Evolvability, epigenetics and transposable elements

2011 ◽  
Vol 2 (5) ◽  
pp. 333-341 ◽  
Author(s):  
Marie Fablet ◽  
Cristina Vieira
Keyword(s):  
Transposable Elements ◽  
Copy Number ◽  
High Rate ◽  
Adaptive Mutations ◽  
A Genome ◽  
Copy Number Regulation ◽  
The Way

AbstractEvolvability can be defined as the capacity of an individual to evolve and thus to capture adaptive mutations. Transposable elements (TE) are an important source of mutations in organisms. Their capacity to transpose within a genome, sometimes at a high rate, and their copy number regulation are environment-sensitive, as are the epigenetic pathways that mediate TE regulation in a genome. In this review we revisit the way we see evolvability with regard to transposable elements and epigenetics.

scholarly journals THE Mu TRANSPOSABLE ELEMENTS OF MAIZE: EVIDENCE FOR TRANSPOSITION AND COPY NUMBER REGULATION DURING DEVELOPMENT

Genetics ◽  
1986 ◽  
Vol 112 (1) ◽  
pp. 107-119
Author(s):  
Mary Alleman ◽  
Michael Freeling
Keyword(s):  
Transposable Elements ◽  
Inbred Line ◽  
Germ Cells ◽  
Copy Number ◽  
First Generation ◽  
High Rate ◽  
Constant Number ◽  
Mutator Activity ◽  
Copy Number Regulation

ABSTRACT The Mu transposon of maize exists in a highly mutagenic strain called Robertson's Mutator. Plants of this strain contain 10-50 copies of the Mu element, whereas most maize strains and other plants have none. When Mutator plants are crossed to plants of the inbred line 1S2P, which does not have copies of Mu, the progeny plants have approximately the same number of Mu sequences as did their Mutator parent. Approximately one-half of these copies have segregated from their parent and one-half have arisen by transposition and are integrated into new positions in the genome. This maintenance of copy number can be accounted for by an extremely high rate of transposition of the Mu elements (10-15 transpositions per gamete per generation). When Mutator plants are self-pollinated, the progeny double their Mu copy number in the first generation, but maintain a constant number of Mu sequences with subsequent self-pollinations. Transposition of Mu and the events that lead to copy number maintenance occur very late in the development of the germ cells but before fertilization. A larger version of the Mu element transposes but is not necessary for transposition of the Mu sequences. The progeny of crosses with a Mutator plant occasionally lack Mutator activity; these strains retain copies of the Mu element, but these elements no longer transpose.

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 Selection against transposable elements in D. simulans and D. melanogaster

1996 ◽  
Vol 68 (1) ◽  
pp. 9-15 ◽  
Author(s):  
C. Vieira ◽  
C. Biémont
Keyword(s):  
In Situ Hybridization ◽  
Transposable Elements ◽  
Copy Number ◽  
Insertion Site ◽  
Natural Populations ◽  
Lower Proportion ◽  
Major Mechanism ◽  
Insertion Sites ◽  
Copy Number Regulation

SummaryThe insertion site numbers of the transposable elements (TEs) copia, mdgl, 412 and gypsy were determined in various natural populations of Drosophila melanogaster and D. simulans by in situ hybridization. We showed that, while all elements except gypsy had many insertion sites scattered over the chromosomes in D. melanogaster, only the 412 element in D. simulans presented a high number of insertions, and this number was lower than in D. melanogaster. This low 412 site number per genome in D. simulans was associated with a lower proportion of insertions on the X chromosome in comparison with D. melanogaster, as determined in diploid genomes (0·090 for D. simulans against 0·137 for D. melanogaster) and in haploid genomes (0·102 against 0·146), each value being, moreover, lower than the value of 0·20 expected on the hypothesis of no selection against insertional mutations. These results suggest that selection is a major mechanism explaining 412 copy number regulation in Drosophila, and is stronger in D. simulans than in D. melanogaster.

scholarly journals Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. II. Accumulation of Variation and Evolution of a New Subfamily

2019 ◽  
Vol 37 (2) ◽  
pp. 355-364
Author(s):  
Watal M Iwasaki ◽  
T E Kijima ◽  
Hideki Innan
Keyword(s):  
Population Genetics ◽  
Transposable Elements ◽  
Dna Sequences ◽  
Copy Number ◽  
Internal Branch ◽  
Ectopic Recombination ◽  
A Genome ◽  
Different Types ◽  
Long Time ◽  
New Type

