Spatially explicit estimates of N2O emissions from croplands suggest climate mitigation opportunities from improved fertilizer management

Acknowledgements We are grateful to Stefan Seibert for advice on reconciling the Monfreda datasets of yield and area and the Portmann dataset for irrigated area of rice. We thank Deepak Ray and Jonathan Foley for helpful comments. Research support to J.G. K.C., N.M, and P.W. was primarily provided by the Gordon and Betty Moore Foundation and the Institute on Environment, with additional support from NSF Hydrologic Sciences grant 1521210 for N.M., and additional support to J.G. and P.W. whose efforts contribute to Belmont Forum/FACCE-JPI funded DEVIL project (NE/M021327/1). M.H. was supported by CSIRO's OCE Science Leaders Programme and the Agriculture Flagship. Funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection

SELECTOR is a software package for studying the evolution of multiallelic genes under balancing or positive selection while simulating complex evolutionary scenarios that integrate demographic growth and migration in a spatially explicit population framework. Parameters can be varied both in space and time to account for geographical, environmental, and cultural heterogeneity. SELECTOR can be used within an approximate Bayesian computation estimation framework. We first describe the principles of SELECTOR and validate the algorithms by comparing its outputs for simple models with theoretical expectations. Then, we show how it can be used to investigate genetic differentiation of loci under balancing selection in interconnected demes with spatially heterogeneous gene flow. We identify situations in which balancing selection reduces genetic differentiation between population groups compared with neutrality and explain conflicting outcomes observed for human leukocyte antigen loci. These results and three previously published applications demonstrate that SELECTOR is efficient and robust for building insight into human settlement history and evolution.

Compositional Divergence and Convergence in Local Communities and Spatially Structured Landscapes

Community structure depends on both deterministic and stochastic processes. However, patterns of community dissimilarity (e.g. difference in species composition) are difficult to interpret in terms of the relative roles of these processes. Local communities can be more dissimilar (divergence) than, less dissimilar (convergence) than, or as dissimilar as a hypothetical control based on either null or neutral models. However, several mechanisms may result in the same pattern, or act concurrently to generate a pattern, and much research has recently been focusing on unravelling these mechanisms and their relative contributions. Using a simulation approach, we addressed the effect of a complex but realistic spatial structure in the distribution of the niche axis and we analysed patterns of species co-occurrence and beta diversity as measured by dissimilarity indices (e.g. Jaccard index) using either expectations under a null model or neutral dynamics (i.e., based on switching off the niche effect). The strength of niche processes, dispersal, and environmental noise strongly interacted so that niche-driven dynamics may result in local communities that either diverge or converge depending on the combination of these factors. Thus, a fundamental result is that, in real systems, interacting processes of community assembly can be disentangled only by measuring traits such as niche breadth and dispersal. The ability to detect the signal of the niche was also dependent on the spatial resolution of the sampling strategy, which must account for the multiple scale spatial patterns in the niche axis. Notably, some of the patterns we observed correspond to patterns of community dissimilarities previously observed in the field and suggest mechanistic explanations for them or the data required to solve them. Our framework offers a synthesis of the patterns of community dissimilarity produced by the interaction of deterministic and stochastic determinants of community assembly in a spatially explicit and complex context.

A geographical analysis of the role of water supply and sanitation in the risk of helminth infections of children in West Africa

Background We investigated the geographical variation of water supply and sanitation indicators (WS&S) and their role to the risk of schistosomiasis and hookworm infection in school age children in West Africa. The aim was to predict large-scale geographical variation in WS&S, quantify the attributable risk of S. haematobium, S. mansoni and hookworm infections due to WS&S and identify communities where sustainable transmission control could be targeted across the region. Methods National cross-sectional household-based demographic health surveys were conducted in 24,542 households in Burkina Faso, Ghana and Mali, in 2003–2006. We generated spatially-explicit predictions of areas without piped water, toilet facilities and finished floors in West Africa, adjusting for household covariates. Using recently published helminth prevalence data we developed Bayesian geostatistical models (MGB) of S. haematobium, S. mansoni and hookworm infection in West Africa including environmental and the mapped outputs for WS&S. Using these models we estimated the effect of WS&S on parasite risk, quantified their attributable fraction of infection, and mapped the risk of infection in West Africa. Findings Our maps show that most areas in West Africa are very poorly served by water supply except in major urban centers. There is a better geographical coverage for toilet availability and improved household flooring. We estimated smaller attributable risks for water supply in S. mansoni (47%) compared to S. haematobium (71%), and 5% of hookworm cases could be averted by improving sanitation. Greater levels of inadequate sanitation increased the risk of schistosomiasis, and increased levels of unsafe water supply increased the risk of hookworm. The role of floor type for S. haematobium infection (21%) was comparable to that of S. mansoni (16%), but was significantly higher for hookworm infection (86%). S. haematobium and hookworm maps accounting for WS&S show small clusters of maximal prevalence areas in areas bordering Burkina Faso and Mali smaller. The map of S. mansoni shows that this parasite is much more wide spread across the north of the Niger River basin than previously predicted. Interpretation Our maps identify areas where the Millennium Development Goal for water and sanitation is lagging behind. Our results show that WS&S are important contributors to the burden of major helminth infections of children in West Africa. Including information about WS&S as well as the “traditional” environmental risk factors in spatial models of helminth risk yielded a substantial gain both in model fit and at explaining the proportion of spatial variance in helminth risk. Mapping the distribution of infection risk adjusted for WS&S allowed the identification of communities in West Africa where integrative preventive chemotherapy and engineering interventions will yield the greatest public health benefits.

