Effect of species richness and relative abundance on the shape of the species accumulation curve

Abstract We explain how species accumulation curves are influenced by species richness (total number of species), relative abundance and diversity using computer‐generated simulations. Species richness defines the boundary of the horizontal asymptote value for a species accumulation curve, and the shape of the curve is influenced by both relative abundance and diversity. Simulations with a high proportion of rare species and a few abundant species have a species accumulation curve with a low ‘shoulder’ (inflection point on the ordinate axis) and a long upward slope to the asymptote. Simulations with a high proportion of relatively abundant species have a steeply rising initial slope to the species accumulation curve and plateau early. Diversity (as measured by Simpson's and Shannon–Weaver indices) for simulations is positively correlated with the initial slope of the species accumulation curve. Species accumulation curves cross when one simulation has a high proportion of both rare and abundant species compared with another that has a more even distribution of abundance among species.     

Determining adequate trapping effort and species richness using species accumulation curves for environmental impact assessments

Abstract Environmental impact assessments (EIA) require that the proponent indicates the potential impact that a development will have on the biodiversity of the area. As part of this assessment it is normal practice to inventory the vertebrate species in the area. We show here how species accumulation curves can be used as a tool by environmental consultants to indicate the adequacy of their trapping effort and predict species richness for a disturbance site. The shape of a species accumulation curve is influenced by the number of species in an assemblage and the proportional number of singletons (rarely caught species) in the survey sample. We provide guidelines for the number of individuals that need to be caught in a trapping program to achieve 80% and 90% of the species in a habitat, and we indicate how this number can be adjusted to accommodate variations in relative species abundance.     

Using species accumulation curves to estimate trapping effort in fauna surveys and species richness

Abstract The shape of species accumulation curves is influenced by the relative abundance and diversity of the fauna being sampled, and the order in which individuals are caught. We use resampling to show the variation in species accumulation curves caused by the order of trapping periods. Averaged species accumulation curves calculated by randomly assigning the order of trapping periods are smooth curves that are a better estimate of species richness and a more useful tool for determining the trapping effort required to adequately survey a site. We extend this concept of randomly resampling the trapping period to show that randomizing the number of individuals caught for each species over the number of collection periods (e.g. days) can provide an accurate estimate of the averaged species accumulation curve. This is particularly useful as it enables an accurate estimation of the proportion of the total number of species caught in an area during a survey from information on the number of individuals caught for each species and the number of trapping periods, and is not dependent on having knowledge of the trapping period in which each individual was caught. This calculation also enables an assessment to be made of the adequacy of fauna surveys to report a species inventory in environmental impact assessments when only a species list and relative abundance data are provided.     

Applications of species accumulation curves in large-scale biological data analysis

The species accumulation curve, or collector’s curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional sampling. Traditional applications have focused on ecological populations but emerging large-scale applications, for example in DNA sequencing, are orders of magnitude larger and present new challenges. We developed a method to estimate accumulation curves for predicting the complexity of DNA sequencing libraries. This method uses rational function approximations to a classical non-parametric empirical Bayes estimator due to Good and Toulmin [Biometrika, 1956, 43, 45–63]. Here we demonstrate how the same approach can be highly effective in other large-scale applications involving biological data sets. These include estimating microbial species richness, immune repertoire size, and k-mer diversity for genome assembly applications. We show how the method can be modified to address populations containing an effectively infinite number of species where saturation cannot practically be attained. We also introduce a flexible suite of tools implemented as an R package that make these methods broadly accessible.     

