Exploring the evolution of Wolbachia compatibility types: a simulation approach

Wolbachia-induced cytoplasmic incompatibility (CI) is observed when males bearing the bacterium mate with uninfected females or with females bearing a different Wolbachia variant; in such crosses, paternal chromosomes are lost at the first embryonic mitosis, most often resulting in developmental arrest. The molecular basis of CI is currently unknown, but it is useful to distinguish conceptually the male and female sides of this phenomenon: in males, Wolbachia must do something, before it is shed from maturing sperm, that will disrupt paternal chromosomes functionality [this is usually termed "the modification (mod) function"]; in females, Wolbachia must somehow restore embryonic viability, through what is usually called "the rescue (resc) function." The occurrence of CI in crosses between males and females bearing different Wolbachia variants demonstrates that the mod and resc functions interact in a specific manner: different mod resc pairs make different compatibility types. We are interested in the evolutionary process allowing the diversification of compatibility types. In an earlier model, based on the main assumption that the mod and resc functions can mutate independently, we have shown that compatibility types can evolve through a two-step process, the first involving drift on mod variations and the second involving selection on resc variations. This previous study has highlighted the need for simulation-based models that would include the effects of nondeterministic evolutionary forces. This study is based on a simulation program fulfilling this condition, allowing us to follow the evolution of compatibility types under mutation, drift, and selection. Most importantly, simulations suggest that in the frame of our model, the evolution of compatibility types is likely to be a gradual process, with new compatibility types remaining partially compatible with ancestral ones.     

Rapid evolution of Wolbachia incompatibility types

In most insects, the endosymbiont Wolbachia induces cytoplasmic incompatibility (CI), an embryonic mortality observed when infected males mate either with uninfected females or with females infected by an incompatible Wolbachia strain. Although the molecular mechanism of CI remains elusive, it is classically viewed as a modification–rescue model, in which a Wolbachia mod function disables the reproductive success of the sperm of infected males, unless eggs are infected and express a compatible resc function. The extent to which the modification–rescue model can predict highly complex CI pattern remains a challenging issue. Here, we show the rapid evolution of the mod–resc system in the Culex pipiens mosquito. We have surveyed four incompatible laboratory isofemale lines over 50 generations and observed in two of them that CI has evolved from complete to partial incompatibility (i.e. the production of a mixture of compatible and incompatible clutches). Emergence of the new CI types depends only on Wolbachia determinants and can be simply explained by the gain of new resc functions. Evolution of CI types in Cx. pipiens thus appears as a gradual process, in which one or several resc functions can coexist in the same individual host in addition to the ones involved in the self-compatibility. Our data identified CI as a very dynamic process. We suggest that ancestral and mutant Wolbachia expressing distinct resc functions can co-infect individual hosts, opening the possibility for the mod functions to evolve subsequently. This gives a first clue towards the understanding of how Wolbachia reached highly complex CI pattern in host populations.     

Recombination confounds interpretations of Wolbachia evolution.

Wolbachia are vertically transmitted bacteria known from arthropods and nematode worms, which are maintained in host populations because they either physiologically benefit infected individuals or parasitically manipulate their reproduction. The different manipulation phenotypes are scattered across the Wolbachia phylogeny, suggesting that there have been multiple evolutions of similar phenotypes. This conclusion relies on the assumption of an absence of recombination between bacterial strains, so that the gene used to reconstruct the phylogeny reflects the evolutionary history of the genes involved in the trait. We tested for recombination by reconstructing the phylogeny of two Wolbachia genes from seven B-subdivision strains. The two genes produced mutually incompatible topologies, indicating that these lineages are subject to genetic recombination. This means that many evolutionary patterns inferred from Wolbachia phylogenies must be re-evaluated. Furthermore, recombination may be an important feature both in the evolution of the manipulation phenotypes and avoidance of Müller's ratchet. Finally, we discuss the implications of recombination for attempts to genetically engineer Wolbachia for use in the control of crop pests and human pathogens.     

