How genetic parasites persist despite the purge of natural selection

Iranzo, Jaime; Koonin, Eugene V.

doi:10.1209/0295-5075/122/58001

Cited by 8 publications

(5 citation statements)

References 59 publications

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“…However, more generally, this situation would correspond to the arrival of the parasite from the outside, that is, effectively, to any case of infection of a host population. Together with the previous analyses indicating that genetic parasites could not be purged from prokaryote populations due to the high rate of horizontal gene transfer that is essential to the survival of these populations [39, 40], the present results support the concept of genetic parasites as an intrinsic feature of life.…”

Section: Discussionsupporting

confidence: 87%

A Ratio-Dependent Model of Replicator-Genetic Parasite Coevolution Demonstrates Instability of the Parasite-Free State

Berezovskaya

Karev

Wolf

et al. 2021

Preprint

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Nearly all organisms on earth are hosts to diverse genetic parasites including viruses and various types of mobile genetic elements. The emergence and persistence of genetic parasites was hypothesized to be an intrinsic feature of biological evolution. Here we examine this proposition by analysis of a ratio-dependent Lotka-Volterra type model of replicator(host)-parasite coevolution where the evolutionary outcome depends on the ratio of the host and parasite numbers. In a large, unbounded domain of the space of the model parameters, which include the replicator carrying capacity, the damage inflicted by the parasite, the replicative advantage of the parasites, and its mortality rate, the parasite-free equilibrium takes the form of a saddle and accordingly is unstable. Therefore, the evolutionary outcome is either the stable coexistence of the replicator and the parasite or extinction of both. Thus, the results of ratio-dependent model analysis are compatible with the hypothesis that genetic parasites are inherent to life.

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Section: Discussionsupporting

confidence: 87%

A Ratio-Dependent Model of Replicator-Genetic Parasite Coevolution Demonstrates Instability of the Parasite-Free State

Berezovskaya

Karev

Wolf

et al. 2021

Preprint

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“…This suggests the presence of additional factors governing plasmid acquisition and loss, such as environment-specific parameters. Our model of a balance between parasite invasion and selection is conceptually similar to those developed for transposons [ 41 ], and there are generalized models of mobile genetic elements that rely on a similar mechanism [ 30 ]. However, a major difference is that these models are concerned with the distribution of copy numbers, while we model the distribution of plasmid types.…”

Section: Discussionmentioning

confidence: 99%

“…There has been comparatively little theoretical work on parasitic infectious plasmids, with only a handful of papers exploring this scenario. These papers have generally focused on conjugative plasmids in single well-mixed environments [ 20 , 27 , 28 ], with exploration of more complex scenarios limited to generalized models of mobile genetic elements [ 29 , 30 ].…”

Section: Introductionmentioning

confidence: 99%

Modeling the ecology of parasitic plasmids

2021

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Plasmids are autonomous genetic elements that can be exchanged between microorganisms via horizontal gene transfer (HGT). Despite the central role they play in antibiotic resistance and modern biotechnology, our understanding of plasmids’ natural ecology is limited. Recent experiments have shown that plasmids can spread even when they are a burden to the cell, suggesting that natural plasmids may exist as parasites. Here, we use mathematical modeling to explore the ecology of such parasitic plasmids. We first develop models of single plasmids and find that a plasmid’s population dynamics and optimal infection strategy are strongly determined by the plasmid’s HGT mechanism. We then analyze models of co-infecting plasmids and show that parasitic plasmids are prone to a “tragedy of the commons” in which runaway plasmid invasion severely reduces host fitness. We propose that this tragedy of the commons is averted by selection between competing populations and demonstrate this effect in a metapopulation model. We derive predicted distributions of unique plasmid types in genomes—comparison to the distribution of plasmids in a collection of 17,725 genomes supports a model of parasitic plasmids with positive plasmid–plasmid interactions that ameliorate plasmid fitness costs or promote the invasion of new plasmids.

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“…Genomic comparisons of taxa that have diverged over deep evolutionary time, compared with investigations of genomes within the same contemporary natural communities, may lead to different inferences about the relative importance of genic selection. The diverse interactions a particular genetic element can have with host fitness is why others have recommended that assessments of the fitness impacts of such elements be based on long timescales only ( Iranzo and Koonin 2018 ). Although this is a sensible approach, it will not necessarily provide insight into the causal reasons for why a genetic element is present in a genome.…”

Section: Discussionmentioning

confidence: 99%

“…It has long been hypothesized that mobile elements that have neutral or deleterious impacts on host fitness are maintained in populations through sufficiently high rates of HGT. This question was recently investigated through a modeling approach that focused on DNA transposons, conjugative plasmids, and toxin–antitoxin modules across prokaryotes ( Iranzo and Koonin 2018 ). This investigation inferred that many such MGEs are likely deleterious over long timescales.…”

Section: General Strategies For Mgesmentioning

confidence: 99%

Genic Selection Within Prokaryotic Pangenomes

Douglas

Shapiro

2021

Genome Biology and Evolution

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Understanding the evolutionary forces shaping prokaryotic pangenome structure is a major goal of microbial evolution research. Recent work has highlighted that a substantial proportion of accessory genes appear to confer niche-specific adaptations. This work has primarily focused on selection acting at the level of individual cells. Herein, we discuss a lower level of selection that also contributes to pangenome variation: genic selection. This refers to cases where genetic elements, rather than individual cells, are the entities under selection. The clearest examples of this form of selection are selfish mobile genetic elements, which are those that have either a neutral or deleterious effect on host fitness. We review the major classes of these and other mobile elements and discuss the characteristic features of such elements that could be under genic selection. We also discuss how genetic elements that are beneficial to hosts can also be under genic selection, a scenario that may be more prevalent but not widely appreciated, because disentangling the effects of selection at different levels (i.e., organisms vs genes) is challenging. Nonetheless, an appreciation for the potential action and implications of genic selection provides a useful conceptual lens with which to study the evolution of prokaryotic pangenomes.

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How genetic parasites persist despite the purge of natural selection

Cited by 8 publications

References 59 publications

A Ratio-Dependent Model of Replicator-Genetic Parasite Coevolution Demonstrates Instability of the Parasite-Free State

A Ratio-Dependent Model of Replicator-Genetic Parasite Coevolution Demonstrates Instability of the Parasite-Free State

Modeling the ecology of parasitic plasmids

Genic Selection Within Prokaryotic Pangenomes

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