Computing β-diversity with Rao's quadratic entropy: a change of perspective

Ecologists have traditionally viewed β-diversity as the ratio between γ-diversity and average α-diversity. More recently, an alternative way of partitioning diversity has been proposed for which β-diversity is obtained as the difference between γ-diversity and average α-diversity. Although this additive model of diversity decomposition is generally considered superior to its multiplicative counterpart, in both models β-diversity is a formally derived quantity without any self-contained ecological meaning; it simply quantifies the diversity excess of γ-diversity with respect to average α-diversity. Taking this excess as an index of β-diversity is a questionable operation. In this paper, we show that a particular family of α-diversity measures, the most celebrated of which is Rao's quadratic entropy, can be adequately used for summarizing β-diversity. Our proposal naturally leads to a new additive model of diversity for which, given two or more sets of plots, overall plot-to-plot species variability can be additively partitioned into two non-negative components: average variability in species composition within each set of plots and the species variability between the set of plots. For conservation purposes, the suggested change of perspective in the summarization of β-diversity allows for a flexible analysis of spatial heterogeneity in ecological diversity so that different hierarchical levels of biotic relevance (i.e. from the genetic to the landscape level) can be expressed in a significant and consistent way.     

Diversity and distribution of ferns in sub-Saharan Africa, Madagascar and some islands of the South Atlantic

Aim This paper reports the diversity and endemism patterns of African ferns, and explores the potential role of diversity refuges and environmental and historical factors in the shaping of these patterns. Material and locations The extant fern taxa occupying Africa south of the Sahara, Madagascar and some islands of the South Atlantic. Methods The number of taxa in each area or operational geographical unit (OGU) was scored, and the correlation between this number and physical and climatic variables analysed by standard pairwise and stepwise multiple regression analysis (SPR and SMR). The effects of biological factors such as dispersal capacity, reproductive biology, genetic features and certain physiological adaptations were evaluated by comparing the number of species in each OGU. Floral affinities among OGUs were analysed using non‐metric multi‐dimensional scaling (NMS) and parsimonic analysis of dispersion (PAD), and compared with β‐turnover and inter‐OGU distances. Results OGU area, elevation and the distance between refuges determined the composition of local floras, but only greater OGU area and the existence of higher maximum elevations increased species richness. The distance between refuges also affected the number of endemic species, especially on islands. The biological features studied only slightly influenced fern distribution. The main climatic predictor of species number was humidity. SPR and SMR revealed three main groups of ferns with different ecological trends. NMS and PAD analyses separated the four areas of highest diversity in Africa, three of which are inhabited by ferns with distinct ecological requirements. The fourth area was Madagascar, which shows an accumulation of endemic and relict diversity that is not easy to explain. Main conclusions The distribution of ferns in Africa has been influenced by refuges. These probably allowed many species to recolonize the neighbouring areas after the extinctions of the Pleistocene. Three major components were detected in the African flora: Guinea‐Congolian thermophilous, cold‐tolerant Afro‐montane, and Southern drought‐tolerant elements. These are related to the three main refuge areas, i.e. the Gulf of Guinea area, the eastern tropical region, and the Cape region. Endemicity in ferns was found to be lower than that of seed plants due to the higher dispersability of fern spores. The distance between OGUs seems to be the main predictor of the number of endemic fern species these areas contain.     

