scholarly journals The rugged adaptive landscape of an emerging plant RNA virus

2014 ◽  
Author(s):  
Jasna Lalic ◽  
Santiago F. Elena
Keyword(s):  
Fitness Landscape ◽  
Rna Virus ◽  
Large Population ◽  
Emerging Infectious Diseases ◽  
Evolutionary Process ◽  
Adaptive Landscape ◽  
Evolutionary Potential ◽  
Recombination Rates ◽  
New Host ◽  
Population Sizes

RNA viruses are the main source of emerging infectious diseases owed to the evolutionary potential bestowed by their fast replication, large population sizes and high mutation and recombination rates. However, an equally important parameter, which is usually neglected, is the topography of the fitness landscape, that is, how many fitness maxima exist and how well connected they are, which determines the number of accessible evolutionary pathways. To address this question, we have reconstructed the fitness landscape describing the adaptation of Tobacco etch potyvirus to its new host, Arabidopsis thaliana. Fitness was measured for most of the genotypes in the landscape, showing the existence of peaks and holes. We found prevailing epistatic effects between mutations, with cases of reciprocal sign epistasis being common at latter stages. Therefore, results suggest that the landscape was rugged and holey, with several local fitness peaks and a very limited number of potential neutral paths. The viral genotype fixed at the end of the evolutionary process was not on the global fitness optima but stuck into a suboptimal peak.

scholarly journals Adaptive fitness landscape for replicator systems: to maximize or not to maximize

2018 ◽  
Vol 13 (3) ◽  
pp. 25 ◽  
Author(s):  
Alexander S. Bratus ◽  
Yuri S. Semenov ◽  
Artem S. Novozhilov
Keyword(s):  
Natural Selection ◽  
Fitness Landscape ◽  
Evolutionary Process ◽  
Hill Climbing ◽  
Adaptive Landscape ◽  
Basic Model ◽  
Mean Fitness ◽  
The Mean ◽  
The Hill ◽  
Fisher’S Fundamental Theorem

Sewall Wright’s adaptive landscape metaphor penetrates a significant part of evolutionary thinking. Supplemented with Fisher’s fundamental theorem of natural selection and Kimura’s maximum principle, it provides a unifying and intuitive representation of the evolutionary process under the influence of natural selection as the hill climbing on the surface of mean population fitness. On the other hand, it is also well known that for many more or less realistic mathematical models this picture is a severe misrepresentation of what actually occurs. Therefore, we are faced with two questions. First, it is important to identify the cases in which adaptive landscape metaphor actually holds exactly in the models, that is, to identify the conditions under which system’s dynamics coincides with the process of searching for a (local) fitness maximum. Second, even if the mean fitness is not maximized in the process of evolution, it is still important to understand the structure of the mean fitness manifold and see the implications of this structure on the system’s dynamics. Using as a basic model the classical replicator equation, in this note we attempt to answer these two questions and illustrate our results with simple well studied systems.

scholarly journals High heritability of coral calcification rates and evolutionary potential under ocean acidification

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Christopher P. Jury ◽  
Mia N. Delano ◽  
Robert J. Toonen
Keyword(s):  
Large Population ◽  
Local Environment ◽  
Evolutionary Potential ◽  
Seawater Chemistry ◽  
Porites Compressa ◽  
Management Actions ◽  
Ph Tolerance ◽  
Population Sizes ◽  
Protected Polymorphism ◽  
High Heritability

