GBIF information is not enough: national database improves the inventory completeness of Amazonian epiphytes

Distribution data sharing in global databases (e.g. GBIF) allowed the knowledge synthesis in several biodiversity areas. However, their Wallacean shortfalls still reduce our capacity to understand distribution patterns. Including exclusive records from other databases, such as national ones (e.g. SpeciesLink), could mitigate these shortfall problems, but it remains not evaluated. Therefore, we assessed whether (i) the inventory completeness, (ii) taxonomic contribution and (iii) spatial biases could be improved when integrating both global and national biodiversity databases. Using Amazonian epiphytes as a model, we compared the available taxonomic information spatially between GBIF and SpeciesLink databases using a species contribution index. We obtained the inventory completeness from sources using species accumulation curves and assessed their spatial biases by constructing spatial autoregressive models. We found that both databases have a high amount of exclusive records (GBIF: 36.7%; SpeciesLink: 21.7%) and species (17.8%). Amazonia had a small epiphyte inventory completeness, but it was improved when we analyzed both databases together. Individually, both database records were biased to sites with higher altitude, population and herbarium density. Together, river density appeared as a new predictor, probably due to the higher species contribution of SpeciesLink along them. Our findings provide strong evidence that using both global and national databases increase the overall biodiversity knowledge and reduce inventory gaps, but spatial biases may persist. Therefore, we highlight the importance of aggregating more than one database to understand biodiversity patterns, to address conservation decisions and direct shortfalls more efficiently in future studies.

     

Macrofungi diversity in cork-oak and holm-oak forests in Andalusia (southern Spain); an efficient parameter for establishing priorities for its evaluation and conservation

In this work, the fungal diversity of holm-oak and cork-oak woodlands in southern Spain is studied in order to analyse the macrofungi component and its ecological characteristics, as well as to establish priorities for its conservation. For this, we have compiled published as well as unpublished data, and applied compositional analysis and statistical methods (basic statistics, non-parametric and multivariate analyses). Priority areas were selected based on complementarity analysis. As a result, 838 taxa were recorded, 78.6% in cork-oak and 76.4% in holm-oak forests, with 55.1% in common. The ratio of mycorrhizal to saprophitic species indicated that cork-oak woodlands present a higher diversity and conservation degree of its macrofungal community than holm-oak woodlands, since the mycorrhizal component is more important for the conservation of these forests (due to nutritional relations). Both forests types appear well differentiated in the multivariate analysis. In the complementarity analysis, with only one site, we recorded 40% of the total species encountered. The percentage increased to 80% with four sites. This type of approach, by highlighting the important areas for conservation of fungal diversity, constitutes a powerful tool to optimise conservation efforts.     

Using species distribution models to locate animal aggregations: a case study with Hippodamia undecimnotata (Schneider) overwintering aggregation sites

1. The protection of animals' aggregation sites is increasingly seen as a key conservation strategy. However, to efficiently protect aggregation sites, they need to be accurately located. Species distribution models (SDMs) are an important tool in biological conservation to predict spatial distribution of species and they are used here to predict the distribution of the aggregation sites of a ladybird (Coleoptera: Coccinellidae) species. 2. Hippodamia undecimnotata forms spectacular overwintering aggregations at the same locations every year across southern and eastern Europe. In this study, an SDM was developed and its performance tested for H. undecimnotata aggregations in southwest France. Moreover, the study looked at how environmental variables correlate with ladybirds' abundance in the aggregation sites. 3. The occurrence of aggregations was best described by one model including isolated prominent object, pesticide risk, altitude and vegetation coverage. Furthermore, ladybird abundance at the aggregation sites is positively correlated with altitude. The SDM occurrence model performance was found to be high (area under the curve = 0.92 and true skill statistic = 0.78). 4. It is suggested that H. undecimnotata may be an umbrella species, because some aggregation sites were also used by other ladybird species. Therefore, the protection of the aggregation sites of this species may benefit several other species. 5. This study provides nature conservation stakeholders with a tool to locate overwintering aggregations, a first step towards the protection of these sites.     