Abstract In order to understand how DNA sequences of transposable elements (TEs) evolve, extensive simulations were carried out. We first used our previous model, in which the copy number of TEs is mainly controlled by selection against ectopic recombination. It was found that along a simulation run, the shape of phylogeny changes quite much, from monophyletic trees to dimorphic trees with two clusters. Our results demonstrated that the change of the phase is usually slow from a monomorphic phase to a dimorphic phase, accompanied with a growth of an internal branch by accumulation of variation between two types. Then, the phase immediately changes back to a monomorphic phase when one group gets extinct. Under this condition, monomorphic and dimorphic phases arise repeatedly, and it is very difficult to maintain two or more different types of TEs for a long time. Then, how a new subfamily can evolve? To solve this, we developed a new model, in which ectopic recombination is restricted between two types under some condition, for example, accumulation of mutations between them. Under this model, because selection works on the copy number of each types separately, two types can be maintained for a long time. As expected, our simulations demonstrated that a new type arises and persists quite stably, and that it will be recognized as a new subfamily followed by further accumulation of mutations. It is indicated that how ectopic recombination is regulated in a genome is an important factor for the evolution of a new subfamily.

scholarly journals Fitness effects of Ty transposition in Saccharomyces cerevisiae.

Genetics ◽  
1992 ◽  
Vol 131 (1) ◽  
pp. 31-42 ◽  
Author(s):  
C M Wilke ◽  
J Adams
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transposable Elements ◽  
Stationary Phase ◽  
Copy Number ◽  
Induced Mutations ◽  
Negative Effects ◽  
Adaptive Mutations ◽  
Positive Effects ◽  
Negative Effect

Abstract It has been suggested that the primary evolutionary role of transposable elements is negative and parasitic. Alternatively, the target specificity and gene regulatory capabilities of many transposable elements raise the possibility that transposable element-induced mutations are more likely to be adaptively favorable than other types of mutations. Populations of Saccharomyces cerevisiae containing large amounts of variation for Ty1 genomic insertions were constructed, and the effects of Ty1 copy number on two components of fitness, yield and growth rate were determined. Although mean stationary phase density decreased with increased Ty1 copy number, the variance and range increased. The distributions of stationary phase densities indicate that many Ty1 insertions have negative effects on fitness, but also that some may have positive effects. To test directly for adaptively favorable Ty1 insertions, populations containing large amounts of variability for Ty1 copy number were grown in continuous culture. After 98-112 generations the frequency of clones containing zero Ty1 elements had decreased to approximately 0.0, and specific Ty1-containing clone families had predominated. Considering that most of the genetic variation in the populations was due to Ty1 transposition, and that Ty1 insertions had, on average, a negative effect on fitness, we conclude that Ty1 transposition events were directly responsible for the production of adaptive mutations in the clones that predominated in the populations.

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

scholarly journals Rapid evolution at the Drosophila telomere: transposable element dynamics at an intrinsically unstable locus

Genetics ◽  
2020 ◽  
Vol 217 (2) ◽  
Author(s):  
Michael P McGurk ◽  
Anne-Marie Dion-Côté ◽  
Daniel A Barbash
Keyword(s):  
Copy Number ◽  
Large Scale ◽  
Insertion Site ◽  
Rapid Evolution ◽  
Interspecific Variation ◽  
High Rate ◽  
Evolutionary Strategy ◽  
Control Mechanisms ◽  
Genetic Conflict ◽  
Number Variation

AbstractDrosophila telomeres have been maintained by three families of active transposable elements (TEs), HeT-A, TAHRE, and TART, collectively referred to as HTTs, for tens of millions of years, which contrasts with an unusually high degree of HTT interspecific variation. While the impacts of conflict and domestication are often invoked to explain HTT variation, the telomeres are unstable structures such that neutral mutational processes and evolutionary tradeoffs may also drive HTT evolution. We leveraged population genomic data to analyze nearly 10,000 HTT insertions in 85  Drosophila melanogaster genomes and compared their variation to other more typical TE families. We observe that occasional large-scale copy number expansions of both HTTs and other TE families occur, highlighting that the HTTs are, like their feral cousins, typically repressed but primed to take over given the opportunity. However, large expansions of HTTs are not caused by the runaway activity of any particular HTT subfamilies or even associated with telomere-specific TE activity, as might be expected if HTTs are in strong genetic conflict with their hosts. Rather than conflict, we instead suggest that distinctive aspects of HTT copy number variation and sequence diversity largely reflect telomere instability, with HTT insertions being lost at much higher rates than other TEs elsewhere in the genome. We extend previous observations that telomere deletions occur at a high rate, and surprisingly discover that more than one-third do not appear to have been healed with an HTT insertion. We also report that some HTT families may be preferentially activated by the erosion of whole telomeres, implying the existence of HTT-specific host control mechanisms. We further suggest that the persistent telomere localization of HTTs may reflect a highly successful evolutionary strategy that trades away a stable insertion site in order to have reduced impact on the host genome. We propose that HTT evolution is driven by multiple processes, with niche specialization and telomere instability being previously underappreciated and likely predominant.

Who is allowed to read and write?

