How important are species richness,species evenness and interspecific differences to productivity? A mathematical model

We present a theoretical model to quantify the influence of diversity on productivity and nutrient acquisition in plant communities during exponential growth. The model fractionates diversity into three components, namely species richness ( S ), species evenness ( E ) and the degree of difference between species ( D ). The influence of each of these components is assessed individually: S is varied by changing the number of species, E by changing their population size, and D by changing the range of species traits critical to productivity (specific nutrient uptake rate, Σ _r , or nutrient use efficiency, NUE ). D was quantified as the coefficient of variation of Σ _r or NUE . All three components of diversity enhance the biomass and nutrient stocks in the community, but the response patterns are different. Species richness has a saturating influence, whereas effects of E and D are linear and exponential, respectively. In all cases the non-linear dependence of productivity and nutrient acquisition on Σ _r and NUE during exponential growth was the single mechanism underlying these effects. This causes the presence of plants with extreme traits to promote productivity, and S , E and D all affect the abundance and/or intensity of these extremes. The model offers a framework to explain differences between experimental observations, and suggests a concept of diversity where S and E are structural components and D a qualitative or functional component, which modulates the influence of the two others. We propose to explicitly recognise D as an integral constituent of plant diversity in future studies.     

Palynological richness and evenness: insights from the taxa accumulation curve

Palynology provides the opportunity to make inferences on changes in diversity of terrestrial vegetation over long time scales. The often coarse taxonomic level achievable in pollen analysis, differences in pollen production and dispersal, and the lack of pollen source boundaries hamper the application of diversity indices to palynology. Palynological richness, the number of pollen types at a constant pollen count, is the most robust and widely used diversity indicator for pollen data. However, this index is also influenced by the abundance distribution of pollen types in sediments. In particular, where the index is calculated by rarefaction analysis, information on taxonomic richness at low abundance may be lost. Here we explore information that can be extracted from the accumulation of taxa over consecutive samples. The log-transformed taxa accumulation curve can be broken up into linear sections with different slope and intersect parameters, describing the accumulation of new taxa within the section. The breaking points may indicate changes in the species pool or in the abundance of high versus low pollen producers. Testing this concept on three pollen diagrams from different landscapes, we find that the break points in the taxa accumulation curves provide convenient zones for identifying changes in richness and evenness. The linear regressions over consecutive samples can be used to inter- and extrapolate to low or extremely high pollen counts, indicating evenness and richness in taxonomic composition within these zones. An evenness indicator, based on the rank-order-abundance is used to assist in the evaluation of the results and the interpretation of the fossil records. Two central European pollen diagrams show major changes in the taxa accumulation curves for the Lateglacial period and the time of human induced land-use changes, while they do not indicate strong changes in the species pool with the onset of the Holocene. In contrast, a central Swedish pollen diagram shows comparatively little change, but high richness during the early Holocene forest establishment. Evenness and palynological richness are related for most periods in the three diagrams, however, sections before forest establishment and after forest clearance show high evenness, which is not necessarily accompanied by high palynological richness, encouraging efforts to separate the two.     

Assessing the diversity pattern of cryophilous plant species in high elevation habitats

This study aimed to better document the diversity and distribution patterns of vascular cryophilous species across major habitat types in a high-elevation Mediterranean system in central Italy. The research addressed the following questions: (a) whether different habitats support similar levels of biodiversity in terms of total vascular plants richness and cryophilous species richness, and (b) how each habitat contributes to the total cryophilous species diversity. A random stratified sampling approach based on a habitat map was applied to construct rarefaction curves for overall cryophilous species richness and habitat type-specific cryophilous richness. Rarefaction curves were also constructed for all-species and exclusive species. To determine whether the targeted species represented a constant proportion of all species, the ratio between the rarefaction curves of the cryophilous species and all species was also calculated. The results highlight the importance of the different habitat types in overall and cryophilous species conservation because these different habitat types had progressively higher richness values. At the regional scale, steep slopes had the highest species diversity, the greatest exclusive species richness and a steep rarefaction curve. The diversity pattern of cryophilous taxa was not related to the general pattern of total species richness, with these species being more common in three habitat types with extreme environmental conditions: ridges, cliffs, and screes. For the establishment of successful biodiversity conservation programs, it is imperative to include species-poor habitats containing a high proportion of cryophilous species, which are considered to be threatened by climate warming.     

