Pyrosequence Analysis of the hsp65 Genes of Nontuberculous Mycobacterium Communities in Unchlorinated Drinking Water in the Netherlands

Studies have shown that certain opportunistic pathogenic species of nontuberculous mycobacteria (NTM) can be present in distributed drinking water. However, detailed information about NTM population composition in drinking water is lacking. Therefore, NTM communities in unchlorinated drinking water from the distribution system of five treatment plants in the Netherlands were characterized using 454 pyrosequencing of the hsp65 gene. Results showed high diversities in unchlorinated drinking water, with up to 28 different NTM operational taxonomic units (OTUs) in a single sample. Each drinking water sample had a unique NTM community, and most (81.1%) OTUs were observed only once. One OTU was observed in 14 of 16 drinking water samples, indicating that this NTM species is well adapted to unchlorinated drinking water conditions. A clear influence of season, source type (groundwater, surface water), easily assimilable organic carbon (AOC) concentration, biofilm formation rate, and active biomass in treated water on the establishment of an NTM community in drinking water was not observed. Apparently, local conditions are more important for the development of a specific NTM community in the drinking water distribution system. A low (4.2%) number of hsp65 gene sequences showed more than 97% similarity to sequences of the opportunistic pathogens M. avium, M. genavense, and M. gordonae. However, most (95.8%) NTM hsp65 gene sequences were related to not-yet-described NTM species that have not been linked to disease, indicating that most NTM species in unchlorinated drinking water from distribution systems in the Netherlands have a low public health significance.     

Copepods distribution in relation to a Cape Ghir upwelling filament (Moroccan Atlantic coast)

The study of the Cape Ghir upwelling filament (31°N) focalizes to describe the dispersive mechanism, caused by the upwelling. The zooplankton was sampled during five oceanographic cruises conducted between 2008 and 2009. Surface temperature and chlorophyll “a” were also measured along with sampling. The distribution of environmental parameters accused extensions that show the path of the filament. Copepods constitute the largest fraction of zooplankton community and represented by 86 species, majorly dominated by Acartia clausi and Oncaea venusta. A number of species of deep or cold waters have been recorded in the area corresponding to a net resurgence of cold water. The analysis of the copepods distribution allowed to view the path of the filament at different times of the year. The distribution of the species A. clausi, neritic specie was observed in the open ocean, shows a result of this dynamic.     

Target theory and survival curves

A general theoretical treatment of cellular radiation damage is presented. The basic assumptions are: (1) the initial damage (“hit”) is not harmful per se, but may be either developed into a biologically significant “lesion” or repaired; (2) each lesion has a certain probability to be lethal, this probability does not depend on the number of lesions per cell; (3) the initial “hits” follow Poisson's distribution. It is shown that under these assumptions the shape of survival curves can be explained. The classical “single-hit” and “multi-hit” curves are obtained as limiting cases.     

A measure of species diversity related to the lognormal distribution of individuals among species

An investigation has been made of the relation between species diversity and the lognormal distribution of individuals among species, using phytoplankton samples from the Indian Ocean. The area under the truncated lognormal curve representing a sample gives the total number of species, S, while the logarithmic standard deviation, σ, gives a measure of the scatter of distribution of individuals among species, the other factor affecting diversity. Using a method described by Hald, truncated lognormal curves were fitted to the phytoplankton data and estimates obtained for the mean, ξ, the logarithmic standard deviation, σ, the number of species in the modal octave, N_o, and the number of species in the population universe, N. Since one is interested in a sample only in so far as it reflects the properties of the population from whence it came, estimated population parameters were used to define measures of diversity by which means it was hoped to obtain a diversity index independent of sample size, i.e., a diversity value related more to the population than to the sample.     

