The Importance of Biodiversity E-infrastructures for Megadiverse Countries

Addressing the challenges of biodiversity conservation and sustainable development requires global cooperation, support structures, and new governance models to integrate diverse initiatives and achieve massive, open exchange of data, tools, and technology. The traditional paradigm of sharing scientific knowledge through publications is not sufficient to meet contemporary demands that require not only the results but also data, knowledge, and skills to analyze the data. E-infrastructures are key in facilitating access to data and providing the framework for collaboration. Here we discuss the importance of e-infrastructures of public interest and the lack of long-term funding policies. We present the example of Brazil’s speciesLink network, an e-infrastructure that provides free and open access to biodiversity primary data and associated tools. SpeciesLink currently integrates 382 datasets from 135 national institutions and 13 institutions from abroad, openly sharing ~7.4 million records, 94% of which are associated to voucher specimens. Just as important as the data is the network of data providers and users. In 2014, more than 95% of its users were from Brazil, demonstrating the importance of local e-infrastructures in enabling and promoting local use of biodiversity data and knowledge. From the outset, speciesLink has been sustained through project-based funding, normally public grants for 2–4-year periods. In between projects, there are short-term crises in trying to keep the system operational, a fact that has also been observed in global biodiversity portals, as well as in social and physical sciences platforms and even in computing services portals. In the last decade, the open access movement propelled the development of many web platforms for sharing data. Adequate policies unfortunately did not follow the same tempo, and now many initiatives may perish.     

An ED-based Protocol for Optimal Sampling of Biodiversity

While conservation planning requires good biodiversity data, our knowledge of most living groups is scarce and patchy even in well-sampled regions. Therefore, we need methodologies for rapid assessments for particular groups and regions. Maps of any biodiversity surrogate can be interpolated from even a few well-known sites, but such places are usually lacking. We therefore propose a protocol for designing field surveys to obtain good coverage of pattern variations of biodiversity in a given region. To represent biodiversity patterns comprehensively, we use a rule step site-allocation procedure, partially based on Faith and Walker's ED criterion that takes environmental and spatial variation into account, together with other criteria such as survey costs. A preliminary assessment of the adequacy of this site sampling strategy is made. Then a set of complementary sites is selected for further sampling. Using the ED criterion, during the stepwise process a p-median analysis is applied both to an environmental distance matrix and to a spatial distance matrix, to maximize the amount of variation covered by our survey planning. This rule-set allocation procedure is integrated into a continuous sampling design protocol directed to ensure we can sample all biodiversity of a region. This protocol requires the gathering of both biological and environmental information, an assessment of previously available information, the choice of sampling methods and dates, and a continuous assessment of the success of the survey being carried out. An example of the application of this protocol to the survey design of dung beetle (Coleoptera, Scarabaeoidea) diversity in the Comunidad de Madrid (Spain) is included.     

The Importance of Rotational Crops for Biodiversity Conservation in Mediterranean Areas

Nowadays we are seeing the largest biodiversity loss since the extinction of the dinosaurs. To conserve biodiversity it is essential to plan protected areas using a prioritization approach, which takes into account the current biodiversity value of the sites. Considering that in the Mediterranean Basin the agro-ecosystems are one of the most important parts of the landscape, the conservation of crops is essential to biodiversity conservation. In the framework of agro-ecosystem conservation, farmland birds play an important role because of their representativeness, and because of their steady decline in the last Century in Western Europe. The main aim of this research was to define if crop dominated landscapes could be useful for biodiversity conservation in a Mediterranean area in which the landscape was modified by humans in the last thousand years and was affected by the important biogeographical phenomenon of peninsula effect. To assess this, we identify the hotspots and the coldspots of bird diversity in southern Italy both during the winter and in the breeding season. In particular we used a scoring method, defining a biodiversity value for each cell of a 1-km grid superimposed on the study area, using data collected by fieldwork following a stratified random sampling design. This value was analysed by a multiple linear regression analysis and was predicted in the whole study area. Then we defined the hotspots and the coldspots of the study area as 15% of the cells with higher and lower value of biodiversity, respectively. Finally, we used GAP analysis to compare hotspot distribution with the current network of protected areas. This study showed that the winter hotspots of bird diversity were associated with marshes and water bodies, shrublands, and irrigated crops, whilst the breeding hotspots were associated with more natural areas (e.g. transitional wood/shrubs), such as open areas (natural grasslands, pastures and not irrigated crops). Moreover, the results underlined the negative effects of permanent crops, such as vineyards, olive groves, and orchards, in particular during the winter season. This research highlights the importance of farmland areas mainly for wintering species and the importance of open areas for breeding species in the Mediterranean Basin. This may be true even when the species’ spatial distribution could be affected by biogeography. An important result showed that the hotspots for breeding species cannot be used as a surrogate for the wintering species, which were often not considered in the planning of protected areas.     