It's all relative: ranking the diversity of aquatic bacterial communities

The study of microbial diversity patterns is hampered by the enormous diversity of microbial communities and the lack of resources to sample them exhaustively. For many questions about richness and evenness, however, one only needs to know the relative order of diversity among samples rather than total diversity. We used 16S libraries from the Global Ocean Survey to investigate the ability of 10 diversity statistics (including rarefaction, non-parametric, parametric, curve extrapolation and diversity indices) to assess the relative diversity of six aquatic bacterial communities. Overall, we found that the statistics yielded remarkably similar rankings of the samples for a given sequence similarity cut-off. This correspondence, despite the different underlying assumptions of the statistics, suggests that diversity statistics are a useful tool for ranking samples of microbial diversity. In addition, sequence similarity cut-off influenced the diversity ranking of the samples, demonstrating that diversity statistics can also be used to detect differences in phylogenetic structure among microbial communities. Finally, a subsampling analysis suggests that further sequencing from these particular clone libraries would not have substantially changed the richness rankings of the samples.     

Effects of anthropogenic habitat disturbance on local pollinator diversity and species turnover across a precipitation gradient

Anthropogenic habitat disturbance can have profound effects on multiple components of forest biotas including pollinator assemblages. We assessed the effect of small-scale disturbance on local richness, abundance, diversity and evenness of insect pollinator fauna; and how habitat disturbance affected species turnover across the landscape and overall diversity along a precipitation gradient in NW Patagonia (Argentina). We evaluated the effect of disturbance on overall pollinator fauna and then separately for bees (i.e. Apoidea) and non-bee pollinators. Locally, disturbed habitats had significantly higher pollinator species richness and abundances than undisturbed habitats for the whole pollinator assemblage, but not for bees or non-bees separately. However, significant differences in species richness between habitats vanished after accounting for differences in abundance between habitat types. At a local scale Shannon–Weaver diversity and evenness did not vary with disturbance. A β diversity index indicated that, across forest types, species turnover was lower between disturbed habitats than between undisturbed habitats. In addition, rarefaction curves showed that disturbed habitats as a whole accumulated fewer species than undisturbed habitats at equivalent sample sizes. We concluded that small patches of disturbed habitat have a negligible effect on local pollinator diversity; however, habitat disturbance reduced β diversity through a homogenization of the pollinator fauna (in particular of bees) across the landscape.     

Phenology of Stomoxyinae in a Kenyan forest

Abstract. The biology of nineteen taxa of African Stomoxyinae was studied during experiments with odour-baited Vavoua traps in Nairobi National Park, Kenya. Both male and female Stomoxys were captured in similar numbers with C0₂ released at 2 1/min or octenol released at 2 mg/h. Some species of Haematobosca reacted synergistically to a combination of these two attractants, producing large increases in catch. Stygeromyia and Rhinomusca responded only to C0₂, and Prostomoxys did not respond to either bait. Many different activity patterns were documented in these genera, but most activity was concentrated just prior to sunset. For example, at peak densities nearly 1500 Stomoxyinae representing fourteen taxa were caught in a single trap between 18.00 and 19.00 hours. The Stomoxyinae community was exceptionally diverse when compared with other biting fly communities. Using data from traps set with different odour baits in the park forest, Shannon-Wiener diversity indices (H') varied from 2.5 to 2.8, and evenness (J') varied between 0.61 and 0.68. The Stomoxys population was extremely female-biased at the start of the rainy season, with species such as S.inornatus and S.boueti consisting of nearly 100% females. Sex ratios equalized when the first rainy-season generation emerged. Population doubling times estimated from trap indices were approximately 12–16 days in two habitats (forest and riverine woodland).     

