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.     

Biodiversity of vespid wasps in spatial and temporal dimensions in northern Zanjan Province of Iran

Vespidae is one of the major families of Hymenoptera with more than 115000 described species. In the present paper, Simpson and Shannon-Wiener diversity indices, Simpson,Camargo, Smith and Wilson, and modified Nee evenness indices, and richness index based on rarefaction method were adopted to study the biodiversity of vespid wasps in spatial and temporal dimensions in northern Zanjan Province of Iran. In spatial dimension, Zanjan and Gilvan showed the highest and the lowest species diversity, evenness, and richness, respectively; while in tem-poral dimension, 16 July-6 August showed the highest species diversity and richness, and 18 May -27 May and 23 August -2 September showed the highest and the lowest species evenness,respectively. Significant differences in species abundance between localities of study area were observed by Kruskal-Wallis nonparametric test.     

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.     

长白山北坡阔叶红松林及其次生白桦林高等植物物种多样性比较

应用Ｓｉｍｐｓｏｎ和Ｓｈａｎｎｏｎ多样性指数及其相应的均匀度,对阔叶红松林及其次生白桦林的高等植物物种多样性进行了对比研究．结果表明,对于木本植物,次生白桦林物种多样性高于阔叶红松林;而对于草本植物,情况正好相反．但在次生白桦林中,无论木本植物还是草本植物,占优势的物种都是一些常见种,而许多阔叶红松林中的珍稀或特有物种在次生白桦林中数量很少,有些甚至完全消失．对群落各种群多度分布的检验表明,２种森林类型中,无论木本植物还是草本植物,各种群的多度分布都遵从对数级数分布．     

Simultaneous confidence intervals for comparing biodiversity indices estimated from overdispersed count data

Diversity indices might be used to assess the impact of treatments on the relative abundance patterns in species communities. When several treatments are to be compared, simultaneous confidence intervals for the differences of diversity indices between treatments may be used. The simultaneous confidence interval methods described until now are either constructed or validated under the assumption of the multinomial distribution for the abundance counts. Motivated by four example data sets with background in agricultural and marine ecology, we focus on the situation when available replications show that the count data exhibit extra‐multinomial variability. Based on simulated overdispersed count data, we compare previously proposed methods assuming multinomial distribution, a method assuming normal distribution for the replicated observations of the diversity indices and three different bootstrap methods to construct simultaneous confidence intervals for multiple differences of Simpson and Shannon diversity indices. The focus of the simulation study is on comparisons to a control group. The severe failure of asymptotic multinomial methods in overdispersed settings is illustrated. Among the bootstrap methods, the widely known Westfall–Young method performs best for the Simpson index, while for the Shannon index, two methods based on stratified bootstrap and summed count data are preferable. The methods application is illustrated for an example.     

Analyzing the (mis)behavior of Shannon index in eutrophication studies using field and simulated phytoplankton assemblages

The Shannon index of diversity H′ is a commonly used metric in ecology. The tendency of this index to show a unimodal relationship with productivity has been the subject of several studies. In the present work, the behavior of H′ and three related ecological indices (Simpson, Hill, and Evenness) was investigated using phytoplankton assemblages along a eutrophication gradient. We used both natural and simulated assemblages, whereby the comparison enabled us to assess the role of environmental ‘noise’ on index behavior. We developed simulated assemblages based on phytoplankton distributions predicted by two model types: the log series statistical model and the random fraction niche-based model. Using field data, H′ and the related Simpson index showed expected unimodal relationships with eutrophication. The same unimodal relationships were reproduced with simulated assemblages. Comparing the simulations with natural assemblages along a eutrophication gradient showed that there was much unexplained variance in the real-world data, suggesting that these diversity indices are sensitive to stochastic processes. An analysis of the simulated assemblages using relative abundance distributions suggested that increasing H′ and Simpson index values in the low range of the eutrophication gradient were due to increasing species richness, and that decreasing index values in the high range of the eutrophication gradient were due to decreasing evenness. In addition, this analysis revealed how assemblages of identical H′ values arose from contrasting community structures found in the low- and high-range of eutrophication. The high variability and non-linearity of the Shannon and Simpson indices along a eutrophication gradient suggests that these measures of diversity are inappropriate for use as water quality monitoring assessment tools. Indeed, when calculating ecological quality ratios that are employed by the European Water Framework Directive, unreliable (non-monotonic) predictions of water quality resulted.     

