Monte Carlo Permutation Tests Research Articles

Accurate Assignment of Significance to Neuropeptide Identifications Using Monte Carlo K-Permuted Decoy Databases

In support of accurate neuropeptide identification in mass spectrometry experiments, novel Monte Carlo permutation testing was used to compute significance values. Testing was based on k-permuted decoy databases, where k denotes the number of permutations. These databases were integrated with a range of peptide identification indicators from three popular open-source database search software (OMSSA, Crux, and X! Tandem) to assess the statistical significance of neuropeptide spectra matches. Significance p-values were computed as the fraction of the sequences in the database with match indicator value better than or equal to the true target spectra. When applied to a test-bed of all known manually annotated mouse neuropeptides, permutation tests with k-permuted decoy databases identified up to 100% of the neuropeptides at p-value < 10−5. The permutation test p-values using hyperscore (X! Tandem), E-value (OMSSA) and Sp score (Crux) match indicators outperformed all other match indicators. The robust performance to detect peptides of the intuitive indicator “number of matched ions between the experimental and theoretical spectra” highlights the importance of considering this indicator when the p-value was borderline significant. Our findings suggest permutation decoy databases of size 1×105 are adequate to accurately detect neuropeptides and this can be exploited to increase the speed of the search. The straightforward Monte Carlo permutation testing (comparable to a zero order Markov model) can be easily combined with existing peptide identification software to enable accurate and effective neuropeptide detection. The source code is available at http://stagbeetle.animal.uiuc.edu/pepshop/MSMSpermutationtesting.

Characterising expert representations during real-time action: A Skill Theory application to soccer

In various domains, experts are found to possess elaborate domain-specific representations they developed over years. In this study, we provide the first systematic attempt to characterise the short-term representations among individuals with different expertise levels. We showed videos of soccer game plays to expert, near-expert and non-expert soccer players and asked them to describe the actions taking place. Verbalisations were coded based on Fischer's Skill Theory. Monte Carlo permutation tests revealed that players with higher expertise constructed representations of higher complexity (regardless of their specific content). Taking the content of the representations into account, we found that higher expertise soccer players relatively more often included high complexity levels of actions not including the ball and (moving) players on the field. These findings improve our understanding of perceptual-cognitive expertise by demonstrating how actors with different levels of expertise integrate the information they perceive to construct their representations in real time.

Morphological forms of two macrophytes (yellow water-lily and arrowhead) along velocity gradient

We investigated morphological response of yellow water-lily and arrowhead to water velocity gradient in the lowland Welna river (Western Poland). Percentage cover of floating and submerged forms of yellow water-lily and arrowhead had been measured in randomly selected sites of 16 m2. We analyzed 62 stands of Nuphar lutea and 80 stands of Sagittaria sagittifolia using 13 environmental variables. Redundancy analysis (RDA), the Monte Carlo permutation test, ranges of chemical and hydrological data, Generalized Additive Models (GAMs) and transfer function were used to describe reaction of investigated species to water velocity. Among the analyzed parameters of microhabitats with the floating and submerged forms of investigated species, velocity, pH, water colour, hydration and organic matter in bottom sediments were statistically significant. In S. sagittifolia case, the velocity was the most important parameter, while in N. lutea — both velocity and content of organic matter in river substrate were statistically significant.

Long-term changes in abundance of Calanus finmarchicus south and north of Iceland in relation to environmental conditions and regional diversity in spring 1990–2013

Abstract A 24-year time series of the abundance of Calanus finmarchicus from two standard sections differing in hydrographical conditions (Atlantic Water south of Iceland, Subarctic Water north of Iceland) was examined in relation to hydrography, phytoplankton dynamics, and large-scale climatic forcing (North Atlantic Oscillation, NAO). In the sea area around Iceland, C. finmarchicus is the most abundant mesozooplankter. The long-term variations were evaluated using multivariate statistics, principal component analyses, redundancy analyses (RDA), and principal response curves. Both south and north of Iceland, significant (RDA, p &lt; 0.05, Monte-Carlo permutation tests) fluctuations in abundance and stages structure of C. finmarchicus between years were observed. The variations were, however, not in tune in south and north, indicating that the C. finmarchicus abundance may be influenced by different forcing factors in the two regions. South of Iceland, the analyses failed to find an effect of any of the environmental variables tested, whereas in the north the year-to-year variability was related to freshwater thickness west of Iceland and temperature north of the island (RDA, p &lt; 0.05, Monte-Carlo permutation tests), indicating that advection of animals with currents from the south is important. In neither of the two regions was it possible to detect a unidirectional temporal trend in abundance of C. finmarchicus (RDA, p &lt; 0.05, Monte-Carlo permutation tests). Based on a comparison with time series from nearby areas and the lack of a relationship with NAO, it is hypothesized that the growth and development of C. finmarchicus in Icelandic waters is more affected by local conditions than large-scale climatic forcing.

