Only Simpson Diversity can be Estimated Accurately from Microbial Community Fingerprints

Lalande et al. (Microb. Ecol. 66(3):647–658, 2013) introduced a promising approach to quantify microbial diversity from fingerprinting profiles. Their analysis is based on extrapolating the abundance of the phylotypes detectable in a fingerprint towards the rare phylotypes of the community. By considering a set of reconstructed communities, Lalande et al. obtained a range of estimates for phylotype richness, Shannon diversity and Simpson diversity. They reported narrow ranges indicating accurate estimation, especially for Shannon and Simpson diversities. Here, we show that a much larger set of reconstructed communities than the one considered by Lalande et al. is consistent with the fingerprint. We find that the estimates for phylotype richness and Shannon diversity vary over orders of magnitude, but that the estimates for Simpson diversity are restricted to a narrow range (around 10 %). We conclude that only Simpson diversity can be estimated accurately from fingerprints.     

A conceptual guide to measuring species diversity

Three metrics of species diversity – species richness, the Shannon index and the Simpson index – are still widely used in ecology, despite decades of valid critiques leveled against them. Developing a robust diversity metric has been challenging because, unlike many variables ecologists measure, the diversity of a community often cannot be estimated in an unbiased way based on a random sample from that community. Over the past decade, ecologists have begun to incorporate two important tools for estimating diversity: coverage and Hill diversity. Coverage is a method for equalizing samples that is, on theoretical grounds, preferable to other commonly used methods such as equal-effort sampling, or rarefying datasets to equal sample size. Hill diversity comprises a spectrum of diversity metrics and is based on three key insights. First, species richness and variants of the Shannon and Simpson indices are all special cases of one general equation. Second, richness, Shannon and Simpson can be expressed on the same scale and in units of species. Third, there is no way to eliminate the effect of relative abundance from estimates of any of these diversity metrics, including species richness. Rather, a researcher must choose the relative sensitivity of the metric towards rare and common species, a concept which we describe as ‘leverage.' In this paper we explain coverage and Hill diversity, provide guidelines for how to use them together to measure species diversity, and demonstrate their use with examples from our own data. We show why researchers will obtain more robust results when they estimate the Hill diversity of equal-coverage samples, rather than using other methods such as equal-effort sampling or traditional sample rarefaction.     

Community assessment techniques and the implications for rarefaction and extrapolation with Hill numbers

Diversity estimates play a key role in ecological assessments. Species richness and abundance are commonly used to generate complex diversity indices that are dependent on the quality of these estimates. As such, there is a long‐standing interest in the development of monitoring techniques, their ability to adequately assess species diversity, and the implications for generated indices. To determine the ability of substratum community assessment methods to capture species diversity, we evaluated four methods: photo quadrat, point intercept, random subsampling, and full quadrat assessments. Species density, abundance, richness, Shannon diversity, and Simpson diversity were then calculated for each method. We then conducted a method validation at a subset of locations to serve as an indication for how well each method captured the totality of the diversity present. Density, richness, Shannon diversity, and Simpson diversity estimates varied between methods, despite assessments occurring at the same locations, with photo quadrats detecting the lowest estimates and full quadrat assessments the highest. Abundance estimates were consistent among methods. Sample‐based rarefaction and extrapolation curves indicated that differences between Hill numbers (richness, Shannon diversity, and Simpson diversity) were significant in the majority of cases, and coverage‐based rarefaction and extrapolation curves confirmed that these dissimilarities were due to differences between the methods, not the sample completeness. Method validation highlighted the inability of the tested methods to capture the totality of the diversity present, while further supporting the notion of extrapolating abundances. Our results highlight the need for consistency across research methods, the advantages of utilizing multiple diversity indices, and potential concerns and considerations when comparing data from multiple sources.     

