Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria

A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations

(2019) Philip Arevalo et al.   CELL

Phylogenetic conservatism of thermal traits explains dispersal limitation and genomic differentiation of Streptomyces sister-taxa

(2018) Mallory J. Choudoir et al.   ISME Journal

Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics

(2018) Eduardo P C Rocha   MOLECULAR BIOLOGY AND EVOLUTION

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

(2018) David Couvin et al.   NUCLEIC ACIDS RESEARCH

Emergence of Soil Bacterial Ecotypes Along a Climate Gradient

(2018) Alexander B. Chase et al.   ENVIRONMENTAL MICROBIOLOGY

Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits

(2017) Alexander B. Chase et al.   mBio

Latitude delineates patterns of biogeography in terrestrial Streptomyces

(2016) Mallory J. Choudoir et al.   ENVIRONMENTAL MICROBIOLOGY

A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus

(2016) Sébastien Wielgoss et al.   ISME Journal

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces

(2016) Cheryl P. Andam et al.   mBio

What Is Speciation?

(2016) B. Jesse Shapiro et al.   PLoS Genetics

Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium

(2016) Alexander B. Chase et al.   Frontiers in Microbiology

A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse

(2016) Jacob E. Lemieux et al.   Nature Microbiology

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils

(2015) David VanInsberghe et al.   ISME Journal

Epidemic Clones, Oceanic Gene Pools, and Eco-LD in the Free Living Marine Pathogen Vibrio parahaemolyticus

(2015) Yujun Cui et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic isolation between two recently diverged populations of a symbiotic fungus

(2015) Sara Branco et al.   MOLECULAR ECOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

LEA: AnRpackage for landscape and ecological association studies

(2015) Eric Frichot et al.   Methods in Ecology and Evolution

Inferring Horizontal Gene Transfer

(2015) Matt Ravenhall et al.   PLoS Computational Biology

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Intraspecies comparison of Streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic origin

(2014) James R Doroghazi et al.   BMC GENOMICS

Fast and Efficient Estimation of Individual Ancestry Coefficients

(2014) Eric Frichot et al.   GENETICS

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Isolation by environment

(2014) Ian J. Wang et al.   MOLECULAR ECOLOGY

Explaining microbial genomic diversity in light of evolutionary ecology

(2014) Otto X. Cordero et al.   NATURE REVIEWS MICROBIOLOGY

Competition-dispersal tradeoff ecologically differentiates recently speciated marine bacterioplankton populations

(2014) Y. Yawata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

GENETIC ISOLATION BY ENVIRONMENT OR DISTANCE: WHICH PATTERN OF GENE FLOW IS MOST COMMON?

(2013) Jason P. Sexton et al.   EVOLUTION

Horizontal gene transfer and the evolution of bacterial and archaeal population structure

(2013) Martin F. Polz et al.   TRENDS IN GENETICS

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

(2012) Sajia Akhter et al.   NUCLEIC ACIDS RESEARCH

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

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria

(2011) Dexi Bi et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

(2010) Sara Vieira-Silva et al.   PLoS Genetics

Isolation by landscape in populations of a prized edible mushroom Tricholoma matsutake

(2009) Anthony Amend et al.   CONSERVATION GENETICS

Nearly Neutrality and the Evolution of Codon Usage Bias in Eukaryotic Genomes

(2008) S. Subramanian   GENETICS

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal

Convergence of Campylobacter Species: Implications for Bacterial Evolution

(2008) S. K. Sheppard et al.   SCIENCE

Resource Partitioning and Sympatric Differentiation Among Closely Related Bacterioplankton

(2008) D. E. Hunt et al.   SCIENCE