A global synthesis of the effects of diversified farming systems on arthropod diversity within fields and across agricultural landscapes

Agricultural intensification is a leading cause of global biodiversity loss, which can reduce the provisioning of ecosystem services in managed ecosystems. Organic farming and plant diversification are farm management schemes that may mitigate potential ecological harm by increasing species richness and boosting related ecosystem services to agroecosystems. What remains unclear is the extent to which farm management schemes affect biodiversity components other than species richness, and whether impacts differ across spatial scales and landscape contexts. Using a global metadataset, we quantified the effects of organic farming and plant diversification on abundance, local diversity (communities within fields), and regional diversity (communities across fields) of arthropod pollinators, predators, herbivores, and detritivores. Both organic farming and higher in‐field plant diversity enhanced arthropod abundance, particularly for rare taxa. This resulted in increased richness but decreased evenness. While these responses were stronger at local relative to regional scales, richness and abundance increased at both scales, and richness on farms embedded in complex relative to simple landscapes. Overall, both organic farming and in‐field plant diversification exerted the strongest effects on pollinators and predators, suggesting these management schemes can facilitate ecosystem service providers without augmenting herbivore (pest) populations. Our results suggest that organic farming and plant diversification promote diverse arthropod metacommunities that may provide temporal and spatial stability of ecosystem service provisioning. Conserving diverse plant and arthropod communities in farming systems therefore requires sustainable practices that operate both within fields and across landscapes.     

Challenges in estimating past plant diversity from fossil pollen data: statistical assessment, problems, and possible solutions

Fossil pollen data from sediment cores may be used as a measure for past plant diversity. According to the theory of probability, palynological richness is positively related to the pollen count. In a low pollen count, only common taxa are detected, whereas rare taxa are only detected by chance. The detection of all pollen taxa requires a very high pollen count, which is time-consuming. In regular palynological investigations, the detected richness in pollen spectra varies with the pollen count. Rarefaction analysis estimates palynological richness in an exactly equal-sum count for all samples, so that comparison between samples is meaningful. However, the over-representation of some taxa suppresses the detection probability of rare taxa; low total pollen abundance in a sample enhances the detection probability of rare taxa and long-distance transported pollen grains. These factors bias the observed palynological richness and distort comparisons. Palynological richness in a pollen count proportional to its pollen influx may be one proxy for reconstructing diversity trends through time. The use of this proxy overcomes most problems encountered in rarefaction analysis, but is constrained by inaccuracy in estimating pollen influx due to the imprecise time control of sediment cores. Estimating palynological richness by mathematical methods may be another way of reconstructing pollen diversity. Pollen data tend to reflect diversity on a regional scale. Sites from small basins have the advantage of recording diversity at both local and regional scales, if the detection of each taxon is independent. By associating one site from a large basin with a series of sites from very small basins (e.g. forest-hollows), information about both regional and local diversity may be obtained. Entomophilous pollen taxa may have to be measured using a different strategy than anemophilous taxa.     

Community differentiation on landscapes: drift, migration and speciation

Theories of the differentiation of ecological communities on landscapes have typically not considered evolutionary dynamics. Here we analytically study the expected differentiation among local communities in a large metacommunity, undergoing speciation, ecological drift and intercommunity dispersal, in the context of neutral theory. We demonstrate that heterogeneity in species diversity and abundance arises among communities when local communities are small and intercommunity migration is infrequent. We propose a new measure to describe community differentiation, defined as the average correlation or the average probability (C_st) that two randomly sampled individuals of the same species within local communities are from the same ancestor. The effects of driving forces (migration, mutation, and ecological drift) are incorporated into the two-level hierarchical community structure in a finite island model of neutral communities. Community differentiation can increase the effective metacommunity size or the Hubbell's fundamental species diversity in the metacommunity by a factor (1−C_st)⁻¹. Significant community differentiation arises when C_st≠0. Intercommunity migration promotes species diversity in local communities but reduce species diversity in the metacommunity. In either the finite or infinite island case, one can estimate the number of intercommunity migrants by using multiple local community datasets when the speciation is negligible in the neutral local communities, or by using the metacommunity dataset when the speciation is included in the local neutral communities. These results highlight the significance of the evolutionary mechanisms in generating heterogeneous communities in the absence of complicated ecological processes on large landscapes.     

