Towards Faster Method Search Through Static Ecosystem Analysis

Software developers are often unsure of the exact name of the method they need to use to invoke the desired behavior in a given context. This results in a process of searching for the correct method name in documentation, which can be lengthy and distracting to the developer. We can decrease the method search time by enhancing the documentation of a class with the most frequently used methods. Usage frequency data for methods is gathered by analyzing other projects from the same ecosystem - written in the same language and sharing dependencies. We implemented a proof of concept of the approach for Pharo Smalltalk and Java. In Pharo Smalltalk, methods are commonly searched for using a code browser tool called "Nautilus", and in Java using a web browser displaying HTML based documentation - Javadoc. We developed plugins for both browsers and gathered method usage data from open source projects, in order to increase developer productivity by reducing method search time. A small initial evaluation has been conducted showing promising results in improving developer productivity.

Mining the Ecosystem to Improve Type Inference For Dynamically Typed Languages

Dynamically typed languages lack information about the types of variables in the source code. Developers care about this information as it supports program comprehension. Ba- sic type inference techniques are helpful, but may yield many false positives or negatives. We propose to mine information from the software ecosys- tem on how frequently given types are inferred unambigu- ously to improve the quality of type inference for a single system. This paper presents an approach to augment existing type inference techniques by supplementing the informa- tion available in the source code of a project with data from other projects written in the same language. For all available projects, we track how often messages are sent to instance variables throughout the source code. Predictions for the type of a variable are made based on the messages sent to it. The evaluation of a proof-of-concept prototype shows that this approach works well for types that are sufficiently popular, like those from the standard librarie, and tends to create false positives for unpopular or domain specific types. The false positives are, in most cases, fairly easily identifiable. Also, the evaluation data shows a substantial increase in the number of correctly inferred types when compared to the non-augmented type inference.

Climate change impacts on tree species, forest properties, and ecosystem services

– Swiss forests experience strong impacts under the CH2011 scenarios, partly even for the low greenhouse gas scenario RCP3PD. Negative impacts prevail in low-elevation forests, whereas mostly positive impacts are expected in high-elevation forests. – Major changes in the distribution of the two most important tree species, Norway spruce and European beech, are expected. Growth conditions for spruce improve in a broad range of scenarios at presently cool high-elevation sites with plentiful precipitation, but in the case of strong warming (A1B and A2) spruce and beech are at risk in large parts of the Swiss Plateau. – High elevation forests that are temperature-limited will show little change in species composition but an increase in biomass. In contrast, forests at low elevations in warm-dry inner-Alpine valleys are sensitive to even moderate warming and may no longer sustain current biomass and species. – Timber production potential, carbon storage, and protection from avalanches and rockfall react differently to climate change, with an overall tendency to deteriorate at low elevations, and improve at high elevations. – Climate change will affect forests also indirectly, e.g., by increasing the risk of infestation by spruce bark beetles, which will profit from an extended flight period and will produce more generations per year.

Direct and indirect effects of invasion by the alien tree Ailanthus altissima on riparian plant communities and ecosystem multifunctionality

Most existing studies addressing the effects of invasive species on biodiversity focus on species richness ignoring better indicators of biodiversity and better predictors of ecosystem functioning such as the diversity of evolutionary histories (phylodiversity). Moreover, no previous study has separated the direct effect of alien plants on multiple ecosystem functions simultaneously (multifunctionality) from those indirect ones mediated by the decrease on biodiversity caused by alien plants. We aimed to analyze direct and indirect effects, mediated or not by its effect on biodiversity, of the invasive tree Ailanthus altissima on ecosystem multifunctionality of riparian habitats under Mediterranean climate. We measured vegetation attributes (species richness and phylodiversity) and several surrogates of ecosystem functioning (understory plant biomass, soil enzyme activities, available phosphorous and organic matter) in plots infested by A. altissima and in control (non-invaded) ones. We used structural equation modelling to tease apart the direct and indirect effects of A. altissima on ecosystem multifunctionality. Our results suggest that lower plant species richness, phylodiversity and multifunctionality were associated to the presence of A. altissima. When analyzing each function separately, we found that biodiversity has the opposite effect of the alien plant on all the different functions measured, therefore reducing the strength of the effect (either positive or negative) of A. altissima on them. This is one of the few existing studies addressing the effect of invasive species on phylodiversity and also studying the effect of invasive species on multiple ecosystem functions simultaneously.

