Dioon Lindl. (Zamiaceae): Perspectives from phylogeny and a population genetic study of Dioon edule

Dioon Lindl. (Zamiaceae) is a small genus restricted to Mexico (12 species) and Honduras (one species). Previous systematic studies have been unable to fully resolve species relationships within the genus. Phylogenetic analyses were conducted with data from several sources, including Restriction Fragment Length Polymorphisms from the chloroplast genome, morphology, two introns of the low copy nuclear gene S-adenosyl-L-homocysteine hydrolase (SAHH) and the 5.8S/ITS2 regions of the nuclear ribosomal DNA. The goals of the study were to construct a total evidence species level phylogeny and to explore current biogeographical hypotheses. None of the analyses performed produced a fully resolved topology. Dioon is comprised of two main lineages (the Edule and Spinulosum Clades), which represents an ancient divergence within the genus. The two introns of the nuclear gene SAHH offer additional evidence for the split into two lineages. Intron 2 contains a 18 bp deletion in the Spinulosum Clade, providing a synapomorphy for that group. The 5.8S/ITS2 regions were highly polymorphic and subsequently omitted from the combined analyses. In order to visualize congruence between morphology and molecular data, morphological characters were mapped onto the combined molecular tree. Current biogeographical hypotheses of a general northward pattern of migration and speciation are supported here. However, sister relationships within the Edule Clade are not fully resolved. Seven DNA microsatellite markers were developed to investigate patterns of genetic variation of seven populations of D. edule, a species restricted to Eastern Mexico. We found that most of the genetic variation lies within populations (Ho = 0.2166–0.3657) and that levels of population differentiation are low (Fst = 0.088); this finding is congruent with the breeding system of this species, dioicy. Four of the populations deviate from Hardy Weinberg Equilibrium and have a high number of identical genotypes, we suggest that this unexpected pattern is due to the life-history strategy of the species coupled with the few number of polymorphic loci detected in these populations. Our results are not congruent with earlier evidence from morphology and allozyme markers that suggest that the two northernmost populations represent a distinct entity that is recognized by some taxonomists as D. angustifolium.

AIDS workplace *policy adoption and implementation in local government: An analysis of departmental variation

This is an empirical study whose purpose was to examine the process of innovation adoption as an adaptive response by a public organization and its subunits existing under varying degrees of environmental uncertainty. Meshing organization innovation research and contingency theory to form a theoretical framework, an exploratory case study design was undertaken in a large, metropolitan government located in an area with the fourth highest prevalence rate of HIV/AIDS in the country. A number of environmental and organizational factors were examined for their influence upon decision making in the adoption/non-adoption as well as implementation of any number of AIDS-related policies, practices, and programs.^ The major findings of the study are as follows. For the county government itself (macro level), no AIDS-specific workplace policies have been adopted. AIDS activities (AIDS education, AIDS Task Force, AIDS Coordinator, etc.), adopted county-wide early in the epidemic, have all been abandoned. Worker infection rates, in the aggregate and throughout the epidemic have been small. As a result, absent co-worker conflict (isolated and negligible), no increase in employee health care costs, no litigation regarding discrimination, and no major impact on workforce productivity, AIDS has basically become a non-issue at the strategic core of the organization. At the departmental level, policy adoption decisions varied widely. Here the predominant issue is occupational risk, i.e., both objective as well as perceived. As expected, more AIDS-related activities (policies, practices, and programs) were found in departments with workers known to have significant risk for exposure to the AIDS virus (fire rescue, medical examiner, police, etc.). AIDS specific policies, in the form of OSHA's Bloodborn Pathogen Standard, took place primarily because they were legislatively mandated. Union participation varied widely, although not necessarily based upon worker risk. In several departments, the union was a primary factor bringing about adoption decisions. Additional factors were identified and included organizational presence of AIDS expertise, availability of slack resources, and the existence of a policy champion. Other variables, such as subunit size, centralization of decision making, and formalization were not consistent factors explaining adoption decisions. ^

(Table 2) Collection sites and number of specimens of Usnea subgenus Neuropogon species

