Use of invertebrate traits for the biomonitoring of European large rivers: the effects of sampling effort on genus richness and functional diversity

1. Studies on biodiversity and ecosystem function require considering metrics for accurately describing the functional diversity of communities. The number of taxa (richness) is commonly used to characterise biological diversity. The disadvantage of richness as a measure of biological diversity is that all taxa are taken into account on an equal basis regardless of their abundance, their biological characteristics or their function in the ecosystem. 2. To circumvent this problem, we applied a recently described measure of biological diversity that incorporates dissimilarities among taxa. Dissimilarities were defined from biological traits (e.g. life history, morphology, physiology and behaviour) of stream invertebrate taxa and the resulting biological diversity index was considered as a surrogate for functional diversity. 3. As sampling effort is known to affect the number of taxa collected within a reach, we investigated how change in functional diversity is affected by sampling effort. We used stream invertebrate community data from three large European rivers to model accumulation curves and to assess the number of samples required to estimate (i.e. closeness to the maximal value) functional diversity and genera richness. We further evaluated the precision of estimates (i.e. similarity of temporal or spatial replicates) of the total functional diversity. 4. As expected, richness estimates were strongly dependent on sampling effort, and 10 replicate samples were found to underestimate actual richness. Moreover, richness estimates showed much variation with season and location. In contrast, functional diversity had greater accuracy with less sampling effort and the precision of the estimates was higher than richness both across sampling occasions and sampling reaches. These results are further arguments towards conducting research on the design of a biomonitoring tool based on biological traits.     

Stream order-dependent diversity metrics of epilithic diatom assemblages

Diatoms are considered as an appropriate indicator group for ecological status assessment of surface waters. These organisms can be indicative not only of the waterchemical but also of the hydro-morphological characteristics (e.g., stream size, physical habitat diversity) of running waters. In this study, diatom diversity metrics (species number, Shannon diversity, and evenness) from 506 sites in Pannon ecoregion (Hungary) were compared to the Strahler stream order system established with ArcView GIS 3.2. SOM analyses were performed to exclude the effect of nutrients on diversity metrics along the stream orders. Mixed-effects linear models and Tukey’s post hoc test revealed a linear relationships between species number, diversity and stream orders on ecoregion level from first- to eighth-order streams. The species number increases with an average of 8%, and the diversity by 10% per unit increase of the stream order. However, we could not find relationships with evenness. Autotrophic diversity metrics based on diatom species data appear to increase parallel with the stream order while those of heterotrophic metrics (published in the literature) maximize at medium stream orders. We argue that stream order is a relevant typological parameter which can basically determine the diatom diversity metrics, and it is well applicable in biomonitoring.     

Enhancing the performance and interpretation of freshwater biological indices: An application in arid zone streams

We assessed the performance of biological indices developed for invertebrate assemblages occurring in arid zone streams: a multimetric index (MMI) and an O/E index of taxonomic completeness. Our overall goal was to advance our understanding of the factors that affect performance and interpretation of biological indices. Our specific objectives were to (1) develop biological indices that are insensitive to natural environmental gradients, (2) develop a general method to determine if the biological potential of an assessed site is adequately represented by the population of reference sites, (3) develop a robust method to select metrics for inclusion in MMIs that ensures maximum independence of metrics, and (4) determine if a fundamental sample property (the evenness of taxa counts within a sample) affects index performance. Random Forest modeling revealed that both individual metrics and taxa composition were strongly associated with natural environmental heterogeneity, which meant both the MMI and O/E index needed to be based on site-specific expectations. We produced a precise, responsive, and ecologically robust MMI by using principal components analysis to identify 7 statistically independent metrics from a list of 31 candidate assemblage-level metrics. However, the O/E index we developed was relatively imprecise compared with O/E indices developed for other regions. This imprecision may be the consequence of low predictability in local taxa composition associated with the relatively high spatial isolation of aquatic habitats within arid regions. We were also able to assess the likelihood that the biological potential of assessed sites were adequately characterized by the population of reference sites by developing and applying a multivariate, nearest-neighbor test that determined if an assessed site occurred within the environmental space of the reference site network. This approach is robust and applicable to all biological indices. We also demonstrate that the evenness of taxa counts within a sample is positively related to estimates of sample taxa richness and thus the scores of both indices. The relationship between richness and sample evenness can potentially compromise inferences regarding biological condition, and post hoc adjustments for the effects of evenness on index scores might be desirable. Further improvements in the performance and interpretation of biological indices will require simultaneous consideration of the effects of incomplete sampling on characterization of biological assemblages and the physical and biological factors that influence community assembly.     

