生物多样性和均匀度显著性的随机化检验及计算软件

多样性指数和均匀度以其简单易用而被广泛应用于群落生物学和生物多样性等研究中,然而由于缺乏合适的统计检验方法等原因,其分析的可信性往往较低,因而限制了其应用。鉴于生物多样性研究中广泛应用主观和直接的比较不,有必要建立和使用较为严格的多样性统计检验。本研究建立和应用了如下随机化检验方法：单群落多样性指数和均匀度的显著性检验,单群落多样性指数和均匀度的置认区间,群落间多群样和均匀度的差异显著性检验。随机化方法已被成功地应用于群落生态学研究,其原理是：随机排序某一向量中的元素,或随机交换两向量中的对应元素。计算该随机化数据的多样性和均匀度,重复该过程多次,统计和计算显著性检验的p值,由向量中的对应元素。计算该随机化数据的多样性和均匀度,重复该过程多次,统计和显著性检验的p值。由此可确定多样性和差异的统计显著性。同时,研制了相应的Internet计算软件BiodiverisytTest。该软件由7个Java类和1个HTML文件组成,可运行于多种操作系统和网络浏览器上,可读取多种类型的ODBC数据库文件如Access,Excel,FoxPro,Dbase等。该软件中包括Shannon-Wiener多样性指数,Simpson多样性指数,McIntosh多样性指数,Berger-Parker多样性指数,Hrlbert多样性指数以及Brillouin多样性指数。基于Shannon-Wiener多样性指数和Berger-Parker多样性指数,用BiodiversityTest软件对水稻田节肢动物群落多样性（15个地点,17个功能群,125个节肢动物种）进行了比较和分析。结果显示,两组结果可较好地反映水稻节肢动物群落多样性的差异显著性,这些检验方法可有效地反映多样性指数和均匀度的变化。与水稻田节肢动物群落间多样性的直接比较法相比,该随机化检验方法获得更客观的结果。本算法与软件有助于改进生物多样性研究中使用的某些不甚严格的分析方法,为随机化检验方法在生物多样性研究中的进一步应用提供了一种可用的工具。     

The biodiversity of zooplankton communities of the west arctic seas

Based on the data from ten cruises that were carried out in 2001–2009, the structure of zooplankton communities was assessed in the Western Arctic seas using the estimated biodiversity indices. The greatest number of taxa was revealed in the south, southeast, and north of the Barents Sea. The average number of taxa in the sample was at a maximum off the coast of the Svalbard Archipelago. The greatest value of the Shannon index was registered within the Murmansk coastal water mass (Barents Sea) and Svalbard Archipelago. The median values of the evenness of the abundance of fauna were 0.5–0.6. A trend to a reduction of the biodiversity parameters of zooplankton communities with increasing square of water area water area was found. An inverse correlation between the Shannon and evenness indices for the total zooplankton abundance was revealed.     

Sampled‐based estimation of diversity sensu stricto by transforming Hurlbert diversities into effective number of species

A theoretical framework based on Hill numbers has recently been advocated to measure and partition diversity sensu stricto. Hill numbers can be interpreted intuitively as effective number of species (ENS). They conform to the so‐called replication principle allowing a mathematically coherent multiplicative partitioning of diversity. They form a family of ENS defined by the parameter q which controls the weight attributed to rare species. Despite its advantages, this framework was developed without considering its robustness when treating community samples. In this study, we first show that Hurlbert diversity indices (expected number of species among k individuals) can be transformed into ENS that conform asymptotically to the replication principle while controlling the weight given to rare species through parameter k. We investigate the statistical properties of Hill and Hurlbert ENS using simulated communities with contrasted diversity. The properties of multiplicative beta diversity estimators based on ENS are also characterized by simulating communities with different levels of differentiation. We show that Hurlbert ENS provides a better statistical performance than Hill numbers when dealing with small sample sizes. By contrast, Hill numbers and their estimators suffer from substantial bias except when rare species have a low weight (q= 2). An estimator of ENS estimating both Hill numbers for q= 2 and Hurlbert ENS for k= 2 is shown to give the best performance and is recommended for processing real datasets when rare species receive low weight. In order to better take account of rare species, current estimators of Hill numbers are not recommended when sample size is too low while Hurlbert’s ENS performs reliably. In conclusion, while Hill numbers possess some interesting mathematical properties that are not shared by Hurlbert’s ENS, the latter outperforms Hill numbers in terms of statistical properties and is well suited to processing community samples, as illustrated on a real dataset.     