黄土丘陵沟壑区80种植物繁殖体形态特征及其物种分布

植物繁殖体的形态特征及其物种分布是植物长期适应环境的结果,对退化生态系统的更新与恢复具有重要的理论与实践指导意义。研究了80种植物的繁殖体形态特征及与其物种分布的关系,结果表明：1）繁殖体重量差别较大（0. 020—357.428 mg）,主要集中在1—9.999 mg（占52.5%）。2）繁殖体的形状指数FI变化范围较大（1.06—12.93）,61.3%的植物繁殖体的形状近圆球形。3）33种植物繁殖体具有明显的附属物,包括毛、翅、芒和刺等。4）87.5%的植物繁殖体表面具有各种纹饰（棱、被毛、纹和颗粒状等）;繁殖体颜色以褐色和黑色为主,少数繁殖体颜色鲜艳;6种植物繁殖体具有吸水分泌粘液的特性。5）黄土丘陵沟壑区繁殖体重量小或形状近圆球形的植物分布数量多、范围广。6）繁殖体具有毛、翅和芒附属物或吸湿分泌粘液的植物在黄土丘陵沟壑区较繁殖体无附属物的植物能够分布更多、更广。繁殖体这些有利于物种分布的形态特征对于植物适应该区干旱与土壤侵蚀干扰具有重要的生态学意义,而且可用于指导该区人工补播促进植被恢复的物种选择。     

长白山云冷杉林幼苗幼树空间分布格局及其更新特征

长白山云冷杉针阔混交林是我国东北主要的森林类型之一,其乔木树种幼苗幼树的结构和动态决定着未来林分的结构和生长动态。在长白山地区设置一块具有代表性的云冷杉针阔混交林幼苗幼树更新样地,统计分析幼苗幼树更新特征,绘制地径结构图、树高结构图及其空间分布图。运用点格局分析中的单变量O-ring统计方法,分析更新树种的空间分布格局;用双变量O-ring统计方法,分析更新树种种间的空间关联性。研究结果表明:(1)更新树种组成有冷杉(Abies nephrolepis)、色木槭(Acer mono)、紫椴(Tilia amurensis)、红皮云杉(Picea koraiensis)、红松(Pinus koraiensis)、蒙古栎(Quercus mongolica)、春榆(Ulmus japonica)7种,其中以冷杉、色木槭为主,更新幼苗幼树的地径近似呈倒J型分布,树高结构近似呈双峰分布;(2)所有更新树种、冷杉、色木槭在小尺度1—10 m的范围内呈聚集分布,随着尺度增加,聚集程度减弱,逐渐趋于均匀分布和随机分布,紫椴、云杉和红松在空间所有尺度上以随机分布为主;(3)更新树种之间的空间关联性在小尺度范围上正关联性比较多,较大尺度范围上负关联性比较多,随着尺度增加,空间关联性减弱。     

吉林磨盘山次生落叶阔叶林群落特征和稳定性分析

东北地区的次生落叶阔叶林一般是由阔叶红松林干扰后形成的,这一群落类型在长白山林区具有广泛的分布.为了解东北次生落叶阔叶林的组成、结构与稳定程度,按照CTFS样地建设标准,于2005年在吉林磨盘山建立了一块5.76 hm² (240 m×240 m)的长期监测样地.本研究以样地内所有胸径(DBH)≥1 cm的木本植物为对象,分析了物种组成、径级结构、主要树种的存活曲线及群落稳定性.结果表明: DBH≥1 cm的木本植物共有39种13368株,隶属于19科31属.重要值≥1的物种有12种,群落树种组成复杂,表现出明显的阔叶混交杂木林特征.种间多度相差较大,稀有种和偶见种的比例分别为23.1%和43.6%.样地内所有个体的径级分布呈倒“J”型,表示群落的生长状态稳定、正常.6个主要树种中花曲柳、蒙古栎、色木槭和怀槐径级结构也呈倒“J”型,胡桃楸近于正态分布,春榆为“L”型分布.结合6个主要树种的存活曲线发现,花曲柳、蒙古栎、色木槭和怀槐为稳定种群,胡桃楸为衰退种群,春榆为增长种群.利用改进M-Godron法对群落的稳定性分析表明,该群落目前处于相对稳定状态.     

