Assessment of coyote-wolf-dog admixture using ancestry-informative diagnostic SNPs.

The evolutionary importance of hybridization as a source of new adaptive genetic variation is rapidly gaining recognition. Hybridization between coyotes and wolves may have introduced adaptive alleles into the coyote gene pool that facilitated an expansion in their geographic range and dietary niche. Furthermore, hybridization between coyotes and domestic dogs may facilitate adaptation to human-dominated environments. We genotyped 63 ancestry-informative single-nucleotide polymorphisms in 427 canids to examine the prevalence, spatial distribution and the ecology of admixture in eastern coyotes. Using multivariate methods and Bayesian clustering analyses, we estimated the relative contributions of western coyotes, western and eastern wolves, and domestic dogs to the admixed ancestry of Ohio and eastern coyotes. We found that eastern coyotes form an extensive hybrid swarm, with all our samples having varying levels of admixture. Ohio coyotes, previously thought to be free of admixture, are also highly admixed with wolves and dogs. Coyotes in areas of high deer density are genetically more wolf-like, suggesting that natural selection for wolf-like traits may result in local adaptation at a fine geographic scale. Our results, in light of other previously published studies of admixture in Canis, revealed a pattern of sex-biased hybridization, presumably generated by male wolves and dogs mating with female coyotes. This study is the most comprehensive genetic survey of admixture in eastern coyotes and demonstrates that the frequency and scope of hybridization can be quantified with relatively few ancestry-informative markers.

Clonal and pathotypic analysis of archetypal Escherichia coli cystitis isolate NU14.

Escherichia coli NU14, a cystitis isolate used to study the pathogenesis of cystitis and to develop a FimH (type 1 fimbrial adhesin) vaccine, was assessed for extended virulence genotype, phylogenetic background, and FimH sequence and binding phenotype(s). NU14 exhibited the same virulence genotype and was derived from the same (meningitis- and cystitis-associated) subclone of E. coli O18:K1:H7 as the archetypal neonatal bacterial meningitis (NBM) isolate RS218. NU14 also displayed the same Ser62Ala FimH polymorphism as did NBM isolates RS218 and IHE3034-conferring both collagen binding and a distinct monomannose binding capability (which characterizes uropathogenic but not commensal E. coli and dramatically increases adherence to uroepithelial cells). These findings establish that strain NU14 exhibits numerous urovirulence-associated traits and derives from the single most prevalent clonal group in acute cystitis. They provide further evidence of clonal and pathotypic similarities between cystitis and NBM isolates of E. coli O18:K1:H7.

The implications of a low rate of horizontal transfer in Borrelia.

The nature and rate of recombination can be studied by comparing the sequences of multiple genes across a set of strains. When this approach is applied to Borrelia burgdorferi, four results emerge: (1) chromosomal genes are clonal; (2) there is little or no plasmid exchange; (3) the major mode of horizontal transfer of genetic material inserts a small fragment of DNA, typically <1 kb, during recombination; and (4) the level of horizontal transfer in Borrelia is so low that there is evidence for horizontal transfer only in genes where there is positive selection for diversity, that is, positive selection for the recombinant. Thus, Borrelia can serve as a model of a low recombination taxon. The implications of these results lead us to postulate that an unknown agent that is part of the Borrelia genome mediates the horizontal transfer of small fragments of DNA; the rare transfer of small fragments of DNA excludes both DNA parasites and virulence factors from the genome.

Variation of enzyme activities at a branched pathway involved in the utilization of gluconate in Escherichia coli.

Twenty-four strains of Escherichia coli from the ECOR collection were characterized for growth rate in gluconate minimal salts medium and for Vmax and Km of the three enzymes (gluconokinase, 6-phosphogluconate dehydrogenase, and 6-phosphogluconate dehydratase) that form a branch point for the utilization of gluconate. A total of 11 characters--growth rate, three Vmax values, four Km values, and three Vmax/Km values--were determined for these 24 ECOR strains. Most of the characters were normally distributed. Statistical tests showed that growth rate is significantly less variable than enzyme activities. Also, analyses of variance showed significant differences among strains and among the extant five genetic groups of E. coli for the characters measured. A Mantel test showed that, for some characters, closely related strains shared similar character values. Two hypotheses regarding the relationships between growth rate and enzyme activity and between various enzyme activities were tested. None of the expected correlations between growth rate and enzyme activity or between enzyme activities was detected. The results were discussed in terms of metabolic control analysis and neutral theory.