The Importance of Hydrodynamics for Protected and Endangered Biodiversity of Lowland Rivers

This paper examines the relationship between protected and endangered riverine species (target species) and hydrodynamics in river-floodplain ecosystems, combining ecological and policy-legal aspects of biodiversity conservation in river management. The importance of different hydrodynamic conditions along a lateral gradient was quantified for various taxonomic groups. Our results show that (i) target species require ecotopes along the entire hydrodynamic gradient; (ii) different parts of the hydrodynamic gradient are important to different species, belonging to different taxonomic groups; (iii) in particular low-dynamic parts are important for many species and (iv) species differ in their specificity for hydrodynamic conditions. Many species of higher plants, fish and butterflies have a narrow range for hydrodynamics and many species of birds and mammals use ecotopes along the entire gradient. Even when focussing only on target species, the entire natural hydrodynamic gradient is important. This means that the riverine species assemblage as a whole can benefit from measures focussing on target species only. River reconstruction and management should aim at re-establishing the entire hydrodynamic gradient, increasing the spatial heterogeneity of hydrodynamic conditions.     

Biodiversity of Jinggangshan Mountain: The Importance of Topography and Geographical Location in Supporting Higher Biodiversity

Diversity is mainly determined by climate and environment. In addition, topography is a complex factor, and the relationship between topography and biodiversity is still poorly understood. To understand the role of topography, i.e., altitude and slope, in biodiversity, we selected Jinggangshan Mountain (JGM), an area with unique topography, as the study area. We surveyed plant and animal species richness of JGM and compared the biodiversity and the main geographic characteristics of JGM with the adjacent 4 mountains. Gleason’s richness index was calculated to assess the diversity of species. In total, 2958 spermatophyte species, 418 bryophyte species, 355 pteridophyte species and 493 species of vertebrate animals were recorded in this survey. In general, the JGM biodiversity was higher than that of the adjacent mountains. Regarding topographic characteristics, 77% of JGM’s area was in the mid-altitude region and approximately 40% of JGM’s area was in the 10°–20° slope range, which may support more vegetation types in JGM area and make it a biodiversity hotspot. It should be noted that although the impact of topography on biodiversity was substantial, climate is still a more general factor driving the formation and maintenance of higher biodiversity. Topographic conditions can create microclimates, and both climatic and topographic conditions contribute to the formation of high biodiversity in JGM.     

Importance Sampling Via the Estimated Sampler

Monte Carlo importance sampling for evaluating numerical integrationis discussed. We consider a parametric family of sampling distributionsand propose the use of the sampling distribution estimated bymaximum likelihood. The proposed method of importance samplingusing the estimated sampling distribution is shown to improvethe asymptotic variance of the ordinary method using the truesampling distribution. The argument is closely related to thediscussion of the paradox in Henmi & Eguchi (2004). We focuson a condition under which the estimated integration value obtainedby the proposed method has asymptotic zero variance.     

The Function of Marine Critical Transition Zones and the Importance of Sediment Biodiversity

Estuaries and coastal wetlands are critical transition zones (CTZs) that link land, freshwater habitats, and the sea. CTZs provide essential ecological functions, including decomposition, nutrient cycling, and nutrient production, as well as regulation of fluxes of nutrients, water, particles, and organisms to and from land, rivers, and the ocean. Sediment-associated biota are integral to these functions. Functional groups considered essential to CTZ processes include heterotrophic bacteria and fungi, as well as many benthic invertebrates. Key invertebrate functions include shredding, which breaks down and recycles organic matter; suspension feeding, which collects and transports sediments across the sediment–water interface; and bioturbating, which moves sediment into or out of the seabed. In addition, macrophytes regulate many aspects of nutrient, particle, and organism dynamics above- and belowground. Animals moving within or through CTZs are vectors that transport nutrients and organic matter across terrestrial, freshwater, and marine interfaces. Significant threats to biodiversity within CTZs are posed by anthropogenic influences; eutrophication, nonnutrient pollutants, species invasions, overfishing, habitat alteration, and climate change affect species richness or composition in many coastal environments. Because biotic diversity in marine CTZ sediments is inherently low whereas their functional significance is great, shifts in diversity are likely to be particularly important. Species introductions (from invasion) or loss (from overfishing or habitat alteration) provide evidence that single-species changes can have overt, sweeping effects on CTZ structure and function. Certain species may be critically important to the maintenance of ecosystem functions in CTZs even though at present there is limited empirical evidence that the number of species in CTZ sediments is critical. We hypothesized that diversity is indeed important to ecosystem function in marine CTZs because high diversity maintains positive interactions among species (facilitation and mutualism), promoting stability and resistance to invasion or other forms of disturbance. The complexity of interactions among species and feedbacks with ecosystem functions suggests that comparative (mensurative) and manipulative approaches will be required to elucidate the role of diversity in sustaining CTZ functions. Received 25 February 2000; accepted 31 January 2001.     

