Crossing the Rift valley: using complete mitogenomes to infer the diversification and biogeographic history of ethiopian highlands Ptychadena (anura: Ptychadenidae).

The Ethiopian Highlands are considered a biodiversity hotspot, harboring a high number of endemic species. Some of the endemic species probably diversified in situ; this is, for example, the case of a monophyletic clade containing 12 known species of grass frogs of the genus Ptychadena. The different species occur at elevations ranging from 1,500 to above 3,400 m and constitute excellent models to study the process of diversification in the highlands as well as adaptations to high elevations. In this study, we sampled 294 specimens across the distribution of this clade and used complete mitogenomes and genome-wide SNP data to better understand how landscape features influenced the population structure and dispersal of these grass frogs across time and space. Using phylogenetic inference, population structure analyses, and biogeographic reconstructions, we found that the species complex probably first diversified on the south-east side of the Great Rift Valley. Later on, species dispersed to the north-west side, where more recent diversification occurred. We further demonstrate that Ptychadena species have dispersed across the Great Rift Valley at different times. Our analyses allowed for a more complete understanding of the contribution of geological events, biogeographic barriers and climatic changes as drivers of species diversification and adaptation in this important biogeographic region.

Formation of topological defects in nematic shells with a dumbbell-like shape.

The present study investigates dumbbell-shaped nematic liquid crystal shells. Using molecular dynamics (MD) simulations, we consider the effects of an external electric field on nematic ordering by computing the average molecular alignment's time evolution and equilibrium configuration. We show that the number and location of topological defects are strongly affected by the external field, with the orientational ordering's equilibrium configuration depending on field direction about the shell's long axis. For a transverse external field, it is verified that the defect rearrangement presents a non-linear dynamics, with a field independent characteristic time scale delimiting the short and long time regimes. Effects associated with varying the shell's Gaussian curvature are also analyzed.

Universal dynamical scaling laws in three-state quantum walks.

We perform a finite-time scaling analysis over the detrapping point of a three-state quantum walk on the line. The coin operator is parametrized by ρ that controls the wave packet spreading velocity. The input state prepared at the origin is set as a symmetric linear combination of two eigenstates of the coin operator with a characteristic mixing angle θ, one of them being the component that results in full spreading occurring at θ_{c}(ρ) for which no fraction of the wave packet remains trapped near the initial position. We show that relevant quantities, such as the survival probability and the participation ratio assume single parameter scaling forms at the vicinity of the detrapping angle θ_{c}. In particular, we show that the participation ratio grows linearly in time with a logarithmic correction, thus, shedding light on previous reports of sublinear behavior.

Asymmetric acoustic wave scattering by a nonreciprocal and position-dependent mass defect.

We investigate the asymmetric wave scattering in a phononic one-dimensional lattice with a nonreciprocal defect and position dependent masses coupled by the defect spring. The nonreciprocal interaction is characterized by a single parameter Δ while the nonlinear contribution due to position-dependent masses are controlled by a parameterχ. The transmission and reflection coefficients are analytically computed and the effects of the nonreciprocity and nonlinearity are detailed. We show that, in opposite with the linear case, the rectification factor has a frequency dependence, which leads to a more efficient diode-like action at large wavevectors. Further, the nonlinearity leads to an asymmetry of the reflected component, absent in the linear regime. We extend our analysis to a system with frictional forces which suppresses the multistability window promoted by the nonlinear mass contribution without compromising the rectification action.

Low-temperature pseudo-phase-transition in an extended Hubbard diamond chain.

We consider the extended Hubbard diamond chain with an arbitrary number of particles driven by chemical potential. The interaction between dimer diamond chain and nodal couplings is considered in the atomic limit (no hopping), whereas the dimer interaction includes the hopping term. We demonstrate that this model exhibits a pseudo-transition effect in the low-temperature regime. Here, we explore the pseudo-transition rigorously by analyzing several physical quantities. The internal energy and entropy depict sudden, although continuous, jumps which closely resembles discontinuous or first-order phase-transition. At the same time, the correlation length and specific heat exhibit astonishing strong sharp peaks quite similar to a second-order phase-transition. We associate the ascending and descending parts of the peak with power-law "pseudo-critical" exponents. We determine the pseudo-critical exponents in the temperature range where these peaks are developed, namely, ν=1 for the correlation length and α=3 for the specific heat. We also study the behavior of the electron density and isothermal compressibility around the pseudo-critical temperature.

