Viral diversity limits immune diversity in asymptomatic phase of HIV infection

We propose a new diversity threshold theory which states that the specific CTLs to the viral strain become inactivated (that is, some HIV strain can escape from its specific immune response) when the diversity of HIV strains exceeds some threshold number. We call this number “immune diversity threshold”. Our theory can explain the inactivation of specific immune response and a limit of maximum immune diversity. We can conclude that the accumulation of viral diversity eventually leads to AIDS.     

Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity

Almost half a century after Whittaker (Ecol Monogr 30:279–338, 1960) proposed his influential diversity concept, it is time for a critical reappraisal. Although the terms alpha, beta and gamma diversity introduced by Whittaker have become general textbook knowledge, the concept suffers from several drawbacks. First, alpha and gamma diversity share the same characteristics and are differentiated only by the scale at which they are applied. However, as scale is relative––depending on the organism(s) or ecosystems investigated––this is not a meaningful ecological criterion. Alpha and gamma diversity can instead be grouped together under the term “inventory diversity.” Out of the three levels proposed by Whittaker, beta diversity is the one which receives the most contradictory comments regarding its usefulness (“key concept” vs. “abstruse concept”). Obviously beta diversity means different things to different people. Apart from the large variety of methods used to investigate it, the main reason for this may be different underlying data characteristics. A literature review reveals that the multitude of measures used to assess beta diversity can be sorted into two conceptually different groups. The first group directly takes species distinction into account and compares the similarity of sites (similarity indices, slope of the distance decay relationship, length of the ordination axis, and sum of squares of a species matrix). The second group relates species richness (or other summary diversity measures) of two (or more) different scales to each other (additive and multiplicative partitioning). Due to that important distinction, we suggest that beta diversity should be split into two levels, “differentiation diversity” (first group) and “proportional diversity” (second group). Thus, we propose to use the terms “inventory diversity” for within-sample diversity, “differentiation diversity” for compositional similarity between samples, and “proportional diversity” for the comparison of inventory diversity across spatial and temporal scales. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Resource availability controls fungal diversity across a plant diversity gradient

Despite decades of research, the ecological determinants of microbial diversity remain poorly understood. Here, we test two alternative hypotheses concerning the factors regulating fungal diversity in soil. The first states that higher levels of plant detritus production increase the supply of limiting resources (i.e. organic substrates) thereby increasing fungal diversity. Alternatively, greater plant diversity increases the range of organic substrates entering soil, thereby increasing the number of niches to be filled by a greater array of heterotrophic fungi. These two hypotheses were simultaneously examined in experimental plant communities consisting of one to 16 species that have been maintained for a decade. We used ribosomal intergenic spacer analysis (RISA), in combination with cloning and sequencing, to quantify fungal community composition and diversity within the experimental plant communities. We used soil microbial biomass as a temporally integrated measure of resource supply. Plant diversity was unrelated to fungal diversity, but fungal diversity was a unimodal function of resource supply. Canonical correspondence analysis (CCA) indicated that plant diversity showed a relationship to fungal community composition, although the occurrence of RISA bands and operational taxonomic units (OTUs) did not differ among the treatments. The relationship between fungal diversity and resource availability parallels similar relationships reported for grasslands, tropical forests, coral reefs, and other biotic communities, strongly suggesting that the same underlying mechanisms determine the diversity of organisms at multiple scales.     

Rarity facets of biodiversity: Integrating Zeta diversity and Dark diversity to understand the nature of commonness and rarity

Measuring commonness and rarity is pivotal to ecology and conservation. Zeta diversity, the average number of species shared by multiple sets of assemblages, and Dark diversity, the number of species that could occur in an assemblage but are missing, have been recently proposed to capture two aspects of the commonness‐rarity spectrum. Despite a shared focus on commonness and rarity, thus far, Zeta and Dark diversities have been assessed separately. Here, we review these two frameworks and suggest their integration into a unified paradigm of the “rarity facets of biodiversity.” This can be achieved by partitioning Alpha and Beta diversities into five components (the Zeta, Eta, Theta, Iota, and Kappa rarity facets) defined based on the commonness and rarity of species. Each facet is assessed in traditional and multiassemblage fashions to bridge conceptual differences between Dark diversity and Zeta diversity. We discuss applications of the rarity facets including comparing the taxonomic, functional, and phylogenetic diversity of rare and common species, or measuring species'' prevalence in different facets as a metric of species rarity. The rarity facets integrate two emergent paradigms in biodiversity science to better understand the ecology of commonness and rarity, an important endeavor in a time of widespread changes in biodiversity across the Earth.     

