Development of a Novel Rabies Simulation Model for Application in a Non-endemic Environment.

Domestic dog rabies is an endemic disease in large parts of the developing world and also epidemic in previously free regions. For example, it continues to spread in eastern Indonesia and currently threatens adjacent rabies-free regions with high densities of free-roaming dogs, including remote northern Australia. Mathematical and simulation disease models are useful tools to provide insights on the most effective control strategies and to inform policy decisions. Existing rabies models typically focus on long-term control programs in endemic countries. However, simulation models describing the dog rabies incursion scenario in regions where rabies is still exotic are lacking. We here describe such a stochastic, spatially explicit rabies simulation model that is based on individual dog information collected in two remote regions in northern Australia. Illustrative simulations produced plausible results with epidemic characteristics expected for rabies outbreaks in disease free regions (mean R0 1.7, epidemic peak 97 days post-incursion, vaccination as the most effective response strategy). Systematic sensitivity analysis identified that model outcomes were most sensitive to seven of the 30 model parameters tested. This model is suitable for exploring rabies spread and control before an incursion in populations of largely free-roaming dogs that live close together with their owners. It can be used for ad-hoc contingency or response planning prior to and shortly after incursion of dog rabies in previously free regions. One challenge that remains is model parameterisation, particularly how dogs' roaming and contacts and biting behaviours change following a rabies incursion in a previously rabies free population.

A Method for Detecting Population Genetic Structure in Diverse, High Gene-Flow Species

Detecting small amounts of genetic subdivision across geographic space remains a persistent challenge. Often a failure to detect genetic structure is mistaken for evidence of panmixia, when more powerful statistical tests may uncover evidence for subtle geographic differentiation. Such slight subdivision can be demographically and evolutionarily important as well as being critical for management decisions. We introduce here a method, called spatial analysis of shared alleles (SAShA), that detects geographically restricted alleles by comparing the spatial arrangement of allelic co-occurrences with the expectation under panmixia. The approach is allele-based and spatially explicit, eliminating the loss of statistical power that can occur with user-defined populations and statistical averaging within populations. Using simulated data sets generated under a stepping-stone model of gene flow, we show that this method outperforms spatial autocorrelation (SA) and UST under common real-world conditions: at relatively high migration rates when diversity is moderate or high, especially when sampling is poor. We then use this method to show clear differences in the genetic patterns of 2 nearshore Pacific mollusks, Tegula funebralis (5 Chlorostoma funebralis) and Katharina tunicata, whose overall patterns of within-species differentiation are similar according to traditional population genetics analyses. SAShA meaningfully complements UST/FST, SA, and other existing geographic genetic analyses and is especially appropriate for evaluating species with high gene flow and subtle genetic differentiation.

Geographic information system-based decision support for soil conservation planning in Tajikistan

Soil erosion on sloping agricultural land poses a serious problem for the environment, as well as for production. In areas with highly erodible soils, such as those in loess zones, application of soil and water conservation measures is crucial to sustain agricultural yields and to prevent or reduce land degradation. The present study, carried out in Faizabad, Tajikistan, was designed to evaluate the potential of local conservation measures on cropland using a spatial modelling approach to provide decision-making support for the planning of spatially explicit sustainable land use. A sampling design to support comparative analysis between well-conserved units and other field units was established in order to estimate factors that determine water erosion, according to the Revised Universal Soil Loss Equation (RUSLE). Such factor-based approaches allow ready application using a geographic information system (GIS) and facilitate straightforward scenario modelling in areas with limited data resources. The study showed first that assessment of erosion and conservation in an area with inhomogeneous vegetation cover requires the integration of plot-based cover. Plot-based vegetation cover can be effectively derived from high-resolution satellite imagery, providing a useful basis for plot-wise conservation planning. Furthermore, thorough field assessments showed that 25.7% of current total cropland is covered by conservation measures (terracing, agroforestry and perennial herbaceous fodder). Assessment of the effectiveness of these local measures, combined with the RUSLE calculations, revealed that current average soil loss could be reduced through low-cost measures such as contouring (by 11%), fodder plants (by 16%), and drainage ditches (by 53%). More expensive measures such as terracing and agroforestry can reduce erosion by as much as 63% (for agroforestry) and 93% (for agroforestry combined with terracing). Indeed, scenario runs for different levels of tolerable erosion rates showed that more cost-intensive and technologically advanced measures would lead to greater reduction of soil loss. However, given economic conditions in Tajikistan, it seems advisable to support the spread of low-cost and labourextensive measures.

