XY System Research Articles

Evaluation of Stiffness and Parametric Modelling of XY Flexure Mechanism for Precision Applications

In miniaturized scale electro-mechanical framework (MEMS) flexural instruments are generally utilized in light of their preferences, frictionless and wear less movement and high accuracy. Flexures rely upon material versatility for their usefulness. In flexure component, movement is created because of flexibility of the shaft from which it is made. One of the run of the mill favorable circumstances of flexural system is to increase exact twisting and adaptability to acquire movement wanted way. This paper manages outline, examination and displaying of XY flexure instrument which depends on twofold parallelogram flexure (DFM). The XY system exhibited has solid structure and it depends on twofold parallelogram flexure. Limited component model and investigation is completed in ANSYS 15. Static examination is done to discover constrain avoidance attributes of instrument. Parametric examination is utilized to improve outline parameters of flexure shaft. Limited component examination (FEA) result approves investigative outcomes of component.

Monogamy quantum correlation near the quantum phase transitions in the two-dimensional XY spin systems**Project supported by the Natural Science Foundation of Jiangsu Province, China (Grant No. BK20171397), the National Natural Science Foundation of China (Grant Nos. 11535004, 11375086, 1175085, and 11120101005), the Foundation for Encouragement of College of Sciences (Grant No. LYLZJJ1616), and the Pre-research Foundation of Army Engineering University

We investigate the role of quantum correlation around the quantum phase transitions by using quantum renormalization group theory. Numerical analysis indicates that quantum correlation as well as quantum nonlocality can efficiently detect the quantum critical point in the two-dimensional XY systems. The nonanalytic behavior of the first derivative of quantum correlation is observed at the critical point as the size of the model increases. Furthermore, we discuss the quantum correlation distribution in this system based on the square of concurrence (SC) and square of quantum discord (SQD). The monogamous properties of SC and SQD are obtained. Particularly, we prove that the quantum critical point can also be achieved by monogamy score.

Novel Sex Chromosomes in 3 Cichlid Fishes from Lake Tanganyika.

African cichlids are well known for their adaptive radiations, but it is now apparent that they also harbor an extraordinary diversity of sex chromosome systems. In this study, we sequenced pools of males and females from species in 3 different genera of cichlids from Lake Tanganyika. We then searched for regions that were differentiated following the patterns expected for sex chromosomes. We report 2 novel sex chromosomes systems, an XY system on LG19 in Tropheus sp. "black" and a ZW system on LG7 in Hemibates stenosoma. We also identify a ZW system on LG5 in Cyprichromis leptosoma that may be convergent with a system previously described in Lake Malawi cichlids. Our data also identify candidate single nucleotide polymorphisms for the blue/yellow tail color polymorphism observed among male C. leptosoma.

Defects in Nematic Shells: A Γ-Convergence Discrete-to-Continuum Approach

In this paper we rigorously investigate the emergence of defects on Nematic Shells with a genus different from one. This phenomenon is related to a non-trivial interplay between the topology of the shell and the alignment of the director field. To this end, we consider a discrete XY system on the shell M, described by a tangent vector field with unit norm sitting at the vertices of a triangulation of the shell. Defects emerge when we let the mesh size of the triangulation go to zero, namely in the discrete-to-continuum limit. In this paper we investigate the discrete-to-continuum limit in terms of Γ-convergence in two different asymptotic regimes. The first scaling promotes the appearance of a finite number of defects whose charges are in accordance with the topology of shell M, via the Poincare–Hopf Theorem. The second scaling produces the so called Renormalized Energy that governs the equilibrium of the configurations with defects.

Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage.

Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and revisit dosage compensation evolution in representative mammals and birds with substantial new expression data. Our analyses show that Anolis sex chromosomes represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage. The age of this system approximately coincides with the ages of the avian and two mammalian sex chromosomes systems. To compensate for the almost complete Y Chromosome degeneration, X-linked genes have become twofold up-regulated, restoring ancestral expression levels. The highly efficient dosage compensation mechanism of Anolis represents the only vertebrate case identified so far to fully support Ohno's original dosage compensation hypothesis. Further analyses reveal that X up-regulation occurs only in males and is mediated by a male-specific chromatin machinery that leads to global hyperacetylation of histone H4 at lysine 16 specifically on the X Chromosome. The green anole dosage compensation mechanism is highly reminiscent of that of the fruit fly, Drosophila melanogaster. Altogether, our work unveils the convergent emergence of a Drosophila-like dosage compensation mechanism in an ancient reptilian sex chromosome system and highlights that the evolutionary pressures imposed by sex chromosome dosage reductions in different amniotes were resolved in fundamentally different ways.

Chromosomal Evolution in Lower Vertebrates: Sex Chromosomes in Neotropical Fishes.

Fishes exhibit the greatest diversity of species among vertebrates, offering a number of relevant models for genetic and evolutionary studies. The investigation of sex chromosome differentiation is a very active and striking research area of fish cytogenetics, as fishes represent one of the most vital model groups. Neotropical fish species show an amazing variety of sex chromosome systems, where different stages of differentiation can be found, ranging from homomorphic to highly differentiated sex chromosomes. Here, we draw attention on the impact of recent developments in molecular cytogenetic analyses that helped to elucidate many unknown questions about fish sex chromosome evolution, using excellent characiform models occurring in the Neotropical region, namely the Erythrinidae family and the Triportheus genus. While in Erythrinidae distinct XY and/or multiple XY-derived sex chromosome systems have independently evolved at least four different times, representatives of Triportheus show an opposite scenario, i.e., highly conserved ZZ/ZW system with a monophyletic origin. In both cases, recent molecular approaches, such as mapping of repetitive DNA classes, comparative genomic hybridization (CGH), and whole chromosome painting (WCP), allowed us to unmask several new features linked to the molecular composition and differentiation processes of sex chromosomes in fishes.

The Discovery of XY Sex Chromosomes in a Boa and Python

For over 50 years, biologists have accepted that all extant snakes share the same ZW sex chromosomes derived from a common ancestor [1-3], with different species exhibiting sex chromosomes at varying stages of differentiation. Accordingly, snakes have been a well-studied model for sex chromosome evolution in animals [1, 4]. A review of the literature, however, reveals no compelling support that boas and pythons possess ZW sex chromosomes [2, 5]. Furthermore, phylogenetic patterns of facultative parthenogenesis in snakes and a sex-linked color mutation in the ball python (Python regius) are best explained by boas and pythons possessing an XY sex chromosome system [6, 7]. Here we demonstrate that a boa (Boa imperator) and python (Python bivittatus) indeed possess XY sex chromosomes, based on the discovery of male-specific genetic markers in both species. We use these markers, along with transcriptomic and genomic data, to identify distinct sex chromosomes in boas and pythons, demonstrating that XY systems evolved independently in each lineage. This discovery highlights the dynamic evolution of vertebrate sex chromosomes and further enhances the value of snakes as a model for studying sex chromosome evolution.

A test for Y-linked additive and epistatic effects on surviving bacterial infections in Drosophila melanogaster.

Y- and W-chromosomes offer a theoretically powerful way for sexual dimorphism to evolve. Consistent with this possibility, Drosophila melanogaster Y-chromosomes can influence gene regulation throughout the genome; particularly immune-related genes. In order for Y-linked regulatory variation (YRV) to contribute to adaptive evolution it must be comprised of additive genetic variance, such that variable Ys induce consistent phenotypic effects within the local gene pool. We assessed the potential for Y-chromosomes to adaptively shape gram-negative and gram-positive bacterial defence by introgressing Ys across multiple genetic haplotypes from the same population. We found no Y-linked additive effects on immune phenotypes, suggesting a restricted role for the Y to facilitate dimorphic evolution. We did find, however, a large magnitude Y by background interaction that induced rank order reversals of Y-effects across the backgrounds (i.e. sign epistasis). Thus, Y-chromosome effects appeared consistent within backgrounds, but highly variable among backgrounds. This large sign epistatic effect could constrain monomorphic selection in both sexes, considering that autosomal alleles under selection must spend half of their time in a male background where relative fitness values are altered. If the pattern described here is consistent for other traits or within other XY (or ZW) systems, then YRV may represent a universal constraint to autosomal trait evolution.

