The taxonomic status of the endangered thin-spined porcupine, Chaetomys subspinosus (Olfers, 1818), based on molecular and karyologic data

Background: The thin-spined porcupine, also known as the bristle-spined rat, Chaetomys subspinosus (Olfers, 1818), the only member of its genus, figures among Brazilian endangered species. In addition to being threatened, it is poorly known, and even its taxonomic status at the family level has long been controversial. The genus Chaetomys was originally regarded as a porcupine in the family Erethizontidae, but some authors classified it as a spiny-rat in the family Echimyidae. Although the dispute seems to be settled in favor of the erethizontid advocates, further discussion of its affinities should be based on a phylogenetic framework. In the present study, we used nucleotide-sequence data from the complete mitochondrial cytochrome b gene and karyotypic information to address this issue. Our molecular analyses included one individual of Chaetomys subspinosus from the state of Bahia in northeastern Brazil, and other hystricognaths. Results: All topologies recovered in our molecular phylogenetic analyses strongly supported Chaetomys subspinosus as a sister clade of the erethizontids. Cytogenetically, Chaetomys subspinosus showed 2n = 52 and FN = 76. Although the sexual pair could not be identified, we assumed that the X chromosome is biarmed. The karyotype included 13 large to medium metacentric and submetacentric chromosome pairs, one small subtelocentric pair, and 12 small acrocentric pairs. The subtelocentric pair 14 had a terminal secondary constriction in the short arm, corresponding to the nucleolar organizer region (Ag-NOR), similar to the erethizontid Sphiggurus villosus, 2n = 42 and FN = 76, and different from the echimyids, in which the secondary constriction is interstitial. Conclusion: Both molecular phylogenies and karyotypical evidence indicated that Chaetomys is closely related to the Erethizontidae rather than to the Echimyidae, although in a basal position relative to the rest of the Erethizontidae. The high levels of molecular and morphological divergence suggest that Chaetomys belongs to an early radiation of the Erethizontidae that may have occurred in the Early Miocene, and should be assigned to its own subfamily, the Chaetomyinae.

Testing Evolutionary and Dispersion Scenarios for the Settlement of the New World

Background: Discussion surrounding the settlement of the New World has recently gained momentum with advances in molecular biology, archaeology and bioanthropology. Recent evidence from these diverse fields is found to support different colonization scenarios. The currently available genetic evidence suggests a ""single migration'' model, in which both early and later Native American groups derive from one expansion event into the continent. In contrast, the pronounced anatomical differences between early and late Native American populations have led others to propose more complex scenarios, involving separate colonization events of the New World and a distinct origin for these groups. Methodology/Principal Findings: Using large samples of Early American crania, we: 1) calculated the rate of morphological differentiation between Early and Late American samples under three different time divergence assumptions, and compared our findings to the predicted morphological differentiation under neutral conditions in each case; and 2) further tested three dispersal scenarios for the colonization of the New World by comparing the morphological distances among early and late Amerindians, East Asians, Australo-Melanesians and early modern humans from Asia to geographical distances associated with each dispersion model. Results indicate that the assumption of a last shared common ancestor outside the continent better explains the observed morphological differences between early and late American groups. This result is corroborated by our finding that a model comprising two Asian waves of migration coming through Bering into the Americas fits the cranial anatomical evidence best, especially when the effects of diversifying selection to climate are taken into account. Conclusions: We conclude that the morphological diversity documented through time in the New World is best accounted for by a model postulating two waves of human expansion into the continent originating in East Asia and entering through Beringia.

