Genetic bottlenecks and population passages cause profound fitness differences in RNA viruses

Repeated clone-to-clone (genetic bottleneck) passages of an RNA phage and vesicular stomatitis virus have been shown previously to result in loss of fitness due to Muller's ratchet. We now demonstrate that Muller's ratchet also operates when genetic bottleneck passages are carried out at 37 rather than 32 degrees C. Thus, these fitness losses do not depend on growth of temperature-sensitive (ts) mutants at lowered temperatures. We also demonstrate that during repeated genetic bottleneck passages, accumulation of deleterious mutations does occur in a stepwise (ratchet-like) manner as originally proposed by Muller. One selected clone which had undergone significant loss of fitness after only 20 genetic bottleneck passages was passaged again in clone-to-clone series. Additional large losses of fitness were observed in five of nine independent bottleneck series; the relative fitnesses of the other four series remained close to the starting fitness. In sharp contrast, when the same selected clone was transferred 20 more times as large populations (10(5) to 10(6) PFU transferred at each passage), significant increases in fitness were observed in all eight passage series. Finally, we selected several clones which had undergone extreme losses of fitness during 20 bottleneck passages. When these low-fitness clones were passaged many times as large virus populations, they always regained very high relative fitness. We conclude that transfer of large populations of RNA viruses regularly selects those genomes within the quasispecies population which have the highest relative fitness, whereas bottleneck transfers have a high probability of leading to loss of fitness by random isolation of genomes carrying debilitating mutations. Both phenomena arise from, and underscore, the extreme mutability and variability of RNA viruses.

The strands of both polarities of a small circular RNA from carnation self-cleave in vitro through alternative double- and single-hammerhead structures

The sequence of a circular RNA from carnation has been determined and found to consist of 275 nucleotide residues adopting a branched secondary structure of minimum free energy. Both plus and minus strands of this RNA can form the hammerhead structures proposed to mediate the in vitro self-cleavage of a number of small infectious plant RNAs and the transcript of satellite 2 DNA from the newt. Minus full- and partial-length transcripts of the carnation circular RNA including the hammerhead structure showed self-cleavage during transcription and after purification, indicating the involvement of a single-hammerhead structure in the self-cleavage reaction. In the case of the plus transcripts only a dimeric RNA, but not a monomeric one, self-cleaved efficiently during transcription and after purification, strongly supporting the implication in this process of a double-hammerhead structure theoretically more stable than the corresponding single cleavage domain. However, a plus monomeric transcript self-cleaved after purification at a slow rate in a concentration-independent reaction which most probably occurs through an intramolecular mechanism. Comparative sequence analysis has revealed that the circular RNA from carnation shares similarities with some representative members of the viroid and viroid-like satellites RNAs from plants, suggesting that it is a new member of either these two groups of small pathogenic RNAs.

Pear blister canker viroid is a member of the apple scar skin subgroup (apscaviroids) and also has sequence homology with viroids from other subgroups

The sequence of pear blister canker viroid (PBCVd), the putative causal agent of pear blister canker (PBC) disease, has been determined. PBCVd consists of a single-stranded circular RNA of 315 nucleotide residues which assumes a branched conformation when it is folded in the model of lowest free energy. PBCVd has highest sequence similarity with grapevine 1B viroid (52.4%), but also contains sequences related to regions present in viroids that belong to different subgroups, suggesting that PBCVd could have developed from RNA recombination between viroids replicating in a common host plant. PBCVd contains almost the entire central sequence which is conserved in the members of the apple scar skin subgroup (apscaviroids) as well as a conserved sequence located in the left-terminal region of apscaviroids and pospiviroids (whose type member is potato spindle tuber viroid). A consensus phylogenetic tree has been obtained in which PBCVd and other viroids previously classified as apscaviroids appear closely related, allowing consideration of PBCVd as a new member of this subgroup.

GEOSEQ: a Pascal program to calculate statistical geometry parameters of aligned nucleic acid sequences

Statistical geometry in sequence space is a statistical method used mainly to determine the topology of the divergence (i.e. tree, bundle or net) of a set of aligned sequences by combining horizontal and vertical positional information. GEOSEQ is a documented program written in Pascal that calculates the statistical geometry parameters necessary to choose between phylogenetic topologies. The input file is an optimal alignment of nucleic acid sequences in PHYLIP format (v. 3.3) with a first line containing information regarding sequences as well as some options. In order to check the randomization level associated with the obtained topology, the program has been implemented with a random generator of sequences under specified set conditions.

