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.

Mitogenome analyses elucidate the evolutionary relationships of a probable Eocene wet tropics relic in the xerophile lizard genus Acanthodactylus

Climate has a large impact on diversity and evolution of the world's biota. The Eocene-Oligocene transition from tropical climate to cooler, drier environments was accompanied by global species turnover. A large number of Old World lacertid lizard lineages have diversified after the Eocene-Oligocene boundary. One of the most speciose reptile genera in the arid Palearctic, Acanthodactylus, contains two sub-Saharan species with unresolved phylogenetic relationship and unknown climatic preferences. We here aim to understand how and when adaptation to arid conditions occurred in Acanthodactylus and when tropical habitats where entered. Using whole mitogenomes from fresh and archival DNA and published sequences we recovered a well-supported Acanthodactylus phylogeny and underpinned the timing of diversification with environmental niche analyses of the sub-Saharan species A. guineensis and A. boueti in comparison to all arid Acanthodactylus. We found that A. guineensis represents an old lineage that splits from a basal node in the Western clade, and A. boueti is a derived lineage and probably not its sister. Their long branches characterize them-and especially A. guineensis-as lineages that may have persisted for a long time without further diversification or have undergone multiple extinctions. Environmental niche models verified the occurrence of A. guineensis and A. boueti in hot humid environments different from the other 42 arid Acanthodactylus species. While A. guineensis probably remained in tropical habitat from periods prior to the Eocene-Oligocene boundary, A. boueti entered tropical environments independently at a later period. Our results provide an important baseline for studying adaptation and the transition from humid to arid environments in Lacertidae.

Skin microbiome correlates with bioclimate and Batrachochytrium dendrobatidis infection intensity in Brazil's Atlantic Forest treefrogs

In Brazil’s Atlantic Forest (AF) biodiversity conservation is of key importance since the fungal pathogen Batrachochytrium dendrobatidis (Bd) has led to the rapid loss of amphibian populations here and worldwide. The impact of Bd on amphibians is determined by the host's immune system, of which the skin microbiome is a critical component. The richness and diversity of such cutaneous bacterial communities are known to be shaped by abiotic factors which thus may indirectly modulate host susceptibility to Bd. This study aimed to contribute to understanding the environment-host–pathogen interaction determining skin bacterial communities in 819 treefrogs (Anura: Hylidae and Phyllomedusidae) from 71 species sampled across the AF. We investigated whether abiotic factors influence the bacterial community richness and structure on the amphibian skin. We further tested for an association between skin bacterial community structure and Bd co-occurrence. Our data revealed that temperature, precipitation, and elevation consistently correlate with richness and diversity of the skin microbiome and also predict Bd infection status. Surprisingly, our data suggest a weak but significant positive correlation of Bd infection intensity and bacterial richness. We highlight the prospect of future experimental studies on the impact of changing environmental conditions associated with global change on environment-host–pathogen interactions in the AF.

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 β ∕ 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.

Multiple origins of green coloration in frogs mediated by a novel biliverdin-binding serpin

Many vertebrates have distinctive blue-green bones and other tissues due to unusually high biliverdin concentrations-a phenomenon called chlorosis. Despite its prevalence, the biochemical basis, biology, and evolution of chlorosis are poorly understood. In this study, we show that the occurrence of high biliverdin in anurans (frogs and toads) has evolved multiple times during their evolutionary history, and relies on the same mechanism-the presence of a class of serpin family proteins that bind biliverdin. Using a diverse combination of techniques, we purified these serpins from several species of nonmodel treefrogs and developed a pipeline that allowed us to assemble their complete amino acid and nucleotide sequences. The described proteins, hereafter named biliverdin-binding serpins (BBS), have absorption spectra that mimic those of phytochromes and bacteriophytochromes. Our models showed that physiological concentration of BBSs fine-tune the color of the animals, providing the physiological basis for crypsis in green foliage even under near-infrared light. Additionally, we found that these BBSs are most similar to human glycoprotein alpha-1-antitrypsin, but with a remarkable functional diversification. Our results present molecular and functional evidence of recurrent evolution of chlorosis, describe a biliverdin-binding protein in vertebrates, and introduce a function for a member of the serpin superfamily, the largest and most ubiquitous group of protease inhibitors.

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.