Coupled human and natural system dynamics as key to the sustainability of Lake Victoria's ecosystem services

East Africa’s Lake Victoria provides resources and services to millions of people on the lake’s shores and abroad. In particular, the lake’s fisheries are an important source of protein, employment, and international economic connections for the whole region. Nonetheless, stock dynamics are poorly understood and currently unpredictable. Furthermore, fishery dynamics are intricately connected to other supporting services of the lake as well as to lakeshore societies and economies. Much research has been carried out piecemeal on different aspects of Lake Victoria’s system; e.g., societies, biodiversity, fisheries, and eutrophication. However, to disentangle drivers and dynamics of change in this complex system, we need to put these pieces together and analyze the system as a whole. We did so by first building a qualitative model of the lake’s social-ecological system. We then investigated the model system through a qualitative loop analysis, and finally examined effects of changes on the system state and structure. The model and its contextual analysis allowed us to investigate system-wide chain reactions resulting from disturbances. Importantly, we built a tool that can be used to analyze the cascading effects of management options and establish the requirements for their success. We found that high connectedness of the system at the exploitation level, through fisheries having multiple target stocks, can increase the stocks’ vulnerability to exploitation but reduce society’s vulnerability to variability in individual stocks. We describe how there are multiple pathways to any change in the system, which makes it difficult to identify the root cause of changes but also broadens the management toolkit. Also, we illustrate how nutrient enrichment is not a self-regulating process, and that explicit management is necessary to halt or reverse eutrophication. This model is simple and usable to assess system-wide effects of management policies, and can serve as a paving stone for future quantitative analyses of system dynamics at local scales.

Quick divergence but slow convergence during ecotype formation in lake and stream stickleback pairs of variable age

When genetic constraints restrict phenotypic evolution, diversification can be predicted to evolve along so-called lines of least resistance. To address the importance of such constraints and their resolution, studies of parallel phenotypic divergence that differ in their age are valuable. Here, we investigate the parapatric evolution of six lake and stream threespine stickleback systems from Iceland and Switzerland, ranging in age from a few decades to several millennia. Using phenotypic data, we test for parallelism in ecotypic divergence between parapatric lake and stream populations and compare the observed patterns to an ancestral-like marine population. We find strong and consistent phenotypic divergence, both among lake and stream populations and between our freshwater populations and the marine population. Interestingly, ecotypic divergence in low-dimensional phenotype space (i.e. single traits) is rapid and seems to be often completed within 100 years. Yet, the dimensionality of ecotypic divergence was highest in our oldest systems and only there parallel evolution of unrelated ecotypes was strong enough to overwrite phylogenetic contingency. Moreover, the dimensionality of divergence in different systems varies between trait complexes, suggesting different constraints and evolutionary pathways to their resolution among freshwater systems.

Divergent Macroparasite Infections in Parapatric Swiss Lake-Stream Pairs of Threespine Stickleback (Gasterosteus aculeatus)

Spatial heterogeneity in diversity and intensity of parasitism is a typical feature of most host-parasite interactions, but understanding of the evolutionary implications of such variation is limited. One possible outcome of infection heterogeneities is parasite-mediated divergent selection between host populations, ecotypes or species which may facilitate the process of ecological speciation. However, very few studies have described infections in population-pairs along the speciation continuum from low to moderate or high degree of genetic differentiation that would address the possibility of parasite-mediated divergent selection in the early stages of the speciation process. Here we provide an example of divergent parasitism in freshwater fish ecotypes by examining macroparasite infections in threespine stickleback (Gasterosteus aculeatus) of four Swiss lake systems each harbouring parapatric lake-stream ecotype pairs. We demonstrate significant differences in infections within and between the pairs that are driven particularly by the parasite taxa transmitted to fish from benthic invertebrates. The magnitude of the differences tended to correlate positively with the extent of neutral genetic differentiation between the parapatric lake and stream populations of stickleback, whereas no such correlation was found among allopatric populations from similar or contrasting habitats. This suggests that genetic differentiation is unrelated to the magnitude of parasite infection contrasts when gene flow is constrained by geographical barriers while in the absence of physical barriers, genetic differentiation and the magnitude of differences in infections tend to be positively correlated.

Land use intensification alters ecosystem multifunctionality via loss of biodiversity and changes to functional composition

Global change, especially land-use intensification, affects human well-being by impacting the deliv-ery of multiple ecosystem services (multifunctionality). However, whether biodiversity loss is amajor component of global change effects on multifunctionality in real-world ecosystems, as inexperimental ones, remains unclear. Therefore, we assessed biodiversity, functional compositionand 14 ecosystem services on 150 agricultural grasslands differing in land-use intensity. We alsointroduce five multifunctionality measures in which ecosystem services were weighted according torealistic land-use objectives. We found that indirect land-use effects, i.e. those mediated by biodi-versity loss and by changes to functional composition, were as strong as direct effects on average.Their strength varied with land-use objectives and regional context. Biodiversity loss explainedindirect effects in a region of intermediate productivity and was most damaging when land-useobjectives favoured supporting and cultural services. In contrast, functional composition shifts,towards fast-growing plant species, strongly increased provisioning services in more inherentlyunproductive grasslands.