Land snail diversity and composition in relation to ecological variations in Central European floodplain forests and their history

We explored patterns of land snail assemblages using 93 alluvial forest sites in six river floodplains of the Elbe drainage basin (northwestern Bohemia, Czech Republic). Differences in species richness and composition across the four floodplain forest types (i.e., alder carrs, ash-alder forests, willow-poplar softwood forests, and hardwood forests) were analysed using generalized linear models, multidimensional scaling and redundancy analysis with the Monte Carlo permutation test. The studied floodplain forest types did not differ in species richness, except for the alder carrs which were significantly poorer. The number of species expressed a significant unimodal response along with elevation and Ellenberg nutrients, and further significantly decreased towards the most humid sites. Contrary to species richness, the main forest types clearly differed based on land snail species composition, with the exception of the ash-alder and willow-poplar forest sites which became completely overlapped in the ordination space. The main changes in species composition were mostly associated with elevation and Ellenberg moisture on the first MDS axis: Ellenberg nutrients and light were fitted on the second and the third axes, respectively. These variables, along with calcium content estimated using Ellenberg indicator values for soil reaction, had significant effects on the variation and snail species composition in the final RDA model. No response of either species richness or compositional changes was found for the measured content of topsoil calcium, most likely due to the higher importance of other variables. On the basis of some recently published data we can conclude that historical development and long-term human activities on the succession of floodplain assemblages have resulted in a sharp impoverishment of strictly land snail species of several hardwood forest sites in the majority of lower river stretches. Whilst in most areas there are no exact palaeoecological data available, these historical influences were closely correlated with the site elevation in our dataset as the main difference in species composition was hard to explain solely using environmental predictors.

Valid Monte Carlo permutation tests for genetic case-control studies with missing genotypes.

Monte Carlo permutation tests can be formally constructed by choosing a set of permutations of individual indices and a real-valued test statistic measuring the association between genotypes and affection status. In this paper, we develop a rigorous theoretical framework for verifying the validity of these tests when there are missing genotypes. We begin by specifying a nonparametric probability model for the observed genotype data in a genetic case-control study with unrelated subjects. Under this model and some minimal assumptions about the test statistic, we establish that the resulting Monte Carlo permutation test is exact level α if (1) the chosen set of permutations of individual indices is a group under composition and (2) the distribution of the observed genotype score matrix under the null hypothesis does not change if the assignment of individuals to rows is shuffled according to an arbitrary permutation in this set. We apply these conditions to show that frequently used Monte Carlo permutation tests based on the set of all permutations of individual indices are guaranteed to be exact level α only for missing data processes satisfying a rather restrictive additional assumption. However, if the missing data process depends on covariates that are all identified and recorded, we also show that Monte Carlo permutation tests based on the set of permutations within strata of individuals with identical covariate values are exact level α. Our theoretical results are verified and supplemented by simulations for a variety of missing data processes and test statistics.

