Domestication history and geographical adaptation inferred from a SNP map of African rice

African rice (Oryza glaberrima Steud.) is a cereal crop species closely related to Asian rice (Oryza sativa L.) but was independently domesticated in West Africa-3,000 years ago. African rice is rarely grown outside sub-Saharan Africa but is of global interest because of its tolerance to abiotic stresses. Here we describe a map of 2.32 million SNPs of African rice from whole-genome resequencing of 93 landraces. Population genomic analysis shows a population bottleneck in this species that began-13,000-15,000 years ago with effective population size reaching its minimum value-3,500 years ago, suggesting a protracted period of population size reduction likely commencing with predomestication management and/or cultivation. Genome-wide association studies (GWAS) for six salt tolerance traits identify 11 significant loci, 4 of which are within-300 kb of genomic regions that possess signatures of positive selection, suggesting adaptive geographical divergence for salt tolerance in this species

Independent, Rapid and Targeted Loss of Highly Repetitive DNA in Natural and Synthetic Allopolyploids of Nicotiana tabacum

Allopolyploidy (interspecific hybridisation and polyploidy) has played a significant role in the evolutionary history of angiosperms and can result in genomic, epigenetic and transcriptomic perturbations. We examine the immediate effects of allopolyploidy on repetitive DNA by comparing the genomes of synthetic and natural Nicotiana tabacum with diploid progenitors N. tomentosiformis (paternal progenitor) and N. sylvestris (maternal progenitor). Using next generation sequencing, a recently developed graph-based repeat identification pipeline, Southern blot and fluorescence in situ hybridisation (FISH) we characterise two highly repetitive DNA sequences (NicCL3 and NicCL7/30). Analysis of two independent high-throughput DNA sequencing datasets indicates NicCL3 forms 1.6–1.9% of the genome in N. tomentosiformis, sequences that occur in multiple, discontinuous tandem arrays scattered over several chromosomes. Abundance estimates, based on sequencing depth, indicate NicCL3 is almost absent in N. sylvestris and has been dramatically reduced in copy number in the allopolyploid N. tabacum. Surprisingly elimination of NicCL3 is repeated in some synthetic lines of N. tabacum in their forth generation. The retroelement NicCL7/30, which occurs interspersed with NicCL3, is also under-represented but to a much lesser degree, revealing targeted elimination of the latter. Analysis of paired-end sequencing data indicates the tandem component of NicCL3 has been preferentially removed in natural N. tabacum, increasing the proportion of the dispersed component. This occurs across multiple blocks of discontinuous repeats and based on the distribution of nucleotide similarity among NicCL3 units, was concurrent with rounds of sequence homogenisation

The evolutionary history of wild, domesticated, and feral Brassica oleracea (Brassicaceae)

Understanding the evolutionary history of crops, including identifying wild relatives, helps to provide insight for conservation and crop breeding efforts. Cultivated Brassica oleracea has intrigued researchers for centuries due to its wide diversity in forms, which include cabbage, broccoli, cauliflower, kale, kohlrabi, and Brussels sprouts. Yet, the evolutionary history of this species remains understudied. With such different vegetables produced from a single species, B. oleracea is a model organism for understanding the power of artificial selection. Persistent challenges in the study of B. oleracea include conflicting hypotheses regarding domestication and the identity of the closest living wild relative. Using newly generated RNA-seq data for a diversity panel of 224 accessions, which represents 14 different B. oleracea crop types and nine potential wild progenitor species, we integrate phylogenetic and population genetic techniques with ecological niche modeling, archaeological, and literary evidence to examine relationships among cultivars and wild relatives to clarify the origin of this horticulturally important species. Our analyses point to the Aegean endemic B. cretica as the closest living relative of cultivated B. oleracea, supporting an origin of cultivation in the Eastern Mediterranean region. Additionally, we identify several feral lineages, suggesting that cultivated plants of this species can revert to a wild-like state with relative ease. By expanding our understanding of the evolutionary history in B. oleracea, these results contribute to a growing body of knowledge on crop domestication that will facilitate continued breeding efforts including adaptation to changing environmental conditions

Search for R-Parity Breaking Sneutrino Exchange at LEP

We report on a search for R--parity breaking effects due to supersymmetric tau--sneutrino exchange in the reactions e+e- to e+e- and e+e- to mu+mu- at centre--of--mass energies from 91~{\GeV} to 172~{\GeV}, using the L3 detector at LEP. No evidence for deviations from the Standard Model expectations of the measured cross sections and forward--backward asymmetries for these reactions is found. Upper limits for the couplings $\lambda_{131}$ and $\lambda_{232}$ for sneutrino masses up to m_{\SNT} \leq 190~\GeV are determined from an analysis of the expected effects due to tau sneutrino exchange

