The second Southern African Bird Atlas Project: Causes and consequences of geographical sampling bias

Using the Southern African Bird Atlas Project (SABAP2) as a case study, we examine the possible determinants of spatial bias in volunteer sampling effort and how well such biased data represent environmental gradients across the area covered by the atlas. For each province in South Africa, we used generalized linear mixed models to determine the combination of variables that explain spatial variation in sampling effort (number of visits per 5′ × 5′ grid cell, or “pentad”). The explanatory variables were distance to major road and exceptional birding locations or “sampling hubs,” percentage cover of protected, urban, and cultivated area, and the climate variables mean annual precipitation, winter temperatures, and summer temperatures. Further, we used the climate variables and plant biomes to define subsets of pentads representing environmental zones across South Africa, Lesotho, and Swaziland. For each environmental zone, we quantified sampling intensity, and we assessed sampling completeness with species accumulation curves fitted to the asymptotic Lomolino model. Sampling effort was highest close to sampling hubs, major roads, urban areas, and protected areas. Cultivated area and the climate variables were less important. Further, environmental zones were not evenly represented by current data and the zones varied in the amount of sampling required representing the species that are present. SABAP2 volunteers' preferences in birding locations cause spatial bias in the dataset that should be taken into account when analyzing these data. Large parts of South Africa remain underrepresented, which may restrict the kind of ecological questions that may be addressed. However, sampling bias may be improved by directing volunteers toward undersampled regions while taking into account volunteer preferences.     

Geographical sampling bias and its implications for conservation priorities in Africa

Aim To design and apply statistical tests for measuring sampling bias in the raw data used to the determine priority areas for conservation, and to discuss their impact on conservation analyses for the region. Location Sub‐Saharan Africa. Methods An extensive data set comprising 78,083 vouchered locality records for 1068 passerine birds in sub‐Saharan Africa has been assembled. Using geographical information systems, we designed and applied two tests to determine if sampling of these taxa was biased. First, we detected possible biases because of accessibility by measuring the proximity of each record to cities, rivers and roads. Second, we quantified the intensity of sampling of each species inside and surrounding proposed conservation priority areas and compared it with sampling intensity in non‐priority areas. We applied statistical tests to determine if the distribution of these sampling records deviated significantly from random distributions. Results The analyses show that the location and intensity of collecting have historically been heavily influenced by accessibility. Sampling localities show dense, significant aggregation around city limits, and along rivers and roads. When examining the collecting sites of each individual species, the pattern of sampling has been significantly concentrated within and immediately surrounding areas now designated as conservation priorities. Main conclusions Assessment of patterns of species richness and endemicity at the scale useful for establishing conservation priorities, below the continental level, undoubtedly reflects biases in taxonomic sampling. This is especially problematic for priorities established using the criterion of complementarity because the estimated spatial costs of this approach are highly sensitive to sampling artefacts. Hence such conservation priorities should be interpreted with caution proportional to the bias found. We argue that conservation priority setting analyses require (1) statistical tests to detect these biases, and (2) data treatment to reflect species distribution rather than patterns of collecting effort.     

Population and geographic range dynamics: implications for conservation planning

Continuing downward trends in the population sizes of many species, in the conservation status of threatened species, and in the quality, extent and connectedness of habitats are of increasing concern. Identifying the attributes of declining populations will help predict how biodiversity will be impacted and guide conservation actions. However, the drivers of biodiversity declines have changed over time and average trends in abundance or distributional change hide significant variation among species. While some populations are declining rapidly, the majority remain relatively stable and others are increasing. Here we dissect out some of the changing drivers of population and geographic range change, and identify biological and geographical correlates of winners and losers in two large datasets covering local population sizes of vertebrates since 1970 and the distributions of Galliform birds over the last two centuries. We find weak evidence for ecological and biological traits being predictors of local decline in range or abundance, but stronger evidence for the role of local anthropogenic threats and environmental change. An improved understanding of the dynamics of threat processes and how they may affect different species will help to guide better conservation planning in a continuously changing world.     