Dynamics of Shifting Cultivation Landscapes in Northern Lao PDR Between 2000 and 2009 Based on an Analysis of MODIS Time Series and Landsat Images

The rotational nature of shifting cultivation poses several challenges to its detection by remote sensing. Consequently, there is a lack of spatial data on the dynamics of shifting cultivation landscapes on a regional, i.e. sub-national, or national level. We present an approach based on a time series of Landsat and MODIS data and landscape metrics to delineate the dynamics of shifting cultivation landscapes. Our results reveal that shifting cultivation is a land use system still widely and dynamically utilized in northern Laos. While there is an overall reduction in the areas dominated by shifting cultivation, some regions also show an expansion. A review of relevant reports and articles indicates that policies tend to lead to a reduction while market forces can result in both expansion and reduction. For a better understanding of the different factors affecting shifting cultivation landscapes in Laos, further research should focus on spatially explicit analyses.

The Importance of Place Names in the Search for Ecosystem-Like Concepts in Indigenous Societies: An Example from the Bolivian Andes

This paper aims to deepen the search for ecosystem-like concepts in indigenous societies by highlighting the importance of place names used by Quechua indigenous farmers from the central Bolivian Andes. Villagers from two communities in the Tunari Mountain Range were asked to list, describe, map and categorize the places they knew on their community’s territory. Results show that place names capture spatially explicit units which integrate biotic and abiotic nature and humans, and that there is an emphasis on topographic terms, highlighting the importance of geodiversity. Farmers’ perspectives differ from the classical view of ecosystems because they ‘humanize’ places, considering them as living beings with agency. Consequently, they do not make a distinction between natural and cultural heritage. Their perspective of the environment is that of a personalized, dynamic relationship with the elements of the natural world that are perceived as living entities. A practical implication of the findings for sustainable development is that since places names make the links between people and the elements of the landscape, toponymy is a tool for ecosystem management rooted in indigenous knowledge. Because place names refer to holistic units linked with people’s experience and spatially explicit, they can be used as an entry point to implement an intercultural dialogue for more sustainable land management.

From Statistical Data to Spatial Knowledge - informing decision making in Vietnam

Vietnam has developed rapidly over the past 15 years. However, progress was not uniformly distributed across the country. Availability, adequate visualization and analysis of spatially explicit data on socio-economic and environmental aspects can support both research and policy towards sustainable development. Applying appropriate mapping techniques allows gleaning important information from tabular socio-economic data. Spatial analysis of socio-economic phenomena can yield insights into locally-specifi c patterns and processes that cannot be generated by non-spatial applications. This paper presents techniques and applications that develop and analyze spatially highly disaggregated socioeconomic datasets. A number of examples show how such information can support informed decisionmaking and research in Vietnam.

Does Sex Speed Up Evolutionary Rate and Increase Biodiversity?

Most empirical and theoretical studies have shown that sex increases the rate of evolution, although evidence of sex constraining genomic and epigenetic variation and slowing down evolution also exists. Faster rates with sex have been attributed to new gene combinations, removal of deleterious mutations, and adaptation to heterogeneous environments. Slower rates with sex have been attributed to removal of major genetic rearrangements, the cost of finding a mate, vulnerability to predation, and exposure to sexually transmitted diseases. Whether sex speeds or slows evolution, the connection between reproductive mode, the evolutionary rate, and species diversity remains largely unexplored. Here we present a spatially explicit model of ecological and evolutionary dynamics based on DNA sequence change to study the connection between mutation, speciation, and the resulting biodiversity in sexual and asexual populations. We show that faster speciation can decrease the abundance of newly formed species and thus decrease long-term biodiversity. In this way, sex can reduce diversity relative to asexual populations, because it leads to a higher rate of production of new species, but with lower abundances. Our results show that reproductive mode and the mechanisms underlying it can alter the link between mutation, evolutionary rate, speciation and biodiversity and we suggest that a high rate of evolution may not be required to yield high biodiversity.