SNP genotypes reveal breed substructure,selection signatures and highly inbred regions in Piétrain pigs

The Piétrain pig originates from the Belgian village Piétrain some time between 1920 and 1950. Owing to its superior conformation, the Piétrain has spread worldwide since the 1960s. As initial population sizes were limited and close inbreeding was commonplace, the breed’s genetic diversity has been questioned. Therefore, this study examines Piétrain breed substructure, diversity and selection signatures using SNP data in comparison with Duroc, Landrace and Large White populations. Principal component analysis indicated three subpopulations, and F_ST analysis showed that US Piétrains differ most from European Piétrains. Average inbreeding based on runs of homozygosity (ROH) segments larger than 4 Mb ranged between 16.7 and 20.9%. The highest chromosomal inbreeding levels were found on SSC8 (42.7%). ROH islands were found on SSC8, SSC15 and SSC18 in all Piétrain populations, but numerous population-specific ROH islands were also detected. Moreover, a large ROH island on SSC8 (34–126 Mb) appears nearly fixed in all Piétrain populations, with a unique genotype. Chromosomal ROH patterns were similar between Piétrain populations. This study shows that Piétrain populations are genetically diverging, with at least three genetically distinct populations worldwide. Increasing genetic diversity in local Piétrain populations by introgression from other Piétrain populations seems to be only limited. Moreover, a unique 90 Mb region on SSC8 appeared largely fixed in the Piétrain breed, indicating that fixation was already present before the 1960s. We believe that strong selection and inbreeding during breed formation fixed these genomic regions in Piétrains. Finally, we hypothesize that independent coat color selection may have led to large ROH pattern similarities on SSC8 between unrelated pig breeds.     

The parasitic communities of the minnow (Phoxinus phoxinus L>)

Phoxinus phoxinus being a widely distributed through Palaearctic and ecologically specialised species is a good model to study parasite communities. 72 specimens of P. phoxinus from 5 localities of the Siberia and Mongolia has been studied by the author and 651 specimens--from 5 localities in Kola Peninsula by the other researches. 595 specimens were studied by B. S. Shulman (1983) year around. To describe infra- and component parasite communities the Brillouin, Shannon, Berger-Parker indexes were used. Communities within individual fish were compared within, and between localities with quantitative percentage similarity index (Esch e. a., 1988). The Brillouin, Shannon and Berger-Parker indexes can be calculated based on abundance or total number of parasites of each species for component or compound communities. Intensity cannot be used. Significant negative correlation was observed between the Brillouin and Berger-Parker dominance indexes (r = -0.984, p < 0.01, n = 66) in infracommunities. The Brillouin index was significant positive correlated with the number of parasites in infracommunity (r = 0.407, p < 0.01, n = 66) and with the number of species in infracommunity (r = 0.92, p < 0.01, n = 66). Berger-Parker dominance index was significant negative correlated with the number of parasite in infacommunity (r = -0.815, p < 0.01, n = 66) and with the number of species in infracommunity (r = -0.268, p < 0.05). Total number of parasites and the number of species in infracommunity was positive correlated significantly (r = 0.565, p < 0.01, n = 66). These correlations remain the same at the component community level for the Shannon/Berger-Parker indexes (r = -0.965, p < 0.01, n = 10) and total number of parasites/number of species (r = 0.789, p < 0.01, n = 10) only. Similarity index was not correlate with any other indexes and parameters. No significant correlation was found between the Brillouin, Berger-Parker indexes and geographical characters of localities (longitude, latitude, altitude above sea-level). Weak correlation (r = 0.551, p < 0.098, n = 10) was observed only between the Berger-Parker dominance index and the latitude. 37 metazoan parasites have been found in all localities (specialists--40%, allogenic species--22%, rare species--40%). Allogenic generalist species of the genus Diplostomum (D. phoxini in most cases) were dominant in 60% of the component communities and 36% of infracommunities on average. 20% of the component communities were dominant by autogenic specialists Gyrodactylus magnificus and only 12% of the infracommunities were dominated by this species. Trematode and nematode larvae were core species in most localities. Frequency distribution of infracommunity richness varied from locality to locality being overdispersed in combine sample. Parasite communities at least on the infracommunity level demonstrate high variability of all parameters. Some tendency to decrease the diversity seems to be present depending on remoteness from prospective centre of origin of the genus Phoxinus.     

