Inversions In Natural Populations Research Articles

Inversion Genotyping in the Anopheles gambiae Complex Using High-Throughput Array and Sequencing Platforms.

Chromosomal inversion polymorphisms have special importance in the Anopheles gambiae complex of malaria vector mosquitoes, due to their role in local adaptation and range expansion. The study of inversions in natural populations is reliant on polytene chromosome analysis by expert cytogeneticists, a process that is limited by the rarity of trained specialists, low throughput, and restrictive sampling requirements. To overcome this barrier, we ascertained tag single nucleotide polymorphisms (SNPs) that are highly correlated with inversion status (inverted or standard orientation). We compared the performance of the tag SNPs using two alternative high throughput molecular genotyping approaches vs. traditional cytogenetic karyotyping of the same 960 individual An. gambiae and An. coluzzii mosquitoes sampled from Burkina Faso, West Africa. We show that both molecular approaches yield comparable results, and that either one performs as well or better than cytogenetics in terms of genotyping accuracy. Given the ability of molecular genotyping approaches to be conducted at scale and at relatively low cost without restriction on mosquito sex or developmental stage, molecular genotyping via tag SNPs has the potential to revitalize research into the role of chromosomal inversions in the behavior and ongoing adaptation of An. gambiae and An. coluzzii to environmental heterogeneities.

Comparative Cytology of Female Meiosis I Among Drosophila Species.

The physical connections established by recombination are normally sufficient to ensure proper chromosome segregation during female Meiosis I. However, nonexchange chromosomes (such as the Muller F element or “dot” chromosome in D. melanogaster) can still segregate accurately because they remain connected by heterochromatic tethers. A recent study examined female meiosis in the closely related species D. melanogaster and D. simulans, and found a nearly twofold difference in the mean distance the obligately nonexchange dot chromosomes were separated during Prometaphase. That study proposed two speculative hypotheses for this difference, the first being the amount of heterochromatin in each species, and the second being the species’ differing tolerance for common inversions in natural populations. We tested these hypotheses by examining female meiosis in 12 additional Drosophila species. While neither hypothesis had significant support, we did see 10-fold variation in dot chromosome sizes, and fivefold variation in the frequency of chromosomes out on the spindle, which were both significantly correlated with chromosome separation distances. In addition to demonstrating that heterochromatin abundance changes chromosome behavior, this implies that the duration of Prometaphase chromosome movements must be proportional to the size of the F element in these species. Additionally, we examined D. willistoni, a species that lacks a free dot chromosome. We observed that chromosomes still moved out on the meiotic spindle, and the F element was always positioned closest to the spindle poles. This result is consistent with models where one role of the dot chromosomes is to help organize the meiotic spindle.

Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype.

Both models and case studies suggest that chromosomal inversions can facilitate adaptation and speciation in the presence of gene flow by suppressing recombination between locally adapted alleles. Until recently, however, it has been laborious and time-consuming to identify and genotype inversions in natural populations. Here we apply RAD sequencing data and newly developed population genomic approaches to identify putative inversions that differentiate a sand dune ecotype of the prairie sunflower (Helianthus petiolaris) from populations found on the adjacent sand sheet. We detected seven large genomic regions that exhibit a different population structure than the rest of the genome and that vary in frequency between dune and nondune populations. These regions also show high linkage disequilibrium and high heterozygosity between, but not within, arrangements, consistent with the behaviour of large inversions, an inference subsequently validated in part by comparative genetic mapping. Genome-environment association analyses show that key environmental variables, including vegetation cover and soil nitrogen, are significantly associated with inversions. The inversions colocate with previously described "islands of differentiation," and appear to play an important role in adaptive divergence and incipient speciation within H. petiolaris.

Stimulated X-rays in resonant atom Majorana mixing

Massive neutrinos demand to ask whether they are Dirac or Majorana particles. Majorana neutrinos are an irrefutable proof of physics beyond the Standard Model. Neutrinoless double electron capture is not a process but a virtual ΔL = 2 mixing between a parent AZ atom and a daughter A(Z — 2) excited atom with two electron holes. As a mixing between two neutral atoms and the observable signal in terms of emitted two-hole X-rays, the strategy, experimental signature and background are different from neutrinoless double beta decay. The mixing is resonantly enhanced for almost degeneracy and, under these conditions, there is no irreducible background from the standard two-neutrino channel. We reconstruct the natural time history of a nominally stable parent atom since its production either by nature or in the laboratory. After the time periods of atom oscillations and the decay of the short-lived daughter atom, at observable times the relevant “stationary” states are the mixed metastable long-lived state and the short-lived excited state, as well as the ground state of the daughter atom. Their natural population inversion is most appropriate for exploiting the bosonic nature of the observed X-rays by means of stimulating X-ray beams. Among different observables of the atom Majorana mixing, we include the enhanced rate of stimulated X-ray emission from the long-lived metastable state by a high-intensity X-ray beam. A gain factor of 100 can be envisaged in a facility like European XFEL.