The relationship between local and regional diversity of indigenous forest fauna in KwaZulu-Natal Province, South Africa

The relationship between local and regional diversity was tested by regressing local community richness against regional species diversity for three taxa, birds, butterflies and mammals, in subtropical forest. The quadratic model best fits the relationship between local and regional diversity for birds. Local bird species richness is theoretically independent of the size of the regional pool of species and may represent saturated communities. A linear model best describes the relationship for mammals and butterflies. For mammals, the slope is shallow (0.264) and regional richness overestimates local species richness, suggesting communities are undersaturated. Extinction filtering may explain this pattern. Past climatic changes have filtered out many mammalian species, these changes have been too recent for autochthanous speciation, and the relatively low vagility of mammals has prevented extensive recolonisation. Differences in the nature of the diversity relationship between taxa are as much due to independent evolutionary histories as to differences in vagility and colonising potential. A pervasive role is suggested for regional biogeographic processes in the development of faunal assemblage structure. Large-scale processes are not considered in current conservation plans. We encourage the shift of conservation emphasis from local ecological processes and species interactions, to whole communities and consideration of regional processes.     

Evidence that niche specialization explains species-energy relationships in lake fish communities

1. Interspecific niche differences have long been identified as a major explanation for the occurrence of species-rich communities. However, much fieldwork studying variation in local species richness has focused upon physical habitat attributes or regional factors, such as the size of the regional species pool. 2. We applied indices of functional diversity and niche overlap to data on the species niche to examine the importance of interspecific niche differentiation for species richness in French lake fish communities. We combined this information with environmental data to test generalizations of the physiological tolerance and niche specialization hypotheses for species-energy relationships. 3. We found evidence for a largely non-saturating relationship (relative to random expectation) between species richness and functional evenness (evenness of spacing between species in niche space), while functional richness (volume of niche space occupied) peaked at moderate levels of species richness and niche overlap showed an initial decrease followed by saturation. This suggests that increased niche specialization may have allowed species to coexist in the most species-rich communities. 4. We tested for evidence that increased temperature, local habitat area, local habitat diversity and immigration affected species richness via increased niche specialization. Temperature explained by far the largest amount of variation in species richness, functional diversity and niche overlap. These results, combined with the largely non-saturating species richness-functional evenness relationship, suggest that increased temperature may have permitted increased species richness by allowing increased niche specialization. 5. These results emphasize the importance of niche differences for species coexistence in species-rich communities, and indicate that the conservation of functional diversity may be vital for the maintenance of species diversity in biological communities. Our approach may be applied readily to many types of community, and at any scale, thus providing a flexible means of testing niche-based hypotheses for species richness gradients.     

Disturbance and diversity at two spatial scales

The spatial scale of disturbance is a factor potentially influencing the relationship between disturbance and diversity. There has been discussion on whether disturbances that affect local communities and create a mosaic of patches in different successional stages have the same effect on diversity as regional disturbances that affect the whole landscape. In a microcosm experiment with metacommunities of aquatic protists, we compared the effect of local and regional disturbances on the disturbance–diversity relationship. Local disturbances destroyed entire local communities of the metacommunity and required reimmigration from neighboring communities, while regional disturbances affected the whole metacommunity but left part of each local community intact. Both disturbance types led to a negative relationship between disturbance intensity and Shannon diversity. With strong local disturbance, this decrease in diversity was due to species loss, while strong regional disturbance had no effect on species richness but reduced the evenness of the community. Growth rate appeared to be the most important trait for survival after strong local disturbance and dominance after strong regional disturbance. The pattern of the disturbance–diversity relationship was similar for both local and regional diversity. Although local disturbances at least temporally increased beta diversity by creating a mosaic of differently disturbed patches, this high dissimilarity did not result in regional diversity being increased relative to local diversity. The disturbance–diversity relationship was negative for both scales of diversity. The flat competitive hierarchy and absence of a trade-off between competition and colonization ability are a likely explanation for this pattern.     

Taxonomic and functional homogenisation of macroinvertebrate communities in recently intermittent Alpine watercourses