PhosphoBlast, a computational tool for comparing phosphoprotein signatures among large datasets

Identification of specific protein phosphorylation sites provides predicative signatures of cellular activity and specific disease states such as cancer, diabetes, Alzheimer disease, and rheumatoid arthritis. Recent progress in phosphopeptide isolation technology and tandem mass spectrometry has provided the means to identify thousands of phosphorylation sites from a single biological sample. These advances now make it possible to profile global changes in the phosphoproteome at an unprecedented level. However, although this technology is generating a wealth of information, there is currently no efficient means to identify phosphoprotein signatures shared among large phosphoprotein databases. Identification of common phosphoprotein signatures found in biologically relevant systems and their conservation throughout evolution would provide valuable insight into mechanisms of signal transduction and cell function. Here we describe the development of a computational program (PhosphoBlast) that can rapidly match thousands of phosphopeptides that share phosphorylation sites within and across species. PhosphoBlast analysis of several large phosphoprotein datasets from the literature revealed common phosphorylation signatures shared across diverse experimental platforms and species. Moreover PhosphoBlast is a powerful analysis tool to identify specific phosphosite mutations. Comparison of the mouse and human phosphoproteomes revealed more than 130 specific phosphoamino acid mutations, some of which are predicted to alter protein function. Further analysis revealed that known phosphorylated amino acids are more evolutionally conserved than the Ser/Thr/Tyr amino acids not known to be phosphorylated. Together our results demonstrate that PhosphoBlast is a versatile mining tool capable of identifying related phosphorylation signatures and phosphoamino acid mutations among complex proteomics datasets in a highly efficient and accurate manner. PhosphoBlast will aid in the informatics analysis of the phosphoproteome and the identification of phosphoprotein biomarkers of disease.     

Quantitative method for identifying networks of minimum priority sites for protection of rare and endangered plant species in Guangdong,China

The approaches to enlarge the protected areas are deeply embedded in the conservation planning.In practice,however,even in some sites of top conservation priority,there exist problems of inefficient conservation for lack of funding,to say nothing of assisting all species under threat from the viewpoint of conservationists.Identifying priority sites for conservation and establishing networks of minimum priority sites (NOMPS) are helpful for promoting the transition from number and size oriented,to quality and effectiveness oriented practices of biological conservation,and for realizing the target of biodiversity conservation with the most benefits for the least costs.Based on heuristic algorithm and integer linear programming (ILP),we propose a refined method of heuristic integer linear programming (HILP) for quantitative identification of the NOMPS to protect rare and endangered plant species (REPS) in Guangdong Province,China.The results indicate that there are 19 priority sites which are essential for protecting all of the 107 REPS distributed in 83 sites in Guangdong.These should be the paramount targets of financing and management.Compared with the ILP,which uses minimum number of sites as the only constraint,HILP takes into consideration of the effect of species richness,and is thus more suitable for conservation practices though with a little more number of priority sites selected.It is suggested that ILP and HILP are both effective quantitative methods for identifying NOMPS and can yield important information for decision making,especially when economic factors are constraints for biological conservation.     

Quantitative method for identifying networks of minimum priority sites for protection of rare and endangered plant species in Guangdong, China

