Assessing modern ground survey methods and airborne laser scanning for digital terrain modelling:A case study from the Lake District, England

This paper compares the applicability of three ground survey methods for modelling terrain: one man electronic tachymetry (TPS), real time kinematic GPS (GPS), and terrestrial laser scanning (TLS). Vertical accuracy of digital terrain models (DTMs) derived from GPS, TLS and airborne laser scanning (ALS) data is assessed. Point elevations acquired by the four methods represent two sections of a mountainous area in Cumbria, England. They were chosen so that the presence of non-terrain features is constrained to the smallest amount. The vertical accuracy of the DTMs was addressed by subtracting each DTM from TPS point elevations. The error was assessed using exploratory measures including statistics, histograms, and normal probability plots. The results showed that the internal measurement accuracy of TPS, GPS, and TLS was below a centimetre. TPS and GPS can be considered equally applicable alternatives for sampling the terrain in areas accessible on foot. The highest DTM vertical accuracy was achieved with GPS data, both on sloped terrain (RMSE 0.16. m) and flat terrain (RMSE 0.02. m). TLS surveying was the most efficient overall but veracity of terrain representation was subject to dense vegetation cover. Therefore, the DTM accuracy was the lowest for the sloped area with dense bracken (RMSE 0.52. m) although it was the second highest on the flat unobscured terrain (RMSE 0.07. m). ALS data represented the sloped terrain more realistically (RMSE 0.23. m) than the TLS. However, due to a systematic bias identified on the flat terrain the DTM accuracy was the lowest (RMSE 0.29. m) which was above the level stated by the data provider. Error distribution models were more closely approximated by normal distribution defined using median and normalized median absolute deviation which supports the use of the robust measures in DEM error modelling and its propagation. © 2012 Elsevier Ltd.

Modelling local-scale determinants and the probability of microarthropod species occurrence in Antarctic soils

Soil fauna in the extreme conditions of Antarctica consists of a few microinvertebrate species patchily distributed at different spatial scales. Populations of the prostigmatic mite Stereotydeus belli and the collembolan Gressittacantha terranova from northern Victoria Land (Antarctica) were used as models to study the effect of soil properties on microarthropod distributions. In agreement with the general assumption that the development and distribution of life in these ecosystems is mainly controlled by abiotic factors, we found that the probability of occurrence of S. belli depends on soil moisture and texture and on the sampling period (which affects the general availability of water); surprisingly, none of the analysed variables were significantly related to the G. terranova distribution. Based on our results and literature data, we propose a theoretical model that introduces biotic interactions among the major factors driving the local distribution of collembolans in Antarctic terrestrial ecosystems. (c) 2007 Elsevier Ltd. All rights reserved.

Identifying optimal feeding habitat and proposed Marine Protected Areas (pMPAs) for the black-legged kittiwake (Rissa tridactyla) suggests a need for complementary management approaches

Marine Protected Areas (MPAs) are an important conservation tool. For marine predators, recent research has focused on the use of Species Distribution Models (SDMs) to identify proposed sites. We used a maximum entropy modelling approach based on static and dynamic oceanographic parameters to determine optimal feeding habitat for black-legged kittiwakes (Rissa tridactyla) at two colonies during two consecutive breeding seasons (2009 and 2010). A combination of Geographic Positioning System (GPS) loggers and Time-Depth Recorders (TDRs) attributed feeding activity to specific locations. Feeding areas were <30 km from the colony, <40 km from land, in productive waters, 25–175m deep. The predicted extent of optimal habitat declined at both colonies between 2009 and 2010 coincident with declines in reproductive success. Whilst the area of predicted optimal habitat changed, its location was spatially stable between years. There was a close match between observed feeding locations and habitat predicted as optimal at one colony (Lambay Island, Republic of Ireland), but a notable mismatch at the other (Rathlin Island, Northern Ireland). Designation of an MPA at Rathlin may, therefore, be less effective than a similar designation at Lambay perhaps due to the inherent variability in currents and sea state in the North Channel compared to the comparatively stable conditions in the central Irish Sea. Current strategies for designating MPAs do not accommodate likely future redistribution of resources due to climate change. We advocate the development of new approaches including dynamic MPAs that track changes in optimal habitat and non-colony specific ecosystem management.

