João M F Silva, María J Olmo-Uceda, Valerie J Morley, Paul E Turner, Santiago F Elena
{"title":"泰勒幂律规定了病毒进化过程中等位基因频率的动态变化,以响应宿主的变化。","authors":"João M F Silva, María J Olmo-Uceda, Valerie J Morley, Paul E Turner, Santiago F Elena","doi":"10.1098/rsif.2025.0146","DOIUrl":null,"url":null,"abstract":"<p><p>Sudden and gradual changes from permissive to resistant hosts affect viral fitness, virulence and rates of molecular evolution. We analysed the roles of stochasticity and selection in evolving populations of Sindbis virus under different rates of host replacement. First, approximate Markov models within the Wright-Fisher diffusion framework revealed a reduction in effective population size by approximately half under sudden host changes. These scenarios were also associated with fewer weak beneficial mutations. Second, genetic distance between populations at consecutive time points indicated that populations undergoing gradual host changes evolved steadily until the original host disappeared. Distances to the ancestral sequence in these cases exhibited occasional leapfrog phenomena, where the rise of certain haplotypes is not predictable based on their relatedness to previously dominant ones. In contrast, populations exposed to sudden changes exhibited less-stable compositions and diverged from the ancestral sequence at a consistent rate. Third, we observed that the distribution of allele frequencies followed Taylor's Power Law. Both treatments exhibited high levels of allele aggregation and significant fluctuations, with neutral, beneficial and deleterious alleles distinguishable by their behaviour and position on Taylor's plot. Finally, we found evidence that the host replacement regime influences the temporal distribution of mutations across the genome.</p>","PeriodicalId":17488,"journal":{"name":"Journal of The Royal Society Interface","volume":"22 228","pages":"20250146"},"PeriodicalIF":3.5000,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12303090/pdf/","citationCount":"0","resultStr":"{\"title\":\"Taylor's Power Law rules the dynamics of allele frequencies during viral evolution in response to host changes.\",\"authors\":\"João M F Silva, María J Olmo-Uceda, Valerie J Morley, Paul E Turner, Santiago F Elena\",\"doi\":\"10.1098/rsif.2025.0146\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Sudden and gradual changes from permissive to resistant hosts affect viral fitness, virulence and rates of molecular evolution. We analysed the roles of stochasticity and selection in evolving populations of Sindbis virus under different rates of host replacement. First, approximate Markov models within the Wright-Fisher diffusion framework revealed a reduction in effective population size by approximately half under sudden host changes. These scenarios were also associated with fewer weak beneficial mutations. Second, genetic distance between populations at consecutive time points indicated that populations undergoing gradual host changes evolved steadily until the original host disappeared. Distances to the ancestral sequence in these cases exhibited occasional leapfrog phenomena, where the rise of certain haplotypes is not predictable based on their relatedness to previously dominant ones. In contrast, populations exposed to sudden changes exhibited less-stable compositions and diverged from the ancestral sequence at a consistent rate. Third, we observed that the distribution of allele frequencies followed Taylor's Power Law. Both treatments exhibited high levels of allele aggregation and significant fluctuations, with neutral, beneficial and deleterious alleles distinguishable by their behaviour and position on Taylor's plot. Finally, we found evidence that the host replacement regime influences the temporal distribution of mutations across the genome.</p>\",\"PeriodicalId\":17488,\"journal\":{\"name\":\"Journal of The Royal Society Interface\",\"volume\":\"22 228\",\"pages\":\"20250146\"},\"PeriodicalIF\":3.5000,\"publicationDate\":\"2025-07-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12303090/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of The Royal Society Interface\",\"FirstCategoryId\":\"103\",\"ListUrlMain\":\"https://doi.org/10.1098/rsif.2025.0146\",\"RegionNum\":2,\"RegionCategory\":\"综合性期刊\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/7/16 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q1\",\"JCRName\":\"MULTIDISCIPLINARY SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of The Royal Society Interface","FirstCategoryId":"103","ListUrlMain":"https://doi.org/10.1098/rsif.2025.0146","RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/7/16 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"MULTIDISCIPLINARY SCIENCES","Score":null,"Total":0}
Taylor's Power Law rules the dynamics of allele frequencies during viral evolution in response to host changes.
Sudden and gradual changes from permissive to resistant hosts affect viral fitness, virulence and rates of molecular evolution. We analysed the roles of stochasticity and selection in evolving populations of Sindbis virus under different rates of host replacement. First, approximate Markov models within the Wright-Fisher diffusion framework revealed a reduction in effective population size by approximately half under sudden host changes. These scenarios were also associated with fewer weak beneficial mutations. Second, genetic distance between populations at consecutive time points indicated that populations undergoing gradual host changes evolved steadily until the original host disappeared. Distances to the ancestral sequence in these cases exhibited occasional leapfrog phenomena, where the rise of certain haplotypes is not predictable based on their relatedness to previously dominant ones. In contrast, populations exposed to sudden changes exhibited less-stable compositions and diverged from the ancestral sequence at a consistent rate. Third, we observed that the distribution of allele frequencies followed Taylor's Power Law. Both treatments exhibited high levels of allele aggregation and significant fluctuations, with neutral, beneficial and deleterious alleles distinguishable by their behaviour and position on Taylor's plot. Finally, we found evidence that the host replacement regime influences the temporal distribution of mutations across the genome.
期刊介绍:
J. R. Soc. Interface welcomes articles of high quality research at the interface of the physical and life sciences. It provides a high-quality forum to publish rapidly and interact across this boundary in two main ways: J. R. Soc. Interface publishes research applying chemistry, engineering, materials science, mathematics and physics to the biological and medical sciences; it also highlights discoveries in the life sciences of relevance to the physical sciences. Both sides of the interface are considered equally and it is one of the only journals to cover this exciting new territory. J. R. Soc. Interface welcomes contributions on a diverse range of topics, including but not limited to; biocomplexity, bioengineering, bioinformatics, biomaterials, biomechanics, bionanoscience, biophysics, chemical biology, computer science (as applied to the life sciences), medical physics, synthetic biology, systems biology, theoretical biology and tissue engineering.