A regional interpretation of rules and good practice for greenhouse accounting : Northern Australian savanna systems

Land-use change, particularly clearing of forests for agriculture, has contributed significantly to the observed rise in atmospheric carbon dioxide concentration. Concern about the impacts on climate has led to efforts to monitor and curtail the rapid increase in concentrations of carbon dioxide and other greenhouse gases in the atmosphere. Internationally, much of the current focus is on the Kyoto Protocol to the United Nations Framework Convention on Climate Change (UNFCCC). Although electing to not ratify the Protocol, Australia, as a party to the UNFCCC, reports on national greenhouse gas emissions, trends in emissions and abatement measures. In this paper we review the complex accounting rules for human activities affecting greenhouse gas fluxes in the terrestrial biosphere and explore implications and potential opportunities for managing carbon in the savanna ecosystems of northern Australia. Savannas in Australia are managed for grazing as well as for cultural and environmental values against a background of extreme climate variability and disturbance, notably fire. Methane from livestock and non-CO2 emissions from burning are important components of the total greenhouse gas emissions associated with management of savannas. International developments in carbon accounting for the terrestrial biosphere bring a requirement for better attribution of change in carbon stocks and more detailed and spatially explicit data on such characteristics of savanna ecosystems as fire regimes, production and type of fuel for burning, drivers of woody encroachment, rates of woody regrowth, stocking rates and grazing impacts. The benefits of improved biophysical information and of understanding the impacts on ecosystem function of natural factors and management options will extend beyond greenhouse accounting to better land management for multiple objectives.

Geographical and morphological variation within and between colour phases in Coris julis (L. 1758), a protogynous marine fish

The possible differences between sexes in patterns of morphological variation in geographical space have been explored only in gonochorist freshwater species. We explored patterns of body shape variation in geographical space in a marine sequential hermaphrodite species, Coris julis (L. 1758), analyzing variation both within and between colour phases, through the use of geometric morphometrics and spatially-explicit statistical analyses. We also tested for the association of body shape with two environmental variables: temperature and chlorophyll a concentration, as obtained from time-series of satellite-derived data. Both colour phases showed a significant morphological variation in geographical space and patterns of variation divergent between phases. Although the morphological variation was qualitatively similar, individuals in the initial colour phase showed a more marked variation than individuals in the terminal phase. Body shape showed a weak but significant correlation with environmental variables, which was more pronounced in primary specimens.

Modelling predicts positive and negative interactions between three Australian tropical tree species in monoculture and binary mixture

Computer modelling promises to be an important tool for analysing and predicting interactions between trees within mixed species forest plantations. This study explored the use of an individual-based mechanistic model as a predictive tool for designing mixed species plantations of Australian tropical trees. The `spatially explicit individually based-forest simulator' (SeXI-FS) modelling system was used to describe the spatial interaction of individual tree crowns within a binary mixed-species experiment. The three-dimensional model was developed and verified with field data from three forest tree species grown in tropical Australia. The model predicted the interactions within monocultures and binary mixtures of Flindersia brayleyana, Eucalyptus pellita and Elaeocarpus grandis, accounting for an average of 42% of the growth variation exhibited by species in different treatments. The model requires only structural dimensions and shade tolerance as species parameters. By modelling interactions in existing tree mixtures, the model predicted both increases and reductions in the growth of mixtures (up to +/-50% of stem volume at 7 years) compared to monocultures. This modelling approach may be useful for designing mixed tree plantations.