Multiple gene movements into and out of haploid sex chromosomes

BackgroundLong-term evolution of sex chromosomes is a dynamic process shaped by gene gain and gene loss. Sex chromosome gene traffic has been studied in XY and ZW systems but no detailed analyses have been carried out for haploid phase UV sex chromosomes. Here, we explore sex-specific sequences of seven brown algal species to understand the dynamics of the sex-determining region (SDR) gene content across 100 million years of evolution.ResultsA core set of sex-linked genes is conserved across all the species investigated, but we also identify modifications of both the U and the V SDRs that occurred in a lineage-specific fashion. These modifications involve gene loss, gene gain and relocation of genes from the SDR to autosomes. Evolutionary analyses suggest that the SDR genes are evolving rapidly and that this is due to relaxed purifying selection. Expression analysis indicates that genes that were acquired from the autosomes have been retained in the SDR because they confer a sex-specific role in reproduction. By examining retroposed genes in Saccharina japonica, we demonstrate that UV sex chromosomes have generated a disproportionate number of functional orphan retrogenes compared with autosomes. Movement of genes out of the UV sex chromosome could be a means to compensate for gene loss from the non-recombining region, as has been suggested for Y-derived retrogenes in XY sexual systems.ConclusionThis study provides the first analysis of gene traffic in a haploid UV system and identifies several features of general relevance to the evolution of sex chromosomes.

Genetic sex determination in Astatotilapia calliptera, a prototype species for the Lake Malawi cichlid radiation.

East African cichlids display extensive variation in sex determination systems. The species Astatotilapia calliptera is one of the few cichlids that reside both in Lake Malawi and in surrounding waterways. A. calliptera is of interest in evolutionary studies as a putative immediate outgroup species for the Lake Malawi species flock and possibly as a prototype ancestor-like species for the radiation. Here, we use linkage mapping to test association of sex in A. calliptera with loci that have been previously associated with genetic sex determination in East African cichlid species. We identify a male heterogametic XY system segregating at linkage group (LG) 7 in an A. calliptera line that originated from Lake Malawi, at a locus previously shown to act as an XY sex determination system in multiple species of Lake Malawi cichlids. Significant association of genetic markers and sex produce a broad genetic interval of approximately 26 megabases (Mb) using the Nile tilapia genome to orient markers; however, we note that the marker with the strongest association with sex is near a gene that acts as a master sex determiner in other fish species. We demonstrate that alleles of the marker are perfectly associated with sex in Metriaclima mbenjii, a species from the rock-dwelling clade of Lake Malawi. While we do not rule out the possibility of other sex determination loci in A. calliptera, this study provides a foundation for fine mapping of the cichlid sex determination gene on LG7 and evolutionary context regarding the origin and persistence of the LG7 XY across diverse, rapidly evolving lineages.

The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB.

Variation in social behaviour is common, yet little is known about the genetic architectures underpinning its evolution. A rare exception is in the fire ant Solenopsis invicta: Alternative variants of a supergene region determine whether a colony will have exactly one or up to dozens of queens. The two variants of this region are carried by a pair of ‘social chromosomes’, SB and Sb, which resemble a pair of sex chromosomes. Recombination is suppressed between the two chromosomes in the supergene region. While the X‐like SB can recombine with itself in SB/SB queens, recombination is effectively absent in the Y‐like Sb because Sb/Sb queens die before reproducing. Here, we analyse whole‐genome sequences of eight haploid SB males and eight haploid Sb males. We find extensive SB–Sb differentiation throughout the >19‐Mb‐long supergene region. We find no evidence of ‘evolutionary strata’ with different levels of divergence comparable to those reported in several sex chromosomes. A high proportion of substitutions between the SB and Sb haplotypes are nonsynonymous, suggesting inefficacy of purifying selection in Sb sequences, similar to that for Y‐linked sequences in XY systems. Finally, we show that the Sb haplotype of the supergene region has 635‐fold less nucleotide diversity than the rest of the genome. We discuss how this reduction could be due to a recent selective sweep affecting Sb specifically or associated with a population bottleneck during the invasion of North America by the sampled population.

