Ochman, H.O., J.G. Lawrence, and E.A. Groisman. 2000. The nature of bacterial innovation. Nature 405:299-304
Unlike eukaryotes, which evolve principally through the modification of existing genetic information, a significant portion of the diversity observed in bacteria has originated through the acquisition of sequences from distantly related organisms. Horizontal genetic processes result in extremely dynamic genomes in which substantial amounts of DNA are introduced into, and deleted from, the chromosome and have effectively changed the ecological and pathogenic character of bacterial species.
Lawrence, J.G. 1999. Gene transfer and minimal genome size. Pp 32-38 in Size Limits of Very Small Microorganisms, , Ed. National Research Council, Washington, D.C.
Throughout all domains of life, genetic material is exchanged within and among genomes. Horizontal transfer typically denotes rare transfer of genetic material between diverse lineages. This process does not constrain genome size in significant ways. Intraspecific recombination is more common than horizontal exchange, allows for the removal of deleterious mutations, and helps maintenance of species identity. Recombination enables organisms to maintain maximum genome sizes that are larger than those capable without gene exchange (escape of Muller's ratchet), but does not mediate potential reduction of genome size. In these cases, gene exchange allows transfer of non-essential gene among organisms, or reassortment of essential genes within a taxon. Neither process permits a cell to maintain fewer than the minimal complement of genes required for life. A model is presented whereby the frequency of gene exchange is much greater than the frequency of cell division. In this model, cells may be considered way-stations for gene replication and transfer; such organisms need not maintain a full complement of genes, and genome sizes may decrease. Simulations predict the propagation of organisms where the average cell contains, on average over time, fewer than 1 gene.
Lawrence, J.G., and J.R. Roth. 1999. Genomic flux : Genome evolution by gene loss and acquisition. Pp 263 - 289 in Bacterial Genomics, Charlebois, R., Ed. ASM Press, Washington, D.C.
Genome evolution is the process by which the content and organization of a species' genetic information changes over time. This process involves four sorts of changes: (a) Point mutations and gene conversion events gradually alter internal information; (b) rearrangements (e.g. inversions, translocations, plasmid integration, and transpositions) alter chromosome topology with little change in information content; (c) deletions cause irreversible loss of information; (d) insertions of foreign material can add novel information to a genome. Although the first two processes can create new genes, they act very slowly. Gene loss and acquisition are genomic changes that can radically and rapidly increase fitness or alter some aspect of lifestyle.
Most evolutionary thought on genome evolution has focused on how the slow sequence changes can cause divergence of gene functions. This is understandable, because available data suggests that horizontal genetic transfer has been a minor contributor to the evolution of eukaryotic lineages (with notable exceptions such as the introduction mitochondria and chloroplasts). In bacteria, however, both genetics and genome analysis provide extensive evidence for gene loss and horizontal genetic transfer. Analyses of these data suggest that gene loss and acquisition are likely to be the primary mechanisms by which bacteria adapt genetically to novel environments, and by which bacterial populations diverge and form separate, evolutionarily distinct species. We suggest that bacterial adaptation and speciation is determined predominantly by acquisition of selectively valuable genes (by horizontal transfer) and by loss of weakly contributing genes (by mutation, deletion and drift from the population) during periods of relaxed selection.
We propose that a limitation of genome expansion couples the rates of gene acquisition and loss. Genome size may be limited in part by population-based factors that limit the ability of cells to selectively maintain information; some limitation may also be imposed by physiological considerations. The balance between selective gene acquisition and secondarily-imposed gene loss, implies that addition of a foreign gene increases the probability of loss of some resident function of lower selective value. The interaction of these factors, we suggest, drives divergence of bacterial types.
Lawrence, J.G. 1999. Gene transfer, speciation, and the evolution of bacterial genomes. Curr. Op. Microbiol. 2:519-523
Studies in microbial evolution have focused on the origin and vertical transmission of genetic variation within populations experiencing limited recombination. Genomic analyses have highlighted the importance of horizontal genetic transfer in shaping the composition of microbial genomes, providing novel metabolic capabilities, and catalyzing the diversification of bacterial lineages.
Lawrence, J.G. 1999. Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes. Curr. Op. Genet. Dev. 9:642-648
The Selfish Operon Model postulates that the organization of bacterial genes into operons is beneficial to the constituent genes in that proximity allows horizontal cotransfer of all genes required for a selectable phenotype; eukaryotic operons formed for very different reasons. Horizontal transfer of selfish operons likely promotes bacterial diversification.