State-dependent sampling bias in insects: implications for monitoring western tarnished plant bugs

Insect populations vary in the proportion of individuals exhibiting a particular ‘state’ (e.g., developmental stage, sex, egg load, or nutritional status). Because an insect's developmental state often determines both its size and its behavior, it is likely that this will also affect the probability of being sampled. We propose that a comprehensive approach to pest management must consider the interaction between the structure of a pest population (i.e., the relative number of individuals in each state) and any state‐dependent sampling bias. To illustrate the usefulness of this method we sampled populations of the western tarnished pest bug, Lygus hesperus Knight (Heteroptera: Miridae), in cotton fields. Our sampling technique utilized large cages to measure the absolute densities of each L. hesperus stage and adult sex within a population. This technique allowed us to document a wide range of absolute stage structures and sex ratios across 10 L. hesperus populations in California. Using a combination of cage samples and sweep net samples, we quantified the state‐dependent sampling bias by calculating the efficiency of sweep sampling as a function of L. hesperus developmental stage and sex. We found that the efficiency of sweep nets increased steadily with each successive developmental stage (i.e., nymphal instar) of L. hesperus. We also found that sweep nets are slightly more efficient in capturing male vs. female L. hesperus adults. Since other studies have documented that the stage and sex of L. hesperus can affect feeding impact on cotton flower buds, our results suggest that accurate predictions of Lygus damage will need to incorporate stage and sex‐dependent sampling biases.     

Modelling the distribution of Bonelli's eagle in Spain: implications for conservation planning

Bonelli's eagle, Hieraaetus fasciatus, has recently suffered a severe population decline and is currently endangered. Spain supports about 70% of the European population. We used stepwise logistic regression on a set of environmental, spatial and human variables to model Bonelli's eagle distribution in the 5167 UTM 10 × 10 km quadrats of peninsular Spain. We obtained a model based on 16 variables, which allowed us to identify favourable and unfavourable areas for this species in Spain, as well as intermediate favourability areas. We assessed the stepwise progression of the model by comparing the model's predictions in each step with those of the final model, and selected a parsimonious explanatory model based on three variables — slope, July temperature and precipitation — comprising 76% of the predictive capacity of the final model. The reported presences in favourable and unfavourable areas suggest a source–sink dynamics in Bonelli's eagle populations. The fragmented spatial structure of the favourable areas suggests the existence of a superimposed metapopulation dynamics. Previous LIFE (The Financial Instrument of the European Union for the Environment and Nature) projects for the conservation of this species have focused mainly on the northern limit of its range, where the sharpest population decline has been recorded. In these areas, favourability is low and Bonelli's eagle populations are probably maintained by the immigration of juveniles produced in more favourable zones. However, southern populations, although stable, show signs of reduction in productivity, which could menace the population sizes in the whole study area. We suggest that conservation efforts should focus also on known favourable areas, which might favour population persistence in unfavourable areas through dispersal.     

Priority areas for the conservation of South African vegetation: a coarse-filter approach

Abstract.  South Africa has an important responsibility to global biodiversity conservation, but a largely inadequate conservation area network for addressing this responsibility. This study employs a coarse-filter approach based on 68 potential vegetation units to identify areas that are largely transformed, degraded or impacted upon by road-effects. The assessment highlights broad vegetation types that face high biodiversity losses currently or in the near future due to human impacts. Most vegetation types contain large tracts of natural vegetation, with little degradation, transformation or impacts from road networks. Regions in the grasslands, fynbos and forest biomes are worst affected. Very few of the vegetation types are adequately protected according to the IUCN's 10% protected area conservation target, with the fynbos and savanna biomes containing a few vegetation types that do achieve this arbitrary goal. This investigation identifies areas where limited conservation resources should be concentrated by identifying vegetation types with high levels of anthropogenic land use threats and associated current and potential biodiversity loss.     

Spatial ecology of freshwater eels in South Africa: implications for conservation

Hydrobiologia - Four freshwater eel species (Anguilla spp.) occur in southern African rivers that are increasingly anthropogenically modified. Information on movements, habitat use and overlap by...     