Stimulated transitions in resonant atom Majorana mixing

Massive neutrinos demand to ask whether they are Dirac or Majorana particles. Majorana neutrinos are an irrefutable proof of physics beyond the Standard Model. Neutrinoless double electron capture is not a process but a virtual ΔL = 2 mixing between a parent AZ atom and a daughter A(Z − 2) excited atom with two electron holes. As a mixing between two neutral atoms and the observable signal in terms of emitted two-hole X-rays, the strategy, experimental signature and background are different from neutrinoless double beta decay. The mixing is resonantly enhanced for almost degeneracy and, under these conditions, there is no irreducible background from the standard two-neutrino channel. We reconstruct the natural time history of a nominally stable parent atom since its production either by nature or in the laboratory. After the time periods of atom oscillations and the decay of the short-lived daughter atom, at observable times the relevant “stationary” states are the mixed metastable long-lived state and the non-orthogonal short-lived excited state, as well as the ground state of the daughter atom. We find that they have a natural population inversion which is most appropriate for exploiting the bosonic nature of the observed atomic transitions radiation. Among different observables of the atom Majorana mixing, we include the enhanced rate of stimulated X-ray emission from the long-lived metastable state by a high-intensity X-ray beam: a gain factor of 100 can be envisaged at current XFEL facilities. On the other hand, the historical population of the daughter atom ground state can be probed by exciting it with a current pulsed optical laser, showing the characteristic absorption lines: the whole population can be excited in a shorter time than typical pulse duration.

Pool and conquer: new tricks for (c)old problems

The early period of genetics is closely associated with the study of chromosomal inversions. For almost a century, evolutionary biologists found evidence for the role of inversions in central processes such as adaptation and speciation. In spite of huge efforts, many questions remain about the evolutionary forces underlying the distribution and dynamics of inversions in natural populations. Fortunately, old problems can be solved with new tools. In this issue, Kapun et al. (2014) present a remarkable combination of resources and techniques, including publicly available data, karyotyping, statistical estimation of haplotypes, Pool-Seq data and experimental evolution, setting the ground for exciting developments in the field.

Striking structural dynamism and nucleotide sequence variation of the transposon Galileo in the genome of Drosophila mojavensis

BackgroundGalileo is a transposable element responsible for the generation of three chromosomal inversions in natural populations of Drosophila buzzatii. Although the most characteristic feature of Galileo is the long internally-repetitive terminal inverted repeats (TIRs), which resemble the Drosophila Foldback element, its transposase-coding sequence has led to its classification as a member of the P-element superfamily (Class II, subclass 1, TIR order). Furthermore, Galileo has a wide distribution in the genus Drosophila, since it has been found in 6 of the 12 Drosophila sequenced genomes. Among these species, D. mojavensis, the one closest to D. buzzatii, presented the highest diversity in sequence and structure of Galileo elements.ResultsIn the present work, we carried out a thorough search and annotation of all the Galileo copies present in the D. mojavensis sequenced genome. In our set of 170 Galileo copies we have detected 5 Galileo subfamilies (C, D, E, F, and X) with different structures ranging from nearly complete, to only 2 TIR or solo TIR copies. Finally, we have explored the structural and length variation of the Galileo copies that point out the relatively frequent rearrangements within and between Galileo elements. Different mechanisms responsible for these rearrangements are discussed.ConclusionsAlthough Galileo is a transposable element with an ancient history in the D. mojavensis genome, our data indicate a recent transpositional activity. Furthermore, the dynamism in sequence and structure, mainly affecting the TIRs, suggests an active exchange of sequences among the copies. This exchange could lead to new subfamilies of the transposon, which could be crucial for the long-term survival of the element in the genome.