Taxonomic and functional diversity covary in rock pool microalgal communities despite their different drivers

Local biodiversity has traditionally been estimated with taxonomic diversity metrics such as species richness. Recently, the concept of biodiversity has been extended beyond species identity by ecological traits determining the functional role of a species in a community. This interspecific functional diversity typically responds more strongly to local environmental variation compared with taxonomic diversity, while taxonomic diversity may mirror more strongly dispersal processes compared with functional metrics. Several trait‐based indices have been developed to measure functional diversity for various organisms and habitat types, but studies of their applicability on aquatic microbial communities have been underrepresented. We examined the drivers and covariance of taxonomic and functional diversity among diatom rock pool communities on the Baltic Sea coast. We quantified three taxonomic (species richness, Shannon''s diversity, and Pielou''s evenness) and three functional (functional richness, evenness, and divergence) diversity indices and determined abiotic factors best explaining variation in these indices by generalized linear mixed models. The six diversity indices were highly collinear except functional evenness, which merely correlated significantly with taxonomic evenness. All diversity indices were always explained by water conductivity and temperature–sampling month interaction. Taxonomic diversity was further consistently explained by pool distance to the sea, and functional richness and divergence by pool location. The explained variance in regression models did not markedly differ between taxonomic and functional metrics. Our findings do not clearly support the superiority of neither set of diversity indices in explaining coastal microbial diversity, but rather highlight the general overlap among the indices. However, as individual metrics may be driven by different factors, the greatest advantage in assessing biodiversity is nevertheless probably achieved with a simultaneous application of the taxonomic and functional diversity metrics.     

Impact of the activities of beaver on the zooplankton of a piedmont river (Mongolia)

The activities of beavers, even in the absence of construction, promote the increase of abundance and the change of community composition in zooplankton. Size of populations, biomass, abundance of copepods, number of species, and value of the Shannon biodiversity indices all increase in parts of the river with some water flow. Biomass and abundance of cladocerans increase in stagnant floodplain waterbodies, along with the reduction of the number of species and of the uniformity of communities.     

On the use of sample indices to reflect changes in benthic fauna biodiversity

This paper focuses on the difference between the value of some commonly used diversity indices (Simpson, Shannon, abundance, richness) calculated from benthic grab samples and their value in the population or region from which the samples are taken. The ability of the sample indices, as well as a recently derived relative Shannon index, to reflect change in biodiversity is examined in a short simulation study based on changing one of the diversity parameters (abundance, richness and evenness) in the population, whilst keeping the other two components constant. Our results suggest that, whilst their population equivalents do not always reflect biodiversity changes, the sample Simpson, Shannon and Richness indices perform well. We note that this will be true for any surveys where the sampling programme fails to detect many species in a population, and hence will be applicable for most benthic surveys. The use of sample indices to detect changes in biodiversity from long-running time series in the Thames and Tyne estuaries is illustrated.     

黑龙江省不同纬度梯度农田大型土壤动物群落分布特征

沿着由高到低的纬度梯度,分别在塔河、带岭、帽儿山的农田生境选择研究样地,采用手捡法调查不同纬度农田生态系统大型土壤动物的群落组成、水平结构、垂直结构和多样性特征,并运用双变量相关分析及典范对应分析阐明土壤动物群落和环境因子的相互关系,旨在揭示黑龙江省不同纬度梯度农田大型土壤动物群落分布特征及其影响因素。调查共捕获大型土壤动物35类2339只,隶属于2门6纲14目35科。其中线蚓科(Enchytraeidae)、正蚓科(Lumbricidae)、步甲科(Carabida)、隐翅虫科(Staphylinidae)为优势类群,其个体数占总个体数的58.84%;常见类群为蚁科(Formicidae)、蜘蛛目(Araneida)和地蜈蚣目(Geophilomorpha)等8类,其个体数占总个体数的32.79%。结果表明:(1)水平分布上:大型土壤动物个体密度和丰富度(即类群数)的水平分布均表现为帽儿山带岭塔河,单因素方差分析表明大型土壤动物的个体密度和丰富度在不同纬度地区无显著差异。Shannon-wiener多样性指数(H')和Pielou均匀度指数(E)均为帽儿山带岭塔河;Simpson优势度指数(C)表现为塔河和带岭最高,帽儿山最少;Margalef丰富度指数(D)则是塔河最多,其次为帽儿山和带岭。(2)垂直分布上:3个不同纬度样地的农田土壤动物个体密度和丰富度在同垂直层次间不存在明显差异(P0.05)。除帽儿山5—10 cm土层土壤动物类群数量较表层增加之外,其他样地大型土壤动物个体密度和丰富度均随土层深度的增加而逐渐降低,表聚性明显。(3)与土壤环境因子关系上:双变量相关分析表明,不同纬度农田大型土壤动物的类群数、个体密度、多样性指数、均匀度指数和优势度指数与土壤p H值、有机质、全氮、全磷和速效磷均没有显著的相关性;典范对应分析(CCA)进一步表明,优势类群和常见类群对环境因子具有较强的适应能力,广泛的分布在3个样地内。研究表明,农田生态系统大型土壤动物的类群数、个体密度和多样性指数随纬度梯度的增加先增加后减少,但不同纬度间均无显著性差异。不同土壤动物类群受到环境变量的影响程度不同,在局地尺度环境因子对土壤动物的影响不容忽视。研究为区域尺度农田生态系统土壤动物空间格局和生物多样性维持机制研究奠定基础。     

