Integrating species and habitat data for nature conservation in Great Britain: data sources and methods

1. Britain is unusual in the quantity and quality of species and habitat data available, at both national and regional scales. This paper reviews the sources, coverage and quality of these data. 2. Habitat and species data are used by conservation agencies in England, Scotland and Wales for site selection and for monitoring habitat quality. The paper argues, however, that neither habitat data nor species distribution data on their own are sufficient to locate and monitor habitats for nature conservation purposes effectively. 3. Differences in sampling methodologies between habitat and species surveys present methodological difficulties for the development of an integrated monitoring system that uses both types of data. These problems need to be overcome if habitat and species data are to be used more effectively for nature conservation in the wider countryside. 4. A more integrated system based on the concept of biotope occupancy is proposed and discussed. The implementation of the system would assist with understanding those factors that explain observed patterns in species distribution and diversity, thereby helping to improve the effectiveness of policies for nature conservation.     

Assessing disturbance-sensitivity and generalism in mammals: Corroborating a hump-shaped relationship using a hemerobiotic approach

Hemeroby is an indicator widely used in plant ecology to evaluate the level of disturbance of the optimal habitat of a species. Hemeroby can be scaled on a range of ten point scores, higher scores of hemeroby meaning higher level of disturbance. In this study we applied two indicators of sensitivity to disturbance based on the concept of hemeroby: HS_i (mean hemeroby score), calculated on the habitat types where each species occurs, and the recently proposed HH_i (mean hemerobiotic entropy), i.e. the level of generalism of a species with respect to the range of levels of disturbance where the species occurs. Both indices are based on the position and range of species along a gradient of disturbance, from pristine to completely human-made habitats. From a recent regional atlas of mammals, it was possible to calculate the ecological preferences for a large number of habitat types for 36 common mammal species for Latium (Central Italy). From the occurrences of mammals in each habitat, we calculated the HS_i (here rescaled: HS_rescaled) and HH_i indices. The relationship between habitat-related disturbance (HS_rescaled) vs. generalism (HH_i) of species showed a hump-shaped relationship peaking at intermediate levels of HS_rescaled, suggesting that generalism is maximum at intermediate levels of disturbance and corroborating analogous results obtained for birds. Alien mammal species exhibited higher averaged values of HS_i when compared to autochthonous species, supporting the evidence regarding the close relationship between alien species and more disturbed ecosystems. The application of the two indices to mammals could open new perspectives in conservation and management of species inhabiting a wide range of differently disturbed habitat types.     

Relationship among settling,demography and habitat selection: an approach and a case study

Summary We explore the demographic consequences of site selection by animals on their abundance among habitats. We found that pre and post settling survivorship are important links between the behavioral decisions where to settle and the distribution of a population among habitats. This was demonstrated for 10 generations of the desert isopod, Hemilepistus reaumuri, in three habitats in the Negev Desert, Israel. The populations exhibit low survivorship before settling (12%) and high survivorship (55%) after settling. According to our model this implies high site selection. Theoretical considerations and the case study led us to suggest the following relationship among settling, demography and habitat selection: 1) Individuals search for suitable settling sites to inhabit and reproduce. 2) Their decision where and when to settle is a cost benefit decision. They weigh the benefit of searching for a high quality site against mortality due to increased searching time. 3) The individual's decision to settle determines the pre and post settling survivorship pattern. 4) Survivorship pattern dictates density pattern in time and space. 5) Density pattern in a given habitat determines its quality for the individual. 6) Settling selection among habitats and the number of safe sites controls the distribution of densities among habitats.     

Measuring the efficiency of fen restoration on carabid beetles and vascular plants: a case study from north‐eastern Germany

The aim of the study was to assess the effects of fen rewetting on carabid beetle and vascular plant assemblages within riverine fens along the river Peene in north‐eastern Germany. Drained (silage grassland), rewetted (restored formerly drained silage grassland), and near‐natural (fairly pristine) stands were compared. Eighty‐four beetle species (7,267 individuals) and 135 plant species were recorded. The richness of vascular plant species and the number of endangered species were highest on near‐natural fens. Fourteen years of rewetting did not increase plant species numbers compared with drained fens. For carabid beetles, however, species richness and the number of stenotopic species were highest on rewetted fens. Rewetting caused the replacement of generalist carabids by wetland specialists, but did not provide suitable habitat for specialist fen carabids or for plant species of oligo‐ or mesotrophic fen communities. Therefore, raising the water table on fens with nutrient‐rich, degraded peat was not sufficient for restoring species assemblages of intact fens, although water level was the most important environmental factor separating species assemblages. Our study illustrated that insects and plants may respond differentially to restoration, stressing the need to consider different taxa when assessing the efficiency of fen restoration. Furthermore, species assemblages of intact fens could not be restored within 14 years, highlighting the importance of conserving pristine habitat.     

