The Tree of Life: Metaphor, Model, and Heuristic Device

Evolutionary Implications of Horizontal Gene Transfer

(2012) Michael Syvanen   Annual Review of Genetics

On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence

(2011) Douglas L Theobald   Biology Direct

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

(2011) Maureen A O'Malley et al.   Biology Direct

A Rooted Net of Life

(2011) David Williams et al.   Biology Direct

Why do RNA viruses recombine?

(2011) Etienne Simon-Loriere et al.   NATURE REVIEWS MICROBIOLOGY

Towards an accurate identification of mosaic genes and partial horizontal gene transfers

(2011) Alix Boc et al.   NUCLEIC ACIDS RESEARCH

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

(2011) Dongying Wu et al.   PLoS One

Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses

(2011) Tom A. Williams et al.   PLoS One

Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting

(2011) Yun Yu et al.   SYSTEMATIC BIOLOGY

Darwin's Theory of Descent with Modification, versus the Biblical Tree of Life

(2011) David Penny   PLOS BIOLOGY

On the need for integrative phylogenomics, and some steps toward its creation

(2010) Eric Bapteste et al.   BIOLOGY & PHILOSOPHY

Trashing life’s tree

(2010) L. R. Franklin-Hall   BIOLOGY & PHILOSOPHY

The attempt on the life of the Tree of Life: science, philosophy and politics

(2010) W. Ford Doolittle   BIOLOGY & PHILOSOPHY

The common ancestry of life

(2010) Eugene V Koonin et al.   Biology Direct

Species, Genes, and the Tree of Life

(2010) J. D. Velasco   BRITISH JOURNAL FOR THE PHILOSOPHY OF SCIENCE

Willi Hennig’s dichotomization of nature

(2010) Olivier Rieppel   CLADISTICS

Trees before and after Darwin

(2010) Pascal Tassy   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

A formal test of the theory of universal common ancestry

(2010) Douglas L. Theobald   NATURE

Was the universal common ancestry proved?

(2010) Takahiro Yonezawa et al.   NATURE

Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE

Defining Life: The Virus Viewpoint

(2010) Patrick Forterre   ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES

Phylogenetic and Phyletic Studies of Informational Genes in Genomes Highlight Existence of a 4th Domain of Life Including Giant Viruses

(2010) Mickaël Boyer et al.   PLoS One

Inferring and Validating Horizontal Gene Transfer Events Using Bipartition Dissimilarity

(2010) Alix Boc et al.   SYSTEMATIC BIOLOGY

Gene Transfer and Diversification of Microbial Eukaryotes

(2009) Jan O. Andersson   Annual Review of Microbiology

The Role of Hybridization in Plant Speciation

(2009) Pamela S. Soltis et al.   Annual Review of Plant Biology

Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective

(2009) Yan Boucher et al.   BIOESSAYS

Trees and networks before and after Darwin

(2009) Mark A Ragan   Biology Direct

Prokaryotic evolution and the tree of life are two different things

(2009) Eric Bapteste et al.   Biology Direct

Viruses are essential agents within the roots and stem of the tree of life

(2009) Luis P. Villarreal et al.   JOURNAL OF THEORETICAL BIOLOGY

Coalescent methods for estimating phylogenetic trees

(2009) Liang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Yet viruses cannot be included in the tree of life

(2009) Purificación López-García et al.   NATURE REVIEWS MICROBIOLOGY

The network of life: genome beginnings and evolution

(2009) M. A. Ragan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Identifying Hybridization Events in the Presence of Coalescence via Model Selection

(2009) Laura Salter Kubatko   SYSTEMATIC BIOLOGY

Species Trees from Highly Incongruent Gene Trees in Rice

(2009) Karen A. Cranston et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Assumption 0 Analysis: Comparative Phylogenetic Studies in the Age of Complexity1,2,3

(2008) Daniel R. Brooks et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

Phylogenetic Inference Using Whole Genomes

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

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Edward Hitchcock’s Pre-Darwinian (1840) “Tree of Life”

(2008) J. David Archibald   JOURNAL OF THE HISTORY OF BIOLOGY

The Apicomplexan Whole-Genome Phylogeny: An Analysis of Incongruence among Gene Trees

(2008) C.-H. Kuo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Horizontal gene transfer in eukaryotic evolution

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

Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation

(2008) J. Mallet   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

(2008) T. Dagan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Massive Horizontal Gene Transfer in Bdelloid Rotifers

(2008) E. A. Gladyshev et al.   SCIENCE

Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model

(2008) Chen Meng et al.   THEORETICAL POPULATION BIOLOGY

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

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

Lateral transfer of the gene for a widely used marker, α-tubulin, indicated by a multi-protein study of the phylogenetic position of Andalucia (Excavata)

(2007) Alastair G.B. Simpson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION