111 research outputs found
Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes
Few pan-genomic studies have been conducted in plants, and none of them have focused on the intraspecific diversity and evolution of their plastid genomes. We address this issue in Brachypodium distachyon and its close relatives B. stacei and B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and intraspecific plastid comparative genomics and phylogenomic relationships within a family-wide framework. Major indel differences were detected between Brachypodium plastomes. Within B. distachyon, we detected two main lineages, a mostly Extremely Delayed Flowering (EDF+) clade and a mostly Spanish (S+) – Turkish (T+) clade, plus nine chloroplast capture and two plastid DNA (ptDNA) introgression and micro-recombination events. Early Oligocene (30.9 million yr ago (Ma)) and Late Miocene (10.1 Ma) divergence times were inferred for the respective stem and crown nodes of Brachypodium and a very recent Mid-Pleistocene (0.9 Ma) time for the B. distachyon split. Flowering time variation is a main factor driving rapid intraspecific divergence in B. distachyon, although it is counterbalanced by repeated introgression between previously isolated lineages. Swapping of plastomes between the three different genomic groups, EDF+, T+, S+, probably resulted from random backcrossing followed by stabilization through selection pressure
Chaos in resonant-tunneling superlattices
Spatio-temporal chaos is predicted to occur in n-doped semiconductor
superlattices with sequential resonant tunneling as their main charge transport
mechanism. Under dc voltage bias, undamped time-dependent oscillations of the
current (due to the motion and recycling of electric field domain walls) have
been observed in recent experiments. Chaos is the result of forcing this
natural oscillation by means of an appropriate external microwave signal.Comment: 3 pages, LaTex, RevTex, 3 uuencoded figures (1.2M) are available upon
request from [email protected], to appear in Phys.Rev.
Dynamics of Electric Field Domains and Oscillations of the Photocurrent in a Simple Superlattice Model
A discrete model is introduced to account for the time-periodic oscillations
of the photocurrent in a superlattice observed by Kwok et al, in an undoped 40
period AlAs/GaAs superlattice. Basic ingredients are an effective negative
differential resistance due to the sequential resonant tunneling of the
photoexcited carriers through the potential barriers, and a rate equation for
the holes that incorporates photogeneration and recombination. The
photoexciting laser acts as a damping factor ending the oscillations when its
power is large enough. The model explains: (i) the known oscillatory static I-V
characteristic curve through the formation of a domain wall connecting high and
low electric field domains, and (ii) the photocurrent and photoluminescence
time-dependent oscillations after the domain wall is formed. In our model, they
arise from the combined motion of the wall and the shift of the values of the
electric field at the domains. Up to a certain value of the photoexcitation,
the non-uniform field profile with two domains turns out to be metastable:
after the photocurrent oscillations have ceased, the field profile slowly
relaxes toward the uniform stationary solution (which is reached on a much
longer time scale). Multiple stability of stationary states and hysteresis are
also found. An interpretation of the oscillations in the photoluminescence
spectrum is also given.Comment: 34 pages, REVTeX 3.0, 10 figures upon request, MA/UC3M/07/9
Chaotic dynamics of electric-field domains in periodically driven superlattices
Self-sustained time-dependent current oscillations under dc voltage bias have
been observed in recent experiments on n-doped semiconductor superlattices with
sequential resonant tunneling. The current oscillations are caused by the
motion and recycling of the domain wall separating low- and high-electric-
field regions of the superlattice, as the analysis of a discrete drift model
shows and experimental evidence supports. Numerical simulation shows that
different nonlinear dynamical regimes of the domain wall appear when an
external microwave signal is superimposed on the dc bias and its driving
frequency and driving amplitude vary. On the frequency - amplitude parameter
plane, there are regions of entrainment and quasiperiodicity forming Arnol'd
tongues. Chaos is demonstrated to appear at the boundaries of the tongues and
in the regions where they overlap. Coexistence of up to four electric-field
domains randomly nucleated in space is detected under ac+dc driving.Comment: 9 pages, LaTex, RevTex. 12 uuencoded figures (1.8M) should be
requested by e-mail from the autho
Molecular phylogeny, diagnostics, and diversity of plant-parasitic nematodes of the genus Hemicycliophora (Nematoda: Hemicycliophoridae)
