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The Earth Hologenome Initiative (EHI) is a global collaboration to generate and analyse hologenomic data from wild animals and associated microorganisms using standardised methodologies underpinned by open and inclusive research principles. Initially focused on vertebrates, it aims to re-examine ecological and evolutionary questions by studying host–microbiota interactions from a systemic perspective.

Computer simulations are invaluable tools for scientific discovery. However, accurate simulations are often slow to execute, which limits their applicability to extensive parameter exploration, large-scale data analysis, and uncertainty quantification. A promising route to accelerate simulations by building fast emulators with machine learning requires large training datasets, which can be prohibitively expensive to obtain with slow simulations. Here we present a method based on neural architecture search to build accurate emulators even with a limited number of training data. The method successfully emulates simulations in 10 scientific cases including astrophysics, climate science, biogeochemistry, high energy density physics, fusion energy, and seismology, using the same super-architecture, algorithm, and hyperparameters. Our approach also inherently provides emulator uncertainty estimation, adding further confidence in their use. We anticipate this work will accelerate research involving expensive simulations, allow more extensive parameters exploration, and enable new, previously unfeasible computational discovery.

Bakgrund Inom hälso-och sjukvården är vårdrelaterade infektioner den mest förkommande typen av vårdskador. Vårdrelaterade infektioner kan leda till lidande för patienten samtidigt som det medför stora kostnader för samhället. Den basala handhygienrutinen är en grundläggande faktor för att kunna arbeta preventivt gentemot vårdrelaterade infektioner. Ämnet är viktigt att studera i syfte att förstå hur rutiner för handhygien ser ut i vården ur ett globalt perspektiv. Syfte Syftet var att belysa sjukvårdspersonalens efterlevnad av handhygienrutiner. Metod Denna studie har skrivits som en litteraturöversikt. Resultatet är baserat på tio vetenskapliga originaltitlar av både kvantitativ samt kvalitativ design som svarade på studien syfte. Sökmotorerna som användes för att hitta artiklarna var PubMed och Cinahl complete. Resultat I resultatet påvisade sjukvårdspersonalen en förhållandevis låg efterlevnad av handhygienrutiner. Personliga uppfattningar, tid, kunskap och utförande var faktorer som påverkade sjukvårdpersonalens efterlevnad. Det framkom att det fanns en stor variation av kunskap gällande handhygienrutiner. Kunskapsbristen berodde på personalens förhållningssätt samt i vilken utsträckning de fått utbildning i handhygienrutiner. En faktor som ökade sjukvårdspersonalens efterlevnad var kontinuerlig utbildning. Sammanfattning I studien framgick det att det fanns ett stort behov av att öka sjukvårdspersonalens efterlevnad av handhygienrutiner runt om i världen. Interventionen grundar sig att sjukvårdspersonalen bör följa de rekommenderade handhygienrutinerna så som handhygiens utförande, tidsåtgång samt aseptisk teknik. Regelbunden utbildning inom handhygien var en viktig faktor för efterlevnaden. Fortsättningsvis finns ett stort behov för vidareutbildning och kontinuerlig träning hos sjukvårdspersonalen., Background In healthcare, healthcare-associated infections (HRI) are the most common type of healthcare injuries. Healthcare related infections can lead to unnecessary suffering for the patient, and it entails great costs for the society. The basic hand hygiene routine is a fundamental factor to be able to work preventively against healthcare related infections. The subject is important to study in order to understand what the routines for hand hygiene looks like in healthcare from a global perspective. Aim The purpose was to highlight healthcare workers compliance regarding hand hygiene routines. Method This study has been written as a literature review. Based on ten original articles of both quantitative and qualitative design which answered the purpose of the study. The search engines used to find the articles were PubMed and Cinahl complete. Results Healthcare personnel showed relatively low compliance with hand hygiene routines. Attitudes, time, knowledge and hand performance were factors that had an influence on the health care workers compliance. It emerged that there was a large variation in knowledge regarding hand hygiene routines. The lack of knowledge was due to the healthcare workers approach and the extent to which they received training in hand hygiene routines. One factor that increased healthcare workers compliance was further education. Summary The study shows that there is a great need to increase healthcare personnel's compliance with hand hygiene routines around the world. The intervention is based on the fact that healthcare workers should follow the recommended hand hygiene routines such as hand hygiene washing technique, time consumption and aseptic technique. Regular training in hand hygiene proved to be an important factor for compliance.