Phylogeography and historical demography of the neotropical stingless bee Melipona quadrifasciata (Hymenoptera, Apidae): incongruence between morphology and mitochondrial DNA

The stingless bees are among the most abundant and ecologically important social invertebrates in tropical communities. The Neotropical stingless bee Melipona quadrifasciata has two subspecies: M. quadrifasciata quadrifasciata and M. quadrifasciata anthidioides. The main difference between subspecies are the yellow metassomal stripes, which are continuous in M. q. quadrifasciata and discontinuous in M. q. anthidioides. Recently, two populations were described with continuous stripes and inhabiting clearly disjunct areas in relation to M. q. quadrifasciata. We sequenced 852 bp of the mtDNA COI gene from 145 colonies from 56 localities, and for the first time performed a detailed phylogeographic study of a neotropical stingless bee. Phylogenetic analyses revealed the existence of two clades exhibiting a south to north distribution: southern populations comprise the subspecies M. q. quadrifasciata, and northern populations are composed of M. q. anthidioides and two disjunct populations with continuous stripes. The divergence time of these two phylogroups was estimated between 0.233 and 0.840 million years ago in the Pleistocene, a period of climatic changes and geomorphological alterations in the Neotropical region. No evidence of genetic structure in relation to the tergal stripes was found, indicating that the morphological trait regarding the pattern of stripes on tergites is not an accurate diagnostic for the subspecies of M. quadrifasciata.

Complete Genome Viral Phylogenies Suggests the Concerted Evolution of Regulatory Cores and Accessory Satellites

We consider the concerted evolution of viral genomes in four families of DNA viruses. Given the high rate of horizontal gene transfer among viruses and their hosts, it is an open question as to how representative particular genes are of the evolutionary history of the complete genome. To address the concerted evolution of viral genes, we compared genomic evolution across four distinct, extant viral families. For all four viral families we constructed DNA-dependent DNA polymerase-based (DdDp) phylogenies and in addition, whole genome sequence, as quantitative descriptions of inter-genome relationships. We found that the history of the polymerase gene was highly predictive of the history of the genome as a whole, which we explain in terms of repeated, co-divergence events of the core DdDp gene accompanied by a number of satellite, accessory genetic loci. We also found that the rate of gene gain in baculovirus and poxviruses proceeds significantly more quickly than the rate of gene loss and that there is convergent acquisition of satellite functions promoting contextual adaptation when distinct viral families infect related hosts. The congruence of the genome and polymerase trees suggests that a large set of viral genes, including polymerase, derive from a phylogenetically conserved core of genes of host origin, secondarily reinforced by gene acquisition from common hosts or co-infecting viruses within the host. A single viral genome can be thought of as a mutualistic network, with the core genes acting as an effective host and the satellite genes as effective symbionts. Larger virus genomes show a greater departure from linkage equilibrium between core and satellites functions.

PARTIAL STABILITY FOR A CLASS OF NONLINEAR SYSTEMS

This paper studies a nonlinear, discrete-time matrix system arising in the stability analysis of Kalman filters. These systems present an internal coupling between the state components that gives rise to complex dynamic behavior. The problem of partial stability, which requires that a specific component of the state of the system converge exponentially, is studied and solved. The convergent state component is strongly linked with the behavior of Kalman filters, since it can be used to provide bounds for the error covariance matrix under uncertainties in the noise measurements. We exploit the special features of the system-mainly the connections with linear systems-to obtain an algebraic test for partial stability. Finally, motivated by applications in which polynomial divergence of the estimates is acceptable, we study and solve a partial semistability problem.

Hidden vorticity in binary Bose-Einstein condensates

We consider a binary Bose-Einstein condensate (BEC) described by a system of two-dimensional (2D) Gross-Pitaevskii equations with the harmonic-oscillator trapping potential. The intraspecies interactions are attractive, while the interaction between the species may have either sign. The same model applies to the copropagation of bimodal beams in photonic-crystal fibers. We consider a family of trapped hidden-vorticity (HV) modes in the form of bound states of two components with opposite vorticities S(1,2) = +/- 1, the total angular momentum being zero. A challenging problem is the stability of the HV modes. By means of a linear-stability analysis and direct simulations, stability domains are identified in a relevant parameter plane. In direct simulations, stable HV modes feature robustness against large perturbations, while unstable ones split into fragments whose number is identical to the azimuthal index of the fastest growing perturbation eigenmode. Conditions allowing for the creation of the HV modes in the experiment are discussed too. For comparison, a similar but simpler problem is studied in an analytical form, viz., the modulational instability of an HV state in a one-dimensional (1D) system with periodic boundary conditions (this system models a counterflow in a binary BEC mixture loaded into a toroidal trap or a bimodal optical beam coupled into a cylindrical shell). We demonstrate that the stabilization of the 1D HV modes is impossible, which stresses the significance of the stabilization of the HV modes in the 2D setting.

