Reproductive clonality of pathogens: A perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa

The impact of clonality on parasite population genetic structure

(2013) F. Prugnolle et al.   Parasite

The evolution of the Escherichia coli phylogeny

(2012) Roy R. Chaudhuri et al.   INFECTION GENETICS AND EVOLUTION

Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania

(2011) M. B. Rogers et al.   GENOME RESEARCH

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance

(2011) T. Downing et al.   GENOME RESEARCH

Phylogeography and epidemiological history of West Nile virus genotype 1a in Europe and the Mediterranean basin

(2011) Gianguglielmo Zehender et al.   INFECTION GENETICS AND EVOLUTION

Evidence for inter- and intra-clade recombinations in rabies virus

(2011) Wei Liu et al.   INFECTION GENETICS AND EVOLUTION

An evolutionary legacy of sex and clonal reproduction in the protistan oyster parasite Perkinsus marinus

(2011) Peter C. Thompson et al.   INFECTION GENETICS AND EVOLUTION

Genetic exchange and emergence of novel strains in directly transmitted trypanosomatids

(2011) Regula Schmid-Hempel et al.   INFECTION GENETICS AND EVOLUTION

Current status of the taxonomic position of Fusarium oxysporum formae specialis cubense within the Fusarium oxysporum complex

(2011) G. Fourie et al.   INFECTION GENETICS AND EVOLUTION

Hepatitis B virus infection from an evolutionary point of view: How viral, host, and environmental factors shape genotypes and subgenotypes

(2011) Natalia M. Araujo et al.   INFECTION GENETICS AND EVOLUTION

Guns, germs and dogs: On the origin of Leishmania chagasi

(2011) Raphaël Leblois et al.   INFECTION GENETICS AND EVOLUTION

Phylogeny and homologous recombination in Chikungunya viruses

(2011) Jin Cui et al.   INFECTION GENETICS AND EVOLUTION

Molecular evolution of human species D adenoviruses

(2011) Christopher M. Robinson et al.   INFECTION GENETICS AND EVOLUTION

Animal and human pathogenic Escherichia coli strains share common genetic backgrounds

(2011) Olivier Clermont et al.   INFECTION GENETICS AND EVOLUTION

The revised Trypanosoma cruzi subspecific nomenclature: Rationale, epidemiological relevance and research applications

(2011) Bianca Zingales et al.   INFECTION GENETICS AND EVOLUTION

The global distribution and phylogeography of Mycobacterium bovis clonal complexes

(2011) Noel H. Smith   INFECTION GENETICS AND EVOLUTION

Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex

(2011) Tim Downing et al.   INFECTION GENETICS AND EVOLUTION

West Nile virus population genetics and evolution

(2011) Kendra N. Pesko et al.   INFECTION GENETICS AND EVOLUTION

Extraordinary Trypanosoma cruzi diversity within single mammalian reservoir hosts implies a mechanism of diversifying selection

(2011) Martin S. Llewellyn et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Genetic analyses of atypical Toxoplasma gondii strains reveal a fourth clonal lineage in North America

(2011) Asis Khan et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Population genetics and evolution of the pan-genome of Streptococcus pneumoniae

(2011) Alessandro Muzzi et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

The molecular epidemiology of parasite infections: Tools and applications

(2011) A.J. Lymbery et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Reproductive strategies and population structure in Leishmania: substantial amount of sex in Leishmania Viannia guyanensis

(2011) VIRGINIE ROUGERON et al.   MOLECULAR ECOLOGY

Why do RNA viruses recombine?