Usnea species of the Neuropogon group are amongst the most widespread and abundant macrolichens in Antarctic regions. Four principal species, U. antarctica, U. aurantiaco-atra, U. sphacelata and U. subantarctica, have been described on morphological grounds. However, identification to species level is often difficult and atypical morphologies frequently arise. Over 400 specimens were collected on the Antarctic Peninsula and Falkland Islands. Both morphological and molecular characters (ITS and RPB1) were used to compare samples to clarify taxonomic relationships. Morphological characteristics used included presence of apothecia, apothecial rays, soredia, papillae, fibrils, pigmentation and the diameter of the central axis as a proportion of branch diameter. Results revealed a very close relationship between U. antarctica and U. aurantiaco-atra, suggesting that they might constitute a species pair or be conspecific. Usnea sphacelata was comprised of at least two genetically distinct groups with no clear differences in morphology. One group included the first reported fertile specimen of this species. Usnea subantarctica was phylogenetically distinct from the other main Antarctic Usnea species, but clustered with U. trachycarpa. Genetic variation was evident within all species although there was no clear correlation between geographic origin and genetic relatedness. Phylogenetic analyses indicated that species circumscription in the Neuropogon group needs revision, with the principal species being non-monophyletic. None of the morphological characters, or groups of characters, used in this study proved to be completely unambiguous markers for a single species. However, axis thickness was supported as being informative for the identification of monophyletic lineages within the group.

Parties, Mandates and Multilevel Politics : Sub-National Variation in British General Election Manifestos

Earlier versions were presented at the ECPR Joint Sessions Workshop on ‘How and Why of Party Manifestos in New and Established Democracies’, University of St. Gallen, April 2011, and at PSA and EPOP Conferences in 2011. We are grateful to all participants for their feedback, and particularly Bob Harmel and Lars Svasand for their comments and leading this project. We are also grateful to Dai Moon for discussions around Welsh manifestos and highlighting some otherwise unavailable literature. The usual disclaimers naturally apply. Alistair Clark gratefully acknowledges the financial support of a British Academy Overseas Conference Grant, Award Number OC100383 for travel to the 2011 ECPR Joint Sessions. The final definitive version of this paper has been published in Party Politics by SAGE Publications Ltd and is available on the journal website at: http://ppq.sagepub.com/ All Rights Reserved © Alistair Clark and Lynn Bennie.

Seasonal and Species Variation of the Hepatotoxin Indospicine in Australian Indigofera Legumes as Measured by UPLC−MS/MS

Livestock industries have maintained a keen interest in pasture legumes because of the high protein content and nutritive value. Leguminous Indigofera plant species have been considered as having high feeding values to be utilized as pasture, but the occurrence of the toxic constituent indospicine in some species has restricted this utility. Indospicine has caused both primary and secondary hepatotoxicosis and also reproductive losses, but has only previously been determined in a small number of Indigofera species. This paper validates a high throughput ultra-performance liquid chromatography−tandem mass spectrometry (UPLC−MS/MS) method to determine indospicine content of various Indigofera species found in Australian pasture. Twelve species of Indigofera together with Indigastrum parviflorum plants were collected and analysed. Out of the 84 samples analyzed, *I. spicata contained the highest indospicine level (1003 ± 328 mg/kg DM, n = 4) followed by I. linnaei (755 ± 490 mg/kg DM, n = 51). Indospicine was not detected in 9 of the remaining 11 species, and at only low levels (<10 mg/kg DM) in 2 out of 8 I. colutea specimens and in 1 out of 5 I. linifolia specimens. Indospicine concentrations were below quantitation levels for other Indigofera spp. (I. adesmiifolia, I. georgei, I. hirsuta, I. leucotricha,* I. oblongifolia, I. australis and I. trita) and Indigastrum parviflorum. One of the more significant findings to emerge from this study is that the indospicine content of I. linnaei is highly variable (159 to 2128 mg/kg DM, n = 51), and differs across both regions and seasons. Its first re-growth after spring rain has a higher (p < 0.01) indospicine content than growth following more substantial summer rain. The species collected include the predominant Indigofera in Australia pasture, and of these, only *I. spicata and I. linnaei contain high enough levels of indospicine to pose a potential toxic threat to grazing herbivores.