On the PAM matrix model of protein evolution

The internal consistency of the PAM matrix model of protein evolution ishere investigated. The 1 PAM matrix has been constructed from amino acidreplacements observed in closely related sequences. Such replacements areof two types, those that do not require an intermediate amino acidreplacement and those that do. The second type of replacement mustgenerally be produced by a repetition of the first. This allows data on thefirst type to be used in predicting data on the second type so that someelements of the 1 PAM matrix may be used to predict others. A discrepancyof more than two orders of magnitude is found between the predictions andthe data when this is carried out. This is partly accounted for by an errorin constructing the matrix. However, it also seems necessary that the basicmodel be modified. Several possibilities are considered. One of these is toincorporate a site-dependent spectrum of mutabilities associated with eachamino acid.     

Genome evolution of Wolbachia strain wPip from the Culex pipiens group

The obligate intracellular bacterium Wolbachia pipientis strain wPip induces cytoplasmic incompatibility (CI), patterns of crossing sterility, in the Culex pipiens group of mosquitoes. The complete sequence is presented of the 1.48-Mbp genome of wPip which encodes 1386 coding sequences (CDSs), representing the first genome sequence of a B-supergroup Wolbachia. Comparisons were made with the smaller genomes of Wolbachia strains wMel of Drosophila melanogaster, an A-supergroup Wolbachia that is also a CI inducer, and wBm, a mutualist of Brugia malayi nematodes that belongs to the D-supergroup of Wolbachia. Despite extensive gene order rearrangement, a core set of Wolbachia genes shared between the 3 genomes can be identified and contrasts with a flexible gene pool where rapid evolution has taken place. There are much more extensive prophage and ankyrin repeat encoding (ANK) gene components of the wPip genome compared with wMel and wBm, and both are likely to be of considerable importance in wPip biology. Five WO-B-like prophage regions are present and contain some genes that are identical or highly similar in multiple prophage copies, whereas other genes are unique, and it is likely that extensive recombination, duplication, and insertion have occurred between copies. A much larger number of genes encode ankyrin repeat (ANK) proteins in wPip, with 60 present compared with 23 in wMel, many of which are within or close to the prophage regions. It is likely that this pattern is partly a result of expansions in the wPip lineage, due for example to gene duplication, but their presence is in some cases more ancient. The wPip genome underlines the considerable evolutionary flexibility of Wolbachia, providing clear evidence for the rapid evolution of ANK-encoding genes and of prophage regions. This host-Wolbachia system, with its complex patterns of sterility induced between populations, now provides an excellent model for unraveling the molecular systems underlying host reproductive manipulation.     

A population genetical model for sequence evolution under multiple types of mutation

DNA sequencing and restriction mapping provide us with information on DNA sequence evolution within populations, from which the phylogenetic relationships among the sequences can be inferred. Mutations such as base substitutions, deletions, insertions and transposable element insertions can be identified in each sequence. Theoretical study of this type of sequence evolution has been initiated recently. In this paper, population genetical models for sequence evolution under multiple types of mutation are developed. Models of infinite population size with neutral mutation, infinite population size with deleterious mutation and finite population size with neutral mutation are considered.     

Sequential evolution of a symbiont inferred from the host: Wolbachia and Drosophila simulans

This study aims to unravel the biogeography of a model symbiont/host system by exploiting the prediction that a symbiont will leave a signature of infection on the host. Specifically, a global sample of 1,442 Drosophila simulans from 33 countries and 64 sampling localities was employed to infer the phylogeography of the maternally inherited alpha-proteobacteria Wolbachia. Phylogenetic analyses, from three symbiont genes and 24 mtDNA genomes (excluding the A + T-rich region), showed that each of four Wolbachia strains infected D. simulans once. The global distribution and abundance of the Wolbachia strains and the three mtDNA haplogroups (D. simulans siI, siII and siIII) was then determined. Finally, network analyses of variable regions within siI (584 bp from seven additional lines) and siII (1,701 bp from 383 lines) facilitated a detailed biogeographic discussion. There is little variation in siIII and the haplogroup is restricted in its distribution. These data show how the history of an infection can be mapped by combining data from the symbiont and the host. They say little about the organismal history of the host because the mtDNA genome is a biased representation of the whole genome.     

