Development and testing of a risk indexing framework to determine field-scale critical source areas of faecal bacteria on grassland.

This paper draws on lessons from a UK case study in the management of diffuse microbial pollution from grassland farm systems in the Taw catchment, south west England. We report on the development and preliminary testing of a field-scale faecal indicator organism risk indexing tool (FIORIT). This tool aims to prioritise those fields most vulnerable in terms of their risk of contributing FIOs to water. FIORIT risk indices were related to recorded microbial water quality parameters (faecal coliforms [FC] and intestinal enterococci [IE]) to provide a concurrent on-farm evaluation of the tool. There was a significant upward trend in Log[FC] and Log[IE] values with FIORIT risk score classification (r2 =0.87 and 0.70, respectively and P<0.01 for both FIOs). The FIORIT was then applied to 162 representative grassland fields through different seasons for ten farms in the case study catchment to determine the distribution of on-farm spatial and temporal risk. The high risk fields made up only a small proportion (1%, 2%, 2% and 3% for winter, spring, summer and autumn, respectively) of the total number of fields assessed (and less than 10% of the total area), but the likelihood of the hydrological connection of high FIO source areas to receiving watercourses makes them a priority for mitigation efforts. The FIORIT provides a preliminary and evolving mechanism through which we can combine risk assessment with risk communication to end-users and provides a framework for prioritising future empirical research. Continued testing of FIORIT across different geographical areas under both low and high flow conditions is now needed to initiate its long term development into a robust indexing tool

Transients drive the demographic dynamics of plant populations in variable environments

The dynamics of structured plant populations in variable environments can be decomposed into the ‘asymptotic’ growth contributed by vital rates, and ‘transient’ growth caused by deviation from stable stage structure. We apply this framework to a large, global data base of longitudinal studies of projection matrix models for plant populations. We ask, what is the relative contribution of transient boom and bust to the dynamic trajectories of plant populations in stochastic environments? Is this contribution patterned by phylogeny, growth form or the number of life stages per population and per species? We show that transients contribute nearly 50% or more to the resulting trajectories, depending on whether transient and stable contributions are partitioned according to their absolute or net contribution to population dynamics. Both transient contributions and asymptotic contributions are influenced heavily by the number of life stages modelled. We discuss whether the drivers of transients should be considered real ecological phenomena, or artefacts of study design and modelling strategy. We find no evidence for phylogenetic signal in the contribution of transients to stochastic growth, nor clear patterns related to growth form. We find a surprising tendency for plant populations to boom rather than bust in response to temporal changes in vital rates and that stochastic growth rates increase with increasing tendency to boom. Synthesis. Transient dynamics contribute significantly to stochastic population dynamics but are often overlooked in ecological and evolutionary studies that employ stochastic analyses. Better understanding of transient responses to fluctuating population structure will yield better management strategies for plant populations, and better grasp of evolutionary dynamics in the real world

A revised position for the rotated Falkland Islands microplate

The early stages of transform margin formation are associated with crustal fragmentation and block rotation. The restricted size of the resultant microcontinental blocks precludes palaeogeographical reconstructions and reliable estimations of the amount of rotation they can undergo. An example considered here is the Falkland Plateau. This is located adjacent to the Agulhas–Falkland Fracture Zone and its westernmost province is the Falkland Islands microcontinent. The position of the plateau and the islands prior to Gondwana break-up remains contentious. This study integrates seismic reflection and gravity data to propose a revised position of the Falkland Islands microcontinent constrained by (1) the presence of a mega-décollement, controlling the Gondwanide Orogen, described north of the Falkland Islands and underneath South Africa and the Outeniqua Basin, and (2) the similar architecture of fault networks mapped north of the islands and in the northernmost Outeniqua Basin. This revised position requires a re-evaluation of the timing and rate of rotation of the Falkland Islands microcontinent and affects the expected crustal architecture adjacent to the islands. Our model yields rotation rates between 5.5° and 8° Ma−1 and two potential times for rotation, and predicts more unstretched crust beneath the basin east of the Falkland Islands than previous model

Social structure contains epidemics and regulates individual roles in disease transmission in a group-living mammal

Population structure is critical to infectious disease transmission. As a result, theoretical and empirical contact network models of infectious disease spread are increasingly providing valuable insights into wildlife epidemiology. Analyzing an exceptionally detailed dataset on contact structure within a high‐density population of European badgers Meles meles, we show that a modular contact network produced by spatially structured stable social groups, lead to smaller epidemics, particularly for infections with intermediate transmissibility. The key advance is that we identify considerable variation among individuals in their role in disease spread, with these new insights made possible by the detail in the badger dataset. Furthermore, the important impacts on epidemiology are found even though the modularity of the Badger network is much lower than the threshold that previous work suggested was necessary. These findings reveal the importance of stable social group structure for dis‐ease dynamics with important management implications for socially structured populations

