Three geographically separate domestications of Asian rice

Domesticated rice (Oryza sativa L.) accompanied the dawn of Asian civilization(1) and has become one of world's staple crops. From archaeological and genetic evidence various contradictory scenarios for the origin of different varieties of cultivated rice have been proposed, the most recent based on a single domestication(2,3). By examining the footprints of selection in the genomes of different cultivated rice types, we show that there were three independent domestications in different parts of Asia. We identify wild populations in southern China and the Yangtze valley as the source of the japonica gene pool, and populations in Indochina and the Brahmaputra valley as the source of the indica gene pool. We reveal a hitherto unrecognized origin for the aus variety in central India or Bangladesh. We also conclude that aromatic rice is a result of a hybridization between japonica and aus, and that the tropical and temperate versions of japonica are later adaptations of one crop. Our conclusions are in accord with archaeological evidence that suggests widespread origins of rice cultivation(1,4). We therefore anticipate that our results will stimulate a more productive collaboration between genetic and archaeological studies of rice domestication, and guide utilization of genetic resources in breeding programmes aimed at crop improvement.European Research Council [339941]info:eu-repo/semantics/publishedVersio

Domestication as innovation : the entanglement of techniques, technology and chance in the domestication of cereal crops

The origins of agriculture involved pathways of domestication in which human behaviours and plant genetic adaptations were entangled. These changes resulted in consequences that were unintended at the start of the process. This paper highlights some of the key innovations in human behaviours, such as soil preparation, harvesting and threshing, and how these were coupled with genetic ‘innovations’ within plant populations. We identify a number of ‘traps’ for early cultivators, including the needs for extra labour expenditure on crop-processing and soil fertility maintenance, but also linked gains in terms of potential crop yields. Compilations of quantitative data across a few different crops for the traits of nonshattering and seed size are discussed in terms of the apparently slow process of domestication, and parallels and differences between different regional pathways are identified. We highlight the need to bridge the gap between a Neolithic archaeobotanical focus on domestication and a focus of later periods on crop-processing activities and labour organization. In addition, archaeobotanical data provide a basis for rethinking previous assumptions about how plant genetic data should be related to the origins of agriculture and we contrast two alternative hypotheses: gradual evolution with low selection pressure versus metastable equilibrium that prolonged the persistence of ‘semi-domesticated’ populations. Our revised understanding of the innovations involved in plant domestication highlight the need for new approaches to collecting, modelling and integrating genetic data and archaeobotanical evidence

Global Study of Electron-Quark Contact Interactions

We perform a global fit of data relevant to $eeqq$ contact interactions, including deep inelastic scattering at high $Q^2$ from ZEUS and H1, atomic physics parity violation in Cesium from JILA, polarized $e^-$ on nuclei scattering experiments at SLAC, Mainz and Bates, Drell-Yan production at the Tevatron, the total hadronic cross section $\sigma_{had}$ at LEP, and neutrino-nucleon scattering from CCFR. With only the new HERA data, the presence of contact interactions improves the fit compared to the Standard Model. When other data sets are included, the size of the contact contributions is reduced and the overall fit represents no real improvement over the Standard Model.Comment: 26 pages (now single-spaced), Revtex, 2 eps figures, uses epsf.sty. Some clarifications, minor corrections, 2 new references, also 3 new tables which present 95% CL bounds on the contact interaction scales Lambd

Neutrino Interactions In Oscillation Experiments

We calculate neutrino induced cross-sections relevant for oscillation experiments, including the $\tau$-lepton threshold for quasi-elastic, resonance and deep inelastic scattering. In addition to threshold effects, we include nuclear corrections for heavy targets which are moderate for quasi-elastic and large for single pion production. Nuclear effects for deep inelastic reactions are small. We present cross sections together with their nuclear corrections for various channels which are useful for interpreting the experimental results and for determining parameters of the neutrino sector..Comment: 24 pages, 18 figure

A Precise Measurement of the Weak Mixing Angle in Neutrino-Nucleon Scattering

We report a precise measurement of the weak mixing angle from the ratio of neutral current to charged current inclusive cross-sections in deep-inelastic neutrino-nucleon scattering. The data were gathered at the CCFR neutrino detector in the Fermilab quadrupole-triplet neutrino beam, with neutrino energies up to 600 GeV. Using the on-shell definition, ${\rm sin ^2\theta_W} \equiv 1 - \frac{{\rm M_W} ^2}{{\rm M_Z} ^2}$, we obtain ${\rm sin ^2\theta_W} = 0.2218 \pm 0.0025 ({\rm stat.}) \pm 0.0036 ({\rm exp.\: syst.}) \pm 0.0040 ({\rm model})$.Comment: 10 pages, Nevis Preprint #1498 (Submitted to Phys. Rev. Lett.

