On the theory of speciation induced by transposable elements

Structural Variants and Speciation: Multiple Processes at Play

Research on the genomic architecture of speciation has increasingly revealed the importance of structural variants (SVs) that affect the presence, abundance, position, and/or direction of a nucleotide sequence. SVs include large chromosomal rearrangements such as fusion/fissions and inversions and translocations, as well as smaller variants such as duplications, insertions, and deletions (CNVs). Although we have ample evidence that SVs play a key role in speciation, the underlying mechanisms differ depending on the type and length of the SV, as well as the ecological, demographic, and historical context. We review predictions and empirical evidence for classic processes such as underdominance due to meiotic aberrations and the coupling effect of recombination suppression before exploring how recent sequencing methodologies illuminate the prevalence and diversity of SVs. We discuss specific properties of SVs and their impact throughout the genome, highlighting that multiple processes are at play, and possibly interacting, in the relationship between SVs and speciation.

P-elements strengthen reproductive isolation within the Drosophila simulans species complex

Determining mechanisms that underlie reproductive isolation (RI) is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in modulating the strength of RI between species is poorly understood. Several species of Drosophila have been found to harbor P-elements (PEs), yet only D. simulans is known to be currently polymorphic for their presence in wild populations. PEs can cause RI between PE-containing (P) and PE-lacking (M) lineages of the same species. However, it is unclear whether they also contribute to the magnitude of RI between species. Here, we use the simulans species complex to assess whether differences in PE status between D. simulans and its sister species, which do not harbor PEs, contribute to multiple barriers to gene flow between species. We show that crosses involving a P D. simulans father and an M mother from a sister species exhibit lower F1 female fecundity than crosses involving an M D. simulans father and an M sister-species mother. We also find that another TE, I-element, might play a minor role in determining the frequency of dysgenesis between species. Our results suggest that the presence of PEs in a species can strengthen isolation from its sister species, providing evidence that TEs can play a role in RI.

Tirant Stealthily Invaded Natural Drosophila melanogaster Populations during the Last Century

It was long thought that solely three different transposable elements (TEs)-the I-element, the P-element, and hobo-invaded natural Drosophila melanogaster populations within the last century. By sequencing the "living fossils" of Drosophila research, that is, D. melanogaster strains sampled from natural populations at different time points, we show that a fourth TE, Tirant, invaded D. melanogaster populations during the past century. Tirant likely spread in D. melanogaster populations around 1938, followed by the I-element, hobo, and, lastly, the P-element. In addition to the recent insertions of the canonical Tirant, D. melanogaster strains harbor degraded Tirant sequences in the heterochromatin which are likely due to an ancient invasion, likely predating the split of D. melanogaster and D. simulans. These degraded insertions produce distinct piRNAs that were unable to prevent the novel Tirant invasion. In contrast to the I-element, P-element, and hobo, we did not find that Tirant induces any hybrid dysgenesis symptoms. This absence of apparent phenotypic effects may explain the late discovery of the Tirant invasion. Recent Tirant insertions were found in all investigated natural populations. Populations from Tasmania carry distinct Tirant sequences, likely due to a founder effect. By investigating the TE composition of natural populations and strains sampled at different time points, insertion site polymorphisms, piRNAs, and phenotypic effects, we provide a comprehensive study of a natural TE invasion.

The Role of Transposable Elements in Speciation

Understanding the phenotypic and molecular mechanisms that contribute to genetic diversity between and within species is fundamental in studying the evolution of species. In particular, identifying the interspecific differences that lead to the reduction or even cessation of gene flow between nascent species is one of the main goals of speciation genetic research. Transposable elements (TEs) are DNA sequences with the ability to move within genomes. TEs are ubiquitous throughout eukaryotic genomes and have been shown to alter regulatory networks, gene expression, and to rearrange genomes as a result of their transposition. However, no systematic effort has evaluated the role of TEs in speciation. We compiled the evidence for TEs as potential causes of reproductive isolation across a diversity of taxa. We find that TEs are often associated with hybrid defects that might preclude the fusion between species, but that the involvement of TEs in other barriers to gene flow different from postzygotic isolation is still relatively unknown. Finally, we list a series of guides and research avenues to disentangle the effects of TEs on the origin of new species.

