Remote Sensing and GIS for Ecologists: Using Open Source Software

Introduction

Opportunities for Satellite Remote Sensing to Inform Conservation Biology

Nathalie Pettorelli

Our very recent history has been quite distinctive in terms of human expansion and global environmental changes: just looking at the last 100 years, for example, we see that the global human population experienced the highest growth rate in its history, growing from an estimated 1.7 billion inhabitants to well over seven billion (www.census.gov/population/international/data/worldpop/table_history.php; www.census.gov/popclock/). In the same period, the proportion of people living in urban areas increased from 13% to an estimated 50% (Thomas, 2008). It is now well established that modifications in food and energy demands associated with such changes have directly and indirectly caused our planet to lose a significant proportion of its biological diversity (WWF, 2014; Secretariat of the Convention on Biological Diversity, 2014), with local and global species extinctions primarily due to habitat loss and degradation, invasive alien species, overexploitation and climate change (Millennium Ecosystem Assessment, 2005).

In response to these rapid environmental changes, a scientific discipline called conservation biology emerged in the 1970s. What is conservation biology? Michael Soulé originally defined it as the application of science to conservation problems, addressing the biology of species, communities and ecosystems that are perturbed either directly or indirectly by human activities or other agents. This discipline has a clear goal: to provide principles and tools for preserving biological diversity (Soulé, 1985). A quick review of the literature shows that there are now many definitions of conservation biology (for example, Hunter, 1996; Groom, Meffe and Carroll, 2006; Van Dyke, 2008), but Soulé’s definition has the advantage of highlighting four distinctive aspects of the discipline: (1) conservation biology is a mission-driven discipline; (2) conservation biology is a crisis discipline; (3) conservation biology has a strong applied nature; (4) conservation biology is a clear component of environmental and wildlife management (Pettorelli, 2013; Mace, 2014).

Like any scientific discipline, conservation biology requires data. To rise to the challenges posed by global environmental change, the scientific community needs to be able to access global, long-term, reliable information on spatio-temporal changes in the distribution of direct and indirect anthropogenic pressures on biological diversity; in the distribution, structure, composition and functioning of ecosystems; as well as evidence of the effectiveness of various management actions (Collen et al., 2013). The past decade has clearly established that satellite remote sensing (SRS) has considerable potential to address these data needs (Roughgarden, Running and Matson, 1991; Gillespie et al., 2008; Pfeifer et al., 2012). In particular, SRS offers a relatively inexpensive and verifiable means of deriving complete spatial coverage of environmental information for large areas in a consistent manner that may be updated regularly (Muldavin, Neville and Harper, 2001; Duro et al., 2007).

There are many ways by which SRS can support data needs for conservation, ranging from helping to monitor changes in abiotic conditions and disturbances; track human-induced threats to biodiversity; map changes in land cover and vegetation three-dimensional structure; assess primary productivity dynamics; or even directly monitoring species and their migration patterns (Pettorelli et al., 2014a). In this Introduction, I will specifically focus on detailing how SRS can be used to inform management efforts aimed at preventing further biodiversity loss. I will start by detailing how this kind of information can be used to inform the expansion and management of the current protected area network, and will then illustrate how SRS can support the implementation of reintroduction programmes. Landscape-scale connectivity is key to maintaining biodiversity in the face of global environmental change, and SRS can help identify, map and monitor potential wildlife corridors. A clear set of opportunities for science to inform conservation efforts is linked to increasing our understanding of how changes in climatic conditions will impact biodiversity. Satellite remote sensing offers great potential in this arena, and here I will discuss this idea by providing a set of recent examples demonstrating how such information can be used to develop realistic scenarios. The final section of this Chapter will focus on the use of SRS in invasion biology, highlighting how this type of data can be used to detect, map and monitor invasive alien species.

Satellite Remote Sensing and Protected Areas

Protected areas (PAs) play a key role in global biodiversity conservation (Rodrigues et al., 2004; Zimmerer, Galt and Buck, 2004) and represent one of the largest financial investments in conservation efforts (Chape et al., 2005). Their importance is likely to continue to be high for years to come, as one of the Aichi biodiversity targets of the Convention on Biological Diversity is to conserve at least 17% of terrestrial and 10% of marine areas in equitably managed, ecologically representative and well-connected PAs by 2020 (Convention on Biological Diversity, 2013).