Invasion biology examines species originated elsewhere and moved with the help of humans, and those species' impacts on biodiversity, ecosystem services, and human well-being. In a globalized world, the emergence and spread of many human infectious pathogens are quintessential biological invasion events. Some macroscopic invasive species themselves contribute to the emergence and transmission of human infectious agents. We review conceptual parallels and differences between human epidemics and biological invasions by animals and plants. Fundamental concepts in invasion biology regarding the interplay of propagule pressure, species traits, biotic interactions, eco-evolutionary experience, and ecosystem disturbances can help to explain transitions between stages of epidemic spread. As a result, many forecasting and management tools used to address epidemics could be applied to biological invasions and vice versa. Therefore, we advocate for increasing cross-fertilization between the two disciplines to improve prediction, prevention, treatment, and mitigation of invasive species and infectious disease outbreaks, including pandemics.

Biological invasions are a global consequence of an increasingly connected world and the rise in human population size. The numbers of invasive alien species – the subset of alien species that spread widely in areas where they are not native, affecting the environment or human livelihoods – are increasing. Synergies with other global changes are exacerbating current invasions and facilitating new ones, thereby escalating the extent and impacts of invaders. Invasions have complex and often immense long-term direct and indirect impacts. In many cases, such impacts become apparent or problematic only when invaders are well established and have large ranges. Invasive alien species break down biogeographic realms, affect native species richness and abundance, increase the risk of native species extinction, affect the genetic composition of native populations, change native animal behaviour, alter phylogenetic diversity across communities, and modify trophic networks. Many invasive alien species also change ecosystem functioning and the delivery of ecosystem services by altering nutrient and contaminant cycling, hydrology, habitat structure, and disturbance regimes. These biodiversity and ecosystem impacts are accelerating and will increase further in the future. Scientific evidence has identified policy strategies to reduce future invasions, but these strategies are often insufficiently implemented. For some nations, notably Australia and New Zealand, biosecurity has become a national priority. There have been long-term successes, such as eradication of rats and cats on increasingly large islands and biological control of weeds across continental areas. However, in many countries, invasions receive little attention. Improved international cooperation is crucial to reduce the impacts of invasive alien species on biodiversity, ecosystem services, and human livelihoods. Countries can strengthen their biosecurity regulations to implement and enforce more effective management

The number of alien species arriving within new regions has increased at unprecedented rates. Managing the pathways through which alien species arrive and spread is important to reduce the threat of biological invasions. Harmonising information on pathways across individual sectors and user groups is therefore critical to underpin policy and action. The European Alien Species Information Network (EASIN) has been developed to easily facilitate open access to data of alien species in Europe. The Convention on Biological Diversity (CBD) Pathway Classification framework has become a global standard for the classification of pathways. We followed a structured approach to assign pathway information within EASIN for a subset of alien species in Europe, which covered 4169 species, spanning taxonomic groups and environments. We document constraints and challenges associated with implementing the CBD Pathway Classification framework and propose potential amendments to increase clarity. This study is unique in the scope of taxonomic coverage and also in the inclusion of primary (independent introductions to Europe) and secondary (means of dispersal for species expansion within Europe, after their initial introduction) modes of introduction. In addition, we summarise the patterns of introduction pathways within this subset of alien species within the context of Europe. Based on the analyses, we confirm that the CBD Pathway Classification framework offers a robust, hierarchical system suitable for the classification of alien species introduction and spread across a wide range of taxonomic groups and environments. However, simple modifications could improve interpretation of the pathway categories ensuring consistent application across databases and information systems at local, national, regional, continental and global scales. Improving consistency would also help in the development of pathway action plans, as required by EU legislation.