A new statistical framework for the quantification of covariate associations with species distributions

Identifying processes that shape species geographical ranges is a prerequisite for understanding environmental change. Currently, species distribution modelling methods do not offer credible statistical tests of the relative influence of climate factors and typically ignore other processes (e.g. biotic interactions and dispersal limitation). We use a hierarchical model fitted with Markov Chain Monte Carlo to combine ecologically plausible niche structures using regression splines to describe unimodal but potentially skewed response terms. We apply spatially explicit error terms that account for (and may help identify) missing variables. Using three example distributions of European bird species, we map model results to show sensitivity to change in each covariate. We show that the overall strength of climatic association differs between species and that each species has considerable spatial variation in both the strength of the climatic association and the sensitivity to climate change. Our methods are widely applicable to many species distribution modelling problems and enable accurate assessment of the statistical importance of biotic and abiotic influences on distributions.

Marine foundation species shifting ranges and genetic baselines

This thesis revealed the most importance factors shaping the distribution, abundance and genetic diversity of four marine foundation species. Environmental conditions, particularly sea temperatures, nutrient availability and ocean waves, played a primary role in shaping the spatial distribution and abundance of populations, acting on scales varying from tens of meters to hundreds of kilometres. Furthermore, the use of Species Distribution Models (SDMs) with biological records of occurrence and high-resolution oceanographic data, allowed predicting species distributions across time. This approach highlighted the role of climate change, particularly when extreme temperatures prevailed during glacial and interglacial periods. These results, when combined with mtDNA and microsatellite genetic variation of populations allowed inferring for the influence of past range dynamics in the genetic diversity and structure of populations. For instance, the Last Glacial Maximum produced important shifts in species ranges, leaving obvious signatures of higher genetic diversities in regions where populations persisted (i.e., refugia). However, it was found that a species’ genetic pool is shaped by regions of persistence, adjacent to others experiencing expansions and contractions. Contradicting expectations, refugia seem to play a minor role on the re(colonization) process of previously eroded populations. In addition, the available habitat area for expanding populations and the inherent mechanisms of species dispersal in occupying available habitats were also found to be fundamental in shaping the distributions of genetic diversity. However, results suggest that the high levels of genetic diversity in some populations do not rule out that they may have experienced strong genetic erosion in the past, a process here named shifting genetic baselines. Furthermore, this thesis predicted an ongoing retraction at the rear edges and extinctions of unique genetic lineages, which will impoverish the global gene pool, strongly shifting the genetic baselines in the future.

Habitat predictive modelling of demersal fish species in the Azores

Dissertação de Mestrado, Estudos Integrados dos Oceanos, 25 de Março de 2013, Universidade dos Açores.

Mapping multi-species habitat use for marine conservation planning

Tese de Doutoramento, Ciências do Mar (Biologia Marinha)

Scenario-based assessment of future land use change on butterfly species distributions

Species distribution models (SDMs) are increasingly used to predict environmentally induced range shifts of habitats of plant and animal species. Consequently SDMs are valuable tools for scientifically based conservation decisions. The aims of this paper are (1) to identify important drivers of butterfly species persistence or extinction, and (2) to analyse the responses of endangered butterfly species of dry grasslands and wetlands to likely future landscape changes in Switzerland. Future land use was represented by four scenarios describing: (1) ongoing land use changes as observed at the end of the last century; (2) a liberalisation of the agricultural markets; (3) a slightly lowered agricultural production; and (4) a strongly lowered agricultural production. Two model approaches have been applied. The first (logistic regression with principal components) explains what environmental variables have significant impact on species presence (and absence). The second (predictive SDM) is used to project species distribution under current and likely future land uses. The results of the explanatory analyses reveal that four principal components related to urbanisation, abandonment of open land and intensive agricultural practices as well as two climate parameters are primary drivers of species occurrence (decline). The scenario analyses show that lowered agricultural production is likely to favour dry grassland species due to an increase of non-intensively used land, open canopy forests, and overgrown areas. In the liberalisation scenario dry grassland species show a decrease in abundance due to a strong increase of forested patches. Wetland butterfly species would decrease under all four scenarios as their habitats become overgrown

Spectral and statistical characteristics of shoaling waves of Alleppey West coast of India