AbstractEstimates of heritability inform evolutionary potential and the likely outcome of many management actions, but such estimates remain scarce for marine organisms. Here, we report high heritability of calcification rate among the eight most dominant Hawaiian coral species under reduced pH simulating future ocean conditions. Coral colonies were sampled from up to six locations across a natural mosaic in seawater chemistry throughout Hawaiʻi and fragmented into clonal replicates maintained under both ambient and high pCO2 conditions. Broad sense heritability of calcification rates was high among all eight species, ranging from a low of 0.32 in Porites evermanni to a high of 0.61 in Porites compressa. The overall results were inconsistent with short-term acclimatization to the local environment or adaptation to the mean or ideal conditions. Similarly, in ‘local vs. foreign’ and ‘home vs. away’ tests there was no clear signature of local adaptation. Instead, the data are most consistent with a protected polymorphism as the mechanism which maintains differential pH tolerance within the populations. Substantial individual variation, coupled with high heritability and large population sizes, imply considerable scope for natural selection and adaptive capacity, which has major implications for evolutionary potential and management of corals in response to climate change.

scholarly journals Host shifts result in parallel genetic changes when viruses evolve in closely related species

2017 ◽  
Author(s):  
Ben Longdon ◽  
Jonathan P Day ◽  
Joel M Alves ◽  
Sophia CL Smith ◽  
Thomas M Houslay ◽  
...  
Keyword(s):  
Host Species ◽  
Related Species ◽  
Rna Virus ◽  
Parallel Evolution ◽  
Emerging Infectious Diseases ◽  
New Host ◽  
Closely Related Species ◽  
Genetic Changes ◽  
Host Shifts ◽  
Novel Host

AbstractHost shifts, where a pathogen invades and establishes in a new host species, are a major source of emerging infectious diseases. They frequently occur between related host species and often rely on the pathogen evolving adaptations that increase their fitness in the novel host species. To investigate genetic changes in novel hosts, we experimentally evolved replicate lineages of an RNA virus (Drosophila C Virus) in 19 different species of Drosophilidae and deep sequenced the viral genomes. We found a strong pattern of parallel evolution, where viral lineages from the same host were genetically more similar to each other than to lineages from other host species. When we compared viruses that had evolved in different host species, we found that parallel genetic changes were more likely to occur if the two host species were closely related. This suggests that when a virus adapts to one host it might also become better adapted to closely related host species. This may explain in part why host shifts tend to occur between related species, and may mean that when a new pathogen appears in a given species, closely related species may become vulnerable to the new disease.

scholarly journals RNA Virus Fidelity Mutants: A Useful Tool for Evolutionary Biology or a Complex Challenge?

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 600 ◽  
Author(s):  
Tiffany Kautz ◽  
Naomi Forrester
Keyword(s):  
Evolutionary Biology ◽  
Rna Viruses ◽  
Rna Virus ◽  
Large Population ◽  
Genome Replication ◽  
Population Sizes ◽  
Host Infection ◽  
Definition Of

RNA viruses replicate with low fidelity due to the error-prone nature of the RNA-dependent RNA polymerase, which generates approximately one mutation per round of genome replication. Due to the large population sizes produced by RNA viruses during replication, this results in a cloud of closely related virus variants during host infection, of which small increases or decreases in replication fidelity have been shown to result in virus attenuation in vivo, but not typically in vitro. Since the discovery of the first RNA virus fidelity mutants during the mid-aughts, the field has exploded with the identification of over 50 virus fidelity mutants distributed amongst 7 RNA virus families. This review summarizes the current RNA virus fidelity mutant literature, with a focus upon the definition of a fidelity mutant as well as methods to confirm any mutational changes associated with the fidelity mutant. Due to the complexity of such a definition, in addition to reports of unstable virus fidelity phenotypes, the future translational utility of these mutants and applications for basic science are examined.

scholarly journals Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations

2016 ◽  
Vol 283 (1836) ◽  
pp. 20160984 ◽  
Author(s):  
Héctor Cervera ◽  
Jasna Lalić ◽  
Santiago F. Elena
Keyword(s):  
Fitness Landscape ◽  
Rna Virus ◽  
Viral Evolution ◽  
Basin Of Attraction ◽  
Local Optimum ◽  
Historical Contingency ◽  
Recombination Rates ◽  
Local Optima ◽  
Adaptive Landscapes ◽  
Chance Events

