Mike J. Wilkinson

Bio: Mike J. Wilkinson is an academic researcher from Aberystwyth University. The author has contributed to research in topics: Population & DNA methylation. The author has an hindex of 54, co-authored 182 publications receiving 12400 citations. Previous affiliations of Mike J. Wilkinson include University of Adelaide & University of Reading.

A DNA barcode for land plants.

Abstract: DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.

A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars

Abstract: Commercial scale fingerprinting of potato cultivars is made difficult by the need for speed, reliability and the ability to distinguish between large numbers of genotypes. There are also problems in extrapolating the results of small experimental studies to predict the performance of techniques or primers for larger applications. The potential of ISSR-PCR for fingerprinting purposes was evaluated using four primers on 34 potato cultivars. The complex band profiles generated were reproducible between repeat PCRs, DNA extractions, electrophoreses and gel scorings. Two primers were each able to distinguish all cultivars. The combined use of any two of the four primers also allowed complete diagnosis. It is concluded that ISSR-PCR provides a quick, reliable and highly informative system for DNA fingerprinting that is amenable for routine applications. Two possible correlates of the ability of primers to distinguish between genotypes were then examined. Marker Index failed to correlate significantly with genotype diagnosis, but a strong and seemingly linear relationship was observed between Resolving Power of a primer and its ability to distinguish genotypes (r2=0.98). Resolving Power of one or a pair of primers was found to provide a moderately accurate estimate of the number of genotypes identified. Possible implications for future studies on DNA fingerprinting are discussed.

Test of lepton universality with B 0 → K *0 ℓ + ℓ − decays

Abstract: A test of lepton universality, performed by measuring the ratio of the branching fractions of the B$^{0}$ → K$^{*0}$ μ$^{+}$ μ$^{−}$ and B$^{0}$ → K$^{*0}$ e$^{+}$ e$^{−}$ decays, $ {R}_{K^{*0}} $ , is presented. The K$^{*0}$ meson is reconstructed in the final state K$^{+}$ π$^{−}$, which is required to have an invariant mass within 100 MeV/c$^{2}$ of the known K$^{*}$(892)$^{0}$ mass. The analysis is performed using proton-proton collision data, corresponding to an integrated luminosity of about 3 fb$^{−1}$, collected by the LHCb experiment at centre-of-mass energies of 7 and 8 TeV. The ratio is measured in two regions of the dilepton invariant mass squared, q$^{2}$, to be $ {R}_{K^{*0}}=\left\{\begin{array}{l}{0.66_{-}^{+}}_{0.07}^{0.11}\left(\mathrm{stat}\right)\pm 0.03\left(\mathrm{syst}\right)\kern1em \mathrm{f}\mathrm{o}\mathrm{r}\kern1em 0.045<{q}^2<1.1\kern0.5em {\mathrm{GeV}}^2/{c}^4,\hfill \\ {}{0.69_{-}^{+}}_{0.07}^{0.11}\left(\mathrm{stat}\right)\pm 0.05\left(\mathrm{syst}\right)\kern1em \mathrm{f}\mathrm{o}\mathrm{r}\kern1em 1.1<{q}^2<6.0\kern0.5em {\mathrm{GeV}}^2/{c}^4.\hfill \end{array}\right. $

A proposal for a standardised protocol to barcode all land plants

Abstract: Chase, M. W., Cowan, R. S., Hollingsworth, P. M., van den Berg, C., Madrinan, S., Petersen, G., Seberg, O., Jorgsensen, T., Cameron, K. M., Carine, M., Pedersen, N., Hedderson, T. A. J., Conrad, F., Salazar, G. A., Richardson, J. E., Hollingsworth, M. L., Barraclough, T. G., Kelly, L., Wilkinson, M. (2007). A proposal for a standardised protocol to barcode all land plants. Taxon, 56, (2), 295-299.

Measurement of the Ratio of Branching Fractions B (B ¯ 0 →d∗+τ- ν ¯ τ) / B (B ¯ 0 →d∗+μ- ν ¯ μ)

Abstract: The branching fraction ratio R(D-*) = B((B) over bar (0) -> D-*(+)tau(-)(nu) over bar (tau))/B((B) over bar (0) -> D-*(+)mu(-)(nu) over bar (mu)) is measured using a sample of proton-proton collision data corresponding to 3.0 fb(-1) of integrated luminosity recorded by the LHCb experiment during 2011 and 2012. The tau lepton is identified in the decay mode tau(-) -> mu(-)(nu) over bar (mu)nu(tau). The semitauonic decay is sensitive to contributions from non-standard-model particles that preferentially couple to the third generation of fermions, in particular, Higgs-like charged scalars. A multidimensional fit to kinematic distributions of the candidate (B) over bar (0) decays gives R(D-*) = 0.336 +/- 0.027(stat) +/- 0.030(syst). This result, which is the first measurement of this quantity at a hadron collider, is 2.1 standard deviations larger than the value expected from lepton universality in the standard model.