Symbiotic bacterial communities in rainforest fungus-farming ants: evidence for species and colony specificity

Animals may host diverse bacterial communities that can markedly affect their behavioral physiology, ecology, and vulnerability to disease. Fungus-farming ants represent a classical example of mutualism that depends on symbiotic microorganisms. Unraveling the bacterial communities associated with fungus-farming ants is essential to understand the role of these microorganisms in the ant-fungus symbiosis. The bacterial community structure of five species of fungus-farmers (non-leaf-cutters; genera Mycocepurus, Mycetarotes, Mycetophylax, and Sericomyrmex) from three different environments in the Brazilian Atlantic rainforest (lowland forest, restinga forest, and sand dunes) was characterized with amplicon-based Illumina sequencing of 16 S ribosomal RNA gene. Possible differences in bacterial communities between ants internal to the nest (on the fungus garden) and external foragers were also investigated. Our results on the richness and diversity of associated bacteria provide novel evidence that these communities are host- and colony-specific in fungus-farming ants. Indeed, the bacterial communities associated with external foragers differ among the five species, and among colonies of the same species. Furthermore, bacterial communities from internal ants vs. foragers do not differ or differ only slightly within each ant species. This study highlights the importance of describing ant-associated bacterial communities to better understand this host-bacterial interaction in the social environment of insect colonies and provides the foundation for future studies on the ecological and evolutionary processes that drive the success of fungus-farming ants.

High-throughput DNA sequencing of museum specimens sheds light on the long-missing species of the Bokermannohyla claresignata group (Anura: Hylidae: Cophomantini)

The two species of the Bokermannohyla claresignata species group (Anura: Hylidae) have not been collected for the last four decades. It is the only species group of the hyline tribe Cophomantini that has not yet been analysed genetically. Its phylogenetic position is thus uncertain, and it has a combination of adult and larval character states that make this group a crucial missing piece that hinders our understanding of Cophomantini phylogenetics and character evolution. We obtained DNA sequences from a museum larval specimen of Bok. claresignata, using specialized extraction methods and high-throughput DNA sequencing, and combined the molecular phylogenetic results with available phenotypic information to provide new insights into the taxonomy and phylogenetic relationships of its species group. Our phylogenetic results place Bok. claresignata as sister to the Boana pulchella group, supporting its inclusion in Boana, together with Bokermannohyla clepsydra. In light of this new finding, we recognize a newly defined Boana claresignata group to accommodate these species, thus resolving both the polyphyly of Bokermannohyla and the paraphyly of Boana. Considering the phylogenetic relationships of the Boana claresignata group, we also discuss the evolution of suctorial tadpoles and mature oocyte/egg pigmentation in Cophomantini.

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.

Anurans of the Caparaó National Park and surroundings, southeast Brazil

Abstract The Atlantic Forest (AF) is one of the biodiversity hotspots of the world, and the most fragmented biome of Brazil. This biome includes different phytophysiognomies, as riparian, slope, cloudy forests, and grasslands. Such complexity, allied to huge latitudinal and high elevational range, provides diverse habitats and conditions for amphibian speciation. As a result, there are over 600 amphibian species known to occur in the AF. Within this biome the Caparaó National Park (CNP) is relevant, as it includes the highest peak of the biome, the Pico da Bandeira at almost 3,000 m above sea level, as well as different phytophysiognomies as rocky fields and humid forests. In spite of that, its amphibian fauna is still poorly described. We inventoried amphibians at the CNP and surrounding areas from 2016 to 2018 and recorded 47 anuran species, of which two are locally endemic and at least six have not been described yet. Additionally, we compiled data from previous surveys (2004 to 2008) and secondary data from scientific collections. All together, we registered a total of 61 anuran species from 12 families for the CNP and surroundings, placing this area among the 10 amphibian richest sites in the AF. Some of these species are represented by only one or two collected specimens and have not been registered in the CNP since the 1980’s, such as Thoropa lutzi and Hylodes vanzolinii. These species could be examples of population declines or even past local extinctions, highlighting the need of further sampling efforts in that highly biodiverse site.

A review of the elusive bicolored iris Snouted Treefrogs (Anura: Hylidae:Scinax uruguayus group)

The genus Scinax currently includes more than 120 species, recovered in two major clades, the S. catharinae and the S. ruber clades. The latter comprises 75 species, most of which remain unassigned to any species groups, while 12 are included in the S. rostratus and S. uruguayus groups. In this paper we present a taxonomic review of the two species currently included in the S. uruguayus group, discussing some putative phenotypic synapomorphies of this group. Although S. pinima and S. uruguayus have been considered as distinct species, this has been based on scant evidence, and several authors doubted of their distinctiveness. Our study of available specimens of S. pinima and S. uruguayus corroborates that both are valid and diagnosable species based on phenotypic evidence. Furthermore, our results show that S. pinima previously known only from its type locality, has a much widespread distribution than previously thought (including the Brazilian states of Paraná, Santa Catarina, and Rio Grande do Sul), which, added to the biological information presented here allows to suggest the removal of this species from the "Data Deficient" IUCN Red List category to "Least Concern". Also, we describe a new species formerly reported as S. aff. pinima and S. uruguayus from NE Argentina and some localities from the Brazilian State of Rio Grande do Sul. All species are diagnosed and characterized using adult and larval morphology, osteology, vocalizations, cytogenetics, and natural history.