着生藻类和浮游藻类在三峡库区河流健康评价中的适宜性比较研究

藻类对水体环境变化敏感,其种类和数量与环境因素有密切联系并因环境的变化而发生变化,因此藻类常作为河流健康评价的指示生物。水体中的藻类根据生活习性不同分为着生藻类和浮游藻类,在河流健康评价中,以往的工作中有的采用浮游藻类用于河流健康评价,有的采用着生藻类用于评价,但浮游藻类和着生藻类究竟何者用于河流健康评价更适宜,抑或是二者在用于评价的适宜性上没有明显差别,迄今为止未开展过深入研究。选择三峡库区内的两条河流嘉陵江和乌江作为研究对象,于2015年9月,在两条河流上共布设11个研究断面,对嘉陵江、乌江的水环境理化因子、着生藻类和浮游藻类群落进行调查研究,应用着生藻类生物完整性指数(Periphytic algal index of biological integrity,Pe-IBI)和浮游藻类生物完整性指数(Phytoplankton index of biological integrity,Ph-IBI),并结合水体综合污染指数(Comprehensive pollution index,CPI),对嘉陵江、乌江的健康状况进行评价。研究结果表明,采用着生藻类生物完整性评价(Pe-IB...     

UV RADIATION,PHOSPHORUS, AND THEIR COMBINED EFFECTS ON THE TAXONOMIC COMPOSITION OF PHYTOPLANKTON IN A BOREAL LAKE1

We examined how UV radiation and phosphorus (P) affect the taxonomic composition, abundance, and biomass of phytoplankton in an oligotrophic boreal lake. We exposed phytoplankton to three different solar radiation regimes (PAR + UV‐A radiation [UVAR]+ UV‐B radiation [UVBR], PAR + UVAR, and PAR only) and to five levels of P. The biomass of small chrysophytes was reduced by 350% after exposure to PAR + UVAR + UVBR compared with PAR only. No other taxa were found to be negatively affected by exposure to UVBR. Several taxa (e.g. Chry‐ sochromulina laurentiana Kling) were sensitive to UVAR, whereas others (e.g. Tabellaria flocculosa (Roth) Kutzing) were not affected by UV radiation exposure. Principal components analysis ordination separated phytoplankton that were negatively affected by UV radiation and/or positively affected by P treatments (e.g. small chrysophytes, Cryptomonas rostratiformis, T. flocculosa) from those that generally were unaffected by either treatment (e.g. desmids, some Cyanobacteria). Richness, Shannon‐Weaver diversity, and evenness were significantly higher in phytoplankton communities shielded from UVAR and UVBR. The relationship between diversity and richness was positive in all phytoplankton samples except in those exposed to UVBR. Thus, UVBR‐exposed phytoplankton communities were dominated by a few species even though the number of taxa remained relatively unchanged. Consequently, alterations in the UV environments of lakes resulting from climate warming (e.g. drought) and land‐use change (e.g. increased P export) will likely promote shifts in the community composition of lake phytoplankton.     

