The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life

Insights from 20 years of bacterial genome sequencing

(2015) Miriam Land et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes

(2015) Chuan Ku et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes

(2014) Pere Puigbò et al.   BMC BIOLOGY

Estimation of prokaryotic supergenome size and composition from gene frequency distributions

(2014) Alexander E Lobkovsky et al.   BMC GENOMICS

Origins of major archaeal clades correspond to gene acquisitions from bacteria

(2014) Shijulal Nelson-Sathi et al.   NATURE

Genome reduction as the dominant mode of evolution

(2013) Yuri I. Wolf et al.   BIOESSAYS

Seeing the Tree of Life behind the phylogenetic forest

(2013) Pere Puigbò et al.   BMC BIOLOGY

Postgenomic analysis of bacterial pathogens repertoire reveals genome reduction rather than virulence factors

(2013) V. Merhej et al.   Briefings in Functional Genomics

Gene Frequency Distributions Reject a Neutral Model of Genome Evolution

(2013) Alexander E. Lobkovsky et al.   Genome Biology and Evolution

Horizontal Gene Transfer Can Rescue Prokaryotes from Muller’s Ratchet: Benefit of DNA from Dead Cells and Population Subdivision

(2013) Nobuto Takeuchi et al.   G3-Genes Genomes Genetics

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

(2012) Yuri I Wolf et al.   Biology Direct

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

(2012) Franz Baumdicker et al.   Genome Biology and Evolution

Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome

(2012) R. Eric Collins et al.   MOLECULAR BIOLOGY AND EVOLUTION

Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea

(2012) S. Nelson-Sathi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

(2010) M. Csuos   BIOINFORMATICS

The Tree and Net Components of Prokaryote Evolution

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

High Frequency of Horizontal Gene Transfer in the Oceans

(2010) L. D. McDaniel et al.   SCIENCE

Gene Transfer and Diversification of Microbial Eukaryotes

(2009) Jan O. Andersson   Annual Review of Microbiology

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

Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model

(2009) M. Csuros et al.   MOLECULAR BIOLOGY AND EVOLUTION

The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them

(2009) W. F. Doolittle   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mutational Meltdown in Primary Endosymbionts: Selection Limits Muller's Ratchet

(2009) Julie M. Allen et al.   PLoS One

Toolbox model of evolution of prokaryotic metabolic networks and their regulation

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

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY

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

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