Meeting the challenge of DNA barcoding Neotropical amphibians: polymerase chain reaction optimization and new COI primers

Amphibians are one of the most threatened vertebrate classes, yet at the same time new species are being described every year, demonstrating that the number of existing species is grossly underestimated. In groups such as amphibians, with high extinction rates and poorly known species boundaries, DNA barcoding is a tool that can rapidly assess genetic diversity and estimate species richness for prioritizing conservation decisions. However, reliable recovery of the 5' region of the cytochrome c oxidase subunit 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all amphibian species. Here, we provide new PCR conditions and tested new primers that increase the efficiency of barcode recovery in amphibians. We found that a low extension temperature for PCR cycles significantly improves the efficiency of amplification for all combinations of primers. Combining low PCR extension temperature and primers AnF1 + AnR1, we were able to recover COI sequences for 100% of the species analysed (N = 161), encompassing ~15% of the species known from Brazil (representing 77 genera and 23 families), which is an important improvement over previous studies. The preliminary assessment of species diversity suggested that number of species might be underestimated by about 25%. We conclude that DNA barcoding is an efficient, simple, and standardized protocol for identifying cryptic diversity in amphibians and advocate for its use in biodiversity inventories and across widespread populations within known species.

The mitochondrial genomes of Atlas Geckos (Quedenfeldtia): mitogenome assembly from transcriptomes and anchored hybrid enrichment datasets

The nearly complete mitogenomes of the two species of North African Atlas geckos, Quedenfeldtia moerens and Q. trachyblepharus were assembled from anchored hybrid enrichment data and RNAseq data. Congruent assemblies were obtained for four samples included in both datasets. We recovered the 13 protein-coding genes, 22 tRNA genes, and two rRNA genes for both species, including partial control region. The order of genes agrees with that of other geckos.

Phase-shift-controlled logic gates in Y-shaped nonlinearly coupled chains

We introduce a model system composed of two input discrete chains nonlinearly coupled to a single output chain which mimics the geometry of Y-shaped carbon nanotubes, photonic crystal wave guides, and DNA junctions. We explore the capability of the proposed system to perform logic gate operations based on the transmission of phase-shifted harmonic incoming waves. Within a tight-binding approach, we determine the exact transmission spectrum which exhibits a nonlinear induced bistability. Using a digitalization scheme of the output signal based on amplitude modulation, we show that AND, OR, and XOR logic operations can be achieved. Nonlinearity strongly favors the realization of logic operations in the regime of large wavelengths, while phase shifting is required for the OR logic gate to be realizable. A detailed analysis of the contrast ratio shows that optimal operation of the AND and OR logic gates takes place when the nonlinear response is the predominant physical property distinguishing the coupling and regular sites. These results point towards the possibility of Y-branched junctions to perform logic operations based on the transmission of traveling waves.

Tunable topological valence in nematic shells on spherocylindrical colloidal particles

We perform molecular dynamics simulations of the orientational ordering on nematic shells delimited by spherocylindrical nanoscopic colloidal particles. We show that under conditions of degenerate planar anchoring, the equilibrium director field structure in these shells exhibits pairs of +1/2 topological defects at the poles of spherical cups in the absence of an external electric field. In addition, a certain number of pairs of ±1/2 defects occurs on the spherical cups far from the poles, thus resulting in a total of eight valence spots. A strong field applied along the main spherocylindrical axis removes the ±1/2 defect pairs while it coalesces the polar ones into a single +1 topological defect. A strong transverse field destroys all defects on the spherical cups but generates four +1/2 defects in the cylindrical part. Therefore, an external field can be used to control the number of valence centers in spherocylindrical nematic shells, thus unveiling their capability of acting as multivalent building blocks for nanophotonic devices.