西双版纳热带植物园蝴蝶的多样性及变化

中国科学院西双版纳热带植物园（简称“版纳植物园”）保存着上万种植物,且生境多样,具有较高的蝴蝶多样性。本研究选择三类代表性生境：片段化雨林、次生林和专类园,聚焦于环境指示物种蝴蝶这一类群,通过样线法系统调查一年内蝴蝶多样性及其变化。观测结果显示：蝴蝶在版纳植物园内全年发生,共调查到其成虫5科126属218种6 015头,其中蛱蝶科多样性最高。蝴蝶种类及数量随月动态变化,生境间有差异,7-8月种类和数量达到最高峰;1月种类最少,而5-6月数量最低;每月均出现的种类仅有12种,绝大部分种类分散发生于不同月份。影响蝴蝶群落多样性的气候因子中,月最高温显著影响蝴蝶群落的物种丰富度和数量,月最低温显著影响物种丰富度、香农多样性和辛普森多样性,月平均温仅显著影响香农多样性。在版纳的三个典型季节中蝴蝶多样性存在差异,雨季物种丰富度最高,干热季香农和辛普森指数最高;雨季和雾凉季蝴蝶群落组成差异大,仅雾凉季与干热季的蝴蝶群落呈现中等程度相似。此外,在片段化雨林、次生林和专类园这3种不同生境中,蝴蝶群落组成也存在差异,蝴蝶物种丰富度和香农指数在次生林中最高,而辛普森指数则是片段化雨林最高;仅次生林与片段化雨林的蝴蝶群落呈现出中等程度相似。本研究揭示了版纳植物园蝴蝶群落的种类组成与月动态变化规律,并明确了不同季节和生境中蝴蝶群落的多样性变化,可为区域蝴蝶多样性观测及保护提供参考依据。     

不同种植年限香榧根际土壤微生物多样性

为探明不同种植年限对香榧根际土壤微生物群落特征的影响,采用高通量测序技术,分析种植5 a、10 a和15 a香榧根际土壤细菌、真菌的群落结构和多样性特征.结果表明: 在种植15 a的香榧土壤中细菌Chao1指数、ACE指数和Shannon指数显著降低,Simpson指数无显著变化.NMDS分析显示,种植年限对细菌群落结构变化有显著影响,而种植5 a和10 a香榧林地土壤具有相似的细菌群落.细菌相对丰度、多样性以及群落结构(基本上由变形菌、放线菌、酸杆菌和绿弯菌组成)的变化与有机质、C/N、全氮呈极显著相关.香榧根际土壤真菌Chao1指数和ACE指数随种植年限的增加显著降低,Shannon指数和Simpson指数在种植10 a香榧林地中较高.真菌NMDS分析显示,相同种植年限土壤真菌群落聚在一起,不同种植年限之间能明显分开.真菌优势菌群主要包括子囊菌门、担子菌门、接合菌门.有机质是影响真菌丰富度、多样性和群落结构变化的主要因子.综上,香榧根际土壤微生物群落随种植年限不同而发生明显变化,种植年限、C/N、土壤全氮和有机质含量是影响香榧根际土壤微生物群落结构的主要因子.     

Bacterial Communities in the Gut and Reproductive Organs of Bactrocera minax (Diptera: Tephritidae) Based on 454 Pyrosequencing

The citrus fruit fly Bactrocera minax is associated with diverse bacterial communities. We used a 454 pyrosequencing technology to study in depth the microbial communities associated with gut and reproductive organs of Bactrocera minax. Our dataset consisted of 100,749 reads with an average length of 400 bp. The saturated rarefaction curves and species richness indices indicate that the sampling was comprehensive. We found highly diverse bacterial communities, with individual sample containing approximately 361 microbial operational taxonomic units (OTUs). A total of 17 bacterial phyla were obtained from the flies. A phylogenetic analysis of 16S rDNA revealed that Proteobacteria was dominant in all samples (75%–95%). Actinobacteria and Firmicutes were also commonly found in the total clones. Klebsiella, Citrobacter, Enterobacter, and Serratia were the major genera. However, bacterial diversity (Chao1, Shannon and Simpson indices) and community structure (PCA analysis) varied across samples. Female ovary has the most diverse bacteria, followed by male testis, and the bacteria diversity of reproductive organs is richer than that of the gut. The observed variation can be caused by sex and tissue, possibly to meet the host''s physiological demands.     

Responses of the soil fungal communities to the co‐invasion of two invasive species with different cover classes