From Sea to Sea: Canada's Three Oceans of Biodiversity

Evaluating and understanding biodiversity in marine ecosystems are both necessary and challenging for conservation. This paper compiles and summarizes current knowledge of the diversity of marine taxa in Canada''s three oceans while recognizing that this compilation is incomplete and will change in the future. That Canada has the longest coastline in the world and incorporates distinctly different biogeographic provinces and ecoregions (e.g., temperate through ice-covered areas) constrains this analysis. The taxonomic groups presented here include microbes, phytoplankton, macroalgae, zooplankton, benthic infauna, fishes, and marine mammals. The minimum number of species or taxa compiled here is 15,988 for the three Canadian oceans. However, this number clearly underestimates in several ways the total number of taxa present. First, there are significant gaps in the published literature. Second, the diversity of many habitats has not been compiled for all taxonomic groups (e.g., intertidal rocky shores, deep sea), and data compilations are based on short-term, directed research programs or longer-term monitoring activities with limited spatial resolution. Third, the biodiversity of large organisms is well known, but this is not true of smaller organisms. Finally, the greatest constraint on this summary is the willingness and capacity of those who collected the data to make it available to those interested in biodiversity meta-analyses. Confirmation of identities and intercomparison of studies are also constrained by the disturbing rate of decline in the number of taxonomists and systematists specializing on marine taxa in Canada. This decline is mostly the result of retirements of current specialists and to a lack of training and employment opportunities for new ones. Considering the difficulties encountered in compiling an overview of biogeographic data and the diversity of species or taxa in Canada''s three oceans, this synthesis is intended to serve as a biodiversity baseline for a new program on marine biodiversity, the Canadian Healthy Ocean Network. A major effort needs to be undertaken to establish a complete baseline of Canadian marine biodiversity of all taxonomic groups, especially if we are to understand and conserve this part of Canada''s natural heritage.     

Ecological quality scales based on phytoplankton for the implementation of Water Framework Directive in the Eastern Mediterranean

Structural changes of phytoplankton communities, often expressed through ecological indices, constitute one of the metrics for the implementation of the European Water Framework Directive (WFD). In the current study a thorough analysis of the efficiency of 22 ecological indices was performed and a small number was selected for the development of five-level water quality scales (High, Good, Moderate, Poor, and Bad). The analysis was performed on simulated communities free of the noise of field communities due to uncontrolled factors or stochastic processes. Two criteria were set for the sensitivity of indices, namely their monotonicity and linearity across the studied eutrophication spectrum. The whole procedure was based on the development of a five-level quality assessment scheme based on phytoplankton abundance. Among the indices tested, the Menhinick diversity index and three indices of evenness were the most efficient, showing consistency (monotonic behavior) and linearity and were therefore used for the development of quality scales for the WFD. An Integrated Phytoplankton Index (IPI) based on three phytoplankton metrics, chlorophyll a, abundance, and diversity is also proposed. The efficiency of these indices was evaluated for a number of sites in the Aegean, already classified in the past by various methods based on nutrient concentrations or phytoplankton data. The results indicate that the various phytoplankton metrics (chlorophyll a, abundance, and diversity) assessed or proposed in the current study, carry their own information showing differences in the final classification of areas. Therefore the establishment of synthetic indices as the IPI seems to be advantageous for the integrated assessment of coastal water quality in the framework of European policies as the WFD.     

