The dynamics of transposable elements in structured populations

Population genetics of transposable element load: A mechanistic account of observed overdispersion

In 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 300). To obtain insight regarding the evolutionary genetic mechanisms that 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 extends the predictions of the classical theory of TE dynamics in several ways. In particular, moment-based analyses of population distributions of TE load reveal that overdispersion is likely to arise via copy-and-paste proliferation dynamics, especially when the elementary processes of proliferation and excision are approximately balanced. Parameter studies and analytic work confirm this result and further suggest that overdispersed population distributions of TE abundance are probably not a consequence of purifying selection on total element load.

Do pseudogenes pose a problem for metabarcoding marine animal communities?

Because DNA metabarcoding typically employs sequence diversity among mitochondrial amplicons to estimate species composition, nuclear mitochondrial pseudogenes (NUMTs) can inflate diversity. This study quantifies the incidence and attributes of NUMTs derived from the 658 bp barcode region of cytochrome c oxidase I (COI) in 156 marine animal genomes. NUMTs were examined to ascertain if they could be recognized by their possession of indels or stop codons. In total, 309 NUMTs ≥ 150 bp were detected, with an average of 1.98 per species (range = 0-33) and a mean length of 391 bp ± 200 bp. Among this total, 75 (24.3 %) lacked indels or stop codons. NUMTs appear to pose the greatest interpretational risk when short (< 313 bp) amplicons are used, such as in eDNA studies, dietary analyses, or processed fish identification. Employing the standard amplicon length (313 bp) for marine metabarcoding, NUMTs could potentially inflate the OTU count by 21% above the true species count while also raising intraspecific variation at COI by 15%. However, when both amplicon length and position are considered, inflation in OTU counts and in barcode variation were just 9% and 10%, respectively, suggesting NUMTs will not seriously distort biodiversity assessments. There was a weak positive correlation between genome size and NUMT count but no variation among phyla or trophic groups. Until bioinformatic advances improve NUMT detection, the best defense involves targeting long amplicons and developing reference databases that include both mitochondrial sequences and their NUMT derivatives.

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

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.

Invasion of the P elements: Tolerance is not futile

Organisms are locked in an eternal struggle with parasitic DNA sequences that live inside their genomes and wreak havoc on their host's chromosomes as they spread through populations. To combat these parasites, host species have evolved elaborate mechanisms of resistance that suppress their activity. A new study in Drosophila indicates that, prior to the acquisition of resistance, individuals can vary in their ability to tolerate the activity of these genomic parasites, ignoring or repairing the damage they induce. This tolerance results from variation at genes involved in germline development and DNA damage checkpoints and suggests that these highly conserved cellular processes may be influenced by current and historical intragenomic parasite loads.

Accumulation of transposable elements in selfing populations of Arabidopsis lyrata supports the ectopic recombination model of transposon evolution

Transposable elements (TE) can constitute a large fraction of plant genomes, yet our understanding of their evolution and fitness effect is still limited. Here we tested several models of evolution that make specific predictions about differences in TE abundance between selfing and outcrossing taxa, and between small and large populations. We estimated TE abundance in multiple populations of North American Arabidopsis lyrata differing in mating system and long-term size, using transposon insertion display on several TE families. Selfing populations had higher TE copy numbers per individual and higher TE allele frequencies, supporting models which assume that selection against TEs acts predominantly against heterozygotes via the process of ectopic recombination. In outcrossing populations differing in long-term size, the data supported neither a model of density-regulated transposition nor a model of direct deleterious effect. Instead, the population structure of TEs revealed that outcrossing populations tended to split into western and eastern groups - as previously detected using microsatellite markers - whereas selfing populations from west and east were less differentiated. This, too, agrees with the model of ectopic recombination. Overall, our results suggest that TE elements are nearly neutral except for their deleterious potential to disturb meiosis in the heterozygous state.

DYNAMICS OF AN INSERTION SEQUENCE INFECTION IN A SPATIALLY STRUCTURED ENVIRONMENT

Bacterial insertion sequences (ISs), the simplest form of autonomous mobile DNA, depend on their prokaryote hosts to spread in a spatially structured environment. We use a spatially explicit metapopulation model to simulate the spread of an IS that can have both detrimental and beneficial effects on its host cell. We find that, on the one hand, the spatial structure of the metapopulation and cell dispersal between subpopulations have no strong effect on the time to full infection of the metapopulation. On the other hand, factors that influence the IS infection dynamics within a subpopulation have a strong effect on that time. These factors are mainly the fitness benefit of an IS and the rate of horizontal gene transfer. We also find that the infection process of a metapopulation is very erratic in its early phase. Finally, we show that the infection’s success depends critically on the initially infected subpopulation.