Arthropod-bacteria interactions influence assembly of aquatic host microbiome and pathogen defense

The host-associated microbiome is vital to host immunity and pathogen defense. In aquatic ecosystems, organisms may interact with environmental bacteria to influence the pool of potential symbionts, but the effects of these interactions on host microbiome assembly and pathogen resistance are unresolved. We used replicated bromeliad microecosystems to test for indirect effects of arthropod-bacteria interactions on host microbiome assembly and pathogen burden, using tadpoles and the fungal amphibian pathogen Batrachochytrium dendrobatidis as a model host-pathogen system. Arthropods influenced host microbiome assembly by altering the pool of environmental bacteria, with arthropod-bacteria interactions specifically reducing host colonization by transient bacteria and promoting antimicrobial components of aquatic bacterial communities. Arthropods also reduced fungal zoospores in the environment, but fungal infection burdens in tadpoles corresponded most closely with arthropod-mediated patterns in microbiome assembly. This result indicates that the cascading effects of arthropods on the maintenance of a protective host microbiome may be more strongly linked to host health than negative effects of arthropods on pools of pathogenic zoospores. Our work reveals tight links between healthy ecosystem dynamics and the functioning of host microbiomes, suggesting that ecosystem disturbances such as loss of arthropods may have downstream effects on host-associated microbial pathogen defenses and host fitness.

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.

High Genetic Diversity and No Population Structure of the New World Screwworm Fly Cochliomyia hominivorax (Diptera: Calliphoridae) on a Microgeographic Scale: Implications for Management Units

The New World screwworm fly Cochliomyia hominivorax (Coquerel, 1858) (Diptera: Calliphoridae) is an important livestock pest endemic to the Americas that has been eradicated from North and continental Central America with a control program based on the Sterile Insect Technique (SIT). The establishment of target management units is a strategic step in the implementation of new control programs, which can be achieved using genetic studies of natural populations. Previous studies of New World screwworm fly populations were conducted on the continental scale and identified four main groups: two in South America and two in the Caribbean. However, studies within these groups are needed to determine which smaller geographic areas can be treated as management units. Here, we analyze the genetic variability distribution and the population demographic signals of the New World screwworm fly in a 6,000 km2 area located along the border of Brazil and Uruguay. This area was the subject of the first control pilot program conducted in South America. We studied eight microsatellite loci and sequences from two mitochondrial DNA regions in individuals sampled at 20-25 livestock breeding farms. We observed no population structure and found high genetic variability on the geographical scale sampled for both molecular markers. Our microsatellite data suggest that these populations are not in equilibrium, and demographic analyses based on mitochondrial data indicate population expansion. These results suggest that this geographic scale is not adequate for future New World screwworm fly management in South America.

The Intestinal Microbiota of Tadpoles Differs from Those of Syntopic Aquatic Invertebrates

Bacterial communities associated to eukaryotes play important roles in the physiology, development, and health of their hosts. Here, we examine the intestinal microbiota in tadpoles and aquatic invertebrates (insects and gastropods) to better understand the degree of specialization in the tadpole microbiotas. Samples were collected at the same time in one pond, and the V4 region of the bacterial 16S rRNA gene was sequenced with Illumina amplicon sequencing. We found that bacterial richness and diversity were highest in two studied snail individuals, intermediate in tadpoles, and lowest in the four groups of aquatic insects. All groups had substantial numbers of exclusive bacterial operational taxonomic units (OTUs) in their guts, but also shared a high proportion of OTUs, probably corresponding to transient environmental bacteria. Significant differences were found for all pairwise comparisons of tadpoles and snails with the major groups of insects, but not among insect groups or between snails and tadpoles. The similarity between tadpoles and snails may be related to similar feeding mode as both snails and tadpoles scratch biofilms and algae from surfaces; however, this requires confirmation due to low sample sizes. Overall, the gut microbiota differences found among syntopic aquatic animals are likely shaped by both food preferences and host identity.

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.

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.

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.

The mitochondrial genomes of three species of poison frogs (Anura: Dendrobates)

We reconstructed nearly complete mitogenomes for three species of poison frogs, Dendrobates auratus, D. leucomelas, and D. tinctorius, from RNAseq data. We recovered the 13 protein-coding genes, 22 tRNA genes (except tRNA-Val for D. leucomelas), and two rRNA genes for all three species, plus partial sequences of the control region. The order of genes agrees with that known from a previously sequenced D. auratus, being the most commonly found for neobatrachian frogs. Based on full-sibling comparisons we estimate the probable error rate of Illumina-RNAseq reconstructed mitogenomes of up to 0.15%.