1. Mountain streams in southwestern European Alps are currently shifting from perennial to intermittent flow due to the combined effects of climate change and local anthropogenic pressures. Given that flow intermittency is a recently documented phenomenon in the Alps, only scattered studies have investigated functional and taxonomical diversity of benthic invertebrate communities in recently intermittent Alpine streams.
2. We used a hierarchical sampling design to investigate patterns in taxonomic and functional diversity of benthic invertebrate communities in 13 recently intermittent Alpine streams in north-west Italy. in April 2017, we sampled benthic communities in two reaches of each stream with different hydrological conditions: a control reach, with permanent flow; and an intermittent reach, which recently experienced non-flow periods in summer.
3. We tested for the response of taxonomic richness at multiple spatial scales by partitioning total diversity into the average richness of local communities and the richness due to variation among local communities both within and among reaches. By partitioning total diversity (γ) into its local (α) and turnover (β) components we showed a decrease in local and regional species richness both within and among reaches, whereas variation among communities was significantly lower in intermittent reaches at the reach scale only.
4. The analysis of multidimensional trait space of macroinvertebrate communities in reaches with different hydrological conditions revealed a significant reduction of functional diversity, dispersion, and evenness in intermittent reaches. There was trait overdispersion in intermittent reaches, as these hosted both typical Alpine taxa and organisms adapted to flow intermittency. In particular, we observed the replacement of taxa with aquatic respiration and those preferring medium- to fast-flowing oligotrophic waters by taxa adapted to lentic habitats, air breathing and with larval dormancy phases.
5. These results indicate that recent flow intermittency has caused drastic changes in benthic invertebrate communities in Alpine streams. Our work highlights the importance of integrating taxonomic and functional diversity to thoroughly assess the impacts of flow intermittency.

     

Helminth communities of green frogs Rana clamitans Latreille, from southwestern Michigan.

A total of 239 green frogs Rana clamitans, collected between June 3 and August 27, 1998 from 6 locations in southwestern Michigan, was examined for helminths. Of the 26 helminth taxa found, the larval cestode Mesocestoides sp. had the highest mean intensity, followed by the larval trematode Fibricola sp. Of the helminths that mature in frogs, Haematoloechus varioplexus had the highest prevalence and Gorgodera amplicava had the highest mean intensity. Frogs from 118th Pond had the highest species richness (20), mean helminth species richness (5.2), and mean helminth abundance (153.7). Frogs from Constantine East had the highest mean helminth species diversity (0.8778) and evenness (0.6033), followed by frogs from 118th Pond. In all comparisons of mean helminth community species richness, abundance, diversity, and evenness, adult frogs had significantly higher or higher values than did juveniles at each location. Jaccard's coefficients of similarity for the helminth communities for location pairs ranged from 0.545 to 0.823. Nine and 2 core helminth taxa occurred at the local and regional levels, respectively. The differences in several helminth community measures in green frogs among locations stress the importance of local ecological conditions on helminth community structure.     

High reproducibility of ammonia-oxidizing bacterial communities in parallel sequential batch reactors

Aims:  To investigate whether the ammonia-oxidizing bacterial (AOB) communities of replicate nitrifying bioreactors (i) co-evolve or diverge over time and (ii) are stable or dynamic during periods of complete nitrification.
Methods and Results:  Three sequential batch reactors (SBR) were inoculated with sludge from a municipal wastewater treatment plant, fed with ammonium-enriched tap water and operated in parallel for 134 days. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) demonstrated co-evolvement of the AOB communities over time. During start-up, temporary decreases in nitrification were noticed, and the AOB community rate of change values (Δ _{t (week)}) were medium to high (12–22%). During the adjacent period of complete nitrification, low AOB community dynamics were observed (Δ _{t (week)} < 5%). Further pragmatic processing of the DGGE profiles revealed a high range-weighted richness and a medium functional organization of the AOB communities.
Conclusions:  After a start-up period, high functional stability and low dynamics of the AOB communities were observed. Deterministic rather than stochastic driving forces led to AOB community co-evolvement in the replicate SBR.
Significance and Impact of the Study:  Replicates in identical set-ups are reproducible, and pragmatic processing of DGGE patterns is a straightforward tool to score and compare the functionality of the bacterial communities.     

A unified index to measure ecological diversity and species rarity

Several indices have been created to measure diversity, and the most frequently used are the Shannon-Wiener (H) and Simpson (D) indices along with the number of species (S) and evenness (E). Controversies about which index should be used are common in literature. However, a generalized entropy (Tsallis entropy) has the potential to solve part of these problems. Here we explore a family of diversity indices (S_q; where q is the Tsallis index) and evenness (E_q), based on Tsallis entropy that incorporates the most used indices. It approaches S when q=0, H when q→1 and gives D when q=2. In general, varying the value of the Tsallis index (q), S_q varies from emphasis on species richness (q<1) to emphasis on dominance (q>1). Similarly, E_q also works as a tool to investigate diversity. In particular, for a given community, its minimum value represents the maximum deviation from homogeneity (E_q=1) for a particular q (herein named q*). It is remarkable that our analysis indicates that q* and its corresponding evenness, E_q*, are negatively affected by S when using simulated data. They may represent an index related to species rarity. Furthermore, S_q* (i.e. the value of S_q for a specific q*) is positively affected by richness that is an important property of any diversity index. In general, our findings indicate that the indices H, D, S, S_q*, E and E_q* are only part of a whole set of possibilities. In addition, the ecological properties of E_q* and S_q*, proposed here for the first time, show promise in ecology.     