Avian diversity and endemism in Namibia: patterns from the Southern African Bird Atlas Project

Namibia supports a highly diverse avifauna of 644 species, including over 90 species endemic to the southern African subregion and 13 species endemic to the country. Patterns of species diversity in relation to protected areas and habitat types were analysed using data from the Southern African Bird Atlas Project. A modified Shannon index appropriate for atlas data was used to derive an index of diversity for all species, wetland, terrestrial, threatened, and regional endemic species. Species richness for Namibian endemics was mapped. Overall species diversity is highest in the northeast of Namibia where wetland and riparian habitats coincide. Both wetland and terrestrial species show highest diversity in this area. The greatest diversity of southern African endemics falls within the Savanna-Karoo systems. Several key areas are identified for red data species, including the Caprivi Strip, Kunene and Orange Rivers, coastal wetlands and ephemeral river mouths and pans. This highlights the pressures operating on wetland and riparian habitats in arid environments. Concentrations of Namibian endemics are found in the northwestern (Kaoko) escarpment of the country. Although much of the area of high diversity of wetland, terrestrial and red data species falls within protected areas, national and regional endemics are poorly represented within national parks.     

Scale effects in species distribution models: implications for conservation planning under climate change

Predictions of future species' ranges under climate change are needed for conservation planning, for which species distribution models (SDMs) are widely used. However, global climate model-based (GCM) output grids can bias the area identified as suitable when these are used as SDM predictor variables, because GCM outputs, typically at least 50x50 km, are biologically coarse. We tested the assumption that species ranges can be equally well portrayed in SDMs operating on base data of different grid sizes by comparing SDM performance statistics and area selected by four SDMs run at seven grid sizes, for nine species of contrasting range size. Area selected was disproportionately larger for SDMs run on larger grid sizes, indicating a cut-off point above which model results were less reliable. Up to 2.89 times more species range area was selected by SDMs operating on grids above 50x50 km, compared to SDMs operating at 1 km2. Spatial congruence between areas selected as range also diverged as grid size increased, particularly for species with ranges between 20000 and 90000 km2. These results indicate the need for caution when using such data to plan future protected areas, because an overly large predicted range could lead to inappropriate reserve location selection.     

Measurement and mapping of avian diversity in southern Africa: implications for conservation planning

The potential and problems of using species diversity information, derived from the Southern African Bird Atlas Project (SABAP), are examined. Atlas data were analysed and the problem of uneven sampling effort was ameliorated through an application of an index of diversity. Maps of diversity for various suites of species are considered in relation to their implications for conservation planning. An approach to the identification of high-priority areas for conservation, based on an index of diversity, is described and called the Compatible Sets Approach. Birds in the grassland biome are used to illustrate the principles of the approach.     

Sampling mobile oceanic fishes and sharks: implications for fisheries and conservation planning

Tuna, billfish, and oceanic sharks [hereafter referred to as ‘mobile oceanic fishes and sharks’ (MOFS)] are characterised by conservative life‐history strategies and highly migratory behaviour across large, transnational ranges. Intense exploitation over the past 65 years by a rapidly expanding high‐seas fishing fleet has left many populations depleted, with consequences at the ecosystem level due to top‐down control and trophic cascades. Despite increases in both CITES and IUCN Red Listings, the demographic trajectories of oceanic sharks and billfish are poorly quantified and resolved at geographic and population levels. Amongst MOFS trajectories, those of tunas are generally considered better understood, yet several populations remain either overfished or of unknown status. MOFS population trends and declines therefore remain contentious, partly due to challenges in deriving accurate abundance and biomass indices. Two major management strategies are currently recognised to address conservation issues surrounding MOFS: (i) internationally ratified legal frameworks and their associated regional fisheries management organisations (RFMOs); and (ii) spatio‐temporal fishery closures, including no‐take marine protected areas (MPAs). In this context, we first review fishery‐dependent studies relying on data derived from catch records and from material accessible through fishing extraction, under the umbrella of RFMO‐administrated management. Challenges in interpreting catch statistics notwithstanding, we find that fishery‐dependent studies have enhanced the accuracy of biomass indices and the management strategies they inform, by addressing biases in reporting and non‐random effort, and predicting drivers of spatial variability across meso‐ and oceanic scales in order to inform stock assessments. By contrast and motivated by the increase in global MPA coverage restricting extractive activities, we then detail ways in which fishery‐independent methods are increasingly improving and steering management by exploring facets of MOFS ecology thus far poorly grasped. Advances in telemetry are increasingly used to explore ontogenic and seasonal movements, and provide means to consider MOFS migration corridors and residency patterns. The characterisation of trophic relationships and prey distribution through biochemical analysis and hydro‐acoustics surveys has enabled the tracking of dietary shifts and mapping of high‐quality foraging grounds. We conclude that while a scientific framework is available to inform initial design and subsequent implementation of MPAs, there is a shortage in the capacity to answer basic but critical questions about MOFS ecology (who, when, where?) required to track populations non‐extractively, thereby presenting a barrier to assessing empirically the performance of MPA‐based management for MOFS. This sampling gap is exacerbated by the increased establishment of large (>10000 km²) and very large MPAs (VLMPAs, >100000 km²) ‐ great expanses of ocean lacking effective monitoring strategies and survey regimes appropriate to those scales. To address this shortcoming, we demonstrate the use of a non‐extractive protocol to measure MOFS population recovery and MPA efficiency. We further identify technological avenues for monitoring at the VLMPA scale, through the use of spotter planes, drones, satellite technology, and horizontal acoustics, and highlight their relevance to the ecosystem‐based framework of MOFS management.     