Some investigations on the spectral and statistical characteristics of deep water waves are available for Indian waters. But practically no systematic investigation on the shallow water wave spectral and probabilistic characteristics is made for any part of the Indian coast except for a few restricted studies. Hence a comprehensive study of the shallow water wave climate and their spectral and statistical characteristics for a location (Alleppey) along the southwest coast of India is undertaken based on recorded data. The results of the investigation are presented in this thesis.The thesis comprises of seven chapters

Off-road sampling reveals a different grassland bird community than roadside sampling: implications for survey design and estimates to guide conservation

Grassland bird species continue to decline steeply across North America. Road-based surveys such as the North American Breeding Bird Survey (BBS) are often used to estimate trends and population sizes and to build species distribution models for grassland birds, although roadside survey counts may introduce bias in estimates because of differences in habitats along roadsides and in off-road surveys. We tested for differences in land cover composition and in the avian community on 21 roadside-based survey routes and in an equal number of adjacent off-road walking routes in the grasslands of southern Alberta, Canada. Off-road routes (n = 225 point counts) had more native grassland and short shrubs and less fallow land and road area than the roadside routes (n = 225 point counts). Consequently, 17 of the 39 bird species differed between the two route types in frequency of occurrence and relative abundance, measured using an indicator species analysis. Six species, including five obligate grassland species, were more prevalent at off-road sites; they included four species listed under the Canadian federal Species At Risk Act or listed by the Committee on the Status of Endangered Wildlife in Canada: Sprague’s Pipit (Anthus spragueii), Baird’s Sparrow (Ammodramus bairdii), the Chestnut-collared Longspur (Calcarius ornatus), and McCown’s Longspur (Rhynchophanes mccownii). The six species were as much as four times more abundant on off-road sites. Species more prevalent along roadside routes included common species and those typical of farmland and other human-modified habitats, e.g., the European Starling (Sturnus vulgaris), the Black-billed Magpie (Pica hudsonia), and the House Sparrow (Passer domesticus). Differences in avian community composition between roadside and off-road surveys suggest that the use of BBS data when generating population estimates or distribution models may overestimate certain common species and underestimate others of conservation concern. Our results highlight the need to develop appropriate corrections for bias in estimates derived from roadside sampling, and the need to design surveys that sample bird communities across a more representative cross-section of the landscape, both near and far from roads. 

Species-specific responses of Late Quaternary megafauna to climate and humans

Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.

Building the niche through time: using 13,000 years of data to predict the effects of climate change on three tree species in Europe

Aim  Species distribution models (SDMs) based on current species ranges underestimate the potential distribution when projected in time and/or space. A multi-temporal model calibration approach has been suggested as an alternative, and we evaluate this using 13,000 years of data. Location  Europe. Methods  We used fossil-based records of presence for Picea abies, Abies alba and Fagus sylvatica and six climatic variables for the period 13,000 to 1000 yr bp. To measure the contribution of each 1000-year time step to the total niche of each species (the niche measured by pooling all the data), we employed a principal components analysis (PCA) calibrated with data over the entire range of possible climates. Then we projected both the total niche and the partial niches from single time frames into the PCA space, and tested if the partial niches were more similar to the total niche than random. Using an ensemble forecasting approach, we calibrated SDMs for each time frame and for the pooled database. We projected each model to current climate and evaluated the results against current pollen data. We also projected all models into the future. Results  Niche similarity between the partial and the total-SDMs was almost always statistically significant and increased through time. SDMs calibrated from single time frames gave different results when projected to current climate, providing evidence of a change in the species realized niches through time. Moreover, they predicted limited climate suitability when compared with the total-SDMs. The same results were obtained when projected to future climates. Main conclusions  The realized climatic niche of species differed for current and future climates when SDMs were calibrated considering different past climates. Building the niche as an ensemble through time represents a way forward to a better understanding of a species' range and its ecology in a changing climate.