Inferring transposons activity chronology by TRANScendence - TEs database and de-novo mining tool

Background

The constant progress in sequencing technology leads to ever increasing amounts of genomic data. In the light of current evidence transposable elements (TEs for short) are becoming useful tools for learning about the evolution of host genome. Therefore the software for genome-wide detection and analysis of TEs is of great interest.

Results

Here we describe the computational tool for mining, classifying and storing TEs from newly sequenced genomes. This is an online, web-based, user-friendly service, enabling users to upload their own genomic data, and perform de-novo searches for TEs. The detected TEs are automatically analyzed, compared to reference databases, annotated, clustered into families, and stored in TEs repository. Also, the genome-wide nesting structure of found elements are detected and analyzed by new method for inferring evolutionary history of TEs.

We illustrate the functionality of our tool by performing a full-scale analyses of TE landscape in Medicago truncatula genome.

Conclusions

TRANScendence is an effective tool for the de-novo annotation and classification of transposable elements in newly-acquired genomes. Its streamlined interface makes it well-suited for evolutionary studies.

A genome-wide survey of genetic instability by transposition in Drosophila hybrids

Hybridization between species is a genomic instability factor involved in increasing mutation rate and new chromosomal rearrangements. Evidence of a relationship between interspecific hybridization and transposable element mobilization has been reported in different organisms, but most studies are usually performed with particular TEs and do not discuss the real effect of hybridization on the whole genome. We have therefore studied whole genome instability of Drosophila interspecific hybrids, looking for the presence of new AFLP markers in hybrids. A high percentage (27–90%) of the instability markers detected corresponds to TEs belonging to classes I and II. Moreover, three transposable elements (Osvaldo, Helena and Galileo) representative of different families, showed an overall increase of transposition rate in hybrids compared to parental species. This research confirms the hypothesis that hybridization induces genomic instability by transposition bursts and suggests that genomic stress by transposition could contribute to a relaxation of mechanisms controlling TEs in the Drosophila genome.

Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis

Background

Extensive DNA rearrangement of genic colinearity, as revealed by comparison of orthologous genomic regions, has been shown to be a general concept describing evolutionary dynamics of plant genomes. However, the nature, timing, lineages and adaptation of local genomic rearrangement in closely related species (e.g., within a genus) and haplotype variation of genomic rearrangement within populations have not been well documented.

Results

We previously identified a hotspot for genic rearrangement and transposon accumulation in the Orp region of Asian rice (Oryza sativa, AA) by comparison with its orthologous region in sorghum. Here, we report the comparative analysis of this region with its orthologous regions in the wild progenitor species (O. nivara, AA) of Asian rice and African rice (O. glaberrima) using the BB genome Oryza species (O. punctata) as an outgroup, and investigation of transposon insertion sites and a segmental inversion event in the AA genomes at the population level. We found that Orp region was primarily and recently expanded in the Asian rice species O. sativa and O. nivara. LTR-retrotransposons shared by the three AA-genomic regions have been fixed in all the 94 varieties that represent different populations of the AA-genome species/subspecies, indicating their adaptive role in genome differentiation. However, LTR-retrotransposons unique to either O. nivara or O. sativa regions exhibited dramatic haplotype variation regarding their presence or absence between or within populations/subpopulations.

Conclusions

The LTR-retrotransposon insertion hotspot in the Orp region was formed recently, independently and concurrently in different AA-genome species, and that the genic rearrangements detected in different species appear to be differentially triggered by transposable elements. This region is located near the end of the short arm of chromosome 8 and contains a high proportion of LTR-retrotransposons similar to observed in the centromeric region of this same chromosome, and thus may represent a genomic region that has recently switched from euchromatic to heterochromatic states. The haplotype variation of LTR-retrotransposon insertions within this region reveals substantial admixture among various subpopulations as established by molecular markers at the whole genome level, and can be used to develop retrotransposon junction markers for simple and rapid classification of O. sativa germplasm.

Echoes from the past--are we still in an RNP world?