Lawrence, J.G., and H. Ochman.1998. The molecular archaeology of bacterial genomes. Proc Natl Acad Sci., USA 95:9413-9417.
The availability of the complete sequence of Escherichia coli MG1655 provides the first opportunity to assess the overall impact of horizontal genetic transfer on the evolution of bacterial genomes. We found that 755 of 4288 ORFs (547.8 kilobases) have been introduced into the E. coli genome in at least 234 lateral transfer events since this species diverged from the Salmonella lineage 100 million years ago. The average age of introduced genes was 14.4 Myr, yielding a rate of transfer 16 kb per Myr per lineage since divergence. Although most of the acquired genes were subsequently deleted, the sequences that have persisted (~18% of the current chromosome) have conferred properties permitting E. coli to explore otherwise unreachable ecological niches.
Lawrence, J.G., and J.R. Roth. 1998. Roles of horizontal transfer in bacterial evolution. Pp 208 - 225 in 'Horizontal Gene Transfer', M.Syvanen and C.I. Kado, eds. Chapman and Hall, London.
Gene loss and reacquisition may be key aspects of bacterial evolution. This was suggested by the history of B12 metabolism in enteric bacteria, which includes loss of multiple functions and reacquisition of genes from a foreign source. Many bacterial genes are located in cotranscribed clusters or operons; together, the genes in an operon generally provide a single function or selectable phenotype. Conditionally dispensable functions are usually encoded by operons; essential genes are less likely to be clustered. Operon formation may be driven by gene loss (by mutation during periods of dispensability) and reacquisition (by horizontal acquisition of small chromosome fragments followed by selection). Clustered genes can be cotransferred horizontally and therefore can spread faster than identical unclustered alleles; thus clustered alleles have higher fitness. Gene clustering may provide no immediate fitness benefit to the host organism and can be considered a selfish property of genes. Recently acquired genes may show atypical patterns of base composition and codon usage bias. With time, such sequences ameliorate toward the patterns of the new host. From the degree of sequence amelioration, one can estimate the time at which a sequence was introduced. We estimate that 31 kb of foreign DNA are introduced and substantially fixed in the E. coli genome every million years; a corresponding amount of DNA is presumably lost. We predict that the genomes of S. enterica and E. coli each include sequences - up to 30% of each genome - that are absent from the other genome. Horizontal transfer may drive bacterial speciation since it allows an organism to suddenly acquire a well-developed capability.
Lawrence, J.G. 1997. Selfish operons and speciation by gene transfer. Trends Microbiol 5:355-359.
Bacterial genes providing for single metabolic functions may be found in operons because this organization allows efficient horizontal transfer among organisms. Transferred genes can confer novel metabolic phenotypes to their new hosts and allow rapid, effective exploitation of new environmental niches. The mobility of selfish operons may facilitate bacterial speciation.
Lawrence, J.G., and H. Ochman. 1997. Amelioration of bacterial genes: Rates of change and exchange. J Mol Evol 44:383-397
Although bacterial species display wide variation in their overall GC contents, the genes within a particular species' genome are relatively similar in base composition. As a result, sequences that are novel to a bacterial genome - i.e., DNA introduced through recent horizontal transfer - often bear unusual sequence characteristics and can be distinguished from ancestral DNA. At the time of introgression, horizontally-transferred genes reflect the base composition of the donor genome; but, over time, these sequences will ameliorate to reflect the DNA composition of the new genome because the introgressed genes are subject to the same mutational processes affecting all genes in the recipient genome. This process of amelioration is evident in a large group of genes involved in host cell invasion by enteric bacteria and can be modeled to predict the amount of time required after transfer for foreign DNA to resemble native DNA. Furthermore, models of amelioration can be used to estimate the time of introgression of foreign genes in a chromosome. Applying this approach to a 1.43 megabase continuous sequence, we have calculated that the entire Escherichia coli chromosome contains more than 600 kilobases of horizontally-transferred, protein-coding DNA. Estimates of amelioration times indicate that this DNA has accumulated at a rate of 31 kilobases per million years, which is on the order of the amount of variant DNA introduced by point mutations. This rate predicts that the E. coli and Salmonella enterica lineages have each gained and lost more than 3 megabases of novel DNA since their divergence.
The computer program described in the paper is available.
Lawrence, J.G., and J.R. Roth. 1996. Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics 143:1843-1860.
