Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae).

Despite the extensive phenotypic variation that characterizes the Gesneriaceae family, there is a lack of genomic resources to investigate the molecular basis of their diversity. We developed and compared the transcriptomes for two species of the Neotropical lineage of the Gesneriaceae. Illumina sequencing and de novo assembly of floral and leaf samples were used to generate multigene sequence data for Sinningia eumorpha and S. magnifica, two species endemic to the Brazilian Atlantic Forest. A total of 300 million reads were used to assemble the transcriptomes, with an average of 92,038 transcripts and 43,506 genes per species. The transcriptomes showed good quality metrics, with the presence of all eukaryotic core genes, and an equal representation of clusters of orthologous groups (COG) classifications between species. The orthologous search produced 8602 groups, with 15-20% of them annotated using BLAST tools. This study provides the first step toward a comprehensive multispecies transcriptome characterization of the Gesneriaceae family. These resources are the basis for comparative analyses in this species-rich Neotropical plant group; they will also allow the investigation of the evolutionary importance of multiple metabolic pathways and phenotypic diversity, as well as developmental programs in these nonmodel species

Relativistic ionization-rescattering with tailored laser pulses

The interaction of relativistically strong tailored laser pulses with an atomic system is considered. Due to a special tailoring of the laser pulse, the suppression of the relativistic drift of the ionized electron and a dramatic enhancement of the rescattering probability is shown to be achievable. The high harmonic generation rate in the relativistic regime is calculated and shown to be increased by several orders of magnitude compared to the case of conventional laser pulses. The energies of the revisiting electron at the atomic core can approach the MeV domain, thus rendering hard x-ray harmonics and nuclear reactions with single atoms feasible

Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data.

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal-extinction-sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography

Publisher Correction: The impact of endothermy on the climatic niche evolution and the distribution of vertebrate diversity.

In the version of this Article originally published, in Fig. 3a the first boundary was incorrectly labelled the "K/T boundary"; it should have read the "K/Pg boundary". The two equations in the main text were incorrectly omitted from the HTML. In the description of the posterior distribution of an ancestral state, the normal distribution was incorrectly described as being "assigned as prior to the node value"; it should have read "assigned as calibration to the node value". In the associated equation (the second equation in the text), the denominator of the last term was incorrectly given as "Node prior"; it should have read "Node calibration". In the same equation, the numerator of the third term on the right-hand side of the equation contained incorrect superscript notation on the x and this is shown in the full equation in the notice below.In the Acknowledgements, the following two sentences were incorrectly omitted: "The authors thank the Vital-IT facilities of the Swiss Institute of Bioinformatics for the computational support" and "This work was funded by the University of Lausanne and the Swiss National Science Foundation (CRSIII3-147630) to N.S." In the Author contributions section, the first sentence was incorrectly given as "J.R. designed the study. J.R., N.S. and D. Silvestro designed the methodology and ran the analyses"; it should have read "J.R., D.S. and N.S. designed the study and the methodology". In the Supplementary Information, all three instances of the word "prior" were incorrect and should have read "calibration".These errors have now been corrected in all versions of the Article

Theory of high harmonic generation in relativistic laser interaction with overdense plasma

High harmonic generation due to the interaction of a short ultra relativistic laser pulse with overdense plasma is studied analytically and numerically. On the basis of the ultra relativistic similarity theory we show that the high harmonic spectrum is universal, i.e. it does not depend on the interaction details. The spectrum includes the power law part $I_n\propto n^{-8/3}$ for $n<\sqrt{8\alpha}\gamma_{\max}^3$, followed by exponential decay. Here $\gamma_{\max}$ is the largest relativistic $\gamma$-factor of the plasma surface and $\alpha$ is the second derivative of the surface velocity at this moment. The high harmonic cutoff at $\propto \gamma_{\max}^3$ is parametrically larger than the $4 \gamma_{\max}^2$ predicted by the ``oscillating mirror'' model based on the Doppler effect. The cornerstone of our theory is the new physical phenomenon: spikes in the relativistic $\gamma$-factor of the plasma surface. These spikes define the high harmonic spectrum and lead to attosecond pulses in the reflected radiation.Comment: 12 pages, 9 figure

Laser acceleration of ion beams

We consider methods of charged particle acceleration by means of high-intensity lasers. As an application we discuss a laser booster for heavy ion beams provided, e.g. by the Dubna nuclotron. Simple estimates show that a cascade of crossed laser beams would be necessary to provide additional acceleration to gold ions of the order of GeV/nucleon.Comment: 4 pages, 4 figures, Talk at the Helmholtz International Summer School "Dense Matter in heavy Ion Collisions and Astrophysics", August 21 - September 1, 2006, JINR Dubna, Russia; v2, misprints correcte

Microwave-induced control of Free Electron Laser radiation

The dynamical response of a relativistic bunch of electrons injected in a planar magnetic undulator and interacting with a counterpropagating electromagnetic wave is studied. We demonstrate a resonance condition for which the free electron laser (FEL) dynamics is strongly influenced by the presence of the external field. It opens up the possibility of control of short wavelength FEL emission characteristics by changing the parameters of the microwave field without requiring change in the undulator's geometry or configuration. Numerical examples, assuming realistic parameter values analogous to those of the TTF-FEL, currently under development at DESY, are given for possible control of the amplitude or the polarization of the emitted radiation.Comment: 14 pages, 5 figures, accepted for publication in Phys. Rev.

