Volatility of network indices due to undersampling of intraspecific variation in plant–insect interactions

Appropriate sampling effort of interaction networks is necessary to extract robust indices describing the structure of species interactions. Here we show that time-invariant variation in the composition and diversity of interaction partners of plant individuals of the same species explains volatility in aggregate network statistics due to undersampling. Within a multi-species pollinator–plant interaction matrix, we replaced the interactions observed on multiple individuals of a single plant species (Sinapis arvensis, pooled interactions) with the plant–insect interactions observed on a single plant individual. In the resampling approach, we considered the interactions of 1 to 84 S. arvensis individuals in different combinations. For each resampled network, several commonly applied aggregated statistics were calculated to test how intraspecific variation affects the properties of a multi-species network. Our results showed that aggregate statistics are sensitive towards qualitative and quantitative intraspecific variation of flower–visitor interactions within a multi-species network, which may affect the ecological interpretation about the properties of a community. These findings challenge the robustness of commonly applied network indices, confirm the urge for a sufficient and representative sampling of interactions, and emphasize the significance of intraspecific variation in the context of communities and networks.     

Predicting the outcome of trophic manipulation in lakes—a comment on Harris (1994)

1. Harris ( Freshwater Biology , 32 , 143–160, 1994) asserts that while empirical modelling of lake ecosystem properties has yielded general predictions and useful explanations, research into the effects of food-web interactions has not. I provide an explicit example of a useful, quantitative prediction gleaned from experiments on food-web effects—the relationship between total phosphorus and the magnitude of response of algal biomass.
2. I further argue that Harris errs in asserting that food-web effects will be ineffective in eutrophic lakes. This error stems from a misconception about the relevance of ecosystem behaviour in unmanipulated systems for predictions of how an ecosystem will respond to manipulation. I cite empirical evidence demonstrating that, contrary to Harris's contention, the response of algal biomass to a change in food-web structure increases as lakes are enriched.     

Food-web structure of seagrass communities across different spatial scales and human impacts

Seagrass beds provide important habitat for a wide range of marine species but are threatened by multiple human impacts in coastal waters. Although seagrass communities have been well-studied in the field, a quantification of their food-web structure and functioning, and how these change across space and human impacts has been lacking. Motivated by extensive field surveys and literature information, we analyzed the structural features of food webs associated with Zostera marina across 16 study sites in 3 provinces in Atlantic Canada. Our goals were to (i) quantify differences in food-web structure across local and regional scales and human impacts, (ii) assess the robustness of seagrass webs to simulated species loss, and (iii) compare food-web structure in temperate Atlantic seagrass beds with those of other aquatic ecosystems. We constructed individual food webs for each study site and cumulative webs for each province and the entire region based on presence/absence of species, and calculated 16 structural properties for each web. Our results indicate that food-web structure was similar among low impact sites across regions. With increasing human impacts associated with eutrophication, however, food-web structure show evidence of degradation as indicated by fewer trophic groups, lower maximum trophic level of the highest top predator, fewer trophic links connecting top to basal species, higher fractions of herbivores and intermediate consumers, and higher number of prey per species. These structural changes translate into functional changes with impacted sites being less robust to simulated species loss. Temperate Atlantic seagrass webs are similar to a tropical seagrass web, yet differed from other aquatic webs, suggesting consistent food-web characteristics across seagrass ecosystems in different regions. Our study illustrates that food-web structure and functioning of seagrass habitats change with human impacts and that the spatial scale of food-web analysis is critical for determining results.     