A model is presented whereby the formation of gene clusters in bacteria is mediated by transfer of DNA within and among taxa.Bacterial operons are typically comprised of genes whose products contribute to a single function. If this function is subject to weak selection, or to long periods with no selection, the contributing genes may accumulate mutations and be lost by genetic drift. From a cell's perspective, once several genes are lost, the function can be restored only if all missing genes were acquired simultaneously by lateral transfer. The probability of transfer of multiple genes increases when genes are physically proximate. From a gene's perspective, horizontal transfer provides a way to escape evolutionary loss by allowing colonization of organisms lacking the encoded functions. Since organisms bearing clustered genes are more likely to act as successful donors, clustered genes would spread among bacterial genomes. The physical proximity of genes may be considered a selfish property of the operon since it affects the probability of successful horizontal transfer, but may provide no physiological benefit to the host. This process predicts a mosaic structure of modern genomes in which ancestral chromosomal material is interspersed with novel, horizontally transferred operons providing peripheral metabolic functions.
Lawrence, J.G., and J.R. Roth. 1996. Evolution of coenzyme B12 synthesis among enteric bacteria: evidence for loss and reacquisition of a multigene complex. Genetics 142:11-24.
We have examined the distribution of cobalamin (coenzyme B12) synthetic ability and cobalamin-dependent metabolism among enteric bacteria. Most species of enteric bacteria tested synthesize cobalamin under both aerobic and anaerobic conditions and ferment glycerol in a cobalamin-dependent fashion. The group of species including Escherichia coli and S. typhimurium cannot ferment glycerol. E. coli strains cannot synthesize cobalamin de novo, and Salmonella spp. synthesize cobalamin only under anaerobic conditions. In addition, the cobalamin synthetic genes of Salmonella spp. (cob) show a regulatory pattern different from that of other enteric taxa tested. We propose that the cobalamin synthetic genes, as well as genes providing cobalamin-dependent diol dehydratase, were lost by a common ancestor of E. coli and Salmonella spp. and were both reintroduced as a single fragment into the Salmonella lineage from an exogenous source. Consistent with this hypothesis, the S. typhimurium cob genes do not hybridize with the genomes of other enteric species. The Salmonella cob operon may represent a class of genes characterized by periodic loss and reacquisition by host genomes. This process may be an important aspect of bacterial population genetics and evolution.
Roth, J.R., J.G. Lawrence, and T.A. Bobik. 1996. Cobalamin (coenzyme B12): synthesis and biological significance. Ann Rev Microbiol 50:137-181.
The cofactor cobalamin (coenzyme B12) poses a variety of questions. Its large size and chemical complexity have made the study of its biosynthesis a challenge. Cobalamin's uneven distribution among modern life forms and its proposed prebiotic origins raise questions regarding its general biological significance. Although cobalamin is made by some bacteria, is essential to humans (it was discovered by its ability to cure pernicious anemia), it seems to play no role in the metabolism of plants, fungi and some bacteria. Why have some organisms maintained use of this cofactor, while others flourish without it? The discovery of B12 synthesis and use in bacteria with well-developed genetic systems has made it possible to apply genetic methods to these broad questions. In the single organism Salmonella typhimurium, one can approach the synthesis, transport, physiological importance, and evolution of this complex cofactor. We review here the general area of B12 metabolism with an emphasis on biological uses revealed by genetic studies of enteric bacteria.
Ochman, H., and J.G. Lawrence. 1996. Phylogenetics and the amelioration of bacterial genomes. Pp 2627-2637 in 'Escherichia coli and Salmonella: Cellular and molecular biology, Second edition', edited by F. C. Neidhardt, et al. ASM Press, Washington, DC.
When compared to mammals - or even to most other metazoans - bacteria appear to have relatively few characters which might serve as a basis in their classification. Bacteriologists have traditionally relied upon morphological features, supplemented by a suite of metabolic properties, to differentiate among isolates of bacteria and to classify them into species and higher taxonomic units. But to what extent does this classification scheme reflect the actual evolutionary relationships among bacteria? For species constituting the Enterobactericeae, the agreement is reasonably good; however, this conclusion is based on some prior notion about the true phylogeny of these bacterial lineages. While microbiologists have long been aware of the problems associated with establishing the relationships among bacteria, many of these uncertainties have been removed with comparisons macromolecular sequences, particularly ribosomal RNAs. These sequences have allowed both the identification of closely-related species and the hierarchical grouping of species in a manner reflecting the evolutionary histories of the organisms. Our faith in the phylogenies based on biological sequences is founded on considerations of how evolution occurs: cells acquire the majority of genetic material from their direct ancestors (vertical transfer) and these heritable nucleic acids accumulate changes with time. Therefore, the degree of sequence similarity among bacterial lineages will reflect their recent common ancestry. Aside from establishing the relationships among organisms, phylogenetic trees can provide a framework for examining the distribution, patterns of change and relative timing of events in bacterial evolution. In this paper, we examine several aspects genome organization and evolution in bacteria in a phylogenetic perspective. The small size and relative paucity of non-coding DNA in bacterial chromosomes allow investigations into the structure of genes within operons, the physical relationships among operons within chromosomes, and the presence and distribution of genetic elements among chromosomes at levels not attainable in most eukaryotic species. And underlying each of these studies is the need to ascertain the evolutionary relationships of the genes, or organisms, possessing each trait.