Decoupled evolution of floral traits and climatic preferences in a clade of Neotropical Gesneriaceae.

BACKGROUND: Major factors influencing the phenotypic diversity of a lineage can be recognized by characterizing the extent and mode of trait evolution between related species. Here, we compared the evolutionary dynamics of traits associated with floral morphology and climatic preferences in a clade composed of the genera Codonanthopsis, Codonanthe and Nematanthus (Gesneriaceae). To test the mode and specific components that lead to phenotypic diversity in this group, we performed a Bayesian phylogenetic analysis of combined nuclear and plastid DNA sequences and modeled the evolution of quantitative traits related to flower shape and size and to climatic preferences. We propose an alternative approach to display graphically the complex dynamics of trait evolution along a phylogenetic tree using a wide range of evolutionary scenarios. RESULTS: Our results demonstrated heterogeneous trait evolution. Floral shapes displaced into separate regimes selected by the different pollinator types (hummingbirds versus insects), while floral size underwent a clade-specific evolution. Rates of evolution were higher for the clade that is hummingbird pollinated and experienced flower resupination, compared with species pollinated by bees, suggesting a relevant role of plant-pollinator interactions in lowland rainforest. The evolution of temperature preferences is best explained by a model with distinct selective regimes between the Brazilian Atlantic Forest and the other biomes, whereas differentiation along the precipitation axis was characterized by higher rates, compared with temperature, and no regime or clade-specific patterns. CONCLUSIONS: Our study shows different selective regimes and clade-specific patterns in the evolution of morphological and climatic components during the diversification of Neotropical species. Our new graphical visualization tool allows the representation of trait trajectories under parameter-rich models, thus contributing to a better understanding of complex evolutionary dynamics

Optimization strategies for fast detection of positive selection on phylogenetic trees.

MOTIVATION: The detection of positive selection is widely used to study gene and genome evolution, but its application remains limited by the high computational cost of existing implementations. We present a series of computational optimizations for more efficient estimation of the likelihood function on large-scale phylogenetic problems. We illustrate our approach using the branch-site model of codon evolution. RESULTS: We introduce novel optimization techniques that substantially outperform both CodeML from the PAML package and our previously optimized sequential version SlimCodeML. These techniques can also be applied to other likelihood-based phylogeny software. Our implementation scales well for large numbers of codons and/or species. It can therefore analyse substantially larger datasets than CodeML. We evaluated FastCodeML on different platforms and measured average sequential speedups of FastCodeML (single-threaded) versus CodeML of up to 5.8, average speedups of FastCodeML (multi-threaded) versus CodeML on a single node (shared memory) of up to 36.9 for 12 CPU cores, and average speedups of the distributed FastCodeML versus CodeML of up to 170.9 on eight nodes (96 CPU cores in total).Availability and implementation: ftp://ftp.vital-it.ch/tools/FastCodeML/. CONTACT: [email protected] or [email protected]

Genetic consequences of Quaternary climatic oscillations in the Himalayas: Primula tibetica as a case study based on restriction site-associated DNA sequencing.

The effects of Quaternary climatic oscillations on the demography of organisms vary across regions and continents. In taxa distributed in Europe and North America, several paradigms regarding the distribution of refugia have been identified. By contrast, less is known about the processes that shaped the species' spatial genetic structure in areas such as the Himalayas, which is considered a biodiversity hotspot. Here, we investigated the phylogeographic structure and population dynamics of Primula tibetica by combining genomic phylogeography and species distribution models (SDMs). Genomic data were obtained for 293 samples of P. tibetica using restriction site-associated DNA sequencing (RADseq). Ensemble SDMs were carried out to predict potential present and past distribution ranges. Four distinct lineages were identified. Approximate Bayesian computation analyses showed that each of them have experienced both expansions and bottlenecks since their divergence, which occurred during or across the Quaternary glacial cycles. The two lineages at both edges of the distribution were found to be more vulnerable and responded in different ways to past climatic changes. These results illustrate how past climatic changes affected the demographic history of Himalayan organisms. Our findings highlight the significance of combining genomic approaches with environmental data when evaluating the effects of past climatic changes