Conservation, Small Mammals, and the Future of Sacred Groves in West Africa

This article considers the conservation of relict natural habitat in West Africa, especially habitat preserved in traditional sacred groves. Government-sanctioned conservation is contrasted with local grassroots efforts of conservation. Evidence for the ecological value of sacred groves is based on results of a field study of small mammal communities conducted on the Accra Plains of Ghana and on published sources on the conservation and use of sacred groves from various countries. The study employed standard mark-and-recapture techniques for the sampling for terrestrial small mammals, and mist netting for the sampling of bat communities. Pragmatic approaches combining conservation and sustainable use are considered, as are traditional values that have preserved the sacred groves in the past for up to several hundred years in some cases. In part because these groves shelter unique small mammal and plant communities, traditional values and protection mechanisms should be integrated into the newly emerging cultural and religious contexts. The issues encountered during this study reveal that effective conservation involving local peoples requires a concerted interdisciplinary effort. This revised version was published online in November 2006 with corrections to the Cover Date.     

Interpreting recruitment limitation in forests

Studies of tree recruitment are many, but they provide few general insights into the role of recruitment limitation for population dynamics. That role depends on the vital rates (transitions) from seed production to sapling stages and on overall population growth. To determine the state of our understanding of recruitment limitation we examined how well we can estimate parameters corresponding to these vital rates. Our two-part analysis consists of (1) a survey of published literature to determine the spatial and temporal scale of sampling that is basis for parameter estimates, and (2) an analysis of extensive data sets to evaluate sampling intensity found in the literature. We find that published studies focus on fine spatial scales, emphasizing large numbers of small samples within a single stand, and tend not to sample multiple stands or variability across landscapes. Where multiple stands are sampled, sampling is often inconsistent. Sampling of seed rain, seed banks, and seedlings typically span <1 yr and rarely last 5 yr. Most studies of seeding establishment and growth consider effects of a single variable and a single life history stage. By examining how parameter estimates are affected by the spatial and temporal extent of sampling we find that few published studies are sufficiently extensive to capture the variability in recruitment stages. Early recruitment stages are especially variable and require samples across multiple years and multiple stands. Ironically, the longest duration data sets are used to estimate mortality rates, which are less variable (in time) than are early life history stages. Because variables that affect recruitment rates interact, studies of these interactions are needed to assess their full impacts. We conclude that greater attention to spatially extensive and longer duration sampling for early life history stages is needed to assess the role of recruitment limitation in forests.     

Troglochaetus beranecki Delachaux (Annelida, Polychaeta): collecting methods and microscopy techniques for SEM and in vivo observations

The methods and the instruments for sampling and observation in vivo of the polychaete Troglochaetus beranecki are briefly described. Some SEM observations are reported. This revised version was published online in July 2006 with corrections to the Cover Date.     

Strategies for dealing with conformational sampling in structural calculations of flexible or kinked transmembrane peptides.

Peptides corresponding to transmembrane (TM) segments from membrane proteins provide a potential route for the determination of membrane protein structure. We have determined that 2 functionally critical TM segments from the mammalian Na+/H+ exchanger display well converged structure in regions separated by break points. The flexibility of these break points results in conformational sampling in solution. A brief review of available NMR structures of helical membrane proteins demonstrates that there are a number of published structures showing similar properties. Such flexibility is likely indicative of kinks in the full-length protein. This minireview focuses on methods and protocols for NMR structure calculation and analysis of peptide structures under conditions of conformational sampling. The methods outlined allow the identification and analysis of structured peptides containing break points owing to conformational sampling and the differentiation between oligomerization and ensemble-averaged observation of multiple peptide conformations.     

Risk-targeted selection of agricultural holdings for post-epidemic surveillance: estimation of efficiency gains

Current post-epidemic sero-surveillance uses random selection of animal holdings. A better strategy may be to estimate the benefits gained by sampling each farm and use this to target selection. In this study we estimate the probability of undiscovered infection for sheep farms in Devon after the 2001 foot-and-mouth disease outbreak using the combination of a previously published model of daily infection risk and a simple model of probability of discovery of infection during the outbreak. This allows comparison of the system sensitivity (ability to detect infection in the area) of arbitrary, random sampling compared to risk-targeted selection across a full range of sampling budgets. We show that it is possible to achieve 95% system sensitivity by sampling, on average, 945 farms with random sampling and 184 farms with risk-targeted sampling. We also examine the effect of ordering samples by risk to expedite return to a disease-free status. Risk ordering the sampling process results in detection of positive farms, if present, 15.6 days sooner than with randomly ordered sampling, assuming 50 farms are tested per day.     