高寒矮嵩草草甸物种多样性与功能多样性对初级生产力的影响

自然生态系统中植物物种多样性是否随功能多样性变化而影响初级生产力的问题存在很大争议。在高寒矮嵩草草甸,对不同放牧强度、不同利用格局和土壤资源水平的4种生境（Ⅰ.畜圈：重度放牧、资源丰富;Ⅱ.牧道：中度放牧、资源适中;Ⅲ.人工草地：轻-中度放牧、资源贫乏;Ⅳ.封育草地：不放牧、资源贫乏）中物种多样性与功能多样性的变化及其对初级生产力的影响进行了研究。结果表明：物种多样性在牧道生境最高,符合中度干扰理论的预测;人工草地物种多样性低但功能多样性却最高;封育草地物种多样性和功能多样性均较高;物种多样性与地上生物量呈正相关,而功能多样性则与地上生物量呈负相关。表明功能多样性不随物种多样性而变化,二者可能在一定程度上是相互独立地作用于生产力的。群落生产力和生物多样性受生境资源、物种特征、放牧历史和放牧强度等因素的综合影响。     

毛乌素沙地植被不同恢复阶段植物群落物种多样性、功能多样性和系统发育多样性

进入21世纪以来, 中国荒漠化恢复取得显著成效, 荒漠化、沙化土地面积持续减少, 植被覆盖度大幅提升, 但关于植被恢复过程中生物多样性如何变化的研究不足, 这制约着对荒漠化恢复成效的全面评估。本文基于群落调查和叶功能性状(叶片厚度、叶片干物质含量、比叶面积和叶片密度)的测定, 分析了毛乌素沙地不同恢复阶段(半固定沙地、固定沙地、结皮覆盖沙地和草本植物覆盖沙地)的植物群落物种多样性、功能多样性和系统发育多样性特征。结果表明: (1)多数叶功能性状的系统发育信号不显著, 表明环境因子对研究区植物功能性状的塑造作用很强。(2)对于α多样性, 结皮覆盖沙地的物种多样性(Shannon-Wiener多样性, H)、物种丰富度(S)、功能丰富度(FRic)及系统发育多样性(PD)指数均显著低于其他恢复阶段, 而其他3个阶段间无显著差异; 这些指数间均显著正相关, 表明物种多样性、功能多样性和系统发育多样性在植被恢复过程中协同变化。(3) β多样性指数随恢复阶段间隔增加而逐渐增大, 表明物种组成、功能属性及系统发育关系随植被恢复持续变化, 且半固定沙地到固定沙地的群落物种组成、功能属性及系统发育关系更替最快, 导致群落间差异最大。(4)固定沙地、结皮覆盖沙地和草本植物覆盖沙地群落系统发育结构均趋向于发散, 表明竞争排斥是群落构建的主要驱动力; 而半固定沙地群落系统发育结构无一致规律, 表明群落构建可能受到生境过滤和竞争排斥的综合作用。研究结果可为植被建设与管理提供参考, 为毛乌素沙地生态保育和生物多样性的保护提供科学依据。     

Quantifying immigrant diversity in Europe

The notion of increasing immigrant diversity is prevalent in immigration literature. However, little empirical research has examined if immigrant populations have become more diverse during the past two decades. Using data from Pew Research Center's Global Religion and Migration Database and the World Bank's Global Bilateral Migration Database, origin and religious change in immigrant populations since 1990 is presented for six European countries. Findings demonstrate that immigrant origin and religious diversity has been relatively stable during the past ten years, with moderate increases during the 1990s. Further research can examine whether these patterns are true for other countries or what happens when alternative variables are considered.     

