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Use the link below to share a full-text version of this article with your friends and colleagues. Learn more. The evolutionary pathways underlying this dichotomy in bacterial lifestyle were investigated by multilocus sequence typing of a global collection of isolates. Specific pathogen types [enterohaemorrhagic E. Rates of evolution have accelerated in pathogenic lineages, culminating in highly virulent organisms whose genomic contents are altered frequently by increased rates of homologous recombination; thus, the evolution of virulence is linked to bacterial sex.

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At low frequencies, populations are largely asexual clonalwhereas sex becomes more frequent with the frequency of transient mutators. Thus, the most virulent strains of E. Search for more papers by this author. The ancestry of each strain is then estimated as the summed probability of derivation from each group over all polymorphic nucleotides. Old Password. The ultrametric tree used was a upgma tree Anika apar sex from the genetic distances in part A and calibrated to a molecular clock rate Anika apar sex 7. Proportions of ancestry from groups A, B1, B2 and D as inferred by structure and their assignment to six groups as displayed with distruct Rosenberg, This leads us to postulate that virulence is the driving force for more frequent recombination, occurring by the mechanism outlined in Fig. This procedure assigns a probability of ancestry for each polymorphic nucleotide for a given number of groups, Kand also estimates qthe combined probability of ancestry from each Young girls booty shakin the K groups for each individual isolate.

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Use the link below to share a full-text version of this article with your friends and colleagues. Learn more. The evolutionary pathways underlying this dichotomy in bacterial lifestyle were investigated by multilocus sequence typing of a global collection of isolates. Specific pathogen types [enterohaemorrhagic E. Rates of evolution have accelerated in pathogenic lineages, culminating in highly virulent organisms whose genomic contents are altered frequently by increased rates of homologous recombination; thus, the evolution of virulence is linked to bacterial sex.

Pathogenic bacteria present ongoing challenges to human and animal health but the processes by which virulence has evolved remain incompletely understood, even for bacteria as well studied as Escherichia coli. Shigella , neonatal meningitis associated with the K1 capsular polysaccharide , haemolytic uraemic syndrome OH7 as well as a variety of other diseases. However, it remains unclear how virulence affects the overall patterns of evolution within a genome. Addressing such questions requires a global overview of how diversity has evolved within the species at large.

Results of multilocus enzyme electrophoresis MLEE indicated that certain combinations of alleles occurred multiple times, which was interpreted as indicating a clonal population structure with infrequent recombination Selander and Levin, Further support for this conclusion was provided by subsequent MLEE analyses of s of natural and clinical isolates from humans and other sources; 72 of these isolates, the ECOR collection, were chosen to represent the known genetic diversity at that time Ochman and Selander, The ECOR collection was subdivided into four groups, designated A, B1, B2 and D, plus a minor group E that has largely been ignored because it clustered inconsistently in subsequent analyses.

If recombination were frequent in E. However, trees based on different E. Therefore, the contribution of recombination to the population structure of E. Here, we describe a publicly available database of extensive sequence data from housekeeping gene fragments for a global sample of E.

These sequences were used to estimate the population structure of E. As a result, the ancestry of numerous hybrid isolates is derived from multiple sources. Furthermore, it is exactly these hybrid strains that tend to be highly virulent, whereas genetic admixture is less frequent among avirulent isolates, suggesting that sex and virulence are causally related. Fragments of seven housekeeping genes distributed around the E.

The isolates derive from a variety of extraintestinal and intestinal diseases and from the faeces of healthy individuals. To facilitate retrospective analyses, the strains tested include the complete ECOR reference collection. A Genomic locations and B genetic diversity of seven housekeeping genes.

Each gene symbol is followed by the length of the sequenced gene fragment informative sites — polymorphic sites. There is no clear phylogeographic component to the sources of diversity, nor is there a strong correlation between genetic groups and the host species from which bacteria were isolated. The following analyses therefore focus on phylogenetic and population genetic aspects of the entire dataset.

Thus, E. Diversity and population size within E. The dark grey circle represents the main group of isolates within E. Generalized skyline plot showing changes in effective E.

The ultrametric tree used was a upgma tree calculated from the genetic distances in part A and calibrated to a molecular clock rate of 7. Generalized skyline plots can be used to calculate the statistical probability of different demographic scenarios and to estimate when changes in population size occurred Strimmer and Pybus, When applied to the genetic distances estimated for the E.

The two exceptional strains, which are almost as distant from most E. Hereafter, we concentrate on genetic diversity within the main modern group of E. S1 were very low data not shown and the branch lengths to the four clades were very short, both suggesting that the branch order is not reliable.

To resolve such ambiguities, we performed heuristic maximum likelihood analysis, which provides statistical measures of reliability of tree topology. This algorithm yielded an alternate tree topology Fig. Phylogenies of concatenated sequences from the ECOR collection. Original sequences. Sequences purged of recombinant sites. Due to these contradictory results, we attempted to deduce the true branching order by purging recombinant sites see Experimental procedures and then testing all possible topologies of both purged and unpurged maximum likelihood trees by the Shimodaira—Hasegawa likelihood test S—H test , and by likelihood mapping according to quartet puzzling Strimmer and von Haeseler, After purging recombinant sites, the data yielded a higher consistency index and a lower Homoplasy ratio see below , and the major groups were more clearly defined Fig.