Mitogenome assembly from genomic multiplex libraries: comparison of strategies and novel mitogenomes for five species of frogs

Next-generation sequencing continues to revolutionize biodiversity studies by generating unprecedented amounts of DNA sequence data for comparative genomic analysis. However, these data are produced as millions or billions of short reads of variable quality that cannot be directly applied in comparative analyses, creating a demand for methods to facilitate assembly. We optimized an in silico strategy to efficiently reconstruct high-quality mitochondrial genomes directly from genomic reads. We tested this strategy using sequences from five species of frogs: Hylodes meridionalis (Hylodidae), Hyloxalus yasuni (Dendrobatidae), Pristimantis fenestratus (Craugastoridae), and Melanophryniscus simplex and Rhinella sp. (Bufonidae). These are the first mitogenomes published for these species, the genera Hylodes, Hyloxalus, Pristimantis, Melanophryniscus and Rhinella, and the families Craugastoridae and Hylodidae. Sequences were generated using only half of one lane of a standard Illumina HiqSeq 2000 flow cell, resulting in fewer than eight million reads. We analysed the reads of Hylodes meridionalis using three different assembly strategies: (1) reference-based (using bowtie2); (2) de novo (using abyss, soapdenovo2 and velvet); and (3) baiting and iterative mapping (using mira and mitobim). Mitogenomes were assembled exclusively with strategy 3, which we employed to assemble the remaining mitogenomes. Annotations were performed with mitos and confirmed by comparison with published amphibian mitochondria. In most cases, we recovered all 13 coding genes, 22 tRNAs, and two ribosomal subunit genes, with minor gene rearrangements. Our results show that few raw reads can be sufficient to generate high-quality scaffolds, making any Illumina machine run using genomic multiplex libraries a potential source of data for organelle assemblies as by-catch.

Interplay between modulational instability and self-trapping of wavepackets in nonlinear discrete lattices

We investigate the modulational instability of uniform wavepackets governed by the discrete nonlinear Schrodinger equation in finite linear chains and square lattices. We show that, while the critical nonlinear coupling χMI above which modulational instability occurs remains finite in square lattices, it decays as 1/L in linear chains. In square lattices, there is a direct transition between the regime of stable uniform wavefunctions and the regime of asymptotically localized solutions with stationary probability distributions. On the other hand, there is an intermediate regime in linear chains for which the wavefunction dynamics develops complex breathing patterns. We analytically compute the critical nonlinear strengths for modulational instability in both lattices, as well as the characteristic time τ governing the exponential increase of perturbations in the vicinity of the transition. We unveil that the interplay between modulational instability and self-trapping phenomena is responsible for the distinct wavefunction dynamics in linear and square lattices.

Enhanced localization, energy anomalous diffusion and resonant mode in harmonic chains with correlated mass-spring disorder

In this work, we study the vibrational modes and energy spreading in a harmonic chain model with diluted second-neighbors couplings and correlated mass-spring disorder. While all nearest neighbor masses are coupled by an elastic spring, second neighbors springs are introduced with a probability pD. The masses are randomly distributed according to the site connectivity mi = m0 (1 + 1/n(α)(I), where ni is the connectivity of the site i and α is a tunable exponent. We show that maximum localization of the vibrational modes is achieved for α ≃ 3/4. The time-evolution of the energy wave-packet is followed after an initial localized excitation. While the participation number remains finite, the energy spread is shown to be sub-diffusive after a displacement and super-diffusive after an impulse excitation. These features are related to the development of a power-law tail in the wave-packet distribution. Further, we unveil that the spring dilution leads to the emergence of a resonant localized state which is signaled by a van Hove singularity in the density of states.

Stationary and dynamic critical behavior of the contact process on the Sierpinski carpet

We investigate the critical behavior of a stochastic lattice model describing a contact process in the Sierpinski carpet with fractal dimension d=log8/log3. We determine the threshold of the absorbing phase transition related to the transition between a statistically stationary active and the absorbing states. Finite-size scaling analysis is used to calculate the order parameter, order parameter fluctuations, correlation length, and their critical exponents. We report that all static critical exponents interpolate between the line of the regular Euclidean lattices values and are consistent with the hyperscaling relation. However, a short-time dynamics scaling analysis shows that the dynamical critical exponent Z governing the size dependence of the critical relaxation time is found to be larger then the literature values in Euclidean d=1 and d=2, suggesting a slower critical relaxation in scale-free lattices.

Sub-diffusive electronic transport in a DNA single-strand chain with electron-phonon coupling

We investigate the electronic wavepacket dynamics in a finite segment of a DNA single-strand chain considering the electron-phonon coupling. Our theoretical approach makes use of an effective tight-binding Hamiltonian to describe the electron dynamics, together with a classical harmonic Hamiltonian to treat the intrinsic DNA vibrations. An effective time-dependent Schrödinger equation is then settled up and solved numerically for an initially localized wave-packet using the standard Dormand-Prince eighth-order Runge-Kutta method. Our numerical results indicate the presence of a sub-diffusive electronic wavepacket spread mediated by the electron-phonon interaction.