树种多样性和土壤微生物多样性对人工林生产力的影响

林分生产力通常会随着树种多样性增加而增加,但不同营养级生物多样性以及树种和土壤微生物多样性之间的相互作用如何影响生产力目前尚不清楚。以亚热带不同丰富度和树种组成的人工林为研究对象,从物种、功能性状、遗传三个维度的树种多样性以及土壤真菌和细菌系统发育多样性,探究了中国亚热带人工林树种多样性和土壤微生物多样性对林分生产力的影响。研究发现,林分生产力随树种功能多样性(FD)(P<0.001)、比叶面积群落加权均值(CWM-SLA)(P<0.01)、树种系统发育多样性(PD)(P<0.05)和土壤真菌多样性(PDF)(P<0.01)的增加而显著增加,分别解释了林分生产力总变异的12.86%、6.80%、3.67%和3.08%。FD和CWM-SLA可分别通过增加土壤真菌、细菌多样性而间接提高林分生产力。研究结果表明多营养级生物多样性是维持高水平林分生产力的基础,树种多样性和土壤微生物多样性之间的自上而下的级联效应在调节生态系统生产力方面发挥着重要作用。     

Connections between species diversity and genetic diversity

Species diversity and genetic diversity remain the nearly exclusive domains of community ecology and population genetics, respectively, despite repeated recognition in the literature over the past 30 years of close parallels between these two levels of diversity. Species diversity within communities and genetic diversity within populations are hypothesized to co‐vary in space or time because of locality characteristics that influence the two levels of diversity via parallel processes, or because of direct effects of one level of diversity on the other via several different mechanisms. Here, we draw on a wide range of studies in ecology and evolution to examine the theoretical underpinnings of these hypotheses, review relevant empirical literature, and outline an agenda for future research. The plausibility of species diversity–genetic diversity relationships is supported by a variety of theoretical and empirical studies, and several recent studies provide direct, though preliminary support. Focusing on potential connections between species diversity and genetic diversity complements other approaches to synthesis at the ecology–evolution interface, and should contribute to conceptual unification of biodiversity research at the levels of genes and species.     

Notes on compositional diversity

This paper tries to show some ways and means of simple (binary) modelling, whereby diversity can be interconnected with other attributes of a community. A new type of scaling (called characteristic scaling) is introduced for further use.     

红树植物多样性及其研究进展

红树植物是分布于热带、亚热带海岸潮间的木本植物群落。因因适应海岸带和作的生长环境形成了独特的形态结构和生理生态特性。红树林是海岸有重要价值的湿地。论述了红树植物的物 多样性、适应多样性、物侯多样性以及分子水平的多样性及其研究进展。     

Plant species diversity in cape fynbos: Gamma and delta diversity

Summary This paper reports the number of plant species on circumscribed fynbos areas (gamma diversity), ranging in size from 0.27 km² (a site with 364 species) to 471 km² (2351 species). The composition of the floras of four of these sites was analysed to measure delta diversity, the change in flora from one site to the next. Maximum gamma diversity values fitted a species-area curve log S=2.69+0.25 log A. Gamma diversity is apparently higher than in any of the world's biogeographic zones except perhaps the tropical rain forest, and in other South African sites of areas around 1.0 km², which have about as many species. High delta diversities are reflected in differences between fynbos floras of 50 to 70 %, in spite of relative proximity; this degree of diversity is apparently unmatched anywhere. The results support the conventional view that fynbos plant diversity is partly a consequence of the peculiar geography of the zone, and of palaeo-climatic change, which have favoured geographic speciation.This paper would not have been possible without the conscientious work of staff at Jonkershoek, especially that of R.A. Haynes and E.F. Kruger. The information on the floras of each area studied here has been built up through decades of field work by various collectors. Identifications of the many difficult taxa are due to taxonomists at the National Herbarium, at the Compton Herbarium, Kirstenbosch and at the Bolus Herbarium, University of Cape Town. M. F. Thompson and E. E. Esterhuysen contributed materially in this respect.Paper presented at the Annual Congress of the South African Association of Botanists, Stellenbosch, January 1979.This work is based partly on the results of the conservation research programme of the South African Department of Forestry and the Botanical Research Institute's programme on fynbos phytosociology, and is published with permission of our respective heads of Departments.     