Probability distributions of ancestries and genealogical distances on stochastically generated rooted binary trees

The stationary birth-only, or Yule-Furry, process for rooted binary trees has been analysed with a view to developing explicit expressions for two fundamental statistical distributions: the probability that a randomly selected leaf is preceded by N nodes, or “ancestors”, and the probability that two randomly selected leaves are separated by N nodes. For continuous-time Yule processes, the first of these distributions is presented in closed analytical form as a function of time, with time being measured with respect to the moment of “birth” of the common ancestor (which is essentially inaccessible to phylogenetic analysis), or with respect to the instant at which the first bifurcation occurred.The second distribution is shown to follow in an iterative manner from a hierarchy of second-order ordinary differential equations.For Yule trees of a given number n of tips, expressions have been derived for the mean and variance for each of these distributions as functions of n, as well as for the distributions themselves.In addition, it is shown how the methods developed to obtain these distributions can be employed to find, with minor effort, expressions for the expectation values of two statistics on Yule trees, the Sackin index (sum over all root-to-leaf distances), and the sum over all leaf-to-leaf distances.     

Contributions to the sociology and chorology of contrasting plant communities in the southern part of the ‘Wienerwald’ (Austria)

Five plant communities contrasting in successional status and human impact from the southern part of the ‘Wienerwald’ (Austria) are analyzed using vegetation relevés, spectra of area types and a newly proposed disjunction quotient. A climax community (Asperulo-Fagetum), a subclimax community (Querco-Carpinetum s.l.), an anthropogenous substitute community (Mesobromion) and two natural, non-climax permanent communities (Euphorbio saxatilis-Pinetum nigrae and Fumano-Stipetum eriocaulis) are recognized. The disjunction quotient is defined as the number of partial (discontinous) areas divided by the size of the total area of distribution of a species. In particular, the average disjunction quotients of the species in the first two communities reflect relatively table environments only slightly influenced by man, with many ancient, stable taxa. These communities are characterized by species with well-delimited, stable distribution areas. The species in the Mesobromion community have very low average disjunction quotients as its component species are widely and continuously distributed and are often promoted by man. In contrast to these communities, the species linked to the natural permanent, non-climax communities of extreme habitats, have high distribution quotients i.e. small, disconinuous areas; this illustrates the relic character of these plant communities and of the eastern edge of the Alps is a whole. Using the highly variable disjunction quotient of all species and communities examined, the concepts of climax and permanent communities (of different origin) are discussed with regard to European conditions.     

Climatic effects on the distribution of ant- and bat fly-associated fungal ectoparasites (Ascomycota,Laboulbeniales)

Laboulbeniales (Ascomycota: Laboulbeniomycetes) are obligate ectoparasitic fungi of arthropods with a worldwide distribution. Their effects on host physiology and behaviour as well as their ecology have recently gained wider attention. One aspect that is virtually unknown regarding Laboulbeniales and arthropod-associated fungi in general, is how abiotic factors shape the distribution of these parasites. We used ant- and bat fly-associated Laboulbeniales to study whether climatic elements play a role in the distribution of fungal species. We collected uninfected and Laboulbeniales-infected insects belonging to three species: bat flies Nycteribia schmidlii and Penicillidia conspicua (Diptera: Nycteribiidae) and the ant Myrmica scabrinodis (Hymenoptera: Formicidae). We used climatic variables and performed statistical analyses to explain the distribution of Laboulbeniales infection. Our results show a higher likelihood of Laboulbeniales presence in habitats with low annual mean temperature and humidity, suggesting that climatic elements can considerably shape the distribution of Laboulbeniales species.     