A New Reference Genome Assembly for the Microcrustacean Daphnia pulex

Comparing genomes of closely related genotypes from populations with distinct demographic histories can help reveal the impact of effective population size on genome evolution. For this purpose, we present a high quality genome assembly of Daphnia pulex (PA42), and compare this with the first sequenced genome of this species (TCO), which was derived from an isolate from a population with >90% reduction in nucleotide diversity. PA42 has numerous similarities to TCO at the gene level, with an average amino acid sequence identity of 98.8 and >60% of orthologous proteins identical. Nonetheless, there is a highly elevated number of genes in the TCO genome annotation, with ∼7000 excess genes appearing to be false positives. This view is supported by the high GC content, lack of introns, and short length of these suspicious gene annotations. Consistent with the view that reduced effective population size can facilitate the accumulation of slightly deleterious genomic features, we observe more proliferation of transposable elements (TEs) and a higher frequency of gained introns in the TCO genome.

Genomic changes during evolution of animal parasitism in eukaryotes

Understanding how pathogens have evolved to survive in close association with their hosts is an important step in unraveling the biology of host-pathogen interactions. Comparative genomics is a powerful tool to approach this problem as an increasing number of genomes of multiple pathogen species and strains become available. The ever-growing catalog of genome sequences makes comparison of organisms easier, but it also allows us to reconstitute the evolutionary processes occurring at the genomic level that may have led to the acquisition of pathogenic or parasitic mechanisms.

Unique transposon landscapes are pervasive across Drosophila melanogaster genomes

To understand how transposon landscapes (TLs) vary across animal genomes, we describe a new method called the Transposon Insertion and Depletion AnaLyzer (TIDAL) and a database of >300 TLs in Drosophila melanogaster (TIDAL-Fly). Our analysis reveals pervasive TL diversity across cell lines and fly strains, even for identically named sub-strains from different laboratories such as the ISO1 strain used for the reference genome sequence. On average, >500 novel insertions exist in every lab strain, inbred strains of the Drosophila Genetic Reference Panel (DGRP), and fly isolates in the Drosophila Genome Nexus (DGN). A minority (<25%) of transposon families comprise the majority (>70%) of TL diversity across fly strains. A sharp contrast between insertion and depletion patterns indicates that many transposons are unique to the ISO1 reference genome sequence. Although TL diversity from fly strains reaches asymptotic limits with increasing sequencing depth, rampant TL diversity causes unsaturated detection of TLs in pools of flies. Finally, we show novel transposon insertions negatively correlate with Piwi-interacting RNA (piRNA) levels for most transposon families, except for the highly-abundant roo retrotransposon. Our study provides a useful resource for Drosophila geneticists to understand how transposons create extensive genomic diversity in fly cell lines and strains.

Molecular characterization of the piggyBac-like element, a candidate marker for phylogenetic research of Chilo suppressalis (Walker) in China

Background

Transposable elements (TEs, transposons) are mobile genetic DNA sequences. TEs can insert copies of themselves into new genomic locations and they have the capacity to multiply. Therefore, TEs have been crucial in the shaping of hosts’ current genomes. TEs can be utilized as genetic markers to study population genetic diversity. The rice stem borer Chilo suppressalis Walker is one of the most important insect pests of many subtropical and tropical paddy fields. This insect occurs in all the rice-growing areas in China. This research was carried out in order to find diversity between C. suppressalis field populations and detect the original settlement of C. suppressalis populations based on the piggyBac-like element (PLE). We also aim to provide insights into the evolution of PLEs in C. suppressalis and the phylogeography of C. suppressalis.

Results

Here we identify a new piggyBac-like element (PLE) in the rice stem borer Chilo suppressalis Walker, which is called CsuPLE1.1 (GenBank accession no. JX294476). CsuPLE1.1 is transcriptionally active. Additionally, the CsuPLE1.1 sequence varied slightly between field populations, with polymorphic indels (insertion/deletion) and hyper-variable regions including the identification of the 3′ region outside the open reading frame (ORF). CsuPLE1.1 insertion frequency varied between field populations. Sequences variation was found between CsuPLE1 copies and varied within and among field populations. Twenty-one different insertion sites for CsuPLE1 copies were identified with at least two insertion loci found in all populations.