Availability of the human genome sequence and those of other species is unmeasured in their value for a comprehensive understanding of the architecture, function and evolution of genomes and cells. Various mechanisms keep genomes in flux and generate intra- and interspecies variation. The conversion of RNA modules into DNA and their more or less random integration into chromosomes (retroposition) is in many lineages including our own the most pervasive and perhaps the most enigmatic. The proclivity of such events in extant multicellular eukaryotes, even in more recent evolutionary times, gives the impression that the transition period from the RNP (ribonucleoprotein) world to the emergence of modern cells, where DNA became the predominant carrier of genetic information, has lasted billions of years and is an endlessly drawn-out process rather than the punctuated event one might expect. Apart from the impact of such RNA-mediated processes as retroposition, the role of RNA in a wide variety of cellular functions has only recently become more widely appreciated.

Modeling the amplification dynamics of human Alu retrotransposons

Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA) that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed a computer simulation that incorporates several known aspects of primate Alu retrotransposon biology and accommodates sampling effects resulting from the methods by which mobile elements are typically discovered and characterized. By modeling a number of amplification scenarios and comparing simulation-generated expectations to empirical data gathered from existing Alu subfamilies, we were able to statistically reject a number of amplification scenarios for individual subfamilies, including that of a rapid expansion or explosion of Alu amplification at the time of human–chimpanzee divergence.

Nearly 50% of the human genome is composed of mobile elements. While much of this sequence consists of inactive “fossil” elements that are no longer actively moving or generating new copies, three families are currently proliferating in human genomes. Among these, the Alu lineage has reached a copy number of over 1 million and alone accounts for approximately 10% of the genome. While considerable evidence has been gathered concerning the underlying biological mechanisms of Alu mobilization and proliferation, a detailed understanding of Alu amplification history is currently lacking. Researchers are aware, for example, that several thousand Alu elements have inserted within the human genome since the divergence of humans and chimpanzees, but how those insertions were distributed over this ~6-million-year time period is currently unknown. In this work, the authors introduce a simulation framework that seeks to incorporate both sequence diversity and empirically gathered population data from human Alu elements, in order to provide a better understanding of the last several million years of human Alu evolution. The results suggest that a rapid explosion of Alu amplification at the time of the human–chimpanzee divergence is unlikely. Therefore, it is improbable that an increase in Alu retrotransposition activity was involved in the speciation of humans and chimpanzees.

Dynamics of molecular markers linked to the resistance loci in a mosquito-Plasmodium system

Models on the evolution of resistance to parasitism generally assume fitness tradeoffs between the costs of being parasitized and the costs associated with resistance. This study tested this assumption using the yellow fever mosquito Aedes aegypti and malaria parasite Plasmodium gallinaceum system. Experimental mosquito populations were created by mixing susceptible and resistant strains in equal proportions, and then the dynamics of markers linked to loci for Plasmodium resistance and other unlinked neutral markers were determined over 12 generations. We found that when the mixed population was maintained under parasite-free conditions, the frequencies of alleles specific to the susceptible strain at markers closely linked to the loci for resistance (QTL markers) as well as other unlinked markers increased significantly in the first generation and then fluctuated around equilibrium frequencies for all six markers. However, when the mixed population was exposed to an infected blood meal every generation, allele frequencies at the QTL markers for resistance were not significantly changed. Small population size caused significant random fluctuations of allele frequencies at all marker loci. Consistent allele frequency changes in the QTL markers and other unlinked markers suggest that the reduced fitness in the resistant population has a genome-wide effect on the genetic makeup of the mixed population. Continuous exposure to parasites promoted the maintenance of alleles from the resistant Moyo-R strain in the mixed population. The results are discussed in relation to the proposed malaria control strategy through genetic disruption of vector competence.

A theoretical approach to predicting the success of genetic manipulation of malaria mosquitoes in malaria control

BACKGROUND

Mosquitoes that have been genetically modified to better encapsulate the malaria parasite Plasmodium falciparum are being considered as a possible tool in the control of malaria. Hopes for this have been raised with the identification of genes involved in the encapsulation response and with advances in the tools required to transform mosquitoes. However, we have only very little understanding of the conditions that would allow such genes to spread in natural populations.

METHODS

We present here a theoretical model that combines population genetical and epidemiological processes, thereby allowing one to predict not only these conditions (intensity of transmission, evolutionary cost of resistance, tools used to drive the genes) but also the impact of the spread of refractoriness on the prevalence of the disease.