Gauging the effects of sampling failure in biogeographical analysis

Aim Various methods are employed to recover patterns of area relationships in extinct and extant clades. The fidelity of these patterns can be adversely affected by sampling error in the form of missing data. Here we use simulation studies to evaluate the sensitivity of an analytical biogeographical method, namely tree reconciliation analysis (TRA), to this form of sampling failure. Location Simulation study. Methods To approximate varying degrees of taxonomic sampling failure within phylogenies varying in size and in redundancy of biogeographical signal, we applied sequential pruning protocols to artificial taxon–area cladograms displaying congruent patterns of area relationships. Initial trials assumed equal probability of sampling failure among all areas. Additional trials assigned weighted probabilities to each of the areas in order to explore the effects of uneven geographical sampling. Pruned taxon–area cladograms were then analysed with TRA to determine if the optimal area cladograms recovered match the original biogeographical signal, or if they represent false, ambiguous or uninformative signals. Results The results indicate a period of consistently accurate recovery of the true biogeographical signal, followed by a nonlinear decrease in signal recovery as more taxa are pruned. At high levels of sampling failure, false biogeographical signals are more likely to be recovered than the true signal. However, randomization testing for statistical significance greatly decreases the chance of accepting false signals. The primary inflection of the signal recovery curve, and its steepness and slope depend upon taxon–area cladogram size and area redundancy, as well as on the evenness of sampling. Uneven sampling across geographical areas is found to have serious deleterious effects on TRA, with the accuracy of recovery of biogeographical signal varying by an order of magnitude or more across different sampling regimes. Main conclusions These simulations reiterate the importance of taxon sampling in biogeographical analysis, and attest to the importance of considering geographical, as well as overall, sampling failure when interpreting the robustness of biogeographical signals. In addition to randomization testing for significance, we suggest the use of randomized sequential taxon deletions and the construction of signal decay curves as a means to assess the robustness of biogeographical signals for empirical data sets.     

Predicting the outcome of trophic manipulation in lakes—a comment on Harris (1994)

1. Harris ( Freshwater Biology , 32 , 143–160, 1994) asserts that while empirical modelling of lake ecosystem properties has yielded general predictions and useful explanations, research into the effects of food-web interactions has not. I provide an explicit example of a useful, quantitative prediction gleaned from experiments on food-web effects—the relationship between total phosphorus and the magnitude of response of algal biomass.
2. I further argue that Harris errs in asserting that food-web effects will be ineffective in eutrophic lakes. This error stems from a misconception about the relevance of ecosystem behaviour in unmanipulated systems for predictions of how an ecosystem will respond to manipulation. I cite empirical evidence demonstrating that, contrary to Harris's contention, the response of algal biomass to a change in food-web structure increases as lakes are enriched.     

Variability in stream macroinvertebrates at multiple spatial scales

1. We intensively sampled 16 western Oregon streams to characterize: (1) the variability in macroinvertebrate assemblages at seven spatial scales; and (2) the change in taxon richness with increasing sampling effort. An analysis of variance (ANOVA) model calculated spatial variance components for taxon richness, total density, percent individuals of Ephemeroptera, Plecoptera and Trichoptera (EPT), percent dominance and Shannon diversity.
2. At the landscape level, ecoregion and among‐streams components dominated variance for most metrics, accounting for 43–72% of total variance. However, ecoregion accounted for very little variance in total density and 36% of the variance was attributable to differences between streams. For other metrics, variance components were more evenly divided between stream and ecoregion effects.
3. Within streams, approximately 70% of variance was associated with unstructured local spatial variation and not associated with habitat type or transect position. The remaining variance was typically split about evenly between habitat and transect. Sample position within a transect (left, centre or right) accounted for virtually none of the variance for any metric.
4. New taxa per stream increased rapidly with sampling effort with the first four to eight Surber samples (500–1000 individuals counted), then increased more gradually. After counting more than 50 samples, new taxa continued to be added in stream reaches that were 80 times as long as their mean wetted width. Thus taxon richness was highly dependent on sampling effort, and comparisons between sites or streams must be normalized for sampling effort.
5. Characterization of spatial variance structure is fundamental to designing sampling programmes where spatial comparisons range from local to regional scales. Differences in metric responses across spatial scales demonstrate the importance of designing sampling strategies and analyses capable of discerning differences at the scale of interest.     