Critical properties of the SIS model on the clustered homophilic network.

The spreading of epidemics in complex networks has been a subject of renewed interest of several scientific branches. In this regard, we have focused our attention on the study of the susceptible-infected-susceptible (SIS) model, within a Monte Carlo numerical simulation approach, representing the spreading of epidemics in a clustered homophilic network. The competition between infection and recovery that drives the system either to an absorbing or to an active phase is analyzed. We estimate the static critical exponents ß ∕ ν , 1 ∕ ν and γ ∕ ν , through finite-size scaling (FSS) analysis of the order parameter ρ and its fluctuations, showing that they differ from those associated with the contact process on a scale-free network, as well as those predicted by the heterogeneous mean-field theory.

Emerging extreme value and Fermi-Dirac distributions in the Lévy branching and annihilating process.

We study the dynamics of the branching and annihilating process with long-range interactions. Static particles generate an offspring and annihilate upon contact. The branching distance is supposed to follow a Lévy-like power-law distribution with P(r)∝1/r^{α}. We analyze the long term behavior of the mean particles number and its fluctuations as a function of the parameter α that controls the range of the branching process. We show that the dynamic exponent associated with the particle number fluctuations varies continuously for α<4 while the particle number exponent only changes for α<3. A crossover from extreme value Frechet (at α=3) and Gumbell (for 2<α<3) distributions is developed, similar to the one reported in recent experiments with cw-pumped random fiber lasers presenting underlying gain and Lévy processes. We report the dependence of the relevant dynamical power-law exponents on α showing that explosive growth takes place for α≤2. Further, the average occupation number distribution is shown to evolve from the standard Fermi-Dirac form to the generalized one within the context of nonextensive statistics.

Rectification of acoustic phonons in harmonic chains with nonreciprocal spring defects.

The scattering of acoustic phonons by nonreciprocal spring defects inserted in an harmonic chain is investigated. The degree of nonreciprocity of the forces mediated by the defect springs is parameterized by a single quantity Δ that effectively takes into account the interaction of the coupled masses with hidden degrees of freedom of an underlying nonequilibrium system. We demonstrate a pronounced rectification effect with transmission having a preferential direction. Nonreciprocity also allows energy exchange between the system and the medium. Further, we show a cooperative action between defects mediated by resonant cavity modes. The influence of damping forces is also explored and shown to promote the rectification of the reflected vibrational wave component.

Localization-delocalization transition in discrete-time quantum walks with long-range correlated disorder.

We study the effects of spatially long-range correlated phase disorder on the Hadamard quantum walk on a line. The shift operator is built to exhibit an intrinsic disorder distribution featuring long-range correlations. To impose such, we resort to fractional Brownian motion with power-law spectrum 1/k^{2α} with α≥0 being the exponent that controls the degree of correlations. We discuss the scaling behavior of the walker's wave packet and report a localization-delocalization transition controlled by α. We unveil two intermediate dynamical regimes between exponential localization and full delocalization.

Enhanced nonreciprocal transmission through a saturable cubic-quintic nonlinear dimer defect.

The transmission properties through a saturable cubic-quintic nonlinear defect attached to lateral linear chains is investigated. Particular attention is directed to the possible non-reciprocal diode-like transmission when the parity-symmetry of the defect is broken. Distinct cases of parity breaking are considered including asymmetric linear and nonlinear responses. The spectrum of the transmission coefficient is analytically computed and the influence of the degree of saturation analyzed in detail. The transmission of Gaussian wave-packets is also numerically investigated. Our results unveil that spectral regions with high transmission and enhanced diode-like operation can be achieved.

Phase diagram and re-entrant fermionic entanglement in a hybrid Ising-Hubbard ladder.