RESULTS

The main conclusions are 1) that efficient transposons will generally be able to drive genes that confer refractoriness through populations even if there is a substantial (evolutionary) cost of refractoriness, but 2) that this will decrease malaria prevalence in the human population substantially only if refractoriness is close to 100% effective.

CONCLUSIONS

If refractoriness is less than 100% effective (because of, for example, environmentally induced variation in the effectiveness of the mosquito's immune response), control programmes based on genetic manipulation of mosquitoes will have very little impact on the epidemiology of malaria, at least in areas with intense transmission.

The role of selfish genetic elements in eukaryotic evolution

'Selfish genetic elements', such as transposons, homing endonucleases, meiotic drive chromosomes and heritable microorganisms, are common features of eukaryotes. However, their importance in the evolution of eukaryotic genomes is still controversial. In this review, we discuss these diverse elements and their potential importance in the evolution of genetic systems, adaptation, and the extinction and birth of species.

Perspective: transposable elements, parasitic DNA, and genome evolution

The nature of the role played by mobile elements in host genome evolution is reassessed considering numerous recent developments in many areas of biology. It is argued that easy popular appellations such as "selfish DNA" and "junk DNA" may be either inaccurate or misleading and that a more enlightened view of the transposable element-host relationship encompasses a continuum from extreme parasitism to mutualism. Transposable elements are potent, broad spectrum, endogenous mutators that are subject to the influence of chance as well as selection at several levels of biological organization. Of particular interest are transposable element traits that early evolve neutrally at the host level but at a later stage of evolution are co-opted for new host functions.

Phylogenetic analysis of a retroposon family as represented on the human X chromosome

SINE-R elements constitute a class of retroposons derived from the long terminal repeat (LTR) of the human endogenous retrovirus HERV-K family that are present in hominoid primates and active in the human genome. In an investigation of the X chromosome, we identified twenty-five SINE-R elements with between 89.6 and 97.7% homology with the SINE-R.C2 element that is human specific, originally identified in the gene for the C2 component of complement. SINE-R.C2 and a sequence HS307 that we previously identified in a region of Xq21.3 that has a recently created homology with a 4 Mb block in Yp11.2 are amongst the group of elements that have diverged furthest from the parent HERV-K10 sequence. The sequence on the X chromosome resemble those that we previously described on chromosomes 7 and 17 and the Y chromosome, with a similar range of variation. Phylogenetic analysis from the retroposon family including those of African great apes using the neighbor-joining method suggests that the SINE-R retroposon family have evolved independently during primate evolution. Further investigation of SINE-R elements on the sex chromosomes, particularly in recently created regions of X-Y homology, may cast light on the timing of the retroposition process and its possible relevance to recent evolutionary change.

UV light induces IS10 transposition in Escherichia coli

A new mutagenesis assay system based on the phage 434 cI gene carried on a low-copy number plasmid was used to investigate the effect of UV light on intermolecular transposition of IS10. Inactivation of the target gene by IS10 insertion was detected by the expression of the tet gene from the phage 434 PR promoter, followed by Southern blot analysis of plasmids isolated from TetR colonies. UV irradiation of cells harboring the target plasmid and a donor plasmid carrying an IS10 element led to an increase of up to 28-fold in IS10 transposition. Each UV-induced transposition of IS10 was accompanied by fusion of the donor and acceptor plasmid into a cointegrate structure, due to coupled homologous recombination at the insertion site, similar to the situation in spontaneous IS10 transposition. UV radiation also induced transposition of IS10 from the chromosome to the target plasmid, leading almost exclusively to the integration of the target plasmid into the chromosome. UV induction of IS10 transposition did not depend on the umuC and uvrA gene product, but it was not observed in lexA3 and DeltarecA strains, indicating that the SOS stress response is involved in regulating UV-induced transposition. IS10 transposition, known to increase the fitness of Escherichia coli, may have been recruited under the SOS response to assist in increasing cell survival under hostile environmental conditions. To our knowledge, this is the first report on the induction of transposition by a DNA-damaging agent and the SOS stress response in bacteria.

