How stands the Tree of Life a century and a half after The Origin?

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

(2011) O. Popa et al.   GENOME RESEARCH

Save the tree of life or get lost in the woods

(2010) Ruben E Valas et al.   Biology Direct

The Tree and Net Components of Prokaryote Evolution

(2010) Pere Puigbò et al.   Genome Biology and Evolution

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction

(2010) M. D. Rasmussen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rooting the Ribosomal Tree of Life

(2010) G. P. Fournier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths

(2010) T. Kloesges et al.   MOLECULAR BIOLOGY AND 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

Prokaryotic evolution and the tree of life are two different things

(2009) Eric Bapteste et al.   Biology Direct

The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum

(2009) Eugene V Koonin et al.   Biology Direct

On the origin of prokaryotic species

(2009) W. F. Doolittle et al.   GENOME RESEARCH

Mapping the Tree of Life: Progress and Prospects

(2009) N. R. Pace   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient Horizontal Gene Transfer between Plants and Fungi

(2009) T. A. Richards et al.   PLANT CELL

Darwin and the scientific method

(2009) F. J. Ayala   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network analyses structure genetic diversity in independent genetic worlds

(2009) S. Halary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogeny of prokaryotes: does it exist and why should we care?

(2009) Simonetta Gribaldo et al.   RESEARCH IN MICROBIOLOGY

Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes

(2009) L. Lacey Knowles   SYSTEMATIC BIOLOGY

Signature Genes as a Phylogenomic Tool

(2008) B. E. Dutilh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Horizontal gene transfer in eukaryotic evolution

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

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

(2008) E. V. Koonin et al.   NUCLEIC ACIDS RESEARCH

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

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