Formation of vortices in a dense Bose-Einstein condensate

A relaxation method is employed to study a rotating dense Bose-Einstein condensate beyond the Thomas-Fermi approximation. We use a slave-boson model to describe the strongly interacting condensate and derive a generalized nonlinear Schrodinger equation with a kinetic term for the rotating condensate. In comparison with previous calculations, based on the Thomas-Fermi approximation, significant improvements are found in regions where the condensate in a trap potential is not smooth. The critical angular velocity of the vortex formation is higher than in the Thomas-Fermi prediction.

Numerical investigation of the quantum fluctuations of optical fields transmitted through an atomic medium

We have numerically solved the Heisenberg-Langevin equations describing the propagation of quantized fields through an optically thick sample of atoms. Two orthogonal polarization components are considered for the field, and the complete Zeeman sublevel structure of the atomic transition is taken into account. Quantum fluctuations of atomic operators are included through appropriate Langevin forces. We have considered an incident field in a linearly polarized coherent state (driving field) and vacuum in the perpendicular polarization and calculated the noise spectra of the amplitude and phase quadratures of the output field for two orthogonal polarizations. We analyze different configurations depending on the total angular momentum of the ground and excited atomic states. We examine the generation of squeezing for the driving-field polarization component and vacuum squeezing of the orthogonal polarization. Entanglement of orthogonally polarized modes is predicted. Noise spectral features specific to (Zeeman) multilevel configurations are identified.

Double-helicity dependence of jet properties from dihadrons in longitudinally polarized p plus p collisions at root s=200 GeV

It has been postulated that partonic orbital angular momentum can lead to a significant double-helicity dependence in the net transverse momentum of Drell-Yan dileptons produced in longitudinally polarized p + p collisions. Analogous effects are also expected for dijet production. If confirmed by experiment, this hypothesis, which is based on semiclassical arguments, could lead to a new approach for studying the contributions of orbital angular momentum to the proton spin. We report the first measurement of the double-helicity dependence of the dijet transverse momentum in longitudinally polarized p + p collisions at root s = 200 GeV from data taken by the PHENIX experiment in 2005 and 2006. The analysis deduces the transverse momentum of the dijet from the widths of the near-and far-side peaks in the azimuthal correlation of the dihadrons. When averaged over the transverse momentum of the triggered particle, the difference of the root mean square of the dijet transverse momentum between like-and unlike-helicity collisions is found to be -37 +/- 88(stat) +/- 14(sys)t MeV/c.

High-p(T) pi(0) production with respect to the reaction plane in Au plus Au collisions at s(NN)=200 GeV

Measurements of the azimuthal anisotropy of high-p(T) neutral pion (pi(0)) production in Au+Au collisions at s(NN)=200 GeV by the PHENIX experiment are presented. The data included in this article were collected during the 2004 Relativistic Heavy Ion Collider running period and represent approximately an order of magnitude increase in the number of analyzed events relative to previously published results. Azimuthal angle distributions of pi(0) mesons detected in the PHENIX electromagnetic calorimeters are measured relative to the reaction plane determined event-by-event using the forward and backward beam-beam counters. Amplitudes of the second Fourier component (v(2)) of the angular distributions are presented as a function of pi(0) transverse momentum (p(T)) for different bins in collision centrality. Measured reaction plane dependent pi(0) yields are used to determine the azimuthal dependence of the pi(0) suppression as a function of p(T), R(AA)(Delta phi,p(T)). A jet-quenching motivated geometric analysis is presented that attempts to simultaneously describe the centrality dependence and reaction plane angle dependence of the pi(0) suppression in terms of the path lengths of hypothetical parent partons in the medium. This set of results allows for a detailed examination of the influence of geometry in the collision region and of the interplay between collective flow and jet-quenching effects along the azimuthal axis.