The idea that SRS information can represent a great addition to the monitoring toolkit for PAs is not new, with various authors having recommended the use of Earth Observations for PA monitoring and effectiveness assessment (see, for example, Gillespie et al., 2008; Dubois et al., 2011). There are many ways by which SRS can support the establishment and management of terrestrial and marine PAs: for example, a variety of human-induced threats to biological diversity in PAs can be detected from space, including illegal deforestation, extraction activities, oil spills and illegal, undeclared or unreported fishing (for example, see Corbane et al., 2010; Hansen and Loveland, 2012; Ottaviani et al., 2012; Duncan et al., 2014). Satellite remote sensing can also provide information on the occurrence, extent and impact of various natural environmental disturbances, including fires, flood, frost and insect outbreaks (Kerr and Ostrovsky, 2003; Pettorelli, 2013). It can sometimes be used to directly detect and count species (for example, see He et al., 2011; Fretwell et al., 2012), although the direct detection of species from space continues to be one of the greatest challenges of Earth Observations systems.

Moreover, it can be used to track habitat distribution and land cover changes (Nagendra et al., 2013), with the SRS ability to map certain, usually large-scale habitats now being widely recognized (Horning et al., 2010) and going beyond the purely terrestrial realm (Kachelriess et al., 2014). Vegetation indices (VIs), such as the Normalized Difference Vegetation Index (NDVI), can help track potential long-term changes in primary dynamics in PA networks (Alcaraz-Segura et al., 2009; Pettorelli et al., 2012) or derive relevant information for the setting of new PAs. Singh and Milner-Gulland (2011), for example, illustrated how SRS data can help identify good locations for new PAs in Kazakhstan for the benefit of a threatened migratory species, the saiga antelope (Saiga tatarica). To do so, they showed that saiga distribution in spring was determined by an intermediate range of temperature and intermediate primary productivity (as indexed by the NDVI), and by the availability of areas at intermediate distance from water and away from human settlements. Such results then allowed them to derive a habitat suitability map for the country and identify current mismatches between suitable habitats for the saiga and PA distribution.

SRS as a Tool to Support Reintroduction Programmes

As mentioned earlier, global biodiversity is under increasing threat from anthropogenic impacts, leading to an unprecedented rate of species loss (Pereira et al., 2010; Barnosky et al., 2011). A range of management actions are available to slow the rate of species loss; these include setting new PAs and improving PA management, but also reintroducing species in areas where they have become extinct. Successfully reintroducing a species in a given area still remains a difficult task (Seddon, Armstrong and Maloney, 2007); one important step relates to carrying out a detailed habitat assessment of the proposed reintroduction site. One also needs to insure that the area has sufficient carrying capacity to sustain growth of the reintroduced population and support a viable, self-sustaining population in the long run (IUCN, 1998; IUCN/SSC, 2013). The practicalities of habitat assessments can be logistically challenging when dealing with difficult terrain or large-bodied animals that require large areas for their survival. In such circumstances, field-based assessments of potential reintroduction areas can quickly become labour-intensive and time-consuming, leading to SRS sometimes being the only possible standardized, low-cost approach to inform habitat assessment needs (Estes et al., 2011; Freemantle et al., 2013).

Until now, few publications have made use of SRS to assess potential habitat availability before carrying out a reintroduction. One of the few examples is the recent work by Freemantle and colleagues, who assessed the Ouadi Rimé-Ouadi Achim Faunal Reserve (OROAFR) in Chad as a potential reintroduction site for the scimitar-horned oryx, Oryx dammah (Freemantle et al., 2013). Using SRS data collected by the National Oceanic and Atmospheric Administration (NOAA) satellites, the authors were able to show that: (1) average annual primary productivity in the OROAFR has been increasing over the past three decades; (2) this average trend was mainly driven by increasing primary productivity in the southern part of the reserve; (3) annual primary productivity decreased in the northern part of the reserve between 1982 and 2008; and (4) opposite trends are currently leading to an increased contrast in primary productivity dynamics between the north and the south of the reserve. These recent changes in the spatial dynamics of primary productivity are important ones to take into consideration when planning a possible reintroduction of oryx in the area: the sub-desert transition zone is indeed preferred by the oryx, and this habitat is currently narrowing. This implies a potential reduction of favourable habitat for the species, which could have detrimental effects on the success of establishing a self-sustaining reintroduced population (Freemantle et al., 2013).

