We test for LD using three methods: a Mantel test of genetic association, a test using standard metrics of LD (r 2 and D′), and a third method based on measures of phylogenetic congruence. In contrast, frequent genetic reassortment among segments would cause low LD between segments. The rarity of intrasegment recombination documented in laboratory studies of the phage suggests that LD within segments will be high. We test for a correlation between genetic and geographic distance between segments and for LD within and between segments. We use nucleotide sequence data derived from newly and previously isolated strains ( 25, 29) to characterize migration rates and linkage disequilibrium (LD) LD is a measure of the nonrandomness of the association between alleles at different sites. Here, we report the results of a biogeography study involving Cystoviridae isolates from different regions across the United States. However, the frequency of reassortment among Cystoviruses in the wild is unknown. Reassortment between very distantly related phages in the Cystoviridae clade has been documented in vitro ( 28).
These characteristics are biologically similar to those of segmented RNA viruses of medical and agricultural importance, such as Influenza-A. Experimental manipulations have shown that intrasegment recombination in Cystoviruses is infrequent, occurring at a rate of ≈10 -7 per segment per generation ( 26), but reassortment (exchange of segments between viruses) readily occurs when host cells are multiply infected ( 27). Additional phages from this clade were not isolated until 25 years later from the leaves of several agricultural species ( 25). Cystoviridae are characterized by a tripartite dsRNA genome, and the three RNA segments per phage particle are referred to as L, M, and S (large, medium, and small, respectively).
Therefore, from a theoretical standpoint, it is crucial to gauge the rate of genetic exchange in phages and to determine whether sexual processes act to structure biological populations that comprise a major portion of our global ecosystem.īacteriophages from the Cystoviridae clade were first isolated in 1971 from bean straw infested with Pseudomonas syringae pathovar phaseolicola ( Pp) ( 24). Furthermore, it has long been proposed that sex may be generally favored, because it promotes linkage equilibrium, which (in addition to de novo mutations) can provide the genetic variability that is the raw material for natural selection ( 19- 23). It is increasingly evident that phages often exert significant control over the population sizes of their hosts and, thus, influence large-scale ecological and biogeochemical processes attributed to bacteria ( 17, 18). Bacteriophages are an excellent choice for studying the rate and significance of genetic exchange in virus populations. These biases prevent the drawing of general conclusions. However, only a few medically or agriculturally important viruses have been examined, few of which represent random population samples. Several studies have estimated that the rate of genetic exchange in virus populations is relatively low ( 2- 16). Various mechanisms exist for genetic exchange (sex) between individual microbes, but the importance of these processes in structuring virus populations remains unclear. Microbes are the most numerous entities in the biosphere, and viruses that infect bacteria (bacteriophages) constitute the majority of these organisms ( 1). We discuss our results in light of the biological species concept applied to viruses. This extraordinary rate of genetic exchange between highly unrelated individuals is unprecedented in any taxa. The absence of LD within this group of phages is consistent with expectations for a completely sexual population, despite the fact that some segments have >50% nucleotide divergence at 4-fold degenerate sites. An extensive analysis of LD between segments supports frequent reassortment, on a time scale similar to the genomic mutation rate. Analyzing linkage disequilibrium (LD) within segments, we find no significant evidence of intrasegment recombination in wild populations, consistent with ( i). Previous laboratory manipulation has shown that, when multiple Cystoviruses infect a single host cell, they undergo ( i) rare intrasegment recombination events and ( ii) frequent genetic reassortment between segments.
Here, we present a biogeography study involving 25 previously undescribed bacteriophages from the Cystoviridae clade, a group characterized by a dsRNA genome divided into three segments. Despite this numerical dominance, the genetic structure of bacteriophage populations is poorly understood. Bacteriophages are the most numerous entities in the biosphere.
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