CiteULike: Xavier's no-tag

Analyzing patterns of microbial evolution using the mauve genome alignment system.

AE Darling — 2008-04-08T08:45:04-00:00

Methods in molecular biology (Clifton, N.J.), Vol. 396 (2007), pp. 135-152.

During the course of evolution, genomes can undergo large-scale mutation events such as rearrangement and lateral transfer. Such mutations can result in significant variations in gene order and gene content among otherwise closely related organisms. The Mauve genome alignment system can successfully identify such rearrangement and lateral transfer events in comparisons of multiple microbial genomes even under high levels of recombination. This chapter outlines the main features of Mauve and provides examples that describe how to use Mauve to conduct a rigorous multiple genome comparison and study evolutionary patterns.

Detecting recombination from gene trees

Maynard — 2006-03-22T18:32:56-00:00

Mol Biol Evol, Vol. 15, No. 5. (1 May 1998), pp. 590-599.

Barriers to recombination between closely related bacteria: MutS and RecBCD inhibit recombination between Salmonella typhimurium and Salmonella typhi

Thomas Zahrt — 2007-08-08T10:50:05-00:00

PNAS, Vol. 94, No. 18. (2 September 1997), pp. 9786-9791.

Previous studies have shown that inactivation of the MutS or MutL mismatch repair enzymes increases the efficiency of homeologous recombination between Escherichia coli and Salmonella typhimurium and between S. typhimurium and Salmonella typhi. However, even in mutants defective for mismatch repair the recombination frequencies are 102- to 103-fold less than observed during homologous recombination between a donor and recipient of the same species. In addition, the length of DNA exchanged during transduction between S. typhimurium and S. typhi is less than in transductions between strains of S. typhimurium. In homeologous transductions, mutations in the recD gene increased the frequency of transduction and the length of DNA exchanged. Furthermore, in mutS recD double mutants the frequency of homeologous recombination was nearly as high as that seen during homologous recombination. The phenotypes of the mutants indicate that the gene products of mutS and recD act independently. Because S. typhimurium and S. typhi are [approx]98-99% identical at the DNA sequence level, the inhibition of recombination is probably not due to a failure of RecA to initiate strand exchange. Instead, these results suggest that mismatches act at a subsequent step, possibly by slowing the rate of branch migration. Slowing the rate of branch migration may stimulate helicase proteins to unwind rather than extend the heteroduplex and leave uncomplexed donor DNA susceptible to further degradation by RecBCD exonuclease. 10.1073/pnas.94.18.9786

Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities

IJ Wilson — 2007-08-03T14:08:11-00:00

pp. 155-188.

Summary. We develop a flexible class of Metropolis–Hastings algorithms for drawing inferences about population histories and mutation rates from deoxyribonucleic acid (DNA) sequence data. Match probabilities for use in forensic identification are also obtained, which is particularly useful for mitochondrial DNA profiles. Our data augmentation approach, in which the ancestral DNA data are inferred at each node of the genealogical tree, simplifies likelihood calculations and permits a wide class of mutation models to be employed, so that many different types of DNA sequence data can be analysed within our framework. Moreover, simpler likelihood calculations imply greater freedom for generating tree proposals, so that algorithms with good mixing properties can be implemented. We incorporate the effects of demography by means of simple mechanisms for changes in population size and structure, and we estimate the corresponding demographic parameters, but we do not here allow for the effects of either recombination or selection. We illustrate our methods by application to four human DNA data sets, consisting of DNA sequences, short tandem repeat loci, single-nucleotide polymorphism sites and insertion sites. Two of the data sets are drawn from the male-specific Y-chromosome, one from maternally inherited mitochondrial DNA and one from the -globin locus on chromosome 11.

Displaying the relatedness among isolates of bacterial species - the eBURST approach

Brian Spratt — 2007-08-03T10:54:53-00:00

FEMS Microbiology Letters, Vol. 241, No. 2. (2004), pp. 129-134.

Abstract Determining the most appropriate way to represent the relationships between bacterial isolates is complicated by the differing rates of recombination within species. In many cases, a bifurcating tree can be positively misleading. The recently described program eBURST can be used with multilocus data to define groups or clonal complexes of related isolates derived from a common ancestor, the patterns of descent linking them together, and the ancestral genotype. eBURST has recently been extensively updated to include additional tools for exploring the relationships between isolates. We discuss the advantages of this approach and describe its use to explore patterns of descent within clonal complexes identified using multilocus sequence typing.

eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data.

