Diversity and dynamics of rare and of resident bacterial populations in coastal sands

Coastal sands filter and accumulate organic and inorganic materials from the terrestrial and marine environment, and thus provide a high diversity of microbial niches. Sands of temperate climate zones represent a temporally and spatially highly dynamic marine environment characterized by strong physical mixing and seasonal variation. Yet little is known about the temporal fluctuations of resident and rare members of bacterial communities in this environment. By combining community fingerprinting via pyrosequencing of ribosomal genes with the characterization of multiple environmental parameters, we disentangled the effects of seasonality, environmental heterogeneity, sediment depth and biogeochemical gradients on the fluctuations of bacterial communities of marine sands. Surprisingly, only 3–5% of all bacterial types of a given depth zone were present at all times, but 50–80% of them belonged to the most abundant types in the data set. About 60–70% of the bacterial types consisted of tag sequences occurring only once over a period of 1 year. Most members of the rare biosphere did not become abundant at any time or at any sediment depth, but varied significantly with environmental parameters associated with nutritional stress. Despite the large proportion and turnover of rare organisms, the overall community patterns were driven by deterministic relationships associated with seasonal fluctuations in key biogeochemical parameters related to primary productivity. The maintenance of major biogeochemical functions throughout the observation period suggests that the small proportion of resident bacterial types in sands perform the key biogeochemical processes, with minimal effects from the rare fraction of the communities.     

Where the rare species are

Prioritizing geographic areas for conservation attention is important – time and money are in short supply but endangered species are not – and difficult. One popular perspective highlights areas with many species found nowhere else ( Myers et al. 2000 ). Another identifies areas that contain species with fewer close relatives elsewhere ( Faith 1992 ). One might characterize the first as focusing on geographic, and the second on phylogenetic, rarity. To the extent that geographically rare species are at greater risk of extinction ( Gaston & Fuller 2009 ), and that phylogenetically rare species contribute disproportionally to overall biodiversity ( Crozier 1997 ), it would seem reasonable to formally integrate the two approaches. In this issue, Rosauer et al. (2009) do just that; their elegant combined metric pinpoints areas missed out when the two types of rarity are looked at in isolation.     

Spatial distribution of rare species: statistical approach

Many species are locally rare (have low occurrences in a given region). The method is proposed for the analysis of spatial distribution of such species. The procedure is based on the comparison of actual mean distances between records with Monte-Carlo-simulated mean distances expected for random occurrence pattern. The method was applied to two datasets: benthic macrofauna from the Barents and Kara Seas (Kucheruk, Kotov, 2002) and the Black Sea interstitial ciliates (original data). For both datasets, the number of rare species positively correlates with number of common species per site and with the total number of species. Furthermore (and irrespectively of total diversity pattern), rare species usually were locally clumped in their distribution: each of the species was mostly found at sites that were close together. This tendency, however, was significant for the macrofauna species but not for ciliates.     

Influence of management on butterflies of rare grassland ecosystems in Germany

Traditional hay-meadows in the Alps and fens at the edge of the Alps are habitats for many rare and endangered butterfly species. Conservation efforts aim at preserving these species, but the biotopes depend on regular mowing, which in turn requires intensive financial support. The feasibility of substituting mowing of these sites by grazing is discussed and considered as a more cost effective management type which produces agriculturally valuable goods as well. In this study the butterfly fauna of mown and grazed sites were compared. Species composition, species number, and the occurrence of rare species under the two management types were in most cases rather similar for both grassland ecosystems. Nevertheless, there are hints that for single rare species this might not be true. Additionally, at one site, grazing intensity on a former hay-meadow was too high to preserve the species-rich community. Overall the results are encouraging: grazing does not have to be as detrimental as formerly thought, although details (compartments of pastures, intensity) still have to be confirmed. Experimental grazing management of aban-doned grasslands of the studied types should be started.     

The good, the bad, and the rare: memory for partners in social interactions

For cooperation to evolve via direct reciprocity, individuals must track their partners' behavior to avoid exploitation. With increasing size of the interaction group, however, memory becomes error prone. To decrease memory effort, people could categorize partners into types, distinguishing cooperators and cheaters. We explored two ways in which people might preferentially track one partner type: remember cheaters or remember the rare type in the population. We assigned participants to one of three interaction groups which differed in the proportion of computer partners' types (defectors rare, equal proportion, or cooperators rare). We extended research on both hypotheses in two ways. First, participants experienced their partners repeatedly by interacting in Prisoner's Dilemma games. Second, we tested categorization of partners as cooperators or defectors in memory tests after a short and long retention interval (10 min and 1 week). Participants remembered rare partner types better than they remembered common ones at both retention intervals. We propose that the flexibility of responding to the environment suggests an ecologically rational memory strategy in social interactions.     

