On the evolution and population genetics of hybrid-dysgenesis-causing transposable elements in Drosophila

1986 ◽  
Vol 312 (1154) ◽  
pp. 205-215 ◽  
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Transposable Elements ◽  
Transposable Element ◽  
Natural Populations ◽  
Element Composition ◽  
Hybrid Dysgenesis ◽  
Evolutionary Significance ◽  
Genetic Elements ◽  
Transposable Genetic Elements

Much has been learned about transposable genetic elements in Drosophila , but questions still remain, especially concerning their evolutionary significance. Three such questions are considered here, (i) Has the behaviour of transposable elements been most influenced by natural selection at the level of the organism, the population, or the elements themselves? (ii) How did the elements originate in the genome of the species? (iii) Why are laboratory stocks different from natural populations with respect to their transposable element composition? No final answers to these questions are yet available, but by focusing on the two families of hybrid dysgenesis-causing elements, the P and I factors, we can draw some tentative conclusions.

scholarly journals The transposable elements of the Drosophila serrata reference panel

2020 ◽  
Author(s):  
Zachary Tiedeman ◽  
Sarah Signor
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Copy Number ◽  
Genetic Background ◽  
Natural Populations ◽  
Inbred Lines ◽  
Transposable Element Insertion ◽  
Defense Systems ◽  
Drosophila Serrata ◽  
Transposable Element Copy

AbstractTransposable elements are an important element of the complex genomic ecosystem, proving to be both adaptive and deleterious - repressed by the piRNA system and fixed by selection. Transposable element insertion also appears to be bursty – either due to invasion of new transposable elements that are not yet repressed, de-repression due to instability of organismal defense systems, stress, or genetic variation in hosts. Here, we characterize the transposable element landscape in an important model Drosophila, D. serrata, and investigate variation in transposable element copy number between genotypes and in the population at large. We find that a subset of transposable elements are clearly related to elements annotated in D. melanogaster and D. simulans, suggesting they spread between species more recently than other transposable elements. We also find that transposable elements do proliferate in particular genotypes, and that often if an individual is host to a proliferating transposable element, it is host to more than one proliferating transposable element. In addition, if a transposable element is active in a genotype, it is often active in more than one genotype. This suggests that there is an interaction between the host and the transposable element, such as a permissive genetic background and the presence of potentially active transposable element copies. In natural populations an active transposable element and a permissive background would not be held in association as in inbred lines, suggesting the magnitude of the burst would be much lower. Yet many of the inbred lines have actively proliferating transposable elements suggesting this is an important mechanism by which transposable elements maintain themselves in populations.

scholarly journals Models of repression of transposition in P-M hybrid dysgenesis by P cytotype and by zygotically encoded repressor proteins.

Genetics ◽  
1991 ◽  
Vol 128 (2) ◽  
pp. 471-486 ◽  
Author(s):  
J F Brookfield
Keyword(s):  
Computer Simulation ◽  
Transposable Elements ◽  
Transposable Element ◽  
Evolutionary Dynamics ◽  
Hybrid Dysgenesis ◽  
P Elements ◽  
Infinite Population ◽  
Repressor Proteins ◽  
P Transposable Element ◽  
Harmful Effects

Abstract By analytical theory and computer simulation the expected evolutionary dynamics of P transposable element spread in an infinite population are investigated. The analysis is based on the assumption that, unlike transposable elements which move via RNA intermediates, the harmful effects of P elements arise primarily in the act of transposition, and that this causes their evolutionary dynamics to be unusual. It is suggested that a situation of transposition-selection balance will be superceded by the buildup of a cytoplasmically inherited repression or by the elimination of active transposase-encoding elements from the chromosomes, a process which may be accompanied by the evolution of elements which encode proteins which repress transposition.

scholarly journals Models of the population genetics of transposable elements

2005 ◽  
Vol 85 (3) ◽  
pp. 171-181 ◽  
Author(s):  
ARNAUD LE ROUZIC ◽  
GRÉGORY DECELIERE
Keyword(s):  
Population Genetics ◽  
Drosophila Melanogaster ◽  
Natural Selection ◽  
Transposable Elements ◽  
Genetic Drift ◽  
Self Regulation ◽  
Evolutionary Forces ◽  
Classical Models

Although transposable elements (TEs) have been found in all organisms in which they have been looked for, the ways in which they invade genomes and populations are still a matter of debate. By extending the classical models of population genetics, several approaches have been developed to account for the dynamics of TEs, especially in Drosophila melanogaster. While the formalism of these models is based on simplifications, they enable us to understand better how TEs invade genomes, as a result of multiple evolutionary forces including duplication, deletion, self-regulation, natural selection and genetic drift. The aim of this paper is to review the assumptions and the predictions of these different models by highlighting the importance of the specific characteristics of both the TEs and the hosts, and the host/TE relationships. Then, perspectives in this domain will be discussed.

