How citizen science could improve species distribution models and their independent assessment

1. Species distribution models (SDM) have been increasingly developed in recent years, but their validity is questioned. Their assessment can be improved by the use of independent data, but this can be difficult to obtain and prohibitive to collect. Standardized data from citizen science may be used to establish external evaluation datasets and to improve SDM validation and applicability.
2. We used opportunistic presence‐only data along with presence–absence data from a standardized citizen science program to establish and assess habitat suitability maps for 9 species of amphibian in western France. We assessed Generalized Additive and Random Forest Models’ performance by (1) cross‐validation using 30% of the opportunistic dataset used to calibrate the model or (2) external validation using different independent datasets derived from citizen science monitoring. We tested the effects of applying different combinations of filters to the citizen data and of complementing it with additional standardized fieldwork.
3. Cross‐validation with an internal evaluation dataset resulted in higher AUC (Area Under the receiver operating Curve) than external evaluation causing overestimation of model accuracy and did not select the same models; models integrating sampling effort performed better with external validation. AUC, specificity, and sensitivity of models calculated with different filtered external datasets differed for some species. However, for most species, complementary fieldwork was not necessary to obtain coherent results, as long as the citizen science data were strongly filtered.
4. Since external validation methods using independent data are considered more robust, filtering data from citizen sciences may make a valuable contribution to the assessment of SDM. Limited complementary fieldwork with volunteer''s participation to complete ecological gradients may also possibly enhance citizen involvement and lead to better use of SDM in decision processes for nature conservation.

     

The Sampled Red List Index for Plants,phase II: ground-truthing specimen-based conservation assessments

The IUCN Sampled Red List Index (SRLI) is a policy response by biodiversity scientists to the need to estimate trends in extinction risk of the world''s diminishing biological diversity. Assessments of plant species for the SRLI project rely predominantly on herbarium specimen data from natural history collections, in the overwhelming absence of accurate population data or detailed distribution maps for the vast majority of plant species. This creates difficulties in re-assessing these species so as to measure genuine changes in conservation status, which must be observed under the same Red List criteria in order to be distinguished from an increase in the knowledge available for that species, and thus re-calculate the SRLI. However, the same specimen data identify precise localities where threatened species have previously been collected and can be used to model species ranges and to target fieldwork in order to test specimen-based range estimates and collect population data for SRLI plant species. Here, we outline a strategy for prioritizing fieldwork efforts in order to apply a wider range of IUCN Red List criteria to assessments of plant species, or any taxa with detailed locality or natural history specimen data, to produce a more robust estimation of the SRLI.     

A noninvasive method for distinguishing among canid species: amplification and enzyme restriction of DNA from dung

Endangered San Joaquin kit foxes Vulpes macrotis mutica can be sympatrically distributed with as many as four other canids: red fox, gray fox, coyote and domestic dog. Canid scats are often found during routine fieldwork, but cannot be reliably identified to species. To detect and study the endangered kit fox, we developed mitochondrial DNA markers that can be amplified from small amounts of DNA extracted from scats. We amplified a 412-bp fragment of the mitochondrial cytochrome- b gene from scat samples and digested it with three restriction enzymes. The resulting restriction profiles discriminated among all five canid species and correctly identified 10 'unknown' fox scats to species in blind tests. We have applied our technique to identify canids species for an environmental management study and a conservation study. We envision that our protocol, and similar ones developed for other endangered species will be greatly used for conservation management in the future.     

Diversity of Alticinae in Oaxaca,Mexico: A preliminary study (Coleoptera,Chrysomelidae)

This is a preliminary study of the diversity of the Flea Beetles (Alticinae) of the Mexican state of Oaxaca based on fieldwork by the author in 1991, 1997, and 2010, the literature, and specimens in several institutional collections. The number of genera and species for Mexico as well as for Oaxaca increased significantly from previous studies. There are now 625 species in 90 genera recorded from Mexico with 275 species in 68 genera recorded from Oaxaca. There are 113 species known only from the state of Oaxaca and another 38 species known only from Oaxaca and the surrounding states. Oaxaca has a relatively high diversity as well as a high percentage of endemism. This study also demonstrates the effects of how even a small amount of fieldwork together with extracting specimen data from institutional collections can significantly increase the total faunistic and diversity knowledge of an area. A complete list of the genera and species known from Oaxaca is included.     

