The power of time: spatiotemporal scaling of species diversity

The species–area relationship (SAR) provides the foundation for much of theoretical ecology and conservation practice. However, by ignoring time the SAR offers an incomplete model for biodiversity dynamics. We used long‐term data from permanent plots in Kansas grasslands, USA, to show that the increase in the number of species found with increasing periods of observation takes the same power‐law form as the SAR. A statistical model including time, area, and their interaction explains 98% of variation in mean species number and demonstrates that while the effect of time depends on area, and vice versa, time has strong effects on species number even at relatively broad spatial scales. Our results suggest equivalence of underlying processes in space and time and raise questions about the diversity estimates currently used by basic researchers and conservation practitioners.     

Scale dependency of diversity components estimated from primary biodiversity data and distribution maps

Different sources of information about biodiversity may lead to unrealistic or biased estimation of its components, with different patterns according to the scale of analysis. In this study, we analyse patterns of species richness at the local (average alpha) and regional (gamma) scales, and the relationship between them (Whittaker's beta), in central Mexico, using as a source of data for the species' distributions: (1) museum specimen occurrence data for birds, and (2) distribution maps based on ecological niche models developed and refined by experts. We performed analyses at five spatial resolutions (1/32°−1/2°). Scale changes (grain and extent) affected significantly the estimates of average alpha, gamma, and beta. Use of raw occurrence data vs. distribution maps yielded contrasting results, with raw data underestimating alpha and overestimating beta, as functions of area. As regards species–area relationships, our results suggest a natural decomposition of factors into an area-invariant component (related to alpha), and an area dependent factor (related to beta). Most of our results are maintained in a null model that randomizes occurrences without changing observed range-size distributions. From this result we argue that average alpha and Whittaker's beta capture little information about the spatial covariation of species distribution patterns.     

Monitoring an Arizona Ponderosa Pine Restoration: Sampling Efficiency and Multivariate Analysis of Understory Vegetation

As monitoring plans for the restoration of Pinus ponderosa forests in the southwestern United States evolve toward examining multifactor ecosystem responses to ecological restoration, designing efficient sampling procedures for understory vegetation will become increasingly important. The objective of this study was to compare understory composition and diversity among thin/burn and control treatments in a P. ponderosa restoration, while simultaneously examining the effects of sampling design and multivariate analyses on which conclusions were based. Using multi‐response permutation procedures (MRPP), we tested the null hypothesis of no difference in understory species composition among treatments using different data matrices (e.g., frequency and cover) for two different sampling methods. Treatment differences were subtle and were detected by an intensive 50, 1‐m² subplot sampling method for all data matrices but were not detected by a less intensive point‐intercept sampling method for any matrix. Sampling methods examined in this study controlled results of multivariate analyses more than the data matrices used to summarize data generated by a sampling method. We partitioned data into plant life form and native/exotic species categories for MRPP, and this partitioning isolated plant groups most responsible for treatment differences. We also examined the effects of number of 1‐m² subplots sampled on mean‐species‐richness/m² estimates and found that estimates based on 10 subplots and based on 50 subplots were highly correlated (r = 0.99). Species–area curves indicated that the 50, 1‐m² subplot sampling method detected the common species of sites but failed to detect the majority of rare species. Additional sampling‐design studies are needed to develop single sampling designs that produce multifactor data on plant composition, diversity, and spatial patterns amenable to multivariate analyses as part of monitoring plans of vegetation responses to ecological restoration.     

Global patterns of diversity among the specialist birds of riverine landscapes

1. Despite the growing view that biodiversity provides a unifying theme in river ecology, global perspectives on richness in riverine landscapes are limited. As a result, there is little theory or quantitative data on features that might have influenced global patterns in riverine richness, nor are there clear indications of which riverine landscapes are important to conservation at the global scale. As conspicuous elements of the vertebrate fauna of riverine landscapes, we mapped the global distributions of all of the world's specialist riverine birds and assessed their richness in relation to latitude, altitude, primary productivity and geomorphological complexity (surface configuration). 2. Specialist riverine birds, typical of high‐energy riverine landscapes and dependent wholly or partly on production from river ecosystems, occur in 16 families. They are represented by an estimated 60 species divided equally between the passerines and non‐passerines. Major radiation has occurred among different families on different continents, indicating that birds have evolved several times into the niches provided by riverine landscapes. 3. Continental richness varies from four species in Europe to 28 in Asia, with richness on the latter continent disproportionately larger than would be expected from a random distribution with respect to land area. Richness is greatest in mountainous regions at latitudes of 20–40°N in the riverine landscapes of the Himalayan mountains, where 13 species overlap in range. 4. Family, genus and species richness in specialist riverine birds all increase significantly with productivity and surface configuration (i.e. relief). However, family richness was the best single predictor of the numbers of species or genera. In keeping with the effect of surface configuration, river‐bird richness peaks globally at 1300–1400 m altitude, and most species occur typically on small, fast rivers where they feed predominantly on invertebrates. Increased lengths of such streams in areas of high relief and rainfall might have been responsible for species–area effects. 5. We propose the hypothesis that the diversity in channel forms and habitats in riverine landscapes, in addition to high temperature and primary productivity, have been prerequisites to the development of global patterns in the richness of specialist riverine organisms. We advocate tests of this hypothesis in other taxonomic groups. We draw attention, however, to the challenges of categorically defining riverine organisms in such tests because (i) rivers grade into many other habitat types across several different ecotones and (ii) `terrestrialisation' processes in riverine landscapes means that they offer habitat for organisms whose evolutionary origins are not exclusively riverine.     