辽东山区次生林物种多样性的空间分布及尺度效应

以辽东山区次生林为研究对象,分析4 hm²样地Gleason丰富度指数、Simpson优势度指数、Shannon多样性指数和Pielou均匀度指数的空间分布特征及其与尺度的关系.结果表明: 4个多样性指数的空间分布均表现出较高的空间异质性;4个多样性指数的方差随尺度的增加其变化趋势有所差异;4个多样性指数的变异系数随尺度的增加呈下降趋势;乔木层的4个多样性指数值高于灌木层,且随尺度增加其变化趋势有所差异.在分析辽东山区次生林物种多样性时应考虑尺度效应.     

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.     

鹞落坪自然保护区蝽类昆虫区系与多样性

2006～2007年期间对鹞落坪自然保护区蝽类昆虫多样性进行调查,在不同的生境、月份及海拔对该地区的蝽类昆虫种类及数量进行抽样统计,将调查到的物种进行编目,并采用Margalof丰富度指数、Simpson多样性指数、Shannon-Wiener指数、Pielou指数和Whittaker多样性指数对其群落多样性进行分析。结果表明,鹞落坪共有蝽类昆虫102种,分别隶属于13科,77属。其中有33种为安徽省新记录种。区系分析表明该地区东洋种成分占优势,古北种次之,古北、东洋共有种最少。蝽类群落α多样性分析结果显示:不同生境多样性指数高低顺序是:阔叶灌丛、阔叶林、灌草丛、竹林、农田;不同月份多样性指数高低顺序是:5,7,6,4,9和8月;不同海拔多样性指数高低顺序是:1100,800,700,600,900,1000,1200,500和1300m以上。多样性、均匀性及丰富度的相关分析说明:在不同生境、不同月份、不同海拔,鹞落坪蝽类群落多样性H′指数与Simpson多样性指数及丰富度是一致的,H′与均匀度均不一致。鹞落坪蝽类群落β多样性指数受生境影响最大。     

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.     

吕梁山森林群落草本层植物物种多样性的空间格局及其对模拟增温的响应

为研究气候变暖背景下森林群落草本层植物物种多样性对温度升高的响应及其随海拔、纬度的空间分布格局,按照纬度梯度选择吕梁山系北段的管涔山和南段的五鹿山为研究区,并在每个山地的不同海拔梯度(高、中、低)分别设置对照(CK)、低度增温(OTC1)和高度增温(OTC2) 3种试验样地。于2017年植被生长季对植物多度、频度、盖度、高度进行调查,计算物种多样性指数(Simpson指数、Shannon指数、Pielou指数、Patrick指数)。结果表明:(1)吕梁山森林群落草本层植物物种多样性随海拔呈"v型"变化格局,即在中间海拔梯度处最低,且海拔梯度对各多样性指数的影响均达到极显著水平(P0.01)。(2)物种多样性随纬度升高呈递增趋势(P0.05),即较高纬度山地具有较高的物种多样性。(3)物种多样性随温度升高整体呈递减趋势(P0.05),即温度升高可抑制林下草本层植物物种多样性。(4)在增温处理下,五鹿山草本植物的Simpson指数、Shannon指数和Patrick指数呈递减趋势,Pielou指数先降低后升高;管涔山草本植物的Simpson指数、Shannon指数和Pielou指数先增加后减小,Patrick指数呈递增趋势。整体来说,在吕梁山较低海拔,持续增温会使物种多样性降低;在中等海拔,物种多样性随温度升高呈现先下降后上升的变化趋势;在较高海拔,适度增温可提高物种多样性,持续增温则抑制多样性。因此,增温对吕梁山森林群落草本植物物种多样性的影响随海拔升高整体呈下降趋势。     

