Archaeogenetic evidence of ancient Nubian barley evolution from six to two-row indicates local adaptation

Background Archaeobotanical samples of barley (Hordeum vulgare L.) found at Qasr Ibrim display a two-row phenotype that is unique to the region of archaeological sites upriver of the first cataract of the Nile, characterised by the development of distinctive lateral bracts. The phenotype occurs throughout all strata at Qasr Ibrim, which range in age from 3000 to a few hundred years. Methodology and Findings We extracted ancient DNA from barley samples from the entire range of occupancy of the site, and studied the Vrs1 gene responsible for row number in extant barley. Surprisingly, we found a discord between the genotype and phenotype in all samples; all the barley had a genotype consistent with the six-row condition. These results indicate a six-row ancestry for the Qasr Ibrim barley, followed by a reassertion of the two-row condition. Modelling demonstrates that this sequence of evolutionary events requires a strong selection pressure. Conclusions The two-row phenotype at Qasr Ibrim is caused by a different mechanism to that in extant barley. The strength of selection required for this mechanism to prevail indicates that the barley became locally adapted in the region in response to a local selection pressure. The consistency of the genotype/phenotype discord over time supports a scenario of adoption of this barley type by successive cultures, rather than the importation of new barley varieties associated with individual cultures

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 QCD Analysis and the CTEQ Parton Distributions

The CTEQ program for the determination of parton distributions through a global QCD analysis of data for various hard scattering processes is fully described. A new set of distributions, CTEQ3, incorporating several new types of data is reported and compared to the two previous sets of CTEQ distributions. Comparison with current data is discussed in some detail. The remaining uncertainties in the parton distributions and methods to further reduce them are assessed. Comparisons with the results of other global analyses are also presented.Comment: (Change in Latex style only: 2up style removed since many don't have it.) 35 pages, 23 figures separately submitted as uuencoded compressed ps-file; Michigan State Report # MSU-HEP/41024 and CTEQ 40

Simulations from a new neutrino event generator

We construct a new Monte Carlo generator of events for neutrino interactions. The dynamical models for quasi-elastic reactions, $\Delta$ excitation and more inelastic events described by the DIS formalism with the PDFs modified according to recent JLab data are used. We describe in detail single pion production channels, which combine the $\Delta$ excitation and DIS contribution. Many comparisons of the outcome of simulations with experimental data are presented.Comment: To appear in the proceedings of 4th International Workshop on Neutrino Nucleus Interactions in the Few GeV Region (NuInt05), Okayama, Japan, 26-29 September, 200

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.

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

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