Markus Metz

GRASS GIS: A multi-purpose open source GIS

The GIS software sector has developed rapidly over the last ten years. Open Source GIS applications are gaining relevant market shares in academia, business, and public administration. In this paper, we illustrate the history and features of a key Open Source GIS, the Geographical Resources Analysis Support System (GRASS). GRASS has been under development for more than 28 years, has strong ties into academia, and its review mechanisms led to the integration of well tested and documented algorithms into a joint GIS suite which has been used regularly for environmental modelling. The development is community-based with developers distributed globally. Through the use of an online source code repository, mailing lists and a Wiki, users and developers communicate in order to review existing code and develop new methods. In this paper, we provide a functionality overview of the more than 400 modules available in the latest stable GRASS software release. This new release runs natively on common operating systems (MS-Windows, GNU/Linux, Mac OSX), giving basic and advanced functionality to casual and expert users. In the second part, we review selected publications with a focus on environmental modelling to illustrate the wealth of use cases for this open and free GIS.

Bat echolocation calls facilitate social communication

Bat echolocation is primarily used for orientation and foraging but also holds great potential for social communication. The communicative function of echolocation calls is still largely unstudied, especially in the wild. Eavesdropping on vocal signatures encoding social information in echolocation calls has not, to our knowledge, been studied in free-living bats so far. We analysed echolocation calls of the polygynous bat Saccopteryx bilineata and found pronounced vocal signatures encoding sex and individual identity. We showed experimentally that free-living males discriminate approaching male and female conspecifics solely based on their echolocation calls. Males always produced aggressive vocalizations when hearing male echolocation calls and courtship vocalizations when hearing female echolocation calls; hence, they responded with complex social vocalizations in the appropriate social context. Our study demonstrates that social information encoded in bat echolocation calls plays a crucial and hitherto underestimated role for eavesdropping conspecifics and thus facilitates social communication in a highly mobile nocturnal mammal.

Surface Temperatures at the Continental Scale: Tracking Changes with Remote Sensing at Unprecedented Detail

Temperature is a main driver for most ecological processes, and temperature time series provide key environmental indicators for various applications and research fields. High spatial and temporal resolutions are crucial for detailed analyses in various fields of research. A disadvantage of temperature data obtained by satellites is the occurrence of gaps that must be reconstructed. Here, we present a new method to reconstruct high-resolution land surface temperature (LST) time series at the continental scale gaining 250-m spatial resolution and four daily values per pixel. Our method constitutes a unique new combination of weighted temporal averaging with statistical modeling and spatial interpolation. This newly developed reconstruction method has been applied to greater Europe, resulting in complete daily coverage for eleven years. To our knowledge, this new reconstructed LST time series exceeds the level of detail of comparable reconstructed LST datasets by several orders of magnitude. Studies on emerging diseases, parasite risk assessment and temperature anomalies can now be performed on the continental scale, maintaining high spatial and temporal detail. We illustrate a series of applications in this paper. Our dataset is available online for download as time aggregated derivatives for direct usage in GIS-based applications.

A new GRASS GIS toolkit for Hortonian analysis of drainage networks

The aim of this paper is to present a new GRASS GIS toolset designed for Hortonian analysis of drainage networks. The r.stream toolset uses a multiple flow direction algorithm for stream network extraction as well as for calculating other hydrogeomorphological features in the catchments area. As all GRASS GIS toolsets, r.stream consists of several separate modules that can extract stream networks from a spectrum of accumulation maps, order the extracted network using several ordering methods, do advanced modeling of basins boundary, perform Hortonian statistics, calculate additional parameters such as flow path distance to watershed elements, partition ordered and unordered networks into near-straight-line sectors, and calculate sector directions. The package is free and open-source software, available for GRASS version 6.4 and later.

Early warning of West Nile virus mosquito vector: climate and land use models successfully explain phenology and abundance of Culex pipiens mosquitoes in North-Western Italy

BackgroundWest Nile Virus (WNV) is an emerging global health threat. Transmission risk is strongly related to the abundance of mosquito vectors, typically Culex pipiens in Europe. Early-warning predictors of mosquito population dynamics would therefore help guide entomological surveillance and thereby facilitate early warnings of transmission risk.MethodsWe analysed an 11-year time series (2001 to 2011) of Cx. pipiens mosquito captures from the Piedmont region of north-western Italy to determine the principal drivers of mosquito population dynamics. Linear mixed models were implemented to examine the relationship between Cx. pipiens population dynamics and environmental predictors including temperature, precipitation, Normalized Difference Water Index (NDWI) and the proximity of mosquito traps to urban areas and rice fields.ResultsWarm temperatures early in the year were associated with an earlier start to the mosquito season and increased season length, and later in the year, with decreased abundance. Early precipitation delayed the start and shortened the length of the mosquito season, but increased total abundance. Conversely, precipitation later in the year was associated with a longer season. Finally, higher NDWI early in the year was associated with an earlier start to the season and increased season length, but was not associated with abundance. Proximity to rice fields predicted higher total abundance when included in some models, but was not a significant predictor of phenology. Proximity to urban areas was not a significant predictor in any of our models. Predicted variations in start of the season and season length ranged from one to three weeks, across the measured range of variables. Predicted mosquito abundance was highly variable, with numbers in excess of 1000 per trap per year when late season temperatures were low (average 21°C) to only 150 when late season temperatures were high (average 30°C).ConclusionsClimate data collected early in the year, in conjunction with local land use, can be used to provide early warning of both the timing and magnitude of mosquito outbreaks. This potentially allows targeted mosquito control measures to be implemented, with implications for prevention and control of West Nile Virus and other mosquito borne diseases.