Variation, correlation and heritability of interest characters for selection of African eggplant

The eggplant ( Solanum aethiopicum ) is the species of the Solanum genus, whose geographical distribution is broadest. It is grown throughout tropical Africa, and includes three groups of cultivars commonly called African or indigenous eggplant. Kumba group or “bitter eggplant” is an important Solanaceous vegetable crop in Burkina Faso. The objective of this study was to determine genetic variability, strength of association and level of heritability among agronomic interest traits. Phenotypic and genotypic variations and heritability of 14 traits were estimated in 61 accessions at Institut de Développement Rural (IDR), Gampela in Burkina Faso. High phenotypic and genotypic coefficients of variation were observed for fruit diameter, number of seeds per fruit, fruit weight, leaf blade length and width, and height at flowering. In addition, genetic and phenotypic variances were high for the number of seed, fruit weight, plant height at flowering and days to 50% flowering. High heritability estimates were recorded for all traits. Fruit weight showed a positive association with fruit diameter and thickness. The fifty percent flowering cycle registered positive correlations with plant height and fruit diameter. Fruit number showed a negative association with fruit weight and diameter, and 50% flowering cyle.

Temporal variation in the diet of gentoo penguins at the Falkland Islands

Knowledge of diet is critical in interpreting the ecological roles of marine top predators and provides information towards their conservation and management. The Falkland Islands hold the largest number of breeding gentoo penguins. Yet knowledge of gentoo penguin diet at the Falklands is limited to either broad taxonomic divisions of prey items or dietary samples collected only on a single day. This study is the first to investigate gentoo penguin diet at Cow Bay, Falklands, to the species level, over repeated sampling intervals during the breeding period. Through stomach content analysis, we determined diet over a large temporal scale (2002/2003/2004–2011/2012/2013) and between the guard and crèche periods of chick rearing. The principle prey item by reconstituted mass was rock cod fish Patagonotothen spp., for all periods (47–78 %) except that of the 2012/2013 crèche period (19 %) when Falkland herring Sprattus fugensis made up the bulk of the diet (52 %). Of the cephalopods recovered, Patagonian squid Doryteuthis gahi was prominent (1–24 %), while crustaceans contributed negligibly to gentoo penguin diet. Our findings revealed that gentoo penguins breeding at the Falkland Islands were primarily demersal foragers with an ability for pelagic feeding. Diet choice appears to reflect prey availability.

Mapping variation in children’s mathematical reasoning: the case of ‘what else belongs?’

Explaining appears to dominate primary teachers’ understanding of mathematical reasoning when it is not confused with problem solving. Drawing on previous literature of mathematical reasoning, we generate a view of the critical aspects of reasoning that may assist primary teachers when designing and enacting tasks to elicit and develop mathematical reasoning. The task used in this study of children’s reasoning is a number commonality problem. We analysed written and verbal samples of reasoning gathered from children in grades 3 and 4 from three primary schools in Australia and one elementary school in Canada to map the variation in their reasoning. We found that comparing and contrasting was a critical aspect of forming conjectures when generalising in this context, an action not specified in frameworks for generalising in early algebra. The variance in children’s reasoning elicited through this task also illuminated the difference between explaining and justifying.

Adding fuel to the "fire of life": energy budgets across levels of variation in ectotherms and endotherms

Energy metabolism - the "fire of life" - is the sum of the processes by which animals acquire energy, channel energy into useful functions, and dissipate energy from their bodies. Acquisition and allocation processes deal with energy mainly as a quantity, but energy is absorbed or expended over a period of time; therefore, the most relevant way to conceptualize energy budgets is with the use of rate functions. A large number of recent studies have examined co-variation in metabolic and behavioral traits among individuals. A general finding stemming from this body of work is that there is no single cause-and-effect mechanism driving these relationships, but that the direction of the effects is dynamic and shifts in different contexts and environments. However, the remarkable energetic differences between endotherms and ectotherms are an unexploited basis for achieving a further understanding of such relationships.

