scholarly journals The population dynamics of transposable elements

1983 ◽  
Vol 42 (1) ◽  
pp. 1-27 ◽  
Author(s):  
Brian Charlesworth ◽  
Deborah Charlesworth
Keyword(s):  
Population Dynamics ◽  
Transposable Elements ◽  
Copy Number ◽  
Probability Distributions ◽  
General Pattern ◽  
Simulation Models ◽  
Theoretical Models ◽  
Infinite Population ◽  
Individual Fitness ◽  
Set Up

SUMMARYThis paper describes analytical and simulation models of the population dynamics of transposable elements in randomly mating populations. The models assume a finite number of chromosomal sites that are occupable by members of a given family of elements. Element frequencies can change as a result of replicative transposition, loss of elements from occupied sites, selection on copy number per individual, and genetic drift. It is shown that, in an infinite population, an equilibrium can be set up such that not all sites in all individuals are occupied, allowing variation between individuals in both copy number and identity of occupied sites, as has been observed for several element families in Drosophila melanogaster. Such an equilibrium requires either regulation of transposition rate in response to copy number per genome, a sufficiently strongly downwardly curved dependence of individual fitness on copy number, or both. The probability distributions of element frequencies, generated by the effects of finite population size, are derived on the assumption of independence between different loci, and compared with simulation results. Despite some discrepancies due to violation of the independence assumption, the general pattern seen in the simulations agrees quite well with theory.Data from Drosophila population studies are compared with the theoretical models, and methods of estimating the relevant parameters are discussed.

scholarly journals The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. I. Element frequencies and distribution

1992 ◽  
Vol 60 (2) ◽  
pp. 103-114 ◽  
Author(s):  
Brian Charlesworth ◽  
Angela Lapid ◽  
Darlene Canada
Keyword(s):  
Population Dynamics ◽  
Drosophila Melanogaster ◽  
Linkage Disequilibrium ◽  
Transposable Elements ◽  
Copy Number ◽  
Polytene Chromosomes ◽  
Chromosome Band ◽  
High Frequencies ◽  
Copy Numbers

SummaryData were collected on the distribution of nine families of transposable elements among second and third chromosomes isolated from a natural population of Drosophila melanogaster, by means of in situ hybridization of element probes to polytene chromosomes. It was found that the copy numbers per chromosome in the distal sections of the chromosome arms followed a Poisson distribution. Elements appeared to be distributed randomly along the distal sections of the chromosome arms. There was no evidence for linkage disequilibrium in the distal sections of the chromosomes, but some significant disequilibrium was detected in proximal regions. There were many significant correlations between different element families with respect to the identity of the sites that were occupied in the sample. There were also significant correlations between families with respect to sites at which elements achieved relatively high frequencies. Element frequencies per chromosome band were generally low in the distal sections, but were higher proximally. These results are discussed in the light of models of the population dynamics of transposable elements. It is concluded that they provide strong evidence for the operation of a force or forces opposing transpositional increase in copy number. The data suggest that the rate of transposition perelement per generation is of the order of 10−4, for the elements included in this study.

POPULATION DYNAMICS OF TRANSPOSABLE ELEMENTS: COPY NUMBER REGULATION AND SPECIES INVASION REQUIREMENTS

2005 ◽  
Vol 13 (04) ◽  
pp. 455-475 ◽  
Author(s):  
CLAUDIO J. STRUCHINER ◽  
MARGARET G. KIDWELL ◽  
JOSÉ M. C. RIBEIRO
Keyword(s):  
Population Dynamics ◽  
Transposable Elements ◽  
Parameter Space ◽  
Copy Number ◽  
Host Population ◽  
Reproductive Capacity ◽  
Dynamics Model ◽  
Population Extinction ◽  
Population Dynamics Model ◽  
Copy Number Regulation

A deterministic population dynamics model of the spread of transposable elements (TE) in sexually reproducing populations is presented. The population is modeled by a three-parameter equation describing host reproductive capacity, population size and the strength of the density dependence, while TE dynamics were modeled based also on three parameters, the maximum ability of the element to copy itself in the absence of regulation (T0), the regulatory effect of copy number decreasing transposition (C0.5), and the deleterious effect of each new transposition on host fitness (d). The mechanism of transposition control is therefore a function of the number of new TE copies. Our results indicate that non-regulated elements cannot fix in host populations, and that prediction of stable copy number following successful invasion is mainly a function of the combination of T0 and C0.5 values. Fitness reduction does not affect the final copy number after successful invasion of the element. Fitness reduction, however, will affect the surface of the {T0 × C0.5} parameter space leading to successful invasion of the TE. Invasion of host populations by eight or more individuals containing elements with appropriate parameters will lead to successful element fixation at any size of the host population. Host population extinction due to the invasion of TE's is observed in a small area of the {T0 × C0.5} parameter space. These results are qualitatively preserved under alternative choices for the shape of the functions defining regulation of transposition and distinct sets of parameters determining host population dynamics.