Predicting dispersal and recruitment of Miconia calvescens (Melastomataceae) in Australian tropical rainforests

Miconia calvescens (Melastomataceae) is a serious invader in the tropical Pacific, including the Hawaiian and Tahitian Islands, and currently poses a major threat to native biodiversity in the Wet Tropics of Australia. The species is fleshy-fruited, small-seeded and shade tolerant, and thus has the potential to be dispersed widely and recruit in relatively intact rainforest habitats, displacing native species. Understanding and predicting the rate of spread is critical for the design and implementation of effective management actions. We used an individual-based model incorporating a dispersal function derived from dispersal curves for similar berry-fruited native species, and life-history parameters of fecundity and mortality to predict the spatial structure of a Miconia population after a 30 year time period. We compared the modelled population spatial structure to that of an actual infestation in the rainforests of north Queensland. Our goal was to assess how well the model predicts actual dispersion and to identify potential barriers and conduits to seed movement and seedling establishment. The model overpredicts overall population size and the spatial extent of the actual infestation, predicting individuals to occur at a maximum 1,750 m from the source compared with the maximum distance of any detected individual in the actual infestation of 1,191 m. We identify several characteristic features of managed invasive populations that make comparisons between modelled outcomes and actual infestations difficult. Our results suggest that the model’s ability to predict both spatial structure and spread of the population will be improved by incorporating a spatially explicit element, with dispersal and recruitment probabilities that reflect the relative suitability of different parts of the landscape for these processes.

New efforts at biological control of Mikania micrantha H.B.K. (Asteraceae) in Papua New Guinea and Fiji.

New efforts at biological control of Miconia calvescens (Melastomataceae) is a serious invader in the tropical Pacific, including the Hawaiian and Tahitian Islands, and currently poses a major threat to native biodiversity in the Wet Tropics of Australia. The species is fleshy-fruited, small-seeded and shade tolerant, and thus has the potential to be dispersed widely and recruit in relatively intact rainforest habitats, displacing native species. Understanding and predicting the rate of spread is critical for the design and implementation of effective management actions. We used an individual-based model incorporating a dispersal function derived from dispersal curves for similar berry-fruited native species, and life-history parameters of fecundity and mortality to predict the spatial structure of a Miconia population after a 30 year time period. We compared the modelled population spatial structure to that of an actual infestation in the rainforests of north Queensland. Our goal was to assess how well the model predicts actual dispersion and to identify potential barriers and conduits to seed movement and seedling establishment. The model overpredicts overall population size and the spatial extent of the actual infestation, predicting individuals to occur at a maximum 1,750 m from the source compared with the maximum distance of any detected individual in the actual infestation of 1,191 m. We identify several characteristic features of managed invasive populations that make comparisons between modelled outcomes and actual infestations difficult. Our results suggest that the model’s ability to predict both spatial structure and spread of the population will be improved by incorporating a spatially explicit element, with dispersal and recruitment probabilities that reflect the relative suitability of different parts of the landscape for these processes. Mikania micrantha H.B.K. (Asteraceae) in Papua New Guinea and Fiji.

Surveillance protocols for management of invasive plants: modelling Chilean needle grass (Nassella neesiana) in Australia

Aim: To develop a surveillance support model that enables prediction of areas susceptible to invasion, comparative analysis of surveillance methods and intensity and assessment of eradication feasibility. To apply the model to identify surveillance protocols for generalized invasion scenarios and for evaluating surveillance and control for a context-specific plant invasion. Location: Australia. Methods: We integrate a spatially explicit simulation model, including plant demography and dispersal vectors, within a Geographical Information System. We use the model to identify effective surveillance protocols using simulations of generalized plant life-forms spreading via different dispersal mechanisms in real landscapes. We then parameterize the surveillance support model for Chilean needle grass [CNG; Nassella neesiana (Trin. & Rupr.) Barkworth], a highly invasive tussock grass, which is an eradication target in south-eastern Queensland, Australia. Results: General surveillance protocols that can guide rapid response surveillance were identified; suitable habitat that is susceptible to invasion through particular dispersal syndromes should be targeted for surveillance using an adaptive seek-and-destroy method. The search radius of the adaptive method should be based on maximum expected dispersal distances. Protocols were used to define a surveillance strategy for CNG, but simulations indicated that despite effective and targeted surveillance, eradication is implausible at current intensities. Main conclusions: Several important surveillance protocols emerged and simulations indicated that effectiveness can be increased if they are followed in rapid response surveillance. If sufficient data are available, the surveillance support model should be parameterized to target areas susceptible to invasion and determine whether surveillance is effective and eradication is feasible. We discovered that for CNG, regardless of a carefully designed surveillance strategy, eradication is implausible at current intensities of surveillance and control and these efforts should be doubled if they are to be successful. This is crucial information in the face of environmentally and economically damaging invasive species and large, expensive and potentially ineffective control programmes.