Distribution pattern of the invasive alien plant Bunias orientalis in Rów Podtatrzański trench,north of the Tatra Mts,Poland

Bunias orientalis is an alien species that has spread greatly in recent decades in Central Europe. This coloniser is particularly well (pre)adapted to anthropogenic disturbances and human-mediated dispersal, allowing it to spread mainly along roads and railways. Here, its distribution and population structure is investigated for the sub-montane region located in the northern foothills of the Tatra Mts. Based on 70 phytosociological samples of invading vegetation, the relationships between B. orientalis cover and species diversity, together with the composition of vegetation, were analysed using regression analysis. Comparison of the current distribution of B. orientalis within the investigated area with published records indicates that the expansion rate of this alien species is not particularly high, despite its increased frequency in anthropogenic habitats and meadows. Meadows invaded by this species revealed that increased B. orientalis cover was accompanied by a significant reduction in the values of the Inverse Simpson diversity index and Pielou’s measure of evenness. Reduced diversity was caused by considerable decrease in cover by species of the Molinio-Arrhenatheretea class. However, for anthropogenic habitats, no statistically significant relationships were found to occur between the abundance of B. orientalis, species diversity and vegetation composition.     

The enigmatic molar from Gondolin, South Africa: Implications for Paranthropus paleobiology

The specific attribution of the large hominin M₂ (GDA-2) from Gondolin has significant implications for the paleobiology of Paranthropus. If it is a specimen of Paranthropus robustus it impacts that species' size range, and if it belongs to Paranthropus boisei it has important biogeographic implications. We evaluate crown size, cusp proportions and the likelihood of encountering a large-bodied mammal species in both East and South Africa in the Early Pleistocene. The tooth falls well outside the P. robustus sample range, and comfortably within that for penecontemporaneous P. boisei. Analyses of sample range, distribution and variability suggest that it is possible, albeit unlikely to find a M₂ of this size in the current P. robustus sample. However, taphonomic agents - carnivore (particularly leopard) feeding behaviors - have likely skewed the size distribution of the Swartkrans and Drimolen P. robustus assemblage. In particular, assemblages of large-bodied mammals accumulated by leopards typically display high proportions of juveniles and smaller adults. The skew in the P. robustus sample is consistent with this type of assemblage. Morphological evidence in the form of cusp proportions is congruent with GDA-2 representing P. robustus rather than P. boisei. The comparatively small number of large-bodied mammal species common to both South and East Africa in the Early Pleistocene suggests a low probability of encountering an herbivorous australopith in both. Our results are most consistent with the interpretation of the Gondolin molar as a very large specimen of P. robustus. This, in turn, suggests that large, presumptive male, specimens are rare, and that the levels of size variation (sexual dimorphism) previously ascribed to this species are likely to be gross underestimates.     

Distribution of cicadas of the genus Lyristes (Hemiptera: Cicadidae) in the eastern Mediterranean area

The present study gives an updated overview on the distribution of species of the genus Lyristes Horváth, 1926 in the eastern Mediterranean area. Besides occurring in southern continental Europe, specimens of L. plebejus were also found along the southern Greek mainland and in the western Aegean island of Kithira. Moreover, the new data presented give L. gemellus as a new record for Greece (appearing only along most of the Anatolian coast) as well as for Cyprus. The genus seems to be absent from the Cyclades as well as from the islands of Crete and Karpathos. Therefore, the results revealed a faunal discontinuity between the Greek western and eastern islands in the Aegean Sea. Hence, the persistence of a deep sea barrier between these two groups of islands seems to explain the present distribution of Lyristes species, which is also in accordance with the paleogeography of the area and with the fact that dispersal to more geographically isolated islands might have been virtually impossible for species of this genus.     