A physical approach on flood risk vulnerability of buildings

The design of efficient hydrological risk mitigation strategies and their subsequent implementation relies on a careful vulnerability analysis of the elements exposed. Recently, extensive research efforts were undertaken to develop and refine empirical relationships linking the structural vulnerability of buildings to the impact forces of the hazard processes. These empirical vulnerability functions allow estimating the expected direct losses as a result of the hazard scenario based on spatially explicit representation of the process patterns and the elements at risk classified into defined typological categories. However, due to the underlying empiricism of such vulnerability functions, the physics of the damage-generating mechanisms for a well-defined element at risk with its peculiar geometry and structural characteristics remain unveiled, and, as such, the applicability of the empirical approach for planning hazard-proof residential buildings is limited. Therefore, we propose a conceptual assessment scheme to close this gap. This assessment scheme encompasses distinct analytical steps: modelling (a) the process intensity, (b) the impact on the element at risk exposed and (c) the physical response of the building envelope. Furthermore, these results provide the input data for the subsequent damage evaluation and economic damage valuation. This dynamic assessment supports all relevant planning activities with respect to a minimisation of losses, and can be implemented in the operational risk assessment procedure.

Pattern and process: competition causes regular spacing of individuals within plant populations

1 We used simulated and experimental plant populations to analyse mortality-driven pattern formation under size-dependent competition. Larger plants had an advantage under size-asymmetric but not under symmetric competition. Initial patterns were random or clumped. 2 The simulations were individual-based and spatially explicit. Size-dependent competition was modelled with different rules to partition overlapping zones of influence. 3 The experiment used genotypes of Arabidopsis thaliana with different morphological plasticity and hence size-dependent competition. Compared with wild types, transgenic individuals over-expressed phytochrome A and had decreased plasticity because of disabled phytochrome-mediated shade avoidance. Therefore, competition among transgenics was more asymmetric compared with wild-types. 4 Density-dependent mortality under symmetric competition did not substantially change the initial spatial pattern. Conversely, simulations under asymmetric competition and experimental patterns of transgenic over-expressors showed patterns of survivors that deviated substantially from random mortality independent of initial patterns. 5 Small-scale initial patterns of wild types were regular rather than random or clumped. We hypothesize that this small-scale regularity may be explained by early shade avoidance of seedlings in their cotyledon stage. 6 Our experimental results support predictions from an individual-based simulation model and support the conclusion that regular spatial patterns of surviving individuals should be interpreted as evidence for strong, asymmetric competitive interactions and subsequent density-dependent mortality.

An initiative for participatory monitoring of large scale acquisitions: Opportunities and results thus far