Potential of remote sensing to predict species invasions A modelling perspective

Understanding the causes and effects of species invasions is a priority in ecology and conservation biology. One of the crucial steps in evaluating the impact of invasive species is to map changes in their actual and potential distribution and relative abundance across a wide region over an appropriate time span. While direct and indirect remote sensing approaches have long been used to assess the invasion of plant species, the distribution of invasive animals is mainly based on indirect methods that rely on environmental proxies of conditions suitable for colonization by a particular species. The aim of this article is to review recent efforts in the predictive modelling of the spread of both plant and animal invasive species using remote sensing, and to stimulate debate on the potential use of remote sensing in biological invasion monitoring and forecasting. Specifically, the challenges and drawbacks of remote sensing techniques are discussed in relation to: i) developing species distribution models, and ii) studying life cycle changes and phenological variations. Finally, the paper addresses the open challenges and pitfalls of remote sensing for biological invasion studies including sensor characteristics, upscaling and downscaling in species distribution models, and uncertainty of results.

Highly diversified coronaviruses in neotropical bats

Bats host a broad diversity of coronaviruses (CoVs), including close relatives of human pathogens. There is only limited data on neotropical bat CoVs. We analysed faecal, blood and intestine specimens from 1562 bats sampled in Costa Rica, Panama, Ecuador and Brazil for CoVs by broad-range PCR. CoV RNA was detected in 50 bats representing nine different species, both frugivorous and insectivorous. These bat CoVs were unrelated to known human or animal pathogens, indicating an absence of recent zoonotic spill-over events. Based on RNA-dependent RNA polymerase (RdRp)-based grouping units (RGUs) as a surrogate for CoV species identification, the 50 viruses represented five different alphacoronavirus RGUs and two betacoronavirus RGUs. Closely related alphacoronaviruses were detected in Carollia perspicillata and C. brevicauda across a geographical distance exceeding 5600 km. Our study expands the knowledge on CoV diversity in neotropical bats and emphasizes the association of distinct CoVs and bat host genera.

Robust rectification of aerial photographs in an open source environment

Aerial photographs provide the basis for developing indices of landscape composition and structure as sensitive measures of large-scale environmental change over relatively long periods of time. In view of this, proper image rectification is needed to enable geometrically unbiased application of landscape metrics in order to obtain meaningful results. It is also particularly important to provide researchers with image rectification tools within an open source environment, in order to: (i) guarantee free and robust tools for processing remote sensing data, (ii) facilitate customization, and (iii) provide useful support via forums and email lists. In this paper we provide a complete description of a robust and freely licensed toolchain for orthorectifying images, which is available in the open source software GRASS GIS. We will first sketch the theoretical background behind rectification and then illustrate the workflow of the orthorectification procedure in GRASS GIS.

Is Switzerland Suitable for the Invasion of Aedes albopictus

Background Over the last 30 years, the Asian tiger mosquito, Aedes albopictus, has rapidly spread around the world. The European distribution comprises the Mediterranean basin with a first appearance in Switzerland in 2003. Early identification of the most suitable areas in Switzerland allowing progressive invasion by this species is considered crucial to suggest adequate surveillance and control plans. Methodology/Principal Findings We identified the most suitable areas for invasion and establishment of Ae. albopictus in Switzerland. The potential distribution areas linked to the current climatic suitability were assessed using remotely sensed land surface temperature data recorded by the MODIS satellite sensors. Suitable areas for adult survival and overwintering of diapausing eggs were also identified for future climatic conditions, considering two different climate change scenarios (A1B, A2) for the periods 2020–2049 and 2045–2074. At present, the areas around Lake Geneva in western Switzerland provide suitable climatic conditions for Ae. albopictus. In northern Switzerland, parts of the Rhine valley, around Lake Constance, as well as the surroundings of Lake Neuchâtel, appear to be suitable for the survival at least of adult Ae. albopictus. However, these areas are characterized by winters currently being too cold for survival and development of diapausing eggs. In southern Switzerland, Ae. albopictus is already well-established, especially in the Canton of Ticino. For the years 2020–2049, the predicted possible spread of the tiger mosquito does not differ significantly from its potential current distribution. However, important expansions are obtained if the period is extended to the years 2045–2074, when Ae. albopictus may invade large new areas. Conclusions/Significance Several parts of Switzerland provide suitable climatic conditions for invasion and establishment of Ae. albopictus. The current distribution and rapid spread in other European countries suggest that the tiger mosquito will colonize new areas in Switzerland in the near future.

Identifying the environmental conditions favouring West Nile Virus outbreaks in Europe

West Nile Virus (WNV) is a globally important mosquito borne virus, with significant implications for human and animal health. The emergence and spread of new lineages, and increased pathogenicity, is the cause of escalating public health concern. Pinpointing the environmental conditions that favour WNV circulation and transmission to humans is challenging, due both to the complexity of its biological cycle, and the under-diagnosis and reporting of epidemiological data. Here, we used remote sensing and GIS to enable collation of multiple types of environmental data over a continental spatial scale, in order to model annual West Nile Fever (WNF) incidence across Europe and neighbouring countries. Multi-model selection and inference were used to gain a consensus from multiple linear mixed models. Climate and landscape were key predictors of WNF outbreaks (specifically, high precipitation in late winter/early spring, high summer temperatures, summer drought, occurrence of irrigated croplands and highly fragmented forests). Identification of the environmental conditions associated with WNF outbreaks is key to enabling public health bodies to properly focus surveillance and mitigation of West Nile virus impact, but more work needs to be done to enable accurate predictions of WNF risk.