Conclusions

Our results indicate that the initial invasion of CsuPLE1 into C. suppressalis occurred before C. suppressalis populations spread throughout China, and suggest that C. suppressalis populations have a common ancestor in China. Additionally, the lower reaches of the Yangtze River are probably the original settlement of C. suppressalis in China. Finally, the CsuPLE1 insertion site appears to be a candidate marker for phylogenetic research of C. suppressalis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12867-014-0028-y) contains supplementary material, which is available to authorized users.

Population genetics and molecular evolution of DNA sequences in transposable elements. I. A simulation framework

A population genetic simulation framework is developed to understand the behavior and molecular evolution of DNA sequences of transposable elements. Our model incorporates random transposition and excision of transposable element (TE) copies, two modes of selection against TEs, and degeneration of transpositional activity by point mutations. We first investigated the relationships between the behavior of the copy number of TEs and these parameters. Our results show that when selection is weak, the genome can maintain a relatively large number of TEs, but most of them are less active. In contrast, with strong selection, the genome can maintain only a limited number of TEs but the proportion of active copies is large. In such a case, there could be substantial fluctuations of the copy number over generations. We also explored how DNA sequences of TEs evolve through the simulations. In general, active copies form clusters around the original sequence, while less active copies have long branches specific to themselves, exhibiting a star-shaped phylogeny. It is demonstrated that the phylogeny of TE sequences could be informative to understand the dynamics of TE evolution.

New insights into the population structure of Anopheles gambiae s.s. in the Gulf of Guinea Islands revealed by Herves transposable elements

Transposable elements (TEs) are mobile portions of DNA that are able to replicate and spread in the genome of many organisms. TEs can be used as a means to insert transgenes in insects, being stably inherited throughout generations. Anopheles gambiae is the main vector of human malaria in Sub-Saharan Africa. Given the extraordinary burden this disease imposes, the mosquito became a choice target for genetic control approaches with the purpose of reducing malaria transmission. In this study, we investigated the abundance and distribution of Herves TE in An. gambiae s.s. from Cameroon and four islands in the Gulf of Guinea, in order to determine their genetic structure. We have detected a population subdivision between Equatorial Guinea islands and the islands of São Tomé, Príncipe and mainland. This partitioning associates more with political rather than geographic boundaries, possibly reflecting different mainland source populations colonizing the islands.

What makes transposable elements move in the Drosophila genome?

Transposable elements (TEs), by their capacity of moving and inducing mutations in the genome, are considered important drivers of species evolution. The successful invasions of TEs in genomes, despite their mutational properties, are an apparent paradox. TEs' transposition is usually strongly regulated to low value, but in some cases these elements can also show high transposition rates, which has been associated sometimes to changes in environmental conditions. It is evident that factors susceptible to induce transpositions in natural populations contribute to TE perpetuation. Different factors were proposed as causative agents of TE mobilization in a wide range of organisms: biotic and abiotic stresses, inter- and intraspecific crosses and populational factors. However, there is no clear evidence of the factors capable of inducing TE mobilization in Drosophila, and data on laboratory stocks show contradictory results. The aim of this review is to have an update critical revision about mechanisms promoting transposition of TEs in Drosophila, and to provide to the readers a global vision of the dynamics of these genomic elements in the Drosophila genome.

Evolutionary Implications of Mechanistic Models of TE-Mediated Hybrid Incompatibility

New models of TE repression in plants (specifically Arabidopsis) have suggested specific mechanisms by which TE misregulation in hybrids might result in the expression of hybrid inviability. If true, these models suggest as yet undescribed consequences for (1) mechanistic connections between hybrid problems expressed at different postzygotic stages (e.g., inviability versus sterility), (2) the predicted strength, stage, and direction of isolation between diverging lineages that differ in TE activity, and (3) the association between species attributes that influence TE dynamics (e.g., mode of reproduction, geographical structure) and the rate at which they could accumulate incompatibilities. In this paper, we explore these implications and outline future empirical directions for generating data necessary to evaluate them.

Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes

A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Early computational analyses of TEs in genome sequences focused on filtering out "junk" sequences to facilitate gene annotation. When the high abundance and diversity of TEs in eukaryotic genomes were recognized, these early efforts transformed into the systematic genome-wide categorization and classification of TEs. The availability of genomic sequence data reversed the classical genetic approaches to discovering new TE families and superfamilies. Curated TE databases and their accurate annotation of genome sequences in turn facilitated the studies on TEs in a number of frontiers including: (1) TE-mediated changes of genome size and structure, (2) the influence of TEs on genome and gene functions, (3) TE regulation by host, (4) the evolution of TEs and their population dynamics, and (5) genomic scale studies of TE activity. Bioinformatics and genomic approaches have become an integral part of large-scale studies on TEs to extract information with pure in silico analyses or to assist wet lab experimental studies. The current revolution in genome sequencing technology facilitates further progress in the existing frontiers of research and emergence of new initiatives. The rapid generation of large-sequence datasets at record low costs on a routine basis is challenging the computing industry on storage capacity and manipulation speed and the bioinformatics community for improvement in algorithms and their implementations.