Recombinant chimeric Borrelia proteins for diagnosis of Lyme disease.

Current serologic Lyme disease tests use whole borrelia cells as the source of antigen. These assays are difficult to standardize and to optimize for sensitivity and specificity. To help solve these problems, we constructed a library of recombinant chimeric proteins composed of portions of key antigens of Borrelia burgdorferi. These proteins were then used to develop an enzyme-linked immunosorbent assay. We compared our assay with the most sensitive of three whole-cell borrelia assays. We found that the recombinant assay could detect antibodies significantly better from early Lyme disease sera (P<0.05), and had the same sensitivity for late Lyme disease sera, as the most sensitive whole-cell borrelia assay. On potentially cross-reactive sera, the recombinant assay was more specific, but not significantly so, than the best whole-cell borrelia assay. Optimization of the recombinant assay offers the potential for a significant improvement in both sensitivity and specificity.

Methods for estimating gene frequencies and detecting selection in bacterial populations.

Recent breakthroughs in molecular technology, most significantly the polymerase chain reaction (PCR) and in situ hybridization, have allowed the detection of genetic variation in bacterial communities without prior cultivation. These methods often produce data in the form of the presence or absence of alleles or genotypes, however, rather than counts of alleles. Using relative allele frequencies from presence-absence data as estimates of population allele frequencies tends to underestimate the frequencies of common alleles and overestimate those of rare ones, potentially biasing the results of a test of neutrality in favor of balancing selection. In this study, a maximum-likelihood estimator (MLE) of bacterial allele frequencies designed for use with presence-absence data is derived using an explicit stochastic model of the host infection (or bacterial sampling) process. The performance of the MLE is evaluated using computer simulation and a method is presented for evaluating the fit of estimated allele frequencies to the neutral infinite alleles model (IAM). The methods are applied to estimate allele frequencies at two outer surface protein loci (ospA and ospC) of the Lyme disease spirochete, Borrelia burgdorferi, infecting local populations of deer ticks (Ixodes scapularis) and to test the fit to a neutral IAM.

Infection with multiple strains of Borrelia burgdorferi sensu stricto in patients with Lyme disease.

OBJECTIVE: To assess human skin biopsy specimens from erythema migrans lesions for the presence of infection with multiple strains of the Lyme disease spirochete, Borrelia burgdorferi. DESIGN: Skin biopsy specimens were obtained prospectively from patients with erythema migrans. To determine allelic differences and strain identification of B burgdorferi, the biopsy specimens were analyzed by cold single-strand conformation polymorphism of an amplified fragment of the outer surface protein C (ospC) gene. Further single-strand conformation polymorphism patterns of amplified ospC genes from culture isolates were compared with polymerase chain reaction products obtained directly from erythema migrans biopsy specimens. SETTING: A private dermatology office and a university medical center outpatient department. PATIENTS: Sixteen patients presenting with erythema migrans. RESULTS: Two of the 16 patients in this cohort were infected with 2 B burgdorferi sensu stricto strains, as evidenced by 2 ospC alleles in their skin biopsy results. CONCLUSION: This is the first documented description of the existence of more than a single strain of B burgdorferi sensu stricto in a human specimen.

Four clones of Borrelia burgdorferi sensu stricto cause invasive infection in humans.

Lyme disease begins at the site of a tick bite, producing a primary infection with spread of the organism to secondary sites occurring early in the course of infection. A major outer surface protein expressed by the spirochete early in infection is outer surface protein C (OspC). In Borrelia burgdorferi sensu stricto, OspC is highly variable. Based on sequence divergence, alleles of ospC can be divided into 21 major groups. To assess whether strain differences defined by ospC group are linked to invasiveness and pathogenicity, we compared the frequency distributions of major ospC groups from ticks, from the primary erythema migrans skin lesion, and from secondary sites, principally from blood and spinal fluid. The frequency distribution of ospC groups from ticks is significantly different from that from primary sites, which in turn is significantly different from that from secondary sites. The major groups A, B, I, and K had higher frequencies in the primary sites than in ticks and were the only groups found in secondary sites. We define three categories of major ospC groups: one that is common in ticks but very rarely if ever causes human disease, a second that causes only local infection at the tick bite site, and a third that causes systemic disease. The finding that all systemic B. burgdorferi sensu stricto infections are associated with four ospC groups has importance in the diagnosis, treatment, and prevention of Lyme disease.

Pathoadaptive mutations: gene loss and variation in bacterial pathogens.