The approaches to enlarge the protected areas are deeply embedded in the conservation planning. In practice, however, even in some sites of top conservation priority, there exist problems of inefficient conservation for lack of funding, to say nothing of assisting all species under threat from the viewpoint of conservationists. Identifying priority sites for conservation and establishing networks of minimum priority sites (NOMPS) are helpful for promoting the transition from number and size oriented, to quality and effectiveness oriented practices of biological conservation, and for realizing the target of biodiversity conservation with the most benefits for the least costs. Based on heuristic algorithm and integer linear programming (ILP), we propose a refined method of heuristic integer linear programming (HILP) for quantitative identification of the NOMPS to protect rare and endangered plant species (REPS) in Guangdong Province, China. The results indicate that there are 19 priority sites which are essential for protecting all of the 107 REPS distributed in 83 sites in Guangdong. These should be the paramount targets of financing and management. Compared with the ILP, which uses minimum number of sites as the only constraint, HILP takes into consideration of the effect of species richness, and is thus more suitable for conservation practices though with a little more number of priority sites selected. It is suggested that ILP and HILP are both effective quantitative methods for identifying NOMPS and can yield important information for decision making, especially when economic factors are constraints for biological conservation.     

Can We Distinguish Plant Species that are Rare and Endangered from Other Plants Using Their Biological Traits?

Understanding the factors responsible for species rarity is crucial for effective species conservation. One possible approach to obtaining information about causes of species rarity is to compare rare and common species. We analyzed the biological and ecological traits of critically endangered (CR) plant species of the Czech Republic. We compared the vegetative, generative and ecological traits of CR species with: i) common closely related species (a form of phylogenetic correction), ii) common closely related species sharing the same habitat (i.e., excluding pairs not sharing the same habitat, because many differences in species traits can be caused by adaptation to a specific habitat type) and iii) all plants of the Czech Republic. Information about species traits was mainly obtained from literature and databases. Comparison with common closely related species showed that CR species are smaller, flower for shorter periods, and have higher proportions of self-compatibility and higher terminal velocities. CR species also differ in their mode of dispersion, and their ecology and distribution. Comparison with species from the same habitat gave similar results. Comparison with the whole flora produced slightly different results, with additional differences in pollination mode and seed mass. The results of all three types of comparison suggest that critically endangered species of the Czech Republic are small, competitively inferior species, with some differences in the generative part of their life cycle, and occur mainly in open, unproductive habitats.     

Biodiversity assessment: a case study in predicting richness from the potential distributions of plant species in the forests of south-western Australia

Distributions were predicted for 1430 native plant species as part of a biodiversity assessment in the forests of south‐west Western Australia. From these predicted distributions, an index of plant species richness was generated for the forest area. The most common predictors for distribution were found to be climatic surfaces incorporating some aspect of seasonality in temperature and precipitation. Although coarse, the index confirmed existing knowledge of areas of high biodiversity within the study area and introduced a new area, the Blackwood Plateau, for consideration as a conservation reserve with high species richness. An additional survey was conducted to sample actual species richness in 11 test sites. When actual richness was regressed against predicted richness, a significant correlation was obtained if both annuals and geophytes were excluded from the analysis. With refinement of the model and further data collection targeted at areas of low effort, the species richness index is proposed as a useful tool for conservation planning.     

Biogeography, current knowledge and conservation of threatened vascular plants characteristic of Mexican temperate forests

The main goal of this study is to document the biogeographical patterns, current status and conservation of 24 species of vascular plants in Mexico, all of them recorded in some risk category in the Mexican official publication named ‘Norma Oficial Mexicana 059’ (NOM-059) and some of them in the IUCN red lists (the World Conservation Union) and CITES (Convention on International Trade in Endangered Species); many of these species are linked to Mexican cloud forests and other temperate vegetation types. Distribution maps of these 24 species were generated with information obtained from specialized literature, herbarium specimens, institutional databases, and field work; with this information, the patterns of richness and endemism of these species were obtained. For this, the Mexican territory was divided using a grid system based on a chart index (scale 1:50,000 system composed by grids of 15' × 20'). Also, we up to date the knowledge of these species and their populations and current habitats, and evaluate their geographic distribution in relation to the current Mexican National Parks and Reserves System and Mexican Priority Regions for Conservation. We also discuss some changes of categories in the NOM-059 and suggest the urgent incorporation of some of the species in the recent IUCN Red Data List of Threatened Species (2003). Most of the species studied require special policies for their conservation due to problems that affect their natural populations; also we consider that these taxa are underrepresented in the current Mexican System of Natural Protected Areas, especially those with restricted distributions.     