On the evolution of recombination and meiosis.

Theories on the evolution of recombination in regard to its ability to increase mean fitness require a consistent source of negative linkage disequilibrium among loci affecting fitness to show an advantage to recombination. Here we present evidence that, at least theoretically, genetic variation for recombination can spread in very large populations under a strictly multiplicative-fitness, deleterious-allele model. The model uses only Mendelian genetics in a multi-locus context to show that a dominant gene for recombination can spread when rare and resist invasion when common. In non-equilibrium populations driven by Muller's ratchet, the gene increases its probability of fixation by increasing the probability of being associated with the best individuals. This occurs at an optimal level of recombination. Its action results in both an immediate and a long-term advantage to recombination amongst the proto-meiotic organisms modelled. The genetic mechanism lends itself naturally to a model for the evolution of meiosis, where modern-day gametes are seen as derivative of ancient unicellular organisms.     

Behavior,body types and the irreversibility of evolution

A functional approach to evolutionary morphology is emphasized in this paper. This perspective differs from the current structuralist trend, which emphasizes the constraining role of developmental paths. In addition, the present approach agrees with the adaptationist paradigm. It is further argued that three types of phenomena are better understood in this light: i.- the existence of evolutionary trends, ii.- the maintenance of certain structural features within a given taxon, and iii.- the irreversibility of evolution.     

Sexual compatibility between two types of Hylocerus (Cactaceae)

There are two types of pitahaya that are cultivated in Yucatan Peninsula of Mexico. They differ mainly in the skin color of the fruit, one of them has a red skin (Uqroo1), while the other has a light yellow skin (Uqroo2) both belong to Hylocereus undatus (Haworth) Britt. & Rose. The yellow skin pitahaya is the sweetest. The studies were conducted using the methods of self pollination and cross pollination, with direct crosses and reciprocal pollination in order to evaluate the effect related to the quantity of fruits that accomplish their growing process. Some characteristic parameters of fruits, thus obtained, were used to detect the possible xenic effect. The control samples were collected from naturally pollinated flowers. The experimental design used was completely random and the experiment was repeated fifteen times. The results revealed that the Uqroo1 turned out to be self-compatible, and their fruits reached one hundred percent of development. On the other hand, Uqroo2 was self-incompatible, that is, it did not accept self pollen. The control samples of both types reached the same weight, and the fruits of the Uqroo2 produced by cross pollination had the same or more weight than the control samples. Several parameters were positively correlated. The coefficient between the number of seeds and the fruit weight was r = 0.84. The highest correlation that was found (r = 0.97) in the fruit weight and the pulp weight within both types. The fruits obtained by cross-pollination maintained the characteristic of the female progenitor. It is suggest intercalate the yellow pitahaya plants with another types or species of pitahaya, other than the Uqroo1.     

Multiple Wolbachia determinants control the evolution of cytoplasmic incompatibilities in Culex pipiens mosquito populations

Wolbachia are maternally inherited endosymbionts that can invade arthropod populations through manipulation of their reproduction. In mosquitoes, Wolbachia induce embryonic death, known as cytoplasmic incompatibility (CI), whenever infected males mate with females either uninfected or infected with an incompatible strain. Although genetic determinants of CI are unknown, a functional model involving the so-called mod and resc factors has been proposed. Natural populations of Culex pipiens mosquito display a complex CI relationship pattern associated with the highest Wolbachia (wPip) genetic polymorphism reported so far. We show here that C. pipiens populations from La Réunion, a geographically isolated island in the southwest of the Indian Ocean, are infected with genetically closely related wPip strains. Crossing experiments reveal that these Wolbachia are all mutually compatible. However, crosses with genetically more distant wPip strains indicate that Wolbachia strains from La Réunion belong to at least five distinct incompatibility groups (or crossing types). These incompatibility properties which are strictly independent from the nuclear background, formally establish that in C. pipiens, CI is controlled by several Wolbachia mod/resc factors.     

