOURNAL OF BOTANY

On the brink: the highly reduced plastomes of nonphotosynthetic Ericaceae

(2017) Thomas W. A. Braukmann et al.   NEW PHYTOLOGIST

Plastomes on the edge: the evolutionary breakdown of mycoheterotroph plastid genomes

(2017) Sean W. Graham et al.   NEW PHYTOLOGIST

A few-gene plastid phylogenetic framework for mycoheterotrophic monocots

(2016) Vivienne K.Y. Lam et al.   AMERICAN JOURNAL OF BOTANY

Drastic reduction of plastome size in the mycoheterotrophic Thismia tentaculata relative to that of its autotrophic relative Tacca chantrieri

(2016) Gwynne S. Lim et al.   AMERICAN JOURNAL OF BOTANY

Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasiteCytinus hypocistis(Cytinaceae)

(2016) Cristina Roquet et al.   ANNALS OF BOTANY

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV

(2016)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Phylogenomics and historical biogeography of the monocot order Liliales: out of Australia and through Antarctica

(2016) Thomas J. Givnish et al.   CLADISTICS

Assembled Plastid and Mitochondrial Genomes, as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales

(2016) Sidonie Bellot et al.   Genome Biology and Evolution

Detecting and Characterizing the Highly Divergent Plastid Genome of the Nonphotosynthetic Parasitic PlantHydnora visseri(Hydnoraceae)

(2016) Julia Naumann et al.   Genome Biology and Evolution

Lineage-Specific Reductions of Plastid Genomes in an Orchid Tribe with Partially and Fully Mycoheterotrophic Species

(2016) Yan-Lei Feng et al.   Genome Biology and Evolution

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

The elusive predisposition to mycoheterotrophy in Ericaceae

(2016) Félix Lallemand et al.   NEW PHYTOLOGIST

Mechanistic model of evolutionary rate variation en route to a nonphotosynthetic lifestyle in plants

(2016) Susann Wicke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic relationships at the base of Ericaceae: Implications for vegetative and mycorrhizal evolution

(2016) John V. Freudenstein et al.   TAXON

Comparative analysis of plastid genomes of non-photosynthetic Ericaceae and their photosynthetic relatives

(2016) Maria D. Logacheva et al.   Scientific Reports

The complete chloroplast genome of parasitic flowering plant Monotropa hypopitys: extensive gene losses and size reduction

(2016) Eugene V. Gruzdev et al.   Mitochondrial DNA Part B-Resources

Evolution of mycoheterotrophy in Polygalaceae: The case of Epirixanthes

(2015) Constantijn B. Mennes et al.   AMERICAN JOURNAL OF BOTANY

Plastid phylogenomics and molecular evolution of Alismatales

(2015) T. Gregory Ross et al.   CLADISTICS

The Plastomes of Two Species in the Endoparasite GenusPilostyles(Apodanthaceae) Each Retain Just Five or Six Possibly Functional Genes

(2015) Sidonie Bellot et al.   Genome Biology and Evolution

The Highly Reduced Plastome of MycoheterotrophicSciaphila(Triuridaceae) Is Colinear with Its Green Relatives and Is under Strong Purifying Selection

(2015) Vivienne K.Y. Lam et al.   Genome Biology and Evolution

Exploring the Limits for Reduction of Plastid Genomes: A Case Study of the Mycoheterotrophic Orchids Epipogium aphyllum and Epipogium roseum

(2015) Mikhail I. Schelkunov et al.   Genome Biology and Evolution

Ancient Gondwana break-up explains the distribution of the mycoheterotrophic family Corsiaceae (Liliales)

(2015) Constantijn B. Mennes et al.   JOURNAL OF BIOGEOGRAPHY

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

Phylogenetic Inferences and the Evolution of Plastid DNA in Campynemataceae and the Mycoheterotrophic Corsia dispar D.L Jones & B. Gray (Corsiaceae)

(2015) Sarah Silvia Bodin et al.   PLANT MOLECULAR BIOLOGY REPORTER

Isotopic evidence of partial mycoheterotrophy inBurmannia coelestis(Burmanniaceae)

(2015) Jay F. Bolin et al.   PLANT SPECIES BIOLOGY

Orchid phylogenomics and multiple drivers of their extraordinary diversification

(2015) Thomas J. Givnish et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

The Plastid Genome of Mycoheterotrophic Monocot Petrosavia stellaris Exhibits Both Gene Losses and Multiple Rearrangements

(2014) Maria D. Logacheva et al.   Genome Biology and Evolution

Investigating the Path of Plastid Genome Degradation in an Early-Transitional Clade of Heterotrophic Orchids, and Implications for Heterotrophic Angiosperms

(2014) Craig F. Barrett et al.   MOLECULAR BIOLOGY AND EVOLUTION

Should genes with missing data be excluded from phylogenetic analyses?