The contribution of common and rare species to species abundance patterns in alpine meadows: The effect of elevation gradients

Ecological niche modeling uses environmental variables associated with species distribution points to simulate species distribution and its importance in biodiversity conservation. This study aimed to quantify plant community composition and species abundance distribution (SAD) in alpine meadows at different elevations and to assess the contribution of rare and common species to SAD. We established a permanent study plot of 210 hm² in Gannan Tibetan Autonomous Prefecture, China, surveyed 315 sample squares (0.5 m × 0.5 m), and calculated the Hill numbers. The results showed that (1) a total of 72 species were surveyed at different altitudes, with Kobresia humilis and Kobresia macrantha as the main dominant species; (2) the SADs of overall and common species fit the ecological niche model (GSM (Geometric Sequence Model)), indicating that ecological niche differentiation is the main factor influencing SAD. The fitted model for rare species SAD varied with elevation, suggesting that various ecological processes influence rare species SAD. (3) Hill numbers showed a “single peak” pattern with increasing elevation. The number of rare species was higher than that of common species. Still, the distribution frequency of common species was significantly higher than rare species. The correlation between common-rare species sequences and cumulative species distribution was high. This indicates that common species dominate the species diversity pattern of the community, are the main contributors to the SAD pattern, and should be protected first. Rare species are also important carriers of community function and include much spatial information. Rare and common species work together in different ways to influence and maintain the species diversity patterns of alpine meadow plant communities.     

Butterflies (Lepidoptera, Rhopalocera) in the Arctic fauna

The Arctic fauna includes 106 species of diurnal butterflies: Papilionidae (6 species), Pieridae (20), Lycaenidae (18), Nymphalidae (30), Satyridae (27), and Hesperiidae (5). Among them, representatives of the family Nymphalidae predominate as to the features characterizing the biological progress in the Arctic, as well as to the number of the most strongly pronounced arctic forms. The family Satyridae shares the first place with Nymphalidae by the number of species, but differs from the latter in the uneven or local distribution. The family Pieridae demonstrates a wide distribution of polyzonal and boreal species in the tundra zone. The distribution patterns of Lycaenidae are different in the Eurasian and Beringian-American sectors. Species of Papilionidae and Hesperiidae occur only in the southern part of the tundra zone. Each family is characterized by specific distribution in the Arctic subzones and landscapes and by latitudinal trends in its specific ratio in the faunas. There are 30 to 40 arctic species, including arctic proper (euarctic and hemiarctic) and hypoarctic, arctoalpine, arctomontane, and arctoboreal species. The species developing successfully under high-latitude conditions are Boloria chariclea, B. polaris, B. improba, Colias nastes, C. hecla, and Erebia fasciata; the first two species can be considered true euarctic forms. Specific features of the latitudinal and longitudinal distribution of the butterfly species in different parts of the Arctic are discussed.     

Drivers of Solidago species invasion in Central Europe—Case study in the landscape of the Carpathian Mountains and their foreground

AimThe invasion process is a complex, context‐dependent phenomenon; nevertheless, it can be described using the PAB framework. This framework encompasses the joint effect of propagule pressure (P), abiotic characteristics of the environment (A), and biotic characteristics of both the invader and recipient vegetation (B). We analyzed the effectiveness of proxies of PAB factors to explain the spatial pattern of Solidago canadensis and S. gigantea invasion using invasive species distribution models.LocationCarpathian Mountains and their foreground, Central Europe.MethodsThe data on species presence or absence were from an atlas of neophyte distribution based on a 2 × 2 km grid, covering approximately 31,200 km² (7,752 grid cells). Proxies of PAB factors, along with data on historical distribution of invaders, were used as explanatory variables in Boosted Regression Trees models to explain the distribution of invasive Solidago. The areas with potentially lower sampling effort were excluded from analysis based on a target species approach.ResultsProxies of the PAB factors helped to explain the distribution of both S. canadensis and S. gigantea. Distributions of both species were limited climatically because a mountain climate is not conducive to their growth; however, the S. canadensis distribution pattern was correlated with proxies of human pressure, whereas S. gigantea distribution was connected with environmental characteristics. The varied responses of species with regard to distance from their historical distribution sites indicated differences in their invasion drivers.Main conclusionsProxies of PAB are helpful in the choice of explanatory variables as well as the ecological interpretation of species distribution models. The results underline that human activity can cause variation in the invasion of ecologically similar species.     