Background and aims: Since its emergence in the mid-20th century, invasion biology has matured into a productive research field addressing questions of fundamental and applied importance. Not only has the number of empirical studies increased through time, but also has the number of competing, overlapping and, in some cases, contradictory hypotheses about biological invasions. To make these contradictions and redundancies explicit, and to gain insight into the field’s current theoretical structure, we developed and applied a Delphi approach to create a consensus network of 39 existing invasion hypotheses. Results: The resulting network was analysed with a link-clustering algorithm that revealed five concept clusters (resource availability, biotic interaction, propagule, trait and Darwin’s clusters) representing complementary areas in the theory of invasion biology. The network also displays hypotheses that link two or more clusters, called connecting hypotheses, which are important in determining network structure. The network indicates hypotheses that are logically linked either positively (77 connections of support) or negatively (that is, they contradict each other; 6 connections). Significance: The network visually synthesizes how invasion biology’s predominant hypotheses are conceptually related to each other, and thus, reveals an emergent structure – a conceptual map – that can serve as a navigation tool for scholars, practitioners and students, both inside and outside of the field of invasion biology, and guide the development of a more coherent foundation of theory. Additionally, the outlined approach can be more widely applied to create a conceptual map for the larger fields of ecology and biogeography.

Aim Invasive alien species (IAS) are recognized as major drivers of biodiversity loss, but few causal relationships between IAS and species declines have been documented. In this study, we compare the distribution (Belgium and Britain) and abundance (Belgium, Britain and Switzerland) of formerly common and widespread native ladybirds before and after the arrival of Harmonia axyridis, a globally rapidly expanding IAS

Electronic version excludes material for which permission has not been granted by the rights holder, A robust and consistent taxonomy underpins the use of fossil material in palaeoenvironmental research and long-term assessments of biodiversity. However, the successful identification of benthic foraminiferal species is often challenged by enigmatic morphological species boundaries, nomenclatural uncertainty and the recent advent of molecular techniques and the identification of cryptic species. This thesis sought to reconcile molecules and morphology in two scientifically important yet taxonomically challenging groups of benthic foraminifera, the genus Ammonia and the family Elphidiidae, in samples obtained widely across the NE Atlantic shelf seas. Through the production of detailed quantitative morphometric analysis of over 750 genetically sequenced specimens, coupled with assessments of their biogeographical distributions, this thesis provides the most comprehensive re-evaluation of these taxa conducted to date. The integration of these new lines of taxonomic evidence has refined interspecific boundaries, clarified key diagnostic morphological features and has unveiled the presence of a number of enigmatic species boundaries (particularly within the genus Ammonia). The results highlight that classical morphospecies concepts may not always accurately reflect the genetic diversity currently found within this region, which could have important repercussions for applied taxonomic investigations. The extensive sampling across the NE Atlantic has also enabled one of the first re-evaluations of intraspecific morphological variability, revealing that many specimens taken from distinct sampling localities can be morphologically delineated. In a first step to addressing temporal dynamics of previously unrecognised cryptic species, a time series study was conducted in the NW Scottish shelf seas, which unveiled subtle seasonal partitioning between two sympatric species of Ammonia. Finally, a new taxonomic framework was developed which bridges the current discontinuity betwee

Soil carbon storage in tropical ecosystems is important in the global carbon cycle, yet consensus is lacking on how soil organic carbon stocks are altered under anthropogenic land-use change. This thesis seeks to quantify soil carbon stocks, the associated soil carbon emissions and explores the drivers of soil respiration in managed tropical Andean lands over a 2600 m elevation gradient. It investigates: grazing and burning on high altitude montane grasslands, burning in montane forests and agriculture in premontane forests. Changes among land-uses were quantified using belowground carbon stocks, the carbon distribution among density fractions, soil carbon emissions and environmental drivers of soil respiration. Soil respiration was a good proxy of soil carbon loss in premontane pastures and montane grassland soils. The total carbon stocks on some land-uses appeared to be unaffected but the distribution of carbon within the soil had changed and even when there were no net changes in soil carbon emissions, the drivers of respiration were different. The synergistic effect of burning and grazing in montane grasslands was the most detrimental to soil carbon stocks, whereas montane forests were unaffected. In the premontane elevation, soil carbon loss was dependent on the type of agricultural practice but the succession of secondary forest allowed soil carbon to recover to similar levels measured in the mature forest. These findings highlight the fact that although land-use does not always appear to have an obvious effect on total soil carbon stocks, the loss of carbon from short-term labile pools can cause higher carbon emissions and dominate soil-atmospheric feedbacks. Furthermore, the drivers of soil respiration and the synergistic relationship between soil moisture and temperature alter under different land uses. These factors should be taken into consideration with regards to predictions of regional temperature/precipitation climate change and soil carbon management