Macroinvertebrate diversity in headwater streams: a review

1. Headwater streams are ubiquitous in the landscape and are important sources of water, sediments and biota for downstream reaches. They are critical sites for organic matter processing and nutrient cycling, and may be vital for maintaining the 'health' of whole river networks.
2. Macroinvertebrates are an important component of biodiversity in stream ecosystems and studies of macroinvertebrate diversity in headwater streams have mostly viewed stream systems as linear reaches rather than as networks, although the latter may be more appropriate to the study of diversity patterns in headwater systems.
3. Studies of macroinvertebrate diversity in headwater streams from around the world illustrated that taxonomic richness is highly variable among continents and regions, and studies addressing longitudinal changes in taxonomic richness of macroinvertebrates generally found highest richness in mid-order streams.
4. When stream systems are viewed as networks at the landscape-scale, α-diversity may be low in individual headwater streams but high β-diversity among headwater streams within catchments and among catchments may generate high γ-diversity.
5. Differing ability and opportunity for dispersal of macroinvertebrates, great physical habitat heterogeneity in headwater streams, and a wide range in local environmental conditions may all contribute to high β-diversity among headwater streams both within and among catchments.
6. Moving beyond linear conceptual models of stream ecosystems to consider the role that spatial structure of river networks might play in determining diversity patterns at the landscape scale is a promising avenue for future research.     

Do body size and diet breadth affect partitioning of species diversity? A test with forest Lepidoptera

Two of the major themes resulting from recent macroecological research are the central roles that body size and niche breadth may play as determinants of species geographical distribution. Unanswered questions, however, linger regarding how similarities in body size or niche breadth affect the allocation of α‐ and β‐diversity across spatial scales. Using data on moth diversity in the eastern deciduous forest of North America, we tested the predictions that smaller‐bodied and diet‐restricted species would have lower levels of α‐diversity within forest stands and greater β‐diversity at higher sampling scales compared to larger or more generalist species. Moths were sampled using a nested sampling design consisting of three hierarchical levels: 20 forest stands, 5 sites and 3 ecoregions. Body size for 492 species was estimated as mean forewing length, and diet breadth was assessed from the published literature. Moth species were then classified according to body size (small or large) or diet breadth (generalist or restricted), and partitioning was conducted on each group. Diversity partitions for large‐ and small‐bodied species yielded similar patterns. When observed diversity components differed from those derived from our null model, a consistent pattern was observed: α‐diversity was greater than expected, β‐diversity among forest stands was less than expected, and β‐diversity among sites and ecoregions was higher than expected. In contrast, diet‐restricted moths contributed significantly less to stand‐level α‐diversity than generalist feeders. Furthermore, specialists contributed to a greater proportion of β‐diversity across scales compared to generalist moths. Because absolute measures of β‐diversity among stands were greater for generalists than for restricted feeders, we suggest that regional β‐diversity of forest moths may be influenced by several possible factors: intraspecific aggregation of diet‐restricted species, local fluctuations in population size of eruptive generalists and small geographical distributions of generalist moths than predicted by the geographical extent of putative host plants     

Spatial gradients in species diversity of microscopic animals: the case of bdelloid rotifers at high altitude

Aim Organisms smaller than 2 mm appear not to follow the spatial patterns in richness and diversity commonly observed in macroscopic organisms. We describe spatial patterns in species diversity in a group of microscopic organisms, bdelloid rotifers, living in moss and lichen patches, in order to test the hypotheses of no relationship between species richness and composition and spatial gradients, suggested by previously published patterns in microscopic organisms. Location Moss and lichen patches as habitats for bdelloids, on high‐elevation peaks at altitudes between 2984 and 4527 m a.s.l. across the Italian, French and Swiss Alps, with distances among sample sites ranging from 1 m to 420 km, in comparison with lower‐elevation samples at altitudes from 850 to 1810 m a.s.l. Methods We sampled species assemblages of bdelloid rotifers living in isolated moss and lichen patches in 47 sites. We described the observed α, β and γ diversities; the heterogeneity of species assemblages; and the estimated number of species (incidence‐based coverage estimator). Patterns in species distribution were analysed at three different levels: (1) habitat, comparing species richness on moss and lichen substrates, testing differences in α diversity and heterogeneity (anova ), species composition (analysis of similarities test), and γ diversity (rarefaction curves); (2) altitude, comparing the observed richness with previously published data from locations well below 2000 m; and (3) distances between sites, correlating the matrix of Jaccard dissimilarities and the matrix of geographical distances with a Mantel test. Results Both species richness and species composition of bdelloid rotifers differed significantly between mosses and lichens at high elevations, but no difference was found in the heterogeneity of species assemblages. Alpha diversity was significantly lower at high‐elevation than at low‐elevation sites, but the estimated number of species was not reduced when compared with sites at low elevations. Geographical distance between sites had no effect on species composition in either mosses or lichens. The distribution of species was highly heterogeneous, with a low similarity among assemblages. Main conclusions As expected, bdelloids appear to occupy habitats selectively. The altitudinal gradient in species richness for bdelloid rotifers is limited to a decrease in α diversity only; such a decrease is not caused by a lower number of species (low γ diversity) being able to tolerate harsh conditions, and high‐altitude species are not a subset of species living at lower elevations. The observed values of α, β and γ diversity at high altitudes in the Alps are compatible with the scenario of a very low number of available propagules because of the low density of patches of favourable habitat. Our results suggest that the geographical distribution of animals, and therefore biodiversity patterns, may be strongly influenced by animal size, as small organisms such as bdelloids appear to show spatial patterns that differ from those known in larger animals. Differences in body size should be taken into account carefully in future studies of biodiversity patterns.     