Predicting viral evolution has proven to be a particularly difficult task, mainly owing to our incomplete knowledge of some of the fundamental principles that drive it. Recently, valuable information has been provided about mutation and recombination rates, the role of genetic drift and the distribution of mutational, epistatic and pleiotropic fitness effects. However, information about the topography of virus' adaptive landscapes is still scarce, and to our knowledge no data has been reported so far on how its ruggedness may condition virus' evolvability. Here, we show that populations of an RNA virus move efficiently on a rugged landscape and scape from the basin of attraction of a local optimum. We have evolved a set of Tobacco etch virus genotypes located at increasing distances from a local adaptive optimum in a highly rugged fitness landscape, and we observed that few evolved lineages remained trapped in the local optimum, while many others explored distant regions of the landscape. Most of the diversification in fitness among the evolved lineages was explained by adaptation, while historical contingency and chance events contribution was less important. Our results demonstrate that the ruggedness of adaptive landscapes is not an impediment for RNA viruses to efficiently explore remote parts of it.

scholarly journals Evolution by Small Steps and Rugged Landscapes in the RNA Virus ϕ6

Genetics ◽  
1999 ◽  
Vol 151 (3) ◽  
pp. 921-927 ◽  
Author(s):  
Christina L Burch ◽  
Lin Chao
Keyword(s):  
Adaptive Evolution ◽  
Deleterious Mutation ◽  
Rna Virus ◽  
Geometric Model ◽  
Viral Fitness ◽  
Adaptive Landscape ◽  
Step Size ◽  
Large Step ◽  
Population Sizes ◽  
Compensatory Mutations

Abstract Fisher’s geometric model of adaptive evolution argues that adaptive evolution should generally result from the substitution of many mutations of small effect because advantageous mutations of small effect should be more common than those of large effect. However, evidence for both evolution by small steps and for Fisher’s model has been mixed. Here we report supporting results from a new experimental test of the model. We subjected the bacteriophage ϕ6 to intensified genetic drift in small populations and caused viral fitness to decline through the accumulation of a deleterious mutation. We then propagated the mutated virus at a range of larger population sizes and allowed fitness to recover by natural selection. Although fitness declined in one large step, it was usually recovered in smaller steps. More importantly, step size during recovery was smaller with decreasing size of the recovery population. These results confirm Fisher’s main prediction that advantageous mutations of small effect should be more common. We also show that the advantageous mutations of small effect are compensatory mutations whose advantage is conditional (epistatic) on the presence of the deleterious mutation, in which case the adaptive landscape of ϕ6 is likely to be very rugged.

scholarly journals Determining asymptotically large population sizes in insect swarms

2014 ◽  
Vol 11 (99) ◽  
pp. 20140710 ◽  
Author(s):  
James G. Puckett ◽  
Nicholas T. Ouellette
Keyword(s):  
Group Dynamics ◽  
Large Population ◽  
Environmental Cues ◽  
Multi Agent Systems ◽  
Strong Constraint ◽  
Agent Systems ◽  
Self Organized ◽  
Large Numbers ◽  
Population Sizes ◽  
Multi Agent

Social animals commonly form aggregates that exhibit emergent collective behaviour, with group dynamics that are distinct from the behaviour of individuals. Simple models can qualitatively reproduce such behaviour, but only with large numbers of individuals. But how rapidly do the collective properties of animal aggregations in nature emerge with group size? Here, we study swarms of Chironomus riparius midges and measure how their statistical properties change as a function of the number of participating individuals. Once the swarms contain order 10 individuals, we find that all statistics saturate and the swarms enter an asymptotic regime. The influence of environmental cues on the swarm morphology decays on a similar scale. Our results provide a strong constraint on how rapidly swarm models must produce collective states. But our findings support the feasibility of using swarms as a design template for multi-agent systems, because self-organized states are possible even with few agents.