Reconstructing pre-impact vegetation cover in modified landscapes using environmental modelling, historical surveys and remnant vegetation data: a case study in the Fleurieu Peninsula, South Australia

Aim To investigate the application of environmental modelling to reconstructive mapping of pre‐impact vegetation using historical survey records and remnant vegetation data. Location The higher elevation regions of the Fleurieu Peninsula region in South Australia were selected as a case study. The Fleurieu Peninsula is an area typical of many agricultural regions in temperate Australia that have undergone massive environmental transformation since European settlement. Around 9% of the present land cover is remnant vegetation and historical survey records from the ad 1880s exist. It is a region with strong gradients in climate and topography. Methods Records of pre‐impact vegetation distribution made in surveyors’ field notebooks were transcribed into a geographical information system and the spatial and classificatory accuracy of these records was assessed. Maps of remnant vegetation distribution were obtained. Analysis was undertaken to quantify the environmental domains of historical survey record and remnant vegetation data to selected meso‐scaled climatic parameters and topo‐scaled terrain‐related indices at a 20 m resolution. An exploratory analytical procedure was used to quantify the probability of occurrence of vegetation types in environmental domains. Probability models spatially extended to geographical space produce maps of the probability of occurrence of vegetation types. Individual probability maps were combined to produce a pre‐impact vegetation map of the region. Results Surveyors’ field notebook records provide reliable information that is accurately locatable to levels of resolution such that the vegetation data can be spatially correlated with environmental variables generated on 20 m resolution environmental data sets. Historical survey records of vegetation were weakly correlated with the topo‐scaled environmental variables but were correlated with meso‐scaled climate. Remnant vegetation records similarly not only correlated to climate but also displayed stronger relationships with the topo‐scaled environmental variables, particularly slope. Main conclusions A major conclusion of this study is that multiple sources of evidence are required to reconstruct past vegetation patterns in heavily transformed region. Neither the remnant vegetation data nor historical survey records provided adequate data sets on their own to reconstruct the pre‐impact vegetation of the Fleurieu Peninsula. Multiple sources of evidence provide the only means of assessing the environmental and historical representativeness of data sets. The spatial distribution of historical survey records was more environmentally representative than remnant vegetation data, which reflect biases due to land clearance. Historical survey records were also shown to be classificatory and spatially accurate, thus are suitable for quantitative spatial analyses. Analysis of different spatial vegetation data sets in an environmental modelling framework provided a rigorous means of assessing and comparing respective data sets as well as mapping their predicted distributions based on quantitative correlations. The method could be usefully applied to other regions where predictions of pre‐impact vegetation cover are required.     

The historical context of contemporary climatic adaptation: a case study in the climatically dynamic and environmentally complex southwestern United States

The process of adaptation can be highly dependent upon historical and contemporary factors, especially in environmentally and topographically complex regions affected by Pleistocene glaciations. Here, we investigate Hilaria jamesii (Poaceae), a dryland C₄ graminoid, to test how patterns of adaptive genetic variation are linked to its glacial and post-glacial history. We show that the species persisted in a single, southern refugium during the last glacial period and subsequently migrated throughout its current distribution concurrent with post-glacial warming. The species’ putative adaptive genetic variation correlates with climatic gradients (e.g. monsoon precipitation and mean diurnal temperature range) that covary with the species’ probable route of demographic expansion. The short timescale and multiple climatic dimensions of adaptation imply that natural selection acted primarily upon standing genetic variation. These findings suggest that restoration and conservation practices should prioritize the maintenance of standing genetic variation to ensure that species have the capacity to respond to future environmental changes.     

Assessing extinction-risk of endangered plants using species distribution models: a case study of habitat depletion caused by the spread of greenhouses

The species distribution models (SDMs) are useful tools for investigating rare and endangered species as well as the environmental variables affecting them. In this paper, we propose the application of SDMs to assess the extinction-risk of plant species in relation to the spread of greenhouses in a Mediterranean landscape, where habitat depletion is one of the main causes of biodiversity loss. For this purpose, presence records of the model species (Linaria nigricans, a endemic and threatened species) and the greenhouses, a dataset of environmental variables, and different only presence-based modelling algorithms (Bioclim, Domain, GARP, MaxEnt and ENFA) were used to build SDMs for L. nigricans as well as for greenhouses. To evaluate the models a modified approach of the area-under-curve ROC was applied. Combining the most accurate models, we generated an extinction-risk model of L. nigricans populations, which enabled us to assess the sustainability of the most threatened populations. Our results show that is possible to model greenhouses spreading as a “biological invasion”. The procedure explained and used in this work is quite novel, and offers an objective spatial criterion intended for the management of natural resources and for the conservation of the biodiversity in areas threatened by habitat depletion processes as particular as greenhouses expansion.     