How meaningful are Bayesian support values?

In this study, we used an empirical example based on 100 mitochondrial genomes from higher teleost fishes to compare the accuracy of parsimony-based jackknife values with Bayesian support values. Phylogenetic analyses of 366 partitions, using differential taxon and character sampling from the entire data matrix of 100 taxa and 7,990 characters, were performed for both phylogenetic methods. The tree topology and branch-support values from each partition were compared with the tree inferred from all taxa and characters. Using this approach, we quantified the accuracy of the branch-support values assigned by the jackknife and Bayesian methods, with respect to each of 15 basal clades. In comparing the jackknife and Bayesian methods, we found that (1) both measures of support differ significantly from an ideal support index; (2) the jackknife underestimated support values; (3) the Bayesian method consistently overestimated support; (4) the magnitude by which Bayesian values overestimate support exceeds the magnitude by which the jackknife underestimates support; and (5) both methods performed poorly when taxon sampling was increased and character sampling was not increases. These results indicate that (1) the higher Bayesian support values are inappropriate (in magnitude), and (2) Bayesian support values should not be interpreted as probabilities that clades are correctly resolved. We advocate the continued use of the relatively conservative bootstrap and jackknife approaches to estimating branch support rather than the more extreme overestimates provided by the Markov Chain Monte Carlo-based Bayesian methods.     

Effects of spatial scale of sampling on food web structure

This study asks whether the spatial scale of sampling alters structural properties of food webs and whether any differences are attributable to changes in species richness and connectance with scale. Understanding how different aspects of sampling effort affect ecological network structure is important for both fundamental ecological knowledge and the application of network analysis in conservation and management. Using a highly resolved food web for the marine intertidal ecosystem of the Sanak Archipelago in the Eastern Aleutian Islands, Alaska, we assess how commonly studied properties of network structure differ for 281 versions of the food web sampled at five levels of spatial scale representing six orders of magnitude in area spread across the archipelago. Species (S) and link (L) richness both increased by approximately one order of magnitude across the five spatial scales. Links per species (L/S) more than doubled, while connectance (C) decreased by approximately two‐thirds. Fourteen commonly studied properties of network structure varied systematically with spatial scale of sampling, some increasing and others decreasing. While ecological network properties varied systematically with sampling extent, analyses using the niche model and a power‐law scaling relationship indicate that for many properties, this apparent sensitivity is attributable to the increasing S and decreasing C of webs with increasing spatial scale. As long as effects of S and C are accounted for, areal sampling bias does not have a special impact on our understanding of many aspects of network structure. However, attention does need be paid to some properties such as the fraction of species in loops, which increases more than expected with greater spatial scales of sampling.     

Global versus Chinese perspectives on the phylogeny of the N-fixing clade

There has been increasing interest in integrating a regional tree of life with community assembly rules in the ecological research. This raises questions regarding the impacts of taxon sampling strategies at the regional versus global scales on the topology. To address this concern, we constructed two trees for the nitrogen-fixing clade: (i) a genus-level global tree including 1023 genera; and (ii) a regional tree comprising 303 genera, with taxon sampling limited to China. We used the supermatrix approach and performed maximum likelihood analyses on combined matK, rbcL, and trnL-F plastid sequences. We found that the topology of the global and the regional tree of the N-fixing clade were generally congruent. However, whereas relationships among the four orders obtained with the global tree agreed with the accepted topology obtained in focused analyses with more genes, the regional topology obtained different relationships, albeit weakly supported. At a finer scale, the phylogenetic position of the family Myricaceae was found to be sensitive to sampling density. We expect that internal support throughout the phylogeny could be improved with denser taxon sampling. The taxon sampling approach (global vs. regional) did not have a major impact on fine-level branching patterns of the N-fixing clade. Thus, a well-resolved phylogeny with relatively dense taxon sampling strategy at the regional scale appears, in this case, to be a good representation of the overall phylogenetic pattern and could be used in ecological research. Otherwise, the regional tree should be adjusted according to the correspondingly reliable global tree.     

