Nonparametric Lower Bounds for Species Richness and Shared Species Richness under Sampling without Replacement

Summary A number of species richness estimators have been developed under the model that individuals (or sampling units) are sampled with replacement. However, if sampling is done without replacement so that no sampled unit can be repeatedly observed, then the traditional estimators for sampling with replacement tend to overestimate richness for relatively high-sampling fractions (ratio of sample size to the total number of sampling units) and do not converge to the true species richness when the sampling fraction approaches one. Based on abundance data or replicated incidence data, we propose a nonparametric lower bound for species richness in a single community and also a lower bound for the number of species shared by multiple communities. Our proposed lower bounds are derived under very general sampling models. They are universally valid for all types of species abundance distributions and species detection probabilities. For abundance data, individuals' detectabilities are allowed to be heterogeneous among species. For replicated incidence data, the selected sampling units (e.g., quadrats) need not be fully censused and species can be spatially aggregated. All bounds converge correctly to the true parameters when the sampling fraction approaches one. Real data sets are used for illustration. We also test the proposed bounds by using subsamples generated from large real surveys or censuses, and their performance is compared with that of some previous estimators.     

Estimating species richness from quadrat sampling data: a general approach

We consider the problem of estimating the number of species (denoted by S) of a biological community located in a region divided into n quadrats. To address this question, different hierarchical parametric approaches have been recently developed. Despite a detailed modeling of the underlying biological processes, they all have some limitations. Indeed, some assume that n is theoretically infinite; as a result, n and the sampling fraction are not a part of such models. Others require some prior information on S to be efficiently implemented. Our approach is more general in that it applies without limitation on the size of n, and it can be used in the presence, as well as in the absence, of prior information on S. Moreover, it can be viewed as an extension of the approach of Dorazio and Royle (2005, Journal of the American Statistical Association 100, 389-398) in that n is a part of the model and a prior distribution is placed on S. Despite serious computational difficulties, we have perfected an efficient Markov chain Monte Carlo algorithm, which allows us to obtain the Bayesian estimate of S. We illustrate our approach by estimating the number of species of a bird community located in a forest.     

Bayesian estimation of species richness from quadrat sampling data in the presence of prior information

We consider the problem of estimating the number of species of an animal community. It is assumed that it is possible to draw up a list of species liable to be present in this community. Data are collected from quadrat sampling. Models considered in this article separate the assumptions related to the experimental protocol and those related to the spatial distribution of species in the quadrats. Our parameterization enables us to incorporate prior information on the presence, detectability, and spatial density of species. Moreover, we elaborate procedures to build the prior distributions on these parameters from information furnished by external data. A simulation study is carried out to examine the influence of different priors on the performances of our estimator. We illustrate our approach by estimating the number of nesting bird species in a forest.     

西藏地衣物种多样性的海拔梯度分析

根据西藏地衣分类和区系的文献资料,对西藏地衣物种多样性的海拔梯度进行了分析。267个分类群按照生长型或者基物被分为六组。每一组地衣的物种丰度随海拔增加呈现单峰曲线形式的变化。多数组物种丰度的峰值出现在海拔3400~3900m之间,对应于山地寒温带针叶林带的上半部分,比尼泊尔对应类群出现极值的海拔要高。此植物带谱内复杂的生态系统可能是物种多样性高的主要原因。壳状地衣物种丰度的峰值出现在5100~5400m区间则可能是因为该区内高大的树木的消失以及具有充裕的阳光。西藏的地衣物种多样性远低于尼泊尔,两地共有的物种数量很少。对西藏地衣物种多样性的调查不充分应当是其主要原因,因此今后中国地衣学工作者应当加强西藏地衣多样性的研究。     

