Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria (2009)
Kuo, Chih-Horng, Ochman, Howard
Abstract Background Because bacteria do not have a robust fossil record, attempts to infer the timing of events in their evolutionary history requires comparisons of molecular sequences. This use of...
The consequences of genetic drift for bacterial genome complexity (2009)
Kuo, Chih-Horng, Moran, Nancy A., Ochman, Howard
Genetic drift, which is particularly effective within small populations, can shape the size and complexity of genomes by affecting the fixation of deleterious mutations. In Bacteria, assessing the...
Habilitation à Diriger des Recherches (2008)
Eduardo Pimentel, Manolo Gouy, Patrick Forterre, Didier Mazel, Bénédicte Michel, Pierre Netter, ...
Ordre et désordre dans les génomes bactériens
The nature and dynamics of bacterial genomes (2006)
Ochman, Howard, Davalos, Liliana M.
Though generally small and gene rich, bacterial genomes are constantly subjected to both mutational and population-level processes that operate to increase amounts of functionless DNA. As a result,...
Sex and virulence in Escherichia coli: an evolutionary perspective (2006)
Wirth, Thierry, Falush, Daniel, Lan, Ruiting, Colles, Frances, Mensa, Patience, Wieler, Lothar H., ...
Pathogenic Escherichia coli cause over 160 million cases of dysentery and one million deaths per year, whereas non-pathogenic E. coli constitute part of the normal intestinal flora of healthy mammals...
Evolutionary Origins of Genomic Repertoires in Bacteria (2005)
Emmanuelle Lerat, Vincent Daubin, Howard Ochman, Nancy A. Moran
Lateral gene transfer, rather than duplication, is responsible for most gene diversity present in gamma-Protobacteria; however, these genes are then vertically transmitted and have little impact on...
Evolutionary Origins of Genomic Repertoires in Bacteria (2005)
Emmanuelle Lerat, Vincent Daubin, Howard Ochman, Nancy A. Moran
Explaining the diversity of gene repertoires has been a major problem in modern evolutionary biology. In eukaryotes, this diversity is believed to result mainly from gene duplication and loss, but in...
Recognizing the pseudogenes in bacterial genomes (2005)
Lerat, Emmanuelle, Ochman, Howard
Pseudogenes are now known to be a regular feature of bacterial genomes and are found in particularly high numbers within the genomes of recently emerged bacterial pathogens. As most pseudogenes are...
Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli (2004)
Daubin, Vincent, Ochman, Howard
Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of...
{Psi}-{Phi}: Exploring the outer limits of bacterial pseudogenes (2004)
Lerat, Emmanuelle, Ochman, Howard
Because bacterial chromosomes are tightly packed with genes and were traditionally viewed as being optimized for size and replication speed, it was not surprising that the early annotations of...
{Psi}-{Phi}: Exploring the outer limits of bacterial pseudogenes (2004)
Lerat, Emmanuelle, Ochman, Howard
Because bacterial chromosomes are tightly packed with genes and were traditionally viewed as being optimized for size and replication speed, it was not surprising that the early annotations of...
Quartet Mapping and the Extent of Lateral Transfer in Bacterial Genomes (2004)
Daubin, Vincent, Ochman, Howard
Several recent analyses have used quartet-based methods to assess the congruence among phylogenies derived for large sets of genes from prokaryotic genomes. The principal conclusion from these...
MBE Advance Access published August 29, 2003 (2003)
Quartet mapping and the extent of lateral transfer in bacterial genomes
Loss of DNA Recombinational Repair Enzymes in the Initial Stages of Genome Degeneration (2003)
Dale, Colin, Wang, Ben, Moran, Nancy, Ochman, Howard
Many obligate intracellular pathogens and symbionts undergo genome degeneration during long-term association with eukaryotic hosts; however, very little is known about genome changes that occur in...
Neutral Mutations and Neutral Substitutions in Bacterial Genomes (2003)
Molecular evolutionary biologists usually assess the underlying spectrum of mutations within a bacterial genome by examining substitutions that occur at sites that are believed to be under no...
Quartet Mapping and the Extent of Lateral Transfer in Bacterial Genomes (2003)
Daubin, Vincent, Ochman, Howard
Several recent analyses have used quartet-based methods to assess the congruence among phylogenies derived for large sets of genes from prokaryotic genomes. The principal conclusion from these...
Neutral Mutations and Neutral Substitutions in Bacterial Genomes (2003)
Molecular evolutionary biologists usually assess the underlying spectrum of mutations within a bacterial genome by examining substitutions that occur at sites believed to be under no selective...
Loss of DNA Recombinational Repair Enzymes in the Initial Stages of Genome Degeneration (2003)
Dale, Colin, Wang, Ben, Moran, Nancy, Ochman, Howard
Many obligate intracellular pathogens and symbionts undergo genome degeneration during long-term association with eukaryotic hosts; however, very little is known about genome changes that occur in...
