Reductive genome evolution at both ends of the bacterial population size spectrum

Implications of streamlining theory for microbial ecology

(2014) Stephen J Giovannoni et al.   ISME Journal

Strong Genome-Wide Selection Early in the Evolution of Prochlorococcus Resulted in a Reduced Genome through the Loss of a Large Number of Small Effect Genes

(2014) Zhiyi Sun et al.   PLoS One

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

Genomic Taxonomy of the Genus Prochlorococcus

(2013) Cristiane C. Thompson et al.   MICROBIAL ECOLOGY

Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution

(2013) Laurent Guéguen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Confounders of mutation-rate estimators: Selection and phenotypic lag in Thermus thermophilus

(2013) Grace E. Kissling et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus

(2013) P. Flombaum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Is junk DNA bunk? A critique of ENCODE

(2013) W. F. Doolittle   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of variation in presence and absence of genes in bacterial pathways

(2012) Andrew R Francis et al.   BMC EVOLUTIONARY BIOLOGY

Virtual Genomes in Flux: An Interplay of Neutrality and Adaptability Explains Genome Expansion and Streamlining

(2012) Thomas D. Cuypers et al.   Genome Biology and Evolution

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

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

Altered tRNA characteristics and 3′ maturation in bacterial symbionts with reduced genomes

(2012) Allison K. Hansen et al.   NUCLEIC ACIDS RESEARCH

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

The Repatterning of Eukaryotic Genomes by Random Genetic Drift

(2011) Michael Lynch et al.   Annual Review of Genomics and Human Genetics

The Rare Bacterial Biosphere

(2011) Carlos Pedrós-Alió   Annual Review of Marine Science

Eco-evolutionary dynamics, coding structure and the information threshold

(2011) Folkert K de Boer et al.   BMC EVOLUTIONARY BIOLOGY

NONADAPTIVE EVOLUTION OF MITOCHONDRIAL GENOME SIZE

(2011) Bastien Boussau et al.   EVOLUTION

The Evolution of Multimeric Protein Assemblages

(2011) M. Lynch   MOLECULAR BIOLOGY AND EVOLUTION

Independent Genome Reduction and Phylogenetic Reclassification of the Oceanic SAR11 Clade

(2011) J. Viklund et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome Reduction by Deletion of Paralogs in the Marine Cyanobacterium Prochlorococcus

(2011) H. Luo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Codon usage patterns and adaptive evolution of marine unicellular cyanobacteria Synechococcus and Prochlorococcus

(2011) Tonghai Yu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genomic island variability facilitates Prochlorococcus–virus coexistence

(2011) Sarit Avrani et al.   NATURE

The spontaneous mutation frequencies of Prochlorococcus strains are commensurate with those of other bacteria

(2011) Marcia S. Osburne et al.   Environmental Microbiology Reports

Drift and Genome Complexity Revisited

(2011) Kenneth D. Whitney et al.   PLoS Genetics

Sequence Conservation and Functional Constraint on Intergenic Spacers in Reduced Genomes of the Obligate Symbiont Buchnera

(2011) Patrick H. Degnan et al.   PLoS Genetics

Statistical Inference on the Mechanisms of Genome Evolution

(2011) Michael Lynch   PLoS Genetics

Distinct, ecotype-specific genome and proteome signatures in the marine cyanobacteria Prochlorococcus

(2010) Sandip Paul et al.   BMC GENOMICS

The Rate of Establishment of Complex Adaptations

(2010) M. Lynch et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary microbial genomics: insights into bacterial host adaptation

(2010) Christina Toft et al.   NATURE REVIEWS GENETICS

Ecosystem-specific selection pressures revealed through comparative population genomics

(2010) M. L. Coleman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Did Genetic Drift Drive Increases in Genome Complexity?

(2010) Kenneth D. Whitney et al.   PLoS Genetics

Prochlorococcus: Advantages and Limits of Minimalism

(2009) Frédéric Partensky et al.   Annual Review of Marine Science

Databases of homologous gene families for comparative genomics

(2009) Simon Penel et al.   BMC BIOINFORMATICS

Deletional Bias across the Three Domains of Life

(2009) Chih-Horng Kuo et al.   Genome Biology and Evolution

Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus

(2009) Olga Zhaxybayeva et al.   Genome Biology and Evolution

The consequences of genetic drift for bacterial genome complexity

(2009) C.-H. Kuo et al.   GENOME RESEARCH

Ecological Genomics of Marine Picocyanobacteria

(2009) D. J. Scanlan et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria

(2009) N. A. Moran et al.   SCIENCE

Genomics and Evolution of Heritable Bacterial Symbionts

(2008) Nancy A. Moran et al.   Annual Review of Genetics

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

(2008) Julien Dutheil et al.   BMC EVOLUTIONARY BIOLOGY

POPULATION STRUCTURE, LEVELS OF SELECTION, AND THE EVOLUTION OF INTRACELLULAR SYMBIONTS

(2008) Brendan O'Fallon   EVOLUTION

Environmental Sequence Data from the Sargasso Sea Reveal That the Characteristics of Genome Reduction in Prochlorococcus Are Not a Harbinger for an Escalation in Genetic Drift

(2008) J. Hu et al.   MOLECULAR BIOLOGY AND EVOLUTION