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

Virulence Evolution of the Human Pathogen Neisseria meningitidis by Recombination in the Core and Accessory Genome

(2011) Biju Joseph et al.   PLoS One

The Plant Pathogen Phytophthora andina Emerged via Hybridization of an Unknown Phytophthora Species and the Irish Potato Famine Pathogen, P. infestans

(2011) Erica M. Goss et al.   PLoS One

South American Plasmodium falciparum after the Malaria Eradication Era: Clonal Population Expansion and Survival of the Fittest Hybrids

(2011) Sean M. Griffing et al.   PLoS One

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

African monkeys are infected by Plasmodium falciparum nonhuman primate-specific strains

(2011) F. Prugnolle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination

(2011) S. Budroni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Second-Order Selection for Evolvability in a Large Escherichia coli Population

(2011) R. J. Woods et al.   SCIENCE

Rapid Pneumococcal Evolution in Response to Clinical Interventions

(2011) N. J. Croucher et al.   SCIENCE

A cautionary note concerning Plasmodium in apes

(2011) Gediminas Valkiūnas et al.   TRENDS IN PARASITOLOGY

A plethora of Plasmodium species in wild apes: a source of human infection?

(2011) Julian C. Rayner et al.   TRENDS IN PARASITOLOGY

Double peaks reveal rare diplomonad sex

(2011) Jan O. Andersson   TRENDS IN PARASITOLOGY

Population genetics of Toxoplasma gondii: New perspectives from parasite genotypes in wildlife

(2011) Jered M. Wendte et al.   VETERINARY PARASITOLOGY

The molecular epidemiology of hepatitis E virus infection

(2011) Michael A. Purdy et al.   VIRUS RESEARCH

Recombination and Population Structure in Salmonella enterica

(2011) Xavier Didelot et al.   PLoS Genetics

Evolutionary History of Rabies in Ghana

(2011) David T. S. Hayman et al.   PLoS Neglected Tropical Diseases

Phylogeography and Taxonomy of Trypanosoma brucei

(2011) Oliver Balmer et al.   PLoS Neglected Tropical Diseases

Multilocus Sequence Typing (MLST) for Lineage Assignment and High Resolution Diversity Studies in Trypanosoma cruzi

(2011) Matthew Yeo et al.   PLoS Neglected Tropical Diseases

Multi-Locus Sequence Analysis Reveals Profound Genetic Diversity among Isolates of the Human Pathogen Bartonella bacilliformis

(2011) Gemma L. Chaloner et al.   PLoS Neglected Tropical Diseases

Analyses of 32 Loci Clarify Phylogenetic Relationships among Trypanosoma cruzi Lineages and Support a Single Hybridization prior to Human Contact

(2011) Carlos A. Flores-López et al.   PLoS Neglected Tropical Diseases

Multifaceted Population Structure and Reproductive Strategy in Leishmania donovani Complex in One Sudanese Village

(2011) Virginie Rougeron et al.   PLoS Neglected Tropical Diseases

Multilocus Genotyping of Human Giardia Isolates Suggests Limited Zoonotic Transmission and Association between Assemblage B and Flatulence in Children

(2011) Marianne Lebbad et al.   PLoS Neglected Tropical Diseases

Epidemiological Tracking and Population Assignment of the Non-Clonal Bacterium, Burkholderia pseudomallei

(2011) Julia Dale et al.   PLoS Neglected Tropical Diseases

Recent, Independent and Anthropogenic Origins of Trypanosoma cruzi Hybrids

(2011) Michael D. Lewis et al.   PLoS Neglected Tropical Diseases

Endemic Dengue Associated with the Co-Circulation of Multiple Viral Lineages and Localized Density-Dependent Transmission

(2011) Jayna Raghwani et al.   PLoS Pathogens

A Fresh Look at the Origin of Plasmodium falciparum, the Most Malignant Malaria Agent

(2011) Franck Prugnolle et al.   PLoS Pathogens

The Evolutionary Genetics of Emerging Viruses

(2010) Edward C. Holmes   Annual Review of Ecology Evolution and Systematics

Prospects for the Future Using Genomics and Proteomics in Clinical Microbiology

(2010) Pierre-Edouard Fournier et al.   Annual Review of Microbiology

Population Structure and Evolution of Pathogenicity ofYersinia pseudotuberculosis

(2010) Shear Lane Ch'ng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A Population Genetics-Based and Phylogenetic Approach to Understanding the Evolution of Virulence in the Genus Listeria

(2010) H. C. den Bakker et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evolution of Eukaryotic Microbial Pathogens via Covert Sexual Reproduction

