Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes

Recombination Shapes Genome Architecture in an Organism from the Archaeal Domain

(2014) David J. Krause et al.   Genome Biology and Evolution

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

(2014) N. Kashtan et al.   SCIENCE

Ordering microbial diversity into ecologically and genetically cohesive units

(2014) B. Jesse Shapiro et al.   TRENDS IN MICROBIOLOGY

Extensive Cotransformation of Natural Variation into Chromosomes of Naturally Competent Haemophilus influenzae

(2014) Joshua Chang Mell et al.   G3-Genes Genomes Genetics

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

(2014) Martial Marbouty et al.   eLife

Sulfolobus islandicus:a model system for evolutionary genomics

(2013) Changyi Zhang et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species

(2013) Alexander F Koeppel et al.   ISME Journal

Long-Term Dynamics of Adaptation in Asexual Populations

(2013) M. J. Wiser et al.   SCIENCE

Distributive Conjugal Transfer in Mycobacteria Generates Progeny with Meiotic-Like Genome-Wide Mosaicism, Allowing Mapping of a Mating Identity Locus

(2013) Todd A. Gray et al.   PLOS BIOLOGY

Genomic characterization of the Bacillus cereus sensu lato species: Backdrop to the evolution of Bacillus anthracis

(2012) M. E. Zwick et al.   GENOME RESEARCH

A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans

(2012) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic analysis of a key innovation in an experimental Escherichia coli population

(2012) Zachary D. Blount et al.   NATURE

Ecological Populations of Bacteria Act as Socially Cohesive Units of Antibiotic Production and Resistance

(2012) O. X. Cordero et al.   SCIENCE

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Patterns of Gene Flow Define Species of Thermophilic Archaea

(2012) Hinsby Cadillo-Quiroz et al.   PLOS BIOLOGY

A High-Resolution View of Genome-Wide Pneumococcal Transformation

(2012) Nicholas J. Croucher et al.   PLoS Pathogens

Bacterial species may exist, metagenomics reveal

(2011) Alejandro Caro-Quintero et al.   ENVIRONMENTAL MICROBIOLOGY

Pervasive Recombination and Sympatric Genome Diversification Driven by Frequency-Dependent Selection inBorrelia burgdorferi, the Lyme Disease Bacterium

(2011) James Haven et al.   GENETICS

A Model for the Effect of Homologous Recombination on Microbial Diversification

(2011) James R. Doroghazi et al.   Genome Biology and Evolution

Genomic divergence during speciation: causes and consequences

(2011) P. Nosil et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

(2011) M. W. Nachman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic islands of divergence in hybridizingHeliconiusbutterflies identified by large-scale targeted sequencing

(2011) Nicola J. Nadeau et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow

(2011) S. Via   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species

(2011) C. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

(2011) C. E. Ellison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transformation of Natural Genetic Variation into Haemophilus Influenzae Genomes

(2011) Joshua Chang Mell et al.   PLoS Pathogens

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

(2010) Sandip Paul et al.   BMC GENOMICS

Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences

(2010) X. Didelot et al.   GENETICS

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

Biogeography of the Sulfolobus islandicus pan-genome

(2009) M. L. Reno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

E Unibus Plurum: Genomic Analysis of an Experimentally Evolved Polymorphism in Escherichia coli

(2009) Margie A. Kinnersley et al.   PLoS Genetics

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

Isolation by Distance in the Spore-Forming Soil Bacterium Myxococcus xanthus

(2008) Michiel Vos et al.   CURRENT BIOLOGY

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Microbial diversity and the genetic nature of microbial species

(2008) Mark Achtman et al.   NATURE REVIEWS MICROBIOLOGY

Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae

(2008) M. Brochet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics

(2008) A. Koeppel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

(2008) Z. D. Blount et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE

Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton

(2008) D. E. Hunt et al.   SCIENCE