Ecological selection of siderophore-producing microbial taxa in response to heavy metal contamination

Some microbial public goods can provide both individual and community‐wide benefits, and are open to exploitation by non‐producing species. One such example is the production of metal‐detoxifying siderophores. Here, we investigate whether conflicting selection pressures on siderophore production by heavy metals – a detoxifying effect of siderophores, and exploitation of this detoxifying effect – result in a net increase or decrease. We show that the proportion of siderophore‐producing taxa increases along a natural heavy metal gradient. A causal link between metal contamination and siderophore production was subsequently demonstrated in a microcosm experiment in compost, in which we observed changes in community composition towards taxa that produce relatively more siderophores following copper contamination. We confirmed the selective benefit of siderophores by showing that taxa producing large amounts of siderophore suffered less growth inhibition in toxic copper. Our results suggest that ecological selection will favour siderophore‐mediated decontamination, with important consequences for potential remediation strategies

Comparison of Transfer-to-Continuum and Eikonal Models of Projectile Fragmentation Reactions

Spectroscopic properties of nuclei are accessible with projectile fragmentation reactions, but approximations made in the reaction theory can limit the accuracy of the determinations. We examine here two models that have rather different approximations for the nucleon wave function, the target interaction, and the treatment of the finite duration of the reaction. The nucleon-target interaction is treated differently in the eikonal and the transfer-to-continuum model, but the differences are more significant for light targets. We propose a new parameterization with that in mind. We also propose a new formula to calculate the amplitude that combines the better treatment of the wave function in the eikonal model with the better treatment of the target interaction in the transfer-to-continuum model.Comment: 21 pages, latex file including 3 tables. 5 figures. Submitted to Phys. Rev.

The Replicase Gene of Avian Coronavirus Infectious Bronchitis Virus Is a Determinant of Pathogenicity

We have previously demonstrated that the replacement of the S gene from an avirulent strain (Beaudette) of infectious bronchitis virus (IBV) with an S gene from a virulent strain (M41) resulted in a recombinant virus (BeauR-M41(S)) with the in vitro cell tropism of the virulent virus but that was still avirulent. In order to investigate whether any of the other structural or accessory genes played a role in pathogenicity we have now replaced these from the Beaudette strain with those from M41. The recombinant IBV was in effect a chimaeric virus with the replicase gene derived from Beaudette and the rest of the genome from M41. This demonstrated that it is possible to exchange a large region of the IBV genome, approximately 8.4 kb, using our transient dominant selection method. Recovery of a viable recombinant IBV also demonstrated that it is possible to interchange a complete replicase gene as we had in effect replaced the M41 replicase gene with the Beaudette derived gene. Analysis of the chimaeric virus showed that it was avirulent indicating that none of the structural or accessory genes derived from a virulent isolate of IBV were able to restore virulence and that therefore, the loss of virulence associated with the Beaudette strain resides in the replicase gene

The diversity of population responses to environmental change

This is the final version. Available from Wiley via the DOI in this record.Data available from the Dryad Digital Repository: https:// doi.org/10.5061/dryad.d5f54s7The current extinction and climate change crises pressure us to predict population dynamics with ever-greater accuracy. Although predictions rest on the well-advanced theory of age-structured populations, two key issues remain poorly explored. Specifically, how the age-dependency in demographic rates and the year-to-year interactions between survival and fecundity affect stochastic population growth rates. We use inference, simulations and mathematical derivations to explore how environmental perturbations determine population growth rates for populations with different age-specific demographic rates and when ages are reduced to stages. We find that stage- vs. age-based models can produce markedly divergent stochastic population growth rates. The differences are most pronounced when there are survival-fecundity-trade-offs, which reduce the variance in the population growth rate. Finally, the expected value and variance of the stochastic growth rates of populations with different age-specific demographic rates can diverge to the extent that, while some populations may thrive, others will inevitably go extinct.Max Planck Society, Marie Curie FellowshipERCGerman Research FoundationSwiss National Science FoundationNational Science FoundationNational Institute of AgingRamon y Cajal Research GrantWenner-Gren FoundationLeakey FoundationNational Geographic SocietyZoological Society of San DiegoUniversity of PennsylvaniaArgentinean National Council of Researc

A standard protocol to report discrete stage-structured demographic information

Stage-based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open-access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. Over 80% of surveyed researchers (n = 60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardised protocol to present MPMs in publications. This standard is linked to www.compa dre-db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open-access repositories such as DRYAD, Figshare and Zenodo. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility

Integral control for population management

We present a novel management methodology for restocking a declining population. The strategy uses integral control, a concept ubiquitous in control theory which has not been applied to population dynamics. Integral control is based on dynamic feedback-using measurements of the population to inform management strategies and is robust to model uncertainty, an important consideration for ecological models. We demonstrate from first principles why such an approach to population management is suitable via theory and examples