Influence of macroinvertebrate sample size on bioassessment of streams

In order to standardise biological assessment of surface waters in Europe, a standardised method for sampling, sorting and identification of benthic macroinvertebrates in running waters was developed during the AQEM project. The AQEM method has proved to be relatively time-consuming. Hence, this study explored the consequences of a reduction in sample size on costs and bioassessment results. Macroinvertebrate samples were collected from six different streams: four streams located in the Netherlands and two in Slovakia. In each stream 20 sampling units were collected with a pond net (25×25 cm), over a length of approximately 25 cm per sampling unit, from one or two habitats dominantly present. With the collected data, the effect of increasing sample size on variability and accuracy was examined for six metrics and a multimetric index developed for the assessment of Dutch slow running streams. By collecting samples from separate habitats it was possible to examine whether the coefficient of variation (CV; measure of variability) and the mean relative deviation from the “reference” sample (MRD; measure of accuracy) for different metrics depended only on sample size, or also on the type of habitat sampled. Time spent on sample processing (sorting and identification) was recorded for samples from the Dutch streams to assess the implications of changes in sample size on the costs of sample processing. Accuracy of metric results increased and variability decreased with increasing sample size. Accuracy and variability varied depending on the habitat and the metric, hence sample size should be based on the specific habitats present in a stream and the metric(s) used for bioassessment. The AQEM sampling method prescribes a multihabitat sample of 5 m. Our results suggest that a sample size of less than 5 m is adequate to attain a CV and MRD of ≤ 10% for the metrics ASPT (Average Score per Taxon), Saprobic Index and type Aka+Lit+Psa (%) (the percentage of individuals with a preference for the akal, littoral and psammal). The metrics number of taxa, number of individuals and EPT-taxa (%) required a multihabitat sample size of more than 5 m to attain a CV and MRD of ≤ 10%. For the metrics number of individuals and number of taxa a multihabitat sample size of 5 m is not even adequate to attain a CV and MRD of ≤ 20%. Accuracy of the multimetric index for Dutch slow running streams can be increased from ≤ 20 to ≤ 10% with an increase in labour time of 2 h. Considering this low increase in costs and the possible implications of incorrect assessment results it is recommended to strive for this ≤ 10% accuracy. To achieve an accuracy of ≤ 10% a multihabitat sample of the four habitats studied in the Netherlands would require a sample size of 2.5 m and a labour time of 26 h (excluding identification of Oligochaeta and Diptera) or 38 h (including identification of Oligochaeta and Diptera). Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Relationships between the Seasonal Variations of Macroinvertebrates,and Land Uses for Biomonitoring in the Xitiaoxi River Watershed,China

The impacts of differences in watershed land uses, and differences in seasonality on benthic macroinvertebrate communities, were evaluated in 12 stream sites within the Xitiaoxi River watershed, China, from April 2009 to January 2010. The composition of macroinvertebrate community differed significantly among three land use types. Forested sites were characterized by high taxa richness, diversity and the benthic‐index of biotic integrity (B‐IBI), while farmland and urban disturbed stream sites presented contrary patterns. The percentage of urban land use, conductivity, dissolved oxygen, ammonia nitrogen and total phosphorus were the major drivers for the variations. The land use related water quality stress gradients of the four sampling seasons were determined by means of four independent Principal Component Analyses. The responses of macroinvertebrate community metrics, to anthropogenic stressors, were explored using Spearman Rank Correlation analyses. All the selected metrics, including total numbers of taxa, numbers of Ephemeroptera, Plecoptera and Trichoptera taxa, percentage of non‐insect abundance, percentage of scrapers abundance, Pielou’s evenness index, Simpson diversity index, and the Benthic Index of Biotic Integrity were correlated significantly with environmental gradients (PC1) in autumn. In other seasons such correlations were less pronounced. Our results imply that autumn is the optimal time to sample macroinvertebrate communities, and to conduct water quality biomonitoring in this subtropical watershed. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Development of a macroinvertebrate multimetric index for the assessment of low-land streams in the neotropics

The water and habitat quality in Panamanian streams and rivers are being degraded by agriculture, urbanization, industrial activities, mining, and other forms of development. Thus, the need for standards, especially those examining the biological attributes of lotic systems, are urgently required. We describe the development of a multimetric index based on macroinvertebrates collected in low-land streams in the Panama Canal Watershed (PCW), which differed in their levels of human impacts. The index was developed using 12 streams and validated using a further three, all of which were sampled on four occasions, in the dry and wet seasons of 2007 and 2008. We examined 42 metrics related to macroinvertebrate community structure, composition, and function. Based on their ability to distinguish reference from moderately or severely impacted streams, and on their independence, we selected seven metrics (Margalef's index (taxa), Shannon's evenness index (taxa), number of EPT (taxa), % of Trichoptera, ratio of Chironomidae/Diptera individuals, % of scrapers, and % of shredders). These metrics were then standardized and developed into the Neotropical Low-land Stream Multimetric Index (NLSMI). Overall, the NLSMI distinguished well among the different levels of impairment (Reference, Moderate impact, and Severe impact) and showed a strong, significant correlation with principal component analysis (PCA) axis one values, with the PCA based on a set of physico-chemical variables indicative of stream quality. The wet season generally resulted in lower NLSMI values, leading us to suggest that sampling for biomonitoring be carried out in the dry season. Overall, this preliminary macroinvertebrate NLSMI shows promise for developing a biomonitoring programme to assess the ecological integrity of streams, to aid with management, restoration, and conservation, and to serve as a basis to develop a more geographically extensive multimetric index.     