鄱阳湖湿地大型底栖无脊椎动物多样性对群落次级生产力及稳定性的影响

理解生物多样性对生态系统功能及稳定性的影响对于制定有效的保护管理策略有重要意义。然而,目前生物多样性与群落生产力、稳定性的关系仍存在争议。在鄱阳湖湿地布设30个采样点,于2019年秋季开展大型底栖无脊椎动物群落野外调查。基于底栖动物群落数据,采用广义加性模型分析物种、谱系、功能多样性对鄱阳湖湿地底栖动物群落次级生产力与稳定性的影响。结果表明:底栖动物群落的次级生产力与反映物种多样性的指数(Simpson多样性指数、Shannon-Wiener多样性指数、Pielou均匀度指数)、分类多样性指数、平均分类差异指数、功能丰富度指数等呈显著的负相关,其中Pielou均匀度指数与次级生产力的相关度最高(r²=0.33)。功能多样性对群落次级生产力的空间分异有最高的解释度(r²=0.75)。P/B值(次级生产力与生物量之比代表群落稳定性)与物种、谱系、功能多样性指数均呈正相关,其中功能丰富度与P/B值的相关度最高(r²=0.22)。反映物种多样性的三个指数总体上对P/B值的空间分异解释度最高(r²=0.37)。谱系多样性与次级生产力、P/B值的相关性相对较弱。生物多样性指数总体分别解释了次级生产力和群落稳定性中81.9%、54.8%的变异。上述研究结果表明,生物多样性与群落生产力、稳定性的关系可能因具体的生物群落而异。研究结果对于鄱阳湖湿地的底栖生物多样性保护有参考价值。     

The Role of Landscape Patterns of Habitat Types on Plant Species Diversity of a Tropical Forest in Mexico

The relationships among landscape characteristics and plant diversity in tropical forests may be used to predict biodiversity. To identify and characterize them, the number of species, as well as Shannon and Simpson diversity indices were calculated from 157 sampling quadrats (17,941 individuals sampled) while the vegetation classes were obtained from multi-spectral satellite image classification in four landscapes located in the southeast of Quintana Roo, Mexico. The mean number of species of trees, shrubs and vines as well as the mean value of the total number of species and the other two diversity indices were calculated for four vegetation classes in every one of the four landscapes. In addition, the relationships between landscape patterns metrics of patch types and diversity indices were explored. The multiple statistical analyses revealed significant predictor variables for the three diversity indices. Moreover, the shape, similarity and edge contrast metrics of patch types might serve as useful indicators for the number of species and the other two diversity variables at the landscape scale. Although the association between the three diversity indices and patch types metrics showed similar behavior, some differences were appreciated. The Shannon diversity index, with its greater sensitivity to rare species, should be considered as having a greater importance in interpretation analysis than Simpson index.     

中国暖温带若干灌丛群落多样性问题的研究

 暖温带灌丛的生物多样性的研究表明：1．灌丛群落的均一度指数同优势度指数的相关性较丰富度指数同变化度指数的相关性为高;在众多的多样性指数中,D4(Shannon信息度指数)和D6(Gini指数)因最大限度地包含了其它各类多样性指数的信息而被采用。2．灌丛群落的物种多样性指数值随着演替的进行,没有表现出降低的趋势。3．生物多样性较高的荆条灌丛和辽东栎萌丛的物种多度分布是对数分布,而生物多样性较低的鬼见愁灌丛和毛榛灌丛的物种多度分布是几何分布,处于中间的三桠绣线菊灌丛的物种多度分布是Broken-Stick分布;没有正态对数分布类型。     