Increasing commercial pressures on land are provoking fundamental and far-reaching changes in the relationships between people and land. Much knowledge on land-oriented investments projects currently comes from the media. Although this provides a good starting point, lack of transparency and rapidly changing contexts mean that this is often unreliable. The International Land Coalition, in partnership with Oxfam Novib, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), University of Pretoria, Centre for Development and Environment of the University of Bern (CDE), and GIZ, started to compile an inventory of land-related investments. This project aims to better understand the extent, trends and impacts of land-related investments by supporting an ongoing and systematic stocktaking exercise of the various investment projects currently taking place worldwide. It involves a large number of organizations and individuals working in areas where land transactions are being made, and able to provide details of such investments. The project monitors land transactions in rural areas that imply a transformation of land use rights from communities and smallholders to commercial use, and are made both by domestic and foreign investors (private actors, governments, government-back private investors). The focus is on investments for food or agrofuel production, timber extraction, carbon trading, mineral extraction, conservation and tourism. A novel way of using ITC to document land acquisitions in a spatially explicit way and by using an approach called “crowdsourcing” is being developed. This approach will allow actors to share information and knowledge directly and at any time on a public platform, where it will be scrutinized in terms of reliability and cross checked with other sources. Up to now, over 1200 deals have been recorded across 96 countries. Details of such transactions have been classified in a matrix and distributed to over 350 contacts worldwide for verification. The verified information has been geo-referenced and represented in two global maps. This is an open database enabling a continued monitoring exercise and the improvement of data accuracy. More information will be released over time. The opportunities arise from overcoming constraints by incomplete information by proposing a new way of collecting, enhancing and sharing information and knowledge in a more democratic and transparent manner. The intention is to develop interactive knowledge platform where any interested person can share and access information on land deals, their link to involved stakeholders, and their embedding into a geographical context. By making use of new ICT technologies that are more and more in the reach of local stakeholders, as well as open access and web-based spatial information systems, it will become possible to create a dynamic database containing spatial explicit data. Feeding in data by a large number of stakeholders, increasingly also by means of new mobile ITC technologies, will open up new opportunities to analyse, monitor and assess highly dynamic trends of land acquisition and rural transformation.

A 600 years warm-season temperature record from varved sediments of Lago Plomo, Northern Patagonia, Chile (47°S)

High-resolution records of calibrated proxy data for the past millennium are fundamental to place current changes into the context of pre-industrial natural forced and unforced variability. Although the need for regional spatially-explicit comprehensive reconstructions is widely recognized, the proxy data sources are still scarce, particularly for the Southern Hemisphere and especially for South America. We present a 600-year long warm season temperature record from varved sediments of Lago Plomo, a proglacial lake of the Northern Patagonian Ice field in Southern Chile (46°59′S, 72°52′W, 203 m a.s.l.). The thickness of the bright summer sediment layer relative to the dark winter layer (measured as total brightness; % reflectance 400–730 nm) is calibrated against warm season SONDJF temperature (1900–2009; r = 0.58, p(aut) = 0.056, RE = 0.52; CE = 0.15, RMSEP = 0.28 °C; five-year triangular filtered data). In Lago Plomo, warm summer temperatures lead to enhanced glacier melt and suspended sediment transport, which results in thicker light summer layers and to brighter sediments. Although Patagonia shows pronounced regional differences in decadal temperature trends and variability, the 600 years temperature reconstruction from Lago Plomo compares favourably with other regional/continental temperature records, but also emphasizes significant regional differences for which no data and information existed so far. These regional differences seem to be real as they are also reflected in modern climate data sets (1900–2010). The reconstruction shows pronounced subdecadal – multidecadal variability with cold phases during parts of the Little Ice Age (16th and 18th centuries) and in the beginning of the 20th century. The most prominent warm phase is the 19th century which is as warm as the second half of the 20th century. The exceptional summer warmth AD 1780–1810 is also found in other archives of Northern Patagonia and Central Chile. Our record shows the delayed 20th century warming in the Southern Hemisphere. The comparison between winter precipitation and summer temperature (inter-seasonal coupling) from Lago Plomo reveals alternating phases with parallel and contrasting decadal trends of winter precipitation and summer temperature (positive and negative running correlations Rwinter PP; summer TT). This observation from the sediment proxy data is also confirmed by two sets of reanalysis data for the 20th century. Reanalysis data show that phases with negative correlations between winter precipitation and summer temperature (e.g., dry winters and warm summers) at Lago Plomo are characteristic for periods when circumpolar Westerly flow is displaced southward and enhanced around 60°S.

Beyond deforestation monitoring in conservation hotspots: Analysing landscape mosaic dynamics in north-eastern Madagascar

Due to its extraordinary biodiversity and rapid deforestation, north-eastern Madagascar is a conservation hotspot of global importance. Reducing shifting cultivation is a high priority for policy-makers and conservationists; however, spatially explicit evidence of shifting cultivation is lacking due to the difficulty of mapping it with common remote sensing methods. To overcome this challenge, we adopted a landscape mosaic approach to assess the changes between natural forests, shifting cultivation and permanent cultivation systems at the regional level from 1995 to 2011. Our study confirmed that shifting cultivation is still being used to produce subsistence rice throughout the region, but there is a trend of intensification away from shifting cultivation towards permanent rice production, especially near protected areas. While large continuous forest exists today only in the core zones of protected areas, the agricultural matrix is still dominated by a dense cover of tree crops and smaller forest fragments. We believe that this evidence makes a crucial contribution to the development of interventions to prevent further conversion of forest to agricultural land while improving local land users' well-being.