An early evaluation of translocation actions for endangered plant species on Mediterranean islands

In situ conservation is widely considered a primary conservation strategy. Plant translocation, specifically, represents an important tool for reducing the extinction risk of threatened species. However, thus far, few documented translocations have been carried out in the Mediterranean islands. The CareMediflora project, carried out on six Mediterranean islands, tackles both short-and long-term needs for the insular endangered plants through in situ and ex situ conservation actions. The project approach is based on using ex situ activities as a tool to improve in situ conservation of threatened plant species.Fifty island plants(representing 45 taxa) were selected for translocations using common criteria.During the translocations, several approaches were used, which differed in site selection method, origin of genetic material, type of propagative material, planting method, and more. Although only preliminary data are available, some general lessons can be learned from the experience of the CareMediflora project. Among the factors restricting the implementation of translocations, limited financial resources appear to be the most important. Specific preliminary management actions, sometimes to be reiterated after translocation, increase the overall cost, but often are necessary for translocation success. Translocation using juvenile/reproductive plants produces better results over the short term,although seeds may provide good results over the long run(to be assessed in the future). Regardless,plant translocation success can only be detected over long periods; therefore, proper evaluation of plant translocations requires a long-term monitoring protocol. Care-Mediflora project represents the first attempt to combine the existing approaches in a common plant conservation strategy specifically focusing on the Mediterranean islands.     

Molecular identification of Chironomus spp. (Diptera) for biomonitoring of aquatic ecosystems

Abstract   Chironomidae larvae often represent a major component of the benthic fauna in inland water bodies and are used frequently as bioindicators of ecosystem health. The genus Chironomus is a recognised indicator of organic enrichment and has been used extensively in the northern hemisphere and New Zealand in ecotoxicological studies. However, similar use of Chironomus in Australia is limited due to the presence of cryptic species that restrict the collection of information on species-specific responses to environmental stress. To address the problems associated with species identification, we have used PCR-RFLP of the mitochondrial COI gene to develop DNA profiles for nine common Australian Chironomus species. Species-specific haplotypes were identified using reference taxa previously identified by cytological analysis, and verified with field specimens collected from seven wetlands around Melbourne. This research provides an effective tool for species identification of this ubiquitous and often abundant genus that will provide the basis of obtaining species-specific information to inform on the health of aquatic ecosystems.     

Nature reserve selection in the Transvaal, South Africa: what data should we be using?

Iterative reserve selection algorithms were applied to two mammal databases, generalized to sixteenth degree grid squares, for the Transvaal region of South Africa. Based on primary point data, 24 grid squares are required to represent all species at least once, while only 13 grid squares are required when based on distribution map data; only two of these grid squares are common to both analyses. As the number of representations per species is increased from one to five, the number of selected grid squares increased to 86 and 71 or 72 respectively, with only 17 of these common to both analyses. These differences in the selection of sites are further reflected in the degree of congruence between selected grid squares and existing conservation areas which is on average 63.3% for grid squares selected from the primary database and only 42.5% for those selected from the distribution map database. These results emphasize the importance of quality data input when evaluating regional reserve networks. Highly generalized distribution map data sets, on the one hand, are extrapolations of limited data sets and contain non-quantifiable levels of false-positives which could have significant implications if used for establishing regional reserve networks. On the other hand, although there are problems associated with the establishment of primary diversity databases, namely data currency and uneven and non-random sampling (leading to false negatives), they remain our most reliable option for assigning conservation value.     