Incorporating functional dissimilarities into sample‐based rarefaction curves: from taxon resampling to functional resampling

Question: Indices of functional diversity have been seen as the key for integrating information on species richness with measures that focus on those components of community composition related to ecosystem functioning. For comparing species richness among habitats on an equal‐effort basis, so‐called sample‐based rarefaction curves may be used. Given a study area that is sampled for species presence and absence in N plots, sample‐based rarefaction generates the expected number of accumulated species as the number of sampled plots increases from 1 to N. Accordingly, the question for this study is: can we construct a ‘functional rarefaction curve’ that summarizes the expected functional dissimilarity between species when n plots are drawn at random from a larger pool of N plots? Methods: In this paper, we propose a parametric measure of functional diversity that is obtained by combining sample‐based rarefaction techniques that are usually applied to species richness with Rao's quadratic diversity. For a given set of N presence/absence plots, the resulting measure summarizes the expected functional dissimilarity at an increasingly larger cumulative number of plots n (n≤N). Results and Conclusions: Due to its parametric nature, the proposed measure is progressively more sensitive to rare species with increasing plot number, thus rendering this measure adequate for comparing the functional diversity of species assemblages that have been sampled with variable effort.     

What is the extent of prokaryotic diversity?

The extent of microbial diversity is an intrinsically fascinating subject of profound practical importance. The term 'diversity' may allude to the number of taxa or species richness as well as their relative abundance. There is uncertainty about both, primarily because sample sizes are too small. Non-parametric diversity estimators make gross underestimates if used with small sample sizes on unevenly distributed communities. One can make richness estimates over many scales using small samples by assuming a species/taxa-abundance distribution. However, no one knows what the underlying taxa-abundance distributions are for bacterial communities. Latterly, diversity has been estimated by fitting data from gene clone libraries and extrapolating from this to taxa-abundance curves to estimate richness. However, since sample sizes are small, we cannot be sure that such samples are representative of the community from which they were drawn. It is however possible to formulate, and calibrate, models that predict the diversity of local communities and of samples drawn from that local community. The calibration of such models suggests that migration rates are small and decrease as the community gets larger. The preliminary predictions of the model are qualitatively consistent with the patterns seen in clone libraries in 'real life'. The validation of this model is also confounded by small sample sizes. However, if such models were properly validated, they could form invaluable tools for the prediction of microbial diversity and a basis for the systematic exploration of microbial diversity on the planet.     

Predation increases multiple components of microbial diversity in activated sludge communities

Protozoan predators form an essential component of activated sludge communities that is tightly linked to wastewater treatment efficiency. Nonetheless, very little is known how protozoan predation is channelled via bacterial communities to affect ecosystem functioning. Therefore, we experimentally manipulated protozoan predation pressure in activated-sludge communities to determine its impacts on microbial diversity, composition and putative functionality. Different components of bacterial diversity such as taxa richness, evenness, genetic diversity and beta diversity all responded strongly and positively to high protozoan predation pressure. These responses were non-linear and levelled off at higher levels of predation pressure, supporting predictions of hump-shaped relationships between predation pressure and prey diversity. In contrast to predation intensity, the impact of predator diversity had both positive (taxa richness) and negative (evenness and phylogenetic distinctiveness) effects on bacterial diversity. Furthermore, predation shaped the structure of bacterial communities. Reduction in top-down control negatively affected the majority of taxa that are generally associated with increased treatment efficiency, compromising particularly the potential for nitrogen removal. Consequently, our findings highlight responses of bacterial diversity and community composition as two distinct mechanisms linking protozoan predation with ecosystem functioning in activated sludge communities.Subject terms: Microbial communities, Biodiversity