Pathogenicity-adaptive, or pathoadaptive, mutations represent a genetic mechanism for enhancing bacterial virulence without horizontal transfer of specific virulence factors. Pathoadaptive evolution can be important within single infections and for defining the population structure of a pathogenic species.

Genetic diversity of ospC in a local population of Borrelia burgdorferi sensu stricto.

The outer surface protein, OspC, is highly variable in Borrelia burgdorferi sensu stricto, the agent of Lyme disease. We have shown that even within a single population OspC is highly variable. The variation of ospA and ospC in the 40 infected deer ticks collected from a single site on Shelter Island, New York, was determined using PCR-SSCP. There is very strong apparent linkage disequilibrium between ospA and ospC alleles, even though they are located on separate plasmids. Thirteen discernible SSCP mobility classes for ospC were identified and the DNA sequence for each was determined. These sequences, combined with 40 GenBank sequences, allow us to define 19 major ospC groups. Sequences within a major ospC group are, on average, <1% different from each other, while sequences between major ospC groups are, on average, approximately 20% different. The tick sample contains 11 major ospC groups, GenBank contains 16 groups, with 8 groups found in both samples. Thus, the ospC variation within a local population is almost as great as the variation of a similar-sized sample of the entire species. The Ewens-Watterson-Slatkin test of allele frequency showed significant deviation from the neutral expectation, indicating balancing selection for these major ospC groups. The variation represented by major ospC groups needs to be considered if the OspC protein is to be used as a serodiagnostic antigen or a vaccine.

Pathogenic adaptation of Escherichia coli by natural variation of the FimH adhesin.

Conventional wisdom regarding mechanisms of bacterial pathogenesis holds that pathogens arise by external acquisition of distinct virulence factors, whereas determinants shared by pathogens and commensals are considered to be functionally equivalent and have been ignored as genes that could become adapted specifically for virulence. It is shown here, however, that genetic variation in an originally commensal trait, the FimH lectin of type 1 fimbriae, can change the tropism of Escherichia coli, shifting it toward a urovirulent phenotype. Random point mutations in fimH genes that increase binding of the adhesin to mono-mannose residues, structures abundant in the oligosaccharide moieties of urothelial glycoproteins, confer increased virulence in the mouse urinary tract. These mutant FimH variants, however, are characterized by increased sensitivity to soluble inhibitors bathing the oropharyngeal mucosa, the physiological portal of E. coli. This functional trade-off seems to be detrimental for the intestinal ecology of the urovirulent E. coli. Thus, bacterial virulence can be increased by random functional mutations in a commensal trait that are adaptive for a pathologic environment, even at the cost of reduced physiological fitness in the nonpathologic habitat.

Santa Rosalia revisited: why are there so many species of bacteria?

The diversity of bacteria in the world is very poorly known. Usually less than one percent of the bacteria from natural communities can be grown in the laboratory. This has caused us to underestimate bacterial diversity and biased our view of bacterial communities. The tools are now available to estimate the number of bacterial species in a community and to estimate the difference between communities. Using what data are available, I have estimated that thirty grams of forest soil contains over half a million species. The species difference between related communities suggests that the number of species of bacteria may be more than a thousand million. I suppose that the explanation for such a large number of bacterial species is simply that speciation in bacteria is easy and extinction difficult, giving a rate of speciation higher than the rate of extinction, leading to an ever increasing number of species over time. The idea that speciation is easy is justified from the results of recent experimental work in bacterial evolution.

A population genetic study of Borrelia burgdorferi sensu stricto from eastern Long Island, New York, suggested frequency-dependent selection, gene flow and host adaptation.