Another example illustrating the potential for SRS to support reintroduction programmes is the case study presented by Estes and colleagues in 2011, which looked at supporting restoration efforts of the mountain bongo (Tragelaphus eurycerus isaaci), an endangered antelope, in its endemic range in the Kenyan montane forests. Using a combination of remote sensing data, predictive distribution models and multiple validation techniques to improve these distribution models, the authors showed that terrain ruggedness was the strongest habitat use predictor, followed by soil moisture availability, distance from law enforcement outposts, vegetation structural complexity and vegetation edge density. This allowed them to identify areas that should be primarily targeted for bongo conservation (Estes et al., 2011).

Overall, these two examples hopefully support the notion that SRS can greatly enhance the practice and management of species reintroductions and contribute significantly to their success. Admittedly, the level of contribution described here might not be achievable in all situations. Tailoring the type of information that can be extracted from SRS data to the ecosystem and biology of the species considered will be crucial to help increase the contribution of SRS data to the success of reintroduction programmes.

Satellite Remote Sensing to Identify, Map and Monitor Wildlife Corridors

Habitat loss and fragmentation is a major threat to biological diversity, as it can lead to isolated, small populations of wildlife becoming more common. Increases in the number of these small and isolated populations are a concern for conservation biologists because these populations are known to have higher extinction rates (Pimm, Jones and Diamond, 1988). One of the possible strategies to increase the effective size of these populations, and make them more resilient to inbreeding, demographic stochasticity and the Allee effect (Lande, 1988; Stephens, Sutherland and Freckleton, 1999), is to include corridors in conservation plans so that connectivity between otherwise isolated patches of habitat is increased (Meffe and Carroll, 1994). Corridors in this context are defined as strips of native vegetation or habitat connecting otherwise isolated remnants (Hobbs, 1992). They are thought to facilitate movement between connected patches of habitat, and thus increase gene flow, promote the re-establishment of locally extinct populations and increase species diversity within otherwise isolated areas (Fleury and Brown, 1997).

Satellite remote sensing can be a valuable tool for identifying and monitoring corridors, for various species and in various environmental contexts (see, for example, Xiaofeng et al., 2011; Bergl et al., 2012). Pittiglio and colleagues, for example, investigated the environmental and anthropogenic factors directly and indirectly related to the transit corridors of elephants (Loxodonta Africana) in Tanzania (Pittiglio et al., 2012). They demonstrated that elephant presence was correlated with SRS-derived information on the distribution of permanent drinking water sources, topography, anthropogenic activities, land cover and primary productivity dynamics. This showed that the identified transit corridors matched migration routes described in the 1960s, suggesting that corridors in the area are temporally stable. More recently, Wang and colleagues (Wang et al., 2014) supported giant panda (Ailuropoda melanoleuca) conservation efforts at the landscape scale, by providing a quantitative framework for corridor planning in China. Specifically, they combined field survey data with satellite imagery and species occupancy modelling to examine the habitat use of giant panda within the potential corridor area. They then conducted least-cost and circuit models to identify potential paths of dispersal across the (considered) landscape. This allowed them to demonstrate that both forest/bamboo restoration and automobile tunnel construction are the best options to significantly improve the effectiveness of potential corridors.

SRS to Predict Climate Change Effects on Wildlife

Greater greenhouse gas emissions over the past 100 years have led to observable changes in atmospheric gas concentrations, which translated into: increased global surface temperature; shifts in seasonal climatic patterns; extreme climatic events becoming more frequent and occurring with greater intensity; glacier reduction; sea surface ice reduction; and increased sea levels (IPCC, 2007, 2012). Wildlife is directly or indirectly responding to changes in these climatic patterns, with many studies reporting latitudinal and altitudinal distribution range shifts; migrant birds arriving earlier and starting to breed earlier; reduced survival or reproduction; and increased extinction risk (Parmesan, 2006; Foden et al., 2008; Ameca-y-Juárez et al., 2012).

An important set of opportunities for conservation biology to inform environmental management in the face of climate change is linked to increasing our understanding of, and ability to predict, how changes in climatic conditions will have an impact on species. Responses of species to climatic changes can be expected to fall into one of the following three categories: (1) thrive (that is, the species can live under the new set of environmental conditions); (2) adapt (that is, the species can change its ecology or distribution to avoid extinction); (3) go extinct (that is, the species will slowly decline and eventually be lost). There is a need to identify which species will fall into which category, and to understand how to facilitate species’ ability to adapt to change (Pettorelli, 2012).

A range of studies have explored how changes in climatic conditions are likely to have an impact on species distribution (see, for example, Pearson and Dawson, 2003; Perry et al., 2005; Araújo et al., 2011). However, studies that can qualitatively link climate change predictions with SRS-derived information on resource availability to predict the distributional or population dynamic impacts of climate change on particular species are still relatively rare, but examples do exist.