Variable Importance of Macrofaunal Functional Biodiversity for Biogeochemical Cycling in Temperate Coastal Sediments

Coastal marine systems are currently subject to a variety of anthropogenic and climate-change-induced pressures. An important challenge is to predict how marine sediment communities and benthic biogeochemical cycling will be affected by these ongoing changes. To this end, it is of paramount importance to first better understand the natural variability in coastal benthic biogeochemical cycling and how this is influenced by local environmental conditions and faunal biodiversity. Here, we studied sedimentary biogeochemical cycling at ten coastal stations in the Southern North Sea on a monthly basis from February to October 2011. We explored the spatio-temporal variability in oxygen consumption, dissolved inorganic nitrogen and alkalinity fluxes, and estimated rates of nitrification and denitrification from a mass budget. In a next step, we statistically modeled their relation with environmental variables and structural and functional macrobenthic community characteristics. Our results show that the cohesive, muddy sediments were poor in functional macrobenthic diversity and displayed intermediate oxygen consumption rates, but the highest ammonium effluxes. These muddy sites also showed an elevated alkalinity release from the sediment, which can be explained by the elevated rate of anaerobic processes taking place. Fine sandy sediments were rich in functional macrobenthic diversity and had the maximum oxygen consumption and estimated denitrification rates. Permeable sediments were also poor in macrobenthic functional diversity and showed the lowest oxygen consumption rates and only small fluxes of ammonium and alkalinity. Macrobenthic functional biodiversity as estimated from bioturbation potential appeared a better variable than macrobenthic density in explaining oxygen consumption, ammonium and alkalinity fluxes, and estimated denitrification. However, this importance of functional biodiversity was manifested particularly in fine sandy sediments, to a lesser account in permeable sediments, but not in muddy sediments. The strong relationship between macrobenthic functional biodiversity and biogeochemical cycling in fine sandy sediments implies that a future loss of macrobenthic functional diversity will have important repercussions for benthic ecosystem functioning.     

Prey Selection by an Apex Predator: The Importance of Sampling Uncertainty

The impact of predation on prey populations has long been a focus of ecologists, but a firm understanding of the factors influencing prey selection, a key predictor of that impact, remains elusive. High levels of variability observed in prey selection may reflect true differences in the ecology of different communities but might also reflect a failure to deal adequately with uncertainties in the underlying data. Indeed, our review showed that less than 10% of studies of European wolf predation accounted for sampling uncertainty. Here, we relate annual variability in wolf diet to prey availability and examine temporal patterns in prey selection; in particular, we identify how considering uncertainty alters conclusions regarding prey selection.Over nine years, we collected 1,974 wolf scats and conducted drive censuses of ungulates in Alpe di Catenaia, Italy. We bootstrapped scat and census data within years to construct confidence intervals around estimates of prey use, availability and selection. Wolf diet was dominated by boar (61.5±3.90 [SE] % of biomass eaten) and roe deer (33.7±3.61%). Temporal patterns of prey densities revealed that the proportion of roe deer in wolf diet peaked when boar densities were low, not when roe deer densities were highest. Considering only the two dominant prey types, Manly''s standardized selection index using all data across years indicated selection for boar (mean = 0.73±0.023). However, sampling error resulted in wide confidence intervals around estimates of prey selection. Thus, despite considerable variation in yearly estimates, confidence intervals for all years overlapped. Failing to consider such uncertainty could lead erroneously to the assumption of differences in prey selection among years. This study highlights the importance of considering temporal variation in relative prey availability and accounting for sampling uncertainty when interpreting the results of dietary studies.     