Effects of deforestation on structure and diversity of small mammal communities in the Moravskoslezské Beskydy Mts (Czech Republic)

During 1970s and 1980s, a large area of mountains in the Czech Republic was influenced by long-term industrial air pollution. Among the most degraded areas were the peaks of the Moravskoslezské Beskydy Mts, where vast clearings resulted from emissions and subsequent forest destruction. This study is aimed at determining the degree of deforestation that is necessary to cause changes in structure and species diversity of small mammal communities that were observed previously. Communities of rodents and insectivores were monitored for a minimum of 3 years at two mountain ranges of the Moravskoslezské Beskydy Mts (Czech Republic) by standard mouse snap-traps. The localities (Smrk and Kněhyně) differ by the degree of human disturbance. Clearings on Smrk Mt are very large (> 30 ha) with no remaining original forest growth as a result of intensive air pollution, unlike the same habitat type at Kněhyně Mt, where the clearings are minor (< 3 ha) and contain living solitary trees. Structure and diversity of small mammal communities in clearings were compared with those from original forests and other mountain habitats. Communities of small mammals at clearings in Smrk Mt (with dominatingMicrotus agrestis) are structurally very different from all other habitats, while structure of communities at Kněhyně clearings are very similar to those of original mountain forest (Complete linkage clustering based on Renkonen index). The community of the original mountain spruce forest at Kněhyně had the highest species diversity (according to Shannon-Weaver, Brillouin, and Simpson indices, Shannon evenness, and rarefaction), while species diversity at clearings of Smrk was the lowest. Shannon diversity of community at Kněhyně primeval forest is similar to that of Kněhyně clearings, while at Smrk Mt the forest diversity is higher than that of clearings. The species diversity of mountain forest and clearings at Kněhyně Mt was significantly higher than that in the same habitats at Smrk Mt. Our results obtained in disturbed habitats at Kněhyně and Smrk Mts suggest that the degree of deforestation may influence the presence and/or the degree of community changes. If the forest destruction is relatively small (clearings < 3 ha), the structure and diversity of small mammal communities do not differ from those of original forest.     

Responses of species abundance distribution patterns to spatial scaling in subtropical secondary forests

To quantify and assess the processes underlying community assembly and driving tree species abundance distributions(SADs) with spatial scale variation in two typical subtropical secondary forests in Dashanchong state‐owned forest farm, two 1‐ha permanent study plots (100‐m × 100‐m) were established. We selected four diversity indices including species richness, Shannon–Wiener, Simpson and Pielou, and relative importance values to quantify community assembly and biodiversity. Empirical cumulative distribution and species accumulation curves were utilized to describe the SADs of two forests communities trees. Three types of models, including statistic model (lognormal and logseries model), niche model (broken‐stick, niche preemption, and Zipf‐Mandelbrodt model), and neutral theory model, were estimated by the fitted SADs. Simulation effects were tested by Akaike's information criterion (AIC) and Kolmogorov–Smirnov test. Results found that the Fagaceae and Anacardiaceae families were their respective dominance family in the evergreen broad‐leaved and deciduous mixed communities. According to original data and random sampling predictions, the SADs were hump‐shaped for intermediate abundance classes, peaking between 8 and 32 in the evergreen broad‐leaved community, but this maximum increased with size of total sampled area size in the deciduous mixed community. All niche models could only explain SADs patterns at smaller spatial scales. However, both the neutral theory and purely statistical models were suitable for explaining the SADs for secondary forest communities when the sampling plot exceeded 40 m. The results showed the SADs indicated a clear directional trend toward convergence and similar predominating ecological processes in two typical subtropical secondary forests. The neutral process gradually replaced the niche process in importance and become the main mechanism for determining SADs of forest trees as the sampling scale expanded. Thus, we can preliminarily conclude that neutral processes had a major effect on biodiversity patterns in these two subtropical secondary forests but exclude possible contributions of other processes.     

Monitoring change in biodiversity through composite indices

The need to monitor trends in biodiversity raises many technical issues. What are the features of a good biodiversity index? How should trends in abundance of individual species be estimated? How should composite indices, possibly spanning very diverse taxa, be formed? At what spatial scale should composite indices be applied? How might change-points--points at which the underlying trend changes--be identified? We address some of the technical issues underlying composite indices, including survey design, weighting of the constituent indices, identification of change-points and estimation of spatially varying time trends. We suggest some criteria that biodiversity measures for use in monitoring surveys should satisfy, and we discuss the problems of implementing rigorous methods. We illustrate the properties of different composite indices using UK farmland bird data. We conclude that no single index can capture all aspects of biodiversity change, but that a modified Shannon index and the geometric mean of relative abundance have useful properties.     