西藏地衣物种多样性的海拔梯度分析

根据西藏地衣分类和区系的文献资料,对西藏地衣物种多样性的海拔梯度进行了分析。267个分类群按照生长型或者基物被分为六组。每一组地衣的物种丰度随海拔增加呈现单峰曲线形式的变化。多数组物种丰度的峰值出现在海拔3400~3900m之间,对应于山地寒温带针叶林带的上半部分,比尼泊尔对应类群出现极值的海拔要高。此植物带谱内复杂的生态系统可能是物种多样性高的主要原因。壳状地衣物种丰度的峰值出现在5100~5400m区间则可能是因为该区内高大的树木的消失以及具有充裕的阳光。西藏的地衣物种多样性远低于尼泊尔,两地共有的物种数量很少。对西藏地衣物种多样性的调查不充分应当是其主要原因,因此今后中国地衣学工作者应当加强西藏地衣多样性的研究。     

Using Self-Organizing Maps to Explore Patterns in Species Richness and Protection

The combination of species distributions with abiotic and landscape variables using Geographic Information Systems can prioritize areas for biodiversity protection by identifying areas of high richness, although the number of variables and complexity of the relationships between them can prove difficult for traditional statistical methods. The use of these methods, which commonly assume linearity and low correlation between independent variables, can obscure even strong relationships and patterns. Self-Organizing Maps (SOM) is a heuristic statistical tool based on machine learning methods that can be used to explore patterns in large, complex datasets for linear and nonlinear patterns. Here we use SOM to visualize broad patterns in species richness by taxonomic group (birds, mammals, reptiles, and amphibians) and 78 habitat, landscape and environmental variables using data from the Gap analysis project for West Virginia, USA. Soil and habitat variables demonstrated clear relationships with species richness; areas with high species richness occurred in areas with high soil richness. Landscape metrics were less important, although habitat diversity and evenness indices were positively related to species richness in some taxonomic groups. Current coverage of protected areas (e.g., National Forests and state parks) appeared to be insufficient to cover most of the areas of high species richness, especially for reptiles; many of the polygons with the highest richness were not covered by these areas. The identification of polygons with high richness and low protection can be used to focus conservation efforts in those areas.     

铜壁关自然保护区种子植物物种丰富度的海拔梯度格局——兼论物种密度的计算方法

利用对铜壁关自然保护区多次考察形成的种子植物数据库,结合通过GIS生成的区域数字高程模型(DEM)数据,分析了该区域种子植物物种丰富度及物种密度沿海拔梯度的变化特征。结果表明, 科、属、种的丰富度随海拔的升高,先增加后降低,在中海拔区域达到最大值,科、种的丰富度最大值出现在海拔1400~1800 m的范围内,属的丰富度最大值出现在1000~1400 m的海拔范围。科、属、种的密度随海拔升高先下降后上升,再下降后再上升;且最大值都出现在保护区最高海拔3000~3400 m的范围内。物种丰富度和物种密度分布格局明显受到海拔梯度的影响,海拔梯度综合了水热条件等诸多因素。铜壁关种子植物科、属、种水平上的物种丰富度的海拔分布格局符合中域效应假说;同时还对目前常用的计算物种密度的"对数模型"方法的普遍适用性提出质疑。     

Influence of Forest Types and Effects of Forestry Activities on Species Richness and Composition of Chrysomelidae in the Central Mountainous Region of Japan

Species richness and composition of the Chrysomelidae (Coleoptera) were studied in larch (Larix kaempheri [Lamb.] Carrière) plantations, secondary forests, and primary forests. In addition, the effects of forest management practices, such as thinning and long rotation, were examined in the larch plantation. The species richness of Chrysomelidae was higher in the larch plantation than in the secondary forest or in the primary forest. Among the larch plantations, the species richness in old-aged plantations was higher than that in middle-aged plantations. The composition of the beetle assemblages in the larch plantation differed from that in the secondary forest or in the primary forest. Exosoma akkoae (Chujo), Batophila acutangula Heikertinger, and Calomicrus nobyi Chujo were caught with a bias toward the larch plantation. Longitarsus succineus (Foudras) and Sphaeroderma tarsatum Baly were caught more in the secondary forest and the primary forest, respectively. More B. acutangula and S. tarsatum were caught in stands where their host plants occurred at higher rates. Species richness of understory plants was an important factor for chrysomlid species richness, and frequency of host occurrence affected the number of individuals of leaf beetles examined. It seems that forest types and forest management practices affect host plants as well as Chrysomelidae, and that these effects on the host plants also influence chrysomelid assemblages.     