scholarly journals Inferred Clades of Transposable Elements in Drosophila Suggest Co-evolution with piRNAs

2021 ◽  
Author(s):  
Iskander Said ◽  
Michael P. McGurk ◽  
Andrew G. Clark ◽  
Daniel A. Barbash
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Transposable Elements ◽  
Copy Number ◽  
Population Genetic ◽  
General Pattern ◽  
Sequence Evolution ◽  
Genetic Theory ◽  
Copy Number Selection ◽  
Eukaryotic Genomes

AbstractTransposable elements (TEs) are self-replicating “genetic parasites” ubiquitous to eukaryotic genomes. In addition to conflict between TEs and their host genomes, TEs of the same family are in competition with each other. They compete for the same genomic niches while experiencing the same regime of copy-number selection. This suggests that competition among TEs may favor the emergence of new variants that can outcompete their brethren. To investigate the sequence evolution of TEs, we developed a method to infer clades: collections of TEs that share SNP variants and represent distinct TE family lineages. We applied this method to a panel of 85 Drosophila melanogaster genomes and found that the genetic variation of several TE families shows significant population structure that arises from the population-specific expansions of single clades. We used population genetic theory to classify these clades into younger versus older clades and found that younger clades are associated with a greater abundance of sense and antisense piRNAs per copy than older ones. Further, we find that the abundance of younger, but not older clades, is positively correlated with antisense piRNA production, suggesting a general pattern where hosts preferentially produce antisense piRNAs from recently active TE variants. Together these findings suggest a co-evolution of TEs and hosts, where new TE variants arise by mutation, then increase in copy number, and the host then responds by producing antisense piRNAs which may be used to silence these emerging variants.

scholarly journals Population dynamics of the copia, mdg1, mdg3, gypsy, and P transposable elements in a natural population of Drosophila melanogaster

1994 ◽  
Vol 63 (3) ◽  
pp. 197-212 ◽  
Author(s):  
C. Biémont ◽  
F. Lemeunier ◽  
M. P. Garcia Guerreiro ◽  
J. F. Brookfield ◽  
C. Gautier ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transposable Elements ◽  
Natural Population ◽  
Copy Number ◽  
Population Biology ◽  
Insertion Site ◽  
Polytene Chromosomes ◽  
Sharp Decrease ◽  
Theoretical Models ◽  
X Chromosomes

SummaryThe insertion site polymorphism of the copia, mdg1, mdg3, gypsy, and P transposable elements was analysed by in situ hybridization to the polytene chromosomes in genomes of males from a natural population of Drosophila melanogaster. Parameters of various theoretical models of the population biology of transposable elements were estimated from our data, and different hypotheses explaining TE copy number containment were tested. The copia, mdg1 and gypsy elements show evidence for a deficiency of insertions on the X chromosomes, a result consistent with selection against the mutational effects of insertions. On the contrary, mdg3 and P copy numbers fit a neutral model with a balance between regulated transposition and excisions. There is no strong evidence of a systematic accumulation of elements in the distal and proximal regions of the chromosomes where crossing over and ectopic exchanges are reduced. For all chromosome arms but 3L, however, the TE site density increases from the proximal to the distal parts of the chromosomes (the centromeric regions were excluded in this analysis) with sometimes a sharp decrease in density at the extreme tip, following in part the exchange coefficient. The way the copy number of TEs is contained in genomes depends thus on the element considered, and on various forces acting simultaneously, indicating that models of TE dynamics should include details of each element.

scholarly journals Quantitative investigation reveals distinct phases in Drosophila sleep

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xiaochan Xu ◽  
Wei Yang ◽  
Binghui Tian ◽  
Xiuwen Sui ◽  
Weilai Chi ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
General Pattern ◽  
Model Organism ◽  
Infrared Camera ◽  
Fruit Fly ◽  
Genetic Dissection ◽  
Power Law Distribution ◽  
Quantitative Investigation ◽  
Waking Up ◽  
Set Up