Development and field validation of a regional,management‐scale habitat model: A koala Phascolarctos cinereus case study

Species distribution models have great potential to efficiently guide management for threatened species, especially for those that are rare or cryptic. We used MaxEnt to develop a regional‐scale model for the koala Phascolarctos cinereus at a resolution (250 m) that could be used to guide management. To ensure the model was fit for purpose, we placed emphasis on validating the model using independently‐collected field data. We reduced substantial spatial clustering of records in coastal urban areas using a 2‐km spatial filter and by modeling separately two subregions separated by the 500‐m elevational contour. A bias file was prepared that accounted for variable survey effort. Frequency of wildfire, soil type, floristics and elevation had the highest relative contribution to the model, while a number of other variables made minor contributions. The model was effective in discriminating different habitat suitability classes when compared with koala records not used in modeling. We validated the MaxEnt model at 65 ground‐truth sites using independent data on koala occupancy (acoustic sampling) and habitat quality (browse tree availability). Koala bellows (n = 276) were analyzed in an occupancy modeling framework, while site habitat quality was indexed based on browse trees. Field validation demonstrated a linear increase in koala occupancy with higher modeled habitat suitability at ground‐truth sites. Similarly, a site habitat quality index at ground‐truth sites was correlated positively with modeled habitat suitability. The MaxEnt model provided a better fit to estimated koala occupancy than the site‐based habitat quality index, probably because many variables were considered simultaneously by the model rather than just browse species. The positive relationship of the model with both site occupancy and habitat quality indicates that the model is fit for application at relevant management scales. Field‐validated models of similar resolution would assist in guiding management of conservation‐dependent species.     

Phylogeography,historical demography and habitat suitability modelling of freshwater fishes inhabiting seasonally fluctuating Mediterranean river systems: a case study using the Iberian cyprinid Squalius valentinus

The Mediterranean freshwater fish fauna has evolved under constraints imposed by the seasonal weather/hydrological patterns that define the Mediterranean climate. These conditions have influenced the genetic and demographic structure of aquatic communities since their origins in the Mid‐Pliocene. Freshwater species in Mediterranean‐type climates will likely constitute genetically well‐differentiated populations, to varying extents depending on basin size, as a consequence of fragmentation resulting from drought/flood cycles. We developed an integrative framework to study the spatial patterns in genetic diversity, demographic trends, habitat suitability modelling and landscape genetics, to evaluate the evolutionary response of Mediterranean‐type freshwater fish to seasonal fluctuations in weather. To test this evolutionary response, the model species used was Squalius valentinus, an endemic cyprinid of the Spanish Levantine area, where seasonal weather fluctuations are extreme, although our findings may be extrapolated to other Mediterranean‐type species. Our results underscore the significant role of the Mediterranean climate, along with Pleistocene glaciations, in diversification of S. valentinus. We found higher nuclear diversity in larger drainage basins, but higher mitochondrial diversity correlated to habitat suitability rather than basin size. We also found strong correlation between genetic structure and climatic factors associated with Mediterranean seasonality. Demographic and migration analyses suggested population expansion during glacial periods that also contributed to the current genetic structure of S. valentinus populations. The inferred models support the significant contribution of precipitation and temperature to S. valentinus habitat suitability and allow recognizing areas of habitat stability. We highlight the importance of stable habitat conditions, fostered by typical karstic springs found on the Mediterranean littoral coasts, for the preservation of freshwater species inhabiting seasonally fluctuating river systems.     

Constructing and validating a transferable epidemic risk index in data scarce environments using open data: A case study for dengue in the Philippines

Epidemics are among the most costly and destructive natural hazards globally. To reduce the impacts of infectious disease outbreaks, the development of a risk index for infectious diseases can be effective, by shifting infectious disease control from emergency response to early detection and prevention.In this study, we introduce a methodology to construct and validate an epidemic risk index using only open data, with a specific focus on scalability. The external validation of our risk index makes use of distance sampling to correct for underreporting of infections, which is often a major source of biases, based on geographical accessibility to health facilities. We apply this methodology to assess the risk of dengue in the Philippines.The results show that the computed dengue risk correlates well with standard epidemiological metrics, i.e. dengue incidence (p = 0.002). Here, dengue risk constitutes of the two dimensions susceptibility and exposure. Susceptibility was particularly associated with dengue incidence (p = 0.048) and dengue case fatality rate (CFR) (p = 0.029). Exposure had lower correlations to dengue incidence (p = 0.193) and CFR (p = 0.162). Highest risk indices were seen in the south of the country, mainly among regions with relatively high susceptibility to dengue outbreaks.Our findings reflect that the modelled epidemic risk index is a strong indication of sub-national dengue disease patterns and has therefore proven suitability for disease risk assessments in the absence of timely epidemiological data. The presented methodology enables the construction of a practical, evidence-based tool to support public health and humanitarian decision-making processes with simple, understandable metrics. The index overcomes the main limitations of existing indices in terms of construction and actionability.     