Herbivores limit the population size of big-leaf mahogany trees in an Amazonian forest

The Janzen–Connell hypothesis proposes that specialized herbivores maintain high numbers of tree species in tropical forests by restricting adult recruitment so that host populations remain at low densities. We tested this prediction for the large timber tree species, Swietenia macrophylla, whose seeds and seedlings are preyed upon by small mammals and a host-specific moth caterpillar Steniscadia poliophaea, respectively. At a primary forest site, experimental seed additions to gaps – canopy-disturbed areas that enhance seedling growth into saplings – over three years revealed lower survival and seedling recruitment closer to conspecific trees and in higher basal area neighborhoods, as well as reduced subsequent seedling survival and height growth. When we included these Janzen–Connell effects in a spatially explicit individual-based population model, the caterpillar's impact was critical to limiting Swietenia's adult tree density, with a > 10-fold reduction estimated at 300 years. Our research demonstrates the crucial but oft-ignored linkage between Janzen–Connell effects on offspring and population-level consequences for a long-lived, potentially dominant tree species.

Distance from Sub-Saharan Africa Predicts Mutational Load in Diverse Human Genomes

The Out-of-Africa (OOA) dispersal ∼50,000 y ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test this hypothesis, we have sequenced full genomes and high-coverage exomes from seven geographically divergent human populations from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia, and Mexico. We find that individual genomes vary modestly in the overall number of predicted deleterious alleles. We show via spatially explicit simulations that the observed distribution of deleterious allele frequencies is consistent with the OOA dispersal, particularly under a model where deleterious mutations are recessive. We conclude that there is a strong signal of purifying selection at conserved genomic positions within Africa, but that many predicted deleterious mutations have evolved as if they were neutral during the expansion out of Africa. Under a model where selection is inversely related to dominance, we show that OOA populations are likely to have a higher mutation load due to increased allele frequencies of nearly neutral variants that are recessive or partially recessive.

The Effects of Density, Spatial Pattern, and Competitive Symmetry on Size Variation in Simulated Plant Populations

Patterns of size inequality in crowded plant populations are often taken to be indicative of the degree of size asymmetry of competition, but recent research suggests that some of the patterns attributed to size‐asymmetric competition could be due to spatial structure. To investigate the theoretical relationships between plant density, spatial pattern, and competitive size asymmetry in determining size variation in crowded plant populations, we developed a spatially explicit, individual‐based plant competition model based on overlapping zones of influence. The zone of influence of each plant is modeled as a circle, growing in two dimensions, and is allometrically related to plant biomass. The area of the circle represents resources potentially available to the plant, and plants compete for resources in areas in which they overlap. The size asymmetry of competition is reflected in the rules for dividing up the overlapping areas. Theoretical plant populations were grown in random and in perfectly uniform spatial patterns at four densities under size‐asymmetric and size‐symmetric competition. Both spatial pattern and size asymmetry contributed to size variation, but their relative importance varied greatly over density and over time. Early in stand development, spatial pattern was more important than the symmetry of competition in determining the degree of size variation within the population, but after plants grew and competition intensified, the size asymmetry of competition became a much more important source of size variation. Size variability was slightly higher at higher densities when competition was symmetric and plants were distributed nonuniformly in space. In a uniform spatial pattern, size variation increased with density only when competition was size asymmetric. Our results suggest that when competition is size asymmetric and intense, it will be more important in generating size variation than is local variation in density. Our results and the available data are consistent with the hypothesis that high levels of size inequality commonly observed within crowded plant populations are largely due to size‐asymmetric competition, not to variation in local density.