安徽菜子湖湿地鞘翅目昆虫区系分析及多样性研究

在2012年-2013年期间对菜子湖湿地鞘翅目昆虫多样性进行调查,在不同生境、月份对该湿地的鞘翅目昆虫种类及数量进行了统计,对采集的物种进行编目,并采用Shannon-Wiener物种多样性指数、Simpson优势度指数、Pielou均匀度指数、MargMef丰富度指数对其群落多样性进行分析。结果表明：菜子湖湿地共有鞘翅目昆虫种类139种,分别隶属于29科114属,其中安徽新记录种7种。区系分析表明该湿地东洋古北共有种占优势,东洋种次之,古北种最少,其所占比例分别为62．59％、27．34％、10．07％。鞘翅目昆虫多样性分析结果显示：不同生境多样性指数高低顺序为草丛一灌木区〉农田区〉滩涂一草丛;不同月份多样性指数高低顺序为5月、7月、61月和8月。多样性、均匀性及丰富度的相关分析说明：菜子湖湿地鞘翅目昆虫多样性指数与丰富度、均匀度指数呈正相关,表明该湿地鞘翅目昆虫群落较稳定。     

不同母质温带草地植物群落多样性对人为干扰的响应

本研究以赛罕乌拉保护区2种不同土壤母质(黄土和沙母质)与3种利用方式(围栏打草、季节性放牧和自由放牧)草地为对象,基于群落组成调查数据,计算人为干扰指数与物种多样性指数,研究草地植物群落物种多样性与草地退化程度间的关系。结果表明: 土壤母质与人为利用方式的差异使草地处于不同的退化状态,黄土与沙母质类型草地退化程度均随人为利用强度的增加而上升,且当人为利用方式相同时,黄土母质草地人为干扰指数(均值1.21)比沙母质草地(均值1.48)低。各样地物种多样性指数总体随土壤母质的砂质化和人为利用强度的增加而下降,其中Margalef丰富度指数为1.57～4.27,Shannon多样性指数为1.16～2.39,Simpson优势度指数为0.76～0.87,Pielou均匀度指数为0.71～0.80。随着人为干扰指数增加,丰富度指数、多样性指数和优势度指数均下降,而均匀度指数有上升趋势。过度放牧对2种土壤母质草地均会造成严重威胁,黄土与沙母质草地最适宜的利用方式分别为围封打草和季节性放牧。在今后生物多样性保护的实施过程中,需兼顾草地不同土壤母质与人为利用方式的影响,针对不同土壤母质条件规划不同的草地利用方式,实现因地制宜的草地恢复与管理。     

Cellular automata and ecology

Many indices for measuring species diversity have been proposed. In this article, a link is noted between a common family of diversity indices and non-additive statistical mechanics. This makes the Shannon index and the Simpson diversity (or Gini coefficient) special cases of a more general index. The general index includes a parameter q that can be interpreted from a statistical mechanics perspective for systems with an underlying (multi)fractal structure. A q - generalised version of the Zipf–Mandelbrot distribution sometimes used to characterise rank–abundance relationships may be obtained by maximising this entropy.     

西双版纳热带雨林树种多样性的尺度效应

基于西双版纳20hm2森林动态监测样地内直径≥1cm的树种资料,分析了该样地树种香农多样性指数和辛普森多样性指数及其方差和变异系数在7个取样尺度(5m×5m、10m×10m、20m×20m、25m×25m、50m×50m、100m×100m、200m×250m)的变化规律,结果表明:(1)香农指数-面积曲线在尺度100m×100m有一个峰值,而辛普森指数-面积曲线在尺度为20m×20m有一个峰值。(2)香农指数和辛普森指数的方差随尺度的增加而减小,其中香农指数的方差在尺度100m×100m上最小,辛普森指数在尺度20m×20m方差最小,表明香农多样性指数在100m×100m的尺度上所获得的多样性信息比较可靠,而辛普森指数在20m×20m的尺度上所获得信息比较可靠。(3)多样性指数的方差和变异系数远大于随机模型拟合的数值,说明样地内树种不是随机分布。     