Phylogenetic reconstruction of the Drosophila obscura group, on the basis of mitochondrial DNA

We have constructed restriction-site maps of the mtDNAs in 13 species and one subspecies of the Drosophila obscura group. The traditional division of this group into two subgroups (affinis and obscura) does not correspond to the phylogeny of the group, which shows two well-defined clusters (the Nearctic affinis and pseudoobscura subgroups) plus a very heterogeneous set of anciently diverged species (the Palearctic obscura subgroup). The mtDNA of Drosophila exhibits a tendency to evolve toward high A+T values. This leads to a "saturation" effect that (1) begets an apparent decrease in the rate of evolution as the time since the divergence of taxa increases and (2) reduces the value that mtDNA restriction analysis has for the phylogenetic reconstruction of Drosophila species that are not closely related.

Rapid fitness losses in mammalian RNA virus clones due to Muller's ratchet

Muller's ratchet is an important concept in population genetics. It predicts that when mutation rates are high and a significant proportion of mutations are deleterious, a kind of irreversible ratchet mechanism will gradually decrease the mean fitness of small populations of asexual organisms. In contrast, sexual recombination may stop or reverse this mutational ratchet by recombinational repair of genetic damage. Experimental support for Muller's ratchet has previously been obtained in protozoa and in a tripartite RNA bacteriophage. We now show clear evidence that Muller's ratchet can operate on a nonsegmented nonrecombining pathogenic RNA virus of animals and humans. We did genetic bottleneck passages (plaque-to-plaque transfers) of vesicular somatitis virus (VSV) and then quantitated relative fitness of the bottleneck clones by allowing direct replication competition in mixed infections in cell culture. We document variable fitness drops (some severe) following only 20 plaque-to-plaque transfers of VSV. In some clones no fitness changes (or only insignificant changes) were observed. Surprisingly, the most regular and severe fitness losses occurred during virus passages on a new host cell type. These results again demonstrate the extreme genetic and biological variability of RNA virus populations. Muller's ratchet could have significant implications for variability of disease severity during virus outbreaks, since genetic bottlenecks must often occur during respiratory droplet transmissions and during spread of low-yield RNA viruses from one body site to another (as with human immunodeficiency virus). Likewise, the lower-probability generation of increased-fitness clones during repeated genetic bottleneck transfers of RNA viruses in nature might also affect disease pathogenesis in infected individuals and in host populations. Whenever genetic bottlenecks of RNA viruses occur, enhanced biological differences among viral subpopulations may result.

Different mechanisms generating sequence variability are revealed in distinct regions of the hydroxyproline-rich glycoprotein gene from maize and related species

The sequences of the genes coding for a hydroxyproline-rich glycoprotein from two varieties of maize (Zea mays, Ac1503 and W22), a teosinte (Zea diploperennis) and sorghum (Sorghum vulgare) have been obtained and compared. Distinct patterns of variability have been observed along their sequences. The 500 bp region immediately upstream of the TATA box is highly conserved in the Zea species and contains stretches of sequences also found in the sorghum gene. Further upstream, significant rearrangements are observed, even between the two maize varieties. These observations allow definition of a 5' region, which is common to the four genes and is probably essential for their expression. The 3' end shows variability, mostly due to small duplications and single nucleotide substitutions. There is an intron present in this region showing a high degree of sequence conservation among the four genes analyzed. The coding region is the most divergent, but variability arises from duplications of fragments coding for similar protein blocks and from single nucleotide substitutions. These results indicate that a number of distinct mechanisms (probably point mutation, transposon insertion and excision, homologous recombination and unequal crossing-over) are active in the production of sequence variability in maize and related species. They are revealed in different parts of the gene, probably as the result of the different types of functional constraints acting on them, and of the specific nature of the sequence in each region.

Repetitive nucleotide sequencing of a dispensable DNA segment in a clonal population of African swine fever virus

Repetitive nucleotide sequencing of a dispensable genomic segment of a clonal population of African swine fever (ASF) virus has been carried out to estimate the mutant frequency to neutral alleles. Since no mutations have been detected in a total of 54026 nucleotides screened, the maximum mutant frequency is 5.5 x 10(-5) substitutions/nucleotide (95% confidence level). The result renders very unlikely the occurrence of hypermutational events during ASF virus DNA replication, at least within the selected DNA fragment.