Roth, J., N. Benson, T. Galitski, K. Haack, J. Lawrence, and L. Miesel. 1996. Rearrangements of the bacterial chromosome -- Formation and applications. Pp 2256-2276 in Escherichia coli and Salmonella: Cellular and molecular biology, Second edition, edited by F. C. Neidhardt, et al. ASM Press, Washington, DC.
One of the adjuncts to DNA replication and repair is the formation of occassional chromosomal rearrangements - deletions, tandem duplications, and inversions. Several earlier reviews have discussed aspects of this subject. Rearrangments differ greatly from the point mutations that are more often considered in thinking about evolution and analytical genetics. Deletions can remove multiple functions and are irreversible. Duplications can amplify a coding region and are so highly reversible that they might be considered a temporary "regulatory state" rather that a mutation. Inversions change the orientation of a sequence in the chromosome but disrupt the sequence only at the two endpoints. Inversions are not highly reversible. All of these mutations have consequences for the structure of the chromosome and may lead, on an evolutionary timescale, to changes in the genetic map. In this review, we will describe the formal characteristics of these rearrangments and the ways in which they may be formed. Duplications and deletions, despite their distinct properties and consequences, can be generated by similar sister strand exchanges and will be discussed together. Inversions are fundamentally more complicated and will be discussed separately, with some of their implications for chromosome structure.
Lawrence, J.G., and J.R. Roth. 1995. The cobalamin (coenzyme B12) biosynthetic genes of Escherichia coli. J Bacteriol 177:6371-6380.
The enteric bacterium Escherichia coli synthesizes cobalamin (vitamin B12) only when provided with the complex intermediate cobinamide. Three cobalamin biosynthetic genes have been cloned from Escherichia coli K-12 and their nucleotide sequences have been determined. The three genes form an operon (cob) under the control of several promoters and are induced by cobinamide, a precursor of cobalamin. The cob operon of E. coli comprises the cobU gene, encoding the bifunctional cobinamide kinase-guanylyltransferase, the cobS gene, encoding cobalamin synthetase, and the cobT gene, encoding DMB phosphoribosyltransferase. The physiological roles of these sequences were verified by the isolation of Tn10 insertion mutations in the cobS and cobT genes. All genes were named after their Salmonella typhimurium homologues, and are located at the corresponding position on the E. coli genetic map. Although the nucleotide sequences of the Salmonella cob genes and the E. coli cob genes are homologous, they are too divergent to have been derived from an operon present in their most recent common ancestor. Based on comparisons of G+C content, codon usage bias, dinucleotide frequencies, and patterns of synonymous and nonsynonymous substitutions, we conclude that the cob operon was introduced into the Salmonella genome from an exogenous source. The cob operon of E. coli may be related to cobalamin synthetic genes now found among non-Salmonella enteric bacteria.
Roth, J.R., J.G. Lawrence, M. Rubenfield, S. Kieffer-Higgins, and G.C. Church. 1993. Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. J Bacteriol 175:3303-3316.
Salmonella typhimurium synthesizes cobalamin (vitamin B12) de novo under anaerobic conditions. Of the 30 cobalamin synthetic genes, 25 or clustered in one operon, cob, and are arranged in three groups, each group encoding enzymes for a biochemically distinct portion of the biosynthetic pathway. We have determined the DNA sequence for the promoter region and the proximal 17.1 kb of the cob operon. This sequence includes 20 translationally coupled genes that encode the enzymes involved in Parts I and III of the cobalamin biosynthetic pathway. A comparison of these genes with the cobalamin synthetic genes from Pseudomonas denitrificans allows assignment of likely functions to 12 of the 20 sequenced Salmonella genes. Three additional Salmonella genes encode proteins likely to be involved in the transport of cobalt, a component of vitamin B12. However, not all Salmonella and Pseudomonas cobalamin synthetic genes have apparent homologs in the other species. These differences suggest that the cobalamin biosynthetic pathways differ between the two organisms. The evolution of the genes and their chromosomal positions is discussed.