Genetic diversity and population structure of the New World screwworm fly from the Amazon region of Brazil

Cochliomyia hominivorax (Coquerel) is a myiasis fly that causes economic losses to livestock farmers in warmer American regions. Previous studies of this pest had found population structure at north and south of the Amazon Basin, which was considered to be a barrier to dispersal. The present study analyzed three mitochondrial DNA (mtDNA) markers and eight nuclear microsatellite loci to investigate for the first time the genetic diversity and population structure across the Brazilian Amazon region (Amazonia). Both mtDNA and microsatellite data supported the existence of much diversity and significant population structure among nine regional populations of C. hominivorax, which was found to be surprisingly common in Amazonia. Forty-six mtDNA haplotypes were identified, of which 39 were novel and seven had previously been found only at south of Amazonia. Seventy microsatellite alleles were identified by size, moderate to high values of heterozygosity were discovered in all regions, and a Bayesian clustering analysis identified four genetic groups that were not geographically distributed. Reproductive compatibility was also investigated by laboratory crossing, but no evidence of hybrid dysgenesis was found between an Amazonian colony and one each of from Northeast and Southeast Brazil. The results have important implications for area-wide control by the Sterile Insect Technique.

Nonreciprocal transmission through a saturable nonlinear asymmetric dimer

We investigate the nonreciprocal diodelike behavior of a dimer with an asymmetric on-site potential and a saturable nonlinearity. The dimer is coupled to linear side chains. The spectra of transmission and the rectifying factor are analytically obtained using a backward iteration of the set of discrete nonlinear Schrödinger equations used to model the wave propagation through the nonlinear dimer. We show that the windows of bistable behavior leading to a pronounced nonreciprocal diodelike transmission become wider and displaced to higher input field intensities as the saturation coefficient increases. Further, saturation of the nonlinear response has opposite impacts on the rectifying action over short- and long-wavelength input signals within the second bistability window. In the first window, the rectifying action is not compromised by the saturation, thus showing that a weak contribution of high-order susceptibilities to the nonlinear response can improve the efficiency of the nonreciprocal transmission. The rectifying action of a dimer with an asymmetric nonlinearity is also discussed.

Bose-Einstein condensation in diamond hierarchical lattices

The Bose-Einstein condensation of noninteracting particles restricted to move on the sites of hierarchical diamond lattices is investigated. Using a tight-binding single-particle Hamiltonian with properly rescaled hopping amplitudes, we are able to employ an orthogonal basis transformation to exactly map it on a set of decoupled linear chains with sizes and degeneracies written in terms of the network branching parameter q and generation number n. The integrated density of states is shown to have a fractal structure of gaps and degeneracies with a power-law decay at the band bottom. The spectral dimension d(s) coincides with the network topological dimension d(f) = ln(2q)/ln(2). We perform a finite-size scaling analysis of the fraction of condensed particles and specific heat to characterize the critical behavior of the BEC transition that occurs for q > 2 (d(s) > 2). The critical exponents are shown to follow those for lattices with a pure power-law spectral density, with non-mean-field values for q < 8 (d(s) < 4). The transition temperature is shown to grow monotonically with the branching parameter, obeying the relation 1/T(c) = a + b/(q - 2).

The phylogeographic history of the new world screwworm fly, inferred by approximate bayesian computation analysis

Insect pest phylogeography might be shaped both by biogeographic events and by human influence. Here, we conducted an approximate Bayesian computation (ABC) analysis to investigate the phylogeography of the New World screwworm fly, Cochliomyia hominivorax, with the aim of understanding its population history and its order and time of divergence. Our ABC analysis supports that populations spread from North to South in the Americas, in at least two different moments. The first split occurred between the North/Central American and South American populations in the end of the Last Glacial Maximum (15,300-19,000 YBP). The second split occurred between the North and South Amazonian populations in the transition between the Pleistocene and the Holocene eras (9,100-11,000 YBP). The species also experienced population expansion. Phylogenetic analysis likewise suggests this north to south colonization and Maxent models suggest an increase in the number of suitable areas in South America from the past to present. We found that the phylogeographic patterns observed in C. hominivorax cannot be explained only by climatic oscillations and can be connected to host population histories. Interestingly we found these patterns are very coincident with general patterns of ancient human movements in the Americas, suggesting that humans might have played a crucial role in shaping the distribution and population structure of this insect pest. This work presents the first hypothesis test regarding the processes that shaped the current phylogeographic structure of C. hominivorax and represents an alternate perspective on investigating the problem of insect pests.