EJ Feil — 2006-05-18T18:50:37-00:00

J Bacteriol, Vol. 186, No. 5. (March 2004), pp. 1518-1530.

The introduction of multilocus sequence typing (MLST) for the precise characterization of isolates of bacterial pathogens has had a marked impact on both routine epidemiological surveillance and microbial population biology. In both fields, a key prerequisite for exploiting this resource is the ability to discern the relatedness and patterns of evolutionary descent among isolates with similar genotypes. Traditional clustering techniques, such as dendrograms, provide a very poor representation of recent evolutionary events, as they attempt to reconstruct relationships in the absence of a realistic model of the way in which bacterial clones emerge and diversify to form clonal complexes. An increasingly popular approach, called BURST, has been used as an alternative, but present implementations are unable to cope with very large data sets and offer crude graphical outputs. Here we present a new implementation of this algorithm, eBURST, which divides an MLST data set of any size into groups of related isolates and clonal complexes, predicts the founding (ancestral) genotype of each clonal complex, and computes the bootstrap support for the assignment. The most parsimonious patterns of descent of all isolates in each clonal complex from the predicted founder(s) are then displayed. The advantages of eBURST for exploring patterns of evolutionary descent are demonstrated with a number of examples, including the simple Spain(23F)-1 clonal complex of Streptococcus pneumoniae, "population snapshots" of the entire S. pneumoniae and Staphylococcus aureus MLST databases, and the more complicated clonal complexes observed for Campylobacter jejuni and Neisseria meningitidis.

Assessing the reliability of eBURST using simulated populations with known ancestry

Katherine Turner — 2007-04-13T04:13:09-00:00

BMC Microbiology, Vol. 7 (12 April 2007), 30.

The impact of homologous recombination on the generation of diversity in bacteria

William Hanage — 2007-07-16T17:29:47-00:00

Journal of Theoretical Biology, Vol. 239, No. 2. (21 March 2006), pp. 210-219.

The imprint of demographic and selective processes on bacterial population structure needs to be evaluated as deviation from the expectations of an appropriate null neutral model. We explore the impact of varying the population mutation and recombination rates [theta] and [rho] on ideal populations, using a recently developed model of neutral drift at multiple loci. This model may be fitted to experimental data to provide estimates of these parameters, and we do so for seven bacterial species (Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes, Staphylococcus aureus, Helicobacter pylori, Burkholderia pseudomallei and Bacillus cereus), illustrating that bacterial species vary extensively in these fundamental parameters. Historically, the influence of recombination has often been estimated through its influence on the Index of Association IA. We show that this may be relatively insensitive to changes in either mutation or recombination rates. It is known that biased sampling can lead to artificially high estimates of IA. We therefore provide a method of precisely separating the effects of such bias and true linkage between alleles. We also demonstrate that by fitting the neutral model to experimental data, more informative and precise estimates of the relative roles of recombination and mutation may be obtained.

Neutral microepidemic evolution of bacterial pathogens.

C Fraser — 2005-02-11T16:24:23-00:00

Proc Natl Acad Sci U S A, Vol. 102, No. 6. (8 February 2005), pp. 1968-1973.

Understanding bacterial population genetics is vital for interpreting the response of bacterial populations to selection pressures such as antibiotic treatment or vaccines targeted at only a subset of strains. The evolution of transmissible bacteria occurs by mutation and localized recombination and is influenced by epidemiological as well as molecular processes. We demonstrate that the observed population genetic structure of three important human pathogens, Streptococcus pneumoniae, Neisseria meningitidis, and Staphylococcus aureus, can be explained by using a simple evolutionary model that is based on neutral mutational drift, modulated by recombination, and which incorporates the impact of epidemic transmission in local populations. The predictions of this neutral "microepidemic" model are found to closely fit observed genetic relatedness distributions of bacteria sampled from their natural population, and it provides estimates of the relative rate of recombination that agree well with empirical estimates. The analysis suggests the emergence of neutral bacterial population structure from overlapping microepidemics within clustered host populations and provides insight into the nature and size distribution of these clusters. These findings challenge the assumption that strains of bacterial pathogens differ markedly in relative fitness.

Genome-wide association mapping in bacteria?