不同尺度因子对滦河流域大型底栖无脊椎动物群落的影响

PDF HTML阅读 XML下载 导出引用 引用提醒 不同尺度因子对滦河流域大型底栖无脊椎动物群落的影响 DOI: 10.5846/stxb201210181448 作者: 作者单位: 中国科学院生态环境研究中心城市与区域生态国家重点实验室,衡水学院生命科学系,中国科学院生态环境研究中心城市与区域生态国家重点实验室,中国科学院生态环境研究中心城市与区域生态国家重点实验室,中国科学院生态环境研究中心 作者简介: 通讯作者: 中图分类号: 基金项目: 国家水体污染控制与治理科技重大专项（2012ZX07501002002） The influence of variables at different scales on stream benthic macroinvertebrates in Luanhe River Basin Author: Affiliation: State Key Laboratory of Urban Regional Ecology,Research Center for Eco-Environmental Sciences,Chinese Academy of Sciences,College of Life Sciences,Hengshui University,,China,State Key Laboratory of Urban Regional Ecology,Research Center for Eco-Environmental Sciences,Chinese Academy of Sciences,State Key Laboratory of Urban Regional Ecology,Research Center for Eco-Environmental Sciences,Chinese Academy of Sciences,State Key Laboratory of Urban Regional Ecology,Research Center for Eco-Environmental Sciences,Chinese Academy of Sciences Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:通过2011年滦河流域38个河段大型底栖无脊椎动物采集，探讨了河段尺度和流域尺度环境因子对大型底栖无脊椎动物分布的影响。其中，河段尺度因子包括水体/底质特征、河岸带特征和水质，流域尺度因子包括采样位置、流域土地利用结构和缓冲区土地利用结构。RDA（冗余分析）结果表明，河段尺度影响大型底栖无脊椎动物分布的关键因子为：细粒物质比例、河岸带植被盖度、河岸带人类干扰程度、河岸带农田比例、水面宽度和河道改造程度，总解释量为42%；流域尺度影响大型底栖无脊椎动物分布的关键因子为：纬度、海拔、流域内耕地面积百分比和流域面积，总解释量为32%。研究结果表明，河段尺度因子比流域尺度因子对于指示大型底栖无脊椎动物分布更为重要，在环境因子监测中应给以更多的重视。 Abstract:In the context of climate change and human-induced habitat destruction, biodiversity is being destroyed at an unprecedented rate. Moreover, the biodiversities in freshwater ecosystems are decreasing faster than those in terrestrial ecosystems. Less attention, however, has been paid to this issue. Compared with fish and algae, benthic macroinvertebrates, which have more advantages, become the most popular biological indicators of river health. Early studies were mostly focused on the influence of small-scale indicators on macroinvertebrates assemblages. Since the 1990s, some researchers started to pay attention to the impact of large-scale factors. Factors at landscape and watershed scale began to be treated equally or were given more concern. Understanding the relative influence of environmental variables at different scales is important in the distribution of large-scale monitoring points and river restoration.Based on environmental and biotic data of 38 sites within the Luan River Basin, the aims of the study were to identify the key factors related to macroinvertebrates at reach and catchment scales, and to determine which scale is more important in explaining the variation of macroinvertebrates assemblages in this region. Macroinvertebrate assemblages were collected by D-frame net and described by using community structure index and biotic attributes. Such methods were commonly used to describe ecological condition of streams (e.g., richness, feeding type). Water chemistry and physical indicators were involved at reach scale. A majority of reach-scale physical indicators were measured using the method in reference to rapid biological assessment programs in the United States and the Australian community monitoring manual. The covered ratio of forest (%), grassland (%), arable land (%) and construction land (%) in each catchment and buffer zone were summarized as catchment-scale indicators. Redundancy analyses (RDA) was used to quantify macroinvertebrate-reach relationships. Key variables for each ordination at reach scale were selected using the manual forward-selection procedure provided in CANOCO 4.5. The selection was based on Monte Carlo permutation test. Then, the RDA was performed to test for the signicance of the rst RDA axis and all axes, only by the selected reach-scale variables.The following results were captured as follows. First, 117 macroinvertebrate taxa were collected. The dominant population community was aquatic insects which included 107 generas. Second, RDA results showed that the selected reach-scale variables related to macroinvertebrates were %fine sediments, riparian vegetation cover, riparian human disturbance, % cropland in riparian, water width and river transformation. The first axis and all axes explained 0.307 and 0.42, respectively. Both reached a significant level. The first axis and riparian vegetation cover had a highest correlation coefficient. Third, the selected catchment-scale variables were latitude, attitude, % cropland in the whole catchment and catchment area. The first axis and all axes explained 0.234 and 0.32, respectively. Both of them also reached a significant level. The first axis and catchment area had a highest correlation coefficient. The results showed that benthic macoinvertebrate communities in Luanhe River Bsin were affected by the combined effects of natural and human factors at both scales. However, variables at reach scale played a more important role in stream macroinvertebrates distribution, rather than catchment scale. It was suggested that more attention should be paid to reach-scale factors in river ecosystem management and restoration in Luanhe River Basin. 参考文献 相似文献 引证文献

Zooplankton response to organic carbon level in lakes of differing trophic states