Preservation of biodiversity in small rainforest patches: rapid evaluations using butterfly trapping

Determining the capacity of small forest remnants to support biodiversity is of critical importance, especially in the tropics where high rates of land conversion coincide with extraordinarily high species richness and endemism. Using fruit-baited traps, we conducted rapid evaluations in 1993 and 1994 of the forest butterfly diversity of seven small patches (3–30 ha) and a single remaining large patch (227 ha) of Costa Rican mid-elevation moist forest. Our results suggest that even recently isolated 20–30 ha fragments of primary forest retain surprisingly depauperate butterfly faunas relative to that supported by the 227 ha patch only 0.5–1.0 km away. If forest butterflies are an index of the diversity of small-bodied organisms in general, preservation of the latter may require unexpectedly large patches. In 1994 we also surveyed a 16 ha botanical garden, situated between and contiguous to both the 227 ha patch and an exceptionally species-rich 25 ha patch. In the garden, we discovered adults of many butterfly species associated with forest interior, suggesting that even heavily managed systems of largely exotic plants (such as agricultural systems) could be designed to serve as corridors for butterflies and perhaps some other groups of organisms. We discuss some implications for a planned restoration of biotic connections between lowland and montane forests in southern Costa Rica.     

Factors affecting range size differences for plant species on rock outcrops in eastern Australia

Abstract: Rock outcrops are considered as habitat or ecological islands discordant from the adjacent matrix. The floras of 24 aggregated outcrop regions within the New England Batholith of eastern Australia were sampled and investigations made into species range differences. A measure is developed to describe differences in species range sizes across floras (range saturation: RS). Range sizes increased in areas with higher incident radiation (higher available energy) and concordantly in regions with a greater proportion of hemi‐parasites, epiphytes and herbs (which were demonstrated to have large range sizes). Differences in species’ range sizes of granite outcrop occurring species on the New England Batholith of eastern Australia at different scales and extents are regressed against selected environmental variables and against local species richness and abundance. Although species’ range size has been linked in a number of systems with increased species richness and local species abundance, such correlations were not obtained in this investigation. Analyses of species’ range sizes could not be used to infer directly on processes that maintain species richness or abundance within the granitic outcrop flora of the New England Batholith.     

应用物种指示值法解析昆嵛山植物群落类型和植物多样性

生物指示目前被广泛用于各类生态系统恢复的监测和评估、生态系统管理的政策与法规的制定等。本文的目的是采用物种指示值法初步解析昆嵛山植物群落类型及其植物多样性的特点,为进一步开展昆嵛山森林自然恢复评价和森林管理提供参考依据。物种累计曲线分析表明,从昆嵛山自然保护区40块永久性标准样地实际采到的物种占全部物种数（估计值ACE为131.26）的92.9%,显示抽样充分。采用主坐标分析将昆嵛山森林群落进一步划分为六种林分类型,通过物种指示值分析得到了各林分类型的指示物种。其中,黑松、山槐、麻栎是黑松林的指示物种;郁李、赤松、山胡椒是赤松林的指示物种;日本落叶松/刺杉林的显著指示物种包括日本落叶松、水榆花楸、刺杉、白檀和水蜡。针叶树－麻栎混交林的指示物种是麻栎;而针叶树－杂木混交林的指示物种构成复杂,如粘鱼须、楸树、华山松,等。阔叶林的物种组成很不相同,分别有枫香林、麻栎林、刺槐林、和水榆花楸林。综合比较不同林分类型乔灌草的整体多样性特点表明,6种林分类型的物种多度和物种丰富度无显著差异;阔叶林的Fisher α指数（P< 0.001）、Shannon–Wiener指数（P = 0.001）,Simpson指数（P = 0.034）与其它5种林分类型相比差异显著;其他五种林分类型的Fisher α指数和Shannon–Wiener指数无显著差异,但Simpson指数在这些林分间差异显著。昆嵛山林分类型的多样性与30年前树种引进和人工造林等人为干扰密不可分。     