Orchids of the West Indies: predictability of diversity and endemism

Aim We examined phytogeographical patterns of West Indian orchids, and related island area and maximum elevation with orchid species richness and endemism. We expected strong species–area relationships, but that these would differ between low and montane island groups. In so far as maximum island elevation is a surrogate for habitat diversity, we anticipated a strong relationship with maximum elevation and both species richness and endemism for montane islands. Location The West Indies. Methods Our data included 49 islands and 728 species. Islands were classified as either montane (≥ 300 m elevation) or low (< 300 m). Linear and multivariate regression analyses were run to detect relationships between either area or maximum island elevation and species richness or the number of island endemic species. Results For all 49 islands, the species–area relationship was strong, producing a z‐value of 0.47 (slope of the regression line) and explaining 46% of the variation. For 18 relatively homogeneous, low islands we found a non‐significant slope of z = −0.01 that explained only 0.1% of the variation. The 31 montane islands had a highly significant species–area relationship, with z = 0.49 and accounting for 65% of the variation. Species numbers were also strongly related to maximum island elevation. For all islands < 750 km², we found a small‐island effect, which reduced the species–area relationship to a non‐significant z = 0.16, with only 5% of the variation explained by the model. Species–area relationships for montane islands of at least 750 km² were strong and significant, but maximum elevation was the best predictor of species richness and accounted for 79% of the variation. The frequency of single‐island endemics was high (42%) but nearly all occurred on just nine montane islands (300 species). The taxonomic distribution of endemics was also skewed, suggesting that seed dispersability, while remarkable in some taxa, is very limited in others. Montane island endemics showed strong species–area and species–elevation relationships. Main conclusions Area and elevation are good predictors of orchid species diversity and endemism in the West Indies, but these associations are driven by the extraordinarily strong relationships of large, montane islands. The species richness of low islands showed no significant relationship with either variable. A small‐island effect exists, but the montane islands had a significant relationship between species diversity and maximum elevation. Thus, patterns of Caribbean orchid diversity are dependent on an interplay between area and topographic diversity.     

高寒草甸不同草地群落物种多样性与生产力关系研究

生态系统的结构和功能、生物多样性与生产力的关系问题是近年来群落生态学中研究的中心问题,其中,生态系统生产力水平是其功能的重要表现形式,用4种不同草地类型探讨自然群落的物种多样性与生产力关系.结果表明,矮嵩草草甸、小嵩草草甸和金露梅灌丛群落中物种多样性与生产力的关系呈线性增加关系,藏嵩草沼泽化草甸群落中线性增加关系不显著,这表明群落生产力除受物种多样性的影响外,也受物种本身特征和环境资源的影响.不同的环境资源和环境异质性是形成群落结构特征、物种多样性分布格局差异的主要原因之一.     

Towards a more general species–area relationship: diversity on all islands, great and small

Aim

To demonstrate a new and more general model of the species–area relationship that builds on traditional models, but includes the provision that richness may vary independently of island area on relatively small islands (the small island effect).

Location

We analysed species–area patterns for a broad diversity of insular biotas from aquatic and terrestrial archipelagoes.

Methods

We used breakpoint or piecewise regression methods by adding an additional term (the breakpoint transformation) to traditional species–area models. The resultant, more general, species–area model has three readily interpretable, biologically relevant parameters: (1) the upper limit of the small island effect (SIE), (2) an estimate of richness for relatively small islands and (3) the slope of the species–area relationship (in semi‐log or log–log space) for relatively large islands.

Results

The SIE, albeit of varying magnitude depending on the biotas in question, appeared to be a relatively common feature of the data sets we studied. The upper limit of the SIE tended to be highest for species groups with relatively high resource requirements and low dispersal abilities, and for biotas of more isolated archipelagoes.