Insertional variability of four transposable elements and population structure of the midge Chironomus riparius (Diptera)

The dipteran Chironomus riparius is found across the entire Palearctic region; its larvae are among the most abundant macroinvertebrates inhabiting inland waterbodies. Chironomid larvae have been extensively used in ecotoxicological and cytogenetic research, but relatively little is known on the population structure of this species. Transposable elements (TEs) are DNA sequences that are capable of autonomous replication; the number and genomic location of TE insertions varies across individuals; this variability is increasingly being used in population studies. Several TEs had been characterized in Chironomids; this enabled the analysis of insertional variability of four different TEs in six natural populations of C. riparius from Italy, Bulgaria and Russia using a PCR-based method, transposon insertion display (TID). The method allows to obtain dominant markers, similar to AFLP. In all populations, TE insertions showed high individual polymorphism, while median copy numbers of the same TEs did not vary between populations. Analysis of molecular variance (AMOVA) detected significant differentiation between populations for three of the TEs; although no correlation between genetic and geographic distances was found, the corresponding population structures were found to be significantly correlated and indicate a degree of isolation by distance. TEs belonging to different classes have different mechanisms of replication, resulting in different transposition rates of mobilization; the finding of mostly concordant population structuring for three of the TEs indicates that population dynamics contributed significantly in shaping the detected insertional polymorphism.

A brief history of the status of transposable elements: from junk DNA to major players in evolution

The idea that some genetic factors are able to move around chromosomes emerged more than 60 years ago when Barbara McClintock first suggested that such elements existed and had a major role in controlling gene expression and that they also have had a major influence in reshaping genomes in evolution. It was many years, however, before the accumulation of data and theories showed that this latter revolutionary idea was correct although, understandably, it fell far short of our present view of the significant influence of what are now known as "transposable elements" in evolution. In this article, I summarize the main events that influenced my thinking about transposable elements as a young scientist and the influence and role of these specific genomic elements in evolution over subsequent years. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work.

Osvaldo and Isis retrotransposons as markers of the Drosophila buzzatii colonisation in Australia

Background

Transposable elements (TEs) constitute an important source of genetic variability owing to their jumping and regulatory properties, and are considered to drive species evolution. Several factors that are able to induce TE transposition in genomes have been documented (for example environmental stress and inter- and intra-specific crosses) but in many instances the reasons for TE mobilisation have yet to be elucidated. Colonising populations constitute an ideal model for studying TE behaviour and distribution as they are exposed to different environmental and new demographic conditions. In this study, the distribution of two TEs, Osvaldo and Isis, was examined in two colonising populations of D. buzzatii from Australia. Comparing Osvaldo copy numbers between Australian and Old World (reported in previous studies) colonisations provides a valuable tool for elucidating the colonisation process and the effect of new conditions encountered by colonisers on TEs.

Results

The chromosomal distributions of Osvaldo and Isis retrotransposons in two colonising populations of D. buzzatii from Australia revealed sites of high insertion frequency (>10%) and low frequency sites. Comparisons between Osvaldo insertion profiles in colonising populations from the Old World and Australia demonstrate a tendency towards a higher number of highly occupied sites with higher insertion frequency in the Old World than in Australian populations. Tests concerning selection against deleterious TE insertions indicate that Isis is more controlled by purifying selection than Osvaldo. The distribution of both elements on chromosomal arms follows a Poisson distribution and there are non-significant positive correlations between highly occupied sites and chromosomal inversions.

Conclusions

The occupancy profile of Osvaldo and Isis retrotransposons is characterised by the existence of high and low insertion frequency sites in the populations. These results demonstrate that Australian D. buzzatii populations were subjected to a founder effect during the colonisation process. Moreover, there are more sites with high insertion frequency in the Old World colonisation than in the Australian colonisation, indicating a probable stronger bottleneck effect in Australia. The results suggest that selection does not seem to play a major role, compared to demography, in the distribution of transposable elements in the Australian populations.