Natural population inversion in a gaseous molecular filament

We propose a new mechanism/scheme to explain the ultrafast population inversion of molecular ions which takes place in a time scale comparable to the femtosecond laser pulse. The nonlinear pumping process including the pump photons and the self-generated harmonic photons of the pump laser would be responsible for building up population inversion to realize remote molecule lasers in femtosecond laser filaments in gases. It is shown that the remote laser emissions in molecular ions of gases may be a universal process in the femtosecond laser filament.

Viabilities of D. subobscura homo- and heterokaryotypes at optimal and stress temperatures. II. Seasonal component analysis

Here we report the viability of natural chromosomal O-inversion structural homo- and heterokaryotypes in a population of D. subobscura from Avala Mountain, Serbia, subjected to cold and heat stress during spring 2004. These results were compared with those observed in the same population in September 2004. We detected protection of a great number of lethal genes in O-chromosome lethal heterozygous combinations, independently of inversion backgrounds and temperature stress. The positive epistatic interactions of mildly-deleterious genes observed only in O-inversion heterokaryotypes (at distinct temperatures) and lethal genes in O-inversion homokaryotypes (under temperature stress only) could be responsible for reducing the genetic load. The seasonal fluctuations in frequencies of several chromosomal arrangements and karyotypes indicate a seasonal adaptation to changeable environmental conditions. The sample of D. subobscura collected in spring 2004 was tolerant to cold but not to heat, and these results point to tolerance to extreme low temperatures, possibly as a result of natural selection. Also, a non-random distribution of distinct combinations of viability classes among several O-inversion karyotypes (under both optimal conditions and heat stress) was observed. This observation could be taken as evidence of co-adaptation: different capacities of several O-inversion karyotypes with different combinations of genes to tolerate a range of temperatures. We conclude that frequency-dependent and supergene selection are balancing selection mechanisms and are responsible for the protection of chromosomal inversions in natural populations of D. subobscura.

MDH-polymorphism in Drosophila subobscura II. Non-random associations between alleles and chromosomal inversions in natural populations

MDH-polymorphism in Drosophila subobscura II. Non-random associations between alleles and chromosomal inversions in natural populations

Micro-geographic variation of inversions in natural populations of Drosophila pseudoobscura

Chromosomal polymorphism for the third chromosome in Drosophila pseudoobscura has been widely studied for genetic variation in different environments or locations far apart. However, there is less information regarding sites geographically near one another. Targeting on possible micro-geographic variation in the species, a serial study was done on 12 Mexican populations grouped in four regions, including locations in Durango (DU), the border area of Guanajuato-San Luis Potosi states (GP), Chiapas (CH) and Saldilo (SA). Flies were trapped in their natural habitats using fermenting bananas as bait. They were individually cultivated in the laboratory for larvae production. In a given population sample several flies were cultivated together but only one larva per culture provided salivary tissue to observe polytene chromosomes. Gene arrangements or inversions were identified and frequencies were calculated. A total of 767 third chromosomes were studied and 11 different inversions detected. The type and relative frequencies of the arrangements varied among regions. From the 11 inversions observed, 10 were found in Durango, five in Guanajuato-San Luis Potosi and Chiapas, and eight in Saltillo. The inversion frequencies in the Durango locations varied in four cases, but only one in Chiapas, three cases in Guanajuato-San Luis Potosi, and five in Saltillo. It was also observed that there were geographical gradients for inversions within regions as follows: four arrangements in Saltillo and Durango, three in Guanajuato-San Luis Potos? and one in Chiapas. Moreover, all four regions studied showed evidences for micro-geographical variation. Nevertheless, more studies are needed to elucidate the relevance of the inversion frequencies changes in neighboring populations and also any seasonal-annual frequencies observed in the locations studied here.

Maintenance of a large pericentric inversion generated by the hobo transposable element in a transgenic line of Drosophila melanogaster

The impact of the hobo transposable element in the global reorganization of the Drosophila melanogaster genome has been investigated in transgenic lines generated by the injection of hobo elements into the Hikone strain, which lacked them previously. Extensive surveys of transgenic lines followed for 250 generations have identified 13 inversions with hobo inserts at most breakpoints. One of these inversions is pericentric on chromosome 2. It has been maintained in the line where it was discovered and in several sublines at frequencies from 0.19 to 0.45, generating stable chromosomal polymorphisms, similar to cosmopolitan paracentric inversions in natural populations. Individuals homozygous for this inversion were viable and fertile, allowing the creation of a new homozygous strain.