Main conclusions

The breakpoint species–area model can be used to test for the significance, and to explore patterns of variation in small island effects, and to estimate slopes of the species–area (semi‐log or log–log) relationship after adjusting for SIE. Moreover, the breakpoint species–area model can be expanded to investigate three fundamentally different realms of the species–area relationship: (1) small islands where species richness varies independent of area, but with idiosyncratic differences among islands and with catastrophic events such as hurricanes, (2) islands beyond the upper limit of SIE where richness varies in a more deterministic and predictable manner with island area and associated, ecological factors and (3) islands large enough to provide the internal geographical isolation (large rivers, mountains and other barriers within islands) necessary for in situ speciation.

     

Species diversity and endemism of five major Malesian islands: diversity–area relationships

Aim A comparison of biodiversity patterns within Malesia in relation to surface area. Location Analysis of the patterns in species richness and endemism of vascular plants in the five major Malesian islands, i.e. Java, Sulawesi, Sumatra, Borneo and New Guinea. Methods Available data on species richness and species ranges in correlation with the surface area of the respective islands were examined in this work. Estimations of total species numbers for these islands are presented based on extrapolation of all available published Flora Malesiana information and recent checklists, all in all comprising 12,000 different species. The regression analysis of overall species richness and endemism were studied for all species together as well as for different plant families to compare the fit with the Arrhenius species–area model. Results The five islands form a series of independent areas of increasing size suited for an analysis of the species–area relationships at the regional scale. All species taken together and those of families with even distribution throughout Malesia show significant species–area relationships. Non‐significant relationships were detected in families with western or eastern‐centred Malesian distribution patterns. Relationships between number of endemic species and surface area are significant for all species and for the majority of the families with significant species–area relationships. Main conclusions Species–area relationships of families appear to be dependent on species number. Families with high numbers of species usually have a significant species–area relationship whereas small families have not. For the families that display an eastern or western Malesian centred pattern, a historical biogeographical explanation should be invoked. Island surface area appears to be a predictor for island percent endemism in Malesian vascular plants. None of the islands appears to be a hotspot of endemism nor of species diversity, as no significant departure from the Arrhenius model was noted for any of them.     

环境梯度下蒙古栎群落的物种多样性特征

通过样地法研究了东北地区处于不同经度、纬度和海拔的 13个地点蒙古栎群落的物种丰富度、Gini指数、PIE指数、Shannon指数和 Pielou指数 ,利用相关和回归的统计方法分析了不同地点物种的丰富度指数、Simpson多样性指数和 Shannon多样性指数与各地所处的经度、纬度和海拔的关系。结果发现 :不仅不同地点 (较大尺度 )的物种丰富度和多样性指数均有差异 ,即使在相同的地点 (较小尺度 ) ,物种丰富度及多样性指数也有差异 ,有时还具有很大的差异 ,呈现空间异质性分布的特征 ;因为影响这些多样性指数的环境因子更加复杂 ,不仅受经度、纬度和海拔的影响 ,也受地形、群落的年龄、干扰史等多种生态因子影响。不同地点的物种丰富度与海拔和纬度都具有明显的相关性 (p<0 .0 5 ) ,物种丰富度随海拔和纬度的升高而降低 ,依据显著度的大小可以推测物种丰富度与海拔的相关性比与纬度的相关性更密切 ;蒙古栎群落不同类群的植物种的丰富度具有不同的分布格局 ,木本植物的丰富度与当地纬度具有明显的相关性 (p<0 .0 5 ) ,而与所在地的海拔没有显著的关系 (p>0 .0 5 ) ,而草本植物受海拔的影响更显著 (p<0 .0 5 ) ,而与纬度之间没有显著的关系 (p>0 .0 5 )。群落的 Gini指数、PIE指数、Shannon指数和Pielou指数未发现与海     

盐度对滨海土壤细菌多样性和群落构建过程的影响

滨海盐土是重要的农业土地后备资源.微生物是土壤中物质循环的关键动力,然而盐度对土壤微生物群落特征影响的研究还很缺乏.本研究采集滨海地区的土壤样品,研究非盐、轻盐和高盐3组不同盐度对土壤细菌数量、多样性和群落构建的影响.结果表明:与非盐和轻盐土壤相比,高盐土壤的脱氢酶活性和细菌数量显著降低,而细菌α多样性没有变化,细菌群...     