The genus Hemicycliophora (Nematoda: Hemicycliophoridae) contains 132 valid species of plant-parasitic nematodes, collectively known as ‘sheath nematodes’. Hemicycliophora spp. are characterized morphologically by a long stylet with rounded basal knobs and a cuticular sheath, present in juvenile and adult stages. Populations of 20 valid and 14 putative species of Hemicycliophora and Loofia from several countries were characterized morphologically using light (LM) and scanning electron microscopy (SEM) and molecularly using the D2-D3 segments of 28S rRNA and internal transcribed spacer (ITS) rRNA gene sequences. LM and SEM observations provided new details on the morphology of these species. PCR-restriction fragment length polymorphisms (PCR-RFLPs) of the D2-D3 of 28S rDNA were proposed for identification of the species. Phylogenetic relationships within populations of 36 species of the genus Hemicycliophora using 102 D2-D3 of 28S rDNA and 97 ITS rRNA gene sequences as inferred from Bayesian analysis are reconstructed and discussed. Ancestral state reconstructions of diagnostic characters (body and stylet length, number of body annuli, shape of vulval lip and tail), using maximum parsimony and Bayesian inference, revealed that none of the traits are individually reliable characters for classifying the studied sheath nematode. The Shimodaira–Hasegawa test rejected the validity of the genus Loofia. This is the most complete phylogenetic analysis of Hemicycliophora species conducted so far.Fil: Subbotin, Sergei A.. California Department of Food and Agriculture; Estados Unidos. Institute of Ecology and Evolution of the Russian Academy of Sciences; RusiaFil: Chitambar, John J.. California Department of Food and Agriculture; Estados UnidosFil: Chizhov, Vladimir N.. Institute of Ecology and Evolution of the Russian Academy of Sciences; RusiaFil: Stanley, Jason D.. Florida Department of Agriculture and Consumer Services; Estados UnidosFil: Inserra, Renato N.. Florida Department of Agriculture and Consumer Services; Estados UnidosFil: Doucet, Marcelo Edmundo. Universidad Nacional de Cordoba. Facultad de Cs.exactas Fisicas y Naturales. Centro de Zoologia Aplicada; Argentina. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Cordoba. Instituto de Diversidad y Ecologia Animal; ArgentinaFil: Mcclure, Michael. University Of Arizona; Estados UnidosFil: Ye, Weimin. North Carolina Department of Agriculture & Consumer Services; Estados UnidosFil: Yeates, George.Fil: Mollov, Dimitre S.. University Of Minnesota; Estados UnidosFil: Cantalapiedra Navarrete, Carolina. Consejo Superior de Investigaciones CientÃficas. Instituto de Agricultura Sostenible; EspañaFil: Vovlas, Nicola. Istituto per la Protezione delle Piante; ItaliaFil: Van Den Berg, Esther. ARC-Plant Protection Research Institute; SudáfricaFil: Castillo, Pablo. Consejo Superior de Investigaciones CientÃficas. Instituto de Agricultura Sostenible; Españ
Stationary states and phase diagram for a model of the Gunn effect under realistic boundary conditions
A general formulation of boundary conditions for semiconductor-metal contacts
follows from a phenomenological procedure sketched here. The resulting boundary
conditions, which incorporate only physically well-defined parameters, are used
to study the classical unipolar drift-diffusion model for the Gunn effect. The
analysis of its stationary solutions reveals the presence of bistability and
hysteresis for a certain range of contact parameters. Several types of Gunn
effect are predicted to occur in the model, when no stable stationary solution
exists, depending on the value of the parameters of the injecting contact
appearing in the boundary condition. In this way, the critical role played by
contacts in the Gunn effect is clearly stablished.Comment: 10 pages, 6 Post-Script figure
Conserving evolutionary history does not result in greater diversity over geological time scales
Alternative prioritization strategies have been proposed to safeguard biodiversity over macroevolutionary time scales. The first prioritizes the most distantly related species—maximizing phylogenetic diversity (PD)—in the hopes of capturing at least some lineages that will successfully diversify into the future. The second prioritizes lineages that are currently speciating, in the hopes that successful lineages will continue to generate species into the future. These contrasting schemes also map onto contrasting predictions about the role of slow diversifiers in the production of biodiversity over palaeontological time scales. We consider the performance of the two schemes across 10 dated species-level palaeo-phylogenetic trees ranging from Foraminifera to dinosaurs. We find that prioritizing PD for conservation generally led to fewer subsequent lineages, while prioritizing diversifiers led to modestly more subsequent diversity, compared with random sets of lineages. Importantly for conservation, the tree shape when decisions are made cannot predict which scheme will be most successful. These patterns are inconsistent with the notion that long-lived lineages are the source of new species. While there may be sound reasons for prioritizing PD for conservation, long-term species production might not be one of them
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