scholarly journals New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans

2019 ◽  
pp. 505-530 ◽  
Author(s):  
Lain Guio ◽  
Josefa González
Keyword(s):  
Population Dynamics ◽  
Transposable Elements ◽  
Genome Content

Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula

Gene ◽  
2009 ◽  
Vol 448 (2) ◽  
pp. 214-220 ◽  
Author(s):  
Dariusz Grzebelus ◽  
Mirosława Gładysz ◽  
Alicja Macko-Podgórni ◽  
Tomasz Gambin ◽  
Barbara Golis ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Transposable Elements ◽  
Medicago Truncatula ◽  
Inverted Repeat

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 A Comparative Analysis of L1 Retrotransposition Activities in Human Genomes Suggests an Ongoing Increase in L1 Number Despite an Evolutionary Trend Towards Lower Activity

2021 ◽  
Author(s):  
Sawsan Sami Wehbi ◽  
Heinrich zu Dohna
Keyword(s):  
Cell Culture ◽  
Population Dynamics ◽  
Comparative Analysis ◽  
Transposable Elements ◽  
Human Population ◽  
Population Level ◽  
Evolutionary Trend ◽  
Human Genomes ◽  
Long Interspersed Nuclear Elements ◽  
Insight Into

Abstract BackgroundLINE-1 (Long Interspersed Nuclear Elements, L1) retrotransposons are the only autonomously active transposable elements in the human genome. The evolution of L1 retrotransposition rates and its implications for L1 dynamics are poorly understood. Retrotransposition rates are commonly measured in cell culture-based assays, but it is unclear how well these measurements provide insight into L1 population dynamics. This study applied comparative methods to estimate parameters for the evolution of retrotransposition rates, and infer L1 dynamics from these estimates.ResultsOur results show that the rates at which new L1s emerge in the human population correlate positively to cell-culture based retrotransposition activities, that there is an evolutionary trend towards lower retrotransposition activity, and that this evolutionary trend is not sufficient to counter-balance the increase in L1s resulting from continuing retrotransposition. ConclusionsTogether, these findings support a model of the population-level L1 retrotransposition dynamics that is consistent with prior expectations and indicate the remaining gaps in the understanding of L1 dynamics in human genomes.

scholarly journals Transposable elements in natural populations with a mixture of selected and neutral insertion sites

1991 ◽  
Vol 57 (2) ◽  
pp. 127-134 ◽  
Author(s):  
Brian Charlesworth
Keyword(s):  
Population Dynamics ◽  
Transposable Elements ◽  
X Chromosome ◽  
Natural Populations ◽  
Element Abundance ◽  
Weak Selection ◽  
High Frequencies ◽  
Insertion Sites ◽  
Parameter Values

SummaryThis paper examines models of the population dynamics of transposable elements when chromosomal sites vary with respect to the effect on fitness of mutations caused by element insertions. Element abundance is assumed to be stabilised solely by the joint results of transposition, excision, and selection against insertional mutations. When there are only two classes of site, selected and neutral, it is hard to find parameter values for which numbers of elements are maintained that match the findings from surveys of Drosophila populations, as elements tend to accumulate at high frequencies at the neutral sites. It is similarly hard to produce realistic equilibria with three classes of site (strongly selected, weakly selected, and neutral), when elements can transpose out of the neutral sites. If transposition from neutral sites is impossible, as might be the case for elements inserted into centric heterochromatin, then realistic equilibria can be generated if there is very weak selection against elements inserted into the majority of non-neutral sites. This model predicts a modest over-representation of elements at the neutral sites. It also predicts that elements should be under-represented on the X chromosome compared with the autosomes, but this is not generally found to be the case. It is concluded that selection against insertional mutations is unlikely to be the major factor involved in the containment of element abundance.

scholarly journals A comparative analysis of L1 retrotransposition activities in human genomes suggests an ongoing increase in L1 number despite an evolutionary trend towards lower activity

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sawsan Sami Wehbi ◽  
Heinrich zu Dohna
Keyword(s):  
Cell Culture ◽  
Population Dynamics ◽  
Comparative Analysis ◽  
Transposable Elements ◽  
Human Population ◽  
Population Level ◽  
Evolutionary Trend ◽  
Human Genomes ◽  
Long Interspersed Nuclear Elements ◽  
Insight Into

Abstract Background LINE-1 (Long Interspersed Nuclear Elements, L1) retrotransposons are the only autonomously active transposable elements in the human genome. The evolution of L1 retrotransposition rates and its implications for L1 dynamics are poorly understood. Retrotransposition rates are commonly measured in cell culture-based assays, but it is unclear how well these measurements provide insight into L1 population dynamics. This study applied comparative methods to estimate parameters for the evolution of retrotransposition rates, and infer L1 dynamics from these estimates. Results Our results show that the rates at which new L1s emerge in the human population correlate positively to cell-culture based retrotransposition activities, that there is an evolutionary trend towards lower retrotransposition activity, and that this evolutionary trend is not sufficient to counter-balance the increase in active L1s resulting from continuing retrotransposition. Conclusions Together, these findings support a model of the population-level L1 retrotransposition dynamics that is consistent with prior expectations and indicate the remaining gaps in the understanding of L1 dynamics in human genomes.

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