Geographic discrepancies between global and local rarity richness patterns and the implications for conservation

The emerging interest in the biological and conservation significance of locally rare species prompts a number of questions about their correspondence with other categories of biodiversity, especially global rarity. Here we present an analysis of the correspondence between the distributions of globally and locally rare plants. Using biological hotspots of rarity as our framework, we evaluate the extent to which conservation of globally rare plants will act as a surrogate for conservation of locally rare taxa. Subsequently, we aim to identify gaps between rarity hotspots and protected land to guide conservation planning. We compiled distribution data for globally and locally rare plants from botanically diverse Napa County, California into a geographic information system. We then generated richness maps highlighting hotspots of global and local rarity. Following this, we overlaid the distribution of these hotspots with the distribution of protected lands to identify conservation gaps. Based on occupancy of 1 km² grid cells, we found that over half of Napa County is occupied by at least one globally or locally rare plant. Hotspots of global and local rarity occurred in a substantially smaller portion of the county. Of these hotspots, less than 5% were classified as multi-scale hotspots, i.e. they were hotspots of global and local rarity. Although, several hotspots corresponded with the 483 km² of protected lands in Napa County, some of the richest areas did not. Thus, our results show that there are important conservation gaps in Napa County. Furthermore, if only hotspots of global rarity are preserved, only a subset of locally rare plants will be protected. Therefore, conservation of global, local, and multi-scale hotspots needs serious consideration if the goals are to protect a larger variety of biological attributes, prevent extinction, and limit extirpation in Napa County.     

Land management implications for ecosystem services in a South African rangeland

In South Africa, restoration and sustainable management of historically overgrazed and degraded rangelands are promoted to increase biodiversity and ecosystem service provision. This study evaluates different land management scenarios in terms of ecosystem services in a South African rangeland, the Baviaanskloof catchment. As measured data were limited, we used simple models to quantify and map the effect of the different combination of agricultural, nature conservation and restoration practices on multiple ecosystem services. The land management scenarios were evaluated against management targets set for individual ecosystem services. Results highlight how the provision of ecosystem services is related to land management as unmanaged, pristine ecosystems provide a different mix of ecosystem services than ecosystems recently restored or managed as grazing lands. Results also indicate that historically overgrazed lands provide no forage, may retain 40% less sediment and have 38% lower biodiversity, while providing 60% more fuel wood and supplying two and half times more water (i.e. retaining less water), than pristine or restored lands. We conclude that a combination of light grazing, low input agriculture, nature conservation and restoration is the best for the sufficient provision of multiple ecosystem services. Applying such mixed management would improve biodiversity, ecotourism and maintain forage production and regulating services on farmers’ land. This management option also fits into and further optimizes local decision-makers’ vision regarding the future management of the area.     