Management of plant invasions mediated by frugivore interactions

1. Some of the most damaging invasive plants are dispersed by frugivores and this is an area of emerging importance in weed management. It highlights the need for practical information on how frugivores affect weed population dynamics and spread, how frugivore populations are affected by weeds and what management recommendations are available. 2. Fruit traits influence frugivore choice. Fruit size, the presence of an inedible peel, defensive chemistry, crop size and phenology may all be useful traits for consideration in screening and eradication programmes. By considering the effect of these traits on the probability, quality and quantity of seed dispersal, it may be possible to rank invasive species by their desirability to frugivores. Fruit traits can also be manipulated with biocontrol agents. 3. Functional groups of frugivores can be assembled according to broad species groupings, and further refined according to size, gape size, pre- and post-ingestion processing techniques and movement patterns, to predict dispersal and establishment patterns for plant introductions. 4. Landscape fragmentation can increase frugivore dispersal of invasives, as many invasive plants and dispersers readily use disturbed matrix environments and fragment edges. Dispersal to particular landscape features, such as perches and edges, can be manipulated to function as seed sinks if control measures are concentrated in these areas. 5. Where invasive plants comprise part of the diet of native frugivores, there may be a conservation conflict between control of the invasive and maintaining populations of the native frugivore, especially where other threats such as habitat destruction have reduced populations of native fruit species. 6. Synthesis and applications. Development of functional groups of frugivore-dispersed invasive plants and dispersers will enable us to develop predictions for novel dispersal interactions at both population and community scales. Increasingly sophisticated mechanistic seed dispersal models combined with spatially explicit simulations show much promise for providing weed managers with the information they need to develop strategies for surveying, eradicating and managing plant invasions. Possible conservation conflicts mean that understanding the nature of the invasive plant-frugivore interaction is essential for determining appropriate management.

Spatial subdivision among assemblages of Spanish mackerel, Scomberomorus commerson (Pisces: Scombridae) across northern Australia: implications for fisheries management

Aim: This study investigated the use of stable δ13C and δ18O isotopes in the sagittal otolith carbonate of narrow-barred Spanish mackerel, Scomberomorus commerson, as indicators of population structure across Australia. Location: Samples were collected from 25 locations extending from the lower west coast of Western Australia (30°), across northern Australian waters, and to the east coast of Australia (18°) covering a coastline length of approximately 9500 km, including samples from Indonesia. Methods: The stable δ13C and δ18O isotopes in the sagittal otolith carbonate of S. commerson were analysed using standard mass spectrometric techniques. The isotope ratios across northern Australian subregions were subjected to an agglomerative hierarchical cluster analysis to define subregions. Isotope ratios within each of the subregions were compared to assess population structure across Australia. Results: Cluster analysis separated samples into four subregions: central Western Australia, north Western Australia, northern Australia and the Gulf of Carpentaria and eastern Australia. Isotope signatures for fish from a number of sampling sites from across Australia and Indonesia were significantly different, indicating population separation. No significant differences were found in otolith isotope ratios between sampling times (no temporal variation). Main conclusions: Significant differences in the isotopic signatures of S. commerson demonstrate that there is unlikely to be any substantial movement of fish among these spatially discrete adult assemblages. The lack of temporal variation among otolith isotope ratios indicates that S. commerson populations do not undergo longshore spatial shifts in distribution during their life history. The temporal persistence of spatially explicit stable isotopic signatures indicates that, at these spatial scales, the population units sampled comprise functionally distinct management units or separate ‘stocks’ for many of the purposes of fisheries management. The spatial subdivision evident among populations of S. commerson across northern and western Australia indicates that it may be advantageous to consider S. commerson population dynamics and fisheries management from a metapopulation perspective (at least at the regional level).