peer-reviewed, Organically bound sulfur makes up about 90% of the total sulfur in soils, with sulfonates often the dominant fraction. Actinobacteria affiliated to the genus Rhodococcus were able to desulfonate arylsulfonates in wheat rhizospheres from the Broadbalk long-term field wheat experiment, which includes plots treated with inorganic fertilizer with and without sulfate, with farmyard manure, and unfertilized plots. Direct isolation of desulfonating rhizobacteria yielded Rhodococcus strains which grew well with a range of sulfonates, and contained the asfAB genes, known to be involved in sulfonate desulfurization by bacteria. Expression of asfA in vitro increased > 100-fold during growth of the Rhodococcus isolates with toluenesulfonate as sulfur source, compared with growth with sulfate. By contrast, the closely related Rhodococcus erythropolis and Rhodococcus opacus type strains had no desulfonating activity and did not contain asfA homologues. The overall actinobacterial community structure in wheat rhizospheres was influenced by the sulfur fertilization regime, as shown by specific denaturing gradient gel electrophoresis of PCR amplified 16S rRNA gene fragments, and asfAB clone library analysis identified nine different asfAB genotypes closely affiliated to the Rhodococcus isolates. However, asfAB-based multiplex restriction fragment length polymorphism (RFLP)/terminal-RFLP analysis of wheat rhizosphere communities revealed only slight differences between the fertilization regimes, suggesting that the desulfonating Rhodococcus community does not specifically respond to changes in sulfate supply., SUBMITTED, peer-reviewed

peer-reviewed, Forefields of receding glaciers are unique and sensitive environments representing natural soil chronosequences where sulfate availability is assumed to be a limiting factor. Bacterial mineralization of organo-sulfur is an important sulfate-providing process in soils. We analyzed the diversity of sulfonate desulfurizing (desulfonating) bacteria in the Damma glacier forefield on the basis of the key gene asfA by terminal restriction fragment length polymorphism (T-RFLP) and clone libraries. The community structure and sequence diversity of desulfonating bacteria differed significantly between forefield soils deglaciated in the 1990s and the 1950s. Soil age had a strong effect on the desulfonating rhizosphere communities of Agrostis rupestris, but only little impact on the ones from Leucanthemopsis alpina. AsfA affiliated to Polaromonas sp. was predominantly found in the more recent ice-free soils and the corresponding rhizospheres of A. rupestris while a group of unidentified sequences was found to be dominating the matured soils and the corresponding rhizospheres of A. rupestris. The desulfonating bacterial diversity was not affected by varying levels of sulfate concentrations. The level of asfA diversity in recently deglaciated soils suggests that desulfonating bacteria are a critical factor in sulfur cycling with defined groups dominating at different stages of soil formation., SUBMITTED

The Eden Estuary is a small, coastal inlet situated in Fife between the Tay and Forth Estuaries on the east coast of Scotland. A multidisciplinary case study of the estuary was conducted over a three year period observing the dynamic responses of biotic and abiotic behaviour to long term patterns of climate variability. Historical Trend Analysis (HTA) was combined with autocorrelation and spectral density analysis to identify trends, patterns and periodicity in natural cycles. River flow and wind direction data were cross-correlated with the North Atlantic Oscillation Index (NAOI) to link local responses to patterns of northern hemisphere circulation, and with Wolfe Sunspot Numbers representing variable solar activity as a potential driving mechanism for climate driven change. Assessment of the current state of ‘estuary health’ used a proxy analysis of ecosystem function, combining Bray-Curtis similarity nMDS of macrofaunal community diversity with species functional traits. The observed estuary responses were subsequently projected onto the forecasted climate change scenarios reported by the IPCCAR4, UKCIP09 and to modelled projections of solar activity to propose future trajectories of change for the estuary. Autocorrelation analysis of river flow and wind direction data identified significant (95%) correlations corresponding to solar, lunar, planetary and volcanic events. Spectral density analysis similarly identified significant (>95%) frequencies corresponding to known periods of solar activity, lunar cycles and Bruckner climatic cycles. Formal cross -correlation revealed significant (95%) relationships between both river flow and wind data with the NAOI, and using a longer times series, between river Thames annual flow and Wolfe sunspot numbers; correlating solar maximums with high flow. Periods consistent to Schwabe and Hale solar cycles were evident in the wind and river data however the NAOI only displayed Hale periodicity, inferring the river and wind data