ϵ-Proteobacterial diversity from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge

The prokaryotic phylogenetic diversity was determined for a sample associated with an in situ growth chamber deployed for 5 days on a Mid-Atlantic Ridge hydrothermal vent (23 degrees 22'N, 44 degrees 57'W). The DNA was extracted from the sample and the 16S rDNA amplified by PCR. No Archaea were detected in the sample. Eighty-seven clones containing bacterial 16S rDNA inserts were selected. Based on restriction fragment length polymorphism analysis, 47 clones were unique, however, based on comparative sequence analysis some of these were very similar, and thus only 22 clones were selected for full sequence and phylogenetic analysis. The phylotypes were dominated by epsilon-Proteobacteria (66%). The remainder formed a novel lineage within the Proteobacteria (33%). One clone formed a distinct deeply branching lineage, and was a distant relative of the Aquificales. This report further expands the growing evidence that epsilon-Proteobacteria are important members in biogeochemical cycling at deep-sea hydrothermal ecosystems, participating as epibionts and free living bacteria.     

广西扶绥破碎化生境中黑叶猴的食物种类多样性和季节性重叠

动物使用生境中食物种类的方式对其适应性有重要的影响。为了研究黑叶猴在破碎化栖息地中利用食物的方式,2006年1—12月,采用焦点动物取样法和连续记录技术于每月初连续观察8 d,记录破碎化栖息地中黑叶猴取食的种类和时间,分析其食物多样性和月份间种类的重叠度。结果表明,黑叶猴年均食物多样性指数为3.03(范围1.93—2.62),且多样性指数在各月间没有显著的差异(One-sample K-S Test,P=0.99),说明黑叶猴在各月份中取食的食物种数相似,不同季节利用食物种数的变异程度不大。在所有的食物种类中,仅两种食物青檀Pteroceltis tatarinowii和潺槁树Litsea glutinosa在12个月份都被取食,其他种类则表现了月份间明显的季节性替代。各月份间食物种类的相似性在0.42(3—4月)和0.75(9—10月)之间变化。黑叶猴对破碎化生境中食物种类的利用方式是:首先利用常年均有的食物种类以保证食物来源稳定,同时选择性地利用新出现的种类,使食物种类多样化,满足不同的营养需求。     

Mechanisms of positive biodiversity–production relationships: insights provided by δ13C analysis in experimental Mediterranean grassland plots

We investigated the role of water use in a Mediterranean grassland, in which diversity was experimentally manipulated, and a positive relationship was observed between plant species richness and productivity. Soil moisture patterns and stable carbon isotope ratios (δ¹³C) in leaves indicated greater water use by plants growing in species-rich mixtures compared to monocultures. These results suggest that complementarity or facilitation may be the mechanism responsible for the positive relationship between plant diversity and ecosystem processes.     