Selfish DNA as a method of pest control

The inheritance of most genes is tightly controlled, governed by the rules of mendelian inheritance if nuclear or uniparental inheritance if cytoplasmic. A few notable genes and cytoplasmic genomes have escaped this regulation. Such genes may spread by increasing their own rate of transmission despite reducing host fitness and may be regarded as 'selfish'. Their population genetics are described and it appears they may impose a significant genetic load on the host population. Modern molecular techniques may enable similar loads to be imposed on pest species either by transferring selfish genes between species, or by linking deleterious genes to a selfish locus. Alternatively, 'modifier' genes that eliminate the virulent, or disease vectorial capacity, of the pest population may be introduced by linkage to a selfish locus. Selfish elements present in multiple copies may be preferable to single-copy elements as the former are capable of a larger reduction in host fitness. The practical application of these agents depends on five factors: (i) the rate of 'reversion' to a non-selfish form; (ii) the evolution of host repressor systems; (iii) their effect on host fitness, which determines their rate of invasion; (iv) the mechanism regulating host population size in the field; and (v) their ease of manipulation in the laboratory. The first two factors are the most uncertain in most systems, but should be amenable to experimental analysis. It is proposed that the development of such techniques may result in powerful new methods of population control which may be applied to both agricultural pests and disease vectors.

The ebb and flow of a fungal genome

Transposable DNA elements have only recently been described in a few species of filamentous fungi, but may be more abundant than previously believed. Several different elements have been isolated from the rice blast pathogen Magnaporthe grisea. The distribution and amplification of these elements suggest a potential role in the evolution of the fungal genome.

The evolution of coexisting highly divergent LINE-1 subfamilies within the rodent genus Peromyscus

Two distinct members of the LINE-1 (L1) family in Peromyscus were characterized. The two clones, denoted L1Pm55 and L1Pm62, were 1.5 kb and 1.8 kb in length, respectively, and align to the identical region of the L1 sequence of Mus domesticus. Sequence similarity was on the order of 70% between L1Pm55 and L1Pm62, which approximates that between either Peromyscus sequence and Mus L1. L1Pm62 represents a more prevalent subfamily than L1Pm55. L1Pm62 exists in about 500 copies per haploid genome, while L1Pm55 exists in about 100 copies. The existence of major and minor subpopulations of L1 within Peromyscus is in contrast to murine rodents and higher primates, where L1 copy number is on the order of 20,000 to 100,000, and where levels of intraspecific divergence among L1 elements are typically less than 15-20%. Additional Peromyscus clones are similarly divergent from both L1Pm62 and L1Pm55, implying the existence of more than two distinct L1 subfamilies. The highly divergent L1 subfamilies in Peromyscus apparently have been evolving independently for more than 25 million years, preceding the divergence of cricetine and murine rodents. Investigations of the evolution of L1 within Peromyscus by restriction and Southern analysis was performed using species groups represented by the partially interfertile species pairs P. maniculatus-P. polionotus, P. leucopus-P. gossypinus, and P. truei-P. difficilis of the nominate subgenus and P. californicus of the Haplomylomys subgenus. Changes in L1 and species group taxonomic boundaries frequently coincided. The implications for phylogeny are discussed.

Can transposable elements be used to drive disease refractoriness genes into vector populations?

A number of biological procedures are currently being considered as alternatives to insecticide-based methods for the control of insect vectors of disease. Among these are the adaptation of various genetic mechanisms to drive genes of interest, such as refractoriness to malaria in mosquitoes, into natural populations, for vector control purposes. Here, Margaret Kidwell and Jose Ribeiro develop a rationale for the possible use of transposable genetic elements, one of these potential drive mechanisms, and some of the problems being faced in seeking to determine the feasibility of such a strategy are described.

I elements and the Drosophila genome

LINEs are a large class of transposable elements in eukaryotes. They transpose by reverse transcription of an RNA intermediate. I elements of Drosophila melanogaster belong to this class and are responsible for the I-R system of hybrid dysgenesis. Many results indicate that at the beginning of the century natural populations of this species were devoid of active I elements and that they were invaded by functional I elements in the last decades. Many Drosophila species contain both defective and active I elements. It seems that the latter were lost in Drosophila melanogaster before its spread throughout the world, and that the recent invasion results from the spread of functional elements originating either from another species by horizontal transfer or from an isolated population of the same species. These data are discussed, as well as their significance in evolutionary processes.