Micro-spatial distribution of two sibling periwinkle species across the intertidal indicates hybrdization

Populations of periwinkles Littorina saxatilis (Olivi 1792) and L. arcana Hannaford Ellis, 1978 are well suited for microevolutionary studies, being at the same time closely related and intraspecifically diverse. The divergence between these two sibling species, sympatric over large parts of their distribution areas, is small, the only morphological difference being the pallial gland complex structure in females. Molecular identification is possible with the use of a RAPD nuclear marker (cloned A2.8 DNA fragment) typical for L. arcana. However, in some individuals from sympatric populations molecular and morphological criteria suggest conflicting species affiliation, which may be explained either by hybridization or by shared ancestral polymorphism. We tested the hybridization hypotheses examining the micro-spatial distribution of these two species across the intertidal zone in two distant sites at the Barents Sea. We found that (a) the frequency of putative hybrids in sympatric populations was proportional to the frequency of L. arcana; (b) L. saxatilis bearing A2.8 DNA fragment were almost absent in the lower part of the intertidal zone, where L. arcana was absent too; (c) there was a close positive correlation between the distribution of potential parent molluscs and putative hybrids. Moreover, logistic regression models showed a good agreement between the distribution of putative hybrid frequencies and that of parental species frequencies. All our observations taken together support the hypothesis of hybridization between L. saxatilis and L. arcana. Elucidating the mechanisms that support the species status of these sympatric populations is necessary.     

Maintenance of mitotic homeostasis in somatic cell populations

Recent theoretical and experimental studies have indicated that the rate of proliferative activity in somatic cell populations can be modulated by regulation of the transmembrane potential level (E_m). These studies have shown that such modulation is accomplished through control of DNA synthesis preparations, presumably through variations in the intracellular ionic conditions which accompany transmembrane potential changes. This capability for modulating mitotic activity appears to provide a potential mechanism for maintenance of mitotic homeostasis in somatic cell populations. The present paper, after a consideration of the primary kinetic requirement for homeostasis attainment, proceeds to develop two independent concepts of E_m-modulated homeostatic control: (1) “statistical” or “passive” homeostasis obtained by maintenance of a particular, constant E_m level at which proliferation rate equals death rate for the cells under study; and (2) “modulated” or “active” homeostasis obtained by local induction of cellular depolarization, from a high level where mitosis is blocked to a low level where mitosis is stimulated, by loss of intimate surface contact or chemical interaction with a dying cell. The problem of hormone-activated periodic or cyclic proliferative homeostasis is also interpreted in terms of E_m variation.     

Non-invasive genetic sampling of sympatric marten species (Martes martes and Martes foina): assessing species and individual identification success rates on faecal DNA genotyping

The use of non-invasive genetic sampling (NGS) has become increasingly popular in wildlife research but needs well-planned sampling strategies and reliable laboratory protocols. In this study, we planned to assess the reliability and success of species and individual identifications of sympatric martens (European pine marten Martes martes and stone marten Martes foina) by genotyping non-invasively collected faecal samples. First, we developed a novel and accurate multiplex panel of 15 microsatellite loci, selected by cross species amplification of 41 loci. The application of this panel facilitated species distinction, discarding the presence of putative hybrids. Then, we assessed the impact of sample collector skills on the lab protocol performances. The faecal DNA quality was evaluated by (a) the success of polymerase chain reaction–restriction fragment length polymorphism identification of the two Martes species and (b) the genotyping success and error rates of individual pine marten identifications. The survey was conducted over all the sympatric range of the two species in the Iberian Peninsula by three groups of sample collectors with different experience: expert wildlife biologist, trained volunteers and technical staff from natural parks. Results show that the different expertise between sample collectors significantly influences the success rate of pine marten individual genotyping, but not the species identification success rate. Based on our results, we recommend conducting sampling by experienced field biologist to maximise the quality of NGS and ensure accurate genotyping success. Application of our methods to field collected scats can be used in a cost-effective way to investigate distribution, patterns of genetic diversity and structure as well as to estimate population abundance for sympatric martens.