To pluck or not to pluck: the hidden ethical and scientific costs of relying on feathers as a primary source of DNA

This article responds to the recent prominence of ornithological literature advocating the plucking or clipping of feathers to obtain DNA in avian studies. We argue that the practise of feather plucking or clipping should be strongly discouraged on both scientific and ethical grounds in the avian literature. Currently, despite claims to the contrary, it is not clear that feather sampling as a source of DNA has lower ethical impacts on birds than blood sampling. In addition, feather samples provide a smaller and less reliable biological resource, significantly jeopardising the short and long‐term outcomes that can be gained by the sampling. In contrast, blood collection has been experimentally demonstrated to be relatively safe, subject to operators being skilled and following published guidelines, providing large yields of high quality DNA that facilitates archival storage of samples in a manner that the destructive sampling of feathers cannot.     

Diversity and distribution of amphibians in Romania

Nineteen species of amphibians inhabit Romania, 9 of which reach their range limit on this territory. Based on published occurrence reports, museum collections and our own data we compiled a national database of amphibian occurrences. We georeferenced 26779 amphibian species occurrences, and performed an analysis of their spatial patterns, checking for hotspots and patterns of species richness. The results of spatial statistic analyses supported the idea of a biased sampling for Romania, with clear hotspots of increased sampling efforts. The sampling effort is biased towards species with high detectability, protected areas, and large cities. Future sampling efforts should be focused mostly on species with a high rarity score in order to accurately map their range. Our results are an important step in achieving the long-term goals of increasing the efficiency of conservation efforts and evaluating the species range shifts under climate change scenarios.     

本科遗传学教学中的遗传漂变概念探讨

遗传漂变是遗传学教学的难点之一,因其涉及随机性和概率,特别容易引起误解。定义中的“抽样误差”常被误解为遗传漂变是由于“抽样”这一研究方法干扰才导致基因频率的随机变化。本文首先对国内外《遗传学》教材中的遗传漂变定义进行了分析比较,发现“抽样误差”的定义为各教材普遍采用,但只有少数教材对“抽样误差”概念进行了正确的解释,多数未作进一步的说明。文章介绍了遗传漂变的研究历史,亦即Wright、 Fisher和Kimura等学者对遗传漂变研究的贡献。进而,特别介绍了近年来国外关于本科生遗传漂变教学的两篇代表性教学研究论文,指出本科生在学习过程中容易出现错误理解是难以避免的现象,对此也提供了初步的解决办法。作者最后结合自己的教学实践,提出本科生教学中遗传漂变仍然采用含有“抽样误差”概念的定义,只是需要对“抽样误差”做进一步的解释,指出“抽样误差”是等位基因世代传递过程中存在的、配子间的随机结合,“相当于”对整个参与交配的配子库中的配子进行的一次“随机抽样”,而与一般遗传学研究中的人为抽样行为无关。本文旨在为本科遗传学教学中关于遗传源变概念的讲解提供借鉴和参考。     

Airborne microorganisms in a subterranean archaeological area of the basilica of San Lorenzo in Lucina (Rome)

The basilica of San Lorenzo in Lucina in Rome was built in the fifth century on the foundations of a Roman insula used for dwellings and commercial activities, where the first Christian communities had held their meetings. This archaeological area is still rather isolated since it can only be visited by groups for one/two hours once a month. Such a situation is ideal for studying both the quantity of microorganisms in the air under undisturbed conditions and/or conveyed by visitors. The biodeterioration of subterranean remains is determined by the development of bacteria, cyanobacteria, actinomycetes, algae and fungi. On the walls of this underground archaeological area the main form of alteration is the efflorescence. In order to compare the stone and airborne microflora, the microorganisms living on stone and the airborne ones have been detected. Air samples were taken both during the visits and under non-turbulent conditions utilizing three sampling methods: gravitational, intake by multi-stage impact and intake by single-stage impact. The results have made it possible to determine the microbial content of the air, as well as the sampling schedule required for rarely visited underground environments. Furthermore, a comparison of the three methods used showed that the adoption of one or the other sampling method gave different complementary information on airborne microflora. This revised version was published online in June 2006 with corrections to the Cover Date.     

Species Richness and Invasion Vectors: Sampling Techniques and Biases

During a European Union Concerted Action study on species introductions, an intercalibration workshop on ship ballast water sampling techniques considered various phytoplankton and zooplankton sampling methods. For the first time, all the techniques presently in use worldwide were compared using a plankton tower as a model ballast tank spiked with the brine shrimp and oyster larvae while phytoplankton samples were taken simultaneously in the field (Helgoland Harbour, Germany). Three cone-shaped and 11 non-cone shaped plankton nets of different sizes and designs were employed. Net lengths varied from 50 to 300 cm, diameters 9.7–50 cm, and mesh sizes 10–100 μm. Three pumps, a Ruttner sampler, and a bucket previously used in ballast water sampling studies were also compared. This first assessment indicates that for sampling ballast water a wide range of techniques may be needed. Each method showed different results in efficiency and it is unlikely that any of the methods will sample all taxa. Although several methods proved to be valid elements of a hypothetical `tool box' of effective ship sampling techniques. The Ruttner water sampler and the pump P30 provide suitable means for the quantitative phytoplankton sampling, whereas other pumps prevailed during the qualitative trial. Pump P15 and cone-shaped nets were the best methods used for quantitative zooplankton sampling. It is recommended that a further exercise involving a wider range of taxa be examined in a larger series of mesocosms in conjunction with promising treatment measures for managing ballast water. This revised version was published online in July 2006 with corrections to the Cover Date.     