Natural population inversion for the CO 2 vibrational states in Earth's atmosphere

An estimation of population inversion for the (0 0 0 1) and (1 0 0 0) states of the CO 2 molecule in the Earth's atmosphere is presented. The evaluation shows the inversion to occur near a height of 95–100 km in daytime. The principal source of the (0 0 0 1) state pumping is the absorption of solar radiation in the 4.3 μm CO 2 band. The collisional transfer of energy from O( 1D) atoms to the (0 0 0 1) state amplifies the inversion significantly. The maximum value of ([ CO 2(0 0 0 1)]−[ CO 2(1 0 0 0)])/[ CO 2(1 0 0 0)] cannot be less than ≈0.2. However, the maximum order of the total directional gain for laser emission in the 10.4 μm CO 2 band along the tangent path was found to be small, it varies from 0.3×1 0 −5 to 1 0 −5 depending mainly on the extent to which the O( 1D) source contributes to (0 0 0 1) state pumping. The utilization of the natural inversion could be possible by forming a lasing cavity with orbiting mirrors should the engineering problem associated with the slow accumulation of electromagnetic wave energy in the cavity be solved.

Hobo transposons causing chromosomal breakpoints

Several laboratory surveys have shown that transposable elements (TEs) can cause chromosomal breaks and lead to inversions, as in dysgenic crosses involving P-elements. However, it is not presently clear what causes inversions in natural populations of Drosophila. The only direct molecular studies must be taken as evidence against the involvement of mobile elements. Here, in Drosophila lines transformed with the hobo transposable element, and followed for 100 generations, we show the appearance of five different inversions with hobo inserts at breakpoints. Almost all breakpoints occurred in hobo insertion sites detected in previous generations. Therefore, it can be assumed that such elements are responsible for restructuring genomes in natural populations.

Accumulation of P elements in minority inversions in natural populations of Drosophila melanogaster.

The accumulation of a transposable element inside chromosomal inversions is examined theoretically by a mathematical model, and empirically by counts of P elements associated with inversion polymorphisms in natural populations of Drosophila melanogaster. The model demonstrates that, if heterozygosity for an inversion effectively reduces element associated production of detrimental chromosome rearrangements, a differential accumulation of elements is expected, with increased copy number inside the minority inversion. Several-fold differential accumulations are possible with certain parameter values. We present data on P element counts for inversion polymorphisms on all five chromosome arms of 157 haploid genomes from two African populations. Our observations show significantly increased numbers of elements within the regions associated with the least common, or minority arrangements, in natural inversion polymorphisms.

Four decades of inversion polymorphism in Drosophila pseudoobscura.

We report data that continue the studies of Dobzhansky and others on the frequencies of third-chromosome inversions in natural populations of Drosophila pseudoobscura in North America. The common gene arrangements continue to be present in frequencies similar to those described four decades ago, and the broad geographic patterns also remain unchanged. There is only one pronounced trend over time: the increase in frequency of the Tree Line inversion in Pacific coast populations.

Paracentric inversion in the grasshopper Oedipoda charpentieri

One out of ten adult males of the grasshopper Oedipoda charpentieri analysed from a natural population was heterozygous for a paracentric inversion in the megameric M6 chromosome. The inversion involved changes in C-banding pattern which facilitated its detection. Meiotic behaviour was characterised by both an absence of inversion loops at prophase I and dicentric bridges plus acentric fragments in anaphase I, so that this inversion could not have been detected using conventional staining techniques. The possible relationship between the scarcity of reports on paracentric inversions in natural populations of grasshoppers and difficulty to detect them is discussed.

The role of genic selection in the establishment of inversion polymorphism in Drosophila subobscura

A model for explaining the establishment of newly arisen inversions in natural populations, in which the inverted segment may be selected for if its load of deleterious mutations is smaller than the average load of the noninverted segment in the population, is tested for Drosophila subobscura. The results show that for new inversions, originally with no deleterious alleles, the expected cumulative distribution of inversion lengths fits fairly well with the observed one. Therefore, genic selection may be an important cause of the establishment of newly arisen inversions in natural populations of D. subobscura. The applicability of the model to the maintenance of the inversion polymorphism present in this species; is discussed.

High frequency of cosmopolitan inversions in natural populations of Drosophila ananassae from Kerala, South India

High frequency of cosmopolitan inversions in natural populations of Drosophila ananassae from Kerala, South India

High frequency of cosmopolitan inversions in natural populations of Drosophila ananassae from Kerala, South India

High frequency of cosmopolitan inversions in natural populations of Drosophila ananassae from Kerala, South India