A branching-process model for the evolution of transposable elements incorporating selection

We have formulated a very general mathematical model to analyze the evolution of transposable genetic elements in prokaryotic populations. Transposable genetic elements are DNA sequences able to replicate and insert copies of themselves at new locations in the genome. This work characterizes the equilibrium distribution of copy number under the influence of copy number-dependent selection, transposition and deletion. Our principal results concern the equilibrium distribution of copy number in response to various selective regimes. For particular transposition patterns (e.g., unregulated transposition or copy number-dependent transposition), equilibrium distributions are calculated numerically for a variety of specific selection patterns. Selection is quantified through specification of the expected number of offspring for individuals of each type, which is generally a non-increasing function of copy number, in accord with the usual evolutionary speculations.

Nonreciprocal gonadal dysgenesis in hybrids of the chironomid midge Chironomus thummi. IV. Behavior of a female-specific protein, probably a vitellogenin

Using denaturing SDS-polyacrylamide gel electrophoresis, a protein with a subunit MW of about 148,000 daltons could be detected in the fat body of females of the reciprocal hybrids of Chironomus thummi thummi and Chironomus thummi piger, which is not present in males. This protein is presumably a vitellogenin and can be found in both hybrids during the late fourth-instar larval stage until eclosion of the adults, i.e., in early vitellogenesis. After eclosion, the reciprocal hybrids behave differently concerning the 148-kd protein. In females of the piger female x thummi male cross, which are fertile and produce yolky eggs, the 148-kd protein disappears from the fat body immediately after eclosion. In females of the reciprocal cross (thummi female x piger male) which are affected by gonadal dysgenesis and in which the oocytes only rarely contain yolk, the 148-kd protein is still present in the fat body of the adult up to 50 hr after eclosion until the fat body degrades. It is concluded that the inability of the sterile thummi female x piger male females to produce yolky eggs is caused by an impaired uptake of the presumed 148-kd vitellogenin into oocytes and not by a defective vitellogenesis. The impaired vitellogenin deposition into oocytes is taken as another aberrant trait of gonadal dysgenesis of the thummi female x piger male hybrids.

A population genetical model for sequence evolution under multiple types of mutation

DNA sequencing and restriction mapping provide us with information on DNA sequence evolution within populations, from which the phylogenetic relationships among the sequences can be inferred. Mutations such as base substitutions, deletions, insertions and transposable element insertions can be identified in each sequence. Theoretical study of this type of sequence evolution has been initiated recently. In this paper, population genetical models for sequence evolution under multiple types of mutation are developed. Models of infinite population size with neutral mutation, infinite population size with deleterious mutation and finite population size with neutral mutation are considered.

Mutation rates in hybrids between sibling species of Drosophila

It has recently been suggested that sterility or inviability in species hybrids might result from the movement of transposable elements. Because such movement is often detectable by an increased mutation rate, I studied the effect of interspecific hybridization in the Drosophila melanogaster group on the mutation rate of X-linked visibles. This rate did not differ between hybrids and intraspecific controls. This was also true for the germ-line excision rate of a transposable element, although the rate of somatic excision was two to sixfold higher in hybrids than in pure species. Combined with previous work, these results do not support a role for transposable elements in speciation.

The maintenance of transposable elements in natural populations

Models of the maintenance of transposable elements in randomly mating host populations are reviewed. It is shown that the data on the distribution of copy numbers between individuals are largely concordant with what is expected on the basis of the Mendelian transmission of elements. The role of regulation of rates of transposition, and of various modes of natural selection, in maintaining an equilibrium in copy numbers in the face of transpositional increase in copy number is discussed. Tests for the role of selection against insertional mutations and against chromosome rearrangements induced by exchange between homologous elements located at nonhomologous chromosome locations are discussed. Reasons for expecting elements to accumulate in chromosome regions where crossing over is restricted are discussed, and data suggesting the existence of such an effect are described. Theory and data on the probability distribution of element frequencies at individual chromosomal sites are described. It is concluded that the available population data are consistent with the notion that element abundances are largely controlled by the interaction of transpositional increase in copy number with opposing forces.