Taxonomic and functional diversity covary in rock pool microalgal communities despite their different drivers

Local biodiversity has traditionally been estimated with taxonomic diversity metrics such as species richness. Recently, the concept of biodiversity has been extended beyond species identity by ecological traits determining the functional role of a species in a community. This interspecific functional diversity typically responds more strongly to local environmental variation compared with taxonomic diversity, while taxonomic diversity may mirror more strongly dispersal processes compared with functional metrics. Several trait‐based indices have been developed to measure functional diversity for various organisms and habitat types, but studies of their applicability on aquatic microbial communities have been underrepresented. We examined the drivers and covariance of taxonomic and functional diversity among diatom rock pool communities on the Baltic Sea coast. We quantified three taxonomic (species richness, Shannon''s diversity, and Pielou''s evenness) and three functional (functional richness, evenness, and divergence) diversity indices and determined abiotic factors best explaining variation in these indices by generalized linear mixed models. The six diversity indices were highly collinear except functional evenness, which merely correlated significantly with taxonomic evenness. All diversity indices were always explained by water conductivity and temperature–sampling month interaction. Taxonomic diversity was further consistently explained by pool distance to the sea, and functional richness and divergence by pool location. The explained variance in regression models did not markedly differ between taxonomic and functional metrics. Our findings do not clearly support the superiority of neither set of diversity indices in explaining coastal microbial diversity, but rather highlight the general overlap among the indices. However, as individual metrics may be driven by different factors, the greatest advantage in assessing biodiversity is nevertheless probably achieved with a simultaneous application of the taxonomic and functional diversity metrics.     

Sampling strategies for the assessment of tree species diversity

Abstract. This paper aims at proposing efficient vegetation sampling strategies. It describes how the estimation of species richness and diversity of moist evergreen forest is affected by (1) sampling design (simple random sampling, random cluster sampling, systematic cluster sampling, stratified cluster sampling); (2) choice of species richness estimators (number of observed species vs. non-parametric estimators) and (3) choice of diversity index (Simpson vs. Shannon). Two sites are studied: a 28-ha area situated in the Western Ghats of India and a 25-ha area located at Pasoh in Peninsular Malaysia. The results show that: (1) whatever the sampling strategy, estimates of species richness depend on sample size in these very diverse forest ecosystems which contain many rare species; (2) Simpson's diversity index reaches a stable value at low sample sizes while Shannon's index is affected more by the addition of rare species with increasing sample size; (3) cluster sampling strategies provide a good compromise between cost and statistical efficiency; (4) 300 - 400 sample trees grouped in small clusters (10–50 individuals) are enough to obtain unbiased and precise estimates of Simpson's index; (5) the local topography of the Western Ghats has a major influence on forest composition, the steep slopes being richer and more diverse than the ridges and gentle slopes; (6) stratified cluster sampling is thus an interesting alternative to systematic cluster sampling.     

Species–area relationships in the Andaman and Nicobar Islands emerge because rarer species are disproportionately favored on larger islands

The island species–area relationship (ISAR) describes how the number of species increases with increasing size of an island (or island‐like habitat), and is of fundamental importance in island biogeography and conservation. Here, we use a framework based on individual‐based rarefaction to infer whether ISARs result from passive sampling, or whether some processes are acting beyond sampling (e.g., disproportionate effects and/or habitat heterogeneity). Using data on total and relative abundances of four taxa (birds, butterflies, amphibians, and reptiles) from multiple islands in the Andaman and Nicobar archipelago, we examine how different metrics of biodiversity (total species richness, rarefied species richness, and abundance‐weighted effective numbers of species emphasizing common species) vary with island area. Total species richness increased for all taxa, as did rarefied species richness controlling for a given sampling effort. This indicates that the ISAR did not result because of passive sampling, but that instead, some species were disproportionately favored on larger islands. For birds, frogs, and lizards, this disproportionate effect was only associated with species that were rarer in the samples, but for butterflies, both more common and rarer species were affected. Furthermore, for the two taxa for which we had plot‐level data (reptiles and amphibians), within‐island β‐diversity did not increase with island size, suggesting that within‐island compositional effects were unlikely to be driving these ISARs. Overall, our results indicate that the ISARs of these taxa are most likely driven by disproportionate effects, that is, where larger islands are important sources of biodiversity beyond a simple sampling expectation, especially through their influence on rarer species, thus emphasizing their role in the preservation and conservation of species.     