People, protected areas and ecosystem services: a qualitative and quantitative analysis of local people's perception and preferences in Côte d'Ivoire

The long-term integrity of protected areas (PAs), and hence the maintenance of related ecosystem services (ES), are dependent on the support of local people. In the present study, local people's perceptions of ecosystem services from PAs and factors that govern local preferences for PAs are assessed. Fourteen study villages were randomly selected from three different protected forest areas and one control site along the southern coast of Côte d'Ivoire. Data was collected through a mixed-method approach, including qualitative semi-structured interviews and a household survey based on hypothetical choice scenarios. Local people's perceptions of ecosystem service provision was decrypted through qualitative content analysis, while the relation between people's preferences and potential factors that affect preferences were analyzed through multinomial models. This study shows that rural villagers do perceive a number of different ecosystem services as benefits from PAs in Côte d'Ivoire. The results based on quantitative data also suggest that local preferences for PAs and related ecosystem services are driven by PAs' management rules, age, and people's dependence on natural resources.

Soils, agriculture and food security: The interplay between ecosystem functioning and human well-being

Healthy soils are critical to agriculture, and both are essential to enabling food security. Soil-related challenges include using soils and other natural resources sustainably, combating land and soil degradation, avoiding further reduction of soil-related ecosystem services, and ensuring that all agricultural land is managed sustainably. Agricultural challenges include improving the quantity and quality of agricultural outputs to satisfy rising human needs, also in a 2 degrees world; maintaining diversity in agricultural systems while supporting those farms with the highest potential for closing existing yield gaps; and providing a livelihood for about 2.6 billion mostly poor land users. The greatest needs and potentials lie in small-scale farming, although there as elsewhere, trade-offs must be negotiated within the nexus of water, energy, land and food, including the role of soil therein.

Late-Holocene climate variability and ecosystem responses in Alaska inferred from high-resolution multiproxy sediment analyses at Grizzly Lake

The late-Holocene shift from Picea glauca (white spruce) to Picea mariana (black spruce) forests marked the establishment of modern boreal forests in Alaska. To understand the patterns and drivers of this vegetational change and the associated late-Holocene environmental dynamics, we analyzed radiocarbon-dated sediments from Grizzly Lake for chironomids, diatoms, pollen, macrofossils, charcoal, element composition, particle size, and magnetic properties for the period 4100–1800 cal BP. Chironomid assemblages reveal two episodes of decreased July temperature, at ca. 3300–3150 (ca −1 °C) and 2900–2550 cal BP (ca −2 °C). These episodes coincided with climate change elsewhere in the Northern Hemisphere, atmospheric reorganization, and low solar activity. Diatom-inferred lake levels dropped by ca. 5 m at 3200 cal BP, suggesting dry conditions during the period 3200–1800 cal BP. P. glauca declined and P. mariana expanded at ca. 3200 cal BP; this vegetational change was linked to diatom-inferred low lake levels and thus decreased moisture availability. Forest cover declined at 3300–3100, 2800–2500 and 2300–2100 cal BP and soil erosion as inferred from increased values of Al, K, Si, Ti, and Ca intensified, when solar irradiance was low. Plant taxa adapted to disturbance and cold climate (e.g. Alnus viridis, shrub Betula, Epilobium) expanded during these periods of reduced forest cover. This open vegetation type was associated with high fire activity that peaked at 2800 cal BP, when climatic conditions were particularly cold and dry. Forest recovery lagged behind subsequent climate warming (≤+3 °C) by ca. 75–225 years. Our multiproxy data set suggests that P. glauca was dominant under warm-moist climatic conditions, whereas P. mariana prevailed under cold-dry and warm-dry conditions. This pattern implies that climatic warming, as anticipated for this century, may promote P. glauca expansions, if moisture availability will be sufficiently high, while P. mariana may expand under dry conditions, possibly exacerbating climate impacts on the fire regime.

Reviving extinct Mediterranean forest communities may improve ecosystem potential in a warmer future

The Mediterranean Basin is the region of Europe most vulnerable to negative climate-change impacts, including forest decline, increased wildfire, and biodiversity loss. Because humans have affected Mediterranean ecosystems for millennia, it is unclear whether the region's native ecosystems were more resilient to climate change than current ecosystems, and whether they would provide sustainable management options if restored. We simulated vegetation with the LandClim model, using present-day climate as well as future climate-change scenarios, in three representative areas that encompass a broad range of Mediterranean conditions and vegetation types. Sedimentary pollen records that document now-extinct forests help to validate the simulations. Forests modeled under present climate closely resemble the extinct forests when human disturbance is limited; under future scenarios, characterized by increased temperatures and decreased precipitation, extinct forests are projected to re-emerge. When combined with modeling, paleoecological evidence reveals the potential of native vegetation to re-establish under current and future climate conditions, and provides a template for novel management strategies to maintain forest productivity and biodiversity in a warmer and drier future.