Dispersal costs can be classified into energetic, time, risk and opportunity costs and may be levied directly or deferred during departure, transfer and settlement. They may equally be incurred during life stages before the actual dispersal event through investments in special morphologies. Because costs will eventually determine the performance of dispersing individuals and the evolution of dispersal, we here provide an extensive review on the different cost types that occur during dispersal in a wide array of organisms, ranging from micro-organisms to plants, invertebrates and vertebrates. In general, costs of transfer have been more widely documented in actively dispersing organisms, in contrast to a greater focus on costs during departure and settlement in plants and animals with a passive transfer phase. Costs related to the development of specific dispersal attributes appear to be much more prominent than previously accepted. Because costs induce trade-offs, they give rise to covariation between dispersal and other life-history traits at different scales of organismal organisation. The consequences of (i) the presence and magnitude of different costs during different phases of the dispersal process, and (ii) their internal organisation through covariation with other life-history traits, are synthesised with respect to potential consequences for species conservation and the need for development of a new generation of spatial simulation models. © 2011 The Authors. Biological Reviews © 2011 Cambridge Philosophical Society.

Red deer have been subjected to anthropogenic interference for many centuries. Most populations are managed according to hunting schedules, some have been kept long-term in enclosures and other populations have been restocked with foreign deer. The red deer in the Brittany region of north-western France only occupy the largest forests in the region, reaching quite high densities in restricted areas. Here, we aimed to assess the extent of the genetic variability of the populations in four forest fragments and investigate their population genetic structure. We show that, despite relatively large expected heterozygosity values, these geographically isolated populations are genetically impoverished relative to individuals from large continuous forests in other parts of Western Europe. We provide evidence for population genetic structure with large genetic differentiation between geographically close populations, suggesting the absence of effective exchange between the forests. Using samples from the most likely source population, we show that at least two populations were non-indigenous. In order to limit further loss of genetic diversity, it should be a management objective to reduce isolation of the different forests, rather than further increase it by fences and hunting practices that could limit free movement of red deer.

This paper reports the first field deployment and testing of a directional passive air sampler (DPAS) which can be used to cost-effectively identify and quantify air pollutants and their sources. The sampler was used for ambient nitrogen dioxide (NO2) over ten weeks from twelve directional sectors in an urban setting, and tested alongside an automatic chemiluminescent monitor. The time-integrated passive directional results were compared with the directional analysis of the active monitoring results using wind data recorded at a weather station. The DPAS discriminated air pollutant signals directionally. The attempts to derive quantitative data yielded reasonable results-usually within a factor of two of those obtained by the chemiluminescent analyser. Ultimately, whether DPAS approaches are adopted will depend on their reliability, added value and cost. It is argued that added value was obtained here from the DPAS approach applied in a routine monitoring situation, by identifying source sectors. Both the capital and running costs of DPAS were <5% of those for the automatic monitor. It is envisaged that different sorbents or sampling media will enable this rotatable DPAS design to be used for other airborne pollutants. In summary, there are reasons to be optimistic that directional passive air sampling, together with careful interpretation of results, will be of added value to air quality practitioners in future.