2020 ◽  
Vol 19 (3) ◽  
pp. 116-117
Author(s):  
Christian P Subbe ◽  
Keyword(s):  
Information Needs ◽  
Healthcare Professionals ◽  
Personal Health Records ◽  
High Rate ◽  
Personal Health ◽  
Care Needs ◽  
Serious Adverse Events ◽  
Health Records ◽  
Clinical Records ◽  
The Way

What makes us human? In 2015 Jeremy Vine asked this question to a selection of leading British thinkers and writers. The answers were as diverse as the people he interviewed. While you might have your own views about the complexity of being human I would suggest that being able to articulate thoughts and communicate them to others might be one of the characteristics that distinguishes us from other life forms. And if we think more about the achievements of human culture then being able to communicate thoughts in writing and reading other people’s thoughts is one of the unique abilities that humanity has acquired during its evolution: Young humans spend extensive time to learn how to read and write. They write on paper, they read books and they do the same on computers. They become adults. They read and write most days: they e-mail their telephone company, file online forms to the tax office and or write romantic notes to their partner. Then they get older and become unwell and enter large modern building full of the most state-of-the-art technology. But here, in hospitals, none of them are allowed to read or write. They are being asked questions by someone who is often younger and in a rush. That person usually speaks a different language called jargon and try their best to translate their jargon to normal language.1 Patients are not allowed to write their own records and access to read the records is cumbersome. And if this is how we structure communication in our clinical practice then why are we surprised about the hierarchical relationship between patients and healthcare professionals and the high rate of error due to miscommunication? There might be good reasons for the way we document in healthcare: historically only the educated few like doctors were able to read and write and therefore the way to record patient histories had to be by those who were educated to do so. Additionally professions have always defined themselves by their own professional language and jargon that allows their members to describe matters precisely and at the same time create a sense of identity. Things have however changed in the last 100 years and a large proportion of our patients is able to read and write and might be perfectly capable to document their own information (and subsequently read all information that relates to them). The paper from Renggli et al in this issue of Acute Medicine explores the feasibility of documentation by patients on admission to hospital in Switzerland by using a web-based platform: at least half of the patients who were admitted with an emergency to hospital could document important parts their own medical history. The study demonstrated that documentation by patients added additional new information over and beyond of that collected by doctors and improved completeness of records, especially for the increasingly important social history. The paper has three important implications: Good information needs time: Patients can add more information if given the questions and their own time – rushing through an unprepared face-to-face consultation is unlikely to bring out the most relevant information in a reliable fashion. Sharing with patients might improve work-efficiency. Up to 25% of the time of doctors and nurses working in hospitals is taken up by documentation2,3: at a time when so many employed in healthcare are overworked and burnt out it would be reckless not to consider changes in information flow through the lens of work-load and efficiency. Quality care needs joint ownership with patients: Patients participation in the co-design and delivery of new services and shared decision of patients and clinicians in making of complex decision has been challenging to say the least. Co-ownership of clinical records is potentially a key strategic lever to achieve better decisions and services. Patient organisations and policy makers are expecting for patients to access medical records. Personal health records are now compulsory in some countries with roll-out of access for all citizens completed in countries like Estonia since 20084 and Sweden since 2018.5 It is National Health Service (NHS) policy to make a “personalized healthcare” available to everybody by 2020.6 That is now. Despite this there is virtually no evidence for the usage of personal health records in hospital.7,8 There are significant caveats to the current study: Half of the patients approached declined to take part and it is unclear why this was the case. Maybe they did not want to take part in any research. Maybe they felt too unwell to write. And maybe they were unable to read and write. While most people reaching adulthood in European countries have gone to school there is also evidence that up to 7 million adults in England are functionally illiterate and not able to read and write beyond the most basic level9 and relying on friends and family members, signs and symbols to travel through modern life. There is also an increasing body of work about digital exclusion and concerns that those who are unable to navigate the online world are at risk of being left behind by society.10 There are additional questions about ownership: do patients own all data that relates to their care or is documentation by healthcare professionals their intellectual property. There are strong arguments for both perspectives. From a patient safety point of view their would seem to be a strong imperative to come to pragmatic agreements. Research suggests that the majority of serious adverse events was flagged by patients and relatives at a time when they could have been predicted and potentially prevented by clinical teams.11 But safety critical information is often hidden from those who are most affected by it, the patients. The paper by Renggli et all does therefore provide important evidence for the development of a more co-operative and democratic way of providing acute care by using something that is a key part of being human: the ability to read and write.

Copy-number variation in sporadic amyotrophic lateral sclerosis: a genome-wide screen

2008 ◽  
Vol 7 (4) ◽  
pp. 319-326 ◽  
Author(s):  
Hylke M Blauw ◽  
Jan H Veldink ◽  
Michael A van Es ◽  
Paul W van Vught ◽  
Christiaan GJ Saris ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Copy Number Variation ◽  
Copy Number ◽  
Sporadic Amyotrophic Lateral Sclerosis ◽  
Genome Wide ◽  
A Genome ◽  
Number Variation ◽  
Lateral Sclerosis
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