喀斯特常绿落叶阔叶混交林物种多度与丰富度空间分布的尺度效应

物种多样性的空间分布格局及其尺度效应是生态学研究的重点,对于理解物种多样性的形成和维持机制以及生物多样性的管理和保护均具有重要意义。以贵州茂兰国家级自然保护区分布的亚热带原生性喀斯特常绿落叶阔叶混交林为研究对象,分析了2个1hm2(100m×100m)样地中物种多度和丰富度的空间分布特征及其与取样尺度的关系,采用方差和变异系数描述多度和丰富度在5个尺度(5m×5m,10m×10m,20m×20m,25m×25m,50m×50m)上的空间变异性。结果表明:(1)两个样地的物种多度和丰富度具有尺度依赖性特征;(2)由于多度具有叠加性,物种多度的方差随着尺度的增加呈线性增加,而变异系数呈线性下降;(3)丰富度的方差随尺度的增加表现出单峰分布的特征,在25 m×25 m尺度上达到最大值,变异系数则随取样尺度的增加而呈线性下降。研究表明,物种多度具有尺度推演规律,而丰富度却没有,因此,应慎重进行物种丰富度的尺度推演。在分析喀斯特森林物种多样性时,应注重尺度效应带来的影响。     

Effect of species‐counting protocols and the spatial distribution of effort on rarefaction curves in relation to decision making in environmental‐impact assessments

Rarefaction Curves are frequently used in Environmental Impact Assessments to evaluate sampling sufficiency, but without clear guidelines of how to ensure that the assumptions of the methods are met. Infrastructure projects in the Brazilian Amazon and elsewhere often occupy extensive areas in remote locations with difficult access, and random sampling under such conditions is impractical. We tested the influence of sampling unit (sample or individual), and geographic distance between samples on rarefaction curve s, and evaluated the magnitude of errors resulting from the misuse of rarefaction curve in decision making, using frogs from four Amazonian sampling sites. Individual‐based rarefaction curve were steeper than those generated by sample‐based rarefaction curve. Geographic distance influenced the number of exclusive species in a predictable fashion only in one area, and not in the Environmental Impact Assessment site. Misuse of rarefaction curve generated large errors in the identification of vulnerable taxa. Because the rarefaction curve model is sensitive to the assumption of randomness and geographic distance can influence it unpredictably, we suggest that rarefaction curve should generally not be used to estimate sample completeness when making management decisions for environmental licensing purposes.     

Heavy metal pollution negatively correlates with anuran species richness and distribution in south‐eastern Australia

Heavy metal pollution has likely played an important role in global biodiversity decline, but there remains a paucity of information concerning the effects of metals on amphibian diversity. This study assessed anuran species richness and distribution in relation to sediment metal content and water chemistry in wetlands located along the Merri Creek corridor in Victoria, south‐eastern Australia. Anurans were present in 60% (21/35) of study sites, with a total of six species detected: the eastern common froglet (Crinia signifera), the eastern sign‐bearing froglet (Crinia parinsignifera), the southern brown tree frog (Litoria ewingii), the growling grass frog (Litoria raniformis), the eastern banjo frog (Limnodynastes dumerilii) and the spotted marsh frog (Limnodynastes tasmaniensis). Mean species richness was 1.77 ± 0.32 per site, and species richness ranged from zero to six species per site. Across sites, species richness correlated negatively with sediment concentrations of six heavy metals: copper, nickel, lead, zinc, cadmium and mercury. Species richness also correlated negatively with wetland water electrical conductivity (a proxy for salinity) and concentrations of orthophosphate. Distributions of the three most commonly observed frog species (C. signifera, L. tasmaniensis and L. ewingii) were significantly negatively associated with the total level of metal contamination at individual sites. The study is the first to provide evidence for an association between metal contamination and anuran species richness and distribution in the southern hemisphere, adding to a small but growing body of evidence that heavy metal pollution has contributed to global amphibian decline.     