• Soil fungal communities play an important role in the successful invasion of non‐native species. It is common for two or more invasive plant species to co‐occur in invaded ecosystems.
• This study aimed to determine the effects of co‐invasion of two invasive species (Erigeron annuus and Solidago canadensis) with different cover classes on soil fungal communities using high‐throughput sequencing.
• Invasion of E. annuus and/or S. canadensis had positive effects on the sequence number, operational taxonomic unit (OTU) richness, Shannon diversity, abundance‐based cover estimator (ACE index) and Chao1 index of soil fungal communities, but negative effects on the Simpson index. Thus, invasion of E. annuus and/or S. canadensis could increase diversity and richness of soil fungal communities but decrease dominance of some members of these communities, in part to facilitate plant further invasion, because high soil microbial diversity could increase soil functions and plant nutrient acquisition. Some soil fungal species grow well, whereas others tend to extinction after non‐native plant invasion with increasing invasion degree and presumably time. The sequence number, OTU richness, Shannon diversity, ACE index and Chao1 index of soil fungal communities were higher under co‐invasion of E. annuus and S. canadensis than under independent invasion of either individual species.
• The co‐invasion of the two invasive species had a positive synergistic effect on diversity and abundance of soil fungal communities, partly to build a soil microenvironment to enhance competitiveness of the invaders. The changed diversity and community under co‐invasion could modify resource availability and niche differentiation within the soil fungal communities, mediated by differences in leaf litter quality and quantity, which can support different fungal/microbial species in the soil.

     

Pyrosequencing reveals sponge specific bacterial communities in marine sponges of Red Sea,Saudi Arabia

Bacterial communities of marine sponges are believed to be an important partner for host survival but remain poorly studied. Sponges show difference in richness and abundance of microbial population inhabiting them. Three marine sponges belonging to the species of Pione vastifica, Siphonochalina siphonella and Suberea mollis were collected from Red sea in Jeddah and were investigated using high throughput sequencing. Highly diverse communities containing 105 OTUs were identified in S. mollis host. Only 61 and 43 OTUs were found in P. vastifica and S. siphonella respectively. We identified 10 different bacterial phyla and 31 genera using 27,356 sequences. Most of the OTUs belong to phylum Proteobacteria (29%–99%) comprising of Gammaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria where later two were only detected in HMA sponge, S. mollis. A number of 16S rRNA sequences (25%) were not identified to phylum level and may be novel taxa. Richness of bacterial community and Shannon, Simpson diversity revealed that sponge S. mollis harbors high diversity compared to other two LMA sponges. Dominance of Proteobacteria in sponges may indicate an ecological significance of this phylum in the Red sea sponges. These differences in bacterial composition may be due to difference in location site or host responses to environmental conditions. To the best of our knowledge, the microbial communities of these sponges have never been studied before and this is first attempt to unravel bacterial diversity using PCR-based 454-pyrosequencing method.     

太白红杉群落物种多样性与环境因子的关系

定量研究了太白红杉群落物种多样性与环境因子的关系,结果表明:(1)海拔与物种丰富度和种间相遇机率呈极显著的负相关;与Shannon指数、Simpson指数和Pielou指数表现为"中间高度膨胀"的规律,即中等海拔高度上多样性高而低海拔和高海拔多样性较低。(2)岩石裸露度与物种丰富度呈显著的负相关。(3)土壤含水量与物种丰富度呈极显著的正相关;与种间相遇机率呈先降后升的趋势。(4)环境因子与物种多样性逐步回归结果是:海拔和岩石裸露度与物种丰富度关系密切,其回归方程为:S=90.62-0.02E-14.14B(r=0.769,P<0.05)。     

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.     

When species accumulation curves intersect: implications for ranking diversity using small samples

Diversity in biological communities frequently is compared using species accumulation curves, plotting observed species richness versus sample size. When species accumulation curves intersect, the ranking of communities by observed species richness depends on sample size, creating inconsistency in comparisons of diversity. We show that species accumulation curves for two communities are expected to intersect when the community with lower actual species richness has higher Simpson diversity (probability that two random individuals belong to different species). This may often occur when comparing communities that differ in habitat heterogeneity or disturbance, as we illustrate using data from neotropical butterflies. In contrast to observed species richness, estimated Simpson diversity always produces a consistent expected ranking among communities across sample sizes, with the statistical accuracy to confidently rank communities using small samples. Simpson diversity should therefore be particularly useful in rapid assessments to prioritize areas for conservation.     

天童国家森林公园树种多样性的加性分配

根据物种丰富度、Shannon指数和Simpson指数建立的物种多样性分配方法,提出分异度系数,对天童森林公园内不同森林类型的树种多样性进行了分析.结果表明,基于物种丰富度指数,总体的多样性只有小部分归功于样方内多样性,而多样性大多分配在样方间、亚群丛间或群丛间,例如在木荷-栲树群丛中,样方内只贡献了20.3%的物种丰富度.而在Shannon指数和Simpson指数中,多样性大多分配在样方内.这种差异主要是由于后两种指数不仅考虑了物种的存在与否,也考虑了其在样方内的多度.同时比较分析了加性分配与传统方法的结果.     

