The impact of genetic changes during crop domestication

Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These “selective sweeps” can allow mildly deleterious alleles to come to fixation and may create a genetic load in the cultivated gene pool. Although the population-wide genomic consequences of domestication offer several predictions for levels of the genetic diversity in crops, our understanding of how this diversity corresponds to nutritional aspects of crops is not well understood. Many studies have found that modern cultivars have lower levels of key micronutrients and vitamins. We suspect that selection for palatability and increased yield at domestication and during postdomestication divergence exacerbated the low nutrient levels of many crops, although relatively little work has examined this question. Lack of diversity in modern germplasm may further limit our capacity to breed for higher nutrient levels, although little effort has gone into this beyond a handful of staple crops. This is an area where an understanding of domestication across many crop taxa may provide the necessary insight for breeding more nutritious crops in a rapidly changing world

The impact of genetic changes during crop domestication on healthy food development

n/

The Flare-energy Distributions Generated by Kink-unstable Ensembles of Zero-net-current Coronal Loops

It has been proposed that the million degree temperature of the corona is due to the combined effect of barely-detectable energy releases, so called nanoflares, that occur throughout the solar atmosphere. Alas, the nanoflare density and brightness implied by this hypothesis means that conclusive verification is beyond present observational abilities. Nevertheless, we investigate the plausibility of the nanoflare hypothesis by constructing a magnetohydrodynamic (MHD) model that can derive the energy of a nanoflare from the nature of an ideal kink instability. The set of energy-releasing instabilities is captured by an instability threshold for linear kink modes. Each point on the threshold is associated with a unique energy release and so we can predict a distribution of nanoflare energies. When the linear instability threshold is crossed, the instability enters a nonlinear phase as it is driven by current sheet reconnection. As the ensuing flare erupts and declines, the field transitions to a lower energy state, which is modelled by relaxation theory, i.e., helicity is conserved and the ratio of current to field becomes invariant within the loop. We apply the model so that all the loops within an ensemble achieve instability followed by energy-releasing relaxation. The result is a nanoflare energy distribution. Furthermore, we produce different distributions by varying the loop aspect ratio, the nature of the path to instability taken by each loop and also the level of radial expansion that may accompany loop relaxation. The heating rate obtained is just sufficient for coronal heating. In addition, we also show that kink instability cannot be associated with a critical magnetic twist value for every point along the instability threshold

Mind the Gap: Persistent and Mobile Organic Compounds—Water Contaminants That Slip Through

The discharge of persistent and mobile organic chemicals (PMOCs) into the aquatic environment is a threat to the quality of our water resources. PMOCs are highly polar (mobile in water) and can pass through wastewater treatment plants, subsurface environments and potentially also drinking water treatment processes. While a few such compounds are known, we infer that their number is actually much larger. This Feature highlights the issue of PMOCs from an environmental perspective and assesses the gaps that appear to exist in terms of analysis, monitoring, water treatment and regulation. On this basis we elaborate strategies on how to narrow these gaps with the intention to better protect our water resources

Shape Space Methods for Quantum Cosmological Triangleland

With toy modelling of conceptual aspects of quantum cosmology and the problem of time in quantum gravity in mind, I study the classical and quantum dynamics of the pure-shape (i.e. scale-free) triangle formed by 3 particles in 2-d. I do so by importing techniques to the triangle model from the corresponding 4 particles in 1-d model, using the fact that both have 2-spheres for shape spaces, though the latter has a trivial realization whilst the former has a more involved Hopf (or Dragt) type realization. I furthermore interpret the ensuing Dragt-type coordinates as shape quantities: a measure of anisoscelesness, the ellipticity of the base and apex's moments of inertia, and a quantity proportional to the area of the triangle. I promote these quantities at the quantum level to operators whose expectation and spread are then useful in understanding the quantum states of the system. Additionally, I tessellate the 2-sphere by its physical interpretation as the shape space of triangles, and then use this as a back-cloth from which to read off the interpretation of dynamical trajectories, potentials and wavefunctions. I include applications to timeless approaches to the problem of time and to the role of uniform states in quantum cosmological modelling.Comment: A shorter version, as per the first stage in the refereeing process, and containing some new reference

Segmentation of Loops from Coronal EUV Images

We present a procedure which extracts bright loop features from solar EUV images. In terms of image intensities, these features are elongated ridge-like intensity maxima. To discriminate the maxima, we need information about the spatial derivatives of the image intensity. Commonly, the derivative estimates are strongly affected by image noise. We therefore use a regularized estimation of the derivative which is then used to interpolate a discrete vector field of ridge points ``ridgels'' which are positioned on the ridge center and have the intrinsic orientation of the local ridge direction. A scheme is proposed to connect ridgels to smooth, spline-represented curves which fit the observed loops. Finally, a half-automated user interface allows one to merge or split, eliminate or select loop fits obtained form the above procedure. In this paper we apply our tool to one of the first EUV images observed by the SECCHI instrument onboard the recently launched STEREO spacecraft. We compare the extracted loops with projected field lines computed from almost-simultaneously-taken magnetograms measured by the SOHO/MDI Doppler imager. The field lines were calculated using a linear force-free field model. This comparison allows one to verify faint and spurious loop connections produced by our segmentation tool and it also helps to prove the quality of the magnetic-field model where well-identified loop structures comply with field-line projections. We also discuss further potential applications of our tool such as loop oscillations and stereoscopy.Comment: 13 pages, 9 figures, Solar Physics, online firs

Cosmological Histories for the New Variables

Histories and measures for quantum cosmology are investigated through a quantization of the Bianchi IX cosmology using path integral techniques. The result, derived in the context of Ashtekar variables, is compared with earlier work. A non-trivial correction to the measure is found, which may dominate the classical potential for universes on the Planck scale.Comment: 14, CGPG-94/2-

T violation and the unidirectionality of time

An increasing number of experiments at the Belle, BNL, CERN, DA{\Phi}NE and SLAC accelerators are confirming the violation of time reversal invariance (T). The violation signifies a fundamental asymmetry between the past and future and calls for a major shift in the way we think about time. Here we show that processes which violate T symmetry induce destructive interference between different paths that the universe can take through time. The interference eliminates all paths except for two that represent continuously forwards and continuously backwards time evolution. Evidence from the accelerator experiments indicates which path the universe is effectively following. This work may provide fresh insight into the long-standing problem of modeling the dynamics of T violation processes. It suggests that T violation has previously unknown, large-scale physical effects and that these effects underlie the origin of the unidirectionality of time. It may have implications for the Wheeler-DeWitt equation of canonical quantum gravity. Finally it provides a view of the quantum nature of time itself.Comment: 24 pages, 5 figures. Final version accepted for publishing in Foundations of Physics. The final publication is available at http://www.springerlink.com/content/y3h4174jw2w78322

Analytic Solutions of The Wheeler-DeWitt Equation in Spherically Symmetric Space-time

We study the quantum theory of the Einstein-Maxwell action with a cosmological term in the spherically symmetric space-time, and explored quantum black hole solutions in Reissner-Nordstrom-de Sitter geometry. We succeeded to obtain analytic solutions to satisfy both the energy and momentum constraints.Comment: LaTeX file, 15 page