戴云山物种多样性与系统发育多样性海拔梯度分布格局及驱动因子

生物多样性的海拔分布格局是生态学研究的热点。海拔作为综合性因子驱动着植物群落的物种、系统发育与功能多样性的空间分布。以戴云山南坡900-1600 m森林植物群落为研究对象,探讨物种多样性、系统发育指数与环境驱动因子的相互关系以及环境因子在群落构建与多样性维持中的重要意义。结果表明：（1）森林植物群落的系统发育多样性与物种多样性沿海拔均呈现中间高度膨胀格局。（2）物种多样性Margalef指数、Shannon-Wiener指数与系统发育多样性指数呈显著正相关,表明物种多样性越高,系统发育多样性也越高。Shannon-Wiener指数与物种多样性指数（Margalef、Pielou、Simpson指数）、系统发育多样性及系统发育结构都存在显著相关性,一定程度上Shannon-Wiener指数可以代替其他指数。Pielou指数、Simpson指数、Shannon-Wiener指数与系统发育结构NRI （Net relatedness index）指数、NTI （Net nearest taxa index）指数存在显著正相关,表明群落优势度、均匀度与系统发育结构相关性较强。（3）土壤全磷含量是影响系统发育多样性和物种多样性的主要驱动因子,土壤含水量是影响Shannon-Wiener、Pielou、Simpson指数的最显著因子,海拔是影响群落系统发育结构的主要因素。海拔是影响系统发育结构变化的主要环境因子,而土壤因子是影响物种多样性与系统发育多样性的主要因素,进一步验证了物种多样性与系统发育多样性的高度相关,结果旨在揭示物种群落空间分布规律。     

弃管杉木林杉木数量与群落物种多样性间的关系

森林群落物种多样性格局和动态一直是生态学的研究热点,人工林弃管后演替进程中物种多样性变化也很值得研究。杉木(Cunninghamia lanceolata)作为我国南方林区人工栽培最广、经济价值最高的用材树种之一,其人工林分布面积很大,通常群落结构简单、物种多样性低,然而群落中杉木数量如何影响植物物种多样性,迄今缺乏研究。在浙江省自然保护区内,选择不同疏伐强度和弃管时间的杉木人工林,建立了6个1 hm~2长期动态监测样地,在10 m×10 m、20 m×20 m、50 m×50 m和100 m×100 m尺度下,探究群落物种多样性(物种丰富度、Simpson指数、Shannon-Wiener指数和Pielou均匀度指数)的变化规律,分析杉木数量(多度和相对多度)对物种多样性的影响。结果显示：弃管前对杉木林的疏伐强度越高,演替恢复后的群落物种多样性越高。相同疏伐程度下,物种多样性随演替时间的延长有先升高后降低的趋势。取样尺度小于100 m×100 m时,杉木数量与物种多样性呈极显著负相关;100 m×100 m尺度下仅杉木相对多度与3种多样性指数呈显著负相关,杉木多度与各物种多样性均无显...     

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)。     

Diversity of macrophyte communities and their relationship to water quality in different types of lowland rivers in Poland

The aim of the study was to verify botanical and ecological traits of river typology based on macrophytes. We compared diversities of macrophyte communities in different river types and their relationship to water quality. The 240 surveyed rivers were situated in the central-west of Poland in a lowland area. Species compositional similarities were analysed using the Jaccard index. The macrophyte matrix was classified into four groups: Large rivers (LR), Sandy rivers (SaR), Stony rivers (StR) and Organic rivers (OR). The highest level of homogeneity was found for LR, followed by OR, StR and SaR. The greatest differences in species composition were found between LR and StR. Variabilities of indices (species richness, Shannon, Simpson and Pielou indices, and total cover) confirmed the specific diversity patterns in the four types of rivers. All metrics based on relative abundance were strongly correlated with each other, and they were never correlated with water quality. The total covers of LR and OR as well as species richness of LR show some correlation with water quality. The total cover was correlated with water quality in OR and LR. The communities with the highest species richness were related with OR.     

长白山阔叶红松林草本植物多样性季节动态及空间分布格局

基于长白山阔叶红松林25 hm²样地(CBS)一年内草本植物的4次调查数据,对样地内草本植物多样性的季节动态及其空间分布格局进行了初步分析.结果表明：样地内草本植物物种组成丰富,共有102种,隶属于40科84属.Shannon多样性指数、Simpson多样性指数和Pielou均匀度指数分别为3.52、0.96和0.75;物种组成的季节变化比较明显,以初夏物种数最多;各季节的Shannon多样性指数、Simpson多样性指数和Pielou均匀度指数的变化较大,个体数量从早春到秋季逐渐减少;物种丰富度和多度的空间分布连续性较差,主要表现为斑块性分布,说明草本植物对微环境有较强的依赖性;坡向是影响物种丰富度和多度的主要因素, 在早春、夏末和秋季,不同坡向的物种丰富度和多度差异极显著(P<0.01),且早春阶段北坡和东坡的丰富度高于南坡和西坡,夏末和秋季则相反.