祁连山北麓四种天然草地蝗虫物种多样性比较研究

为了研究不同草地类型间草地蝗虫多样性的时空变化特性,于2008和2009年6-10月在祁连山北麓4种天然草地设置采样点,用网捕法调查草地蝗虫物种丰富度和相对多度。共捕获到蝗虫28种（亚种）,隶属于7科15属。结果显示：4种不同草地类型平均蝗虫丰富度变化幅度为7～23种,较低的蝗虫丰富度出现在高山灌丛,2008和2009年其丰富度分别为7和8种;而高山草地蝗虫丰富度值最高,两年分别为16和23种;荒漠草地和高山草甸蝗虫丰富度介于以上两者之间,两年间丰富度值分别为15和15及9和12种。结果提示,水热资源状况、草地植被和地貌地势等特性决定的空间异质性对草地蝗虫群落组成、多样性和空间分布产生重要影响,不同生境间草地蝗虫时空分布呈现明显分化。     

Habitat type as a determinant of species range sizes: the example of lotic–lentic differences in aquatic Goleoptera

Species differ in the size of their geographical ranges, but it is unclear how this is affected by the intrinsic properties of various habitat types. Using data on range sizes for 490 species of aquatic Coleoptera from the Iberian Peninsula we show that running-water (lotic) species have much smaller distributional ranges than those occurring in standing water (lentic). This robust association of habitat type and range size has independently arisen in at least four monophyletic coleopteran lineages, in Hydradephaga, Hydrophiloidea, Hydraenidae and Byrrhoidea, and several more times within these main groups. We propose that this pattern is due to different evolutionary dynamics of both habitat types: stagnant water bodies are more likely to completely disappear, requiring frequent migration of resident populations. Rivers and streams, on the contrary, have more temporal and spatial continuity, and therefore permit the long-term persistence of local populations. In less permanent habitats species will require a greater geographical mobility, which indirectly results in a larger size range. The less dispersive populations of running water should also have reduced gene flow, increasing the probability of allopatric speciation, and thus reducing the average range of more widespread ancestral species. These differences in population parameters, and the frequency of transitions between the two habitat types, may have strong macroevolutionary consequences, in particular regarding speciation rates and possible morphological specializations.     

Performance of nonparametric species richness estimators in a high diversity plant community

Abstract. The efficiency of four nonparametric species richness estimators — first‐order Jackknife, second‐order Jackknife, Chao2 and Bootstrap — was tested using simulated quadrat sampling of two field data sets (a sandy ‘Dune’ and adjacent ‘Swale’) in high diversity shrublands (kwongan) in south‐western Australia. The data sets each comprised > 100 perennial plant species and > 10 000 individuals, and the explicit (x‐y co‐ordinate) location of every individual. We applied two simulated sampling strategies to these data sets based on sampling quadrats of unit sizes 1/400th and 1/100th of total plot area. For each site and sampling strategy we obtained 250 independent sample curves, of 250 quadrats each, and compared the estimators’ performances by using three indices of bias and precision: MRE (mean relative error), MSRE (mean squared relative error) and OVER (percentage overestimation). The analysis presented here is unique in providing sample estimates derived from a complete, field‐based population census for a high diversity plant community. In general the true reference value was approached faster for a comparable area sampled for the smaller quadrat size and for the swale field data set, which was characterized by smaller plant size and higher plant density. Nevertheless, at least 15–30% of the total area needed to be sampled before reasonable estimates of S_t (total species richness) were obtained. In most field surveys, typically less than 1% of the total study domain is likely to be sampled, and at this sampling intensity underestimation is a problem. Results showed that the second‐order Jackknife approached the actual value of S_t more quickly than the other estimators. All four estimators were better than S_obs (observed number of species). However, the behaviour of the tested estimators was not as good as expected, and even with large sample size (number of quadrats sampled) all of them failed to provide reliable estimates. First‐ and second‐order Jackknives were positively biased whereas Chao2 and Bootstrap were negatively biased. The observed limitations in the estimators’ performance suggests that there is still scope for new tools to be developed by statisticians to assist in the estimation of species richness from sample data, especially in communities with high species richness.     