Herbicide resistance modelling: Past, present and future

Computer simulation modelling is an essential aid in building an integrated understanding of how different factors interact to affect the evolutionary and population dynamics of herbicide resistance, and thus in helping to predict and manage how agricultural systems will be affected. In this review, we first discuss why computer simulation modelling is such an important tool and framework for dealing with herbicide resistance. We then explain what questions related to herbicide resistance have been addressed to date using simulation modelling, and discuss the modelling approaches that have been used, focusing first on the earlier, more general approaches, and then on some newer, more innovative approaches. We then consider how these approaches could be further developed in the future, by drawing on modelling techniques that are already employed in other areas, such as individual-based and spatially explicit modelling approaches, as well as the possibility of better representing genetics, competition and economics, and finally the questions and issues of importance to herbicide resistance research and management that could be addressed using these new approaches are discussed. We conclude that it is necessary to proceed with caution when increasing the complexity of models by adding new details, but, with appropriate care, more detailed models will make it possible to integrate more current knowledge in order better to understand, predict and ultimately manage the evolution of herbicide resistance. © 2014 Society of Chemical Industry.

Dynamics of Finnish starlings in 1951-2005 : from monitoring to population modelling

Farmland bird species have been declining in Europe. Many declines have coincided with general intensification of farming practices. In Finland, replacement of mixed farming, including rotational pastures, with specialized cultivation has been one of the most drastic changes from the 1960s to the 1990s. This kind of habitat deterioration limits the persistence of populations, as has been previously indicated from local populations. Integrated population monitoring, which gathers species-specific information of population size and demography, can be used to assess the response of a population to environment changes also at a large spatial scale. I targeted my analysis at the Finnish starling (Sturnus vulgaris). Starlings are common breeders in farmland habitats, but severe declines of local populations have been reported from Finland in the 1970s and 1980s and later from other parts of Europe. Habitat deterioration (replacement of pasture and grassland habitats with specialized cultivation areas) limits reproductive success of the species. I analysed regional population data in order to exemplify the importance of agricultural change to bird population dynamics. I used nestling ringing and nest-card data from 1951 to 2005 in order to quantify population trends and per capita reproductive success within several geographical regions (south/north and west/east aspects). I used matrix modelling, acknowledging age-specific survival and fecundity parameters and density-dependence, to model population dynamics. Finnish starlings declined by 80% from the end of the 1960s up to the end of the 1980s. The observed patterns and the model indicated that the population decline was due to the decline of the carrying capacity of farmland habitats. The decline was most severe in north Finland where populations largely become extinct. However, habitat deterioration was most severe in the southern breeding areas. The deteriorations in habitat quality decreased reproduction, which finally caused the decline. I suggest that poorly-productive northern populations have been partly maintained by immigration from the highly-productive southern populations. As the southern populations declined, ceasing emigration caused the population extinction in north. This phenomenon was explained with source sink population dynamics, which I structured and verified on the basis of a spatially explicit simulation model. I found that southern Finnish starling population exhibits ten-year cyclic regularity, a phenomenon that can be explained with delayed density-dependence in reproduction.

Spatial ecology of food webs : herbivore-parasitoid communities on the pedunculate oak

Herbivorous insects, their host plants and natural enemies form the largest and most species-rich communities on earth. But what forces structure such communities? Do they represent random collections of species, or are they assembled by given rules? To address these questions, food webs offer excellent tools. As a result of their versatile information content, such webs have become the focus of intensive research over the last few decades. In this thesis, I study herbivore-parasitoid food webs from a new perspective: I construct multiple, quantitative food webs in a spatially explicit setting, at two different scales. Focusing on food webs consisting of specialist herbivores and their natural enemies on the pedunculate oak, Quercus robur, I examine consistency in food web structure across space and time, and how landscape context affects this structure. As an important methodological development, I use DNA barcoding to resolve potential cryptic species in the food webs, and to examine their effect on food web structure. I find that DNA barcoding changes our perception of species identity for as many as a third of the individuals, by reducing misidentifications and by resolving several cryptic species. In terms of the variation detected in food web structure, I find surprising consistency in both space and time. From a spatial perspective, landscape context leaves no detectable imprint on food web structure, while species richness declines significantly with decreasing connectivity. From a temporal perspective, food web structure remains predictable from year to year, despite considerable species turnover in local communities. The rate of such turnover varies between guilds and species within guilds. The factors best explaining these observations are abundant and common species, which have a quantitatively dominant imprint on overall structure, and suffer the lowest turnover. By contrast, rare species with little impact on food web structure exhibit the highest turnover rates. These patterns reveal important limitations of modern metrics of quantitative food web structure. While they accurately describe the overall topology of the web and its most significant interactions, they are disproportionately affected by species with given traits, and insensitive to the specific identity of species. As rare species have been shown to be important for food web stability, metrics depicting quantitative food web structure should then not be used as the sole descriptors of communities in a changing world. To detect and resolve the versatile imprint of global environmental change, one should rather use these metrics as one tool among several.