Key-words: zooplankton, Crustacea, total organic carbon, dissolved organic carbon, particulate organic carbon Water eutrophication is associated with an increase in the organic carbon content (both particulate and dissolved forms), which may affect the functioning of the zooplankton community. Mesotrophic and eutrophic lakes in the Masurian Lake District (Poland) were selected to evaluate the relationship between the organic carbon level and the zooplankton community. The lakes differed significantly in most environmental variables. RDA analysis was performed to evaluate the impact of environmental variables on zooplankton. The variables that significantly explained the variance in the zooplankton community abundance (Monte Carlo permutation test) included dissolved and particulate organic carbon, Secchi disc visibility, soluble reactive phosphorus and total nitrogen. The response of zooplankton to an increasing level of organic carbon is functional rather than quantitative. In the mesotrophic system, the results of the redundancy analysis indicated relatively strong positive relationships between dissolved organic carbon and zooplankton biomass, and negative correlations between chlorophyll a and zooplankton biomass. The above suggests that indirect organic carbon utilization by zooplankton could partly compensate for the poor feeding conditions of planktonic animals (decreasedphytoplankton availability). In the eutrophic lake, elevated organic carbon levels are partly limited by zooplankton, which is suggested by the positive relationship between particulate organic matter and the total zooplankton biomass (RDA results). The positive relationship between the biomass of copepods and organic carbon in particulate and dissolved forms implies that copepods benefit from the increased heterotrophic carbon flow that is activated in the eutrophic lake.

Gradient analysis and environmental interpretation of understory herb-layer communities in Xiaoshegou of Lingkong Mountain, Shanxi, China

Aims Many past practices in afforestation and forest management were instrumented for addressing the issues of tree species selection, planting regimes and development of overstory structure, but neglected understory vegetation. Our objective was to determine the controlling factors of herb-layer plant distribution and the importance of topography in determining local-scale spatial patterns of herbaceous plants. Methods The occurrence and distribution of herb-layer plants were investigated on 26 plots in the Xiaoshegou catchment of Lingkong Mountain, Shanxi Province, China. Community types were classified using two-way indicator species analysis (TWINSPAN) and the relationship between the distribution and abundance of herb-layer species and environmental gradients was analyzed using the canonical correspondence analysis (CCA) ordination method. Forward selection and Monte Carlo permutation test were used to select the factors important in determining the herb-layer plant distribution. Partial CCA (PCCA) was also performed to partition the variance that was explainable by categorical habitat and biotic factors studied. Important findings The 26 survey plots were classified into six groups characterized by the dominant overstory tree species. The results of CCA ordination reflected the relationship between herb-layer community structure and selective environmental variables. The classification of 26 plots in CCA ordination was consistent with the result of TWINSPAN. Forward selection and Monte Carlo test suggested that stand type, soil nutrients and slope position were the most important factors determining understory plant distribution. PCCA revealed that habitat and biotic factors together explained 42.9% of variance in the distribution of understory herbaceous plants. Habitat factors alone explained 31.8% of the variance, biotic factors alone explained 7.8% of the variance and interactionbetween habitat and biotic factors explained 3.2% of the variance. The partitioning of variance using the PCCA helped with identifying the important habitat factors regulating understory herbaceous plant distribution at the study site. However, the fact that more than half of the variance was unaccounted for by the factors studied suggests that other factors we did not measure could also play a role in determining the occurrence and distribution of herbaceous plants on the forest floor, e.g., human activities and random events. Our study demonstrates the importance of both topography and overstory tree species in determining the occurrence and distribution of herb-layer plant species in temperate forest of mountainous areas.

The effect of native and introduced biofuel crops on the composition of soil biota communities

Biofuel crops are an accepted alternative to fossil fuels, but little is known about the ecological impact of their production. The aim of this contribution is to study the effect of native (Salix viminalis and Phalaris arundinacea) and introduced (Helianthus tuberosus, Reynoutria sachalinensis and Silphium perfoliatum) biofuel crop plantations on the soil biota in comparison with cultural meadow vegetation used as control. The study was performed as part of a split plot field experiment of the Crop Research Institute in the city of Chomutov (Czech Republic). The composition of the soil meso- and macrofauna community, composition of the cultivable fraction of the soil fungal community, cellulose decomposition (using litter bags), microbial biomass, basal soil respiration and PLFA composition (incl. F/B ratio) were studied in each site. The C:N ratio and content of polyphenols differed among plant species, but these results could not be considered significant between introduced and native plant species. Abundance of the soil meso- and macrofauna was higher in field sites planted with S. viminalis and P. arundinacea than those planted with S. perfoliatum, H. tuberosus and R. sachalinensis. RDA and Monte Carlo Permutation Test showed that the composition of the faunal community differed significantly between various native and introduced plants. Significantly different basal soil respiration was found in sites planted with various energy crops; however, this difference was not significant between native and introduced species. Microbial biomass carbon and cellulose decomposition did not exhibit any statistical differences among the biofuel crops. The largest statistically significant difference we found was in the content of actinobacterial and bacterial (bacteria, G+ bacteria and G− bacteria) PLFA in sites overgrown by P. arundinacea compared to introduced as well as native biofuel crops. In conclusion, certain parameters significantly differ between various native and introduced species of biofuel crops; however, the functional importance of these differences requires further research.