Transcription increases multiple spontaneous point mutations in Salmonella enterica (2003)
Hudson, Richard Ellis, Bergthorsson, Ulfar, Ochman, Howard
The spontaneous rate of G·C→A·T mutations and a hotspot T·A→G·C transversion are known to increase with the frequency of transcription—increases that have been ascribed primarily to...
Loss of DNA Recombinational Repair Enzymes in the Initial Stages of Genome Degeneration (2003)
Dale, Colin, Wang, Ben, Moran, Nancy, Ochman, Howard
Many obligate intracellular pathogens and symbionts undergo genome degeneration during long-term association with eukaryotic hosts; however, very little is known about genome changes that occur in...
Neutral Mutations and Neutral Substitutions in Bacterial Genomes (2003)
Molecular evolutionary biologists usually assess the underlying spectrum of mutations within a bacterial genome by examining substitutions that occur at sites that are believed to be under no...
Quartet Mapping and the Extent of Lateral Transfer in Bacterial Genomes (2003)
Daubin, Vincent, Ochman, Howard
Several recent analyses have used quartet-based methods to assess the congruence among phylogenies derived for large sets of genes from prokaryotic genomes. The principal conclusion from these...
Effect of Chromosome Location on Bacterial Mutation Rates (2002)
Hudson, Richard Ellis, Bergthorsson, Ulfar, Roth, John R., Ochman, Howard
In previous comparisons of enterobacterial sequences, synonymous substitution rates were higher in genes closer to the replication terminus, suggesting that mutation rates increase with distance from...
Gene Location and Bacterial Sequence Divergence (2002)
Previous comparison of a relatively small set of homologous genes from Escherichia coli and Salmonella typhimurium revealed that genes nearer to the origin of replication had substitution rates lower...
Decoupling of genome size and sequence divergence in a symbiotic bacterium (2000)
Wernegreen, Jennifer J., Ochman, Howard, Jones, Isaac B., Moran, Nancy A.
Author Posting. © American Society for Microbiology, 2000. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive...
Decoupling of genome size and sequence divergence in a symbiotic bacterium (2000)
Wernegreen, Jennifer J., Ochman, Howard, Jones, Isaac B., Moran, Nancy A.
Author Posting. © American Society for Microbiology, 2000. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive...
Strand Symmetry Around the {beta}-Globin Origin of Replication in Primates (2000)
Pilar Francino*, M., Ochman, Howard
Certain mutations are known to occur with differing frequencies on the leading and lagging strands of DNA. The extent to which these mutational biases affect the sequences of higher eukaryotes has...
Krane, Dan E., Hartl, Daniel L., Ochman, Howard
We have developed a sensitive, reliable and accurate procedure for estimating the base composition of small samples of DNAs. This method has been applied to the analysis of genomic DNAs from several...
Evolution of parthenogenesis in the spear-winged fly lonchoptera dubia / (1979)
Thesis (M.S.)--University of Rochester. Dept. of Biology.
Molecular archaeology of the Escherichia coli genome
Lawrence, Jeffrey G., Ochman, Howard
The availability of the complete sequence of Escherichia coli strain MG1655 provides the first opportunity to assess the overall impact of horizontal genetic transfer on the evolution of bacterial...
Calibrating bacterial evolution
Ochman, Howard, Elwyn, Susannah, Moran, Nancy A.
Attempts to calibrate bacterial evolution have relied on the assumption that rates of molecular sequence divergence in bacteria are similar to those of higher eukaryotes, or to those of the few...
Long-Term Shifts in Patterns of Antibiotic Resistance in Enteric Bacteria
Several mechanisms are responsible for the ability of microorganisms to tolerate antibiotics, and the incidence of resistance to these compounds within bacterial species has increased since the...
Chromosomal Changes during Experimental Evolution in Laboratory Populations of Escherichia coli
Bergthorsson, Ulfar, Ochman, Howard
Short-term rates of chromosome evolution were analyzed in experimental populations of Escherichia coli B that had been propagated for 2,000 generations under four thermal regimens. Chromosome...
Decoupling of Genome Size and Sequence Divergence in a Symbiotic Bacterium
Wernegreen, Jennifer J., Ochman, Howard, Jones, Isaac B., Moran, Nancy A.
In contrast to genome size variation in most bacterial taxa, the small genome size of Buchnera sp. was shown to be highly conserved across genetically diverse isolates (630 to 643 kb). This...
Type III secretion systems and the evolution of mutualistic endosymbiosis
Dale, Colin, Plague, Gordon R., Wang, Ben, Ochman, Howard, Moran, Nancy A.
The view that parasites can develop cooperative symbiotic relationships with their hosts is both appealing and widely held; however, there is no molecular genetic evidence of such a transition. Here...