Biomass yield in a genetically diverse Miscanthus sacchariflorus germplasm panel phenotyped at five locations in Asia,North America,and Europe

Miscanthus is a high-yielding bioenergy crop that is broadly adapted to temperate and tropical environments. Commercial cultivation of Miscanthus is predominantly limited to a single sterile triploid clone of Miscanthus × giganteus, a hybrid between Miscanthus sacchariflorus and M. sinensis. To expand the genetic base of M. × giganteus, the substantial diversity within its progenitor species should be used for cultivar improvement and diversification. Here, we phenotyped a diversity panel of 605 M. sacchariflorus from six previously described genetic groups and 27 M. × giganteus genotypes for dry biomass yield and 16 yield-component traits, in field trials grown over 3 years at one subtropical location (Zhuji, China) and four temperate locations (Foulum, Denmark; Sapporo, Japan; Urbana, Illinois; and Chuncheon, South Korea). There was considerable diversity in yield and yield-component traits among and within genetic groups of M. sacchariflorus, and across the five locations. Biomass yield of M. sacchariflorus ranged from 0.003 to 34.0 Mg ha⁻¹ in year 3. Variation among the genetic groups was typically greater than within, so selection of genetic group should be an important first step for breeding with M. sacchariflorus. The Yangtze 2x genetic group (=ssp. lutarioriparius) of M. sacchariflorus had the tallest and thickest culms at all locations tested. Notably, the Yangtze 2x genetic group's exceptional culm length and yield potential were driven primarily by a large number of nodes (>29 nodes culm⁻¹ average over all locations), which was consistent with the especially late flowering of this group. The S Japan 4x, the N China/Korea/Russia 4x, and the N China 2x genetic groups were also promising genetic resources for biomass yield, culm length, and culm thickness, especially for temperate environments. Culm length was the best indicator of yield potential in M. sacchariflorus. These results will inform breeders' selection of M. sacchariflorus genotypes for population improvement and adaptation to target production environments.     

小兴安岭森林地表鞘翅目成虫对不同干扰梯度的响应

为探讨小兴安岭凉水自然保护区森林生态系统中地表鞘翅目成虫群落对不同人为干扰梯度的响应,于2015年7月、8月和10月分别对轻度干扰[原始阔叶红松林(KY)和谷地云冷杉林(YL)]、中度干扰[阔叶红松择伐林(ZF)和次生白桦林(BH)]及重度干扰[落叶松人工林(RL)和红松人工林(RHS)]的6个林型进行取样调查。结果表明:(1)整个采样周期共捕获地表鞘翅目成虫879只,隶属9科44物种;其中轻度干扰生境共捕获6科29种251只(KY捕获5科21种150只,YL捕获4科20种101只),中度干扰生境捕获6科27种276只(ZF捕获3科20种144只,BH捕获6科23种132只),重度干扰生境捕获6科29种352只(RL捕获4科22种232只,RHS捕获5科17种120只)。(2)7月和8月步甲科和葬甲科占据数量优势,10月步甲科和葬甲科成虫数量明显减少而隐翅虫科数量占优势;不同林型及不同干扰梯度地表鞘翅目成虫物种总数和总个体数于7、8、10月均表现为下降趋势,且群落多样性也呈不同程度下降。(3)林型和月份对地表鞘翅目成虫群落结构具有显著影响,干扰梯度对群落结构无显著影响;6个林型之间地表鞘翅目成虫个体数量具有显著差异,但在物种组成上无显著差异;不同干扰梯度间地表鞘翅目成虫个体数、物种数无显著差异,且随干扰梯度变化没有明显的梯度性规律;相似性系数和聚类分析表明,属于同一干扰梯度的两个林型没有表现出高度的相似性。本研究表明干扰梯度不是决定各林型间地表鞘翅目成虫群落多样性存在差异的主要原因,凉水森林生态系统地表鞘翅目成虫对不同干扰梯度的响应不符合中度干扰假说,林型和时间则是影响地表鞘翅目成虫群落组成的显著因素,本实验为地表生物多样性保护和森林生态系统管理提供数据支撑。     