Daniel Falush — 2007-08-03T10:51:01-00:00

Trends in Microbiology, Vol. 14, No. 8. (August 2006), pp. 353-355.

Bacteria display many interesting phenotypes such as virulence, tissue specificity and host range, for which it would be useful to know the genetic basis. Association mapping involves identifying causal variants by showing that particular genotypes are statistically associated with a phenotypic trait in a sample of strains taken from a natural population. With the advent of high-throughput genotyping, association mapping is becoming an increasingly powerful approach. However, until recently, association studies had not been used in bacteria because of their strong population structure, which can produce false positives and/or loss of statistical power unless elucidated and taken into account in analyses. Here, we describe how association mapping could be successfully applied to bacteria and outline the necessary sampling and genotyping strategies.

Fit genotypes and escape variants of subgroup III Neisseria meningitidis during three pandemics of epidemic meningitis

Peixuan Zhu — 2007-08-03T10:49:03-00:00

PNAS, Vol. 98, No. 9. (24 April 2001), pp. 5234-5239.

10.1073/pnas.061386098

Mismatch induced speciation in Salmonella: model and data.

D Falush — 2007-08-03T10:47:17-00:00

Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1475. (29 November 2006), pp. 2045-2053.

In bacteria, DNA sequence mismatches act as a barrier to recombination between distantly related organisms and can potentially promote the cohesion of species. We have performed computer simulations which show that the homology dependence of recombination can cause de novo speciation in a neutrally evolving population once a critical population size has been exceeded. Our model can explain the patterns of divergence and genetic exchange observed in the genus Salmonella, without invoking either natural selection or geographical population subdivision. If this model was validated, based on extensive sequence data, it would imply that the named subspecies of Salmonella enterica correspond to good biological species, making species boundaries objective. However, multilocus sequence typing data, analysed using several conventional tools, provide a misleading impression of relationships within S. enterica subspecies enterica and do not provide the resolution to establish whether new species are presently being formed.

How clonal are bacteria?

JM Smith — 2005-11-25T12:32:04-00:00

Proc Natl Acad Sci U S A, Vol. 90, No. 10. (15 May 1993), pp. 4384-4388.

Data from multilocus enzyme electrophoresis of bacterial populations were analyzed using a statistical test designed to detect associations between genes at different loci. Some species (e.g., Salmonella) were found to be clonal at all levels of analysis. At the other extreme, Neisseria gonorrhoeae is panmictic, with random association between loci. Two intermediate types of population structure were also found. Neisseria meningitidis displays what we have called an "epidemic" structure. There is significant association between loci, but this arises only because of the recent, explosive, increase in particular electrophoretic types; when this effect is eliminated the population is found to be effectively panmictic. In contrast, linkage disequilibrium in a population of Rhizobium meliloti exists because the sample consisted of two genetically isolated divisions, often fixed for different alleles: within each division association between loci was almost random. The method of analysis is appropriate whenever there is doubt about the extent of genetic recombination between members of a population. To illustrate this we analyzed data on protozoan parasites and again found panmictic, epidemic, and clonal population structures.

Inference of Bacterial Microevolution Using Multilocus Sequence Data

Xavier Didelot — 2007-08-03T10:43:51-00:00

Genetics, Vol. 175, No. 3. (1 March 2007), pp. 1251-1266.

We describe a model-based method for using multilocus sequence data to infer the clonal relationships of bacteria and the chromosomal position of homologous recombination events that disrupt a clonal pattern of inheritance. The key assumption of our model is that recombination events introduce a constant rate of substitutions to a contiguous region of sequence. The method is applicable both to multilocus sequence typing (MLST) data from a few loci and to alignments of multiple bacterial genomes. It can be used to decide whether a subset of isolates share common ancestry, to estimate the age of the common ancestor, and hence to address a variety of epidemiological and ecological questions that hinge on the pattern of bacterial spread. It should also be useful in associating particular genetic events with the changes in phenotype that they cause. We show that the model outperforms existing methods of subdividing recombinogenic bacteria using MLST data and provide examples from Salmonella and Bacillus. The software used in this article, ClonalFrame, is available from http://bacteria.stats.ox.ac.uk/. 10.1534/genetics.106.063305

Traces of human migrations in Helicobacter pylori populations.

D Falush — 2007-02-26T15:05:02-00:00

Science, Vol. 299, No. 5612. (7 March 2003), pp. 1582-1585.