Fixation of mutations at the VP1 gene of foot-and-mouth disease virus. Can quasispecies define a transient molecular clock?

The number of nucleotide (nt) substitutions found in the VP1 gene (encoding viral capsid protein) between any two of 16 closely related isolates of foot-and-mouth disease virus (FMDV) has been quantified as a function of the time interval between isolations [Villaverde et al., J. Mol. Biol. 204 (1988) 771-776]. One of them (isolate C-S12) includes some replacements found in isolates that preceded it and other replacements found in later isolates. The study has revealed alternating periods of rapid evolution and of relative genetic stability of VP1. During a defined period of acute disease, the rate of fixation of replacements at the VP1 coding segment was 6 x 10(-3) substitutions per nt per year. Only small differences in the rate of evolution were observed between subsegments within the VP1 gene. The observation of a relatively constant rate of evolution during a disease episode was unexpected. We propose that such constancy may be a consequence of random sampling of mutants from the FMDV quasispecies, followed by their amplification in susceptible hosts (to generate a new quasispecies). Successive sampling and amplification events may result in a steady accumulation of mutations.

Phylogeny of viroids, viroidlike satellite RNAs, and the viroidlike domain of hepatitis delta virus RNA

We report a phylogenetic study of viroids, some plant satellite RNAs, and the viroidlike domain of human hepatitis delta virus RNA. Our results support a monophyletic origin of these RNAs and are consistent with the hypothesis that they may be "living fossils" of a precellular RNA world. Moreover, the viroidlike domain of human hepatitis delta virus RNA appears closely related to the viroidlike satellite RNAs of plants, with which it shares some structural and functional properties. On the basis of our phylogenetic analysis, we propose a taxonomic classification of these RNAs.

Fitness alteration of foot-and-mouth disease virus mutants: measurement of adaptability of viral quasispecies

We document the rapid alteration of fitness of two foot-and-mouth disease virus (FMDV) mutants resistant to a neutralizing monoclonal antibody. Both mutants showed a selective disadvantage in BHK-21 cells when passaged in competition with their parental FMDV. Upon repeated replication of the mutants alone, they acquired a selective advantage over the parental FMDV and fixed additional genomic substitutions without reversion of the monoclonal antibody-resistant phenotype. Thus, variants that were previously kept at low frequency in the mutant spectrum of a viral quasispecies rapidly became the master sequence of a new genomic distribution and dominated the viral population.

Two modes of balancing selection in Drosophila melanogaster: overcompensation and overdominance

Overdominance is often invoked to account for the extensive polymorphisms found in natural populations of organisms; overcompensation, however, may be equally or more important. Overcompensation occurs when limiting resources are better exploited by a genetically mixed than by a uniform population, and is often causally related to frequency-dependent selection. We have designed experiments to test whether overcompensation occurs in Drosophila melanogaster, using the Sod locus as a marker. Tests are made at each of two densities and two temperatures for cultures with desired genetic compositions. Both temperature and density have statistically significant effects on the per-female productivity of the cultures. More important, there are strong effects due to overcompensation. Cultures that are more polymorphic are also more productive than less polymorphic ones even when the level of individual heterozygosity is the same in all. There is also overdominance for the Sod locus: the heterozygotes are more productive than either homozygote at every temperature and density, and the differences are statistically significant in several cases. These results corroborate previous studies showing that overdominance may contribute to the maintenance of the Sod polymorphisms. Moreover, our results indicate that the significance of overcompensation as a mechanism to account for polymorphism in natural populations deserves further investigation.

Fertility and viability at the Sod locus in Drosophila melanogaster: non-additive and asymmetric selection

Experiments were designed to test in Drosophila melanogaster the effect of mating type at the Sod locus on fertility and viability. The experiments show that fertility is neither additive (or multiplicative) nor symmetric, i.e. that the fertility of a mating type cannot be predicted from the average fertility of the two genotypes involved in the mating. There is no significant male x female interaction with respect or progeny viability; but the interaction is significant for productivity, i.e. when fertility and viability are jointly taken into account. There is overdominance with respect to female fertility, but not with respect to male fertility or to viability. There also is alloprocoptic selection with respect to fertility and with respect to productivity, i.e. mating between like homozygotes are less fertile and productive than matings between dissimilar homozygotes. Selection at the Sod locus yields stable polymorphic equilibria, with the frequency of the F allele predicted at P = 0.641 or 0.695, respectively for low and high larval density.