Species turnover: the case of stream amphibians of rainforests in the Western Ghats, southern India

We examined species turnover in stream amphibians in rainforest in two hill ranges (Ashambu and Anamalai Hills) in the Western Ghats in south India. In each hill range, six stream segments (100 m in length) belonging to three drainage or rivers were surveyed three to four times in three seasons over 1 year. Species turnover (using 1-Sorenson's index) was estimated between all possible pairs of sites at three spatial scales – within drainage, between drainage and between hill ranges. Similar matrices were also developed for altitudinal difference and geographic distance between sites. A total of 30 species in four families were recorded from 3681 individuals. The hill ranges differed significantly in the composition of the stream community at both the species and family levels. Within the hill range, species turnover was correlated with altitudinal difference and not with geographic distance. Anamalai Hills had a greater species turnover than Ashambu Hills, both within and between drainage. There was also a high turnover between these two hill ranges, with only two shared species. This turnover explains the fact that only 30–40 species have been reported from different hill ranges, although regional diversity is high with about 130 species. The turnover also predicts that several undetected species should occur in hill ranges and drainage that have not been surveyed. The conservation model for mammals and birds, consisting of a few large protected areas, may not adequately address the conservation requirements of amphibians. Protection of rainforest frogs may require many protected areas in different drainages.     

喀斯特山区植物物种丰富度的空间变异分析

应用地统计学对地处滇黔桂连片喀斯特腹地的贵州省毕节地区植物物种丰富度的海拔空间变异进行分析。结果表明,乔木物种丰富度的半变异函数最佳理论模型为球状模型,灌木、草本为线性有基台模型。乔木物种丰富度的空间异质比为0．0052,具有强烈的海拔空间相关性,主要受随海拔梯度变化的自然性控制因素的影响;灌木、草本物种丰富度的空间异质比分别为3．15、34．55,海拔梯度的空间相关性很弱,受随机因素作用较大。乔木物种丰富度的变程为177．37m受因素影响的海拔范围较宽;灌木和草本物种丰富度的变程分别为73．02m和49．97m,受因素影响的海拔范围较窄。灌木、草本物种丰富度的Moran’s I系数随海拔梯度变化的趋势相类似,但乔木的差别较大。     

Multi-scale comparisons of cliff vegetation in Colorado

We developed a nested vegetation sampling protocol to sample the plant diversity on south-facing cliffs and cliff bases in Jefferson County, Colorado. The multi-scale plots included three nested spatial scales, 1 m², 20 m², and 40 m². We compared plant species richness and species diversity among large cliffs, medium cliffs, small cliffs, and non-cliff sites using Hill's diversity numbers (N ₀, N ₁, and N ₂) for the 1-m² quadrats. Species richness (N ₀) was calculated for the 20-m² and 40-m² plots. Our results indicate that plant species diversity on the cliff faces did not increase with increasing cliff area. This pattern was consistent at all three sampling scales. A model selection was run to determine if plant species diversity values on the cliff faces were associated with cliff variables. None of the cliff variables measured were good predictors of diversity at the 1-m² scale. However, at the 20-m² scale, canyon differences and a positive relationship with increasing cliff surface roughness explained 70% of the variability in species richness. Although most plant species sampled on the cliff faces were also found in the base plots, 13 species were sampled only on the cliff faces. Additionally, dry south facing cliffs support a mix of xeric and mesic plants indicating that cliffs may provide unique microenvironments for plant establishment. This revised version was published online in August 2006 with corrections to the Cover Date.     