Testing for an unusual distribution of rare variants

Technological advances make it possible to use high-throughput sequencing as a primary discovery tool of medical genetics, specifically for assaying rare variation. Still this approach faces the analytic challenge that the influence of very rare variants can only be evaluated effectively as a group. A further complication is that any given rare variant could have no effect, could increase risk, or could be protective. We propose here the C-alpha test statistic as a novel approach for testing for the presence of this mixture of effects across a set of rare variants. Unlike existing burden tests, C-alpha, by testing the variance rather than the mean, maintains consistent power when the target set contains both risk and protective variants. Through simulations and analysis of case/control data, we demonstrate good power relative to existing methods that assess the burden of rare variants in individuals.     

The fluorescence of transparent polymer films of rare earth complexes

Fluorescence films of rare earth (Eu³⁺ or Tb³⁺) β-diketone chelates dispersed in a PMMA polymer matrix were prepared and their fluorescence properties were investigated. Dependence of rare earth contents on emission properties and transparencies of the films are also given. Influence of the substituents of the ligand on spectroscopic properties and fluorescence intensities were discussed. The strongest red and green fluorescence was obtained when DBM (dibenzoylmethane) was used as a ligand for the Eu-film and AcA (acetylacetone) for the Tb-film. The relation between the nature of ligands and efficiencies of energy transfer in the film systems was also studied.     

Heavy-weighting rare species in dissimilarity indices improve recovery of multivariate groups

Dissimilarity indices differ in the relative weight given to rare species. Heavy-weighting of rare species may be justified in terms of sampling. An index may erroneously estimate high dissimilarity between two identical communities if they are composed of many rare species and the sampling effort is insufficient to observe most of them in both samples. Heavy-weighting of rare species is thought to compensate for this negative bias. I evaluated two quantitative indices that heavy-weight rare species, NNESS (New Normalized Expected Species Shared) and Goodall, and two probability versions of the Sørensen index, one that takes into account shared unseen rare species and the other that does not. They were compared against the widely used Bray-Curtis (or Sørensen quantitative) and the Morisita-Horn. Indices were computed using raw abundance data or coded data that heavy-weight rare species (frequency in sample units, log-transformation and standardization by the maximum abundance within species). Indices were evaluated for their ability to distinguish, using distance-based MANOVA, season-defined (summer, winter) groups of samples of stream macroinvertebrates and groups of samples obtained by simulation. Sørensen corrected for unseen shared species performed poorly in the empirical study and intermediate in the simulations. NNESS was good in the empirical study and intermediate in the simulations. Goodall scored inversely as NNESS, being intermediate in the empirical assessment and very good in the simulations. The Sørensen uncorrected for unseen shared species, Bray-Curtis and the Morisita-Horn presented poor or intermediate results using raw abundance data. Their performance, however, improved consistently using coded data that heavy-weight rare species and made them good or very good. I conclude that heavy-weighting rare species improves the ability to detect multivariate groups. Heavy-weighting of rare species may be achieved either by using specific formulae (NNESS, Goodall) or using coded data.     

Evolution of mating types in finite populations: The precarious advantage of being rare

Sexually reproducing populations with self‐incompatibility bear the cost of limiting potential mates to individuals of a different type. Rare mating types escape this cost since they are unlikely to encounter incompatible partners, leading to the deterministic prediction of continuous invasion by new mutants and an ever‐increasing number of types. However, rare types are also at an increased risk of being lost by random drift. Calculating the number of mating types that a population can maintain requires consideration of both the deterministic advantages and the stochastic risks. By comparing the relative importance of selection and drift, we show that a population of size N can maintain a maximum of approximately N^1/3 mating types for intermediate population sizes, whereas for large N, we derive a formal estimate. Although the number of mating types in a population is quite stable, the rare‐type advantage promotes turnover of types. We derive explicit formulas for both the invasion and turnover probabilities in finite populations.     