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Abstract: Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

ABGD, Automatic Barcode Gap Discovery for primary species delimitation

Abstract: Within uncharacterized groups, DNA barcodes, short DNA sequences that are present in a wide range of species, can be used to assign organisms into species. We propose an automatic procedure that sorts the sequences into hypothetical species based on the barcode gap, which can be observed whenever the divergence among organisms belonging to the same species is smaller than divergence among organisms from different species. We use a range of prior intraspecific divergence to infer from the data a model-based one-sided confidence limit for intraspecific divergence. The method, called Automatic Barcode Gap Discovery (ABGD), then detects the barcode gap as the first significant gap beyond this limit and uses it to partition the data. Inference of the limit and gap detection are then recursively applied to previously obtained groups to get finer partitions until there is no further partitioning. Using six published data sets of metazoans, we show that ABGD is computationally efficient and performs well for standard prior maximum intraspecific divergences (a few per cent of divergence for the five data sets), except for one data set where less than three sequences per species were sampled. We further explore the theoretical limitations of ABGD through simulation of explicit speciation and population genetics scenarios. Our results emphasize in particular the sensitivity of the method to the presence of recent speciation events, via (unrealistically) high rates of speciation or large numbers of species. In conclusion, ABGD is fast, simple method to split a sequence alignment data set into candidate species that should be complemented with other evidence in an integrative taxonomic approach.

A DNA barcode for land plants.

Abstract: DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.

The model of emissions of gases and aerosols from nature version 2.1 (MEGAN2.1): An extended and updated framework for modeling biogenic emissions

Abstract: . The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1) is a modeling framework for estimating fluxes of biogenic compounds between terrestrial ecosystems and the atmosphere using simple mechanistic algorithms to account for the major known processes controlling biogenic emissions. It is available as an offline code and has also been coupled into land surface and atmospheric chemistry models. MEGAN2.1 is an update from the previous versions including MEGAN2.0, which was described for isoprene emissions by Guenther et al. (2006) and MEGAN2.02, which was described for monoterpene and sesquiterpene emissions by Sakulyanontvittaya et al. (2008). Isoprene comprises about half of the total global biogenic volatile organic compound (BVOC) emission of 1 Pg (1000 Tg or 1015 g) estimated using MEGAN2.1. Methanol, ethanol, acetaldehyde, acetone, α-pinene, β-pinene, t-β-ocimene, limonene, ethene, and propene together contribute another 30% of the MEGAN2.1 estimated emission. An additional 20 compounds (mostly terpenoids) are associated with the MEGAN2.1 estimates of another 17% of the total emission with the remaining 3% distributed among >100 compounds. Emissions of 41 monoterpenes and 32 sesquiterpenes together comprise about 15% and 3%, respectively, of the estimated total global BVOC emission. Tropical trees cover about 18% of the global land surface and are estimated to be responsible for ~80% of terpenoid emissions and ~50% of other VOC emissions. Other trees cover about the same area but are estimated to contribute only about 10% of total emissions. The magnitude of the emissions estimated with MEGAN2.1 are within the range of estimates reported using other approaches and much of the differences between reported values can be attributed to land cover and meteorological driving variables. The offline version of MEGAN2.1 source code and driving variables is available from http://bai.acd.ucar.edu/MEGAN/ and the version integrated into the Community Land Model version 4 (CLM4) can be downloaded from http://www.cesm.ucar.edu/ .

Microsatellites: simple sequences with complex evolution

Abstract: Few genetic markers, if any, have found such widespread use as microsatellites, or simple/short tandem repeats. Features such as hypervariability and ubiquitous occurrence explain their usefulness, but these features also pose several questions. For example, why are microsatellites so abundant, why are they so polymorphic and by what mechanism do they mutate? Most importantly, what governs the intricate balance between the frequent genesis and expansion of simple repetitive arrays, and the fact that microsatellite repeats rarely reach appreciable lengths? In other words, how do microsatellites evolve?