佛坪国家级自然保护区植物群落物种多样性特征

用物种多样性指数（Simpson指数和Shannon指数）、均匀度指数（Pielou均匀度）和物种丰富度,对佛坪国家级自然保护区主要高等植物群落物种多样性进行了测度。结果表明：森林群落的多样性程度高于灌丛和草甸,落叶阔叶林高于针叶林,栎林高于杨桦林。群落物种多样性有随海拔高度的升高而降低的趋势。物种多样性在森林群落垂直结构上的分布特点,表现为一般乔木层与灌木层接近但低于草本层。     

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.     

Severe plant invasions can increase mycorrhizal fungal abundance and diversity

Invasions by non-native plants can alter ecosystem functions and reduce native plant diversity, but relatively little is known about their effect on belowground microbial communities. We show that invasions by knapweed (Centaurea stoebe) and leafy spurge (Euphorbia esula, hereafter spurge)—but not cheatgrass (Bromus tectorum)—support a higher abundance and diversity of symbiotic arbuscular mycorrhizal fungi (AMF) than multi-species native plant communities. The higher AMF richness associated with knapweed and spurge is unlikely due to a co-invasion by AMF, because a separate sampling showed that individual native forbs hosted a similar AMF abundance and richness as exotic forbs. Native grasses associated with fewer AMF taxa, which could explain the reduced AMF richness in native, grass-dominated communities. The three invasive plant species harbored distinct AMF communities, and analyses of co-occurring native and invasive plants indicate that differences were partly driven by the invasive plants and were not the result of pre-invasion conditions. Our results suggest that invasions by mycotrophic plants that replace poorer hosts can increase AMF abundance and richness. The high AMF richness in monodominant plant invasions also indicates that the proposed positive relationship between above and belowground diversity is not always strong. Finally, the disparate responses among exotic plants and consistent results between grasses and forbs suggest that AMF respond more to plant functional group than plant provenance.     

放牧干扰下高寒草甸物种多样性指数评价与选择

在青藏高原东北缘高寒草甸设置6个放牧强度样地,连续4年研究10个多样性指数(Richness和Abundance 2个实测指数,优势度指数、均匀度指数、丰富度指数和综合指数各2个)对放牧强度和年限影响植物群落的解释能力.结果表明: 相对于重要值,利用多度计算的多样性指数对放牧干扰更敏感.优势度指数(Berger-Parker、Dominance)与放牧强度和年限均无关,不能将放牧干扰对群落优势种的影响有效区分.均匀度指数(Equitability、Evenness)均与放牧强度无关,但Evenness指数与放牧年限呈显著负相关,不受偶见种影响且与物种多度的变异系数呈显著正相关,在基于时间尺度的均匀度比较中可以选择Evenness指数.丰富度指数(Menhinick、Margalef)均与放牧年限无关,但Margalef指数与放牧强度呈显著正相关,且不受偶见种影响.综合指数(Shannon、Simpson)均与放牧强度无关,但Shannon指数与物种丰富度和多度呈显著正相关,且随放牧年限增加而显著升高,不受偶见种影响,Shannon指数可用于在长时间尺度下比较物种多样性变化.在所有多样性指数中,只有实测物种丰富度和多度均与放牧强度呈显著负相关,与放牧年限呈显著正相关,且不受偶见种影响,故实测物种丰富度和多度相结合可作为放牧干扰下多样性比较的首选指标.此外,多样性指数选择须考虑放牧干扰的强度与时间特征、多样性组分和研究目的.     

北京东灵山辽东栎林植物物种多样性的多尺度分析

多尺度分析物种多样性格局能够为有效保护生物多样性提供重要信息.利用物种多样性的加法分配法则分析了样方-坡位-坡面等级尺度系统辽东栎林植物物种多样性(gamma多样性)的alpha多样性和beta多样性在各尺度上的分配关系.结果表明以物种丰富度为指标的区域物种多样性的最大贡献来自坡面尺度,表明坡面尺度是维持辽东栎林物种多样性的有效尺度;而对Simpson多样性和Shannon多样性的最大贡献则来自样方内,这决定于群落物种优势度和稀有度格局;各尺度间beta多样性组分随尺度的增大而增大可能是环境异质性和扩散作用的综合结果.各尺度间Shannon多样性对总体多样性的贡献大于Simpson多样性的贡献是偶见种在各尺度间分配的结果.物种多样性分配的加法法则为物种多样性格局的多尺度分析提供了理论框架,是检验物种多样性格局形成机制的有效方法.     