北京市白河和潮河流域生态健康评价

选取北京市重要的饮用水源密云水库上游白河和潮河流域,结合北京山区流域生态现状,构建了涵盖水域生境结构、水生生物、生态压力和陆域生态格局与功能、生态压力5大类13项指标的评价指标体系,开展了流域生态健康评价。结果表明白河和潮河流域的健康状态整体处于良好等级,但水生生物和陆域生态格局状况相对较差。14个子流域的健康状况差异并不显著,琉璃河、白河下段、汤河上游的健康状况相对较好,潮河中下段和小汤河的健康状况相对较差。流域内不合理的畜禽养殖、岸边带种植及民俗旅游是导致流域生态健康退化的主要原因,建议加强污染负荷排放的控制和监管涉水活动对水生生境的干扰以改善流域健康状况,并重点关注可指示水生态系统早期退化的生物指数,以实现可持续性和适应性的流域管理,保障密云水库的水生态安全。     

Tropical niche conservatism as a historical narrative hypothesis for the Neotropics: a case study using the fly family Muscidae

Aim We evaluate the extent to which the tropical conservatism hypothesis can explain the evolutionary development of the Muscidae. Furthermore, we compare the geographical patterns of muscid phylogenetic structure with biogeographical regions that have been identified for Neotropical insects. Location Central and South America. Methods We modelled the geographic distributions of 658 species using Maxent and 19 environmental variables. A generic‐level supertree of the Muscidae was assembled using matrix representation with parsimony and used to map the geographic pattern of mean root distance (MRD), a metric of the relative evolutionary development of assemblages. Regression models (ordinary least squares and regression trees) were used to examine temperature and other environmental correlates of MRD to explore potential environmental drivers of muscid diversification. We used the regression tree results to recognize variable intervals that best explained MRD, and these intervals were mapped to recognize and compare with biogeographical regions of Neotropical insects. Results The geographic pattern of MRD was consistent with the tropical conservatism hypothesis: species in genera that diversified relatively early, as measured by their distance from the tree root, dominate lowland tropical South America, whereas species in genera that diversified more recently occupy extra‐tropical areas, sub‐Antarctic areas and the Andean highlands. Temperature was the strongest correlate of MRD. Three biogeographical regions were recognized and they coincided with two regions known for insects. Main conclusions Evolutionary responses of muscid flies to post‐Eocene climate change taking the form of an expansion of a tropical group into regions with colder climates may be fundamental to explaining their distribution in the Neotropics. Our biogeographical regions delimited by temperature and the phylogenetic metric, surrogates of the tropical conservatism hypothesis, were very similar to general insect patterns, supporting the ‘tropical origin and evolutionary response to climate cooling’ as a broadly based historical narrative for the Neotropics.     

Cork-oak woodlands as key-habitats for biodiversity conservation in Mediterranean landscapes: a case study using rove and ground beetles (Coleoptera: Staphylinidae, Carabidae)

Land-use intensification in Mediterranean agro-forest systems became a pressure on biodiversity, concerning particularly the woodland sensitive species. In 2001, the effects of a land-use gradient from old-growth cork-oak forest to a homogeneous agricultural area were assessed using rove beetles as indicators in a Mediterranean landscape. The aim was to find which species were negatively affected by land-use intensification at the landscape level and whether they benefited from cork-oak patches occurring along the land-use gradient. A total of 3,196 rove beetles from 88 taxa were sampled from all landscape types. Agricultural area recorded significantly higher numbers of abundance and species richness in relation to the cork-oak mosaics, i.e. the old-growth forest and the managed agro-forest landscapes (montados). Moreover, 70% of rove beetle indicator species common enough to be tested by IndVal displayed their highest indicator value for agriculture, showing a lower number of woodland indicators in comparison to ground beetles. Nevertheless, one rove beetle taxon was considered a specialist of closed woodland mosaics while no specialist ground beetle was found for that landscape typology. Some rare rove beetle species were also important in typifying diversity patterns of old-growth cork-oak forests. Hence, future management in Mediterranean landscapes should take into account not only indicator species common enough to be tested by IndVal, but also rare and endemic species. Considering the added value of cork-oak woodland cover for sensitive rove and ground beetle diversity, the strengthening of cork-oak woodland connectivity seems to be a crucial management that is required in agricultural Mediterranean landscapes.