Quantum vorticity at positive temperature for spins systems with continuous symmetry

We propose a definition of vorticity at inverse temperature β for Gibbs states in quantum XY or Heisenberg spin systems on the lattice by testing exp[−βH] on a complete set of observables (“one-point functions”). Imposing a compression of Pauli matrices at the boundary, which stands for the classical environment, we perform some numerical simulations on finite lattices in case of XY model, which exhibit usual vortex patterns.

Rapid sex identification method of spinach (Spinacia oleracea L.) in the vegetative stage using loop-mediated isothermal amplification.

A LAMP-mediated, simple and rapid method for sex identification in spinach was developed. Nutrient compositional analysis showed a higher iron content in male than female plants. Spinach (Spinacia oleracea L.) is a dioecious plant with its sex determined by the XY system. Male and female floral organs differ morphologically, but plants do not differ in the vegetative stage before flowering. PCR with Y chromosome markers has been used to determine the sex of dioecious plants before flowering. In this study, we developed a genotype-specific loop-mediated isothermal amplification (LAMP) for sex identification of individual vegetative-stage spinach plants, using primers designed for the genomic region flanked by male-specific markers. LAMP could specifically detect spinach males. The method was further modified to omit DNA purification and use just an aliquot of crude leaf extract homogenized in water. We compared the nutrient composition of males and females, finding higher amounts of iron in the males. Our method could therefore be used for rapidly discriminating male plants in the field, which is useful for efficient hybrid breeding.

Comparative analysis of a sex chromosome from the blackchin tilapia, Sarotherodon melanotheron

BackgroundInversions and other structural polymorphisms often reduce the rate of recombination between sex chromosomes, making it impossible to fine map sex-determination loci using traditional genetic mapping techniques. Here we compare distantly related species of tilapia that each segregate an XY system of sex-determination on linkage group 1. We use whole genome sequencing to identify shared sex-patterned polymorphisms, which are candidates for the ancestral sex-determination mutation.ResultsWe found that Sarotherodon melanotheron segregates an XY system on LG1 in the same region identified in Oreochromis niloticus. Both species have higher densities of sex-patterned SNPs, as well as elevated number of ancestral copy number variants in this region when compared to the rest of the genome, but the pattern of differentiation along LG1 differs between species. The number of sex-patterned SNPs shared by the two species is small, but larger than expected by chance, suggesting that a novel Y-chromosome arose just before the divergence of the two species. We identified a shared sex-patterned SNP that alters a Gata4 binding site near Wilms tumor protein that might be responsible for sex-determination.ConclusionsShared sex-patterned SNPs, insertions and deletions suggest an ancestral sex-determination system that is common to both S. melanotheron and O. niloticus. Functional analyses are needed to evaluate shared SNPs near candidate genes that might play a role in sex-determination of these species. Interspecific variation in the sex chromosomes of tilapia species provides an excellent model system for understanding the evolution of vertebrate sex chromosomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3163-7) contains supplementary material, which is available to authorized users.

The Evolution of Genome Structure by Natural and Sexual Selection.