scholarly journals The Population Genetics of Ploidy Change in Fungi

2020 ◽  
Author(s):  
Aleeza C. Gerstein ◽  
Nathaniel Sharp
Keyword(s):  
Population Genetics ◽  
Genetic Variation ◽  
Natural Selection ◽  
Genetic Variants ◽  
Natural Populations ◽  
Theoretical Work ◽  
Fungal Species ◽  
Random Genetic Drift ◽  
Lab Experiments ◽  
History Of

Ploidy is a significant type of genetic variation, describing the number of chromosome sets per cell. Ploidy evolves in natural populations, clinical populations, and lab experiments, particularly in fungi. Despite a long history of theoretical work on this topic, predicting how ploidy will evolve has proven difficult, as it is often unclear why one ploidy state outperforms another. Here, we review what is known about contemporary ploidy evolution in diverse fungal species through the lens of population genetics. As with typical genetic variants, ploidy evolution depends on the rate that new ploidy states arise by mutation, natural selection on alternative ploidy states, and random genetic drift. However, ploidy variation also has unique impacts on evolution, with the potential to alter chromosomal stability, the rate and patterns of point mutation, and the nature of selection on all loci in the genome. We discuss how ploidy evolution depends on these general and unique factors and highlight areas where additional experimental evidence is required to comprehensively explain the ploidy transitions observed in the field and the lab.

scholarly journals Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anna Ullastres ◽  
Miriam Merenciano ◽  
Josefa González
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Transposable Elements ◽  
Transposable Element ◽  
Natural Populations ◽  
Regulatory Elements ◽  
Genomic Context ◽  
Specific Expression ◽  
Survival Capacity ◽  
Immune Related Genes

Abstract Background Variation in gene expression underlies interindividual variability in relevant traits including immune response. However, the genetic variation responsible for these gene expression changes remains largely unknown. Among the non-coding variants that could be relevant, transposable element insertions are promising candidates as they have been shown to be a rich and diverse source of cis-regulatory elements. Results In this work, we use a population genetics approach to identify transposable element insertions likely to increase the tolerance of Drosophila melanogaster to bacterial infection by affecting the expression of immune-related genes. We identify 12 insertions associated with allele-specific expression changes in immune-related genes. We experimentally validate three of these insertions including one likely to be acting as a silencer, one as an enhancer, and one with a dual role as enhancer and promoter. The direction in the change of gene expression associated with the presence of several of these insertions is consistent with an increased survival to infection. Indeed, for one of the insertions, we show that this is the case by analyzing both natural populations and CRISPR/Cas9 mutants in which the insertion is deleted from its native genomic context. Conclusions We show that transposable elements contribute to gene expression variation in response to infection in D. melanogaster and that this variation is likely to affect their survival capacity. Because the role of transposable elements as regulatory elements is not restricted to Drosophila, transposable elements are likely to play a role in immune response in other organisms as well.

scholarly journals The meiotic recombination landscape ofDrosophila virilisis robust to mitotic damage during hybrid dysgenesis

2018 ◽  
Author(s):  
Lucas W. Hemmer ◽  
Guilherme Dias ◽  
Brittny Smith ◽  
Kelley Van Vaerenberghe ◽  
Ashley Howard ◽  
...  
Keyword(s):  
Dna Damage ◽  
Transposable Elements ◽  
Transposable Element ◽  
Meiotic Recombination ◽  
Genome Stability ◽  
Double Strand Breaks ◽  
Drosophila Virilis ◽  
Hybrid Dysgenesis ◽  
Male Recombination ◽  
Strand Breaks

ABSTRACTGermline DNA damage is a double-edged sword. Programmed double-strand breaks establish the foundation for meiotic recombination and chromosome segregation. However, double-strand breaks also pose a significant challenge for genome stability. Because of this, meiotic double-strand break formation is tightly regulated. However, natural selection can favor selfish behavior in the germline and transposable elements can cause double-strand breaks independent of the carefully regulated meiotic process. To understand how the regulatory mechanisms of meiotic recombination accommodate unregulated transposition, we have characterized the female recombination landscape in a syndrome of hybrid dysgenesis inDrosophila virilis. In this system, a cross between two strains ofD. viriliswith divergent transposable element and piRNA profiles results in germline transposition of diverse transposable elements, reduced fertility, and male recombination. We sought to determine how increased transposition during hybrid dysgenesis might perturb the meiotic recombination landscape. Our results show that the overall frequency and distribution of meiotic recombination is extremely robust to germline transposable element activation. However, we also find that hybrid dysgenesis can result in mitotic recombination within the female germline. Overall, these results show that landscape of meiotic recombination may be insensitive to the DNA damage caused by transposition during early development.

