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

Thermal age, cytosine deamination and the veracity of 8,000 year old wheat DNA from sediments

YesRecently, the finding of 8,000 year old wheat DNA from submerged marine sediments (1) was challenged on the basis of a lack of signal of cytosine deamination relative to three other data sets generated from young samples of herbarium and museum specimens, and a 7,000 year old human skeleton preserved in a cave environment (2). The study used a new approach for low coverage data sets to which tools such as mapDamage cannot be applied to infer chemical damage patterns. Here we show from the analysis of 148 palaeogenomic data sets that the rate of cytosine deamination is a thermally correlated process, and that organellar generally shows higher rates of deamination than nuclear DNA in comparable environments. We categorize four clusters of deamination rates (alpha,beta,gamma,epsilon) that are associated with cold stable environments, cool but thermally fluctuating environments, and progressively warmer environments. These correlations show that the expected level of deamination in the sedaDNA would be extremely low. The low coverage approach to detect DNA damage by Weiss et al. (2) fails to identify damage samples from the cold class of deamination rates. Finally, different enzymes used in library preparation processes exhibit varying capability in reporting cytosine deamination damage in the 5 prime region of fragments. The PCR enzyme used in the sedaDNA study would not have had the capability to report 5 prime cytosine deamination, as they do not read over uracil residues, and signatures of damage would have better been sought at the 3 prime end. The 8,000 year old sedaDNA matches both the thermal age prediction of fragmentation, and the expected level of cytosine deamination for the preservation environment. Given these facts and the use of rigorous controls these data meet the criteria of authentic ancient DNA to an extremely stringent level

The genomics of domestication special issue editorial

Domestication has been of major interest to biologists for centuries, whether for creating new plants and animal types or more formally exploring the principles of evolution. Such studies have long used combinations of phenotypic and genetic evidence. Recently, the advent of a large number of genomes and genomic tools across a wide array of domesticated plant and animal species has reinvigorated the study of domestication. These genomic data, which can be easily generated for nearly any species, often provide great insight with or without a reference genome. The comparison of genome wide data from domestic and wild species has ignited a wave of insight into human, plant, and animal history with a new range of questions becoming accessible. With this in mind, this issue of Evolutionary Applications includes eleven papers covering a wide range of perspectives and methodologies relevant to understanding genomic variation under domestication

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

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

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

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.

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

NN Core Interactions and Differential Cross Sections from One Gluon Exchange

We derive nonstrange baryon-baryon scattering amplitudes in the nonrelativistic quark model using the ``quark Born diagram" formalism. This approach describes the scattering as a single interaction, here the one-gluon-exchange (OGE) spin-spin term followed by constituent interchange, with external nonrelativistic baryon wavefunctions attached to the scattering diagrams to incorporate higher-twist wavefunction effects. The short-range repulsive core in the NN interaction has previously been attributed to this spin-spin interaction in the literature; we find that these perturbative constituent-interchange diagrams do indeed predict repulsive interactions in all I,S channels of the nucleon-nucleon system, and we compare our results for the equivalent short-range potentials to the core potentials found by other authors using nonperturbative methods. We also apply our perturbative techniques to the N$\Delta$ and $\Delta\Delta$ systems: Some $\Delta\Delta$ channels are found to have attractive core potentials and may accommodate ``molecular" bound states near threshold. Finally we use our Born formalism to calculate the NN differential cross section, which we compare with experimental results for unpolarised proton-proton elastic scattering. We find that several familiar features of the experimental differential cross section are reproduced by our Born-order result.Comment: 27 pages, figures available from the authors, revtex, CEBAF-TH-93-04, MIT-CTP-2187, ORNL-CCIP-93-0

Reticulated origin of domesticated emmer wheat supports a dynamic model for the emergence of agriculture in the fertile crescent

We used supernetworks with datasets of nuclear gene sequences and novel markers detecting retrotransposon insertions in ribosomal DNA loci to reassess the evolutionary relationships among tetraploid wheats. We show that domesticated emmer has a reticulated genetic ancestry, sharing phylogenetic signals with wild populations from all parts of the wild range. The extent of the genetic reticulation cannot be explained by post-domestication gene flow between cultivated emmer and wild plants, and the phylogenetic relationships among tetraploid wheats are incompatible with simple linear descent of the domesticates from a single wild population. A more parsimonious explanation of the data is that domesticated emmer originates from a hybridized population of different wild lineages. The observed diversity and reticulation patterns indicate that wild emmer evolved in the southern Levant, and that the wild emmer populations in south-eastern Turkey and the Zagros Mountains are relatively recent reticulate descendants of a subset of the Levantine wild populations. Based on our results we propose a new model for the emergence of domesticated emmer. During a pre-domestication period, diverse wild populations were collected from a large area west of the Euphrates and cultivated in mixed stands. Within these cultivated stands, hybridization gave rise to lineages displaying reticulated genealogical relationships with their ancestral populations. Gradual movement of early farmers out of the Levant introduced the pre-domesticated reticulated lineages to the northern and eastern parts of the Fertile Crescent, giving rise to the local wild populations but also facilitating fixation of domestication traits. Our model is consistent with the protracted and dispersed transition to agriculture indicated by the archaeobotanical evidence, and also with previous genetic data affiliating domesticated emmer with the wild populations in southeast Turkey. Unlike other protracted models, we assume that humans played an intuitive role throughout the process.Natural Environment Research Council [NE/E015948/1]; Slovak Research and Development Agency [APVV-0661-10, APVV-0197-10]info:eu-repo/semantics/publishedVersio