On the evolution of blue proteins.

Amino acid sequences of 8 plastocyanins, 8 azurins, stellacyanin, two regions in human ceruloplasmin (ferroxidase)--all of which proteins are known to bind a blue (type 1) copper--and subunit II of bovine mitochondrial cytochrome c oxidase were compared by statistical methods to assess similarities and derive possible evolutionary relationships. It is suggested that all of the examined proteins are monophyletic. The two ceruloplasmin partial sequences clearly demonstrate that this protein has undergone a duplication. A calculated most parcimonious phylogenetic tree shows the divergence of the azurin and plastocyanin ancestor to be the earliest event. Stellacyanin and later the blue oxidase (ceruloplasmin) evolved from the plastocyanin branch, which the cytochrome c oxidase subunit evolved from the azurin ancestor.     

Two distinct types of trimethoprim-resistant dihydrofolate reductase specified by R-plasmids of different compatibility groups.

R-Plasmids from a number of trimethoprim-resistant Escherichia coli and Citrobacter sp. were studied after transfer to E. coli K12 hosts. Each was found to specify a dihydrofolate reductase which was resistant to trimethoprim and Methotrexate, and which could be completely separated from the host chromosomal enzyme by gel filtration. Two distinct types of R-plasmid dihydrofolate reductases were identified. Type I enzymes, typified by the R483 enzyme previously described (Sk?ld, O., and Widh, A. (1974) J. Biol. Chem. 249, 4324-4325), are synthesized in amounts severalfold higher than the chromosomal enzyme. The 50% inhibitory concentrations (I50) of trimethoprim, Methotrexate, and aminopterin are increased several thousandfold over the corresponding values for the chromosomal enzyme. Type II R-plasmid dihydrofolate reductases are synthesized in about the same amount, or less, as the chromosomal enzyme, but are practically several hundredfold higher than those for the type I enzymes. Both types of R-plasmid dihydrofolate reductase showed little difference from the chromosomal enzyme in the binding of dihydrofolate, NADPH, folic acid, and 2,4-diaminopyrimidine.     

On the evolution and dynamics of biological networks.

Large numbers of interacting non-genic molecules regulate metabolism and embryonic morphogenesis through often unspecific mechanisms. This lack of specificity suggests that the prevailing viewpoint, that such ordered processes result from the direct control of genes and their products irrespective of local molecular dynamics, is incomplete. Proposed here is a hypothetical type of control dynamics, called indirect, that is exhibited in natural biological networks of interacting and adapting elements. Evidence in the literature suggests that ordinary interactions among such elements - including organisms, cells and molecules - produce six network phenomena that can be attributed to indirect-control dynamics. Although these hypotheses can be disproved, including by showing that the phenomena can be accounted for by an alternative process, the set of ecological dynamics argued to underlie the phenomena is observable, biologically consistent and universal. In contrast, the direct-control dynamics required by the modern synthesis likely is biologically disadvantageous. This biological view of networks suggests new areas of research.     

On the variability of the types ofC. diphtheriae

Conclusion From this investigation it is evident that most strains ofC. diphtheriae can be easily typed; with the typing of some strains difficulties have been encountered. By close examination of the properties some of these can be typed after some delay, superisolation being indispensable.The use of insoluble starch is essential in the fermentation test. All bacteria which differ in one or more respects from the typical ones must be labelled as atypical. This also concerns gravis strains which do not ferment starch and glycogen. If the bacteria are thus typed erroneous typing can be minimized, though faults will be inevitable.The typical as well as the atypical bacteria have great stability. For the moment we wish to consider the types as fixates rather than as subspecies. Notwithstanding the observation of changesin vitro in some cases, the types appear to be sufficiently stable for epidemiological investigation.     