Cost effectiveness of endangered species management: the kokako (

Expenditure on endangered species management is increasing greatly, on a global basis. Managers need tools to evaluate the performance of endangered species programmes because there will always be more demand for resources than there are available. Cost Effectiveness Analysis (CEA) is used here to evaluate the performance of the kokako (Callaeas cinerea) recovery programme. This species is being managed at a number of sites in New Zealand and analysis shows a large variation in costs and effectiveness between these sites. Cost Effectiveness Analysis provides a tool to allow managers to better predict where resources should be invested to most cost-effectively achieve their conservation targets, in this case recovery of an endangered species. Issues of lack of reliable cost data and ongoing policy problems limit the potential of economics to contribute to improved conservation management of threatened species in New Zealand.     

DNA barcoding as an effective tool to complement wetland management: A case study of a protected area in Italy

In recent years, DNA barcoding has been suggested as a useful molecular technique to complement traditional taxonomic expertise for fast species identification and biodiversity inventories. In this study, in situ application of DNA barcodes was tested on the plant community of a wetland area in central Italy. Four cpDNA markers (trnH–psbA, rbcL, rpoC1, and matK) were tested on 40 plant species, 26 of which strictly connected to the aquatic habitat. Universality of the method, ease of data retrieval, and correct assignation of the genetic markers to each species were evaluated. The markers showed different prospects of reliable applicability. The obtained sequences were blasted against the NCBI database to verify the correct species identification. A score ranging between 32% and 67% was achieved. Overall, eight species remained unidentified with all the tested barcodes due to the absence of conspecific sequences in the available databases. This work demonstrates some limitations in the applicability of DNA barcoding to accomplish complete taxonomical surveys. Difficulties encountered in this study urge refinement of technical protocols and accessibility to wider databases. Future technological advances and larger sample sets will certainly reinforce DNA barcoding as a useful tool to address knowledge and conservation of wetlands.     

eDNA metabarcoding: a promising method for anuran surveys in highly diverse tropical forests

Understanding the geographical distribution and community composition of species is crucial to monitor species persistence and define effective conservation strategies. Environmental DNA (eDNA) has emerged as a powerful noninvasive tool for species detection. However, most eDNA survey methods have been developed and applied in temperate zones. We tested the feasibility of using eDNA to survey anurans in tropical streams in the Brazilian Atlantic forest and compared the results with short‐term visual and audio surveys. We detected all nine species known to inhabit our focal streams with one single visit for eDNA sampling. We found a higher proportion of sequence reads and larger number of positive PCR replicates for more common species and for those with life cycles closely associated with the streams, factors that may contribute to increased release of DNA in the water. However, less common species were also detected in eDNA samples, demonstrating the detection power of this method. Filtering larger volumes of water resulted in a higher probability of detection. Our data also show it is important to sample multiple sites along streams, particularly for detection of target species with lower population densities. For the three focal species in our study, the eDNA metabarcoding method had a greater capacity of detection per sampling event than our rapid field surveys, and thus, has the potential to circumvent some of the challenges associated with traditional approaches. Our results underscore the utility of eDNA metabarcoding as an efficient method to survey anuran species in tropical streams of the highly biodiverse Brazilian Atlantic forest.     

Rarefaction method for assessing plant species diversity on a regional scale

In national conservation plans, it is necessary to comparatively assess species pools of different regions and monitor their changes over time. Two specific problems arise: i) species diversity must be standardized per area, because regions differ in size, and ii) the diversity measure should take into account how common or rare the species are on the regional scale. We used the rarefaction method combined with a fitting procedure to calculate the expected number of species E(S). The method takes into account the nonlinearity of species and area, as well as how common or rare each species is and allows analysis of species groups' contribution to total species diversity. The slope parameter of the fitted power function is used as an indicator of species turnover, and thus, of β-diversity. For the analysis, Switzerland was divided into seven biogeographic regions (256–10 642 km²). The diversity of the total species pool and of six ecological species groups was investigated for each region. In every biogeographic region, we find the lowest species turnover in the fertilized meadow group, and the highest species turnover in the pioneer/weedy species and the mountain species groups pioneer/weedy. The results show that among Swiss regions, differences in E(S) are mainly due to the presence or absence of mountain species. Other species groups show a rather constant contribution to the regional species pools. We found the rarefaction method to be a very useful tool for assessing Swiss plant species diversity on a regional scale.     