Mitochondrial genomes in the Hymenoptera and their utility as phylogenetic markers

Abstract.  In this study, we assessed the ability of mitochondrial genome sequences to recover a test phylogeny of five hymenopteran taxa from which phylogenetic relationships are well accepted. Our analyses indicated that the test phylogeny was well recovered in all nucleotide Bayesian analyses when all the available holometabolan (i.e. outgroup) taxa were included, but only in Bayesian analyses excluding third codon positions when only the hymenopteran representatives and a single outgroup were included. This result suggests that taxon sampling of the outgroup might be as important as taxon sampling of the ingroup when recovering hymenopteran phylogenetic relationships using whole mitochondrial genomes. Parsimony analyses were more sensitive to both taxon sampling and the analytical model than Bayesian analyses, and analyses using the protein dataset did not recover the test phylogeny. In general, mitochondrial genomes did not resolve the position of the Hymenoptera within the Holometabola with confidence, suggesting that an increased taxon sampling, both within the Holometabola and among outgroups, is necessary.     

Effects of water-depth and water-level fluctuations on the macroinvertebrate community structure in the littoral zone of Lake Constance

This article presents an evaluation of two sampling methods for assessing the biodiversity of heavily vegetated wetlands. The aim was to establish an effective sampling regime to maximise total taxon richness and minimise sampling effort. Three Integrated Constructed Wetland (ICW) systems in Annetown Valley, Co. Waterford, SE of the Republic of Ireland, were sampled during spring and summer 2005. The two methods that were evaluated were pond netting and two types of horizontal activity traps, namely “horizontal activity traps” (HATs) and modified “horizontal activity traps” (modified HATs). The activity traps provided a one-way funnel system and were constructed from 2 l plastic bottles, allowing for the passive collection of taxa. HATs were designed to capture macroinvertebrates in open water and modified HATs, which were designed specifically for this study, were used to sample within stands of dense emergent vegetation. Results show that a combination of pond netting and activity traps will yield a more complete estimate of taxon richness. The performance of Modified HATs was not significantly different from that of the HATs in dense vegetation. Tests on the sampling effort required for each method are also discussed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Guest editors: R. Céréghino, J. Biggs, B. Oertli and S. Declerck The ecology of European ponds: defining the characteristics of a neglected freshwater habitat     

Comparison of several techniques for sampling macroinvertebrates in different habitats of a North Iberian pond

Several habitats of a Mediterranean pond were sampled for macroinvertebrates using different techniques: quantitative methods, semiquantitative hand-net sweep sampling and a qualitative protocol based on hand-net sweeps with fixed counts of individuals. The taxonomic composition was analyzed by DCA and several indices based on taxon composition or percentage of individuals were calculated. The aim of the study was to compare the results provided by these techniques and, in particular, to check if the qualitative approach could be an appropriate low-cost methodology for use in biomonitoring. The results provided by the three sampling methods in relation to submerged macrophytes were very similar. In soft sediment, certain differences were found between the quantitative and semiquantitative techniques. The qualitative protocol applied to single habitats collected fewer taxa than the corresponding quantitative or semiquantitative techniques. However, the overall protocol, consisting of samples from three habitats, provided higher richness values than all the quantitative and semiquantitative methods together, with 59 taxa out of the 70 collected during the study. It is concluded that this qualitative methodology performed reasonably well since it offers a reliable view of the community and it misses few taxa. Moreover, it is not so time consuming as other techniques and can be applied in a variety of habitats. It, therefore, seems to be an efficient method for bioassessment of the macroinvertebrate communities of ponds or the littoral zone of lakes.     