Bayesian online algorithms for learning in discrete Hidden Markov Models

We propose and analyze two different Bayesian online algorithms for learning in discrete Hidden Markov Models and compare their performance with the already known Baldi-Chauvin Algorithm. Using the Kullback-Leibler divergence as a measure of generalization we draw learning curves in simplified situations for these algorithms and compare their performances.

CMB in a box: Causal structure and the Fourier-Bessel expansion

This paper makes two points. First, we show that the line-of-sight solution to cosmic microwave anisotropies in Fourier space, even though formally defined for arbitrarily large wavelengths, leads to position-space solutions which only depend on the sources of anisotropies inside the past light cone of the observer. This foretold manifestation of causality in position (real) space happens order by order in a series expansion in powers of the visibility gamma = e(-mu), where mu is the optical depth to Thomson scattering. We show that the contributions of order gamma(N) to the cosmic microwave background (CMB) anisotropies are regulated by spacetime window functions which have support only inside the past light cone of the point of observation. Second, we show that the Fourier-Bessel expansion of the physical fields (including the temperature and polarization momenta) is an alternative to the usual Fourier basis as a framework to compute the anisotropies. The viability of the Fourier-Bessel series for treating the CMB is a consequence of the fact that the visibility function becomes exponentially small at redshifts z >> 10(3), effectively cutting off the past light cone and introducing a finite radius inside which initial conditions can affect physical observables measured at our position (x) over right arrow = 0 and time t(0). Hence, for each multipole l there is a discrete tower of momenta k(il) (not a continuum) which can affect physical observables, with the smallest momenta being k(1l) similar to l. The Fourier-Bessel modes take into account precisely the information from the sources of anisotropies that propagates from the initial value surface to the point of observation-no more, no less. We also show that the physical observables (the temperature and polarization maps), and hence the angular power spectra, are unaffected by that choice of basis. This implies that the Fourier-Bessel expansion is the optimal scheme with which one can compute CMB anisotropies.

Noncommutativity due to spin

Using the Berezin-Marinov pseudoclassical formulation of the spin particle we propose a classical model of spin noncommutativity. In the nonrelativistic case, the Poisson brackets between the coordinates are proportional to the spin angular momentum. The quantization of the model leads to the noncommutativity with mixed spatial and spin degrees of freedom. A modified Pauli equation, describing a spin half particle in an external electromagnetic field is obtained. We show that nonlocality caused by the spin noncommutativity depends on the spin of the particle; for spin zero, nonlocality does not appear, for spin half, Delta x Delta y >= theta(2)/2, etc. In the relativistic case the noncommutative Dirac equation was derived. For that we introduce a new star product. The advantage of our model is that in spite of the presence of noncommutativity and nonlocality, it is Lorentz invariant. Also, in the quasiclassical approximation it gives noncommutativity with a nilpotent parameter.

Topology Studies of Hydrodynamics Using Two-Particle Correlation Analysis

The effects of fluctuating initial conditions are studied in the context of relativistic heavy ion collisions where a rapidly evolving system is formed. Two-particle correlation analysis is applied to events generated with the NEXSPHERIO hydrodynamic code, starting with fluctuating nonsmooth initial conditions (IC). The results show that the nonsmoothness in the IC survives the hydroevolution and can be seen as topological features of the angular correlation function of the particles emerging from the evolving system. A long range correlation is observed in the longitudinal direction and in the azimuthal direction a double peak structure is observed in the opposite direction to the trigger particle. This analysis provides clear evidence that these are signatures of the combined effect of tubular structures present in the IC and the proceeding collective dynamics of the hot and dense medium.

Local approximations for polarization potentials

We discuss the derivation of an equivalent polarization potential independent of angular momentum l for use in the optical Schrodinger equation that describes the elastic scattering of heavy ions. Three different methods are used for this purpose. Application of our theory to the low energy scattering of light heavy-ion systems at near-barrier energies is made. It is found that the notion of an l-independent polarization potential has some validity but cannot be a good substitute for the l-dependent local equivalent Feshbach polarization potential.