Singh and Milner-Gulland (2011), for example, developed a set of predictions regarding the impact of climate change on SRS-derived information on vegetation dynamics in central Asia to assess how such changes might affect saiga antelope distributions in the future. Hu and Jiang (2011) developed a habitat suitability model for Przewalski’s gazelle (Procapra przewalskii), an endangered ungulate whose historical and current ranges encompass Mongolia and China, and used this model to explore how projected changes in climate for the region may have an impact on the distribution of the species. To do so, the authors combined occurrence data with environmental predictors across four types of data, namely: (1) climatic data; (2) habitat data, which included a land cover layer and the NDVI for April, May, July and August; (3) a human influence index; and (4) information on topography and elevation. The best fit model was then used to investigate the impact of climate change on Przewalski’s gazelle habitat suitability, by replacing the current values of the retained climate predictors with the values predicted by three global climate models.

A major goal for ecologists and conservation biologists is to be able to transit from correlative approaches linking climatic conditions and resource availability to biodiversity patterns, to predictive approaches that allow quantitatively disentangling the direct and indirect effects of changes in climatic conditions on biodiversity (Berteaux et al., 2006). As the evidence for the usefulness of SRS data as a good proxy for resource availability for many species accumulates, such a transition is becoming increasingly possible.

Satellite Remote Sensing and Invasive Alien Species

Human-mediated introduction of plants and animals to areas beyond their natural geographic range is a major driver of biodiversity loss worldwide (Vitousek et al., 1996; Blackburn et al., 2010). The eradication of invasive alien species, defined as introduced species whose introduction does or is likely to cause economic or environmental harm or harm to human, animal or plant health, is extremely challenging and costly. In the US alone, the estimated cost of environmental damages and associated management and control of invasive alien species was estimated to reach over USD130 billion per year (Pimentel et al., 2000). Prevention of new invasions has been identified as the most efficient way to minimize the impacts of invasive alien species on global biodiversity, human health and the success of human economic and agricultural enterprises (Davis, 2009).

Several studies have now successfully implemented SRS-based methods to predict and map the distribution of invasive alien species, illustrating the huge potential for such data to actively support management decisions on the ground (see He et al., 2011 for a review). Using spectral information collected by the Landsat 5 Thematic Mapper (TM) and Landsat 7 Enhanced Thematic Mapper Plus (ETM+) satellites, for example, Wilfong, Gorchov and Henry (2009) explored the possibility of predicting Amur honeysuckle (Lonicera maackii) cover from VIs in woodlots in south-western Ohio and eastern Indiana. Hoyos and colleagues (2010) used the NDVI to map glossy privet (Ligustrum lucidum) invasion in Argentina. Roura-Pascual and colleagues (2004) used the NDVI to explore the potential distributional expansion of Argentine ants (Linepithema humile) with warming climates. Sanchez-Flores and colleagues (2008) used pan-sharpened 1-m IKONOS satellite imagery in combination with a genetic algorithm to predict the occurrence of African grasses (Schismus arabicus and Brassica tournefortii) in the Sonoran Desert of Mexico. Altogether, accumulated evidence suggests a simple rule when it comes to SRS and invasive alien plant species: alien invasions can be studied using SRS when the invader presents a novel structure, phenology or biochemistry relative to neighbouring native vegetation (Huang and Asner, 2009).

Conclusions

Successfully mitigating the effects of global environmental changes on living organisms can be expected to rely on a good understanding of the processes leading to biodiversity loss, as well as on novel, integrative, applied research that supports decision-making processes at local, national and international scales (Collen et al., 2013). Assessing and predicting the impacts of such changes on biodiversity is a complex task, especially given that threats to biological diversity can, and do, often interact. (This is something that has rarely been taken into account.) This Introduction hopefully demonstrates the potential for a combined use of field data, SRS and state-of-the-art modelling techniques to support the development of conservation biology as a discipline and successfully address the management issues posed by global environmental change.

Clearly, there is a series of challenges that need to be overcome for SRS to reach its potential in terms of making a difference in natural resource management (Pettorelli et al., 2014a, 2014b). For example, the costs of SRS data acquisition and associated logistical requirements for processing and analysing these large data sets can be prohibitive, while integration between in situ data and expert knowledge provided by local biologists and the technical expertise of remote sensing analysts remains too limited. However, chances to overcome these challenges have never been greater, with clear desires expressed by the conservation and remote sensing communities to develop stronger, more efficient ties, which are the keys to a brighter future for both communities – and the planet they share.

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