Mapping first to final uses for rare earth elements,globally and in the United States

Estimating the material flows of rare earth elements (REEs) is essential to understanding which industries are most vulnerable to potential REE supply disruptions which, in turn, may inform policy recommendations aimed at reducing the supply risk. However, the REEs are a group of mineral commodities characterized by highly uncertain estimates of supply and demand due to the REE market's complexity, opacity, and small size. In this study, a streamlined methodology was applied to map mineral commodity first-use to final-use applications and to estimate total requirements at the national level based on available industrial data for final-use finished goods. This analysis examines REEs both as a group and individually, showing that total US requirements are between 15% and 16.5% of world requirements for the year 2015, the latest year with the most complete information available. The findings shed light on US industrial capabilities by revealing the discrepancy between the types of REEs that go into US raw material consumption and those that are contained in embedded consumption. For instance, given the United States’ large oil refining industry, US raw material consumption of lanthanum is quite high. In contrast, US raw material consumption of neodymium is relatively low, whereas embedded demand is comparatively high. This reflects the lack of industrial capacity to process REE concentrates into magnet material combined with the US's high imports of products that contain rare earth permanent magnets.     

Identification of base substitutions in ten types of rare variants of phosphoglucomutase-1 (PGM1) encountered in Japanese.

In a previous starch-gel electrophoresis study of erythrocyte phosphoglucomutase-1 (PGM1) in 23,095 Japanese from Hiroshima and Nagasaki, we detected 14 types of rare variant alleles. To determine sequence differences in these rare alleles, cell lines were established from peripheral B-lymphocytes from 24 unrelated individuals in whom nine types of rare variants are presumed to exist on the basis of earlier electrophoresis studies. cDNAs reverse transcribed from mRNAs extracted from these cell lines were amplified by polymerase chain reaction and sequences determined. Amino acid substitution types were deduced from each cDNA sequence. Although two individuals were reported to have an identical electromorph (PGM1 4HR3), sequence analysis revealed that alleles encoding these electromorphs possessed different base substitutions, and one was renamed PGM1 4HR4. As the amino acid substitution of ten different variants could be deduced by cDNA sequence in this study, the effect of each amino acid substitution on enzyme activity could be precisely simulated. The secondary structure of each variant predicted by computer simulations revealed that very decreased activity observed on PGM1 4HR2 protein was caused by significant secondary structure change introduced by the amino acid substitution. On the basis of the crystal structure, the amino acid substitutions of the ten types of rare variants seem to be outside the active center of this enzyme.     

浙江丽水地区珍稀濒危植物区系研究与保护

浙江丽水地区有珍稀濒危植物 42种 ,隶属于 3 7属 2 5科。其中国家二级珍稀濒危植物 1 8种 ,三级珍稀濒危植物 2 4种 ,大致可分划为 1 0个分布类型 5个变型 ,以木本植物占优势 ,中国特有属、单型属较多。本文根据丽水珍稀濒危植物的现状提出了一些具体的保护措施。     

两种稀有的孔状木生真菌

本文对中国长白山自然保护区两种稀有的新记录多孔菌黑白拟蜡菌Ceriporiopsisalbonigrescens,分支榆孔菌Elmerinacladophora进行了报道,对这两个种进行了详细描述和显微结构绘图。     

CNVs: harbingers of a rare variant revolution in psychiatric genetics

The genetic bases of neuropsychiatric disorders are beginning to yield to scientific inquiry. Genome-wide studies of copy number variation (CNV) have given rise to a new understanding of disease etiology, bringing rare variants to the forefront. A proportion of risk for schizophrenia, bipolar disorder, and autism can be explained by rare mutations. Such alleles arise by de novo mutation in the individual or in recent ancestry. Alleles can have specific effects on behavioral and neuroanatomical traits; however, expressivity is variable, particularly for neuropsychiatric phenotypes. Knowledge from CNV studies reflects the nature of rare alleles in general and will serve as a guide as we move forward into a new era of whole-genome sequencing.     

Comparison of predictor sets for species richness and the number of rare species of butterflies and birds

Aim Accurate inventories of biota are typically restricted to few locations within an extensive region. Accordingly, effective planning must involve some form of surrogate measures coupled with spatial modelling. We conducted a simultaneous comparison of models of both species richness and the number of rare species using three types of surrogates (indicator species, vegetation composition and structure, and topoclimate) as predictors. We evaluated each type of surrogate alone and in combination with others. Location Data for our analyses were collected from 1996–2004 in three adjacent mountain ranges in the central Great Basin (Lander and Nye counties, Nevada, USA), the Shoshone Mountains, Toiyabe Range and Toquima Range. Methods Data on species richness and species composition of butterflies and birds and measures of vegetation composition and structure were obtained in the field. Topoclimatic variables were derived by GIS from digital sources and satellite images. We used Poisson regression with Bayesian model averaging to predict species richness and the number of rare species. We compared the expected prediction success of all models on the basis of internal and external validation trials. Results Same‐taxon indicator species were the most accurate predictors of species richness and of the number of rare species of butterflies and birds. Cross‐taxon indicator species and topoclimate variables were reasonably accurate predictors of species richness of butterflies and birds and of the number of rare butterfly species. Although vegetation variables were more effective for predicting species richness and number of rare species of birds than of butterflies, they were the least accurate predictors overall. Main conclusions Although indicator species may provide the most accurate predictions of species richness, their practical value, like any surrogate measure, depends greatly on ecological considerations and land‐use context. In general, the ability to predict numbers of rare species based on any set of candidate predictors was weaker than the ability to predict species richness, which may result from the high degree of stochasticity that often characterizes distributions of rare species. Our statistical approach for objective examination of different candidate predictors can help ensure that selection of species‐richness surrogates in any system is scientifically reliable and cost‐effective.     