中国农业野生植物原生境保护实践与未来研究方向

农业野生植物原生境保护已成为国内外生物多样性保护热点。截止2011年底,我国利用物理隔离和主流化两种保护方法已建成各类农业野生植物原生境保护点226个,保护物种52个,分布于27个省(自治区、直辖市),其中物理隔离保护点154个,保护物种39个,分布于27个省(自治区、直辖市),主流化保护点72个,保护物种31个,分布于15个省(自治区、直辖市)。本文通过对我国已建成的农业野生植物原生境保护点的调查和分析,比较了物理隔离和主流化两种保护方法的优缺点,总结了两种保护方法建设农业野生植物原生境保护点的经验和存在的主要问题,提出了解决这些问题的思路与对策。在此基础上,结合国际上生物多样性保护的发展趋势,探讨了我国未来农业野生植物原生境保护的发展方向和关键措施。     

Conservation value of low fire frequency in tropical savannas: Ants in monsoonal northern Australia

The conservation values of ‘old‐growth’ forests in landscapes subject to repeated disturbance by fire or logging have received considerable conservation attention. However, little is known of the conservation values of old‐growth sites in ecosystems with an evolutionary history of highly frequent disturbance. Here we address the value of low fire frequency (<1 fire/10 years) in tropical savannas, the world's most fire‐prone biome, in terms of ant biodiversity. We do this by comparing savanna ant communities within the Territory Wildlife Park (TWP) near Darwin in the Australian monsoonal tropics, which has experienced a low incidence of fire over 25 years due to active fire exclusion, with those of adjacent (outside) sites experiencing the ambient fire regime of burning every 2–5 years. Ants were sampled using terrestrial and arboreal pitfall traps at 16 sites, eight each inside and outside TWP. More than 16 000 ants were recorded during the study, representing a total of 98 ant species from 30 genera. More species in total were recorded outside (90) than inside (74) TWP, but there was no difference in mean site species richness or abundance, and overall species composition was similar. All species recorded inside TWP are common and widespread throughout the savanna landscapes of the broader region, in the absence of active fire exclusion. Low fire frequency at the Territory Wildlife Park therefore does not appear to have enhanced regional ant conservation values. Our findings reinforce the importance of targeting fire regimes that are clearly linked to positive conservation outcomes, rather than assuming a need for maximum ‘pyrodiversity’.     

Phylogenetic diversity and its conservation in the presence of phylogenetic uncertainty: a case study of cladoceran communities in urban waterbodies

The need to protect and preserve biodiversity is a pressing issue and requires that conservation projects be based on solid foundations. Knowledge of species evolutionary history can serve as a tool to help guide conservation projects on the basis of evolutionary heritage. We used communities of Cladocera (Crustacea, Branchiopoda) in urban waterbodies to identify which sites should be prioritized for phylogenetic diversity conservation. Phylogenetic trees were inferred using DNA sequences from two mitochondrial genes. Furthermore, we also evaluated the consequences of phylogenetic uncertainty for identifying sites for conservation priority. Using results from Bayesian analyses, we considered the effect of uncertainty in the phylogenetic tree on phylogenetic diversity (PD) estimation. When phylogenetic uncertainty was taken into account, the conservation value of individual sites became uncertain and several potential comparisons between sites could not be supported. Consequently prioritization of one site over the other could not be defended in biodiversity conservation projects. Our study highlights the fact that accounting for phylogenetic uncertainty can alter the relative conservation priority of sites, as assessed by their phylogenetic diversity. Therefore, variability in the phylogenetic estimates should be consistently considered and integrated into estimates of phylogenetic diversity and conservation decisions to avoid making suboptimal choices.