Use of bioluminescence in nucleic acid hybridization reactions

Luminescence reactions can be used to detect specific nucleic acid sequences hybridized with a nucleic probe. Different labels such as cytidine sulphone, fluorescein, and biotin can be incorporated into DNA or oligonucleotide molecules and detected by antibody or avidin conjugates coupled to glucose-6P dehydrogenase. On supports such as nitrocellulose filters, sensitivity is not greatly increased using luminescence, but detection is rapid and easy to perform using polaroid film. Moreover, hybridization can be performed with different labelled probes on the same sample. In solution, luminescence can be used to monitor sandwich reactions. The method is less sensitive than detection on filters but can easily be automated. The performance of these assays can be increased considerably by enzymatic amplification of the target catalysed by a thermostable polymerase.     

Detection of cellulolytic activity of bacteria and fungi growing on agar surfaces

Summary Cellulolytic activity of four fungal species growing on solid medium containing acid-swollen cellulose could be detected much more easily if fungal growth was partly inhibited by the detergent Triton X-100. The dye, aniline blue-black, did not affect growth but increased the sensitivity of detection of cellulolytic activity of both fungi and bacteria. Separating fungi from cellulose fibres by a layer of agar or by filters showed that cell-fibre contact is not necessary for cellulose degradation. Such degradation is clearer when contact is prevented.     

Dispersal and establishment filters influence the assembly of restored prairie plant communities

Community assembly filters, which in theory determine the suite of species that arrive at and establish in a community, have tremendous conceptual relevance to restoration. However, the concept has remained largely theoretical, with a paucity of empirical tests. As such, the applicability of assembly filters theory to ecological restoration remains incompletely known. We tested the relative strengths of dispersal and establishment filters by comparing the plant species composition, measured by species' presence/absence, in 29 restored prairies with the seed mixes used to restore each prairie. We found that both establishment and dispersal filters limited prairie similarity to the seed mix. Sown species responded differentially to filters, with a few species limited only by dispersal (seed density), many others limited only by establishment conditions (i.e. organic matter and sand content of soils, land use history, and fire frequency), and others limited by both dispersal and establishment filters. A few species, typically those sown most often, were not restricted by dispersal or establishment filters, likely because they were sown in high enough densities and all sites had suitable environmental conditions. Finally, one group of species established poorly, but we could not attribute this to either dispersal or establishment filters. This information can help land managers select species likely to establish in restorations when sown at sufficient densities. These results illustrate that dispersal and establishment filters limit the establishment of species in restored communities and these filters are species‐dependent. Identifying the most limiting filter(s) for species will inform strategies to increase their establishment success.     

Are Local Filters Blind to Provenance? Ant Seed Predation Suppresses Exotic Plants More than Natives

The question of whether species’ origins influence invasion outcomes has been a point of substantial debate in invasion ecology. Theoretically, colonization outcomes can be predicted based on how species’ traits interact with community filters, a process presumably blind to species’ origins. Yet, exotic plant introductions commonly result in monospecific plant densities not commonly seen in native assemblages, suggesting that exotic species may respond to community filters differently than natives. Here, we tested whether exotic and native species differed in their responses to a local community filter by examining how ant seed predation affected recruitment of eighteen native and exotic plant species in central Argentina. Ant seed predation proved to be an important local filter that strongly suppressed plant recruitment, but ants suppressed exotic recruitment far more than natives (89% of exotic species vs. 22% of natives). Seed size predicted ant impacts on recruitment independent of origins, with ant preference for smaller seeds resulting in smaller seeded plant species being heavily suppressed. The disproportionate effects of provenance arose because exotics had generally smaller seeds than natives. Exotics also exhibited greater emergence and earlier peak emergence than natives in the absence of ants. However, when ants had access to seeds, these potential advantages of exotics were negated due to the filtering bias against exotics. The differences in traits we observed between exotics and natives suggest that higher-order introduction filters or regional processes preselected for certain exotic traits that then interacted with the local seed predation filter. Our results suggest that the interactions between local filters and species traits can predict invasion outcomes, but understanding the role of provenance will require quantifying filtering processes at multiple hierarchical scales and evaluating interactions between filters.     