Eastern Long Island, New York, is one of the major foci of Lyme disease in the United States. As in almost all other parts of North America, Lyme disease in this region is caused by a single genomic species of spirochete, Borrelia burgdorferi sensu stricto. For three consecutive years, natural populations of Lyme Borrelia in this region were sampled and studied for gene flow among different locations, changes in population structure over time, and selective forces. The genetic diversity of Borrelia populations was measured at the outer surface protein A (ospA) locus using Cold Single-Stranded Conformation Polymorphism (Cold SSCP) analysis. The Borrelia populations were found to be highly polymorphic within any of thirteen local populations. Ewens-Watterson tests of neutrality revealed that the high level of genetic diversity within local Borrelia populations is maintained by balancing selection. Frequency-dependent selection for the different strains distinguished by the ospA alleles is likely the mechanism of the balancing selection. Allele frequency distributions of Borrelia populations were homogeneous across the region in any particular year, although different infection rates of local tick (Ixodes scapularis) populations suggested that the Borrelia populations were at least partially isolated. Since the allele frequency distribution changed over time, while remaining homogeneous over space, the nearly uniform allele frequency distribution across the region cannot be explained by recent geographic expansion from a single population. This uniform distribution across the region thus may be maintained by selection, or by a significant amount of migration or both. The genetic structure of B. burgdorferi sensu stricto also differed between spirochetes infecting nymphal ticks and those infecting adult ticks. Since larval and nymphal ticks have distinctly different host feeding preferences, host adaptation of spirochete populations is implied. This distinction and an animal study using chipmunks suggest that ticks infected by Borrelia as larvae may have high mortality in the wild. This study represents a genetic analysis of local populations of a bacterial species.

Multiple infections of Ixodes scapularis ticks by Borrelia burgdorferi as revealed by single-strand conformation polymorphism analysis.

The genetic heterogeneity of the spirochete Borrelia burgdorferi within single adult black-legged ticks from Shelter Island, N.Y., was determined by cold, single-strand conformation polymorphism (SSCP) analysis. The central region of the ospA gene of B. burgdorferi from infected ticks was amplified by nested PCR. Amplified product of the correct size was obtained from 20 to 45 ticks (44%). This is the fraction of ticks that is expected to be infected with B. burgdorferi. Four variant classes were determined by SSCP analysis. Eight ticks were infected with a single variant, nine ticks were infected with two variants, two ticks were infected with three variants, and one tick was infected with all four variants. DNA from each variant was sequenced. Five different sequences were found. The sequence of each variant was different from that of another variant by a single base. SSCP analysis could distinguish three of the four single-base changes found in the region.

Detecting selective sweeps in naturally occurring Escherichia coli.

The nucleotide sequences of the gapA and pabB genes (separated by approximately 32.5 kb) were determined in 12 natural isolates of Escherichia coli. Three analyses were performed on the data. First, the levels of polymorphism at the loci were compared within and between E. coli and Salmonella strains relative to their degrees of constraint. Second, the gapA and pabB loci were analyzed by the Hudson-Kreitman-Aguadé (HKA) test for selective neutrality. Four additional dispersed genes (crr, putP, trp and gnd) were added to the analysis to provide the necessary frame of reference. Finally, the gene genealogies of gapA and pabB were examined for topological consistency within and between the loci. These lines of evidence indicate that some evolutionary event has recently purged the variability in the region surrounding the gapA and pabB loci in E. coli. This can best be explained by the spread of a selected allele through the global E. coli population by directional selection and the resulting loss in variability in the surrounding regions due to genetic hitchhiking.

Clonal divergence in Escherichia coli as a result of recombination, not mutation.

Nucleotide sequence analysis was performed on 12 natural isolates of Escherichia coli in four loci located in close proximity on the chromosome. A comparison of gene genealogies indicated that three recombination events have occurred in a subset of the strains (ECOR group A) in the time since their divergence from a common ancestor, while during the same time, no mutational divergence has occurred. The common ancestor of this subset existed no more than 2400 years ago, and recombination was shown to occur at a rate of 5.0 x 10(-9) changes per nucleotide per generation--50-fold higher than the mutation rate. Thus, recombination has been the dominant force driving the clonal divergence of the ECOR group A strains and must be considered a significant factor in structuring E. coli populations.

Borrelia burgdorferi is clonal: implications for taxonomy and vaccine development.

The chromosomal genes fla and p93 and the ospA gene from a linear plasmid were sequenced from up to 15 isolates of Borrelia burgdorferi, which causes Lyme borreliosis in man. Comparison of the gene trees provides no evidence for genetic exchange between chromosomal genes, suggesting B. burgdorferi is strictly clonal. Comparison of the chromosomal gene trees with that of the plasmid-encoded ospA reveals that plasmid transfer between clones is rare. Evidence for intragenic recombination was found in only a single ospA allele. The analysis reveals three common clones and a number of rare clones that are so highly divergent that vaccines developed against one are unlikely to provide immunity to organisms from others. Consequently, an understanding of the geographic and genetic variability of B. burgdorferi will prove essential for the development of effective vaccines and programs for control. While the major clones might be regarded as different species, the clonal population structure, the geographic localization, and the widespread incidence of Lyme disease suggest that B. burgdorferi should remain the name for the entire array of organisms.