We conclude that, despite claims that E. Population genetic tools can be more appropriate than phylogenetic trees for deducing deep evolutionary splits in species where homologous recombination is common.

The linkage model of structure assigns probabilities of derivation from ancestral source groups for each polymorphic nucleotide. The ancestry of each strain is then estimated as the summed probability of derivation from each group over all polymorphic nucleotides.

However, within the entire dataset, numerous strains fell into hybrid groups that contain significant ancestry from multiple sources Fig. Ancestry of E. Proportions of ancestry from groups A, B1, B2 and D as inferred by structure and their assignment to six groups as displayed with distruct Rosenberg, Dots are coloured according to group and lines connecting ST complexes see Fig.

Clades that are illustrated in greater detail in part c are indicated by numbers and encircled by lines. Details of microevolution within eight selected clades.

Numbers in contrasting colours indicate the numbers of nucleotides that differ from the allele that was previously present. In addition to A, B1, B2 and D, we defined one hybrid group called AxB1, containing strains which derive most of their ancestry from A and B1, and a second group called ABD, where extensive recombination has yielded a highly heterogeneous set of isolates with multiple sources of ancestry.

Groups ABD and AxB1 contain isolates where recombination has been particularly frequent, but recombination is not exclusive to these hybrid groups. Virtually all E. Both tests confirm that significant levels of recombination had occurred within each of the E.

The lowest Homoplasy ratio 0. We also note that the mutation rate within group D is higher than within the other groups. Each of the four major groups of E. In contrast, the hybrid groups are particularly rich in pathogens, suggesting a link between virulence and homologous recombination.

Sources of ancestry versus pathogenicity. Proportion of pathogens per group. The six groups are represented by circles whose areas are proportional to the numbers of isolates. Notched box and whisker plots of the uniformity of ancestral sources by pathogen group. Within each plot, the central box indicates the two central quartiles, separated by a horizontal line indicating the median value. Lines above and below each box indicate the upper and lower quartiles, and outliers are indicated by small circles.

Uniformity was calculated for each strain as the sum of its squared ancestries from the A, B1, B2 and D groups according to structure , which ranges from 0. Frequency of isolates versus proportion of genome that has been imported from other groups by pathogen type. For each strain, the proportion of imported DNA was estimated conservatively by subtracting its maximal ancestry from any single group A, B1, B2 or D from 1.

These observations indicate that different groups of pathogens may be associated with different frequencies of homologous recombination. We therefore calculated the genetic uniformity of ancestral sources by pathogen group Fig. Similar results were obtained with histograms of the frequency of strains versus the proportion of imported nucleotides Fig. Thus, the most virulent strains of E. The sequence polymorphisms defined 50—82 unique sequences for each of the seven gene loci, which are referred to as alleles.

Each unique combination of alleles was assigned a sequence type ST number, e. STs that did not match the criteria for inclusion within an ST complex are simply referred to by their ST designation. Second, many ST complexes are associated with particular virulence phenotypes Fig. Almost all isolates within the ST complexes , , , and were Shigella, and almost all Shigella were found within these ST complexes.

Each ST is represented by a dot. Dots with uniform colours indicate that all isolates were of the same pathogen type see legend while the small pie charts indicate the fraction of isolates belonging to each pathogen type.

Circled numbers indicate ST complexes, whereas arrows indicate STs 11 and Black lines connecting pairs of STs indicate that they share six thick lines , five thin or four alleles dotted. Grey, dotted lines connecting pairs of STs of increasing line length indicate that they share three to one alleles respectively. In addition, the lines connecting the STs within an ST complex are shaded in grey. None of the five pathogen types is restricted to a single grouping Fig. Not only do these pathogens occur in multiple, distinct ST complexes, but they do not seem to represent distinct genetic entities and are occasionally found within a single ST.

In agreement, each of these three strains belong to a distinct ST within the ST29 complex. Allele sharing between pathogen types. We attempted to sample all natural diversity in E. The resulting sample is unique in its diversity of sources and provided insights not achievable with the more limited sampling strategy of former analyses.

The global sample was so extensive that we identified two strains that are very distinct from the other isolates Fig. The existence of these strains indicates that E. This diversity was reduced an estimated 10—30 million years ago by population contractions and bottlenecks, and most of the genetic diversity observed in contemporary populations has accumulated during extensive expansions in the last 5 million years.

During these population expansions, the descendants of four major lineages, A, B1, B2 and D, have become predominant and represent the majority of modern isolates. Phylogenetic approaches can be used to reconstruct the time scale and branching order of evolutionary events among distinct groups of organisms that rarely interbreed, such as multiple species. They are not necessarily suitable for evolutionary analyses within breeding populations, e.

Initial analyses of the population structure of E.

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