Neotropical Copestylum (Diptera,Syrphidae) breeding in Agavaceae and Cactaceae including seven new species

We studied 42 species of saprophagous, Neotropical Copestylum (Diptera, Syrphidae) reared from decaying Cactaceae and Agavaceae. Thirty‐three species were reared during fieldwork in Bolivia, Costa Rica, Ecuador, Mexico, Peru, and Trinidad from 1998–2007. Nine species came from museum and private collections. Seven were new species. We describe these new species and the third stage larva and/or puparium and breeding sites of 40 species. Not described are two apparent species related to Copestylum apicale (Loew, 1866) reared from Cactaceae. Resolution of their status was beyond the scope of this paper but reference is made to their distinctive larval morphology. Based on early stage characters all reared species can be placed in ten species groups, all but three of which have been recognized previously on the basis of adult characters. A high level of congruence was found between adult and larval characters in terms of these species groups. Eight of the groups appear to be related closely and may represent a monophyletic lineage within Copestylum that has diversified in xeric habitats. Early stage morphology varied within and amongst groups but two trends in functional morphology are recognizable. One trend is towards feeding in watery decay and the other towards feeding in firmer decay. The latter trend is characterized by species that scoop food and use grinding mills in their head skeletons to break it up. They also have armoured thoraces with varying arrangements of sclerotized spicules or stiffened setae for gripping and protection during tunnelling, a short anal segment, and a short posterior breathing tube for protecting the openings. The former trend is characterized by species with opposite and contrasting features. They filter food and have well‐developed pre‐oral setal filters but they lack grinding mills or only have poorly developed grinding mills. They have reduced thoracic armature, elongate anal segments, and posterior breathing tubes which facilitates simultaneous feeding and respiration. Comparison with 23 Copestylum species reared from bromeliads (Bromeliaceae) suggests a common pattern of diversification in that species groups with the largest body sizes are more specialized.     

Determination of the filamentous cyanobacteria Planktothrix rubescens in environmental water samples using an image processing system

Cyanobacteria occur in surface waters worldwide. Many of these produce peptides and/or alkaloids, which can present a risk for animal and human health. Effective risk assessment and management requires continuous and precise observation and quantification of cyanobacterial cell densities. In this respect, quantification of filamentous Planktothrix species is problematic. The aim of this study was to develop an automated system to count filamentous Planktothrix rubescens using image processing. Furthermore, this study aimed to assess optimum sample volumes and filament density for measurement precision and to validate image processing measurement of P. rubescens for an effective risk assessment.Three environmental samples and one cultured sample of P. rubescens were collected by filtration onto nitrocellulose filters. Filament lengths were determined using fluorescence microscopy combined with an image processor. Cell density could be calculated from the resulting images. Cyanobacteria could easily be discriminated from algae via their fluorescence properties. The results were found to be independent of the mode of image acquisition. The precision of total filament length determination was dependent on the total filament length on the filter, i.e. analyses of highest precision could be expected for filters containing 2000–20,000 μm filaments per mm². When using suitable filtration volumes, the detection limits of the described method are sufficient for an effective risk assessment. To summarise, this procedure is a fast, easy and accurate method to determine cell densities of filamentous P. rubescens in water samples without costly and tedious manual handling.     

Modelling geographical patterns in species richness using eigenvector-based spatial filters

Aim To test the mechanisms driving bird species richness at broad spatial scales using eigenvector‐based spatial filtering. Location South America. Methods An eigenvector‐based spatial filtering was applied to evaluate spatial patterns in South American bird species richness, taking into account spatial autocorrelation in the data. The method consists of using the geographical coordinates of a region, based on eigenanalyses of geographical distances, to establish a set of spatial filters (eigenvectors) expressing the spatial structure of the region at different spatial scales. These filters can then be used as predictors in multiple and partial regression analyses, taking into account spatial autocorrelation. Autocorrelation in filters and in the regression residuals can be used as stopping rules to define which filters will be used in the analyses. Results Environmental component alone explained 8% of variation in richness, whereas 77% of the variation could be attributed to an interaction between environment and geography expressed by the filters (which include mainly broad‐scale climatic factors). Regression coefficients of environmental component were highest for AET. These results were unbiased by short‐scale spatial autocorrelation. Also, there was a significant interaction between topographic heterogeneity and minimum temperature. Conclusion Eigenvector‐based spatial filtering is a simple and suitable statistical protocol that can be used to analyse patterns in species richness taking into account spatial autocorrelation at different spatial scales. The results for South American birds are consistent with the climatic hypothesis, in general, and energy hypothesis, in particular. Habitat heterogeneity also has a significant effect on variation in species richness in warm tropical regions.     