scholarly journals 2000 Fleming Lecture. The origin and evolution of hepatitis viruses in humans

2001 ◽  
Vol 82 (4) ◽  
pp. 693-712 ◽  
Author(s):  
Peter Simmonds
Keyword(s):  
Large Population ◽  
Human Populations ◽  
Hepatitis Viruses ◽  
Hepatitis G Virus ◽  
Origin And Evolution ◽  
Wide Range ◽  
Population Sizes ◽  
History Of ◽  
Virus C ◽  
Time Of Divergence

The spread and origins of hepatitis C virus (HCV) in human populations have been the subject of extensive investigations, not least because of the importance this information would provide in predicting clinical outcomes and controlling spread of HCV in the future. However, in the absence of historical and archaeological records of infection, the evolution of HCV and other human hepatitis viruses can only be inferred indirectly from their epidemiology and by genetic analysis of contemporary virus populations. Some information on the history of the latter may be obtained by dating the time of divergence of various genotypes of HCV, hepatitis B virus (HBV) and the non-pathogenic hepatitis G virus (HGV)/GB virus-C (GBV-C). However, the relatively recent times predicted for the origin of these viruses fit poorly with their epidemiological distributions and the recent evidence for species-associated variants of HBV and HGV/GBV-C in a wide range of non-human primates. The apparent conservatism of viruses over long periods implied by these latter observations may be the result of constraints on sequence change peculiar to viruses with single-stranded genomes, or with overlapping reading frames. Large population sizes and intense selection pressures that optimize fitness may be the factors that set virus evolution apart from that of their hosts.

scholarly journals Pairwise genetic interactions modulate lipid plasma levels and cellular uptake

2020 ◽  
Author(s):  
Magdalena Zimon ◽  
Yunfeng Huang ◽  
Anthi Trasta ◽  
Jimmy Z. Liu ◽  
Chia-Yen Chen ◽  
...  
Keyword(s):  
Complex Traits ◽  
Drug Target ◽  
Human Genetics ◽  
Large Population ◽  
Genetic Interactions ◽  
Model Systems ◽  
Lipid Lowering ◽  
Gene Pairs ◽  
Population Sizes ◽  
The Uk

SUMMARYGenetic interactions (GIs), the joint impact of different genes or variants on a phenotype, are foundational to the genetic architecture of complex traits. However, identifying GIs through human genetics is challenging since it necessitates very large population sizes, while findings from model systems not always translate to humans. Here, we combined exome-sequencing and genotyping in the UK Biobank with combinatorial RNA-interference (coRNAi) screening to systematically test for pairwise GIs between 30 lipid GWAS genes. Gene-based protein-truncating variant (PTV) burden analyses from 240,970 exomes revealed additive GIs for APOB with PCSK9 and LPL, respectively. Both, genetics and coRNAi identified additive GIs for 12 additional gene pairs. Overlapping non-additive GIs were detected only for TOMM40 at the APOE locus with SORT1 and NCAN. Our study identifies distinct gene pairs that modulate both, plasma and cellular lipid levels via additive and non-additive effects and nominates drug target pairs for improved lipid-lowering combination therapies.

Looking forwards and backwards in a bisexual moran model

1989 ◽  
Vol 26 (04) ◽  
pp. 880-885 ◽  
Author(s):  
K. Kämmerle
Keyword(s):  
Diffusion Approximation ◽  
Large Population ◽  
Extinction Probability ◽  
Single Pair ◽  
Approximation Methods ◽  
Moran Model ◽  
Population Sizes ◽  
Limit Result

In this paper a bisexual Moran model is introduced. The population consists of N pairs of individuals. At times t = 1, 2, ·· ·two individuals are born, who ‘choose their parents randomly' and independently of each other. Then one of the pairs is removed and replaced by the two individuals born at that instant. The extinction probability of the descendants of a single pair and the number of ancestors of a whole generation are studied. A limit result for large population sizes has been derived by diffusion approximation methods.

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