Progress on understanding how genome structure evolves is accelerating with the arrival of new genomic, comparative, and theoretical approaches. This article reviews progress in understanding how chromosome inversions and sex chromosomes evolve, and how their evolution affects species' ecology. Analyses of clines in inversion frequencies in flies and mosquitoes imply strong local adaptation, and roles for both over- and under dominant selection. Those results are consistent with the hypothesis that inversions become established when they capture locally adapted alleles. Inversions can carry alleles that are beneficial to closely related species, causing them to introgress following hybridization. Models show that this "adaptive cassette" scenario can trigger large range expansions, as recently happened in malaria mosquitoes. Sex chromosomes are the most rapidly evolving genome regions of some taxa. Sexually antagonistic selection may be the key force driving transitions of sex determination between different pairs of chromosomes and between XY and ZW systems. Fusions between sex-chromosomes and autosomes most often involve the Y chromosome, a pattern that can be explained if fusions are mildly deleterious and fix by drift. Sexually antagonistic selection is one of several hypotheses to explain the recent discovery that the sex determination system has strong effects on the adult sex ratios of tetrapods. The emerging view of how genome structure evolves invokes a much richer constellation of forces than was envisioned during the Golden Age of research on Drosophila karyotypes.

Comparative cytogenetic analysis in 13 tortoise beetles (Coleoptera: Chrysomelidae: Cassidinae) from Brazil

In the present work, we have characterized the chromosomes of 13 Cassidinae beetles, belonging to four tribes, the broad aim being to increase the cytogenetic data and establish the mechanisms involved in chromosome evolution of this subfamily, which appear to be conserved karyotypically, i.e. 2n = 16 + Xyp. The analysis of mitotic and meiotic cells revealed a high diversity of diploid numbers (2n = 18, 2n = 22, 2n = 26, 2n = 32, 2n = 36, 2n = 40, 2n = 42), and the presence of sex chromosome system of the Xyp type in most species, with the exception of two representatives that exhibited Xyr and XY systems. C-banding showed constitutive heterochromatin predominantly localized in the pericentromeric region of the chromosomes, but differences regarding the number of chromosomes with positive C-bands, intensity of the blocks, and presence of additional bands in autosomes and/or sex chromosomes were observed among the species investigated. Our data revealed that the karyotype 2n = 16 + Xyp does not occur in all 13 tribes of the Cassidinae characterized cytogenetically, seeming to be only a shared feature among the species of the Cassidini. Variations in the C-band pattern, mainly in closely related species, suggest that the interspecific karyotype diversification occurred as a result of changes in the quantity and distribution of constitutive heterochromatin. The occurrence of the Xyp sex chromosome system in the tribe Mesomphaliini, which showed the highest diversity of simple and multiple systems among the coleopteran as a whole, reinforces the view that derived systems originated by chromosome rearrangements involving the Xyp ancestral system.

Magnetic Ground States of the Rare-Earth Tripod Kagome Lattice Mg_{2}RE_{3}Sb_{3}O_{14} (RE=Gd,Dy,Er).

We present the structural and magnetic properties of a new compound family, Mg_{2}RE_{3}Sb_{3}O_{14} (RE=Gd,Dy,Er), with a hitherto unstudied frustrating lattice, the "tripod kagome" structure. Susceptibility (ac, dc) and specific heat exhibit features that are understood within a simple Luttinger-Tisza-type theory. For RE=Gd, we found long-ranged order (LRO) at 1.65K, which is consistent with a 120° structure, demonstrating the importance of diople interactions for this 2D Heisenberg system. For RE=Dy, LRO at 0.37K is related to the "kagome spin ice" physics for a 2D system. This result shows that the tripod kagome structure accelerates the transition to LRO predicted for the related pyrochlore systems. For RE=Er, two transitions, at 80mK and 2.1K are observed, suggesting the importance of quantum fluctuations for this putative XY system.

Deciphering evolutionary strata on plant sex chromosomes and fungal mating-type chromosomes through compositional segmentation