Critical behavior of the ideal-gas Bose-Einstein condensation in the Apollonian network

We show that the ideal Boson gas displays a finite-temperature Bose-Einstein condensation transition in the complex Apollonian network exhibiting scale-free, small-world, and hierarchical properties. The single-particle tight-binding Hamiltonian with properly rescaled hopping amplitudes has a fractal-like energy spectrum. The energy spectrum is analytically demonstrated to be generated by a nonlinear mapping transformation. A finite-size scaling analysis over several orders of magnitudes of network sizes is shown to provide precise estimates for the exponents characterizing the condensed fraction, correlation size, and specific heat. The critical exponents, as well as the power-law behavior of the density of states at the bottom of the band, are similar to those of the ideal Boson gas in lattices with spectral dimension d(s)=2ln(3)/ln(9/5)~/=3.74.

Critical properties of a superdiffusive epidemic process

We introduce a superdiffusive one-dimensional epidemic process model on which infection spreads through a contact process. Healthy (A) and infected (B) individuals can jump with distinct probabilities D(A) and D(B) over a distance ℓ distributed according to a power-law probability P(ℓ)[proportionality]1/ℓ(μ). For μ≥3 the propagation is equivalent to diffusion, while μ<3 corresponds to Lévy flights. In the D(A)>D(B) diffusion regime, field-theoretical results have suggested a first-order transition, a prediction not supported by several numerical studies. An extensive numerical study of the critical behavior in both the diffusive (μ≥3) and superdiffusive (μ<3) D(A)>D(B) regimes is also reported. We employed a finite-size scaling analysis to obtain the critical point as well as the static and dynamic critical exponents for several values of μ. All data support a second-order phase transition with continuously varying critical exponents which do not belong to the directed percolation universality class.

Spiroplasma in Drosophila melanogaster populations: prevalence, male-killing, molecular identification, and no association with Wolbachia

Spiroplasma endosymbionts are maternally transmitted bacteria that may kill infected sons resulting in the production of female-biased broods. The prevalence of male killers varies considerably both between and within species. Here, we evaluate the spatial and temporal status of male-killing and non-male-killing Spiroplasma infection in three Brazilian populations of Drosophila melanogaster, nearly a decade after the first occurrence report for this species. The incidence of the male-killing Spiroplasma ranged from close to 0 to 17.7 % (so far the highest estimate for a Drosophila species) with a suggestion of temporal decline in a population. We also found non-male-killing Spiroplasma coexisting in one population at lower prevalence (3-5 %), and we did not detect it in the other two. This may be taken as a suggestion of a spreading advantage conferred by the male-killing strategy. Sequencing two loci, we identified the phylogenetic position of Spiroplasma strains from the three localities, showing that all strains group closely in the poulsonii clade. Due to intensive sampling effort, we were able to test the association between Spiroplasma infections and another widespread endosymbiont, Wolbachia, whose prevalence ranged from 81.8 to 100 %. The prevalence of Wolbachia did not differ between Spiroplasma-infected and uninfected strains in our largest sample nor were the prevalences of the two endosymbionts associated across localities.

Resonant localized states and quantum percolation on random chains with power-law-diluted long-range couplings

We investigate the nature of one-electron eigenstates in power-law-diluted chains for which the probability of occurrence of a bond between sites separated by a distance r decays as p(r) = p/r(1+σ). Using an exact diagonalization scheme and a phenomenological finite-size scaling analysis, we determine the quantum percolation transition phase diagram in the full parameter space (p,σ). We show that the density of states displays singularities at some resonance energies associated with degenerate eigenstates localized in a pair of sites with special symmetries. This model is shown to present an intermediate phase for which there is classical percolation but no quantum percolation. Quantum percolation only takes place for σ < 0.78, a value larger than the corresponding one for the Anderson transition in long-ranged coupled chains with random diagonal disorder. The fractality of critical wavefunctions is also characterized.