Woody plant encroachment reduces species richness of herb‐rich woodlands in southern Australia

Abstract Woody plants have been increasing in many woodland and savanna ecosystems owing to land use changes in recent decades. We examined the effects of encroachment by the indigenous shrub Leptospermum scoparium (Myrtaceae) on herb‐rich Eucalyptus camaldulensis woodlands in southern Australia. Species richness and compositional patterns were examined under the canopy of L. scoparium and in surrounding open areas to determine the species most susceptible to structural changes. Richness was significantly lower in areas of moderate to high L. scoparium cover (>15%), suggesting that a threshold shrub cover caused major change in this ecosystem. Shrubs were associated with a significant reduction in above‐ground biomass of the ground‐layer flora and a significant shift in community composition. The few species that were positively associated with high L. scoparium cover were also common in the woodland flora; no new species were recorded under the shrub canopy. Important environmental changes associated with L. scoparium cover were decreased light availability and increased litter cover, which were likely a consequence of encroachment. Leptospermum scoparium cover was also associated with greater surface soil moisture, which may be a consequence of increased shading under the shrub canopy or indicate favourable soil conditions for L. scoparium establishment. Reductions in species richness and abundance of the germinable seed bank were found in soil samples taken from under L. scoparium. With ongoing recruitment of L. scoparium and consequent increases in shrub cover, ground‐layer diversity in these species‐rich woodlands should continue to decline over time.     

Effects of Tree Genotypic Diversity and Species Diversity on the Arthropod Community Associated with Big‐leaf Mahogany

Despite potential interactive effects of plant species and genotypic diversity (SD and GD, respectively) on consumers, studies have usually examined these effects separately. We evaluated the individual and combined effects of tree SD and mahogany (Swietenia macrophylla) GD on the arthropod community associated with mahogany. We conducted this study within the context of a tree diversity experiment consisting of 74 plots with 64 saplings/plot. We sampled 24 of these plots, classified as monocultures of mahogany or polycultures of four species (including mahogany). Within each plot type, mahogany was represented by either one or four maternal families. We surveyed arthropods on mahogany and estimated total arthropod abundance and species richness, as well as abundance and richness separately for herbivorous and predatory arthropods. Overall tree SD and mahogany GD had positive effects on total arthropod species richness and abundance on mahogany, and also exerted interactive effects on total species richness (but not abundance). Analyses conducted by trophic level group showed contrasting patterns; SD positively influenced herbivore species richness but not abundance, and did not affect either predator richness or abundance. GD influenced predator species richness but not abundance, and did not influence herbivore abundance or richness. There were interactive effects of GD and SD only for predator species richness. These results provide evidence that intra‐ and inter‐specific plant diversity exert interactive controls on associated consumer communities, and that the relative importance of SD and GD may vary among higher trophic levels, presumably due to differences in the underlying mechanisms or consumer traits.     

Processes involved in species saturation of ground‐dwelling ant communities (Hymenoptera,Formicidae)

The species saturation hypothesis in ground‐dwelling ant communities was tested, the relationship between local and regional species richness was studied and the possible processes involved in this relationship were evaluated in the present paper. To describe the relationship between local and regional species richness, the ground‐dwelling ant fauna of 10 forest remnants was sampled, using 10 1 m² quadrats in each remnant. The ants were extracted from the litter by using Winkler sacs. Using regression analyses, an asymptotic pattern between local and regional species richness was detected. This saturated pattern may be related to three processes: (i) high interspecific competition; (ii) habitat species specialization; or (iii) stochastic equilibrium. It is concluded that non‐interactive processes, such as stochastic equilibrium and habitat specialization may act as factors regulating species richness in this community. The predominance of locally restricted species, in all sampled remnants, seems to indicate the occurrence of a high degree of habitat specialization by the ant species. This result is evidence for the hypothesis that community saturation has been generated by non‐interactive processes. Although ants are frequently described as highly interactive, it is possible that interspecific competition is not important in the structuring of ground‐dwelling ant communities.