A unified mathematical framework for the measurement of richness and evenness within and among multiple communities

Biodiversity can be divided into two aspects: richness (the number of species or other taxa in a community or sample) and evenness (a measure of the distribution of relative abundances of different taxa in a community or sample). Sample richness is typically evaluated using rarefaction, which normalizes for sample size. Evenness is typically summarized in a single value. It is shown here that Hurlbert's probability of interspecific encounter (Δ₁), a commonly used sample-size independent measure of evenness, equals the slope of the steepest part of the rising limb of a rarefaction curve. This means that rarefaction curves provide information on both aspects of diversity. In addition, regional diversity (gamma) can be broken down into the diversity within local communities (alpha) and differences in taxonomic composition among local communities (beta). Beta richness is expressed by the difference between the composite rarefaction curve of all samples in a region with the collector's curve for the same samples. The differences of the initial slopes of these two curves reflect the beta evenness thanks to the relationship between rarefaction and Δ₁. This relationship can be further extended to help interpret species-area curves (SAC's). As previous authors have described, rarefaction provides the null hypothesis of passive sampling for SAC's, which can be interpreted as regional collector's curves. This allows evaluation of richness and evenness at local and regional scales using a single family of well-established, mathematically related techniques.     

Reexamining Sample Size Requirements for Multivariate,Abundance-Based Community Research: When Resources are Limited,the Research Does Not Have to Be

Community ecologists commonly perform multivariate techniques (e.g., ordination, cluster analysis) to assess patterns and gradients of taxonomic variation. A critical requirement for a meaningful statistical analysis is accurate information on the taxa found within an ecological sample. However, oversampling (too many individuals counted per sample) also comes at a cost, particularly for ecological systems in which identification and quantification is substantially more resource consuming than the field expedition itself. In such systems, an increasingly larger sample size will eventually result in diminishing returns in improving any pattern or gradient revealed by the data, but will also lead to continually increasing costs. Here, we examine 396 datasets: 44 previously published and 352 created datasets. Using meta-analytic and simulation-based approaches, the research within the present paper seeks (1) to determine minimal sample sizes required to produce robust multivariate statistical results when conducting abundance-based, community ecology research. Furthermore, we seek (2) to determine the dataset parameters (i.e., evenness, number of taxa, number of samples) that require larger sample sizes, regardless of resource availability. We found that in the 44 previously published and the 220 created datasets with randomly chosen abundances, a conservative estimate of a sample size of 58 produced the same multivariate results as all larger sample sizes. However, this minimal number varies as a function of evenness, where increased evenness resulted in increased minimal sample sizes. Sample sizes as small as 58 individuals are sufficient for a broad range of multivariate abundance-based research. In cases when resource availability is the limiting factor for conducting a project (e.g., small university, time to conduct the research project), statistically viable results can still be obtained with less of an investment.     

Impact of biased sampling effort and spatial uncertainty of locations on models of plant invasion patterns in Croatia