Structural genomics: correlation blocks, population structure, and genome architecture

An integration of the pattern of genome-wide inter-site associations with evolutionary forces is important for gaining insights into the genomic evolution in natural or artificial populations. Here, we assess the inter-site correlation blocks and their distributions along chromosomes. A correlation block is broadly termed as the DNA segment within which strong correlations exist between genetic diversities at any two sites. We bring together the population genetic structure and the genomic diversity structure that have been independently built on different scales and synthesize the existing theories and methods for characterizing genomic structure at the population level. We discuss how population structure could shape correlation blocks and their patterns within and between populations. Effects of evolutionary forces (selection, migration, genetic drift, and mutation) on the pattern of genome-wide correlation blocks are discussed. In eukaryote organisms, we briefly discuss the associations between the pattern of correlation blocks and genome assembly features in eukaryote organisms, including the impacts of multigene family, the perturbation of transposable elements, and the repetitive nongenic sequences and GC-rich isochores. Our reviews suggest that the observable pattern of correlation blocks can refine our understanding of the ecological and evolutionary processes underlying the genomic evolution at the population level.

The impact of genome defense on mobile elements in Microbotryum

Repeat induced point mutation (RIP), a mechanism causing hypermutation of repetitive DNA sequences in fungi, has been described as a 'genome defense' which functions to inactivate mobile elements and inhibit their deleterious effects on genome stability. Here we address the interactions between RIP and transposable elements in the Microbotryum violaceum species complex. Ten strains of M. violaceum, most of which belong to different species of the fungus, were all found to contain intragenomic populations of copia-like retrotransposons. Intragenomic DNA sequence variation among the copia-like elements was analyzed for evidence of RIP. Among species with RIP, there was no significant correlation between the frequency of RIP-induced mutations and inferred transposition rate based on diversity. Two strains of M. violaceum, from two different plant species but belonging to the same fungal lineage, contained copia-like elements with very low diversity, as would result from a high transposition rate, and these were also unique in showing no evidence of the hypermutation patterns indicative of the RIP genome defense. In this species, evidence of RIP was also absent from a Class II helitron-like transposable element. However, unexpectedly the absolute repetitive element load was lower than in other strains.

Dynamics of transposable elements: towards a community ecology of the genome

Like ecological communities, which vary in species composition, eukaryote genomes differ in the amount and diversity of transposable elements (TEs) that they harbor. Given that TEs have a considerable impact on the biology of their host species, we need to better understand whether their dynamics reflects some form of organization or is primarily driven by stochastic processes. Here, we borrow ecological concepts on species diversity to explore how interactions between TEs can contribute to structure TE communities within their genomic ecosystem. Whereas the niche theory predicts a stable diversity of TEs because of their divergent characteristics, the neutral theory of biodiversity predicts the assembly of TE communities from stochastic processes acting at the level of the individual TE. Contrary to ecological communities, however, TE communities are shaped by selection at the level of their ecosystem (i.e. the host individual). Developing ecological models specific to the genome will thus be a prerequisite for modeling the dynamics of TEs.

Dynamics of transposable elements: towards a community ecology of the genome

Like ecological communities, which vary in species composition, eukaryote genomes differ in the amount and diversity of transposable elements (TEs) that they harbor. Given that TEs have a considerable impact on the biology of their host species, we need to better understand whether their dynamics reflects some form of organization or is primarily driven by stochastic processes. Here, we borrow ecological concepts on species diversity to explore how interactions between TEs can contribute to structure TE communities within their genomic ecosystem. Whereas the niche theory predicts a stable diversity of TEs because of their divergent characteristics, the neutral theory of biodiversity predicts the assembly of TE communities from stochastic processes acting at the level of the individual TE. Contrary to ecological communities, however, TE communities are shaped by selection at the level of their ecosystem (i.e. the host individual). Developing ecological models specific to the genome will thus be a prerequisite for modeling the dynamics of TEs.

Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata

Transposable elements (TEs) are the major component of most plant genomes, and characterizing their population dynamics is key to understanding plant genome complexity. Yet there have been few studies of TE population genetics in plant systems. To study the roles of selection, transposition, and demography in shaping TE population diversity, we generated a polymorphism dataset for six TE families in four populations of the flowering plant Arabidopsis lyrata. The TE data indicated significant differentiation among populations, and maximum likelihood procedures suggested weak selection. For strongly bottlenecked populations, the observed TE band-frequency spectra fit data simulated under neutral demographic models constructed from nucleotide polymorphism data. Overall, we propose that TEs are subjected to weak selection, the efficacy of which varies as a function of demographic factors. Thus, demographic effects could be a major factor driving distributions of TEs among plant lineages.

