Deep mitochondrial divergence within a Heliconius butterfly species is not explained by cryptic speciation or endosymbiotic bacteria.

BACKGROUND: Cryptic population structure can be an indicator of incipient speciation or historical processes. We investigated a previously documented deep break in the mitochondrial haplotypes of Heliconius erato chestertonii to explore the possibility of cryptic speciation, and also the possible presence of endosymbiont bacteria that might drive mitochondrial population structure. RESULTS: Among a sample of 315 individuals from 16 populations of western Colombia, two principal mtDNA clades were detected with 2.15% divergence and we confirmed this structure was weakly associated with geography. The first mtDNA clade included 87% of individuals from northern populations and was the sister group of H. erato members of Andes western, while the second clade contained most individuals from southern populations (78%), which shared haplotypes with an Ecuadorian race of H. erato. In contrast, analysis using AFLP markers showed H. e. chestertonii to be a genetically homogeneous species with no association between mitochondrial divergence and AFLP structure. The lack of congruence between molecular markers suggests that cryptic speciation is not a plausible explanation for the deep mitochondrial divergence in H. e chestertonii. We also carried out the first tests for the presence of endosymbiontic bacteria in Heliconius, and identified two distinct lineages of Wolbachia within H. e. chestertonii. However, neither of the principal mitochondrial clades of H. e. chestertonii was directly associated with the patterns of infection. CONCLUSIONS: We conclude that historical demographic processes are the most likely explanation for the high mitochondrial differentiation in H. e. chestertonii, perhaps due to gene flow between Cauca valley H. e. chestertonii and west Pacific slope populations of H. erato.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Interacting anyons in topological quantum liquids: The golden chain

We discuss generalizations of quantum spin Hamiltonians using anyonic degrees of freedom. The simplest model for interacting anyons energetically favors neighboring anyons to fuse into the trivial (`identity') channel, similar to the quantum Heisenberg model favoring neighboring spins to form spin singlets. Numerical simulations of a chain of Fibonacci anyons show that the model is critical with a dynamical critical exponent z=1, and described by a two-dimensional conformal field theory with central charge c=7/10. An exact mapping of the anyonic chain onto the two-dimensional tricritical Ising model is given using the restricted-solid-on-solid (RSOS) representation of the Temperley-Lieb algebra. The gaplessness of the chain is shown to have topological origin.Comment: 5 pages, 4 figure

Active Semantic Relations in Layered Enterprise Architecture Development

Enterprise Architecture (EA) metamodels align an organisation’s business, information and technology resources so that these assets best meet the organisation’s purpose. The Layered EA Development (LEAD) Ontology enhances EA practices by a metamodel with layered metaobjects as its building blocks interconnected by semantic relations. Each metaobject connects to another metaobject by two semantic relations in opposing directions, thus highlighting how each metaobject views other metaobjects from its perspective. While the resulting two directed graphs reveal all the multiple pathways in the metamodel, more desirable would be to have one directed graph that focusses on the dependencies in the pathways. Towards this aim, using CG-FCA (where CG refers to Conceptual Graph and FCA to Formal Concept Analysis) and a LEAD case study, we determine an algorithm that elicits the active as opposed to the passive semantic relations between the metaobjects resulting in one directed graph metamodel. We also identified the general applicability of our algorithm to any metamodel that consists of triples of objects with active and passive relations

Absence of Phase Transition for Antiferromagnetic Potts Models via the Dobrushin Uniqueness Theorem

We prove that the $q$-state Potts antiferromagnet on a lattice of maximum coordination number $r$ exhibits exponential decay of correlations uniformly at all temperatures (including zero temperature) whenever $q > 2r$. We also prove slightly better bounds for several two-dimensional lattices: square lattice (exponential decay for $q \ge 7$), triangular lattice ($q \ge 11$), hexagonal lattice ($q \ge 4$), and Kagom\'e lattice ($q \ge 6$). The proofs are based on the Dobrushin uniqueness theorem.Comment: 32 pages including 3 figures. Self-unpacking file containing the tex file, the needed macros (epsf.sty, indent.sty, subeqnarray.sty, and eqsection.sty) and the 3 ps file

Fuel Performance Models for High-Temperature Gas-Cooled Reactor Core Design

Mechanistic fuel performance models are used in high-temperature gas-cooled reactor core design and licensing to predict failure and fission product release. Fuel particles manufactured with defective or missing SiC, IPyC, or fuel dispersion in the buffer fail at a level of less than 5 x 10/sup -4/ fraction. These failed particles primarily release metallic fission products because the OPyC remains intact on 90% of the particles and retains gaseous isotopes. The predicted failure of particles using performance models appears to be conservative relative to operating reactor experience

Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling.