Transcription increases multiple spontaneous point mutations in Salmonella enterica
Ellis Hudson, Richard, Bergthorsson, Ulfar, Ochman, Howard
The spontaneous rate of G·C→A·T mutations and a hotspot T·A→G·C transversion are known to increase with the frequency of transcription—increases that have been ascribed primarily to...
Evolutionary dynamics of full genome content in Escherichia coli
Ochman, Howard, Jones, Isaac B.
The evolutionary history of the entire Escherichia coli chromosome was traced by examining the distribution of the ∼4300 open reading frames (ORFs) from E.coli MG1655 among strains of known...
Molecular area effects in Cepaea
Ochman, Howard, Jones, J. S., Selander, Robert K.
Enzyme polymorphisms in the land snail Cepaea nemoralis in the central Pyrenees show concordant geographic patterns of strong differentiation that are not correlated with the distributions of...
Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli
Daubin, Vincent, Ochman, Howard
Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of...
Ψ-Φ: Exploring the outer limits of bacterial pseudogenes
Lerat, Emmanuelle, Ochman, Howard
Because bacterial chromosomes are tightly packed with genes and were traditionally viewed as being optimized for size and replication speed, it was not surprising that the early annotations of...
Evolutionary Origins of Genomic Repertoires in Bacteria
Lerat, Emmanuelle, Daubin, Vincent, Ochman, Howard, Moran, Nancy A
Explaining the diversity of gene repertoires has been a major problem in modern evolutionary biology. In eukaryotes, this diversity is believed to result mainly from gene duplication and loss, but in...
Examining bacterial species under the specter of gene transfer and exchange
Ochman, Howard, Lerat, Emmanuelle, Daubin, Vincent
Even in lieu of a dependable species concept for asexual organisms, the classification of bacteria into discrete taxonomic units is considered to be obstructed by the potential for lateral gene...
Recognizing the pseudogenes in bacterial genomes
Lerat, Emmanuelle, Ochman, Howard
Pseudogenes are now known to be a regular feature of bacterial genomes and are found in particularly high numbers within the genomes of recently emerged bacterial pathogens. As most pseudogenes are...
Dale, Colin, Dunbar, Helen, Moran, Nancy A., Ochman, Howard
Analysis of many bacterial genomes is impeded by the inability to separate individual species from complex mixtures of cells or to propagate cells in pure culture. This problem is an obstacle to the...
The players in a mutualistic symbiosis: Insects, bacteria, viruses, and virulence genes
Moran, Nancy A., Degnan, Patrick H., Santos, Scott R., Dunbar, Helen E., Ochman, Howard
Aphids maintain mutualistic symbioses involving consortia of coinherited organisms. All possess a primary endosymbiont, Buchnera, which compensates for dietary deficiencies; many also contain...
Sex and virulence in Escherichia coli: an evolutionary perspective
Wirth, Thierry, Falush, Daniel, Lan, Ruiting, Colles, Frances, Mensa, Patience, Wieler, Lothar H, ...
Pathogenic Escherichia coli cause over 160 million cases of dysentery and one million deaths per year, whereas non-pathogenic E. coli constitute part of the normal intestinal flora of healthy mammals...
Molecular archaeology of the Escherichia coli genome
Lawrence, Jeffrey G., Ochman, Howard
The availability of the complete sequence of Escherichia coli strain MG1655 provides the first opportunity to assess the overall impact of horizontal genetic transfer on the evolution of bacterial...
Calibrating bacterial evolution
Ochman, Howard, Elwyn, Susannah, Moran, Nancy A.
Attempts to calibrate bacterial evolution have relied on the assumption that rates of molecular sequence divergence in bacteria are similar to those of higher eukaryotes, or to those of the few...
Long-Term Shifts in Patterns of Antibiotic Resistance in Enteric Bacteria
Several mechanisms are responsible for the ability of microorganisms to tolerate antibiotics, and the incidence of resistance to these compounds within bacterial species has increased since the...
Chromosomal Changes during Experimental Evolution in Laboratory Populations of Escherichia coli
Bergthorsson, Ulfar, Ochman, Howard
Short-term rates of chromosome evolution were analyzed in experimental populations of Escherichia coli B that had been propagated for 2,000 generations under four thermal regimens. Chromosome...
Decoupling of Genome Size and Sequence Divergence in a Symbiotic Bacterium
Wernegreen, Jennifer J., Ochman, Howard, Jones, Isaac B., Moran, Nancy A.
In contrast to genome size variation in most bacterial taxa, the small genome size of Buchnera sp. was shown to be highly conserved across genetically diverse isolates (630 to 643 kb). This...
Type III secretion systems and the evolution of mutualistic endosymbiosis
Dale, Colin, Plague, Gordon R., Wang, Ben, Ochman, Howard, Moran, Nancy A.