Downscaling European species atlas distributions to a finer resolution: implications for conservation planning

Aim One of the limitations to using species’ distribution atlases in conservation planning is their coarse resolution relative to the needs of local planners. In this study, a simple approach to downscale original species atlas distributions to a finer resolution is outlined. If such a procedure yielded accurate downscaled predictions, then it could be an aid to using available distribution atlases in real‐world local conservation decisions. Location Europe. Methods An iterative procedure based on generalized additive modelling is used to downscale original European 50 × 50 km distributions of 2189 plant and terrestrial vertebrate species to c. 10 × 10 km grid resolution. Models are trained on 70% of the original data and evaluated on the remaining 30%, using the receiver operating characteristic (ROC) procedure. Fitted models are then interpolated to a finer resolution. A British dataset comprising distributions of 81 passerine‐bird species in a 10 × 10 km grid is used as a test bed to assess the accuracy of the downscaled predictions. European‐wide, downscaled predictions are further evaluated in terms of their ability to reproduce: (1) spatial patterns of coincidence in species richness scores among different groups; and (2) spatial patterns of coincidence in richness, rarity and complementarity hotspots. Results There was a generally good agreement between downscaled and observed fine‐resolution distributions for passerine species in Britain (median Jaccard similarity = 70%; lower quartile = 36%; upper quartile = 88%). In contrast, the correlation between downscaled and observed passerine species richness was relatively low (rho = 0.31) indicating a pattern of error propagation through the process of overlaying downscaled distributions for many species. It was also found that measures of model accuracy in fitting original data (ROC) were a poor predictor of models’ ability to interpolate distributions at fine resolutions (rho = ?0.10). Although European hotspots were not fully coincident between observed and modelled coarse‐resolution data, or between modelled coarse resolution and modelled downscaled data, there was evidence that downscaled distributions were able to maintain original cross‐taxon coincidence of species‐richness scores, at least for terrestrial vertebrate groups. Downscaled distributions were also able to uncover important environmental gradients otherwise blurred by coarse‐resolution data. Main conclusions Despite uncertainties, downscaling procedures may prove useful to identify reserves that are more meaningfully related to local patterns of environmental variation. Potential errors arising from the presence of false positives may be reduced if downscaled‐distribution records projected to occur outside the range of original coarse‐resolution data are excluded. However, the usefulness of this procedure may be limited to data‐rich regions. If downscaling procedures are applied to data‐poor regions, then there is a need to undertake further research to understand the structure of error in models. In particular, it would be important to investigate which species are poorly modelled, where and why. Without such an assessment it is difficult to support unsupervised use of downscaled data in most real‐world situations.     

Geographic patterns of genetic variation in four Neotropical rodents: conservation implications for small game mammals in French Guiana

The Neotropics contributes significantly to global biodiversity yet little is known about its mammalian fauna. Given our limited knowledge, concerns are that extinctions at the local level may cause a decline in genetic diversity through the loss of unique alleles. Here we report the geographical population structure of four rodent species from French Guiana: Dasyprocta leporina , Agouti paca , Proechimys cayennensis and P. cuvieri . Two of them ( Dasyprocta and Agouti ) are commonly harvested throughout the country for subsistence and/or game hunting. Cytochrome b and control region sequences revealed the presence of a number of maternal lineages occurring in sympatry throughout French Guiana. We applied two cytochrome b rodent clock calibrations (7.5% and 12% per million years) to our data, and placed the divergence of the maternal lineages to between 160 000 and 260 000 years ago for the more diverse D. leporina and P. cuvieri , and between 66 000 and 46 000 years ago for the more recent A. paca and P. cayennensis . The clades appear to be widespread throughout South America as indicated by specimens sampled in Brazil, Peru, and Venezuela. At the population level, AMOVA revealed little or no geographical structure within French Guiana. However, this conclusion is based on a single genetic marker and relatively few specimens.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 203–218.     