高寒草地植物物种多样性与功能多样性的关系

物种多样性与功能多样性的关系是生态学当前研究的热点问题之一,不同区域典型生态系统物种多样性和功能多样性的关系研究有利于生物多样性保护理论的全面发展。以青藏高原地区的主要草地生态系统—高寒草甸和高寒草原为研究对象,采用4个物种多样性指数(Patrick丰富度指数、Shannon-Weiner多样性指数、Pielou均匀度指数和Simpson优势度指数)和9个功能多样性指数(FAD功能性状距离指数、MFAD功能性状平均距离指数、基于样地的FDp和基于群落的FDc功能树状图指数、FRic功能体积指数、FEve功能均匀度指数、Rao功能离散度常二次熵指数、FDiv功能离散指数、FDis功能分散指数),分析了高寒草地植物物种多样性、功能多样性关系及其与初级生产力的关系,以期阐明3个科学问题:不同草地类型的高寒草地生态系统植物物种多样性和功能多样性有何差异?高寒草地生态系统的植物物种多样性和功能多样性有何关系?高寒草地生态系统物种多样性、功能多样性对生态系统功能的影响有何异同?研究结果表明:(1)与高寒草原相比,高寒草甸具有更高的物种多样性、功能丰富度和功能离散度;(2)高寒草甸中,Patrick丰富度与功能丰富度指数(FAD、MFAD、FDp、FDc)和功能离散度指数(FDiv)的具有较强的相关性,最优拟合方程分别为幂函数和二次多项式函数;(3)高寒草原中,Patrick丰富度与功能丰富度指数(FAD、MFAD、FDp、FDc、FRic)、Shannon指数和Simpson指数与FEve指数的相关性较强,最优拟合方程为二次多项式函数,Pielou指数与FEve指数的相关性较强,最优拟合方程为指数函数;(4)高寒草甸的初级生产力分别与物种丰富度指数Patrick、功能离散指数FDiv具有较强的相关性;而高寒草原的初级生产力与4个物种多样性指数间均具有较强的相关性,与功能离散指数FDiv具有较强的相关性,最佳拟合方程均为二次多项式函数。研究的总体结论为:物种多样性、功能多样性、二者之间的关系以及二者与生态系统服务功能(以初级生产力为例)之间的关系在高寒草甸和高寒草原群落中表现迥异,因此在研究青藏高原高寒草地的生态功能时,不能仅仅测度传统的物种多样性,还应测度与物种多样性、生态功能密切相关的功能多样性。     

西南地区生物文化多样性空间格局定量研究

自然条件的丰富性与独特性以及多民族聚居的特征使得西南地区成为我国生物多样性和文化多样性的热点地区,但当前仍然缺乏对区域生物文化多样性格局的定量研究。以西南地区603个县级行政区为基本单元,探讨了西南地区的文化多样性与生物多样性的分布格局,在此基础上定量计算了生物文化多样性,从而识别西南地区生物文化多样性空间格局,并分析不同因素对多样性空间分布的影响。文化多样性与生物多样性存在一定的空间分布差异,同时也存在高低值聚类的重叠区域。高生物文化多样性的区域与高生物多样性的区域分布较为相似,而低生物文化多样性的区域与低文化多样性的区域分布较为接近;生物文化多样性的高低值聚类区呈现明显的片状格局。由于生境条件与人为干扰等原因,西南地区文化多样性、生物多样性与生物文化多样性沿河流流向大多呈现"低-高"或"低-高-低"的变化状态。影响因素分析表明,文化多样性与生物多样性产生相互促进的作用;三种多样性的空间分布都受到平均坡度的重要影响;多样性高的单元聚集在地形坡度大、海拔与坡度的差异程度较大而水体覆盖率较低的区域。文化多样性与生物多样性的密切联系表现在地理空间上的交叉重合,因此,对文化多样性与生物多样性的保护应统筹兼顾,并更多从生物文化多样性的视角或者途径来开展相关研究与保护实践。     

生物群落多样性的测度方法VI：与多样性测度有关的统计问题

物种多样性测度是（群落的）总体参数,它们常常是未知的,需要通过抽样将它们估计出来,因此,必须了解估计量的抽样性质。本文对与一些多样性测度的均值、方差的估计和假设检验以及大、小样本分布等有关的问题作了综述。可以看出大多数多样性测度的抽样性质还不清楚,有些甚至根本就没有研究过。Ｐｉｅｌｏｕ的合并样方法和刀切法是两个比较通用的方法,用它们可以解决其中的一些问题。但相比之下,刀切法更实用。     