The degree of fermionic entanglement is examined in an exactly solvable Ising-Hubbard ladder, which involves interacting electrons on the ladder's rungs described by Hubbard dimers at half-filling on each rung, accounting for intrarung hopping and Coulomb terms. The coupling between neighboring Hubbard dimers is assumed to have an Ising-like nature. The ground-state phase diagram consists of four distinct regions corresponding to the saturated paramagnetic, the classical antiferromagnetic, the quantum antiferromagnetic, and the mixed classical-quantum phase. We have exactly computed the fermionic concurrence, which measures the degree of quantum entanglement between the pair of electrons on the ladder rungs. The effects of the hopping amplitude, the Coulomb term, temperature, and magnetic fields on the fermionic entanglement are explored in detail. It is shown that the fermionic concurrence displays a re-entrant behavior when quantum entanglement is being generated at moderate temperatures above the classical saturated paramagnetic ground state.

More sex chromosomes than autosomes in the Amazonian frog Leptodactylus pentadactylus.

Heteromorphic sex chromosomes are common in eukaryotes and largely ubiquitous in birds and mammals. The largest number of multiple sex chromosomes in vertebrates known today is found in the monotreme platypus (Ornithorhynchus anatinus, 2n = 52) which exhibits precisely 10 sex chromosomes. Interestingly, fish, amphibians, and reptiles have sex determination mechanisms that do or do not involve morphologically differentiated sex chromosomes. Relatively few amphibian species carry heteromorphic sex chromosomes, and when present, they are frequently represented by only one pair, either XX:XY or ZZ:ZW types. Here, in contrast, with several evidences, from classical and molecular cytogenetic analyses, we found 12 sex chromosomes in a Brazilian population of the smoky jungle frog, designated as Leptodactylus pentadactylus Laurenti, 1768 (Leptodactylinae), which has a karyotype with 2n = 22 chromosomes. Males exhibited an astonishing stable ring-shaped meiotic chain composed of six X and six Y chromosomes. The number of sex chromosomes is larger than the number of autosomes found, and these data represent the largest number of multiple sex chromosomes ever found among vertebrate species. Additionally, sequence and karyotype variation data suggest that this species may represent a complex of species, in which the chromosomal rearrangements may possibly have played an important role in the evolution process.

Bose-Einstein condensation in chains with power-law hoppings: Exact mapping on the critical behavior in d-dimensional regular lattices.

Recent experimental progress on the realization of quantum systems with highly controllable long-range interactions has impelled the study of quantum phase transitions in low-dimensional systems with power-law couplings. Long-range couplings mimic higher-dimensional effects in several physical contexts. Here, we provide the exact relation between the spectral dimension d at the band bottom and the exponent α that tunes the range of power-law hoppings of a one-dimensional ideal lattice Bose gas. We also develop a finite-size scaling analysis to obtain some relevant critical exponents and the critical temperature of the BEC transition. In particular, an irrelevant dangerous scaling field has to be taken into account when the hopping range is sufficiently large to make the effective dimensionality d>4.

Ground-state phase diagram, fermionic entanglement and kinetically-induced frustration in a hybrid ladder with localized spins and mobile electrons.

We introduce an exactly solvable hybrid spin-ladder model containing localized nodal Ising spins and interstitial mobile electrons, which are allowed to perform a quantum-mechanical hopping between the ladder's legs. The quantum-mechanical hopping process induces an antiferromagnetic coupling between the ladder's legs that competes with a direct exchange coupling of the nodal spins. The model is exactly mapped onto the Ising spin ladder with temperature-dependent two- and four-spin interactions, which is subsequently solved using the transfer-matrix technique. We report the ground-state phase diagram and compute the fermionic concurrence to characterize the quantum entanglement between the pair of interstitial mobile electrons. We further provide a detailed analysis of the local spin ordering including the pair and four-spin correlation functions around an elementary plaquette, as well as, the local ordering diagrams. It is shown that a complex sequence of distinct local orderings and frustrated correlations takes place when the model parameters drive the investigated system close to a zero-temperature triple coexistence point.

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.

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.

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.