Geographic distribution of tree species occurring in the region of Manaus, Brazil: implications for regional diversity and conservation

The alpha-diversity of trees found in the region of Manaus, Brazil is among the highest recorded for one-hectare plots in Amazonia or any tropical forest. Based on a survey of the distributions of 2541 Neotropical tree species, we analyzed the geographic distribution of 364 species of terra firme forest trees that occur in the region and that are not edaphic specialists. Fifteen distinct distribution patterns were recognized for trees occurring in Manaus. The great majority of species (84.9%) have continuous, somewhat restricted distributions, 35 (9.6%) show broad distributions and 20 species (5.5%) show disjunction between Amazonia and Eastern Brazil. A remarkable 150 (41.2%) of these species showed the region of Manaus as one of their distribution limits. Using the same pool of 2541 species distributions, the percentage of species with a distribution limit in Manaus was compared with that for other localities known to be centers of botanical collection. The null hypothesis that the difference in proportion of species with distribution limits among these localities and Manaus is insignificant was rejected. We conclude that the results are not an artifact of collecting density, that Manaus is indeed a crossroads of distinct phytogeographic regions, and that this explains part of the high species diversity of trees in the region of Manaus. A number of scenarios proposed for the Pleistocene in Amazonia postulate some degree of fragmentation of Amazonian forests or at least populations. As much as these theories may conflict with each other in some respects, they are compatible with the concept of Manaus as a region of re-convergence of isolated or disrupted floras and faunas. The significance of the vicinity of Manaus in the history of the Amazon flora and its current status as a repository for surprisingly high tree diversity highlights the need to make this region a conservation priority.     

Predicting global abundance of a threatened species from its occurrence: implications for conservation planning

Aim Global abundance is an important characteristic of a species that is correlated with geographical distribution and body size. Despite its importance these estimates are not available since reliable field estimates are either expensive or difficult to obtain. Based on the relationship between a species’ local abundance and distribution, some authors propose that abundance can be obtained through spatial distribution data from maps plotted at different scales. This has never been tested over the entire geographical range of a species. Thus, the aim of this study was to estimate global abundance of the Neotropical primate Brachyteles hypoxanthus (northern muriqui) and compare the results with available field estimates. Location From southern Bahia to Minas Gerais and Espírito Santo states, in the Brazilian Atlantic rain forest. Methods We compiled 25 recent occurrence localities of B. hypoxanthus and plotted them in grid cells of five different sizes (1, 25, 50, 75 and 100 km per side) to evaluate the performance and accuracy of abundance estimates over a wide range of scales. The abundance estimates were obtained by the negative binomial distribution (NBD) method and corrected by average group size to take into account primate social habits. To assess the accuracy of the method, the predicted abundances were then compared to recent independent field estimates. Results The NBD estimates were quite accurate in predicting B. hypoxanthus global abundance, once the gregarious habits of this species are taken into account. The predicted abundance estimates were not statistically different from those obtained from field estimates. Main conclusions The NBD method seems to be a quick and reliable approach to estimate species abundance once several limiting factors are taken into account, and can greatly impact conservation planning, but further applications in macroecological and ecological theory testing needs improvement of the method.     

Quantifying the spatial ecology of wide-ranging marine species in the Gulf of California: implications for marine conservation planning

There is growing interest in systematic establishment of marine protected area (MPA) networks and representative conservation sites. This movement toward networks of no-take zones requires that reserves are deliberately and adequately spaced for connectivity. Here, we test the network functionality of an ecoregional assessment configuration of marine conservation areas by evaluating the habitat protection and connectivity offered to wide-ranging fauna in the Gulf of California (GOC, Mexico). We first use expert opinion to identify representative species of wide-ranging fauna of the GOC. These include leopard grouper, hammerhead sharks, California brown pelicans and green sea turtles. Analyzing habitat models with both structural and functional connectivity indexes, our results indicate that the configuration includes large proportions of biologically important habitat for the four species considered (25-40%), particularly, the best quality habitats (46-57%). Our results also show that connectivity levels offered by the conservation area design for these four species may be similar to connectivity levels offered by the entire Gulf of California, thus indicating that connectivity offered by the areas may resemble natural connectivity. The selected focal species comprise different life histories among marine or marine-related vertebrates and are associated with those habitats holding the most biodiversity values (i.e. coastal habitats); our results thus suggest that the proposed configuration may function as a network for connectivity and may adequately represent the marine megafauna in the GOC, including the potential connectivity among habitat patches. This work highlights the range of approaches that can be used to quantify habitat protection and connectivity for wide-ranging marine species in marine reserve networks.