Sex chromosomes have evolved from a pair of homologous autosomes which differentiated into sex determination systems, such as XY or ZW system, as a consequence of successive recombination suppression between the gametologous chromosomes. Identifying the regions of recombination suppression, namely, the "evolutionary strata", is central to understanding the history and dynamics of sex chromosome evolution. Evolution of sex chromosomes as a consequence of serial recombination suppressions is well-studied for mammals and birds, but not for plants, although 48 dioecious plants have already been reported. Only two plants Silene latifolia and papaya have been studied until now for the presence of evolutionary strata on their X chromosomes, made possible by the sequencing of sex-linked genes on both the X and Y chromosomes, which is a requirement of all current methods that determine stratum structure based on the comparison of gametologous sex chromosomes. To circumvent this limitation and detect strata even if only the sequence of sex chromosome in the homogametic sex (i.e. X or Z chromosome) is available, we have developed an integrated segmentation and clustering method. In application to gene sequences on the papaya X chromosome and protein-coding sequences on the S. latifolia X chromosome, our method could decipher all known evolutionary strata, as reported by previous studies. Our method, after validating on known strata on the papaya and S. latifolia X chromosome, was applied to the chromosome 19 of Populus trichocarpa, an incipient sex chromosome, deciphering two, yet unknown, evolutionary strata. In addition, we applied this approach to the recently sequenced sex chromosome V of the brown alga Ectocarpus sp. that has a haploid sex determination system (UV system) recovering the sex determining and pseudoautosomal regions, and then to the mating-type chromosomes of an anther-smut fungus Microbotryum lychnidis-dioicae predicting five strata in the non-recombining region of both the chromosomes.

Biased introgression of mitochondrial and nuclear genes: a comparison of diploid and haplodiploid systems

Hybridization between recently diverged species, even if infrequent, can lead to the introgression of genes from one species into another. The rates of mitochondrial and nuclear introgression often differ, with some taxa showing biases for mitochondrial introgression and others for nuclear introgression. Several hypotheses exist to explain such biases, including adaptive introgression, sex differences in dispersal rates, sex-specific prezygotic isolation and sex-specific fitness of hybrids (e.g. Haldane's rule). We derive a simple population genetic model that permits an analysis of sex-specific demographic and fitness parameters and measures the relative rates of mitochondrial and nuclear introgression between hybridizing pairs. We do this separately for diploid and haplodiploid species. For diploid taxa, we recover results consistent with previous hypotheses: an excess of one sex among the hybridizing migrants or sex-specific prezygotic isolation causes a bias for one type of marker or the other; when Haldane's rule is obeyed, we find a mitochondrial bias in XY systems and a nuclear bias in ZW systems. For haplodiploid taxa, the model reveals that owing to their unique transmission genetics, they are seemingly assured of strong mitochondrial biases in introgression rates, unlike diploid taxa, where the relative fitness of male and female hybrids can tip the bias in either direction. This heretofore overlooked aspect of hybridization in haplodiploids provides what is perhaps the most likely explanation for differential introgression of mitochondrial and nuclear markers and raises concerns about the use of mitochondrial DNA barcodes for species delimitation in these taxa.

RAD mapping reveals an evolving, polymorphic and fuzzy boundary of a plant pseudoautosomal region.

How loss of genetic exchanges (recombination) evolves between sex chromosomes is a long-standing question. Suppressed recombination may evolve when a sexually antagonistic (SA) polymorphism occurs in a partially sex-linked 'pseudoautosomal' region (or 'PAR'), maintaining allele frequency differences between the two sexes, and creating selection for closer linkage with the fully sex-linked region of the Y chromosome in XY systems, or the W in ZW sex chromosome systems. Most evidence consistent with the SA polymorphism hypothesis is currently indirect, and more studies of the genetics and population genetics of PAR genes are clearly needed. The sex chromosomes of the plant Silene latifolia are suitable for such studies, as they evolved recently and the loss of recombination could still be ongoing. Here, we used RAD sequencing to genetically map sequences in this plant, which has a large genome (c. 3 gigabases) and no available whole-genome sequence. We mapped 83 genes on the sex chromosomes, and comparative mapping in the related species S. vulgaris supports previous evidence for additions to an ancestral PAR and identified at least 12 PAR genes. We describe evidence that recombination rates have been reduced in meiosis of both sexes, and differences in recombination between S. latifolia families suggest ongoing recombination suppression. Large allele frequency differences between the sexes were found at several loci closely linked to the PAR boundary, and genes in different regions of the PAR showed striking sequence diversity patterns that help illuminate the evolution of the PAR.