Perspectives on the state of insect transgenics

Genetic transformation is a critical component to the fundamental genetic analysis of insect species and holds great promise for establishing strains that improve population control and behavior for practical application. This is especially so for insects that are disease vectors, many of which are currently subject to genomic sequence analysis, and intensive population control measures that must be improved for better efficacy and cost-effectiveness. Transposon-mediated germ-line transformation has been the ultimate goal for most fundamental and practical studies, and impressive strides have been made in recent development of transgene vector and marker systems for several mosquito species. This has resulted in rapid advances in functional genomic sequence analysis and new strategies for biological control based on conditional lethality. Importantly, advances have also been made in our ability to use these systems more effectively in terms of enhanced stability and targeting to specific genomic loci. Nevertheless, not all insects are currently amenable to germ-line transformation techniques, and thus advances in transient somatic expression and paratransgenesis have also been critical, if not preferable for some applications. Of particular importance is how this technology will be used for practical application. Early ideas for population replacement of indigenous pests with innocuous transgenic siblings by transposon-vector spread, may require reevaluation in terms of our current knowledge of the behavior of transposons currently available for transformation. The effective implementation of any control program using released transgenics, will also benefit from broadening the perspective of these control measures as being more mainstream than exotic.

Distribution of the transposable elements bilbo and gypsy in original and colonizing populations of Drosophila subobscura

Background

Transposable elements (TEs) constitute a substantial amount of all eukaryotic genomes. They induce an important proportion of deleterious mutations by insertion into genes or gene regulatory regions. However, their mutational capabilities are not always adverse but can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution and activity in the genomes of populations under different environmental and demographic regimes, is important to understand their role in species evolution. In this work we study the chromosomal distribution of two TEs, gypsy and bilbo, in original and colonizing populations of Drosophila subobscura to reveal the putative effect of colonization on their insertion profile.

Results

Chromosomal frequency distribution of two TEs in one original and three colonizing populations of D. subobscura, is different. Whereas the original population shows a low insertion frequency in most TE sites, colonizing populations have a mixture of high (frequency ≥ 10%) and low insertion sites for both TEs. Most highly occupied sites are coincident among colonizing populations and some of them are correlated to chromosomal arrangements. Comparisons of TE copy number between the X chromosome and autosomes show that gypsy occupancy seems to be controlled by negative selection, but bilbo one does not.

Conclusion

These results are in accordance that TEs in Drosophila subobscura colonizing populations are submitted to a founder effect followed by genetic drift as a consequence of colonization. This would explain the high insertion frequencies of bilbo and gypsy in coincident sites of colonizing populations. High occupancy sites would represent insertion events prior to colonization. Sites of low frequency would be insertions that occurred after colonization and/or copies from the original population whose frequency is decreasing in colonizing populations. This work is a pioneer attempt to explain the chromosomal distribution of TEs in a colonizing species with high inversion polymorphism to reveal the putative effect of arrangements in TE insertion profiles. In general no associations between arrangements and TE have been found, except in a few cases where the association is very strong. Alternatively, founder drift effects, seem to play a leading role in TE genome distribution in colonizing populations.

piggyBac-like elements in cotton bollworm, Helicoverpa armigera (Hübner)

Two piggyBac-like elements (PLEs) were identified in the cotton bollworm, Helicoverpa armigera, and were designated as HaPLE1 and HaPLE2. HaPLE1 is flanked by 16 bp inverted terminal repeats (ITRs) and the duplicated TTAA tetranucleotide, and contains an open reading frame (ORF) of 1794 bp with the presumed DDD domain, indicating that this element may be an active autonomously mobile element. HaPLE2 was found with the same ITRs, but lacks the majority of an ORF-encoding transposase. Thus, this element was thought to be a non-autonomous element. Transposable element displays and distribution of the two PLEs in individuals from three different H. armigera populations suggest that transmobilization of HaPLE2 by the transposase of HaPLE1 may be likely, and mobilization of HaPLE1 might occur not only within the same individual, but also among different individuals. In addition, horizontal transfer was probably involved in the evolution of PLEs between H. armigera and Trichoplusia ni.

Demographic histories of ERV-K in humans, chimpanzees and rhesus monkeys

We detected 19 complete endogenous retroviruses of the K family in the genome of rhesus monkey (Macaca mulatta; RhERV-K) and 12 full length elements in the genome of the common chimpanzee (Pan troglodytes; CERV-K). These sequences were compared with 55 human HERV-K and 20 CERV-K reported previously, producing a total data set of 106 full-length ERV-K genomes. Overall, 61% of the human elements compared to 21% of the chimpanzee and 47% of rhesus elements had estimated integration times less than 4.5 million years before present (MYBP), with an average integration times of 7.8 MYBP, 13.4 MYBP and 10.3 MYBP for HERV-K, CERV-K and RhERV-K, respectively. By excluding those ERV-K sequences generated by chromosomal duplication, we used 63 of the 106 elements to compare the population dynamics of ERV-K among species. This analysis indicated that both HERV-K and RhERV-K had similar demographic histories, including markedly smaller effective population sizes, compared to CERV-K. We propose that these differing ERV-K dynamics reflect underlying differences in the evolutionary ecology of the host species, such that host ecology and demography represent important determinants of ERV-K dynamics.