Evolution of P transposable elements: sequences of Drosophila nebulosa P elements

P elements have been cloned and sequenced from Drosophila nebulosa. Their sequences have diverged less than 6% from P elements of Drosophila melanogaster. However D. nebulosa P elements have nucleotide changes that close all four open reading frames found in the D. melanogaster P element. Microinjection experiments show that D. nebulosa P elements cannot provide transposase function for D. melanogaster P elements, nor are D. nebulosa P elements mobilized by the transposase provided by a D. melanogaster P factor. Three D. nebulosa P elements appear to have integrated into the same position of a complex, centromeric repeated sequence. Comparison of nucleotide sequences suggests that D. nebulosa P elements have diverged upon different pathways from a common ancestor that was 99% homologous to the P elements of D. melanogaster.

Pleiotropic effects of environment-sensitive genes affecting fitness in relation to postmating reproductive isolation

With regard to speciation in sexually reproducing organisms, some population geneticists continue to argue about the relative merits of sympatry versus allopatry. However, all workers seem quite comfortable with the conventional scenario depicting how reproductive isolation arises between subpopulations in the state of incipient speciation. This view according to which the evolution of reproductive isolation mainly results from some genetic divergence consecutive to a substantial restriction in gene flow is questioned here. A verbal model is described in which gene flow is no longer seen as being first interrupted by a mere physical barrier. The model is based on limited genetic changes at loci influencing fitness but it places two important constraints on the properties of the genetic elements involved in it. One of them is concerned with the environment-sensitivity of the mutations implicated in the process, and the other with their presumed pleiotropic action on a behavioural trait.

The detection of deleterious selection using ancestors inferred from a phylogenetic history

The widespread use of restriction endonucleases and DNA sequencing provides a wealth of data on the genetic structure of natural populations. From such data, detailed phylogenies can be constructed and qualitatively different kinds of mutational and substitutional processes can be studied. A neutral model can be constructed to describe the frequencies of sequence haplotypes according to the haplotypes from which they arose and the types of substitution that distinguish them. One feature of such a model is that it examines the ancestors of various sequences. Deleterious selection against a character has a distinct effect on descendant sequences. Individuals containing many deleterious characters leave few or no descendants because these individuals are quickly eliminated by selection. Hence, such a model lends itself to the study of deleterious selection. It is possible to determine if selection is required by searching for any set of mutation rates that can explain an observed set of data. Simulations of artificial populations without selection suggest that this method seldom indicates selection when none is present. Furthermore, recent recombination events between the sequences do not induce false indications of deleterious selection. The method may, however, require relatively large simple sizes in order to accurately reflect the true nature of populations. The method is often very conservative and may not indicate selection when it is, in fact, present.

Molecular population genetics of the alcohol dehydrogenase gene region of Drosophila melanogaster

Variation in the DNA restriction map of a 13-kb region of chromosome II including the alcohol dehydrogenase structural gene (Adh) was examined in Drosophila melanogaster from natural populations. Detailed analysis of 48 D. melanogaster lines representing four eastern United States populations revealed extensive DNA sequence variation due to base substitutions, insertions and deletions. Cloning of this region from several lines allowed characterization of length variation as due to unique sequence insertions or deletions [nine sizes; 21-200 base pairs (bp)] or transposable element insertions (several sizes, 340 bp to 10.2 kb, representing four different elements). Despite this extensive variation in sequences flanking the Adh gene, only one length polymorphism is clearly associated with altered Adh expression (a copia element approximately 250 bp 5' to the distal transcript start site). Nonetheless, the frequency spectra of transposable elements within and between Drosophila species suggests they are slightly deleterious. Strong nonrandom associations are observed among Adh region sequence variants, ADH allozyme (Fast vs. Slow), ADH enzyme activity and the chromosome inversion ln(2L)t. Phylogenetic analysis of restriction map haplotypes suggest that the major twofold component of ADH activity variation (high vs. low, typical of Fast and Slow allozymes, respectively) is due to sequence variation tightly linked to and possibly distinct from that underlying the allozyme difference. The patterns of nucleotide and haplotype variation for Fast and Slow allozyme lines are consistent with the recent increase in frequency and spread of the Fast haplotype associated with high ADH activity. These data emphasize the important role of evolutionary history and strong nonrandom associations among tightly linked sequence variation as determinants of the patterns of variation observed in natural populations.