Predicting the geographical distribution of plant communities in complex terrain – a case study in Fushian Experimental Forest, northeastern Taiwan

Ecosystem management and biodiversity conservation are usually implemented using information of several targeted species or cover-types and usually do not include information about communities. This is not because community-level information is unimportant for management purposes, but because the detailed fieldwork required for gathering community-level information at the scale for ecosystem management is usually impractical. We propose two methods to estimate the geographical distribution of plant communities with the objectives of covering large areas with minimal field efforts. The first method estimates the geographical distribution of plant communities by combining clustering methods with vegetation modeling, and the second extrapolates the geographical distribution of gradients in plant communities by combining gradient analysis with vegetation modeling. Vegetation modeling with clustering methods can be used to allocate sites with potentially higher alpha diversity, with the benefit of having a list of species associated with the clustered type. Vegetation modeling with gradient analysis can be used to identify regions with potentially the highest beta diversity by means of selecting regions with the widest range or highest variability in major DCA axes scores, and thereby help to preserve the scope of environmental conditions that lead to diversity in species assemblages. This is especially important because biological entities such as species, communities, or even ecosystems may cease to exist in the long run, and the preservation of processes that lead to biodiversity will eventually become more meaningful. We conclude that new methods to study and manage the processes that contribute to biodiversity at all scales should be and can be developed.     

生物多样性野外调查地理信息管理、路线精细设计和精确导航方法

野外调查是生物多样性研究和保护的基础工作。在野外调查中, 自然地理环境十分复杂, 对相关地理信息的掌握程度、调查路线的设计质量和导航的准确性, 直接影响调查工作的成效, 甚至调查人员的人身安全。使用谷歌地球软件及相关数据转换工具, 能获取海量遥感影像和地形数据, 能将各种地理信息转换、编辑、叠加到三维地球模型上形成地理信息库, 进而精细设计野外考察路线、调查点和调查样方, 并以kml或kmz文件格式保存和分发设计结果。使用Android智能终端设备安装OruxMaps软件, 可以将多种网络地图下载制作成离线地图, 在卫星图上精确显示当前位置、记录走过的轨迹、导入kml或kmz文件进行导航。综合使用这些工具, 可以实现良好的地理信息管理、精细的生物多样性野外调查路线设计和高精度现场导航实施, 有效提高野外调查工作的成效和安全性。     

Screening for microbial strains degrading glass fiber acrylic composite filters

In this study we have assessed the capacity of five fungal and two bacterial species to biodegrade glass fiber acrylic composite filters which are utilized in air conditioners. The strains used were Trichoderma harzianum (2 strains), Trichoderma koningii, Penicillium spp., Aspergillus niger, Pseudomonas aeruginosa and Pseudomonas fluorescens. Pre-sterilized filters were incubated in solid or liquid media at 30 °C for 21 days. Biodegradability was monitored by evaluating microbial colonization, increase in biomass and weight loss of filters coupons. Among the species under investigation, the two strains of T. harzianum (MYA198 and BCC5828) showed the best biodegradability performance and were used to analyse total carbon and esterase activity. Our results clearly indicate that cells grown in the presence of shredded filters display a hydrolytic activity and lead to a consistent removal of the organic portion of the tested filters. This study suggests that a solid state fermentation process in suitable bioreactors based on T. harzianum species could be a suitable approach to acrylic composite filter biodegradation.     

Species richness and composition assessment of spiders in a Mediterranean scrubland

Intensive fieldwork has been undertaken in Portugal in order to develop a standardized and optimized sampling protocol for Mediterranean spiders. The present study had the objectives of testing the use of semi-quantitative sampling for obtaining an exhaustive species richness assessment of spiders and testing the effects of day, time of day, collector and sampling method on the collected species richness and composition of a Mediterranean scrubland. The collecting summed 224 samples corresponding to one person-hour of effective fieldwork each. In total, 115 species were captured, of which 110 were recorded inside a delimited one-hectare plot, corresponding to more than 70% of the about 160 estimated species. Although no estimator reached the asymptote, the Michaelis-Menten curve behaviour indicates that the estimated richness should be accurate. Most different sampling approaches (day, time of day, collector and sampling method) were found to influence richness, abundance or composition of the samples to some extent, although sampling method had the strongest influence whereas “collector” showed no effect at all. The results support the idea that the only variables that need to be controlled in similar protocols are the sampling methods and the time of day when each method is executed. We conclude that populations in structurally simple habitats present narrower peaks of adult abundance, which implies higher percentages of juveniles in samples. Finally, results also indicate that habitats with a relatively simple structure like scrublands may require as much sampling effort, in order to reach similar proportions of captured species in relation to the estimated richness, as habitats that are much more complex.     