Evolutionary pathways of the tirant LTR retrotransposon in the Drosophila melanogaster subgroup of species

Tirant, a LTR retrotransposon with copies scattered over the chromosome arms of Drosophila melanogaster, is in the process of being lost from the chromosome arms of most natural populations of the sister species D. simulans. In an attempt to clarify the dynamics and evolution of tirant, we have studied the regulatory and reverse transcriptase regions in copies of the nine closely related species of the D. melanogaster subgroup. We show that tirant is mainly vertically transmitted in these species, with the exception of a horizontal transfer event from an ancestor of D. melanogaster to D. teissieri. We propose that, in four of the species (D. melanogaster, D. simulans, D. sechellia, and D. mauritiana), the observed patterns of evolution of the regulatory region vary with genome constraints and with the history and biogeography of the species.

Insertion polymorphism of transposable elements and population structure of Anopheles gambiae M and S molecular forms in Cameroon

The insertion polymorphism of five transposable element (TE) families was studied by Southern blots in several populations of the M and S molecular forms of the mosquito Anopheles gambiae sensu stricto from southern Cameroon. We showed that the mean TE insertion site number and the within-population insertion site polymorphism globally differed between the M and S molecular forms. The comparison of the TE insertion profiles of the populations revealed a significant differentiation between these two molecular forms (0.163 < Phi(ST) < 0.371). We cloned several insertions of a non-LTR retrotransposon (Aara8) that were fixed in one form and absent in the other one. The only insertion that could be clearly located on a chromosome arm mapped to cytological division 6 of chromosome X, confirming the importance of this region in the ongoing speciation between the M and S molecular forms.

Genome ecosystem and transposable elements species

Transposable elements are known to be "selfish DNA" sequences able to spread and be maintained in all genomes analyzed so far. Their evolution depends on the interaction they have with the other components of the genome, including genes and other transposable elements. These relationships are complex and have often been compared to those of species living and competing in an ecosystem. The aim of this current work is a proposition to fill the conceptual gap existing between genome biology and ecology, assuming that genomic components, such as transposable elements families, can be compared to species interacting in an ecosystem. Using this framework, some of the main models defined in the population genetics of transposable elements can then been reformulated, and some new kinds of realistic relationships, such as symbiosis between different genomic components, can then be modelled and explored.

Population genetics models of competition between transposable element subfamilies

Transposable elements are one of the major components of genomes. Some copies are fully efficient; i.e., they are able to produce the proteins needed for their own transposition, and they can move and duplicate into the genome. Other copies are mutated. They may have lost their moving ability, their coding capacity, or both, thus becoming pseudogenes slowly eliminated from the genome through deletions and natural selection. Little is known about the dynamics of such mutant elements, particularly concerning their interactions with autonomous copies. To get a better understanding of the transposable elements' evolution after their initial invasion, we have designed a population genetics model of transposable elements dynamics including mutants or nonfunctional sequences. We have particularly focused on the case where these sequences are nonautonomous elements, known to be able to use the transposition machinery produced by the autonomous ones. The results show that such copies generally prevent the system from achieving a stable transposition-selection equilibrium and that nonautonomous elements can invade the system at the expense of autonomous ones. The resulting dynamics are mainly cyclic, which highlights the similarities existing between genomic selfish DNA sequences and host-parasite systems.

The evolution of retrotransposon regulatory regions and its consequences on the Drosophila melanogaster and Homo sapiens host genomes

It has now been established that transposable elements (TEs) make up a variable, but significant proportion of the genomes of all organisms, from Bacteria to Vertebrates. However, in addition to their quantitative importance, there is increasing evidence that TEs also play a functional role within the genome. In particular, TE regulatory regions can be viewed as a large pool of potential promoter sequences for host genes. Studying the evolution of regulatory region of TEs in different genomic contexts is therefore a fundamental aspect of understanding how a genome works. In this paper, we first briefly describe what is currently known about the regulation of TE copy number and activity in genomes, and then focus on TE regulatory regions and their evolution. We restrict ourselves to retrotransposons, which are the most abundant class of eukaryotic TEs, and analyze their evolution and the subsequent consequences for host genomes. Particular attention is paid to much-studied representatives of the Vertebrates and Invertebrates, Homo sapiens and Drosophila melanogaster, respectively, for which high quality sequenced genomes are available.