Determination of the number of light neutrino species from single photon production at LEP

A determination of the number of light neutrino families performed by measuring the cross section of single photon production in \ee\ collision near the \Zo\ resonance is reported. From an integrated luminosity of $100~\mathrm{pb^{-1}}$, collected during the years 1991--94, we have observed 2091 single photon candidates with an energy above 1~\GeV\ in the polar angular region $45^\circ < \theta_\gamma < 135^\circ$. From a maximum likelihood fit to the single photon cross section, the \Zo\ decay width into invisible particles is measured to be \Ginv = 498 \pm 12 \mathrm{(stat)} \pm 12 \mathrm{(sys)~MeV}. Using the Standard Model couplings of neutrinos to the \Zo, the number of light neutrino species is determined to be $N_\nu = 2.98 \pm 0.07 (\mathrm{stat}) \pm 0.07 (\mathrm{sys}).

Search for charged Higgs bosons in e+e−e^+ e^- collisions at centre-of-mass energies between 130 and 183 GeV

A search for pair-produced charged Higgs bosons is performed with the L3 detector at LEP using data collected at centre-of-mass energies from \mbox{130 to 183 \GeV{}}, corresponding to an integrated luminosity of 88.3 \pb. The Higgs decays into a charm and a strange quark or into a tau lepton and its associated neutrino are considered. The observed candidates are consistent with the expectations from Standard Model background processes. A lower limit of 57.5 \GeV{} on the charged Higgs mass is derived at 95\% CL, independent of the decay branching ratio \mathrm{Br(H^\pm\ra \tau\nu)}

Search for new physics phenomena in fermion-pair production at LEP

The measurements of hadron and lepton--pair production cross sections and lepton--pair forward--backward asymmetries performed with the L3 detector at centre--of--mass energies between 130 GeV and 172 GeV are used to search for new physics phenomena. New physics effects involving four fermion vertices -- contact interactions -- are looked for in all channels. For hadron production the exchange of virtual leptoquarks and scalar quarks is studied. No evidence for deviations from the Standard Model expectations is found. Lower limits on the scale $\Lambda$ of contact interactions in the range 1.2 -- 7.1 TeV are obtained at the 95\% confidence level for various models. Upper limits on the coupling strengths of leptoquarks and scalar quarks are derived

Measurement of the inclusive charmless semileptonic branching fraction of beauty hadrons and a determination of |VubV_{ub}| at LEP

A measurement of the inclusive charmless semileptonic branching fraction of beauty hadrons, $\mathrm{b}\rightarrow\mathrm{X}_\mathrm{u }\ell\nu$, has been performed using almost two million hadronic Z decays collected by the L3 experiment at LEP, yielding the result: \begin{displaymath} \mathrm{Br}(\mathrm{b}\rightarrow\mathrm{X}_\mathr m{u}\ell\nu) = (3.3 \pm 1.0 \pm 1.7)\times 10^{-3}. \end{displaymath} The first uncertainty is statistical and the second is systematic. The modulus of the Cabibbo-Kobayashi-Maskawa matrix element $\mathrm{V_{ub}}$ extracted from this measurement is: \begin{displaymath} |\mathrm{V_{ub}}| = (6.0\, ^{+0.8}_{-1.0} \, ^{+1.4}_{-1.9} \pm 0.2)\times 10^{-3}, \end{displaymath} where the uncertainties are statistical, systematic and theoretical, respectively

Heavy Quarkonium Production in Z Decays

We report measurements of the inclusive production of heavy quarkonium states in $\mathrm {Z}$ decays based on the analysis of 3.6 million hadronic events collected by the L3 detector at LEP. The measurement of inclusive J production and an improved $95\%$ confidence level upper limit on $\Upsilon$ production are presented. In addition, two independent measurements of the ratio, $f_{\mathrm{p}}$, of prompt J mesons to those from B decay are made using two different isolation cuts to separate prompt J mesons from J mesons produced in the decays of b hadrons. The results are: % \begin{eqnarray} \mathrm{Br}(\mathrm{Z} \rightarrow \mathrm{J} + \mathrm{X}) & = & (3.21 \pm 0.21 \; \mathrm{(stat.)} \; ^{+ 0.19}_{- 0.28} \; \mathrm{(sys.)} ) \times 10^{-3} \; , \nonumber \\ \mathrm{Br}(\mathrm {Z} \rightarrow \Upsilon(\mathrm{1S} + X) & < & 4.4 \times 10^{-5} \; , \nonumber \\ %% f_{\mathrm{p}} & = & (7.1 \pm 2.1 \; \mathrm{(stat.)} \; \pm 1.2 \; \mathrm{(sys.)} \; ^{+1.5}_{-0.8} \;\mathrm{(theo.)} ) \times 10^{-2} \; . \nonumbe