Helicobacter pylori, a chronic gastric pathogen of human beings, can be divided into seven populations and subpopulations with distinct geographical distributions. These modern populations derive their gene pools from ancestral populations that arose in Africa, Central Asia, and East Asia. Subsequent spread can be attributed to human migratory fluxes such as the prehistoric colonization of Polynesia and the Americas, the neolithic introduction of farming to Europe, the Bantu expansion within Africa, and the slave trade.

An African origin for the intimate association between humans and Helicobacter pylori

Bodo Linz — 2007-02-08T19:36:11-00:00

Nature

Sex and virulence in Escherichia coli: an evolutionary perspective

Thierry Wirth — 2006-05-11T20:23:20-00:00

Molecular Microbiology, Vol. 60, No. 5. (June 2006), pp. 1136-1151.

Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age.

D Falush — 2005-08-23T13:44:01-00:00

Proc Natl Acad Sci U S A, Vol. 98, No. 26. (18 December 2001), pp. 15056-15061.

The bacterium Helicobacter pylori colonizes the gastric mucosa of half of the human population, resulting in chronic gastritis, ulcers, and cancer. We sequenced ten gene fragments from pairs of strains isolated sequentially at a mean interval of 1.8 years from 26 individuals. Several isolates had acquired small mosaic segments from other H. pylori or point mutations. The maximal mutation rate, the import size, and the frequency of recombination were calculated by using a Bayesian model. The calculations indicate that the last common ancestor of H. pylori existed at least 2,500-11,000 years ago. Imported mosaics have a median size of 417 bp, much smaller than for other bacteria, and recombination occurs frequently (60 imports spanning 25,000 bp per genome per year). Thus, the panmictic population structure of H. pylori results from very frequent recombination during mixed colonization by unrelated strains.

Inference of population structure using multilocus genotype data: dominant markers and null alleles

Daniel Falush — 2007-07-07T09:06:29-00:00

Molecular Ecology Notes, Vol. 7, No. 4. (July 2007), pp. 574-578.

Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.

D Falush — 2007-05-01T04:54:23-00:00

Genetics, Vol. 164, No. 4. (August 2003), pp. 1567-1587.

We describe extensions to the method of Pritchard et al. for inferring population structure from multilocus genotype data. Most importantly, we develop methods that allow for linkage between loci. The new model accounts for the correlations between linked loci that arise in admixed populations ("admixture linkage disequilibium"). This modification has several advantages, allowing (1) detection of admixture events farther back into the past, (2) inference of the population of origin of chromosomal regions, and (3) more accurate estimates of statistical uncertainty when linked loci are used. It is also of potential use for admixture mapping. In addition, we describe a new prior model for the allele frequencies within each population, which allows identification of subtle population subdivisions that were not detectable using the existing method. We present results applying the new methods to study admixture in African-Americans, recombination in Helicobacter pylori, and drift in populations of Drosophila melanogaster. The methods are implemented in a program, structure, version 2.0, which is available at http://pritch.bsd.uchicago.edu.

A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination.

Xavier Didelot — 2006-11-29T11:59:30-00:00

Genome Res (7 November 2006)

All Salmonella can cause disease but severe systemic infections are primarily caused by a few lineages. Paratyphi A and Typhi are the deadliest human restricted serovars, responsible for approximately 600,000 deaths per annum. We developed a Bayesian changepoint model that uses variation in the degree of nucleotide divergence along two genomes to detect homologous recombination between these strains, and with other lineages of Salmonella enterica. Paratyphi A and Typhi showed an atypical and surprising pattern. For three quarters of their genomes, they appear to be distantly related members of the species S. enterica, both in their gene content and nucleotide divergence. However, the remaining quarter is much more similar in both aspects, with average nucleotide divergence of 0.18% instead of 1.2%. We describe two different scenarios that could have led to this pattern, convergence and divergence, and conclude that the former is more likely based on a variety of criteria. The convergence scenario implies that, although Paratyphi A and Typhi were not especially close relatives within S. enterica, they have gone through a burst of recombination involving more than 100 recombination events. Several of the recombination events transferred novel genes in addition to homologous sequences, resulting in similar gene content in the two lineages. We propose that recombination between Typhi and Paratyphi A has allowed the exchange of gene variants that are important for their adaptation to their common ecological niche, the human host.