Ghost resonance in the chaotic Chua's circuit

We experimentally investigate the ghost resonance phenomenon in the electronic circuit of Chua operating in the chaotic regime. The circuit can be stimulated to jump between two single-scroll attractors by an external periodic signal with an amplitude above an intrinsic threshold. For subthreshold signals, jumps between the chaotic attractors can be promoted by a superposed white noise. We show that the circuit output can exhibit a well-defined ghost resonance signature, i.e., a resonance on a frequency that is absent in a multicomponent input signal, when the amplitudes of the input components are properly related. Further, we show that ghost resonance can be induced by the Chua's circuit's own chaotic dynamics when it is driven by a suprathreshold multicomponent signal without the need of an external noise source.

Critical short-time dynamics in a system with interacting static and diffusive populations

We study the critical short-time dynamical behavior of a one-dimensional model where diffusive individuals can infect a static population upon contact. The model presents an absorbing phase transition from an active to an inactive state. Previous calculations of the critical exponents based on quasistationary quantities have indicated an unusual crossover from the directed percolation to the diffusive contact process universality classes. Here we show that the critical exponents governing the slow short-time dynamic evolution of several relevant quantities, including the order parameter, its relative fluctuations, and correlation function, reinforce the lack of universality in this model. Accurate estimates show that the critical exponents are distinct in the regimes of low and high recovery rates.

Geometrical and Anderson transitions in harmonic chains with constrained long-range couplings

Low-dimensional systems with long-range couplings usually present phase transitions which are absent in the short-ranged counterpart model. In this work, we show that a harmonic chain with long-range couplings restricted by a cost function proportional to the chain length N exhibits two distinct phase transitions. In the present model, two sites at a distance r>1 are connected by a spring with probability 1/r(α) with the constraint that the total length of the non-nearest-neighbor couplings is limited to λN, where λ is a cost parameter. A geometrical phase transition is found at α=1.5 between a phase with a finite number of long-range couplings and a phase on which the number of long-range couplings is proportional to the system size. Further, the normal vibrational modes of this chain display a phase transition from delocalized to localized modes at a smaller value of α. Maximum effective disorder is reached at α=2 for which the frequency of the lowest vibrational mode exhibits a pronounced peak.

Exploitation of mitochondrial nad6 as a complementary marker for studying population variability in Lepidoptera

The applicability of mitochondrial nad6 sequences to studies of DNA and population variability in Lepidoptera was tested in four species of economically important moths and one of wild butterflies. The genetic information so obtained was compared to that of cox1 sequences for two species of Lepidoptera. nad6 primers appropriately amplified all the tested DNA targets, the generated data proving to be as informative and suitable in recovering population structures as that of cox1. The proposal is that, to obtain more robust results, this mitochondrial region can be complementarily used with other molecular sequences in studies of low level phylogeny and population genetics in Lepidoptera.

Bose-Einstein condensation in the infinitely ramified star and wheel graphs

In this work, we provide exact solutions for the ideal boson lattice gas on the infinitely ramified star and wheel graphs. Within a tight-binding description, we show that Bose-Einstein condensation (BEC) takes place at a finite temperature after a proper rescaling of the hoping integral ɛ connecting a central site to the peripheral ones. Analytical expressions for the transition temperature, the condensed gas fraction, and the specific heat are given for the star graph as a function of the density of particles n. In particular, the specific heat has a mean-field character, being null in the high-temperature noncondensed phase with a discontinuity at T(c). In the wheel graph, on which the peripheral sites form a closed chain with hopping integral t, BEC takes place only above a critical value of the ratio ɛ/t for which a gap ΔE appears between the ground state and a one-dimensional band. A detailed analysis of the BEC characteristics as a function of n and ΔE is provided. The specific heat in the high-temperature phase of the wheel graph remains finite due to correlations among the peripheral sites.

Localization on a two-channel model with cross-correlated disorder

We study the wavepacket dynamics in a two-channel Anderson model with correlated diagonal disorder. To impose correlations in the disorder distribution we construct the on-site energy landscape following both symmetric and antisymmetric rules. Our numerical data show that symmetric cross-correlations have a small impact on the degree of localization of the one-particle eigenstates. In contrast, antisymmetric correlations lead to a reduction of the effective degree of disorder, thus resulting in a substantial increase of the wavepacket spread. A finite-size scaling analysis shows that the antisymmetric cross-correlations, in spite of weakening the localization, do not promote ballistic transport. The present results shed light on recent findings concerning an apparent delocalization transition in a correlated DNA-like ladder model.