Enzyme variation and taxonomy: the estimation of sampling errors in measurements of interspecific genetic similarity

The uses of biochemical genetics as an aid to taxonomy are discussed briefly. A survey is made of published data to establish expected levels of genetic similarity or identity between conspecific populations, between congeneric species and between species of different genera. Existing measures of genetic similarity, identity or distance are discussed and some of the difficulties involved in their use in taxonomy are outlined. A new measure of genetic similarity is proposed specifically designed for use in making interspecific comparisons for taxonomic purposes. This measure offers considerable advantages in ease of calculation and also greatly simplifies the estimation of sampling errors. An empirical comparison is made, using published data, of the measures and confidence limits obtained by the proposed memod against published measures of genetic variation between species.     

Overdispersed logistic regression for SAGE: Modelling multiple groups and covariates

Background  

Two major identifiable sources of variation in data derived from the Serial Analysis of Gene Expression (SAGE) are within-library sampling variability and between-library heterogeneity within a group. Most published methods for identifying differential expression focus on just the sampling variability. In recent work, the problem of assessing differential expression between two groups of SAGE libraries has been addressed by introducing a beta-binomial hierarchical model that explicitly deals with both of the above sources of variation. This model leads to a test statistic analogous to a weighted two-sample t-test. When the number of groups involved is more than two, however, a more general approach is needed.     

On the occurrence of Streptocephalus torvicornis Waga 1842 (Crustacea,Anostraca) on a coastal island off Italy

The presence of Streptocephalus torvicornis on one coastal island off Italy (Cottarelli & Mura, 1995) is confirmed. Two years of sampling revealed an erratic pattern of occurrence, however, likely related to the unstable nature of the environmental characteristics. Such an unpredictability might be alternatively explained by a colonization-extinction process, or by adaptation to variations in annual weather (Donald, 1983). This revised version was published online in July 2006 with corrections to the Cover Date.     

Identifying the source of species invasions: sampling intensity vs. genetic diversity

Population geneticists and community ecologists have long recognized the importance of sampling design for uncovering patterns of diversity within and among populations and in communities. Invasion ecologists increasingly have utilized phylogeographical patterns of mitochondrial or chloroplast DNA sequence variation to link introduced populations with putative source populations. However, many studies have ignored lessons from population genetics and community ecology and are vulnerable to sampling errors owing to insufficient field collections. A review of published invasion studies that utilized mitochondrial or chloroplast DNA markers reveals that insufficient sampling could strongly influence results and interpretations. Sixty per cent of studies sampled an average of less than six individuals per source population, vs. only 45% for introduced populations. Typically, far fewer introduced than source populations were surveyed, although they were sampled more intensively. Simulations based on published data forming a comprehensive mtDNA haplotype data set highlight and quantify the impact of the number of individuals surveyed per source population and number of putative source populations surveyed for accurate assignment of introduced individuals. Errors associated with sampling a low number of individuals are most acute when rare source haplotypes are dominant or fixed in the introduced population. Accuracy of assignment of introduced individuals is also directly related to the number of source populations surveyed and to the degree of genetic differentiation among them ( F _ST). Incorrect interpretations resulting from sampling errors can be avoided if sampling design is considered before field collections are made.     

The relation between fine root density and proximity of stems in closed Douglas-fir plantations on homogenous sandy soils: implications for sampling design

Studies have been carried out in two fully stocked, fast growing Douglas-fir plantations of the Dutch ACIFORN project in three consecutive years, to obtain information on fine root densities (Olsthoorn 1991). For the present paper, data collected in early summer 1987 were used to study the relation of fine root density and proximity to the nearest tree or the dominant tree. A large number of samples (37 in one site and 55 in another) was collected in a small plot (10 × 11 m). Two distances were measured at each sampling point: the distance to the nearest tree and the distance to the tree with a dominant crown above that point. There was large variability in fine root density in the samples. Tests with different regression models showed a distinct rooting pattern for one of the two locations. It is concluded that systematic errors in the assessment of fine root density can arise when sampling points are chosen at a constant distance from trees. For Douglas-fir, this systematic error could have been an overestimation of the fine root density by up to 10%. These systematic errors can be avoided easily, using a stratified random design or a random sampling design. When trees are spaced irregularly, a grid sampling design is also appropriate. This revised version was published online in June 2006 with corrections to the Cover Date.     