浙江仙居俞坑森林群落物种多样性研究

分别采用物种丰富度、物种多样性指数和群落均匀度指标对浙江省仙居县俞坑森林群落的物种多样性进行测定和分析。结果表明：本木植物的物种多样性以生境优越的常绿阔叶林为高,木本植物的物种丰富度、物种多样性指数明显大于草本植物。在群落垂直结构中,木本植物等2层的物种丰富度、物种多样性指数均显著大于第1层。物种丰富度以木本第3层最大,草本层最小;而物种多样性指数、群落均匀度则以木本第2层最大、草本层最小。木本植物各层次、草本层的物种多样性各项指标在群落各样地间均有一定的差异。     

The Relationship between Local Species Richness and Species Pool: A Case Study from the High Mountains of the Greater Caucasus

The causes of linear relationships between local species richness and the size of the actual species pool in closed subalpine meadow communities and open plant communities of the alpine stony substrate (the Greater Caucasus Mountains) were analyzed using a computer simulation model. The results demonstrated that this relationship is insufficient evidence for the variation of local species richness among communities is wholly or partly determined by regional processes (the species-pool hypothesis). A relatively proportional ratio between these variables can also arise where local species richness and the size of the species pool both depend on local processes, or where local species richness is determined by local factors alone while the size of the species pool is determined by both local and regional factors.     

祁连山区不同海拔草地群落的物种多样性

依据植物在各海拔带出现的频率和不同海拔带植物种的生活型,对祁连山区草地群落海拔2500～3000m的物种α多样性变化特征进行了研究．结果表明,随海拔升高,Shahnon-Wiener指数从1．432上升到1．832,Simpson指数的变化较为复杂．海拔2701～2800m带是物种多样性的一个重要转折点,是物种多样性较丰富的地带．在祁连山草地群落中,有毒的与食性较差的物种在各海拔带所占比例均超过50％,生物量占到整个样地生物量的60％以上,物种多样性已呈现衰退．     

热带森林树种多度和丰富度空间分布特征研究

用巴拿马50 hm2森林动态监测样地内直径≥1 cm的树种资料,分析了该样地树种多度(个体数)和丰富度(物种数)及其方差和变异系数在6个取样尺度(5 m×5 m,10 m×10 m,20 m×20 m,25 m×25 m,50 m×50 m,100 m×100 m)的变化规律.结果显示:(1)由于多度的可加性,不同取样尺度在样地内树种多度的变化表现出一致性;随取样尺度的增加,多度方差呈线性增加,而变异系数呈线性减小.(2)丰富度随取样尺度的变化较为复杂,随取样尺度的增加,丰富度方差呈非线性变化,在取样尺度为25 m×25 m时方差最大;变异系数随取样尺度的增加而呈线性减小.研究表明,大尺度的多度值可以由小尺度的多度值通过外推法估计,而丰富度却不能,在生物多样性的保护和管理中不能简单地从一个取样尺度的生物丰富度推测另一个取样尺度丰富度.     

香溪河流域河岸带植物群落物种丰富度格局

通过不同海拔高度的样带调查来研究香溪河流域河岸植物群落物种丰富度格局,并探讨河岸带中生物多样性维持的生态学机制。结果表明：河岸植物群落总的物种丰富度、乔木层物种丰富度和草本层物种丰富度沿海拔梯度均表现出相似的格局特征,利用抛物线方程进行拟合,物种丰富度与海拔之间有显著的相关性。灌木层物种丰富度和藤本植物物种丰富度格局特征不明显,且物种丰富度与坡度相关,在流域尺度上,海拔对物种丰富度有着重要的控制作用;在局部尺度上,季节性洪水干扰导致的空间异质性和小地形对群落的生物多样性有着重要的影响,研究结果支在于总的物种多样性在原始河流的中间河段将达到最大值的预测。     

Species richness patterns and the determinants of larch forests in China

Larch forests are important for species diversity, as well as soil and water conservation in mountain regions. In this study, we determined large-scale patterns of species richness in larch forests and identified the factors that drive these patterns. We found that larch forest species richness was high in southern China and low in northern China, and that patterns of species richness along an elevational gradient depend on larch forest type. In addition, we found that patterns of species richness in larch forests are best explained by contemporary climatic factors. Specifically, mean annual temperature and annual potential evapotranspiration were the most important factors for species richness of tree and shrub layers, while mean temperature of the coldest quarter and anomaly of annual precipitation from the Last Glacial Maximum to the present were the most important for that of herb layer and the whole community. Community structural factors, especially stand density, are also associated with the species richness of larch forests. Our findings that species richness in China''s larch forests is mainly affected by energy availability and cold conditions support the ambient energy hypothesis and the freezing tolerance hypothesis.