Testing projected wild bee distributions in agricultural habitats: predictive power depends on species traits and habitat type

Species distribution models (SDM) are increasingly used to understand the factors that regulate variation in biodiversity patterns and to help plan conservation strategies. However, these models are rarely validated with independently collected data and it is unclear whether SDM performance is maintained across distinct habitats and for species with different functional traits. Highly mobile species, such as bees, can be particularly challenging to model. Here, we use independent sets of occurrence data collected systematically in several agricultural habitats to test how the predictive performance of SDMs for wild bee species depends on species traits, habitat type, and sampling technique. We used a species distribution modeling approach parametrized for the Netherlands, with presence records from 1990 to 2010 for 193 Dutch wild bees. For each species, we built a Maxent model based on 13 climate and landscape variables. We tested the predictive performance of the SDMs with independent datasets collected from orchards and arable fields across the Netherlands from 2010 to 2013, using transect surveys or pan traps. Model predictive performance depended on species traits and habitat type. Occurrence of bee species specialized in habitat and diet was better predicted than generalist bees. Predictions of habitat suitability were also more precise for habitats that are temporally more stable (orchards) than for habitats that suffer regular alterations (arable), particularly for small, solitary bees. As a conservation tool, SDMs are best suited to modeling rarer, specialist species than more generalist and will work best in long-term stable habitats. The variability of complex, short-term habitats is difficult to capture in such models and historical land use generally has low thematic resolution. To improve SDMs’ usefulness, models require explanatory variables and collection data that include detailed landscape characteristics, for example, variability of crops and flower availability. Additionally, testing SDMs with field surveys should involve multiple collection techniques.

Ecological niche similarities of Peponapis bees and non-domesticated Cucurbita species

Peponapis bees are considered specialized pollinators of Cucurbita flowers, a genus that presents several species of economic value (squashes and pumpkins). Both genera originated in the Americas, and their diversity dispersion center is in Mexico. Ten species of Peponapis and ten species of Cucurbita (only non-domesticated species) were analyzed considering the similarity of their ecological niche characteristics with respect to climatic conditions of their occurrence areas (abiotic variables) and interactions between species (biotic variables). The similarity of climatic conditions (temperature and precipitation) was estimated through cluster analyses. The areas of potential occurrence of the most similar species were obtained through ecological niche modeling and summed with geographic information system tools. Three main clusters were obtained: one with species that shared potential occurrence areas mainly in deserts (P. pruinosa, P. timberlakei, C. digitata, C. palmata, C. foetidissima), another in moist forests (P. limitaris, P. atrata, C. lundelliana, C. o. martinezii) and a third mainly in dry forests (C. a. sororia, C. radicans, C. pedatifolia, P. azteca, P. smithi, P. crassidentata, P. utahensis). Some species with similar ecological niche presented potential shared areas that are also similar to their geographical distribution, like those occurring predominantly on deserts. However, some clustered species presented larger geographical areas, such as P. pruinosa and C. foetidissima suggesting other drivers than climatic conditions to shape their distributions. The domestication of Cucurbita and also the natural history of both genera were considered also as important factors. (C) 2011 Elsevier B.V. All rights reserved.

Using ecological niche modelling to infer past, present and future environmental suitability for Leiopelma hochstetteri, an endangered New Zealand native frog

Leiopelma hochstetteri is an endangered New Zealand frog now confined to isolated populations scattered across the North Island. A better understanding of its past, current and predicted future environmental suitability will contribute to its conservation which is in jeopardy due to human activities, feral predators, disease and climate change. Here we use ecological niche modelling with all known occurrence data (N = 1708) and six determinant environmental variables to elucidate current, pre-human and future environmental suitability of this species. Comparison among independent runs, subfossil records and a clamping method allow validation of models. Many areas identified as currently suitable do not host any known populations. This apparent discrepancy could be explained by several non exclusive hypotheses: the areas have not been adequately surveyed and undiscovered populations still remain, the model is over simplistic; the species` sensitivity to fragmentation and small population size; biotic interactions; historical events. An additional outcome is that apparently suitable, but frog-less areas could be targeted for future translocations. Surprisingly, pre-human conditions do not differ markedly highlighting the possibility that the range of the species was broadly fragmented before human arrival. Nevertheless, some populations, particularly on the west of the North Island may have disappeared as a result of human mediated habitat modification. Future conditions are marked with higher temperatures, which are predicted to be favourable to the species. However, such virtual gain in suitable range will probably not benefit the species given the highly fragmented nature of existing habitat and the low dispersal ability of this species. (C) 2010 Elsevier Ltd. All rights reserved.