Enzymatic activities in a moving bed membrane bioreactor for real urban wastewater treatment: Effect of operational conditions

The microbial hydrolytic enzymatic activities (acid phosphatase, alkaline phosphatase and glucosidase) in a moving bed membrane bioreactor (MBMBR system) for real urban wastewater treatment were investigated. This study was conducted in both suspended biomass and attached biofilm present in a MBMBR system. For this, four experimental phases with 20% and 35% (v/v) carrier filling ratios (CFRs) were conducted, which combined two mixed liquor total suspended solid (MLTSS) concentrations (c.a. 2500 and 4500mg/L) and two hydraulic retention times (HRTs) (10 and 24h). Hydrolytic activities of acid phosphatase, alkaline phosphatase and α-glucosidase in the mixed liquor (suspended biomass) were higher than in the biofilm (independent of the carrier concentration), during the four experiments, possibly due to better substrate diffusion in the mixed liquor. A redundancy analysis (RDA) was performed to evaluate the relationship between enzymatic activities and chemical oxygen demand (COD), biological oxygen demand at 5 days (BOD5), mixed liquor volatile suspended solid concentration (MLVSS), biofilm total solids (BTS), HRT, pH, CFR and temperature. According to the results obtained with the Monte Carlo permutation test, CFR, MLVSS, BTS, COD, temperature and HRT significantly contributed to the variation of enzymatic activities in the MBMBR.

Long‐term and contemporary environmental conditions as determinants of the species composition of bog organisms

Summary Environmental change alters ecosystem processes, minding biogeochemical cycles. These changes are accompanied by shifts in species composition. We predicted that long‐term averages of environmental variables would explain more of the variability in species composition than short‐term assessments, but that this difference would be weaker for short‐lived organisms. We further predicted that short‐lived organisms with rapid dispersal would reflect recent environmental change. In 51 plots of ombrotrophic summit bogs in two mountain ranges of Central Europe, we sampled the contemporary species composition of vascular plants, bryophytes, diatoms and testate amoebae. In the same plots, water chemistry (pH, conductivity, Ca, Mg, Na, K, Al, Fe, Pb, Hg, Zn, humic acids, ammonium, nitrates, nitrites, phosphates, sulphates and chlorides) and water level were monitored three times per year for 15 years. We tested species–environmental relationships using Mantel tests and canonical correspondence analyses with Monte Carlo permutation tests for overall, within‐bog and between‐bog effects. The species composition of all four taxa changed along a natural gradient of water level. Diatoms and testate amoebae also changed along a pH/calcium gradient, which has appeared recently in one of the study regions because of aerial liming of forests. Only diatoms reflected variations in humic acid concentration. Spot measurements of environmental factors were sufficient to describe the general pattern while significant effects of phosphates for diatoms and bryophytes, nitrites for vascular plants, potassium for vascular plants and testate amoebae, sodium for all groups except diatoms and sulphates for bryophytes and testate amoebae were evident only by using medium‐ or long‐term averages. Although only long‐term averages of some environmental variables were sufficient to explain species compositions, major patterns were revealed by single (spot) samples. The explanatory power of long‐ and short‐term environmental conditions did not differ substantially between micro‐ and macroorganisms, although short‐lived and well‐dispersed microorganisms reflected the new pH/calcium gradient.

Calciphile alpine vegetation in Southern Norway: importance of snow and possible effects of climate change

Vegetation types confi ned to calcareous bedrocks are often characterized by high species richness, and rare and red- listed plants occur frequently. Snow depth and duration are of particular importance for the fl oristic composition of mountain vegetation and we therefore wanted to quantify the importance of the date of snowmelt and thereby discuss possible effects of future climate change. In two mountain areas with calcium-rich bedrocks, 106 sample plots (2 x 2 m) were selected by a stratifi ed random sampling, to cover a broad range of snow cover, topography and vegetation composition. Study plots include both the northern boreal zone (NB), the low alpine zone (LA), and the middle alpine zone (MA). Soil data, soil temperature and day of snowmelt were sampled from all plots. Fifteen vegetation (cluster) types were classifi ed by the use of TWINSPAN, and these were well separated in a DCA (Detrended Correspondence Analysis) ordination. A CVA (Canonical Variates Analysis) and Monte Carlo Permutation tests showed that the vegetation types were signifi cantly associated with most of the measured environmental variables, with relative altitude, potassium, and Julian day of snowmelt as the most important variables. All study plots showed relatively high values for soil richness and were signifi cantly negatively correlated with the Julian day when the soil temperature threshold (6 °C) was reached. The signifi cant relationships between altitude, Julian day of snowmelt, and vegetation composition indicate that major changes may be expected as a consequence of an earlier snowmelt in a warmer world.