Diversity of rodent and shrew assemblages in different vegetation types of the savannah biome in South Africa: no evidence for nested subsets or competition

Identifying nonrandom species composition patterns predicted by assembly rules has been a central theme in community ecology. Few studies have investigated the prevalence of multiple drivers on species composition patterns in small mammal assemblages in the Old World. This study investigated seasonal changes in rodent and shrew diversity in eleven savannah vegetation types in South Africa. We tested whether species composition patterns are nonrandom with respect to predictions from Diamond's assembly rules, niche limitation hypothesis and nestedness hypothesis. Species richness estimators indicated that inventories for the rodents (80%) and shrews (100%) were relatively complete. Rodent (n = 11 species) diversity and shrew (n = 5 species) diversity were highest in summer and lowest in autumn. Rodent richness was highest in the Terminalia sericea bushveld and woodlands and lowest in the Drypetes arguta sand forest, whilst shrew richness was highest in the T. sericea bushveld and woodlands and lowest in the Acacia nilotica/Dichrostachys cinerea open shrub savannah. We found no support for the predictions of competition and nestedness hypotheses and suggest that this was probably due to the high seasonal and annual variability in rodent and shrew diversity.     

Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach

A highly diverse T-cell receptor (TCR) repertoire is a fundamental property of an effective immune system, and is associated with efficient control of viral infections and other pathogens. However, direct measurement of total TCR diversity is impossible. The diversity is high and the frequency distribution of individual TCRs is heavily skewed; the diversity therefore cannot be captured in a blood sample. Consequently, estimators of the total number of TCR clonotypes that are present in the individual, in addition to those observed, are essential. This is analogous to the ‘unseen species problem’ in ecology. We review the diversity (species richness) estimators that have been applied to T-cell repertoires and the methods used to validate these estimators. We show that existing approaches have significant shortcomings, and frequently underestimate true TCR diversity. We highlight our recently developed estimator, DivE, which can accurately estimate diversity across a range of immunological and biological systems.     

Biodiversity and species competition regulate the resilience of microbial biofilm community

The relationship between biodiversity and ecosystem stability is poorly understood in microbial communities. Biofilm communities in small bioreactors called microbial electrolysis cells (MEC) contain moderate species numbers and easy tractable functional traits, thus providing an ideal platform for verifying ecological theories in microbial ecosystems. Here, we investigated the resilience of biofilm communities with a gradient of diversity, and explored the relationship between biodiversity and stability in response to a pH shock. The results showed that all bioreactors could recover to stable performance after pH disturbance, exhibiting a great resilience ability. A further analysis of microbial composition showed that the rebound of Geobacter and other exoelectrogens contributed to the resilient effectiveness, and that the presence of Methanobrevibacter might delay the functional recovery of biofilms. The microbial communities with higher diversity tended to be recovered faster, implying biofilms with high biodiversity showed better resilience in response to environmental disturbance. Network analysis revealed that the negative interactions between the two dominant genera of Geobacter and Methanobrevibacter increased when the recovery time became longer, implying the internal resource or spatial competition of key functional taxa might fundamentally impact the resilience performances of biofilm communities. This study provides new insights into our understanding of the relationship between diversity and ecosystem functioning.     

Regional patterns of diversity and estimates of global insect species richness

The total number of insect species in the world is an important if elusive figure. We use a fresh approach to estimate global insect species richness, based on biogeographic patterns of diversity of well or better documented taxa. Estimates generated by various calculations, all variations on a theme, largely serve to substantiate suggestions that insect species are likely to number around 10 million or less.     

Community ecology of absent species: hidden and dark diversity

Community ecologists have so far focused mainly on species identified at a site. I suggest that we can understand better patterns and their underlying processes in ecological communities if we also examine those species absent from the sampled community. However, there are various types of absences, which all harbour different information. Hidden diversity comprises species that are absent from our sight: dormant or locally very rare species overlooked by traditional sampling. Fortunately, modern DNA‐based techniques can help us to find hidden species when analysing environmental samples. Depending on habitat type and sampling scale, a large number of co‐existing species might be hidden. Dark diversity comprises absent species that constitute the habitat‐specific species pool. Dark diversity can be determined based on data on species distribution, dispersal potential and ecological requirements. If we know both observed and dark diversity, we can estimate community completeness and infer those processes that determine which species in the species pool actually co‐exist locally. In addition, most species in the world do not actually belong to the habitat‐specific species pool of the community: their ecological requirements differ or their distribution area is elsewhere. Such other absent species are usually not directly relevant to a particular community. However, knowing ecologically suitable species from other regions can give early warning of possible future invasion of alien species (alien dark diversity). To conclude, species presences have meaning only if there are absences (and vice versa). Methods to detect absent species are rapidly developing and will soon form a standard toolbox for community ecology.