Increased taxon sampling greatly reduces phylogenetic error

Several authors have argued recently that extensive taxon sampling has a positive and important effect on the accuracy of phylogenetic estimates. However, other authors have argued that there is little benefit of extensive taxon sampling, and so phylogenetic problems can or should be reduced to a few exemplar taxa as a means of reducing the computational complexity of the phylogenetic analysis. In this paper we examined five aspects of study design that may have led to these different perspectives. First, we considered the measurement of phylogenetic error across a wide range of taxon sample sizes, and conclude that the expected error based on randomly selecting trees (which varies by taxon sample size) must be considered in evaluating error in studies of the effects of taxon sampling. Second, we addressed the scope of the phylogenetic problems defined by different samples of taxa, and argue that phylogenetic scope needs to be considered in evaluating the importance of taxon-sampling strategies. Third, we examined the claim that fast and simple tree searches are as effective as more thorough searches at finding near-optimal trees that minimize error. We show that a more complete search of tree space reduces phylogenetic error, especially as the taxon sample size increases. Fourth, we examined the effects of simple versus complex simulation models on taxonomic sampling studies. Although benefits of taxon sampling are apparent for all models, data generated under more complex models of evolution produce higher overall levels of error and show greater positive effects of increased taxon sampling. Fifth, we asked if different phylogenetic optimality criteria show different effects of taxon sampling. Although we found strong differences in effectiveness of different optimality criteria as a function of taxon sample size, increased taxon sampling improved the results from all the common optimality criteria. Nonetheless, the method that showed the lowest overall performance (minimum evolution) also showed the least improvement from increased taxon sampling. Taking each of these results into account re-enforces the conclusion that increased sampling of taxa is one of the most important ways to increase overall phylogenetic accuracy.     

Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness

Species richness is a fundamental measurement of community and regional diversity, and it underlies many ecological models and conservation strategies. In spite of its importance, ecologists have not always appreciated the effects of abundance and sampling effort on richness measures and comparisons. We survey a series of common pitfalls in quantifying and comparing taxon richness. These pitfalls can be largely avoided by using accumulation and rarefaction curves, which may be based on either individuals or samples. These taxon sampling curves contain the basic information for valid richness comparisons, including category–subcategory ratios (species-to-genus and species-to-individual ratios). Rarefaction methods – both sample-based and individual-based – allow for meaningful standardization and comparison of datasets. Standardizing data sets by area or sampling effort may produce very different results compared to standardizing by number of individuals collected, and it is not always clear which measure of diversity is more appropriate. Asymptotic richness estimators provide lower-bound estimates for taxon-rich groups such as tropical arthropods, in which observed richness rarely reaches an asymptote, despite intensive sampling. Recent examples of diversity studies of tropical trees, stream invertebrates, and herbaceous plants emphasize the importance of carefully quantifying species richness using taxon sampling curves.     

Surber and kick sampling: a comparison for the assessment of macroinvertebrate community structure in streams of south-western Australia

Macroinvertebrate community structure was compared in benthic samples taken by Surber and kick methods from a lotic system in south-western Australia. Eleven sites were sampled concurrently in winter, spring and summer 1987.Surber samples contained fewer individuals and more taxa, particularly those with a low frequency of occurrence. This was attributed to the lower surface area, but greater intensity of Surber sampling. It is proposed that the Surber method is more suited to taking cryptic and closely adherent taxa in sites with a highly heterogeneous substratum.Percentage similarity between paired Surber and kick samples was determined by Sorensen's and Czekanowski's coefficients, with mean values of 66% and 60% for June, 61% and 49% for September and 66% and 49% for December respectively. Ordination demonstrated a division of upland from lowland sites on axis 1, with a separation of paired-samples on axis 2. This pattern held across qualitative and quantitative datasets, with and without a downweighting on rare taxa. At each level of classification fewer paired-samples separated in qualitative than quantitative datasets.Kick sampling provided a substantial saving in costs over Surber sampling, particularly when qualitative data were utilised, making the method suitable for routine, biological monitoring. However, the initial use of replicated Surber sampling, particularly in areas that have not been previously sampled is recommended for environmental impact studies to detect rare taxa, that may be endangered.