Leptoproduction of Heavy Quarks II -- A Unified QCD Formulation of Charged and Neutral Current Processes from Fixed-target to Collider Energies

A unified QCD formulation of leptoproduction of massive quarks in charged current and neutral current processes is described. This involves adopting consistent factorization and renormalization schemes which encompass both vector-boson-gluon-fusion (flavor creation) and vector-boson-massive-quark-scattering (flavor excitation) production mechanisms. It provides a framework which is valid from the threshold for producing the massive quark (where gluon-fusion is dominant) to the very high energy regime when the typical energy scale \mu is much larger than the quark mass m_Q (where the quark-scattering should be prevalent). This approach effectively resums all large logarithms of the type (alpha_s(mu) log(mu^2/m_Q^2)^n which limit the validity of existing fixed-order calculations to the region mu ~ O(m_Q). We show that the (massive) quark-scattering contribution (after subtraction of overlaps) is important in most parts of the (x, Q) plane except near the threshold region. We demonstrate that the factorization scale dependence of the structure functions calculated in this approach is substantially less than those obtained in the fixed-order calculations, as one would expect from a more consistent formulation.Comment: LaTeX format, 29 pages, 11 figures. Revised to make auto-TeX-abl

Can lepton flavor violating interactions explain the atmospheric neutrino problem?

We investigate whether flavor changing neutrino interactions (FCNIs) can be sufficiently large to provide a viable solution to the atmospheric neutrino problem. Effective operators induced by heavy boson exchange that allow for flavor changing neutrino scattering off quarks or electrons are related by an $SU(2)_L$ rotation to operators that induce anomalous tau decays. Since $SU(2)_L$ violation is small for New Physics at or above the weak scale, one can use the upper bounds on lepton flavor violating tau decays or on lepton universality violation to put severe, model-independent bounds on the relevant non-standard neutrino interactions. Also $Z$-induced flavor changing neutral currents, due to heavy singlet neutrinos, are too small to be relevant for the atmospheric neutrino anomaly. We conclude that the FCNI solution to the atmospheric neutrino problem is ruled out.Comment: 16 pages, no figures, Late

Inherited biotic protection in a Neotropical pioneer plant

Chelonanthus alatus is a bat-pollinated, pioneer Gentianaceae that clusters in patches where still-standing, dried-out stems are interspersed among live individuals. Flowers bear circum-floral nectaries (CFNs) that are attractive to ants, and seed dispersal is both barochorous and anemochorous. Although, in this study, live individuals never sheltered ant colonies, dried-out hollow stems - that can remain standing for 2 years - did. Workers from species nesting in dried-out stems as well as from ground-nesting species exploited the CFNs of live C. alatus individuals in the same patches during the daytime, but were absent at night (when bat pollination occurs) on 60.5% of the plants. By visiting the CFNs, the ants indirectly protect the flowers - but not the plant foliage - from herbivorous insects. We show that this protection is provided mostly by species nesting in dried-out stems, predominantly Pseudomyrmex gracilis. That dried-out stems remain standing for years and are regularly replaced results in an opportunistic, but stable association where colonies are sheltered by one generation of dead C. alatus while the live individuals nearby, belonging to the next generation, provide them with nectar; in turn, the ants protect their flowers from herbivores. We suggest that the investment in wood by C. alatus individuals permitting stillstanding, dried-out stems to shelter ant colonies constitutes an extended phenotype because foraging workers protect the flowers of live individuals in the same patch. Also, through this process these dried-out stems indirectly favor the reproduction (and so the fitness) of the next generation including both their own offspring and that of their siblings, alladding up to a potential case of inclusive fitness in plants

Proton-proton scattering above 3 GeV/c

A large set of data on proton-proton differential cross sections, analyzing powers and the double polarization parameter A_NN is analyzed employing the Regge formalism. We find that the data available at proton beam momenta from 3 GeV/c to 50 GeV/c exhibit features that are very well in line with the general characteristics of Regge phenomenology and can be described with a model that includes the rho, omega, f_2, and a_2 trajectories and single Pomeron exchange. Additional data, specifically for spin-dependent observables at forward angles, would be very helpful for testing and refining our Regge model.Comment: 16 pages, 19 figures; revised version accepted for publication in EPJ

Search for Branons at LEP

We search, in the context of extra-dimension scenarios, for the possible existence of brane fluctuations, called branons. Events with a single photon or a single Z-boson and missing energy and momentum collected with the L3 detector in e^+ e^- collisions at centre-of-mass energies sqrt{s}=189-209$ GeV are analysed. No excess over the Standard Model expectations is found and a lower limit at 95% confidence level of 103 GeV is derived for the mass of branons, for a scenario with small brane tensions. Alternatively, under the assumption of a light branon, brane tensions below 180 GeV are excluded