Introns as relict retrotransposons: implications for the evolutionary origin of eukaryotic mRNA splicing mechanisms

A model is presented for the evolutionary origin of intron sequences within eukaryotic protein-coding genes. We propose that introns are the vestiges of transposable elements and, specifically, that they represent a novel class of retrovirus-like transposons. The attraction of the retrotransposon model is that it gives the RNA splicing mechanism a central role in the evolution of introns. There is a growing body of evidence to suggest that several aspects of splicing are intron-encoded. Consequently, it is reasonable to look for evolutionary explanations of the splicing mechanism in the context of the evolution of the intron sequences themselves. According to this model the ancestral intron genomes were replicated into RNA copies simply because of their insertion within transcriptionally active regions of the host genome. Splicing was necessary not only to minimize their negative effects on host gene expression, but also, and perhaps more importantly, to generate new copies of the intron genome free of flanking exon sequences. These spliced intron copies were then available for reverse transcription and reinsertion elsewhere in the genome. Thus, splicing can be seen as an essential step in the intron replication cycle. Most modern introns have probably lost the majority of their original genetic content and may be considered as degenerate evolutionary relicts. An exception to this degeneracy is the set of splicing signals which must be retained because of its continued importance to host cell survival.(ABSTRACT TRUNCATED AT 250 WORDS)

The evolution of self-regulated transposition of transposable elements

This paper examines the conditions under which self-regulated rates of transposition can evolve in populations of transposable elements infecting sexually reproducing hosts. Models of the evolution of both cis-acting regulation (transposition immunity) and trans-acting regulation (transposition repression) are analyzed. The potential selective advantage to regulation is assumed to be derived from the deleterious effects of mutations associated with the insertion of newly replicated elements. It is shown that both types of regulation can easily evolve in hosts with low rates of genetic recombination per generation, such as bacteria or bacterial plasmids. Conditions are much more restrictive in organisms with relatively free recombination. In haploids, the main selective force promoting regulation is the induction of lethal or sterile mutations by transposition; in diploids, a sufficiently high frequency of dominant lethal or sterile mutations associated with transpositions is required. Data from Drosophila and maize suggest that this requirement can sometimes be met. Coupling of regulatory effects across different families of elements would also aid the evolution of regulation. The selective advantages of restricting transposition to the germ line and of excising elements from somatic cells are discussed.

The population biology of transposable elements

A transposable element can be defined as a DNA sequence capable of moving to new sites in the genome. Such DNA sequences have been described in a wide range of organisms. The evolutionary processes affecting transposable elements can thus be divided into two categories: changes in sequence and changes in genomic location. As with other types of evolutionary change, the nature of the evolutionary process will be reflected in the extent and type of genetic variation existing in wild populations. Quantitative models of the evolution of transposable element sequences and positions will be outlined, and related to relevant data. The extent to which models designed to describe obvious transposable elements such as the mobile sequences of Drosophila are also applicable to interspersed repetitive DNAs from other species will be discussed.

Genetic studies of three sibling species of Drosophila with relationship to theories of speciation

Drosophila melanogaster,D. simulansandD. mauritianaare closely related species, the first two cosmopolitan and the last restricted to the oceanic island of Mauritius.D. simulansandD. mauritianaare the most closely related pair, with the latter species probably resulting from a founder event. The relatedness of the three species and their ability to hybridize allow tests of recent theories of speciation. Genetic analysis of two characters differing betweenD. simulansandD. mauritiana(sex comb tooth number and testis colour) show that the differences are due to at least five and three loci respectively. Behavioural tests further demonstrate that sex combs are probably used by males at a crucial step in mating, and that the differences between the two species may be related to differences in their mating ability. These genetic studies and previous work indicate that differences among these species are polygenic and not (as proposed by recent theories) attributable to only one or two loci of large effect. Further studies of interspecific hybrids show that genetic divergence leading to developmental anomalies is more advanced in the older species pairD. simulans/D. melanogaeterthan in the younger pairD. simulans/D. mauritiana. This supports the neo-Darwinian contention that reproductive isolation is one step in a continuous process of genetic change among isolated populations, and does not support current theories that such change occurs only during the evolution of reproductive isolation. Finally, investigations of the degree of gonadal atrophy and its sensitivity to temperature inD. simulans/D. mauritianahybrids fail to support recent speculations that phenomena similar to hybrid dysgenesis (which causes such atrophy inD. melanogaster) play a role in speciation.