Influence of researcher experience and fieldwork intensity on the probability of brood losses in sensitive species: The case of the Red-backed Shrike Lanius collurio

Minimizing disturbance to animals when studying them should be a major consideration in ecological research design, especially when species are known to be sensitive to disturbances. A basic method in the study of bird reproductive ecology involves nest visits, but these can adversely affect birds’ breeding success. Appropriate fieldwork procedures are therefore highly important, especially in the case of timid and sensitive species. This study aimed to assess the impact of the method of searching for nests of Red-backed Shrike Lanius collurio on the probability of these birds abandoning their broods. Our study revealed that observer experience and nest searching intensity did influence the likelihood of brood desertion by this species. Less field experience and a greater nest searching intensity caused the shrikes to abandon their nests more often. We recommend paying scrupulous attention to the behaviour of the birds when searching for nests and when looking for nests after incubation has started.     

Structural Functionalism as a Heuristic Device

The purpose of this article is to argue that structural functionalism as a method for conducting fieldwork and as a format for analysis of ethnographic data remains a powerful model. Because of its mechanical nature, structural functionalism is easily understood by professional educators and useful in solving their problems. As a heuristic device, functionalist theory can provide aid in the solution of a problem that is otherwise incapable of theoretical justification.     

A rapid technique for the analytical and preparative isolation of transfer RNA from reaction mixtures

The isolation of enzymically modified tRNA's from enzyme reaction mixtures is usually achieved by one of two general methods. Amino-acyl synthetase reactions are easily assayed by filter paper techniques (1) in which the tRNA is precipitated on filters of materials such as cellulose ester or glass fiber. After drying, the filters can be counted by several techniques. The limitations of this technique include unknown counting efficiency and loss of the sample. In cases in which recovery of the tRNA is desired the usual procedure involves phenol extraction of the tRNA followed by selective precipitation with salts and/or organic solvents.     

基于标本和分布信息评估中国虾脊兰属 植物的濒危状况

兰科植物是生物多样性保护的旗舰类群之一, 但如何客观准确地评估兰科植物的濒危状况, 一直是生物多样性保护中急需解决的问题。本文以中国虾脊兰属(Calanthe)植物为例, 探讨了基于馆藏标本和野外分布信息进行兰科植物红色名录濒危等级评估的利弊。我们的研究表明, 馆藏标本能够比较客观地反映物种地理分布信息和相应的野外居群状况, 但对于物种分布的历史变化和受威胁因素反映不足; 而野外工作对于物种的实际分布状况和受威胁因素等的反映比较客观, 但能发现的物种和居群数量有限, 部分极小种群物种在短时间野外工作中很难发现。我们的研究认为, 有2种虾脊兰属植物应被评估为野外灭绝(EW), 16种应被评估为极度濒危(CR)。可见, 中国虾脊兰属植物濒危的状况远比前人的评估结果要严重得多。     

Use of DIL-type cava filters for the prevention of thromboembolism of the pulmonary artery]

New type cava filters were employed to prevent pulmonary artery thromboembolism in 12 cases. DIL cava filter was used, that represents a string made of a special alloy that can 'memorize' its shape. The design of this filter is in principle different from all the known filters, for it functions as an intraluminal filter and at the same time stretches the vena cava inferior, enlarging its diameter in the frontal plane. The DIL cava filter proved to be effective in the majority of cases, but if the walls of vena cava inferior were too rigid, for example, if a tumor grew into them, it was difficult to place the filter properly. On the whole this filter is characterized by a number of advantages: it can be easily implanted via 7 F catheter without injuring the vena cava inferior walls. No cases of dislocation of cava filters in relation to bone markers were noted in 9 patients over 60 +/- 17 days.