井冈山自然保护区蛾类多样性及人为干扰的影响

对井冈山自然保护区蛾类群落的多样性及其受人为干扰的影响进行了研究。结果显示：（1）人为干扰导致井冈山自然保护区蛾类群落构成有较大差别,严重干扰导致蛾类科数明显降低;物种数和个体数呈现出随着人为干扰加强而降低的趋势;蛾类各优势科在不同人为干扰样点的相对多度存在差异。（2）人为干扰导致蛾类主要科的物种数和个体数变化不同：尺蛾科、夜蛾科、毒蛾科和舟蛾科的物种数和个体数在人为干扰下降低;轻度和中度干扰导致螟蛾科和天蛾科的物种数和个体数升高,重度干扰下物种数和个体数降低;人为干扰导致灯蛾科的物种数和苔蛾科的个体数升高。（3）人为干扰导致蛾类群落Shannon多样性指数、Pielou均匀度指数降低,Berger-Parker优势度指数升高。（4）人为干扰对蛾类群落的物种数和个体数的时间动态影响较大,对Shannon指数和Pielou均匀度指数时间动态影响较小,导致Berger-Parker优势度指数时间波动幅度增大。（5）人为干扰导致样点间蛾类群落相似性较低。     

Partitioning diversity for conservation analyses

Aim  Differentiation of sites or communities is often measured by partitioning regional or gamma diversity into additive or multiplicative alpha and beta components. The beta component and the ratio of within-group to total diversity (alpha/gamma) are then used to infer the compositional differentiation or similarity of the sites. There is debate about the appropriate measures and partitioning formulas for this purpose. We test the main partitioning methods, using empirical and simulated data, to see if some of these methods lead to false conclusions, and we show how to resolve the problems that we uncover.
Location  South America, Ecuador, Orellana province, Rio Shiripuno.
Methods  We construct sets of real and simulated tropical butterfly communities that can be unambiguously ranked according to their degree of differentiation. We then test whether beta and similarity measures from the different partitioning approaches rank these datasets correctly.
Results  The ratio of within-group diversity to total diversity does not reflect compositional similarity, when the Gini–Simpson index or Shannon entropy are used to measure diversity. Additive beta diversity based on the Gini–Simpson index does not reflect the degree of differentiation between N sites or communities.
Main conclusions  The ratio of within-group to total diversity (alpha/gamma) should not be used to measure the compositional similarity of groups, if diversity is equated with Shannon entropy or the Gini–Simpson index. Conversion of these measures to effective number of species solves these problems. Additive Gini–Simpson beta diversity does not directly reflect the differentiation of N samples or communities. However, when properly transformed onto the unit interval so as to remove the dependence on alpha and N , additive and multiplicative beta measures yield identical normalized measures of relative similarity and differentiation.     

Focal species diversity patterns can provide diagnostic information on plant invasions

In Europe, coastal sandy habitats are considered highly endangered among those included in the EC Directive 92/43/EEC (Habitats Directive). Among the different threats which affect coastal communities, the spread of alien plants has been claimed to induce changes in community diversity and structure. We therefore set out to analyse diversity patterns of native and focal species (diagnostic and characteristic of coastal dune habitats of European conservation interest) in sandy coastal habitats invaded by Carpobrotus aff. acinaciformis, a widespread alien plant. Focal species are a major conservation target for the Habitats Directive and their decline should be considered a serious threat for the whole habitat. The study was performed in the Central Western coast of Italy. We randomly sampled the vegetation of the holocenic dune by 2 m × 2 m plots. First we split the collected data in two sets: invaded and non-invaded. We compared overall native and focal species richness patterns of the two sets by rarefaction curves. Then, in order to describe the singular aspects of species diversity (e.g. richness, Shannon index, Simpson index, Berger–Parker index), we also compared Rènyi's diversity profiles and we tested the significance of the differences between invaded and non invaded sets using a bootstrap procedure. Rarefaction curves of the non-invaded set rise quickly and reach higher accumulation values than the invaded set, but differences between the two curves were not significant. With respect to Rènyi's profiles, the profile for the invaded dataset was always below the non-invaded one, but differences in diversity were significant only when specifically considering the focal species (Shannon, Simpson and Berger–Parker indices). In the analysed case, the invasion is significantly associated with changes in focal species diversity, instead those differences are not evident on the all native species pool. In the case of recent invasions, a consistent decline on focal species diversity may represent an early alarm sign of diversity loss and may help define specific conservation actions to prevent the decrease of overall diversity.