(2010) Joseph Heitman   Cell Host & Microbe

FISH analysis reveals aneuploidy and continual generation of chromosomal mosaicism in Leishmania major

(2010) Yvon Sterkers et al.   CELLULAR MICROBIOLOGY

Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections

(2010) Tommy Tsan-Yuk Lam et al.   CRITICAL REVIEWS IN CLINICAL LABORATORY SCIENCES

Navigating the future of bacterial molecular epidemiology

(2010) Stephen Baker et al.   CURRENT OPINION IN MICROBIOLOGY

Microsatellite typing identifies the major clades of the human pathogen Candida albicans

(2010) Julio Chávez-Galarza et al.   INFECTION GENETICS AND EVOLUTION

Evolution and world-wide distribution of varicella–zoster virus clades

(2010) Jonas Schmidt-Chanasit et al.   INFECTION GENETICS AND EVOLUTION

Genetic recombination of the hepatitis C virus: clinical implications

(2010) V. Morel et al.   JOURNAL OF VIRAL HEPATITIS

Evolutionary Dynamics and Temporal/Geographical Correlates of Recombination in the Human Enterovirus Echovirus Types 9, 11, and 30

(2010) E. C. McWilliam Leitch et al.   JOURNAL OF VIROLOGY

Quantifying Nonvertical Inheritance in the Evolution of Legionella pneumophila

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

Origin of the human malaria parasite Plasmodium falciparum in gorillas

(2010) Weimin Liu et al.   NATURE

The population genetics of commensal Escherichia coli

(2010) Olivier Tenaillon et al.   NATURE REVIEWS MICROBIOLOGY

Multi-Locus Sequence Typing of a Geographically and Temporally Diverse Sample of the Highly Clonal Human Pathogen Bartonella quintana

(2010) Mardjan Arvand et al.   PLoS One

The Population Genetics of Pseudomonas aeruginosa Isolates from Different Patient Populations Exhibits High-Level Host Specificity

(2010) Rosa van Mansfeld et al.   PLoS One

Phylogenetic character mapping of proteomic diversity shows high correlation with subspecific phylogenetic diversity in Trypanosoma cruzi

(2010) J. Telleria et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics

(2010) S. B. Beres et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

African great apes are natural hosts of multiple related malaria species, including Plasmodium falciparum

(2010) F. Prugnolle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

African apes as reservoirs of Plasmodium falciparum and the origin and diversification of the Laverania subgenus

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

Mechanisms of genetic variation in polioviruses

(2010) Carita Savolainen-Kopra et al.   REVIEWS IN MEDICAL VIROLOGY

Recombination among picornaviruses

(2010) A.N. Lukashev   REVIEWS IN MEDICAL VIROLOGY

A multilocus sequence analysis of Xanthomonas campestris reveals a complex structure within crucifer-attacking pathovars of this species

(2010) E. Fargier et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Impact of recombination on bacterial evolution

(2010) Xavier Didelot et al.   TRENDS IN MICROBIOLOGY

A species concept for bacteria based on adaptive divergence

(2010) Michiel Vos   TRENDS IN MICROBIOLOGY

The impact of genetic diversity in protozoa on molecular diagnostics

(2010) C. Rune Stensvold et al.   TRENDS IN PARASITOLOGY

Combined MLST and AFLP typing of Bartonella henselae isolated from cats reveals new sequence types and suggests clonal evolution

(2010) A. Mietze et al.   VETERINARY MICROBIOLOGY

Self-Mating in the Definitive Host Potentiates Clonal Outbreaks of the Apicomplexan Parasites Sarcocystis neurona and Toxoplasma gondii

(2010) Jered M. Wendte et al.   PLoS Genetics

Inference of Population Structure of Leishmania donovani Strains Isolated from Different Ethiopian Visceral Leishmaniasis Endemic Areas

(2010) Tesfaye Gelanew et al.   PLoS Neglected Tropical Diseases

Sex, Subdivision, and Domestic Dispersal of Trypanosoma cruzi Lineage I in Southern Ecuador