Examining the stability of genetic risk effect as evidence accumulates in the context of meta-analysis

The recursive cumulative meta-analysis (RCM) of genetic association studies explores the relative change of the cumulative risk effect (e.g. OR) in time, indicating the stability of risk effect as evidence accumulates. However, the stability in risk effect is currently evaluated empirically with a graphical approach. A Monte Carlo permutation test for examining the instability in RCM is proposed. The statistic used is a function of the difference between the observed change in risk effect and the expected change, and is expressed (stepwise) cumulatively from the last published GAS to the first one. The permutation method is based on the individual studies and the number of studies in each time step. The test was demonstrated using data from two large scale meta-analyses of GAS. The performance of the test was also explored by simulating data from meta-analyses with different settings in terms of heterogeneity and significance. Significance instability was detected when wide oscillations in risk effect were presented and vice versa. The proposed test for assessing stability may provide the framework for claiming or denying the existence of an association as evidence accumulates.

Second Trimester Maternal Urine for the Diagnosis of Trisomy 21 and Prediction of Poor Pregnancy Outcomes

Given the recognized lack of prenatal clinical methods for the early diagnosis of preterm delivery, intrauterine growth restriction, preeclampsia and gestational diabetes mellitus, and the continuing need for optimized diagnosis methods for specific chromosomal disorders (e.g., trisomy 21) and fetal malformations, this work sought specific metabolic signatures of these conditions in second trimester maternal urine, using (1)H Nuclear Magnetic Resonance ((1)H NMR) metabolomics. Several variable importance to the projection (VIP)- and b-coefficient-based variable selection methods were tested, both individually and through their intersection, and the resulting data sets were analyzed by partial least-squares discriminant analysis (PLS-DA) and submitted to Monte Carlo cross validation (MCCV) and permutation tests to evaluate model predictive power. The NMR data subsets produced significantly improved PLS-DA models for all conditions except for pre-premature rupture of membranes. Specific urinary metabolic signatures were unveiled for central nervous system malformations, trisomy 21, preterm delivery, gestational diabetes, intrauterine growth restriction and preeclampsia, and biochemical interpretations were proposed. This work demonstrated, for the first time, the value of maternal urine profiling as a complementary means of prenatal diagnostics and early prediction of several poor pregnancy outcomes.

Disentangling the role of soil in structuring tropical tree communities at Tarap Hill Reserve of Bangladesh

AbstractTarap Hill Reserve, the largest upland reserve of Bangladesh, is situated along the Indo‐Burma Biodiversity Hotspot. It encompasses the last remaining patches of natural vegetation in the Northeastern Tarap Mountain System and harbors 87 % of the nationally declared red‐listed vascular plant species. Despite requiring high conservation priority, this is one of the least studied reserves in the tropics. In this study, we collected vegetation and soil (eight variables) data from 68 sample plots. We identified the tree communities by cluster analysis and verified them using the multi‐response permutation procedure and detrended correspondence analysis. Species richness, diversity, and compositional similarity between the communities were also estimated. In total, 116 tree species representing 69 genera were recorded within the four identified tree community types. Finally, canonical correspondence analysis with associated Monte Carlo permutation tests (499 permutations) was performed to explore the patterns of variation in tree species distribution explained by the soil variables. Soil phosphorus, organic matter content, and pH were most closely correlated with tree compositional variation. Thus, conservation strategies that take into account variations in these influential soil factors may aid in the conservation of trees in the reserve.