Phylogenetic diversity,functional trait diversity and extinction: avoiding tipping points and worst-case losses

The phylogenetic diversity measure, (‘PD’), measures the relative feature diversity of different subsets of taxa from a phylogeny. At the level of feature diversity, PD supports the broad goal of biodiversity conservation to maintain living variation and option values. PD calculations at the level of lineages and features include those integrating probabilities of extinction, providing estimates of expected PD. This approach has known advantages over the evolutionarily distinct and globally endangered (EDGE) methods. Expected PD methods also have limitations. An alternative notion of expected diversity, expected functional trait diversity, relies on an alternative non-phylogenetic model and allows inferences of diversity at the level of functional traits. Expected PD also faces challenges in helping to address phylogenetic tipping points and worst-case PD losses. Expected PD may not choose conservation options that best avoid worst-case losses of long branches from the tree of life. We can expand the range of useful calculations based on expected PD, including methods for identifying phylogenetic key biodiversity areas.     

昆虫多样性三十年研究进展

当前, 全球昆虫数量和多样性均处于下降趋势, 而导致这一趋势的原因主要包括人为干扰及气候变化。本文基于森林、草地、农业、水生和土壤生态系统, 以植食性、访花、捕食性、寄生性、食果以及食腐昆虫为重点功能昆虫群, 综述了近三十年来国内外昆虫多样性研究领域的主要进展, 并分析了发展趋势。近年来, 昆虫多样性的研究维度不断拓展, 形态多样性研究不断深入, 系统发生多样性、功能多样性和遗传多样性等研究也显著加强。此外, 昆虫多样性研究的空间尺度也逐步扩大, 大尺度区域性研究甚至全球范围的调查持续增长。昆虫进化历史也被引入多样性格局研究中, 并随着系统发生信息学方法的普及而被整合到生态系统建成和生物多样性形成机制研究中。未来需要加强关键昆虫类群整合分类学研究、功能性状多样性、林冠昆虫多样性、互作网络结构等方向的研究。     

野生金头闭壳龟栖息地植被多样性

2006年8—9月通过样方法,对安徽黟县、泾县2地记录有野生金头闭壳龟分布的34个栖息地进行了实地调查,分析了植被的改变对野生金头闭壳龟栖息地其它环境因子的影响。结果表明:对金头闭壳龟栖息地产生较大影响的环境因子包括植物群落结构、溪边沙地、溪流水体环境等;野生金头闭壳龟栖息地植被多是天然林砍伐后形成的次生林、人工毛竹林和杉木林;统计样方中共有维管植物443种,分属129科232属,其中,河柳、枫杨、毛竹、水杨梅、鬼针草、线穗苔草、水蓼等植物在样方中出现频度较高(>50%)。植被的改变对金头闭壳龟生存繁殖产生很大影响,是导致金头闭壳龟濒危的主要原因之一。     

Phylogenetic diversity measures based on Hill numbers

We propose a parametric class of phylogenetic diversity (PD) measures that are sensitive to both species abundance and species taxonomic or phylogenetic distances. This work extends the conventional parametric species-neutral approach (based on 'effective number of species' or Hill numbers) to take into account species relatedness, and also generalizes the traditional phylogenetic approach (based on 'total phylogenetic length') to incorporate species abundances. The proposed measure quantifies 'the mean effective number of species' over any time interval of interest, or the 'effective number of maximally distinct lineages' over that time interval. The product of the measure and the interval length quantifies the 'branch diversity' of the phylogenetic tree during that interval. The new measures generalize and unify many existing measures and lead to a natural definition of taxonomic diversity as a special case. The replication principle (or doubling property), an important requirement for species-neutral diversity, is generalized to PD. The widely used Rao's quadratic entropy and the phylogenetic entropy do not satisfy this essential property, but a simple transformation converts each to our measures, which do satisfy the property. The proposed approach is applied to forest data for interpreting the effects of thinning.     

微生物多样性及其保育

大量实验证明因原始环境的改变使放线菌多样性急剧减少。在对微生物资源的特点及保护微生物资源的必要性进行分析的基础上,提出了保护微生物资源及其多样性的若干措施。