A survey of primary homology assessment: different botanists perceive and define characters in different ways

Cladistic analyses begin with an assessment of variation for a group of organisms and the subsequent representation of that variation as a data matrix. The step of converting observed organismal variation into a data matrix has been considered subjective, contentious, under-investigated, imprecise, unquantifiable, intuitive, as a black-box, and at the same time as ultimately the most influential phase of any cladistic analysis (Pimentel and Riggins, 1987; Bryant, 1989; Pogue and Mickevich, 1990; de Pinna, 1991; Stevens, 1991; Bateman et al., 1992; Smith, 1994; Pleijel, 1995; Wilkinson, 1995; Patterson and Johnson, 1997). Despite the concerns of these authors, primary homology assessment is often perceived as reproducible. In a recent paper, Hawkins et al. (1997) reiterated two points made by a number of these authors: that different interpretations of characters and coding are possible and that different workers will perceive and define characters in different ways. One reviewer challenged us: did we really think that two people working on the same group would come up with different data sets? The conflicting views regarding the reproducibility of the cladistic character matrix provoke a number of questions. Do the majority of workers consistently follow the same guidelines? Has the theoretical framework informing primary homology assessment been adequately explored? The objective of this study is to classify approaches to primary homology assessment, and to quantify the extent to which different approaches are found in the literature by examining variation in the way characters are defined and coded in a data matrix.

Role for flagella but not intimin in the persistent infection of the gastrointestinal tissues of specific-pathogen-free chicks by Shiga toxin-negative Escherichia coli O157:H7

Shiga toxin (Stx)-positive Escherichia coli O157:117 readily colonize and persist in specific-pathogen-free (SPF) chicks, and we have shown that an Stx-negative E. coli O157:117 isolate (NCTC12900) readily colonizes SPF chicks for up to 169 days after oral inoculation at 1 day of age. However, the role of intimin in the persistent colonization of poultry remains unclear. Thus, to investigate the role of intimin and flagella, which is a known factor in the persistence of non-O157 E. coli in poultry, isogenic single- and double-intimin and aflagellar mutants were constructed in E. coli O157:117 isolate NCTC12900. These mutants were used to inoculate (10(5) CFU) 1-day-old SPF chicks. In general, significant attenuation of the aflagellate and intiminaflagellate mutants, but not the intimin mutant, was noted at similar time points between 22 and 92 days after inoculation. The intimin-deficient mutant was still being shed at the end of the experiment, which was 211 days after inoculation, 84 days more than the wild type. Shedding of the aflagellar and intimin-aflagellar mutants ceased 99 and 113 days after inoculation, respectively. Histological analysis of gastrointestinal tissues from inoculated birds gave no evidence for true microcolony formation by NCTC12900 or intimin and aflagellar mutants to epithelial cells. However, NCTC12900 mutant derivatives associated with the mucosa were observed as individual cells and/or as large aggregates. Association with luminal contents was also noted. These data suggest that O157 organisms do not require intimin for the persistent colonization of chickens, whereas flagella do play a role in this process.

Persistent reduced ecosystem respiration after insect disturbance in high elevation forests

Amid a worldwide increase in tree mortality, mountain pine beetles (Dendroctonus ponderosae Hopkins) have led to the death of billions of trees from Mexico to Alaska since 2000. This is predicted to have important carbon, water and energy balance feedbacks on the Earth system. Counter to current projections, we show that on a decadal scale, tree mortality causes no increase in ecosystem respiration from scales of several square metres up to an 84 km2 valley. Rather, we found comparable declines in both gross primary productivity and respiration suggesting little change in net flux, with a transitory recovery of respiration 6–7 years after mortality associated with increased incorporation of leaf litter C into soil organic matter, followed by further decline in years 8–10. The mechanism of the impact of tree mortality caused by these biotic disturbances is consistent with reduced input rather than increased output of carbon.

Synoptic-scale controls of persistent low temperature and icy weather over southern China in January 2008

In January 2008, central and southern China experienced persistent low temperatures, freezing rain, and snow. The large-scale conditions associated with the occurrence and development of these snowstorms are examined in order to identify the key synoptic controls leading to this event. Three main factors are identified: 1) the persistent blocking high over Siberia, which remained quasi-stationary around 65°E for 3 weeks, led to advection of dry and cold Siberian air down to central and southern China; 2) a strong persistent southwesterly flow associated with the western Pacific subtropical high led to enhanced moisture advection from the Bay of Bengal into central and southern China; and 3) the deep inversion layer in the lower troposphere associated with the extended snow cover over most of central and southern China. The combination of these three factors is likely responsible for the unusual severity of the event, and hence a long return period

The persistent challenge of encouraging public participation in the low-carbon transition

In order to address the growing urgency of issues around environmental and resource limits, there is a clear need to develop policies that promote changes in behavior and the ways in which society both views and consumes goods and services. However, there is an argument to suggest that, in order to develop effective policies in this area, we need to move beyond a narrow understanding of ‘how individuals behave’ in order to cultivate a more nuanced approach that encompasses behavioral influences in different societies, contexts and settings. In this opinion article we therefore draw on a range of our own recent comparative research studies in order to provide fresh insights into the continued problem of how to engage people individually and collectively in establishing more sustainable, low-carbon societies.