AbstractThe fruit fly, Drosophila melanogaster, has been used as a model organism for the molecular and genetic dissection of sleeping behaviors. However, most previous studies were based on qualitative or semi-quantitative characterizations. Here we quantified sleep in flies. We set up an assay to continuously track the activity of flies using infrared camera, which monitored the movement of tens of flies simultaneously with high spatial and temporal resolution. We obtained accurate statistics regarding the rest and sleep patterns of single flies. Analysis of our data has revealed a general pattern of rest and sleep: the rest statistics obeyed a power law distribution and the sleep statistics obeyed an exponential distribution. Thus, a resting fly would start to move again with a probability that decreased with the time it has rested, whereas a sleeping fly would wake up with a probability independent of how long it had slept. Resting transits to sleeping at time scales of minutes. Our method allows quantitative investigations of resting and sleeping behaviors and our results provide insights for mechanisms of falling into and waking up from sleep.

scholarly journals Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome

PLoS Genetics ◽  
2014 ◽  
Vol 10 (4) ◽  
pp. e1004298 ◽  
Author(s):  
Concepcion M. Diez ◽  
Esteban Meca ◽  
Maud I. Tenaillon ◽  
Brandon S. Gaut
Keyword(s):  
Zea Mays ◽  
Transposable Elements ◽  
Copy Number ◽  
Host Responses ◽  
Number Dynamics

Numerical Studies on Size Effect Behaviors of Glassy Polymers Based on Strain Gradient Elastoviscoplastic Model

2018 ◽  
Vol 86 (2) ◽  
Author(s):  
Yujun Deng ◽  
Jin Wang ◽  
Peiyun Yi ◽  
Linfa Peng ◽  
Xinmin Lai ◽  
...  
Keyword(s):  
Finite Element ◽  
Size Effect ◽  
Strain Gradient ◽  
Simulation Models ◽  
Theoretical Models ◽  
Deformation Energy ◽  
Glassy Polymers ◽  
Traditional Theory ◽  
Fe Model ◽  
Processing Load

The improvement of the accuracy and efficiency of microforming process of polymers is of great significance to meet the miniaturization of polymeric components. When the nonuniform deformation is reduced to the microscopic scale, however, the mechanics of polymers shows a strong reinforcement behavior. Traditional theoretical models of polymers which have not considered material feature lengths are difficult to describe the size effect in micron scale, and the process simulation models based on the traditional theory could not provide effective and precise guidance for polymer microfabrication techniques. The work reported here proposed strategies to simulate size effect behaviors of glassy polymers in microforming process. First, the strain gradient elastoviscoplastic model was derived to describe the size affected behaviors of glassy polymers. Based on the proposed constitutive model, an eight-node finite element with the consideration of nodes' rotation was developed. Then, the proposed finite element method was verified by comparisons between experiments and simulations for both uniaxial compression and microbending. Finally, based on the FE model, under the consideration of the effect of rotation gradient, the strain distribution, the deformation energy, and the processing load were discussed. These strategies are immediately applicable to other wide-ranging classes of microforming process of glassy polymers, thereby foreshadowing their use in process optimizations of microfabrication of polymer components.

scholarly journals HITS: Hurricane Intensity and Track Simulator with North Atlantic Ocean Applications for Risk Assessment

2015 ◽  
Vol 54 (7) ◽  
pp. 1620-1636 ◽  
Author(s):  
J. Nakamura ◽  
U. Lall ◽  
Y. Kushnir ◽  
B. Rajagopalan
Keyword(s):  
Tropical Cyclone ◽  
North Atlantic Ocean ◽  
Probability Distributions ◽  
Model Fitting ◽  
Simulation Models ◽  
Annual Probability ◽  
Cyclone Tracks ◽  
Probabilistic Coverage ◽  
Tropical Cyclone Tracks

AbstractA nonparametric stochastic model is developed and tested for the simulation of tropical cyclone tracks. Tropical cyclone tracks demonstrate continuity and memory over many time and space steps. Clusters of tracks can be coherent, and the separation between clusters may be marked by geographical locations where groups of tracks diverge as a result of the physics of the underlying process. Consequently, their evolution may be non-Markovian. Markovian simulation models, as are often used, may produce tracks that potentially diverge or lose memory quicker than happens in nature. This is addressed here through a model that simulates tracks by randomly sampling track segments of varying length, selected from historical tracks. For performance evaluation, a spatial grid is imposed on the domain of interest. For each grid box, long-term tropical cyclone risk is assessed through the annual probability distributions of the number of storm hours, landfalls, winds, and other statistics. Total storm length is determined at birth by local distribution, and movement to other tropical cyclone segments by distance to neighbor tracks, comparative vector, and age of track. The model is also applied to the conditional simulation of hurricane tracks from specific positions for hurricanes that were not included in the model fitting so as to see whether the probabilistic coverage intervals properly cover the subsequent track. Consequently, tests of both the long-term probability distributions of hurricane landfall and of event simulations from the model are provided.

Sign in / Sign up

Export Citation Format

Share Document