Very frequently biological databases are used for analysing distribution of different taxa. These databases are usually the result of variable sampling effort and location uncertainty. The aim of this study was to test the influence of geographically biased sampling effort and spatial uncertainty of locations on models of species richness. For this purpose, we assessed the pattern of invasive alien plants in Croatia using the Flora Croatica Database. The procedure applied in testing of the sensitivity of models consisted of sample area sectioning into coherent ecological classes (hereinafter Gower classes). The quadrants were then ranked based on sampling effort per class. This resulted in creation of models using varying numbers of quadrants whose performance was tested with independent validation points. From this the best fitting model was determined, as well as a threshold of sampling effort. The data from quadrants with sampling effort below the threshold were considered too unreliable for modelling. Further, spatial uncertainty was simulated by adding a random term to each location and re-running the models using the simulated locations. Biased sampling effort and spatial uncertainty of locations had similar effects on model performance in terms of the magnitude of the affected area, as in both cases 7% of the quadrants showed statistically significant deviations in alien plant species richness. The model using only on the quandrants with the highest 35% quantile sampling effort best balanced the sampling effort per quadrant and overall geographical coverage. It predicted a mean number of 3.2 invasive alien plant species per quadrant for the Alpine region, 5.2 for the Continental, 6.1 for the Mediterranean and 5.3 for the Pannonian region of Croatia. Thus, the observational databases can be considered as a reliable source for species richness models and, most likely, for other types of species distribution models, given that their limitations are accounted for in the data selection process. In order to obtain precise estimates of species richness it is required to sample the whole range of ecological conditions of the study area.     

Biodiversity of traits and species both show weak responses to hydromorphological alteration in lowland river macroinvertebrates

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Combining counts and incidence data: an efficient approach for estimating the log-normal species abundance distribution and diversity indices

Obtaining accurate estimates of diversity indices is difficult because the number of species encountered in a sample increases with sampling intensity. We introduce a novel method that requires that the presence of species in a sample to be assessed while the counts of the number of individuals per species are only required for just a small part of the sample. To account for species included as incidence data in the species abundance distribution, we modify the likelihood function of the classical Poisson log-normal distribution. Using simulated community assemblages, we contrast diversity estimates based on a community sample, a subsample randomly extracted from the community sample, and a mixture sample where incidence data are added to a subsample. We show that the mixture sampling approach provides more accurate estimates than the subsample and at little extra cost. Diversity indices estimated from a freshwater zooplankton community sampled using the mixture approach show the same pattern of results as the simulation study. Our method efficiently increases the accuracy of diversity estimates and comprehension of the left tail of the species abundance distribution. We show how to choose the scale of sample size needed for a compromise between information gained, accuracy of the estimates and cost expended when assessing biological diversity. The sample size estimates are obtained from key community characteristics, such as the expected number of species in the community, the expected number of individuals in a sample and the evenness of the community.     

Patchiness of local species richness and its implication for large-scale diversity patterns: an example from the middle Miocene of the Paratethys

The best hope for understanding global diversity patterns is to compare local assemblages, which are mostly preserved in taphonomically-complex shell beds. The present study investigates the variability in faunal composition and diversity at the scale of a single outcrop. A total of 152 species (3315 shells) occurred in 25 samples from 5 tempestitic shell beds. Although sampling intensity was high, total species richness was not captured by far at the hierarchical levels present (outcrop, shell beds, samples) because the majority of species is rare. In contrast, sampling intensity was sufficient to cover the most abundant species, as indicated by stable evenness values. Four taxa dominate the assemblage, but their rank order differs strongly between individual shell beds and individual samples; significant differences between some shell beds are evident for faunal composition, and one shell bed differs from all others with respect to species accumulation curves. Within shell beds, rarefaction curves are generally characterized by strongly overlapping confidence intervals, but outliers occur in three of five shell beds. Patchiness is additionally indicated by a wide scatter of diversity indices in some shell beds and by a wide scatter of samples of one shell bed in an ordination on faunal composition. Most of the outcrop-scale variability in faunal composition and diversity can be related to differences between shell beds. This suggests that sampling a single shell bed of the outcrop is insufficient to characterize the local fauna and its diversity, even when sampling intensity (i.e. the number of samples and shells) within the shell bed was high. Similarly, a single sample from such a shell bed may not be sufficient to characterize its diversity, even when the number of counted shells was high. It is therefore confirmed that sampling strategy and sampling intensity are crucial to confidently characterize the shelly assemblages at such a small spatial scale and that dispersed sampling effort with many small replicate samples will characterize a local assemblage and its diversity better than a few large samples. Diversity comparisons of individual samples between localities must account for the high variability present at the smaller spatial scale, as observed in our study.