Sequences of isopenicillin N synthetase genes suggest horizontal gene transfer from prokaryotes to eukaryotes

Evolutionary distances between bacterial and fungal isopenicillin N synthetase (IPNS) genes have been compared to distances between the corresponding 5S rRNA genes. The presence of sequences homologous to the IPNS gene has been examined in DNAs from representative prokaryotic organisms and Ascomycotina. The results of both analyses strongly support two different events of horizontal transfer of the IPNS gene from bacteria to filamentous fungi. This is the first example of such a type of transfer from prokaryotes to eukaryotes.

On the analysis of viability data: an example with Drosophila

Larval competition experiments involving two wild type and eight mutant strains of Drosophila melanogaster have been carried out following the substitution procedure proposed by Mather and Caligari (1981). Our main goal has been to compare the competitive abilities of two phenotypically indistinguishable strains (wild and Oregon-R) by means of their responses with eight different mutants. Prior to the analyses of viability data, we have studied the normalizing effect of several transformations in order to determine which was best suited for the analyses. The differences found among the five transformations tested and the untransformed data were not very great. The folded power transformation (Mosteller and Tukey, 1977) was finally chosen. No constant pattern in the responses of the two wild type strains to the mutant competitors was detected. This leads us to conclude that the nature of the competition between the two wild type strains cannot be predicted from a knowledge of their competition with other strains.

Mitochondrial DNA evolution in experimental populations of Drosophila subobscura

When two mitochondrial DNA (mtDNA) haplotypes of Drosophila subobscura compete in experimental populations with discrete generations, one or the other approaches fixation, depending on the nuclear background with which they are associated. The approach to fixation, however, is strongly dependent on the effective number of females in the population, Nf. Whether or not the ultimate fate of a given mtDNA haplotype is determined by random genetic drift depends on Nf as well as on the relative fitnesses. Our experimental results show that the mtDNA polymorphisms observed in natural populations are affected by interactions among nuclear polymorphisms, random genetic drift, and direct selection on the mtDNA haplotypes.

Overcompensation as a mechanism for maintaining polymorphism: egg-to-adult viability in Drosophila

Frequency-dependent selection may be accounted for, in ecological terms, by the differential effectiveness of alternative genotypes in exploiting limiting environmental resources. Differentiation in resource exploitation among genotypes implies in turn that a mix of genotypes may exploit more fully the resources than a genetically uniform population, a phenomenon called 'overcompensation'. Experiments designed to test for overcompensation show that highly polymorphic populations can support larger numbers of individuals per food unit than less polymorphic populations. This difference cannot be attributed to the level of individual heterozygosity, which is the same in both types of populations.

Comparison of vaccine strains and the virus causing the 1986 foot-and-mouth disease outbreak in Spain: epizootiological analysis

RNAs of the most recent foot-and-mouth disease virus isolated in Spain (A5Sp86) during the 1986 outbreak, and of the three vaccine strains in use at that time in that country, have been compared. Although these viruses are serologically indistinguishable, differences have been found among them by T1 fingerprinting. This genetic heterogeneity affects the immunogenic VP1 gene, with amino acid changes located at the carboxyterminal end of the molecule. VP1-coding sequences obtained have been compared with those previously reported for European A5 FMDVs and it has been possible to trace their phylogenetic origin. The most parsimonious evolutionary tree obtained shows that the viruses analyzed are closely related to those previously isolated in 1983 in Spain, Portugal and Morocco. In spite of the VP1 sequence homology shown by this group of viruses, the genetic distances among field isolates and vaccine strains are significantly shorter than the distances found among field isolates. Thus, a significant relationship among virus recovered from recent outbreaks and the vaccine strains in use at that time in Spain, has been obtained.