Subtractive immunization techniques for the production of monoclonal antibodies to rare antigens.

Traditional techniques for the production of monoclonal antibodies usually result in generation of monoclonal antibodies to immunodominant molecules. To enhance the production of monoclonal antibodies to rare or less immunodominant antigens, subtractive immunization techniques have been employed. This study compared the ability of several subtractive immunization techniques to suppress the immune system to a given antigen. Neonatal tolerization, chemical immunosuppression with cyclophosphamide, a combination of the two and various permutations of these techniques were compared. The results from this study indicated that chemical immunosuppression with cyclophosphamide was the most effective subtractive immunization technique and that the cyclophosphamide regime employed was a critical determinant in the success of chemical immunosuppression.     

Rock outcrops in the southeastern part of the West Siberian plain as the northern limit of distribution and refuge of rare moss species

Foothill plains along the northwest periphery of Altai–Sayan Mountain Country are the northern limit of stony substrates in the West Siberian longitudinal sector. Rock outcrops in this area are rare; their areas usually do not exceed few dozens of square meters. Despite small areas, the rocky outcrops keep nearly half of the foothill moss flora. 119 moss species were recorded in the rocky habitat; 26 of them are rare both in Western Siberia and in its mountain ringing. An annotated list of species is given. Features of species distribution in the longitudinal sector of West Siberia are discussed.     

Characteristics of plant communities containing rare conifers in Poyang Lake Basin,China

The endangerment mechanism of rare conifer species is a very critical problem in conservation biodiversity. Thus, the studies on the protection of the rare and endangered coniferous trees have received extensive attention. The objective of this study was to understand the survival and distribution of the rare coniferous tree species in natural forests of the Poyang Lake Basin. Field investigations on plant communities were conducted in 21 plots from Oct. 2014 to Oct. 2015. These plots were distributed in the Nanling Mountains, Luoxiao Mountains, Wuyi Mountains, Huangshan Mountains, and Jiuling Mountain. The dimensions of each plot were 20 m × 20 m. Community species composition and quantitative characteristics in each plot were recorded. The importance values of trees, shrubs and herbs were computed, respectively. The community types and structural properties were analyzed. A total of 23 sets of community sampling data were obtained in details. A number of 11 species of rare conifers were found in 14 different formations. Rare conifer trees mainly occurred in the communities as co-edificatos or companion species. The formations included Form. Taxus wallichiana var. mairei, Form. Pseudotsuga sinensis, Form. Fokienia hodginsii and Form. Torreya grandis, where the dominant species was coniferous trees. In conclusion, our study provides valuable field investigation data of rare coniferous in Poyang Lake basin, which could provide insight into the protection and management of these species.     

鄱阳湖流域含珍稀针叶树种的群落特征

亚热带分布有众多珍稀针叶树种, 珍稀针叶植物的保护与濒危机制研究受到广泛关注。为了解鄱阳湖流域天然森林植被中珍稀针叶树种的分布及其生存状况, 对其所在的植物群落进行调查。调查采用样方法, 样方面积20 m × 20 m, 记录样方信息、群落物种组成及数量特征, 计算物种重要值, 分析了群落的类型及结构特征。样方分布于鄱阳湖流域内南岭山地、罗宵山脉、武夷山脉、黄山山脉、九岭山脉。论文提供了23组详细的群落样方数据, 11种珍稀针叶树种分布于14个不同群系中, 珍稀针叶植物多以共建种或伴生种出现在群落中, 以针叶树为优势种的群系有南方红豆杉(Taxus wallichiana var. mairei)林、黄杉(Pseudotsuga sinensis)林、福建柏(Fokienia hodginsii)林、榧树(Torreya grandis)林。