(2014) Wei Jiang 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

Phylogenetic relationships of the mycoheterotrophic genus Voyria and the implications for the biogeographic history of Gentianaceae

(2013) Vincent S.F.T. Merckx et al.   AMERICAN JOURNAL OF BOTANY

New insights in the long-debated evolutionary history of Triuridaceae (Pandanales)

(2013) Constantijn B. Mennes et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens

(2013) Martijn Staats et al.   PLoS One

The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation

(2012) Craig F. Barrett et al.   AMERICAN JOURNAL OF BOTANY

Phylogeny of the Liliales (Monocotyledons) with special emphasis on data partition congruence and RNA editing

(2012) Gitte Petersen et al.   CLADISTICS

Combined phylogenetic analyses reveal interfamilial relationships and patterns of floral evolution in the eudicot order Fabales

(2012) M. Angélica Bello et al.   CLADISTICS

Plastid genome evolution in mycoheterotrophic Ericaceae

(2012) Thomas Braukmann et al.   PLANT MOLECULAR BIOLOGY

Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling

(2012) John J. Wiens et al.   PLoS One

Angiosperm phylogeny: 17 genes, 640 taxa

(2011) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Sequencing and Analysis of Plastid Genome in Mycoheterotrophic Orchid Neottia nidus-avis

(2011) Maria D. Logacheva et al.   Genome Biology and Evolution

Rampant Gene Loss in the Underground Orchid Rhizanthella gardneri Highlights Evolutionary Constraints on Plastid Genomes

(2011) E. Delannoy et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolutionary ecology of dust seeds

(2011) Ove Eriksson et al.   PERSPECTIVES IN PLANT ECOLOGY EVOLUTION AND SYSTEMATICS

Isotopic evidence of partial mycoheterotrophy in the Gentianaceae: Bartonia virginica and Obolaria virginica as case studies

(2010) Duncan D. Cameron et al.   AMERICAN JOURNAL OF BOTANY

Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1

(2010) Thomas J. Givnish et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

Inference of phylogenetic relationships among the subfamilies of grasses (Poaceae: Poales) using meso-scale exemplar-based sampling of the plastid genome

(2010) Jeffery M. Saarela et al.   Botany

Evolution of mycoheterotrophy in plants: a phylogenetic perspective

(2010) Vincent Merckx et al.   NEW PHYTOLOGIST

15N and 13C natural abundance of two mycoheterotrophic and a putative partially mycoheterotrophic species associated with arbuscular mycorrhizal fungi

(2010) Vincent Merckx et al.   NEW PHYTOLOGIST

Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms

(2009) J Gordon Burleigh et al.   BMC EVOLUTIONARY BIOLOGY

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

(2009)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Bias and conflict in phylogenetic inference of myco-heterotrophic plants: a case study in Thismiaceae

(2009) Vincent Merckx et al.   CLADISTICS

Isotopic evidence of full and partial myco-heterotrophy in the plant tribe Pyroleae (Ericaceae)

(2009) Nicole A. Hynson et al.   NEW PHYTOLOGIST

Different gymnosperm outgroups have (mostly) congruent signal regarding the root of flowering plant phylogeny

(2008) Sean W. Graham et al.   AMERICAN JOURNAL OF BOTANY

Diversification of myco-heterotrophic angiosperms: evidence from Burmanniaceae

(2008) Vincent Merckx et al.   BMC EVOLUTIONARY BIOLOGY

How well do we understand the overall backbone of cycad phylogeny? New insights from a large, multigene plastid data set

(2008) Jessie M. Zgurski et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY

Iridaceae 'Out of Australasia'? Phylogeny, Biogeography, and Divergence Time Based on Plastid DNA Sequences

(2008) Peter Goldblatt et al.   SYSTEMATIC BOTANY