TESD: a transposable element dynamics simulation environment

Various mathematical models have been used to explore the dynamics of transposable elements (TEs) within their host genomes. However, numerous factors can influence their dynamics, and we know only little about the dynamics of TEs when they first began to invade populations. In addition, the influence of population structuring has only recently been investigated. Transposable Element Simulator Dynamics, a population genomics simulation environment, has therefore been developed to provide a simple tool for analyzing the dynamics of TEs in a community based on (i) various TE parameters, such as the transposition and excision rates, the recombination rate and the coefficient of selection against TE insertions; and (ii) population parameters, such as population size and migration rates. The simulations can be used to illustrate the dynamic fate of TEs in structured populations, can be extended by using more specific molecular or demographic models, and can be useful for teaching population genetics and genomics.

AVAILABILITY

TESD is distributed under GPL from the Pôle Bioinformatique Lyonnais (PBIL) web server at http://pbil.univ-lyon1.fr/software/TESD

piggyBac-like elements in the tobacco budworm, Heliothis virescens (Fabricius)

We identified two different groups of piggyBac-like elements (PLE) in the tobacco budworm, Heliothis virescens, and named them HvPLE1 and HvPLE2. An intact copy of HvPLE1 revealed the characteristics of PLE: inverted terminal repeats, inverted subterminal repeats, and an open reading frame encoding transposase, whereas other HvPLE1 copies and all the HvPLE2 copies carried disruptive mutations in the region encoding transposase. We also identified none to two bands per genome hybridized to a probe of Trichoplusia ni piggyBac in genomic Southern blotting, which are different from HvPLE1 or HvPLE2. Analysis of the sequences of multiple copies of HvPLE1 and HvPLE2 suggests that the PLEs are closely related to the T. ni piggyBac, of relatively young age, and independently entered the H. virescens genome.

Ongoing loss of the tirant transposable element in natural populations of Drosophila simulans

Tirant is a long terminal repeat (LTR) retrotransposon with an average of 11 insertion sites on the chromosome arms of Drosophila melanogaster flies collected from natural populations worldwide. In the sibling species Drosophila simulans, tirant is found only in African populations, which harbor a few insertion sites (1 to 5) on the chromosome arms, although some tirant sequences are present in the heterochromatin of most populations. This distribution in D. simulans reflects either the recent genomic invasion of African populations by a new variant of tirant, or a loss of tirant from the entire species apart from some sequence relics still present in Africa. In an attempt to clarify the situation, we focused on the LTR-UTR region of tirant copies from various populations of both D. melanogaster and D. simulans. We found two distinct types of regulatory region: one type was present in both D. melanogaster and D. simulans, and the other was present only in D. simulans. Copies of this latter type of tirant were transcriptionally inactive in gonads. Here we propose that the present day distribution of tirant in D. simulans populations reflects an ancient invasion of D. simulans by tirant copies followed by the loss of active copies from most populations, apart from the African ones, suggesting that this loss is still ongoing in this species.

Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes

Nuclear inserted copies of mitochondrial origin (numts) vary widely among eukaryotes, with human and plant genomes harboring the largest repertoires. Numts were previously thought to be absent from fish species, but the recent release of three fish nuclear genome sequences provides the resource to obtain a more comprehensive insight into the extent of mtDNA transfer in fishes. From the sequence analyses of the genomes of Fugu rubripes, Tetraodon nigroviridis, and Danio rerio, we have identified 2, 5, and 10 recent numt integrations, respectively, which integrated into those genomes less than 0.6 million years (Myr) ago. Such results contradict the hypothesis of absence or rarity of numts in fishes, as (i) the ratio of numts to the total size of the nuclear genome in T. nigroviridis was superior to the ratio observed in several higher vertebrate species (e.g., chicken, mouse, and rat), and only surpassed by humans, and (ii) the mtDNA coverage transferred to the nuclear genome of D. rerio is exceeded only by human and mouse, within the whole range of eukaryotic genomes surveyed for numts. Additionally, 335, 336, and 471 old numts (>12.5 Myr) were detected in F. rubripes, T. nigroviridis, and D. rerio, respectively. Surprisingly, old numts are inserted preferentially into known or predicted genes, as inferred for recent numts in human. However, because in fish genomes such integrations are old, they are likely to represent evolutionary successes and they may be considered a potential important evolutionary mechanism for the enhancement of genomic coding regions.