The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons

Despite the accumulating knowledge on the development and establishment of the gut microbiota, its role as a reservoir for multidrug resistance is not well understood. This study investigated the prevalence and persistence patterns of an integrase gene (int1), used as a proxy for integrons (which often carry multiple antimicrobial resistance genes), in the fecal microbiota of 147 mothers and their children sampled longitudinally from birth to 2 years. The study showed the int1 gene was detected in 15% of the study population, and apparently more persistent than the microbial community structure itself. We found int1 to be persistent throughout the first two years of life, as well as between mothers and their 2-year-old children. Metagenome sequencing revealed integrons in the gut meta-mobilome that were associated with plasmids and multidrug resistance. In conclusion, the persistent nature of integrons in the infant gut microbiota makes it a potential reservoir of mobile multidrug resistance.

Modelling the bioaccumulation of persistent organic pollutants in agricultural food chains for regulatory exposure assessment

New models for estimating bioaccumulation of persistent organic pollutants in the agricultural food chain were developed using recent improvements to plant uptake and cattle transfer models. One model named AgriSim was based on K OW regressions of bioaccumulation in plants and cattle, while the other was a steady-state mechanistic model, AgriCom. The two developed models and European Union System for the Evaluation of Substances (EUSES), as a benchmark, were applied to four reported food chain (soil/air-grass-cow-milk) scenarios to evaluate the performance of each model simulation against the observed data. The four scenarios considered were as follows: (1) polluted soil and air, (2) polluted soil, (3) highly polluted soil surface and polluted subsurface and (4) polluted soil and air at different mountain elevations. AgriCom reproduced observed milk bioaccumulation well for all four scenarios, as did AgriSim for scenarios 1 and 2, but EUSES only did this for scenario 1. The main causes of the deviation for EUSES and AgriSim were the lack of the soil-air-plant pathway and the ambient air-plant pathway, respectively. Based on the results, it is recommended that soil-air-plant and ambient air-plant pathway should be calculated separately and the K OW regression of transfer factor to milk used in EUSES be avoided. AgriCom satisfied the recommendations that led to the low residual errors between the simulated and the observed bioaccumulation in agricultural food chain for the four scenarios considered. It is therefore recommended that this model should be incorporated into regulatory exposure assessment tools. The model uncertainty of the three models should be noted since the simulated concentration in milk from 5th to 95th percentile of the uncertainty analysis often varied over two orders of magnitude. Using a measured value of soil organic carbon content was effective to reduce this uncertainty by one order of magnitude.

Protein identification pipeline for the homology-driven proteomics

Homology-driven proteomics is a major tool to characterize proteomes of organisms with unsequenced genomes. This paper addresses practical aspects of automated homology-driven protein identifications by LC-MS/MS on a hybrid LTQ orbitrap mass spectrometer. All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download. (C) 2008 Elsevier B.V. All rights reserved.

Coding behavioural data for cladistic analysis: using dynamic homology without parsimony

Many of the controversies around the concept of homology rest on the subjectivity inherent to primary homology propositions. Dynamic homology partially solves this problem, but there has been up to now scant application of it outside of the molecular domain. This is probably because morphological and behavioural characters are rich in properties, connections and qualities, so that there is less space for conflicting character delimitations. Here we present a new method for the direct optimization of behavioural data, a method that relies on the richness of this database to delimit the characters, and on dynamic procedures to establish character state identity. We use between-species congruence in the data matrix and topological stability to choose the best cladogram. We test the methodology using sequences of predatory behaviour in a group of spiders that evolved the highly modified predatory technique of spitting glue onto prey. The cladogram recovered is fully compatible with previous analyses in the literature, and thus the method seems consistent. Besides the advantage of enhanced objectivity in character proposition, the new procedure allows the use of complex, context-dependent behavioural characters in an evolutionary framework, an important step towards the practical integration of the evolutionary and ecological perspectives on diversity. (C) The Willi Hennig Society 2010.