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evolutionary dynamics and evolutionary history in the RTE clade of non-LTR retrotransposons

MOLECULAR BIOLOGY AND EVOLUTION 2001年第10期18卷 1849-1863页

作者： Zupunski, V Gubensek, F Kordis, D Jozef Stefan Inst Dept Biochem & Mol Biol Ljubljana 1001 Slovenia Univ Ljubljana Dept Chem & Biochem Fac Chem & Chem Technol Ljubljana Slovenia

This study examined the evolutionary dynamics of Bov-B LINEs in vertebrates and the evolution of the RTE clade of non-LTR retrotransposons. The first full-length reptilian Bov-B LINE clement is described;it is 3.2 kb in length, with a structural organization typical of the RTE clade of non-LTR retrotransposons. The long-term evolution of Bov-B LINEs was studied in 10 species of Squamata by analysis of a PCR-amplified 1.8-kb fragment encoding part of apurinic/apyrmidinic endonuclease, the intervening domain, and the palm/fingers subdomain of reverse transcriptase. A very high level of conservation in Squamata Bov-B long interspersed nuclear elements has been found, reaching 86% identity in the nearly 600 amino acids of ORF2. The same level of conservation exists between the ancestral snake lineage and Ruminantia. Such a high level is exceptional when compared with the level of conservation observed in nuclear and mitochondrial proteins and in other transposable elements. The RTE clade has been found to be much more widely distributed than previously thought, and novel representatives have been discovered in plants, brown algae, annelids, crustaceans, mollusks, echinoderms, and teleost fishes. evolutionary relationships in the RTE clade were deduced at the amino acid level from three separate regions of ORF2. By using different independent methods, including the divergence-versus-age analysis, several examples of horizontal transfer in the RTE clade were recognized, with important implications for the existence of HT in non-LTR retrotransposons.

关键词： non-LTR retrotransposon RTE clade Bov-B LINE horizontal transfer evolutionary dynamics

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evolutionary dynamics of the island model with stochastic resetting

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JOURNAL OF THE KOREAN PHYSICAL SOCIETY 2022年第12期81卷 1274-1279页

作者： Kang, Yung-Gyung Park, Jeong-Man Hanshin Univ Sch Comp Engn Osan 18101 South Korea Catholic Univ Korea Dept Phys Bucheon 14662 South Korea

We study the evolutionary dynamics of the island model which consists of populations confined to two islands with stochastic resetting. The populations on islands follow the evolutionary dynamics. They reproduce according to their fitnesses, die at random, and migrate between two islands. In addition to the evolutionary dynamics, we introduce the stochastic resetting process in the dynamics, by which the state of the system is reset to a certain specified state at constant rate. Without resetting, it has been shown that there is a continuous phase transition in the subpopulations as the migration rate increases. When the system is reset stochastically, depending on the reset state and the resetting rate, the subpopulation distribution of a certain species exhibits a maximum at a nontrivial value of the resetting rate, whereas the continuous phase transition disappears for any non-vanishing value of the resetting rate.

关键词： evolutionary dynamics Island model Stochastic resetting

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evolutionary dynamics of giant viruses and their virophages

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ECOLOGY AND EVOLUTION 2013年第7期3卷 2103-2115页

作者： Wodarz, Dominik Univ Calif Irvine Dept Ecol & Evolutionary Biol Irvine CA 92697 USA

Giant viruses contain large genomes, encode many proteins atypical for viruses, replicate in large viral factories, and tend to infect protists. The giant virus replication factories can in turn be infected by so called virophages, which are smaller viruses that negatively impact giant virus replication. An example is Mimiviruses that infect the protist Acanthamoeba and that are themselves infected by the virophage Sputnik. This study examines the evolutionary dynamics of this system, using mathematical models. While the models suggest that the virophage population will evolve to increasing degrees of giant virus inhibition, it further suggests that this renders the virophage population prone to extinction due to dynamic instabilities over wide parameter ranges. Implications and conditions required to avoid extinction are discussed. Another interesting result is that virophage presence can fundamentally alter the evolutionary course of the giant virus. While the giant virus is predicted to evolve toward increasing its basic reproductive ratio in the absence of the virophage, the opposite is true in its presence. Therefore, virophages can not only benefit the host population directly by inhibiting the giant viruses but also indirectly by causing giant viruses to evolve toward weaker phenotypes. Experimental tests for this model are suggested.