The Point Count Transect Method for Estimates of Biodiversity on Coral Reefs: Improving the Sampling of Rare Species

Understanding patterns in species richness and diversity over environmental gradients (such as altitude and depth) is an enduring component of ecology. As most biological communities feature few common and many rare species, quantifying the presence and abundance of rare species is a crucial requirement for analysis of these patterns. Coral reefs present specific challenges for data collection, with limitations on time and site accessibility making efficiency crucial. Many commonly used methods, such as line intercept transects (LIT), are poorly suited to questions requiring the detection of rare events or species. Here, an alternative method for surveying reef-building corals is presented; the point count transect (PCT). The PCT consists of a count of coral colonies at a series of sample stations, located at regular intervals along a transect. In contrast the LIT records the proportion of each species occurring under a transect tape of a given length. The same site was surveyed using PCT and LIT to compare species richness estimates between the methods. The total number of species increased faster per individual sampled and unit of time invested using PCT. Furthermore, 41 of the 44 additional species recorded by the PCT occurred ≤ 3 times, demonstrating the increased capacity of PCT to detect rare species. PCT provides a more accurate estimate of local-scale species richness than the LIT, and is an efficient alternative method for surveying reef corals to address questions associated with alpha-diversity, and rare or incidental events.     

The Metropolized Partial Importance Sampling MCMC mixes slowly on minimum reversal rearrangement paths

Markov chain Monte Carlo has been the standard technique for inferring the posterior distribution of genome rearrangement scenarios under a Bayesian approach. We present here a negative result on the rate of convergence of the generally used Markov chains. We prove that the relaxation time of the Markov chains walking on the optimal reversal sorting scenarios might grow exponentially with the size of the signed permutations, namely, with the number of syntheny blocks.     

Sampling Plant Diversity and Rarity at Landscape Scales: Importance of Sampling Time in Species Detectability

Documenting and estimating species richness at regional or landscape scales has been a major emphasis for conservation efforts, as well as for the development and testing of evolutionary and ecological theory. Rarely, however, are sampling efforts assessed on how they affect detection and estimates of species richness and rarity. In this study, vascular plant richness was sampled in 356 quarter hectare time-unlimited survey plots in the boreal region of northeast Alberta. These surveys consisted of 15,856 observations of 499 vascular plant species (97 considered to be regionally rare) collected by 12 observers over a 2 year period. Average survey time for each quarter-hectare plot was 82 minutes, ranging from 20 to 194 minutes, with a positive relationship between total survey time and total plant richness. When survey time was limited to a 20-minute search, as in other Alberta biodiversity methods, 61 species were missed. Extending the survey time to 60 minutes, reduced the number of missed species to 20, while a 90-minute cut-off time resulted in the loss of 8 species. When surveys were separated by habitat type, 60 minutes of search effort sampled nearly 90% of total observed richness for all habitats. Relative to rare species, time-unlimited surveys had ∼65% higher rare plant detections post-20 minutes than during the first 20 minutes of the survey. Although exhaustive sampling was attempted, observer bias was noted among observers when a subsample of plots was re-surveyed by different observers. Our findings suggest that sampling time, combined with sample size and observer effects, should be considered in landscape-scale plant biodiversity surveys.     

Establishing Baseline Indices for the Quality of the Biodiversity of Restored Habitats Using a Standardized Sampling Process

The need for standardized biodiversity assessment methods to enable biodiversity quality to be measured is outlined. A general approach to sampling is suggested. The results of the use of this sampling process are given for two case studies of different taxonomic groups. The data assessment is made easier by the use of a bespoke computer program. Examples of the program output are presented. The advantage of this standardized measurement of biodiversity compared to species lists and the use of indicator species are outlined in the case studies macrofungi and butterflies. It was shown that the biodiversity quality of sites can be compared by the use of a range of measured biodiversity indices in a way that allows sites to be compared through time or between sites/treatments. In one case (butterflies), data that have been collected systematically in a recording scheme have been analyzed retrospectively and yielded valuable information on changes in biodiversity quality. The uses of this method in establishing baselines in restoration ecology are discussed. The importance of restoration ecology in the conservation of biodiversity could be underlined by the use of the methods presented in this article.     

The Legislation for Biodiversity Conservation in China

Effectivebiodiverdityconservationneedsasoundlegalsystemthatincludesthelegisla-tionininternational,nationalandlocallevels.TheConventiononBiologicalDiversity(CBD)thatenteredintoforceonDecember29,1993,isaninternationallegalinstrument.Asaframeconvention,ithasformedalegalsystem,togetherwiththeotherinternationalagree-mentssuchastheConventiononWetlandsofInternationalImportanceEspeciallyasWater-fowlHabitat(Ramsar1971),theConventionConcerningtheProtectionoftheWorldCul-turalandNaturalHeritage(P…