Variability and evolution of the plant RNA virus pepper mild mottle virus

The RNA genomes of 26 isolates of pepper mild mottle virus were compared by their RNase T1 fingerprints. Twenty-three isolates came from epidemic outbreaks in greenhouse-grown peppers in Almería (southeastern Spain) from 1983 to 1987; three other isolates, from 1980, came from Sicily (Italy) and Zaragoza (central Spain). The 26 fingerprints can be classified into 10 different types; nucleotide substitution rates show them to be very similar. Cluster and cladistic analyses group types corresponding to the Almería isolates separate from those of 1980. Intraannual and interannual nucleotide differences were estimated. An evolutionary model for pepper mild mottle virus built on these data indicates a highly stable population, maintaining its diversity through time, with a main prevailing haplotype from which closely related variants arise that do not replace it. This high stability could be due to strong functional constraints on variation, as suggested by the high proportion of invariant versus polymorphic sites in fingerprints.

Linkage disequilibrium in natural and experimental populations of Drosophila melanogaster

We have studied linkage disequilibrium in Drosophila melanogaster in two samples from a wild population and in four large laboratory populations derived from the wild samples. We have assayed four polymorphic enzyme loci, fairly closely linked in the third chromosome: Sod Est-6, Pgm, and Odh. The assay method used allows us to identify the allele associations separately in each of the two homologous chromosomes from each male sampled. We have detected significant linkage disequilibrium between two loci in 16.7% of the cases in the wild samples and in 27.8% of the cases in the experimental populations, considerably more than would be expected by chance alone. We have also found three-locus disequilibria in more instances than would be expected by chance. Some disequilibria present in the wild samples disappear in the experimental populations derived from them, but new ones appear over the generations. The effective population sizes required to generate the observed disequilibria by randomness range from 40 to more than 60,000 individuals in the natural population, depending on which locus pair is considered, and from 100 to more than 60,000 in the experimental populations. These population sizes are unrealistic; the fact that different locus-pairs yield disparate estimates within the same population argues against the likelihood that the disequilibria may have arisen as a consequence of population bottlenecks. Migration, or population mixing, cannot be excluded as the process generating the disequilibria in the wild samples, but can in the experimental populations. We conclude that linkage disequilibrium in these populations is most likely due to natural selection acting on the allozymes, or on loci very tightly linked to them.

Mitochondrial DNA evolution in the Drosophila obscura group

We report a restriction-site study of the mitochondrial DNA (mtDNA) of seven species of the Drosophila obscura group. One species (D. azteca) belongs to the affinis subgroup; the other six species are classified in the obscura subgroup, three of them being from the old-world species (D. obscura, D. ambigua, and D. subobscura) and three from the new-world species (D. pseudoobscura, D. persimilis, and D. miranda). The mtDNA patterns suggest that the phylogeny of the group needs to be revised. The Nearctic obscura species appear as more closely related to D. azteca (affinis subgroup) than to the Palearctic species. The three Palearctic species are, in turn, a very heterogeneous group, with D. obscura no more closely related to D. subobscura and D. ambigua than to D. affinis or the Nearctic obscura species. The rates of mtDNA evolution are variable: some lineages have evolved at rates two or three times greater than others. If an average rate of 0.5% nucleotide substitutions/Myr is assumed, the divergence among the four main lineages in the phylogeny would have occurred 12-15 Myr ago, during the Miocene, which is consistent with biogeographic information.

Gene encoding capsid protein VP1 of foot-and-mouth disease virus: a quasispecies model of molecular evolution

A phylogenetic tree relating the VP1 gene of 15 isolates of foot-and-mouth disease virus (FMDV) of serotypes A, C, and O has been constructed. The most parsimonious tree shows that FMDV subtypes and isolates within subtypes constitute sets of related, nonidentical genomes, in agreement with a quasispecies mode of evolution of this virus. The average number of nucleotide replacements per site for all possible pairs of VP1 coding segments is higher among representatives of serotype A than serotype C or O. In comparing amino acid sequences, the values of dispersion index (variance/mean value) are greater than 1, with the highest values scored when all sequences are considered. This indicates an accumulation of mutations at a limited number of residues, suggesting that distributions of sequences fluctuate around points of high stability. Evolution of FMDV follows a path very distant from that of a star phylogeny, and it has not been possible to derive conclusions on constancy of evolutionary rates with the test applied to the analysis. FMDVs, as other RNA viruses, are of limited genetic complexity and their population sizes are extremely large. Their evolution concerns complex, indeterminate mixtures of genomes rather than a single, determinate species.