(2010) Sofía Ocaña-Mayorga et al.   PLoS Neglected Tropical Diseases

An Infectious Topic in Reticulate Evolution: Introgression and Hybridization in Animal Parasites

(2010) Jillian T. Detwiler et al.   Genes

Cryptic Lineages of the Genus Escherichia

(2009) S. T. Walk et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

(2009) Talima Pearson et al.   BMC BIOLOGY

Giardia duodenalis: Genetic recombination and its implications for taxonomy and molecular epidemiology

(2009) Simone M. Cacciò et al.   EXPERIMENTAL PARASITOLOGY

Apparent high recombination rates in clonal parasitic organisms due to inappropriate sampling design

(2009) F Prugnolle et al.   HEREDITY

The quasispecies nature and biological implications of the hepatitis C virus

(2009) Sarah L. Fishman et al.   INFECTION GENETICS AND EVOLUTION

Phylogenetic perspectives on the epidemiology and origins of SARS and SARS-like coronaviruses

(2009) Chi Wai Yip et al.   INFECTION GENETICS AND EVOLUTION

Legionella pneumophila: Population genetics, phylogeny and genomics

(2009) L. Gomez-Valero et al.   INFECTION GENETICS AND EVOLUTION

Molecular evolution of dengue viruses: Contributions of phylogenetics to understanding the history and epidemiology of the preeminent arboviral disease

(2009) Scott C. Weaver et al.   INFECTION GENETICS AND EVOLUTION

Phylogenetic understanding of clonal populations in an era of whole genome sequencing

(2009) Talima Pearson et al.   INFECTION GENETICS AND EVOLUTION

The evolutionary biology of poxviruses

(2009) Austin L. Hughes et al.   INFECTION GENETICS AND EVOLUTION

Population genetic structure of Central African Trypanosoma brucei gambiense isolates using microsatellite DNA markers

(2009) Gustave Simo et al.   INFECTION GENETICS AND EVOLUTION

Trypanosoma vivax displays a clonal population structure

(2009) Craig W. Duffy et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Flow cytometric analysis and microsatellite genotyping reveal extensive DNA content variation in Trypanosoma cruzi populations and expose contrasts between natural and experimental hybrids

(2009) Michael D. Lewis et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Toxoplasma gondii: 25 years and 25 major advances for the field

(2009) John C. Boothroyd   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Sexual recombination punctuated by outbreaks and clonal expansions predicts Toxoplasma gondii population genetics

(2009) Michael E. Grigg et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Genetic Exchange Within and Between Assemblages ofGiardia duodenalis

(2009) ERICA LASEK-NESSELQUIST et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Genealogical typing of Neisseria meningitidis

(2009) X. Didelot et al.   MICROBIOLOGY-SGM

Moving towards an integrated approach to molecular detection and identification of Toxoplasma gondii

(2009) C. SU et al.   PARASITOLOGY

The molecular epidemiology and phylogeography of Trypanosoma cruzi and parallel research on Leishmania: looking back and to the future

(2009) M. A. MILES et al.   PARASITOLOGY

Discovery of Mating in the Major African Livestock Pathogen Trypanosoma congolense

(2009) Liam J. Morrison et al.   PLoS One

Pseudomonas aeruginosa Population Structure Revisited

(2009) Jean-Paul Pirnay et al.   PLoS One

Extreme inbreeding in Leishmania braziliensis

(2009) V. Rougeron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The origin of malignant malaria

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

Hyper-Recombination, Diversity, and Antibiotic Resistance in Pneumococcus

(2009) W. P. Hanage et al.   SCIENCE

Demonstration of Genetic Exchange During Cyclical Development of Leishmania in the Sand Fly Vector

(2009) N. S. Akopyants et al.   SCIENCE

The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

(2009) C. Fraser et al.   SCIENCE

Evolution of pathogenicity in the Bacillus cereus group

(2009) Xavier Didelot et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Signs of sex: what we know and how we know it

(2009) Andrew M. Schurko et al.   TRENDS IN ECOLOGY & EVOLUTION

From clonal to sexual: a step in T. congolense evolution?