关键词： evolutionary dynamics giant viruses mathematical models virophages

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evolutionary dynamics on small-order graphs

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JOURNAL OF INTERDISCIPLINARY MATHEMATICS 2009年第2期12卷 129-140页

作者： Broom, M. Rychtar, J. Stadler, B. Univ Sussex Dept Math Brighton BN1 9RF E Sussex England Univ North Carolina Greensboro Dept Math & Stat Greensboro NC 27402 USA Univ North Carolina Greensboro Dept Comp Sci Greensboro NC 27402 USA

We study the stochastic birth-death model for structured finite populations popularized by Lieberman et al. [E. Lieberman, C. Hauert and M. A. Nowak (2005), evolutionary dynamics on graphs, Nature, Vol. 433, pp. 312-316]. We consider all possible connected undirected graphs of orders three through eight. For each graph, using the Monte Carlo Markov Chain simulations, we determine the fixation probability of a mutant introduced at every possible vertex. We show that the fixation probability depends on the vertex and on the graph. A randomly placed mutant has the highest chances of fixation in a star graph, closely followed by star-like graphs, and the fixation probability is lowest for regular and almost regular graphs. We also find that within a fixed graph, the fixation probability of a mutant has a negative correlation with the degree of the starting vertex.

关键词： evolutionary dynamics fixation probability heterogeneous graphs star graphs

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evolutionary dynamics may eliminate all strategies used in correlated equilibrium

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MATHEMATICAL SOCIAL SCIENCES 2008年第1期56卷 27-43页

作者： Viossat, Yannick Univ Paris 09 CEREMADE CNRS UMR7534 F-75016 Paris France

We show on a 4 x 4 example that many dynamics may eliminate all strategies used in correlated equilibria, and this for an open set of games. This holds for the best-response dynamics, the Brown-von Neumann-Nash dynamics and any monotonic or weakly sign-preserving dynamics satisfying some standard regularity conditions. For the replicator dynamics and the best-response dynamics, elimination of all strategies used in correlated equilibrium is shown to be robust to the addition of mixed strategies as new pure strategies. (C) 2008 Elsevier B.V. All rights reserved.

关键词： correlated equilibrium evolutionary dynamics elimination as-if rationality

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evolutionary dynamics with Migration by Using the Fast-Mode Elimination Method

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JOURNAL OF THE KOREAN PHYSICAL SOCIETY 2017年第9期71卷 528-537页

作者： Kang, Yung-Gyung Park, Jeong-Man Hanshin Univ Sch Comp Engn Osan 18101 South Korea Catholic Univ Korea Dept Phys Bucheon 14662 South Korea

We investigate the evolutionary dynamics of a Moran model which consists of subdivided populations of individuals confined to a set of islands. In subdivided populations, migration acts with selection and genetic drift to determine the evolutionary dynamics. The individuals are assumed to be haploid with two types. They reproduce according to their fitness values, die at random, and migrate between the islands. The evolutionary dynamics of an individual based model is formulated in terms of a master equation and is approximated as the multidimensional Fokker-Planck equation (FPE) and the coupled non-linear stochastic differential equations (SDEs) with multiplicative noise. We first analyze the deterministic part of the SDEs to obtain the fixed points and determine the stability of each fixed point. We find that there is only one stable fixed point to which all populations started from any initial distribution other than the unstable absorbing points will evolve in both the symmetric and antisymmetric selection schemes. Next, we take demographic stochasticity into account and analyze the FPE by eliminating the fast variable to reduce the coupled two-variable FPE to the single-variable FPE. We derive a quasi-stationary distribution of the reduced FPE and predict the fixation probabilities and the mean fixation times to absorbing states. We also carry out numerical simulations in the form of the Gillespie algorithm and find that the results of simulations are consistent with the analytic predictions.

关键词： evolutionary dynamics Demographic stochasticity Fast-mode elimination

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evolutionary dynamics of the Trivers-Willard effect: A nonparametric approach

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ECOLOGY AND EVOLUTION 2021年第18期11卷 12676-12685页

作者： Borgstede, Matthias Univ Bamberg Markuspl 3 D-96047 Bamberg Germany

The Trivers-Willard hypothesis (TWH) states that parents in good condition tend to bias their offspring sex ratio toward the sex with a higher variation in reproductive value, whereas parents in bad condition favor the opposite sex. Although the TWH has been generalized to predict various Trivers-Willard effects (TWE) depending on the life cycle of a species, existing work does not sufficiently acknowledge that sex-specific reproductive values depend on the relative abundances of males and females in the population. If parents adjust their offspring sex ratio according to the TWE, offspring reproductive values will also change. This should affect the long-term evolutionary dynamics and might lead to considerable deviations from the original predictions. In this paper, I model the full evolutionary dynamics of the TWE, using a published two-sex integral projection model for the Columbian ground squirrel (Urocitellus columbianus). Offspring sex ratio is treated as a nonparametric continuous function of maternal condition. evolutionary change is treated as the successive invasion of mutant strategies. The simulation is performed with varying starting conditions until an evolutionarily stable strategy (ESS) is reached. The results show that the magnitude of the evolving TWE can be far greater than previously predicted. Furthermore, evolutionary dynamics show considerable nonlinearities before settling at an ESS. The nonlinear effects depend on the starting conditions and indicate that evolutionary change is fastest when starting at an extremely biased sex ratio and that evolutionary change is weaker for parents of high condition. The results show neither a tendency to maximize average population fitness nor to minimize the deviation between offspring sex ratio and offspring reproductive value ratio. The study highlights the importance of dynamic feedback in models of natural selection and provides a new methodological framework for analyzing the evolution of continuous

