Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer

Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids

(2011) Shinichiro Maruyama et al.   BMC EVOLUTIONARY BIOLOGY

Red and Green Algal Monophyly and Extensive Gene Sharing Found in a Rich Repertoire of Red Algal Genes

(2011) Cheong Xin Chan et al.   CURRENT BIOLOGY

Plastid Origin and Evolution: New Models Provide Insights into Old Problems

(2011) C. X. Chan et al.   PLANT PHYSIOLOGY

A Survey of Combinatorial Methods for Phylogenetic Networks

(2010) Daniel H. Huson et al.   Genome Biology and Evolution

Phylogenomic Evidence for Separate Acquisition of Plastids in Cryptophytes, Haptophytes, and Stramenopiles

(2010) D. Baurain et al.   MOLECULAR BIOLOGY AND EVOLUTION

Algal Genes in the Closest Relatives of Animals

(2010) G. Sun et al.   MOLECULAR BIOLOGY AND EVOLUTION

A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids

(2010) J. Janouskovec et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Causes and evolutionary significance of genetic convergence

(2010) Pascal-Antoine Christin et al.   TRENDS IN GENETICS

Sizing up the genomic footprint of endosymbiosis

(2009) Marek Elias et al.   BIOESSAYS

Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?

(2009) John W Stiller et al.   BMC GENOMICS

The Puzzle of Plastid Evolution

(2009) John M. Archibald   CURRENT BIOLOGY

Chromalveolates and the Evolution of Plastids by Secondary Endosymbiosis

(2009) PATRICK J. KEELING   JOURNAL OF EUKARYOTIC MICROBIOLOGY

The gene evolution model and computing its associated probabilities

(2009) Lars Arvestad et al.   JOURNAL OF THE ACM

Phylogenetic positions of Glaucophyta, green plants (Archaeplastida) and Haptophyta (Chromalveolata) as deduced from slowly evolving nuclear genes

(2009) Hisayoshi Nozaki et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genomic Footprints of a Cryptic Plastid Endosymbiosis in Diatoms

(2009) A. Moustafa et al.   SCIENCE

Chromalveolate plastids: direct descent or multiple endosymbioses?

(2009) Andrzej Bodył et al.   TRENDS IN ECOLOGY & EVOLUTION

Phylogenetic Inference Using Whole Genomes

(2008) Bruce Rannala et al.   Annual Review of Genomics and Human Genetics

Plastid Evolution

(2008) Sven B. Gould et al.   Annual Review of Plant Biology

Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes

(2008) F. Burki et al.   Biology Letters

Broadly sampled multigene trees of eukaryotes

(2008) Hwan Su Yoon et al.   BMC EVOLUTIONARY BIOLOGY

Multiple Genes of Apparent Algal Origin Suggest Ciliates May Once Have Been Photosynthetic

(2008) Adrian Reyes-Prieto et al.   CURRENT BIOLOGY

Chromatophore Genome Sequence of Paulinella Sheds Light on Acquisition of Photosynthesis by Eukaryotes

(2008) Eva C.M. Nowack et al.   CURRENT BIOLOGY

A HYPOTHESIS FOR PLASTID EVOLUTION IN CHROMALVEOLATES1

(2008) M. Virginia Sanchez-Puerta et al.   JOURNAL OF PHYCOLOGY

Difficulties in Testing for Covarion-Like Properties of Sequences under the Confounding Influence of Changing Proportions of Variable Sites

(2008) N. Gruenheit et al.   MOLECULAR BIOLOGY AND EVOLUTION

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

The origin of plastids

(2008) C.J Howe et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Serial Replacement of Diatom Endosymbionts in Two Freshwater Dinoflagellates, Peridiniopsis spp. (Peridiniales, Dinophyceae)

(2008) Yoshihito Takano et al.   PHYCOLOGIA

Testing Congruence in Phylogenomic Analysis

(2008) Jessica W. Leigh et al.   SYSTEMATIC BIOLOGY

The prokaryotic tree of life: past, present…and future?

(2008) James O. McInerney et al.   TRENDS IN ECOLOGY & EVOLUTION

The eukaryotic tree of life: endosymbiosis takes its TOL

(2008) Christopher E. Lane et al.   TRENDS IN ECOLOGY & EVOLUTION