Hartl, D.L., E.R. Lozovskaya, and J.G. Lawrence. 1992. Nonautonomous transposable elements in prokaryotes and eukaryotes. Genetica 86:47-53
Defective (nonautonomous) copies of transposable elements are relatively common in the genomes of eukaryotes but less common in the genomes of prokaryotes. With regard to transposable elements that exist exclusively in the form of DNA (nonretroviral transposable elements), nonautonomous elements may play a role in the regulation of transposition. In prokaryotes, plasmid-mediated horizontal transmission probably imposes a selection against nonautonomous elements, since nonautonomous elements are incapable of mobilizing themselves. The lower relative frequency of nonautonmous elements in prokaryotes may also reflect the coupling of transcription and translation, which may bias toward the cis activation of transposition. The cis bias we suggest nood not be absolute in order to militate against the long-term maintenance of prokaryotic elements unable to transpose on their own. Furthermore, and cis bias in transposition would also decrease the opportunity for trans repression of transposition by nonautonomous elements.
Lawrence, J.G., and D.L. Hartl 1992. Inference of horizontal genetic transfer: An approach using the bootstrap. Genetics 131:753-760
Inconsistencies in taxonomic relationships implicit in different sets of nucleic acid seuences potentially result from horizontal trasnfer of genetic materil between genomes. A nonparametric method is proposed to determine whether such inconsistencies are statistically significant. A similarity coefficient is calculated from ranked pariwise identities and are evaluated against a distribution of similarity coefficients generated from resampled data. Subsequent analyses of partial data sets, obtained by the elemination of individual taxa, identify particular taxa to which the significance may be attributed, and can sometimes help in distinguishing horizontal genetic transfer from inconsistencies doe to convergent evolution or variation in evolutionary rate. The method was successfully applied to data sets that were not found to be statistically significantly different with existing methods that use comparisons of phylogenetic trees. The new statistical framework is also applicable to the inference of horizontal genetic transfer from restriction fragment length polymorphism distributions and protein sequences.
The computer program described in the paper is available.
Lawrence, J.G., H. Ochman, and D.L. Hartl. 1992. The evolution of insertion sequences in enteric bacteria. Genetics 131:9-20
To identify mechanisms that influence the evolution of bacterial transposons, DNA sequence variation was evaluated among homologs of insertion sequences IS1, IS3, and IS30 from natural strains of Escherichia coli and related enteric bacteria. The nucleotide sequences within each class of IS were highly conserved among E. coli strains, over 99.7% similar to a consensus sequence. When compared to the range of nucleotide divergence among chromosomal genes, these data indicate high turnover and rapid movement of the transposons among clonal lineages of E. coli. In addition, length polymorphism among IS appears to be far less frequent than in eukaryotic transposons, indicating that nonfunctional elements comprise a smaller fraction of bacterial transposon populations than found in eukaryotes. IS present in other species of enteric bacteria are substantially divergent from E. coli elements, indicating that IS are mobilized among bacterial species at a reduced rate. However, homologs of IS1 and IS3 from diverse species provide evidence that recombination events and horizontal transfer of IS among species have both played major roles in the evolution of these elements. IS3 elements from E. coli and Shigella show multiple, nested, intragenic recombinations with a distantly related transposon, and IS1 homologs from diverse taxa reveal a mosaic structure indicative of mulitple recombination and horizontal transfer events.
Lawrence, J.G., D.L. Hartl, and H. Ochman. 1991. Molecular considerations in the evolution of bacterial genes. J Mol Evol 33:241-250
Synonymous and nonsynonymous substitution rates at the loci encoding glyceraldehyde-3-phosphate dehydrogenase (gap) and outer membrane protein 3A (ompA) were examined in 12 species of enteric bacteria. By examining homologous sequences in species of varying degrees of relatedness and of known phylogenetic relationhips, we analyzed the patterns of synonymous and nonsynonymous substitutions within and among these genes. Although both loci accumulate synonymous substitutions at reduced rates due to codon usage bias, portions of the gap and ompA reading frames show significant deviation in synonymous substitution rates not attributable to local codon bias. A paucity of synonymous substitutions in portions of the ompA gene may reflect selection for a novel mRNA secondary structure. In addition, these studies allow comparisons of homologous protein-coding sequences (gap) in plants, animals, and bacteria, revealing differences in evolutionary constraints on this glycolytic enzymes in these lineages.