Synonymous co-variation across the E1/E2 gene junction of hepatitis C virus defines virion fitness

Hepatitis C virus is a positive-sense single-stranded RNA virus. The gene junction partitioning the viral glycoproteins E1 and E2 displays concurrent sequence evolution with the 3′-end of E1 highly conserved and the 5′-end of E2 highly heterogeneous. This gene junction is also believed to contain structured RNA elements, with a growing body of evidence suggesting that such structures can act as an additional level of viral replication and transcriptional control. We have previously used ultradeep pyrosequencing to analyze an amplicon library spanning the E1/E2 gene junction from a treatment naïve patient where samples were collected over 10 years of chronic HCV infection. During this timeframe maintenance of an in-frame insertion, recombination and humoral immune targeting of discrete virus sub-populations was reported. In the current study, we present evidence of epistatic evolution across the E1/E2 gene junction and observe the development of co-varying networks of codons set against a background of a complex virome with periodic shifts in population dominance. Overtime, the number of codons actively mutating decreases for all virus groupings. We identify strong synonymous co-variation between codon sites in a group of sequences harbouring a 3 bp in-frame insertion and propose that synonymous mutation acts to stabilize the RNA structural backbone.

Mating system variation among populations, individuals and within and among fruits in Bertholletia excelsa.

The aim of this study was to investigate variation in mating system among three Brazilian Amazon populations of the tree Bertholletia excelsa with different levels of anthropogenic interventions. We collected open-pollinated seeds from one natural population, remnant trees dispersed in a pasture, and trees from a plantation. Outcrossing rate not varied among the populations and indicates that all seeds were originated from outcrossing (tm=1.0). Mating among relatives was significant higher in the plantation than forest and pasture populations, probably due the fact that many trees are related in the plantation. Correlated mating was significantly higher in pasture (rp=0.47) and plantation (rp=0.51) than in the natural population (rp=0.22), suggesting that trees in natural population are pollinated by a higher number of pollen donors. The paternity correlation was significantly higher within (rp(w)=0.41) than among fruits (rp(a)=0.18), showing a higher probability to find full-sibs within than among fruits. The fixation index was generally lower in seed trees than in their seedlings, suggesting selection for heterozygous individuals from seedling to adult stages. Progeny arrays collected from the natural population had a lower proportion of pairwise full-sibs than in pasture and plantation and higher variance effective size (2.75) than trees in pasture (2.15) and plantations (2.22). Results highlight that seed collections for conservation, breeding and reforestation programs preferentially should be carried out in natural populations due low proportion highest variance effective size within progeny.

Smoothing a Discrete Hazard Function for the Number of Patients Colonized with Methicillin-Resistance Staphylococcus Aureus in an Intensive Care Unit

A new method for estimating the time to colonization of Methicillin-resistant Staphylococcus Aureus (MRSA) patients is developed in this paper. The time to colonization of MRSA is modelled using a Bayesian smoothing approach for the hazard function. There are two prior models discussed in this paper: the first difference prior and the second difference prior. The second difference prior model gives smoother estimates of the hazard functions and, when applied to data from an intensive care unit (ICU), clearly shows increasing hazard up to day 13, then a decreasing hazard. The results clearly demonstrate that the hazard is not constant and provide a useful quantification of the effect of length of stay on the risk of MRSA colonization which provides useful insight.

On Ordinal VC-Dimension and Some Notions of Complexity

We generalize the classical notion of Vapnik–Chernovenkis (VC) dimension to ordinal VC-dimension, in the context of logical learning paradigms. Logical learning paradigms encompass the numerical learning paradigms commonly studied in Inductive Inference. A logical learning paradigm is defined as a set W of structures over some vocabulary, and a set D of first-order formulas that represent data. The sets of models of ϕ in W, where ϕ varies over D, generate a natural topology W over W. We show that if D is closed under boolean operators, then the notion of ordinal VC-dimension offers a perfect characterization for the problem of predicting the truth of the members of D in a member of W, with an ordinal bound on the number of mistakes. This shows that the notion of VC-dimension has a natural interpretation in Inductive Inference, when cast into a logical setting. We also study the relationships between predictive complexity, selective complexity—a variation on predictive complexity—and mind change complexity. The assumptions that D is closed under boolean operators and that W is compact often play a crucial role to establish connections between these concepts. We then consider a computable setting with effective versions of the complexity measures, and show that the equivalence between ordinal VC-dimension and predictive complexity fails. More precisely, we prove that the effective ordinal VC-dimension of a paradigm can be defined when all other effective notions of complexity are undefined. On a better note, when W is compact, all effective notions of complexity are defined, though they are not related as in the noncomputable version of the framework.