The view that parasites can develop cooperative symbiotic relationships with their hosts is both appealing and widely held; however, there is no molecular genetic evidence of such a transition. Here...
Transcription increases multiple spontaneous point mutations in Salmonella enterica
Ellis Hudson, Richard, Bergthorsson, Ulfar, Ochman, Howard
The spontaneous rate of G·C→A·T mutations and a hotspot T·A→G·C transversion are known to increase with the frequency of transcription—increases that have been ascribed primarily to...
Evolutionary dynamics of full genome content in Escherichia coli
Ochman, Howard, Jones, Isaac B.
The evolutionary history of the entire Escherichia coli chromosome was traced by examining the distribution of the ∼4300 open reading frames (ORFs) from E.coli MG1655 among strains of known...
Molecular area effects in Cepaea
Ochman, Howard, Jones, J. S., Selander, Robert K.
Enzyme polymorphisms in the land snail Cepaea nemoralis in the central Pyrenees show concordant geographic patterns of strong differentiation that are not correlated with the distributions of...
Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli
Daubin, Vincent, Ochman, Howard
Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of...
Ψ-Φ: Exploring the outer limits of bacterial pseudogenes
Lerat, Emmanuelle, Ochman, Howard
Because bacterial chromosomes are tightly packed with genes and were traditionally viewed as being optimized for size and replication speed, it was not surprising that the early annotations of...
Evolutionary Origins of Genomic Repertoires in Bacteria
Lerat, Emmanuelle, Daubin, Vincent, Ochman, Howard, Moran, Nancy A
Explaining the diversity of gene repertoires has been a major problem in modern evolutionary biology. In eukaryotes, this diversity is believed to result mainly from gene duplication and loss, but in...
Examining bacterial species under the specter of gene transfer and exchange
Ochman, Howard, Lerat, Emmanuelle, Daubin, Vincent
Even in lieu of a dependable species concept for asexual organisms, the classification of bacteria into discrete taxonomic units is considered to be obstructed by the potential for lateral gene...
Recognizing the pseudogenes in bacterial genomes
Lerat, Emmanuelle, Ochman, Howard
Pseudogenes are now known to be a regular feature of bacterial genomes and are found in particularly high numbers within the genomes of recently emerged bacterial pathogens. As most pseudogenes are...
Dale, Colin, Dunbar, Helen, Moran, Nancy A., Ochman, Howard
Analysis of many bacterial genomes is impeded by the inability to separate individual species from complex mixtures of cells or to propagate cells in pure culture. This problem is an obstacle to the...
The players in a mutualistic symbiosis: Insects, bacteria, viruses, and virulence genes
Moran, Nancy A., Degnan, Patrick H., Santos, Scott R., Dunbar, Helen E., Ochman, Howard
Aphids maintain mutualistic symbioses involving consortia of coinherited organisms. All possess a primary endosymbiont, Buchnera, which compensates for dietary deficiencies; many also contain...
Sex and virulence in Escherichia coli: an evolutionary perspective
Wirth, Thierry, Falush, Daniel, Lan, Ruiting, Colles, Frances, Mensa, Patience, Wieler, Lothar H, ...
Pathogenic Escherichia coli cause over 160 million cases of dysentery and one million deaths per year, whereas non-pathogenic E. coli constitute part of the normal intestinal flora of healthy mammals...
Stepwise formation of the bacterial flagellar system
Elucidating the origins of complex biological structures has been one of the major challenges of evolutionary studies. The bacterial flagellum is a primary example of a complex apparatus whose...
Origins of Flagellar Gene Operons and Secondary Flagellar Systems▿ †
Forty-one flagellated species representing 11 bacterial phyla were used to investigate the origin of secondary flagellar systems and the structure and formation of flagellar gene operons over the...
The Emergence and Fate of Horizontally Acquired Genes in Escherichia coli
Marri, Pradeep Reddy, Ochman, Howard
Bacterial species, and even strains within species, can vary greatly in their gene contents and metabolic capabilities. We examine the evolution of this diversity by assessing the distribution and...
The Effect of Chromosome Geometry on Genetic Diversity
Marri, Pradeep Reddy, Harris, Leigh K., Houmiel, Kathryn, Slater, Steven C., Ochman, Howard
Although organisms with linear chromosomes must solve the problem of fully replicating their chromosome ends, this chromosome configuration has emerged repeatedly during bacterial evolution and is...
Pea Aphid as both Host and Vector for the Phytopathogenic Bacterium Pseudomonas syringae▿
Stavrinides, John, McCloskey, Jodi K., Ochman, Howard
Aphids are widespread agricultural pests that are capable of disseminating plant viral diseases; however, despite coming into frequent contact with epiphytic bacteria, aphids are considered to have...