scholarly journals Polymorphism for Y-Linked Suppressors of sex-ratio in Two Natural Populations of Drosophila mediopunctata

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 891-902 ◽  
Author(s):  
Antonio Bernardo Carvalho ◽  
Suzana Casaccia Vaz ◽  
Louis Bernard Klaczko
Keyword(s):  
Population Genetics ◽  
Population Dynamics ◽  
Natural Selection ◽  
Sex Ratio ◽  
Numerical Simulations ◽  
Natural Populations ◽  
Meiotic Drive ◽  
X Chromosomes ◽  
Variable Expression ◽  
Y Chromosomes

In several Drosophila species there is a trait known as “sex-ratio”: males carrying certain X chromosomes (called “SR”) produce female biased progenies due to X-Y meiotic drive. In Drosophila mediopunctata this trait has a variable expression due to Y-linked suppressors of sex-ratio expression, among other factors. There are two types of Y chromosomes (suppressor and nonsuppressor) and two types of SR chromosomes (suppressible and unsuppressible). Sex-ratio expression is suppressed in males with the SRsuppressible/Ysuppressor genotype, whereas the remaining three genotypes produce female biased progenies. Now we have found that ∼10–20% of the Y chromosomes from two natural populations 1500 km apart are suppressors of sex-ratio expression. Preliminary estimates indicate that Ysuppressor has a meiotic drive advantage of 6% over Ynonsuppressor. This Y polymorphism for a nonneutral trait is unexpected under current population genetics theoly. We propose that this polymorphism is stabilized by an equilibrium between meiotic drive and natural selection, resulting from interactions in the population dynamics of X and Y alleles. Numerical simulations showed that this mechanism may stabilize nonneutral Y polymorphisms such as we have found in D. mediopunctata.

scholarly journals Transposable elements in individual genotypes of Drosophila simulans

2019 ◽  
Author(s):  
Sarah Signor
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Dna Sequences ◽  
Copy Number ◽  
Natural Populations ◽  
Population Level ◽  
Drosophila Simulans ◽  
Mobile Dna ◽  
Open Question ◽  
Number Of Individuals

AbstractTransposable elements are mobile DNA sequences that are able to copy themselves within a host’s genome. Within insects they often make up a substantial proportion of the genome. While they are the subject of intense research, often times when copy number is estimated it is estimated only at the population level, or in a limited number of individuals within a population. However, an important aspect of transposable element spread is the variance between individuals in activity. Do transposable elements accumulate at different rates in different genetic backgrounds? Using two populations of Drosophila simulans from California and Africa I estimated transposable element copy number in individual genotypes. Some active transposable elements seem to be a property of the species, while others of the populations. I find that in addition to population level differences in transposable element load certain genotypes accumulate transposable elements at a much higher rate than others. Most likely active transposable elements are fairly rare, and were inherited only by specific genotypes that were used to create the inbred lines. Whether or not this reflects dynamics in natural populations, where transposable elements may accumulate in specific genotypes and maintain themselves in the population rather than being active at low levels population wide, is an open question.

scholarly journals Population genetics of transposable element load: a mechanistic account of observed overdispersion

2020 ◽  
Author(s):  
Ronald D. Smith ◽  
Joshua R. Puzey ◽  
Gregory D. Conradi Smith
Keyword(s):  
Population Genetics ◽  
Transposable Element ◽  
Natural Populations ◽  
Purifying Selection ◽  
Death Process ◽  
Stationary Population ◽  
Population Distributions ◽  
Evolutionary Genetic ◽  
Genetic Mechanisms ◽  
Copy And Paste

AbstractIn an empirical analysis of transposable element (TE) abundance within natural populations of Mimulus guttatus and Drosophila melanogaster, we found a surprisingly high variance of TE count (e.g., variance-to-mean ratio on the order of 10 to 100). To obtain insight regarding those evolutionary genetic mechanisms that are may underlie the overdispersed population distributions of TE abundance, we developed a mathematical model of TE population genetics that includes the dynamics of element proliferation and purifying selection on TE load. The modeling approach begins with a master equation for a birth-death process and it extends the predictions of the classical theory of TE dynamics in several ways. In particular, moment-based analysis of stationary population distributions of TE load reveal that overdispersion is most likely to arise via copy-and-paste (as opposed to cut-and-paste) dynamics. Parameter studies suggest that overdispersed population distributions of TE abundance are probably not a consequence of purifying selection on total element load.

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