On the evolution of the photosynthetic pigments.

During the course of terrestrial evolution, some organisms developed the capability of capturing and utilizing solar radiation. Colored compounds were undoubtedly incorporated within living forms from the earliest times, but during the transition from heterotrophic to a photoautotrophic metabolism only those pigments were selected that were components of the evolving photosynthetic apparatus and were able to catalyze reactions involving storage of light energy in chemical bonds. In this communication, some properties of tetrapyrroles with a closed porphyrin ring containing a metal ion in the center are discussed. These compounds are present in all principal contemporary photosynthetic pigments, and their synthesis has been demonstrated from simpler compounds under prebiotic conditions. It is probable that during intermediate stages in the evolution of photosynthesis, pigments with oxidizing potentials lower than that of chlorophyll were utilized to store light energy although they were not capable of removing electrons from water. The evolution and function of multiple forms of a given photosynthetic pigment in vivo are discussed. 'Accessory' pigments may be regarded as rudiments of the evolutionary development of the photosynthetic apparatus.     

Integrated and independent evolution of heteromorphic sperm types

Sperm are a simple cell type with few components, yet they exhibit tremendous between-species morphological variation in those components thought to reflect selection in different fertilization environments. However, within a species, sperm components are expected to be selected to be functionally integrated for optimal fertilization of eggs. Here, we take advantage of within-species variation in sperm form and function to test whether sperm components are functionally and genetically integrated both within and between sperm morphologies using a quantitative genetics approach. Drosophila pseudoobscura males produce two sperm types with different functions but which positively interact together in the same fertilization environment; the long eusperm fertilizes eggs and the short parasperm appear to protect eusperm from a hostile female reproductive tract. Our analysis found that all sperm traits were heritable, but short sperm components exhibited evolvabilities 10 times that of long sperm components. Genetic correlations indicated functional integration within, but not between, sperm morphs. These results suggest that sperm, despite sharing a common developmental process, can become developmentally and functionally non-integrated, evolving into separate modules with the potential for rapid and independent responses to selection.     

On the evolution of pure winner and loser effects: A game-theoretic model

The persistence of linear dominance hierarchies is often attributed to higher probabilities of a win after a win or a loss after a loss in agonistic interactions, yet there has been no theory on the evolution of such prior-experience effects. Here an analytic model, based on the idea that contests are determined by subjective perceptions of resource-holding potential (RHP) which animals may revise in the light of experience, demonstrates that winner and loser effects can evolve through round-robin competition among triads of animals drawn randomly from their population, and that the probability of a hierarchy increases with the strength of the combined effect. The effects are pure, in the sense that a contestant observes neither its own RHP nor its opponent’s RHP or RHP perception or win—loss record; and so the strength of an effect is unmodified by the RHPs of particular individuals, but depends on the distribution of RHP among the population at large. The greater the difference between an individual’s and its opponent’s RHP perception, the more likely it is to win a contest; however, if it overestimates its RHP, then the cost of fighting increases with the overestimate. A winner or loser effect exists only if the fitness gain of the beta individual in a hierarchy, relative to that of the alpha, is less than 0.5. Then a loser effect can exist alone, or it can coexist with a winner effect; however, there cannot exist a winner effect without a loser effect.     

Directed evolution of AraC for improved compatibility of arabinose- and lactose-inducible promoters

Synthetic biological systems often require multiple, independently inducible promoters in order to control the expression levels of several genes; however, cross talk between the promoters limits this ability. Here, we demonstrate the directed evolution of AraC to construct an arabinose-inducible (P(BAD)) system that is more compatible with IPTG (isopropyl-beta-D-1-thiogalactopyranoside) induction of a lactose-inducible (P(lac)) system. The constructed system is 10 times more sensitive to arabinose and tolerates IPTG significantly better than the wild type. Detailed studies indicate that the AraC dimerization domain and C terminus are important for the increased sensitivity of AraC to arabinose.