(2009) Philippe Holzmuller et al.   TRENDS IN PARASITOLOGY

Giardia Sex? Yes, but how and how much?

(2009) C. William Birky   TRENDS IN PARASITOLOGY

Toward the Use of Genomics to Study Microevolutionary Change in Bacteria

(2009) Daniel Falush   PLoS Genetics

Trypanosoma cruzi IIc: Phylogenetic and Phylogeographic Insights from Sequence and Microsatellite Analysis and Potential Impact on Emergent Chagas Disease

(2009) Martin S. Llewellyn et al.   PLoS Neglected Tropical Diseases

Genome-Scale Multilocus Microsatellite Typing of Trypanosoma cruzi Discrete Typing Unit I Reveals Phylogeographic Structure and Specific Genotypes Linked to Human Infection

(2009) Martin S. Llewellyn et al.   PLoS Pathogens

The Role of Genomics in Tracking the Evolution of Influenza A Virus

(2009) Alice Carolyn McHardy et al.   PLoS Pathogens

Evolutionary History and Phylogeography of Human Viruses

(2008) Edward C. Holmes   Annual Review of Microbiology

Population Structure ofToxoplasma gondii: Clonal Expansion Driven by Infrequent Recombination and Selective Sweeps

(2008) L. David Sibley et al.   Annual Review of Microbiology

Evolution, Population Structure, and Phylogeography of Genetically Monomorphic Bacterial Pathogens

(2008) Mark Achtman   Annual Review of Microbiology

Lineage specific recombination rates and microevolution in Listeria monocytogenes

(2008) Henk C den Bakker et al.   BMC EVOLUTIONARY BIOLOGY

Population genomics: diversity and virulence in the Neisseria

(2008) Martin CJ Maiden   CURRENT OPINION IN MICROBIOLOGY

Inferring genomic flux in bacteria

(2008) X. Didelot et al.   GENOME RESEARCH

Trypanosoma brucei gambiense Type 1 populations from human patients are clonal and display geographical genetic differentiation

(2008) Liam J. Morrison et al.   INFECTION GENETICS AND EVOLUTION

Genetics and evolution of Neisseria meningitidis: Importance for the epidemiology of meningococcal disease

(2008) Dominique A. Caugant   INFECTION GENETICS AND EVOLUTION

Pneumocystis species, co-evolution and pathogenic power

(2008) Cécile-Marie Aliouat-Denis et al.   INFECTION GENETICS AND EVOLUTION

Adaptive value of sex in microbial pathogens

(2008) Richard E. Michod et al.   INFECTION GENETICS AND EVOLUTION

Multilocus microsatellite typing (MLMT) reveals genetic homogeneity of Leishmania donovani strains in the Indian subcontinent

(2008) M ALAM et al.   INFECTION GENETICS AND EVOLUTION

Molecular approaches to diversity of populations of apicomplexan parasites

(2008) Hans-Peter Beck et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Clonal population structure of Legionella pneumophila inferred from allelic profiling

(2008) M. T. Edwards et al.   MICROBIOLOGY-SGM

The rise and fall of bacterial clones: Streptococcus pneumoniae

(2008) Birgitta Henriques-Normark et al.   NATURE REVIEWS MICROBIOLOGY

Microbial diversity and the genetic nature of microbial species

(2008) Mark Achtman et al.   NATURE REVIEWS MICROBIOLOGY

Evolution and Diversity of Clonal Bacteria: The Paradigm of Mycobacterium tuberculosis

(2008) Tiago Dos Vultos et al.   PLoS One

Population genetics of Trypanosoma brucei gambiense, the agent of sleeping sickness in Western Africa

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

Role of selection in the emergence of lineages and the evolution of virulence in Neisseria meningitidis

(2008) C. O. Buckee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The population structure of the Cryptosporidium parvum population in Scotland: A complex picture

(2007) Liam J. Morrison et al.   INFECTION GENETICS AND EVOLUTION