Towards a knowledge of marine boundaries using ascidians as indicators: characterising transition zones for species distribution along Atlantic-Mediterranean shores

Two methodological approaches are compared with regard to their usefulness for providing explanations of observed faunal differences along Atlantic-Mediterranean coasts. A set of distribution data of ascidians containing 519 species and 80 genera was used for this purpose. Similarity methods were applied to establish the faunal affinities between distribution areas, and the measurement of β diversity and ecological distances along unidimensional gradients by non-lineal rescaling (using Detrended Correspondence Analysis) was undertaken for determining the steepness of ecotones existing along spatial gradients; these were analysed to detect the principal faunal changes, as well as their concordance with the commonly accepted limits for the classical biogeographical areas. There are fewer widely distributed species of shallow-water ascidians than in the Indo-Pacific region. Marked environmental changes within the Atlantic Ocean translate into significant differences in the composition of ascidian assemblages both in a latitudinal range and between the western and eastern sides. Few species show an amphi-Adantic range and most of these correspond with typically cosmopolitan species which are in general associated with shipping traffic or other forms of man-made transport. Three main endemism areas can be distinguished for Adantic-Mediterranean ascidian fauna involving genera and species: Caribbean, Mediterranean and south-west African. The rest of the shallow-water regions act as transitional or buffer zones where the genetic flows are generally maintained, although an increase in the number of certain species is found in some areas. This transitional role is mosdy found in the European Adantic coasts from the British Isles towards the Senegalian subregion, where gradual changes in ascidian populations occur: cold-water and tropical species at their southern and northern boundaries are substituted by temperate and subtropical species at the entrance of the Mediterranean.     

Species diversity in neutral metacommunities: a network approach

Biologists seek an understanding of the processes underlying spatial biodiversity patterns. Neutral theory links those patterns to dispersal, speciation and community drift. Here, we advance the spatially explicit neutral model by representing the metacommunity as a network of smaller communities. Analytic theory is presented for a set of equilibrium diversity patterns in networks of communities, facilitating the exploration of parameter space not accessible by simulation. We use this theory to evaluate how the basic properties of a metacommunity – connectivity, size, and speciation rate – determine overall metacommunity γ -diversity, and how that is partitioned into α - and β -components. We find spatial structure can increase γ -diversity relative to a well-mixed model, even when θ is held constant. The magnitude of deviations from the well-mixed model and the partitioning into α - and β -diversity is related to the ratio of migration and speciation rates. γ -diversity scales linearly with metacommunity size even as α - and β -diversity scale nonlinearly with size.     

中国温带荒漠区的植物多样性及其易地保护*

^{荒漠植物多样性研究及其保护是生物多样性保护的重要组成部分。 中国荒漠区植物种类贫乏（约1000余种）,分布稀疏,生物量小,起源古老,地理成份复杂（有14个地理分布型）, 特有成份多（80余种）,珍稀濒危植物种类相对较多（50～60种）,在荒漠气候和特殊的土壤基质条件下, 形成了多种生态型和特殊的生活型,为荒漠植物多样性易地保护提供了可能性和必要性。 处于亚洲荒漠区的吐鲁番沙漠植物园的研究工作,正从传统的植物引种驯化和经济植物栽培,向荒漠区系植物多样性保护领域转移,现园内保存的荒漠区系植物成份已达42.2％,特有种和珍稀濒危植物也占相当比例。 长期适应荒漠环境的各类植物具有多种多样的抗逆性基因,因而有着潜在的开发利用前景。}     