关键词： continuous strategies evolutionary dynamics evolutionary invasion analysis integral projection models Trivers-Willard hypothesis two-sex models

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evolutionary dynamics of transposable elements during silkworm domestication

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GENES & GENOMICS 2018年第10期40卷 1041-1051页

作者： Han, Min-Jin Xu, Hong-En Xiong, Xiao-Min Zhang, Hua-Hao Southwest Univ State Key Lab Silkworm Genome Biol Key Lab Sericulture Funct Genom & Biotechnol Agr Minist Chongqing 400715 Peoples R China Zhengzhou Univ Zhengzhou Henan Peoples R China Jiujiang Univ Clin Med Coll Jiujiang 332000 Peoples R China Jiujiang Univ Coll Pharm & Life Sci Jiujiang 332000 Peoples R China

Although there are some documented examples on population dynamics of transposable elements (TEs) in model organisms, the evolutionary dynamics of TEs in domesticated species has not been systematically investigated. The objective of this study is to understand population dynamics of TEs during silkworm domestication. In this work, using transposon-display we examined the polymorphism of seven TE families [they represent about 59% of silkworm (Bombyx mori) total TE content] in four domesticated silkworm populations and one wild silkworm population. Maximum likelihood (ML) was used to estimate selection pressure. Population differentiation and structure were performed by using AMOVA analysis and program DISTRUCT, respectively. The results of transposon-display showed that significant differentiation occurred between the domesticated silkworm and wild silkworm. These TEs have experienced expansions and fixation in the domesticated silkworm but not in wild silkworm. Furthermore, the ML results indicated that purifying selection of TEs in the domesticated silkworm were significantly weaker than that in the wild silkworm. Interestingly, an adaptation insertion induced by BmMITE-2 was found, and this insertion can reduce the polymorphism of the flanking regions of its neighboring COQ7 gene. Our results suggested that TEs expanded and were fixed in the domesticated silkworm might result from demographic effects and artificial selection during domestication. We concluded that the data presented in this study have general implication in animal and crop improvements as well as in domestication of new species.

关键词： Transposable elements evolutionary dynamics Domestication Weak selection Silkworm

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evolutionary dynamics and significance of multiple subclonal mutations in cancer

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DNA REPAIR 2017年 56卷 7-15页

作者： Beckman, Robert A. Loeb, Lawrence A. Georgetown Univ Med Ctr Lombardi Comprehens Canc Ctr Dept Oncol Washington DC 20007 USA Georgetown Univ Med Ctr Lombardi Comprehens Canc Ctr Dept Biostat Bioinfonnat & Biomath Washington DC 20007 USA Georgetown Univ Med Ctr Innovat Ctr Biomed Informat Washington DC 20007 USA Univ Washington Sch Med Joseph Gottstein Mem Canc Res Lab Dept Pathol Seattle WA 98195 USA Univ Washington Sch Med Joseph Gottstein Mem Canc Res Lab Dept Biochem Seattle WA 98195 USA

For the last 40 years the authors have collaborated on trying to understand the complexities of human cancer by formulating testable mathematical models that are based on mutation accumulation in human malignancies. We summarize the concepts encompassed by multiple mutations in human cancers in the context of source, accumulation during carcinogenesis and tumor progression, and therapeutic consequences. We conclude that the efficacious treatment of human cancer by targeted therapy will involve individualized, uniquely directed specific agents singly and in simultaneous combinations, and take into account the importance of targeting resistant subclonal mutations, particularly those subclones with alterations in DNA repair genes, DNA polymerase, and other genes required to maintain genetic stability.

关键词： Cancer Mutator hypothesis DNA replication DNA repair Carcinogenesis evolutionary dynamics Duplex sequencing Mathematical models

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evolutionary dynamics of Multi-agent Formation

Evolutionary Dynamics of Multi-agent Formation

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21st Chinese Control and Decision Conference

作者： Qin, Jin Ban, Xiaojuan Li, Xin Univ Sci & Technol Beijing Coll Informat Engn Beijing 100083 Peoples R China

ISBN: (纸本)9781424427239

To probe into the internal mechanism of multi-agent formation, game theory is used to model the interaction between agents and Win-Stay-Lose-Shift strategy to instruct agents' action. Equations are introduced to formulate how agents update their positions. The Win-Stay-Lose-Shift strategy along with the update equations depicts the dynamics of multi-agent formation. And simulations are designed and performed to observe the development of multi-agent formation. The results of simulation show the feasibility of the idea in this paper.

关键词： Multi-agent formation evolutionary dynamics Game theory Simulation

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