珠海鹤洲水道沿岸红树林湿地大型底栖动物群落特征

对珠海鹤洲水道沿岸围垦湿地的4个红树人工林（包括老鼠簕<em>Acanthus ilicifolius</em>、木榄<em>Bruguiera gymnorrhiza</em>、秋茄<em>Kandelia candel</em>和无瓣海桑<em>Sonneratia apetala</em>）样地和2个挺水植被样地（短叶茳芏<em>Cyperus malaccensis</em> var. <em>brevifolius</em>和芦苇<em>Phragmites australis</em>）的大型底栖动物群落进行为期1a的生物调查。利用大型多元分析软件Primer 5的等级聚类分析CLUSTER（基于Bray-Curtis相似性矩阵）和非参数多变量标序NMDS分析大型底栖动物的群落结构，鹤州北围垦湿地6种生境下大型底栖动物在非相似度55%的条件下被划分为3组（组1：短叶茳芏-老鼠簕-木榄组合；组2：无瓣海桑组合；组3：秋茄-芦苇组合）。组1栖息地其大型底栖动物以谭氏泥蟹（<em>Ilyrplax deschampsi</em>）和多毛类为主，其中老鼠簕样地大型底栖动物物种数目（19种）、物种丰富度（<em>d</em>=1.93±0.11）和多样性指数（<em>H’</em>=1.51±0.13）均为全部6种生境最高；短叶茳芏样地的栖息密度（（254.67±156.81）个/m²）在6种生境中最高。组2栖息地其大型底栖动物以攀援型螺类和无齿螳臂相手蟹（<em>Chiromantes dehaani</em>）为主，生物量（（32.06±19.62）g/m²）在6种生境中最高，物种丰富度（<em>d</em>=1.28±0.45）和多样性指数（<em>H’</em>=1.04±0.27）居中。组3栖息地其大型底栖动物以麦克碟尾虫（<em>Discapseudes mackiei</em>）和多毛类为主，物种数、栖息密度、生物量和多样性指数均较低。SIMPER相似性百分比分析显示对群落划分起重要作用的物种主要为各个生境的优势物种。使用典范对应分析（CCA）对大型底栖动物分布与盐度、深度和温度3个环境因子的关系进行深入分析，并利用蒙特卡罗置换检验（Monte Carlo Permutation Test）鉴定环境因子的显著水平，其中盐度（<em>P</em> < 0.05）和深度（<em>P</em> < 0.05）与大型底栖动物分布差异显著相关，温度（<em>P</em> > 0.05）无显著相关。研究结果表明：不同生境大型底栖动物优势物种存在差异；盐度和深度是影响鹤州北围垦湿地大型底栖动物群落结构最重要的环境因子；围垦区人工湿地与自然滩涂大型底栖动物群落结构差异显著。;Macrobenthic communities were sampled four times over a one year period between December 2010 and September 2011 at six different sites in North Hezhou, Zhuhai, China. The six sites comprised four restored mangrove forest habitats (each dominated by a different mangrove species: <em>Acanthus ilicifolius</em>, <em>Bruguiera gymnorrhiza</em>, <em>Kandelia candel</em> and <em>Sonneratia apetala</em>) and two diked wetland habitats, one of which was composed of <em>Cyperus malaccensis </em>var. <em>brevifolius</em>, and the other <em>Phragmites australis</em>. In total, 35 macrobenthic species were recorded during the study. The dominant taxa recorded were crustaceans (10 taxa) and polychaetes (7 taxa). The number of species recorded at a single site varied from 7 (<em>Kandelia candel</em> habitat) to 19 (<em>Acanthus ilicifolius</em> habitat). Hierarchical clustering (based on the Bray-Curtis similarity index) combined with non-metric multidimensional scaling (NMDS); implemented in PRIMER 5 under the condition of 55% non-similarity), was used to classify sampling sites into three groups based on their macrobenthic fauna. Group 1 comprised <em>Cyperus malaccensis </em>var. <em>brevifolius, Acanthus ilicifolius</em>, and <em>Bruguiera gymnorrhiza </em>habitats; Group 2 comprised the <em>Sonneratia apetala</em> habitat; while Group 3 comprised <em>Kandelia candel</em> and <em>Phragmites australis</em> habitat. However, species composition was similar across all three groups, because <em>Discapseudes mackiei </em>was abundant at all six habitats. The highest number of species (19), highest Margalef index (<em>d</em> = 1.93±0.11), and highest species diversity (Shannon-wiener index, <em>H'</em> = 1.51±0.13)were recorded at the <em>Acanthus ilicifolius </em>habitat, where crustaceans, mainly <em>Ilyrplax deschampsi</em>, were the dominant group recorded. Macrobenthos density was highest at the <em>Cyperus malaccensis </em>var. <em>brevifolius </em>habitat (254.67±156.81) ind./m², while macrobenthos biomass was highest at the <em>Sonneratia apetala</em> habitat (32.06±19.62) g/m²). Interestingly, the faunal community structure at the <em>Sonneratia apetala</em> habitat differed significantly to the other habitats, as it was dominated by climbing species, such as <em>Chiromantes dehaani</em> and <em>Pythia cecillei</em>. <em>Discapseudes mackiei </em>and polychaetes were the dominant species within<em> Kandelia candel </em>and<em> Phragmites australis </em>habitats. Overall, macrobenthos species richness, density, biomass and species diversity were low within all six habitats. We also classified macrobenthic community structure based on functional feeding groups (FFGs) and life form analyses. Results showed that the omnivorous functional feeding group and below-surface life forms were abundant at all habitats within the North Hezhou tidal flat. Similarity percentages analysis (SIMPER) showed that the species that differentiated the macrobenthic communities of different habitats were the dominant species in each habitat. The results of a canonical correspondence analysis (CCA) revealed that macrobenthic communities changed significantly with depth (Monte Carlo permutation test: <em>P</em> < 0.05) and salinity (<em>P</em> < 0.05), but not with temperature (<em>P</em> > 0.05). The findings of this study suggest that macrobenthic communities differ structurally between the diked wetland habitats and the natural tidal flat habitats, with the highest densities and biomasses of macrobenthos occurring at habitats close to the tidal gate. Our results further reveal significant differences in the dominant species of macrobenthos occurring in different habitats. Furthermore, our results show that environmental variables, such as depth and salinity, are the most important factors affecting macrobenthic communities in the North Hezhou tidal flat.