An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in turn controls red pattern variation across Heliconius. Phylogenetic analysis of the two elements demonstrated that they have distinct evolutionary histories and that novel adaptive morphological variation was created by shuffling these cis-regulatory modules through recombination between divergent lineages. In addition, recombination of modules into different combinations within species further contributes to diversity. Analysis of the timing of diversification in these two regions supports the hypothesis of introgression moving regulatory modules between species, rather than shared ancestral variation. The dennis phenotype introgressed into Heliconius melpomene at about the same time that ray originated in this group, while ray introgressed back into H. elevatus much more recently. We show that shuffling of existing enhancer elements both within and between species provides a mechanism for rapid diversification and generation of novel morphological combinations during adaptive radiation.This work was funded by BBSRC grant H01439X/1, ERC grant MimEvol and ANR grant HybEvol to MJ.This is the final version of the article. It was first available from PLOS via http://dx.doi.org/10.1371/journal.pbio.100235

AR and MA representation of partial autocorrelation functions, with applications

We prove a representation of the partial autocorrelation function (PACF), or the Verblunsky coefficients, of a stationary process in terms of the AR and MA coefficients. We apply it to show the asymptotic behaviour of the PACF. We also propose a new definition of short and long memory in terms of the PACF.Comment: Published in Probability Theory and Related Field

Dietary diversity and social determinants of nutrition among late adolescent girls in rural Pakistan

The conditions in which adolescent girls mature shape their health, development and nutrition. Nutrient requirements increase to support growth during adolescence, but gaps between consumption and requirements exist in low- and middle-income countries. We aimed to identify and quantify the relationship between dietary intake and diverse social determinants of nutrition (SDN) among a subset of adolescent girls 15-18.9 years (n = 390) enrolled within the Matiari emPowerment and Preconception Supplementation (MaPPS) Trial. The primary outcome, dietary diversity score (DDS), was derived by applying the Minimum Dietary Diversity for Women 10-item scale to 24-h dietary recall data collected three times per participant. To examine the associations between the SDN-related explanatory variables and DDS, we generated a hierarchical, causal model using mixed effects linear regression to account for the cluster-randomized trial design. Using all data, diets lacked diversity (DDS mean ± SD: 3.35 ± 1.03 [range: 1-7; n = 1170]), and the minimum cut-off for dietary diversity was infrequently achieved (13.5%; 95% CI: 11.6-15.6%). Consumption of starches was reported in all recalls, but micronutrient-rich food consumption was less common. Of the SDN considered, wealth quintile had the strongest association with DDS (P \u3c 0.0001). The diets of the sampled Pakistani adolescent girls were insufficient to meet micronutrient requirements. Poverty was the most important predictor of a diet lacking in diversity, indicating limited purchasing power or access to nutritious foods. Dietary diversification and nutrition education strategies alone are unlikely to lead to improved diets without steps to tackle this barrier, for example, through fortification of staple foods and provision of supplements

Major improvements to the Heliconius melpomene genome assembly used to confirm 10 chromosome fusion events in 6 million years of butterfly evolution

The Heliconius butterflies are a widely studied adaptive radiation of 46 species spread across Central and South America, several of which are known to hybridize in the wild. Here, we present a substantially improved assembly of the Heliconius melpomene genome, developed using novel methods that should be applicable to improving other genome assemblies produced using short read sequencing. First, we whole-genome-sequenced a pedigree to produce a linkage map incorporating 99% of the genome. Second, we incorporated haplotype scaffolds extensively to produce a more complete haploid version of the draft genome. Third, we incorporated ~20x coverage of Pacific Biosciences sequencing, and scaffolded the haploid genome using an assembly of this long-read sequence. These improvements result in a genome of 795 scaffolds, 275 Mb in length, with an N50 length of 2.1 Mb, an N50 number of 34, and with 99% of the genome placed, and 84% anchored on chromosomes. We use the new genome assembly to confirm that the Heliconius genome underwent 10 chromosome fusions since the split with its sister genus Eueides, over a period of about 6 million yr

MAPK Signaling Pathway Alters Expression of Midgut ALP and ABCC Genes and Causes Resistance to \u3cem\u3eBacillus thuringiensis\u3c/em\u3e Cry1Ac Toxin in Diamondback Moth

Insecticidal crystal toxins derived from the soil bacterium Bacillus thuringiensis (Bt) are widely used as biopesticide sprays or expressed in transgenic crops to control insect pests. However, large-scale use of Bt has led to field-evolved resistance in several lepidopteran pests. Resistance to Bt Cry1Ac toxin in the diamondback moth, Plutella xylostella (L.), was previously mapped to a multigenic resistance locus (BtR-1). Here, we assembled the 3.15 Mb BtR-1 locus and found high-level resistance to Cry1Ac and Bt biopesticide in four independent P. xylostella strains were all associated with differential expression of a midgut membrane-bound alkaline phosphatase (ALP) outside this locus and a suite of ATP-binding cassette transporter subfamily C (ABCC) genes inside this locus. The interplay between these resistance genes is controlled by a previously uncharacterized trans-regulatory mechanism via the mitogen-activated protein kinase (MAPK) signaling pathway. Molecular, biochemical, and functional analyses have established ALP as a functional Cry1Ac receptor. Phenotypic association experiments revealed that the recessive Cry1Ac resistance was tightly linked to down-regulation of ALP, ABCC2 and ABCC3, whereas it was not linked to up-regulation of ABCC1. Silencing of ABCC2 and ABCC3 in susceptible larvae reduced their susceptibility to Cry1Ac but did not affect the expression of ALP, whereas suppression of MAP4K4, a constitutively transcriptionally-activated MAPK upstream gene within the BtR-1 locus, led to a transient recovery of gene expression thereby restoring the susceptibility in resistant larvae. These results highlight a crucial role for ALP and ABCC genes in field-evolved resistance to Cry1Ac and reveal a novel trans-regulatory signaling mechanism responsible for modulating the expression of these pivotal genes in P. xylostella