Morphological and physiological alterations in the diatom Gomphonema pseudoaugur due to heavy metal stress

Periphytic diatom communities were analyzed from several heavy metal contaminated water bodies of Haryana, India. Among the analyzed sites, site HO3 (Saraswati Dham, Kurukshetra, Pehowa) showed significant response in the periphytic diatom community in terms of community shift (dominance of Gomphonema pseudoaugur) and lower biodiversity indices (species richness and Shannon index). Gomphonema pseudoaugur responded more specifically through induction of lipid bodies and occurrence of deformities in diatom frustules. PCA analysis showed that site HO3 is contaminated with heavy metals, especially Pb and Se. Pearson's correlation analysis showed a positive and statistically strong relationship between induction of lipid bodies and deformities with heavy metals (Pb and Se). Finally, from the present study, we concluded that heavy metal stress induces increased lipid body (LBs) size and deformities in the diatom species Gomphonema pseudoaugur, which could be a valuable indicator species for biomonitoring and a consideration in biofuel production.     

Species turnover in lake littorals: spatial and temporal variation of benthic macroinvertebrate diversity and community composition

Aims Despite wide consensus that ecological patterns and processes should be studied at multiple spatial scales, the temporal component of diversity variation has remained poorly examined. Specifically, rare species may exhibit patterns of diversity variation profoundly different from those of dominant taxa. Location Southern Finland. Methods We used multiplicative partitioning of true diversities (species richness, Shannon diversity) to identify the most important scale(s) of variation of benthic macroinvertebrate communities across several hierarchical scales, from individual samples to multiple littorals, lakes and years. We also assessed the among‐scale variability of benthic macroinvertebrate community composition by using measures of between‐ and within‐group distances at hierarchical scales. Results On average, a single benthic sample contained 23% of the total regional macroinvertebrate species pool. For both species richness and Shannon diversity, beta‐diversity was clearly the major component of regional diversity, with within‐littoral beta‐diversity (β₁) being the largest component of gamma‐diversity. The interannual component of total diversity was small, being almost negligible for Shannon index. Among‐sample (within‐littoral) diversity was related to variation of substratum heterogeneity at the same scale. By contrast, only a small proportion of rare taxa was found in an average benthic sample. Thus, dominant species among lakes and years were about the same, whereas rare species were mostly detected in a few benthic samples in one lake (or year). For rare species, the temporal component of diversity was more important than spatial turnover at most scales. Main conclusions While individual species occurrences and abundances, particularly those of rare taxa, may vary strongly through space and time, patterns of dominance in lake littoral benthic communities are highly predictable. Consequently, many rare species will be missed in temporally restricted samples of lake littorals. In comprehensive biodiversity surveys, interannual sampling of littoral macroinvertebrate communities is therefore needed.     

Numerical reproduction of traditional classifications and automatic vegetation identification

Questions: Is it possible to develop an expert system to provide reliable automatic identifications of plant communities at the precision level of phytosociological associations? How can unreliable expert‐based knowledge be discarded before applying supervised classification methods? Material: We used 3677 relevés from Catalonia (Spain), belonging to eight orders of terrestrial vegetation. These relevés were classified by experts into 222 low‐level units (associations or sub‐associations). Methods: We reproduced low‐level, expert‐defined vegetation units as independent fuzzy clusters using the Possibilistic C‐means algorithm. Those relevés detected as transitional between vegetation types were excluded in order to maximize the number of units numerically reproduced. Cluster centroids were then considered static and used to perform supervised classifications of vegetation data. Finally, we evaluated the classifier's ability to correctly identify the unit of both typical (i.e. training) and transitional relevés. Results: Only 166 out of 222 (75%) of the original units could be numerically reproduced. Almost all the unrecognized units were sub‐associations. Among the original relevés, 61% were deemed transitional or untypical. Typical relevés were correctly identified 95% of the time, while the efficiency of the classifier for transitional data was only 64%. However, if the second classifier's choice was also considered, the rate of correct classification for transitional relevés was 80%. Conclusions: Our approach stresses the transitional nature of relevé data obtained from vegetation databases. Relevé selection is justified in order to adequately represent the vegetation concepts associated with expert‐defined units.     

Robust estimation of microbial diversity in theory and in practice

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao''s estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics (‘Hill diversities''), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao''s estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.