不同水盐梯度下功能多样性和功能冗余对荒漠植物群落稳定性的影响

功能多样性和功能冗余是物种多样性的两个组成部分,也是影响群落稳定性的两个重要因素。基于不同水盐梯度下植物功能多样性、功能冗余、物种多样性和群落稳定性及其相关关系的计算结果,分析功能多样性和功能冗余对群落稳定性的影响,结果表明:(1)功能多样性、物种多样性和群落稳定性均表现为高水高盐和中水中盐群落显著高于低水低盐群落(P0.05);(2)高水高盐群落,功能多样性与物种多样性的相关系数小于功能冗余与物种多样性的相关系数,且功能多样性与稳定性的相关系数也小于功能冗余与稳定性的相关系数,而中水中盐和低水低盐群落的相关系数则呈现相反的规律;(3)中水中盐和低水低盐群落的功能多样性的标准化偏回归系数均大于功能冗余的标准化偏回归系数;(4)典范对应分析中,土壤含水量可以解释总特征根的22.7%,而土壤含盐量仅可以解释总特征根的1.3%;(5)高水高盐群落的稳定比最接近20/80,稳定性最高;低水低盐群落远离20/80,稳定性最低。改进后的Godron稳定性测定方法与物种种群密度变异系数方法得出的结果相同。综上可知,功能多样性和功能冗余两者中与物种多样性关系更为密切者对群落稳定性的影响也越大,且两者均可提高群落稳定性,也就证明冗余假说在温带干旱荒漠区域的隐域性植物群落中是成立的;群落稳定性、功能多样性、功能冗余及物种多样性主要是受土壤含水量的影响,土壤含盐量对其影响较小。     

中国AM真菌的生物多样性

菌根是真菌与植物根系所建立的互惠共生体 ,其中以丛枝菌根在自然界中分布最广。AM真菌遍布各生态系统 ,不仅大量分布于农田和森林土壤 ,而且还广泛存在于多种逆境环境中。绝大多数的植物包括苔鲜、蕨类、裸子植物、被子植物都能被AM真菌侵染。我国的AM真菌研究始于 2 0世纪 80年代 ,迄今为止 ,已经对多种生态环境中多种寄主植物根围的AM真菌进行了调查研究 ,共报道了 7个属的 99种AM真菌。本文从物种多样性、生境多样性和寄主多样性等三个方面概括介绍了 2 0年来我国在AM真菌生物多样性研究中取得的进展 ,并探讨了未来的研究动向。     

中国燕麦的多样性

中国现拥有燕麦种质资源约4000份,对它们的研究结果表明,中国燕麦具有比较丰富的多样性。本文综述了中国燕麦的物种多样性和普通栽培燕麦的遗传多样性,并建议对中国各地生长的野燕麦进行系统研究。     

Genotypic and symbiotic diversity of native rhizobia nodulating red pea (Lathyrus cicera L.) in Tunisia

Nodulation and genetic diversity of native rhizobia nodulating Lathyrus cicera plants grown in 24 cultivated and marginal soils collected from northern and central Tunisia were studied. L. cicera plants were nodulated and showed the presence of native rhizobia in 21 soils. A total of 196 bacterial strains were selected and three different ribotypes were revealed after PCR-RFLP analysis. The sequence analysis of the rrs and two housekeeping genes (recA and thrC) from 36 representative isolates identified Rhizobium laguerreae as the dominant (53%) rhizobia nodulating L. cicera. To the best of our knowledge, this is the first time that this species has been reported among wild populations of the rhizobia-nodulating Lathyrus genus. Twenty-five percent of the isolates were identified as R. leguminosarum and isolates LS11.5, LS11.7 and LS8.8 clustered with Ensifer meliloti. Interestingly, five isolates (LS20.3, LS18.3, LS19.10, LS1.2 and LS21.20) were segregated from R. laguerreae and clustered as a separate clade. These isolates possibly belong to new species. According to nodC and nodA phylogeny, strains of R. laguerreae and R. leguminosarum harbored the symbiotic genes of symbiovar viciae and clustered in three different clades showing heterogeneity within the symbiovar. Strains of E. meliloti harbored symbiotic genes of Clade V and induced inefficient nodules.