Recommendations for the routine sampling of diatoms for water quality assessments in Europe

Many methods for using diatoms for routine monitoring of water quality have been developed in Europe and, in some countries, these are being used to enforce environmental legislation. In order to facilitate their wider use, particularly with respect to European Union legislation, steps are being taken to harmonize methodology. In this paper, the principles and practice of sampling are described in relation to the main habitat types encountered in Europe. Although details of methods and sampling programmes have to be tailored to particular circumstances and the overall objectives of the monitoring, a number of generalizations can be made. Where available, rocks and other hard surfaces are the preferred substrates and methods for sampling these are described. If such substrata are not available, then introduced ('artificial') substrata have many applications. Various types of introduced substrata can be used successfully, so long as some basic precautions are described. Other types of substrata such as macrophytes and macroalgae may also be useful under certain circumstances, although there is less consensus in the literature on the most appropriate methods, and of the validity of comparisons between indices computed from epiphytic and epilithic communities. When designing surveys, it is recommended that as far as possible, extremes of non-water quality factors (e.g. shade, current speed, etc) are avoided, unless these are characteristic of the system under investigation. Detailed guidelines for sampling epilithon are described. Along with the recommendations for sampling other substrata, it is hoped that these provide a framework that can be adapted to most river types in Europe. This revised version was published online in June 2006 with corrections to the Cover Date.     

The importance of qualitative inventory sampling using electric fishing and nets in a large,tropical river (Brazil)

Qualitative fish sampling (single catch) using three methods (electric fishing, gillnets, seine nets) was assessed at three sites in the Ivai River (Paraná State, Brazil) to check their usefulness for quick inventory investigations. Electric fishing at a constant effort (15 min per each) was considered to be the best sampling technique. Taxon richness was calculated as the expected number of species using a rarefraction technique. Samples of 300–325 individuals, and 6–10 repetitions in neighbouring segments were sufficient. Even though electric fishing was conducted with the same effort in similar segments at each site there were many differences in species abundance. This suggests that the estimated fish specimen number obtained with constant effort is of limited validity on one sampling occasion and may be best considered as an ‘index of density’ only. The differences may partially be caused by the segments being located along the right and left bank of the large river (problem of different habitats). Qualitative and quantitative differences between electric fishing, gill-netting and seine-netting samples were very high at a high significance level. Nevertheless, as 22.4% taxa were caught only by gill or seine nets, these gears were important for complementing the species list. This revised version was published online in July 2006 with corrections to the Cover Date.     

Minimal sampling requirements for a precise assessment of soft-bottom macrobenthic communities, using AMBI

Since AMBI was published originally in 2000, it has been used in an increasing number of investigations with monitoring purposes, or to analyse impacts on soft-bottom macrobenthic communities. Some guidelines for its correct use were published in 2005; however, a main issue remained without an answer — which are the minimal area and number of replicates necessary, to obtain a precise estimate for AMBI? In this study, new methodologies such as bootstrap techniques have been applied to this particular problem.Data were obtained from sampling carried out in 1995, within the framework of the Littoral Water Quality Monitoring and Control Network of the Basque Country (northern Spain). The sampling strategy consisted of 11 intertidal estuarine sampling stations (0.25m², sampled for each of six replicates) and 17 subtidal estuarine and coastal sampling stations (0.125m², sampled for each of six replicates).Two replicates have been established as being sufficient, both for intertidal and subtidal sampling stations, to classify 80% of the pseudosamples into the same disturbance level, in terms of AMBI, for 64% of the stations.For the minimal area, it has been determined also (for both intertidal and subtidal sampling stations) that 0.25m² is sufficient to classify 80% of the iterations into the same disturbance level, for 64% of the stations.     

Towards objectivity in vegetation classification: the example of the Austrian forests

We present a numerical classification of 2145 objectively sampled relevés from the entire forest area of Austria (Central Europe). The sample sites were selected by a combined method involving a systematic matrix and stratified random sampling. A TWINSPAN classification led to 32 clusters which are described in detail. Three main groups can be distinguished: (1) Alpine-dinaric coniferous forests on carbonate soils, (2) Coniferous forests on acid soils and (3) Deciduous forests. These groups correspond with accuracy to the classes Erico-Pinetea, Vaccinio-Piceetea and Querco-Fagetea in the traditional Braun-Blanquet system. Thus, the value of the Braun-Blanquet approach is supported by more or less objective sampling and numerical classification methods. The assumption of the objective existence of ecological species groups is strongly supported, too. Moreover, our results may help to solve some controverse points discussed in the European forest classification regarding the delimination between the three mentioned classes. This revised version was published online in August 2006 with corrections to the Cover Date.