Following Healthy Pregnancy by Nuclear Magnetic Resonance (NMR) Metabolic Profiling of Human Urine

In this work, untargeted NMR metabonomics was employed to evaluate the effects of pregnancy on the metabolite composition of maternal urine, thus establishing a control excretory trajectory for healthy pregnancies. Urine was collected for independent groups of healthy nonpregnant and pregnant women (in first, second, third trimesters) and multivariate analysis performed on the corresponding NMR spectra. Models were validated through Monte Carlo Cross Validation and permutation tests and metabolite correlations measured through Statistical Total Correlation Spectroscopy. The levels of 21 metabolites were found to change significantly throughout pregnancy, with variations observed for the first time to our knowledge for choline, creatinine, 4-deoxyerythronic acid, 4-deoxythreonic acid, furoylglycine, guanidoacetate, 3-hydroxybutyrate, and lactate. Results confirmed increased aminoaciduria across pregnancy and suggested (a) a particular involvement of isoleucine and threonine in lipid oxidation/ketone body synthesis, (b) a relation of excreted choline, taurine, and guanidoacetate to methionine metabolism and urea cycle regulation, and (c) a possible relationship of furoylglycine and creatinine to pregnancy, based on a tandem study of nonfasting confounding effects. Results demonstrate the usefulness of untargeted metabonomics in finding biomarker metabolic signatures for healthy pregnancies, against which disease-related deviations may be confronted in future studies, as a base for improved diagnostics and prediction.

Land-use influence on Mediterranean perennial swards of "Poa bulbosa": a case study in the International Tagus Region

Pastureland abandonment or intensification of livestock activity change the floristic patterns of Mediterranean perennial swards which are very important to the conservation of some bird species. The objectives of this study are: 1) to recognise floristic patterns in Mediterranean perennial swards of Poa bulbosa; 2) to identify the communities that configure the European priority habitat 6220* (Pseudo-steppe with grasses and annuals of the Thero-Brachypodietea); 3) to assess the effects of land-use management on the floristic composition of these communities. Field research was conducted in central eastern and south eastern main land Portugal.Vegetation sampling was carried out in 2009-2010 on 9 sward sites, following the phytosociological concepts. Classification and ordination of relevés were obtained by Two Way Indicator Species Analysis (TWINSPAN), Canonical Correspondence Analysis (CCA) and Detrended Canonical Correspondence Analysis (DCCA). Monte Carlo Permutation Tests were performed to analyse differences in floristic patterns. Livestock load, stoniness and land-use history of the last 10 years were selected as the key variables that best explain the ordination model. The absence of extensive livestock grazing results in a reduction of Trifolium subterraneum-dominated areas and in a density/ cover reduction of Poa bulbosa-dominated areas. High livestock loads change the floristic patterns of Mediterranean short swards by favouring species of the Stellarietea mediae class. The control of woody vegetation through grazing or cutting is a key conservation measure.

A Monte Carlo permutation test for co-occurrence data

Researchers commonly use co-occurrence counts to assess the similarity of objects. This paper illustrates how traditional association measures can lead to misguided significance tests of co-occurrence in settings where the usual multinomial sampling assumptions do not hold. I propose a Monte Carlo permutation test that preserves the original distributions of the co-occurrence data. I illustrate the test on a dataset of organizational categorization, in which I investigate the relations between organizational categories (such as “Argentine restaurants” and “Steakhouses”).