Lawrence, J.G., H. Ochman, and D.L. Hartl 1991. Molecular and evolutionary relationships among enteric bacteria. J Gen Microbiol 137:1911-1921
Classification of bacterial species into genera has traditionally relied upon variation in phenotypic characteristics. However, these phenotypes often have a multifactorial genetic basis, making unambiguous taxonomic placement of new species difficult. By designing evolutionarily conserved oligonucleotide primers, it is possible to amplify homologous regions of genes in diverse taxa using the polymerase chain reaction and to determine their nucleotide sequences. We have constructed a phylogeny of some enteric bacteria, including five species classified as members of the genus Escherichia, based on nucleotide sequence variation at the loci encoding glyceraldehyde-3-phosphate dehydrogenase and outer membrane protein 3A, and compared this genealogy with the relationships inferred by biotyping. The DNA sequences of these genes defined congruent and robust phylogenetic trees indicating that they are an accurate reflection of the evolutionary history of the bacterial species. The five species of Escherichia were found to be distantly related and, contrary to their placement in the same genus, do not form a monophyletic group. These data provide a framework which allows the relationships of additional species of enteric bacteria to be inferred. Tehse procedures have general applicability for analysis of the classification, evolution, and epidemiology of bacterial taxa.
Lawrence, J.G., and D.L. Hartl. 1991. Unusual codon usage bias occurring within insertion sequences in Escherichia coli. Genetica 84:23-29
The large open reading frames of insertion sequences from Escherichia coli were examined for their spatial pattern of codon usage bias and distribution of rarely used codons. There is a bias in codon usage that is generally lower toward the terminus ends of the coding regions, which is reflected in the occurrence of an excess of nonpreffered codons in the 3' portions of the coding regions as compared with the 5' portions. In contrast, typical chromosomal genes have a lower codon usage bias toward the 5' ends of the coding regions. These results imply that the selective forces reflected in codon usage bias may differ according to position within a coding sequence. In addition, these constraints apparently differ in important ways between genes contained in insertion seqeunces and those in the chromosome.
Lawrence, J.G., A.C. Colwell, and O.J. Sexton. 1991. The ecological impact of allelopathy in Ailanthus altissima. Amer J Botany 78(7):948-958
Compounds inhibitory to the growth of neighboring plant species were found in significant concentrations in the leaves and stems of young Ailanthus altissima ramets. The surrounding soil also contained appreciable concentrations of similarly acting toxins. Individuals of neighboring plant species have either incorporated active portions of inhibitory compounds or have responded to Ailanthus by producing growth-inhibiting substances. Under greenhouse conditions, individuals of neighboring plant species previously unexposed to Ailanthus in the field were found to be more susceptible to the Ailanthus toxins than individuals previsouly exposed. Moreover, seeds produced by unexposed populations were also more susceptible to Ailanthus toxins than were seeds produced by previously exposed populations. These differences demonstrated that the allelochemicals of Ailanthus altissima exhibited a measurable impact upon neighboring plant species. Since the progeny of these populations displayed a differential response to Ailanthus toxin, this phenotypic difference between the two populations may have a heritable basis.
Lawrence, J.G., D.E. Dykhuizen, R.F. DuBose, and D.L. Hartl. 1989. Phylogenetic analysis of Escherichia coli using insertion sequence fingerprinting. Mol Biol Evol 6:1-14
Chromosomal DNA from 23 closely related, pathogenic strains of Escherichia coli was digested and probed for the insertion seqeunces IS1, IS2, IS4, IS5, and IS30. Under the assumption that elements residing in DNA restriction fragments fo the same apparent length are identical by descent, parsimony analysis of these characters yielded a unique phylogentic tree. This analysis not only distinguished among bacterial strinas that were otherwise identical in their biochemical characteristics and enzyme electrophoretic mobilities, but certain aspects of the topology of the tree were consistent across several unrelated insertion elements. The distribution of IS elements was then reexamined in light of the inferred phylogentic relationships to investigate the biological properties of the elements, such as rates of insertion and deletion, and to discover apparent recombinational events. The analysis shows that the pattern of distribution of insertion elements in the bacterial genome si sufficiently stable for epidemiological studies. Although the rate of recombination by conjugation has been postulated to be low, at least two such events appear to have taken place.
Last Updated 14 August 2006, by JG Lawrence