Evolutionary transitions between hermaphroditism and dioecy have occurred numerous times in the land plants. We briefly review the factors thought to be responsible for these transitions, and we provide a synthesis of what has been learned from recent studies of the annual herb Mercurialis annua, in which dioecy (males and females), monoecy (functional hermaphrodites), and androdioecy (males and hermaphrodites) occur in different parts of its geographic range. Previous research on M. annua has revealed the importance of genome duplication and hybridization in the origin of much of the observed variation. Here we show, however, that spatial transitions in the sexual system also occur within the same ploidy level. In particular, we present an analysis, using flow cytometry data, of ploidy variation across a previously unstudied transition between hermaphroditism and androdioecy, in which we find that the sexual‐system transition is uncoupled from the shift in ploidy levels. We review recent research that shows that such transitions between sexual systems in M. annua are consistent with differential selection at the regional level for reproductive assurance during colonization. We also present new experimental data that highlight both the importance of the resource status of plants and that of their local mating context in regulating gender strategies and sex ratios. The studies reviewed and the new results presented emphasize the role that shifts in the ecological and genetic context of plant populations may play in causing transitions between sexual systems.

The aim of this thesis is to establish the evolutionary history of relict talus accumulations in the Scottish Highlands through study of their distribution, morphology, structure and sedimentology, and through dating and pollen analysis of buried soil horizons. Analyses of talus morphology demonstrates that though the investigated slopes comprise a basal concavity and upper straight slope, features hitherto interpreted as characteristic of unmodified rockfall accumulations, there is considerable variability in upper slope gradient. Surface relief indicates widespread reworking by slope failure, gullying and debris flows. Sections through gully-side exposures exhibit up to 3.5 m of stacked debris flow deposits, wash layers and buried soils overlying rockfall deposits, indicating a complex history of sediment reworking. Sedimentological analyses indicate that 27-30% of the talus sediments at one site (Trottemish) comprise fine (< 2 mm) particles representing granular weathering of the rockwall and syndepositional accumulation of both fine and coarse debris. The volume of talus on Trottemish implies an average rockwall retreat rate of c. 0.3 mm yr-1 since deglaciation, of which 0.08-0.09 mm yr-1 reflects granular weathering rather than rockfall. Failure and reworking of talus is inferred to reflect reduced infiltration rates (and high porewater pressures during rainstorms) caused by progressive accumulation of fines. Radiocarbon dating of buried soils indicates that reworking commenced prior to c. 6 cal ka BP, and has been intermittently active during the Holocene. Pollen analyses and charcoal concentration counts provide no evidence for accelerated reworking as a result of anthropogenic interference with vegetation cover, but the timing of reworking events provides support for enhanced activity associated with climatic deterioration after c. 2.7-2.3 cal ka BP. The characteristics of the investigated slopes show that models that treat talus as a free-draining accumulat

Two areas of well exposed mid-crustal structures in the axial zone of the Pan-African Damaran orogenic belt show that basement has formed domes which have amoeboid forms on the scale of tens of km with steep sided overturned non-planar, non- cylindrical geometry. These are surrounded by open to tight synclinal cover envelopes that converge at depressions between the domes. The domes are found in association with a strong regional WSW moderately plunging lineation. Strain analysis demonstrates that domes have formed in a moderately plunging constrictional field. Structural features which normally indicate polyphase evolution such as mesoscale fold interference patterns are rare and inconsistent. Regional structural form, described morphogically by cylindrical domains, is defined by one fabric S0/S1. Secondary fabric trajectories and mesoscale fold oreintations are controlled by domain scale structure and not regional deformation trends. Dome formation is thus interpreted as being the result of a simultaneous flow and buckling episode within the middle crust. Deformation was extremely ductile. P-T estimates from thermobarometry with Grt-Bt, Grt-Crd-Bt-Sil assemblages indicate that peak metamorphic conditions during deformation were approximately 3.5kbar and 650°C in the cover envelopes and 7kbar 791°C in the basement domes, approaching the amphibolite-granulite transition. Interactive transpressional collision between three cratons during the latest Neoproterozoic-early Paleozoic: namely the Kalahari, Congo and Rio de la Plata caused constriction and extrusion in the Central Zone. The metamorphic gap between basement and cover occurred when the distance between regional isotherms was reduced by thinning at the basement-cover interface. Higher temperatures where preserved at dome cores. At the cooler margins of the Damara Belt thrust tectonics occurred, albeit obliquely with sinistral transpression. After dome formation granite intruded many domal structures.